From 0db2f006353590374a5107b095623ba8cc9dce5b Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Mon, 20 Apr 2020 14:57:56 -0500
Subject: [PATCH 001/802] PyTorch: remove CUDA conflicts (#16136)

---
 .../repos/builtin/packages/py-torch/package.py | 18 ------------------
 1 file changed, 18 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py
index 31bfb716578..619a621c2b3 100644
--- a/var/spack/repos/builtin/packages/py-torch/package.py
+++ b/var/spack/repos/builtin/packages/py-torch/package.py
@@ -6,7 +6,6 @@
 from spack import *
 
 
-# TODO: try switching to CMakePackage for more control over build
 class PyTorch(PythonPackage, CudaPackage):
     """Tensors and Dynamic neural networks in Python
     with strong GPU acceleration."""
@@ -107,26 +106,9 @@ class PyTorch(PythonPackage, CudaPackage):
     # see https://github.com/pytorch/pytorch/issues/35149
     conflicts('+fbgemm', when='@1.4.0')
 
-    cuda_arch_conflict = ('This version of Torch/Caffe2 only supports compute '
-                          'capabilities ')
-
     conflicts('cuda_arch=none', when='+cuda',
               msg='Must specify CUDA compute capabilities of your GPU, see '
               'https://developer.nvidia.com/cuda-gpus')
-    conflicts('cuda_arch=52', when='@1.3.0:+cuda',
-              msg=cuda_arch_conflict + '>=5.3')
-    conflicts('cuda_arch=50', when='@1.3.0:+cuda',
-              msg=cuda_arch_conflict + '>=5.3')
-    conflicts('cuda_arch=35', when='@1.3.0:+cuda',
-              msg=cuda_arch_conflict + '>=5.3')
-    conflicts('cuda_arch=32', when='@1.3.0:+cuda',
-              msg=cuda_arch_conflict + '>=5.3')
-    conflicts('cuda_arch=30', when='@1.3.0:+cuda',
-              msg=cuda_arch_conflict + '>=5.3')
-    conflicts('cuda_arch=30', when='@1.2.0:+cuda',
-              msg=cuda_arch_conflict + '>=3.2')
-    conflicts('cuda_arch=20', when='@1.0.0:+cuda',
-              msg=cuda_arch_conflict + '>=3.0')
 
     # Required dependencies
     depends_on('cmake@3.5:', type='build')

From 3a9ce3ac4a3b60c43bc8c5c33418008c2675e7d5 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <eafischer2@alaska.edu>
Date: Mon, 20 Apr 2020 12:15:38 -0800
Subject: [PATCH 002/802] glib (#16179)

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
---
 var/spack/repos/builtin/packages/glib/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py
index b7cf326e858..9e71ccdd4bb 100644
--- a/var/spack/repos/builtin/packages/glib/package.py
+++ b/var/spack/repos/builtin/packages/glib/package.py
@@ -159,6 +159,11 @@ def configure_args(self):
         args.append('GTKDOC_REBASE={0}'.format(true))
         return args
 
+    def setup_build_environment(self, env):
+        if self.spec.satisfies('platform=darwin'):
+            # https://github.com/pybind/pybind11/issues/595
+            env.set('STRIP', 'strip -x')
+
     @when('@:2.57.99')
     def install(self, spec, prefix):
         configure('--prefix={0}'.format(prefix), *self.configure_args())

From 742a4b7e2a5baef0c984b20110f99d8d0d7c869f Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <eafischer2@alaska.edu>
Date: Mon, 20 Apr 2020 12:21:36 -0800
Subject: [PATCH 003/802] proj (#16175)

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
---
 var/spack/repos/builtin/packages/proj/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/proj/package.py b/var/spack/repos/builtin/packages/proj/package.py
index 19de7a79095..46a91ab8a0c 100644
--- a/var/spack/repos/builtin/packages/proj/package.py
+++ b/var/spack/repos/builtin/packages/proj/package.py
@@ -20,6 +20,7 @@ class Proj(AutotoolsPackage):
     # Version 6 removes projects.h, while version 7 removes proj_api.h.
     # Many packages that depend on proj do not yet support the newer API.
     # See https://github.com/OSGeo/PROJ/wiki/proj.h-adoption-status
+    version('6.3.1', sha256='6de0112778438dcae30fcc6942dee472ce31399b9e5a2b67e8642529868c86f8')
     version('6.2.0', sha256='b300c0f872f632ad7f8eb60725edbf14f0f8f52db740a3ab23e7b94f1cd22a50')
     version('6.1.0', sha256='676165c54319d2f03da4349cbd7344eb430b225fe867a90191d848dc64788008')
     version('6.0.0', sha256='4510a2c1c8f9056374708a867c51b1192e8d6f9a5198dd320bf6a168e44a3657')

From 1f49fb8cebe5dfe1ca2f5caeb614f266dc5912e6 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 20 Apr 2020 22:32:58 +0200
Subject: [PATCH 004/802] python: Add 3.7.7 (#16170)

---
 var/spack/repos/builtin/packages/python/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 97acde7b59c..94a3f2d6453 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -34,7 +34,8 @@ class Python(AutotoolsPackage):
     version('3.8.2',  sha256='e634a7a74776c2b89516b2e013dda1728c89c8149b9863b8cea21946daf9d561')
     version('3.8.1',  sha256='c7cfa39a43b994621b245e029769e9126caa2a93571cee2e743b213cceac35fb')
     version('3.8.0',  sha256='f1069ad3cae8e7ec467aa98a6565a62a48ef196cb8f1455a245a08db5e1792df')
-    version('3.7.6',  sha256='aeee681c235ad336af116f08ab6563361a0c81c537072c1b309d6e4050aa2114', preferred=True)
+    version('3.7.7',  sha256='8c8be91cd2648a1a0c251f04ea0bb4c2a5570feb9c45eaaa2241c785585b475a', preferred=True)
+    version('3.7.6',  sha256='aeee681c235ad336af116f08ab6563361a0c81c537072c1b309d6e4050aa2114')
     version('3.7.5',  sha256='8ecc681ea0600bbfb366f2b173f727b205bb825d93d2f0b286bc4e58d37693da')
     version('3.7.4',  sha256='d63e63e14e6d29e17490abbe6f7d17afb3db182dbd801229f14e55f4157c4ba3')
     version('3.7.3',  sha256='d62e3015f2f89c970ac52343976b406694931742fbde2fed8d1ce8ebb4e1f8ff')

From 73e0dd9f614a17f89da263d1641a2f0eca5de1fc Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Mon, 20 Apr 2020 15:39:53 -0500
Subject: [PATCH 005/802] prism: new package at 4.5 (#16187)

---
 .../repos/builtin/packages/prism/package.py   | 43 +++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/prism/package.py

diff --git a/var/spack/repos/builtin/packages/prism/package.py b/var/spack/repos/builtin/packages/prism/package.py
new file mode 100644
index 00000000000..a76f33ac7a3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/prism/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Prism(MakefilePackage):
+    """PRISM is a probabilistic model checker, a tool for formal modelling and
+       analysis of systems that exhibit random or probabilistic behaviour."""
+
+    homepage = "https://www.prismmodelchecker.org/"
+    url      = "https://github.com/prismmodelchecker/prism/archive/v4.5.tar.gz"
+
+    version('4.5', sha256='1cb7a77538b5c997d98a8c209030c46f9e8f021f7a8332e5eb2fd3b4a23936fd')
+
+    build_directory = 'prism'
+
+    depends_on('java', type=('build', 'run'))
+
+    def setup_run_environment(self, env):
+        env.set('PRISM_DIR', self.prefix)
+
+    def install(self, spec, prefix):
+        with working_dir(self.build_directory):
+            # after building, remove PRISM_DIR lines from startup scripts,
+            # as they point to the stage and not the prefix
+            for f in ['prism', 'xprism']:
+                filter_file('^PRISM_DIR.*', '', 'bin/{0}'.format(f))
+
+            dirs = [
+                'bin',
+                'classes',
+                'dtds',
+                'etc',
+                'include',
+                'images',
+                'lib',
+            ]
+
+            for d in dirs:
+                install_tree(d, join_path(prefix, d))

From ed13319a4b368e99afc1fd7fe3021a3440d5bfdf Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 21 Apr 2020 04:59:16 +0800
Subject: [PATCH 006/802] Add new Package: accumulo (#16148)

---
 .../builtin/packages/accumulo/package.py      | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/accumulo/package.py

diff --git a/var/spack/repos/builtin/packages/accumulo/package.py b/var/spack/repos/builtin/packages/accumulo/package.py
new file mode 100644
index 00000000000..219d313aa10
--- /dev/null
+++ b/var/spack/repos/builtin/packages/accumulo/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Accumulo(Package):
+    """Apache Accumulo is a sorted, distributed key/value store that
+    provides robust, scalable data storage and retrieval."""
+
+    homepage = "https://accumulo.apache.org/"
+    url      = "https://github.com/apache/accumulo/archive/rel/2.0.0.tar.gz"
+
+    version('2.0.0', sha256='2564056dc24398aa464763c21bae10ef09356fe3261600d27744071cf965c265')
+    version('1.9.3', sha256='d9548d5b9cf9f494f027f0fe59d5d6d45d09064359d7761cade62991ce2a5d0c')
+    version('1.9.2', sha256='11ab028143ad6313cd5fc701b36b4c35e46a4a3fa2ce663869860b9f6bf5ee4d')
+
+    depends_on('maven', type='build')
+    depends_on('java', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mvn = which('mvn')
+        mvn('package', '-DskipTests')
+        install_tree('.', prefix)

From cab1d06d6a3907084aad14c8b66b03741453284c Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 21 Apr 2020 05:06:31 +0800
Subject: [PATCH 007/802] Add new package: collectd (#16144)

---
 .../builtin/packages/collectd/package.py      | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/collectd/package.py

diff --git a/var/spack/repos/builtin/packages/collectd/package.py b/var/spack/repos/builtin/packages/collectd/package.py
new file mode 100644
index 00000000000..35472a4a675
--- /dev/null
+++ b/var/spack/repos/builtin/packages/collectd/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Collectd(AutotoolsPackage):
+    """The system statistics collection daemon."""
+
+    homepage = "http://collectd.org/"
+    url      = "https://github.com/collectd/collectd/archive/collectd-5.11.0.tar.gz"
+
+    version('5.11.0', sha256='639676d09c5980ceea90b5a97811a9647d94e368528cce7cea3d43f0f308465d')
+    version('5.10.0', sha256='bcde95a3997b5eee448d247d9414854994b3592cb9fb4fecd6ff78082cc28a1b')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')

From 126491288a532da08fb3923eae2635a84736798d Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 21 Apr 2020 05:07:18 +0800
Subject: [PATCH 008/802] Add new package: libsamplerate (#16143)

---
 .../builtin/packages/libsamplerate/package.py | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/libsamplerate/package.py

diff --git a/var/spack/repos/builtin/packages/libsamplerate/package.py b/var/spack/repos/builtin/packages/libsamplerate/package.py
new file mode 100644
index 00000000000..fcab8be9d3d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libsamplerate/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libsamplerate(AutotoolsPackage):
+    """libsamplerate (also known as Secret Rabbit Code) is a library for
+    performing sample rate conversion of audio data."""
+
+    homepage = "http://www.mega-nerd.com/libsamplerate/history.html"
+    url      = "http://www.mega-nerd.com/libsamplerate/libsamplerate-0.1.9.tar.gz"
+
+    version('0.1.9', sha256='0a7eb168e2f21353fb6d84da152e4512126f7dc48ccb0be80578c565413444c1')
+    version('0.1.8', sha256='93b54bdf46d5e6d2354b7034395fe329c222a966790de34520702bb9642f1c06')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')

From eb0d82a7e496d47bedc353e9c8227aeb46540d58 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 21 Apr 2020 05:07:44 +0800
Subject: [PATCH 009/802] Add new package: codec2 (#16142)

---
 .../repos/builtin/packages/codec2/package.py    | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/codec2/package.py

diff --git a/var/spack/repos/builtin/packages/codec2/package.py b/var/spack/repos/builtin/packages/codec2/package.py
new file mode 100644
index 00000000000..55a526c8540
--- /dev/null
+++ b/var/spack/repos/builtin/packages/codec2/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Codec2(CMakePackage):
+    """Open source speech codec designed for communications quality speech
+    between 450 and 3200 bit/s. The main application is low bandwidth
+    HF/VHF digital radio."""
+
+    homepage = "http://www.rowetel.com/codec2.html"
+    url      = "https://github.com/drowe67/codec2/archive/v0.9.2.tar.gz"
+
+    version('0.9.2', sha256='19181a446f4df3e6d616b50cabdac4485abb9cd3242cf312a0785f892ed4c76c')

From ac17d0783aa60a918028188794191054f2f01494 Mon Sep 17 00:00:00 2001
From: Hadrien G <knights_of_ni@gmx.com>
Date: Mon, 20 Apr 2020 23:08:44 +0200
Subject: [PATCH 010/802] Add Acts v0.22 (#16141)

---
 var/spack/repos/builtin/packages/acts-core/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/acts-core/package.py b/var/spack/repos/builtin/packages/acts-core/package.py
index ea3498b4f3a..fc5b6cd4784 100644
--- a/var/spack/repos/builtin/packages/acts-core/package.py
+++ b/var/spack/repos/builtin/packages/acts-core/package.py
@@ -34,6 +34,7 @@ class ActsCore(CMakePackage):
     maintainers = ['HadrienG2']
 
     version('master', branch='master')
+    version('0.22.0', commit='2c8228f5843685fc0ae69a8b95dd8fc001139efb')
     version('0.21.0', commit='10b719e68ddaca15b28ac25b3daddce8c0d3368d')
     version('0.20.0', commit='1d37a849a9c318e8ca4fa541ef8433c1f004637b')
     version('0.19.0', commit='408335636486c421c6222a64372250ef12544df6')

From 78f1940646fab40c65ea293a2d0435b50566e1e1 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 20 Apr 2020 23:11:07 +0200
Subject: [PATCH 011/802] update package py-graphviz version (#16131)

---
 var/spack/repos/builtin/packages/py-graphviz/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-graphviz/package.py b/var/spack/repos/builtin/packages/py-graphviz/package.py
index 9fcbd1c5560..144321cccff 100644
--- a/var/spack/repos/builtin/packages/py-graphviz/package.py
+++ b/var/spack/repos/builtin/packages/py-graphviz/package.py
@@ -13,6 +13,9 @@ class PyGraphviz(PythonPackage):
     homepage = "https://github.com/xflr6/graphviz"
     url      = "https://pypi.io/packages/source/g/graphviz/graphviz-0.10.1.zip"
 
+    version('0.13.2', sha256='60acbeee346e8c14555821eab57dbf68a169e6c10bce40e83c1bf44f63a62a01')
+    version('0.13', sha256='dc08677f37c65a4a480f00df4bd0d19a0a103c06aad95f21a37f0b7fd440de81')
+    version('0.12', sha256='c60e232a66e4847f9f644fbaa94730ca4f78385a1314a2cc1e7f4cb2d7461298')
     version('0.11.1', sha256='914b8b124942d82e3e1dcef499c9fe77c10acd3d18a1cfeeb2b9de05f6d24805')
     version('0.10.1', sha256='d311be4fddfe832a56986ac5e1d6e8715d7fcb0208560da79d1bb0f72abef41f')
 

From e3966d2791c827b09f3173a07b07b4fea47a7b62 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 20 Apr 2020 23:16:39 +0200
Subject: [PATCH 012/802] pixman: Add 0.40.0 (#16190)

---
 var/spack/repos/builtin/packages/pixman/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/pixman/package.py b/var/spack/repos/builtin/packages/pixman/package.py
index 31c15b42686..1087dabbbff 100644
--- a/var/spack/repos/builtin/packages/pixman/package.py
+++ b/var/spack/repos/builtin/packages/pixman/package.py
@@ -15,6 +15,7 @@ class Pixman(AutotoolsPackage):
     homepage = "http://www.pixman.org"
     url      = "http://cairographics.org/releases/pixman-0.32.6.tar.gz"
 
+    version('0.40.0', sha256='6d200dec3740d9ec4ec8d1180e25779c00bc749f94278c8b9021f5534db223fc')
     version('0.38.4', sha256='da66d6fd6e40aee70f7bd02e4f8f76fc3f006ec879d346bae6a723025cfbdde7')
     version('0.38.0', sha256='a7592bef0156d7c27545487a52245669b00cf7e70054505381cff2136d890ca8')
     version('0.34.0', sha256='21b6b249b51c6800dc9553b65106e1e37d0e25df942c90531d4c3997aa20a88e')

From 8635c0d804ee0f143e36b08e99b19e83652d27a3 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 20 Apr 2020 23:16:51 +0200
Subject: [PATCH 013/802] rocksdb: Add 6.7.3 (#16189)

This also adds a shared variant, so we can build both the static and
shared libraries at the same time. It also adds a pkg-config file.
---
 .../repos/builtin/packages/rocksdb/package.py | 32 +++++++++++++++++--
 1 file changed, 29 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/rocksdb/package.py b/var/spack/repos/builtin/packages/rocksdb/package.py
index 67b9ddea448..7cb105ba637 100644
--- a/var/spack/repos/builtin/packages/rocksdb/package.py
+++ b/var/spack/repos/builtin/packages/rocksdb/package.py
@@ -13,7 +13,8 @@ class Rocksdb(MakefilePackage):
     url      = 'https://github.com/facebook/rocksdb/archive/v6.5.3.tar.gz'
     git      = 'https://github.com/facebook/rocksdb.git'
 
-    version('develop', git=git, branch='master', submodules=True)
+    version('master',  git=git, branch='master', submodules=True)
+    version('6.7.3',   sha256='c4d1397b58e4801b5fd7c3dd9175e6ae84541119cbebb739fe17d998f1829e81')
     version('6.5.3',   sha256='6dc023a11d61d00c8391bd44f26ba7db06c44be228c10b552edc84e02d7fbde2')
     version('5.18.3',  sha256='7fb6738263d3f2b360d7468cf2ebe333f3109f3ba1ff80115abd145d75287254')
     version('5.17.2',  sha256='101f05858650a810c90e4872338222a1a3bf3b24de7b7d74466814e6a95c2d28')
@@ -22,6 +23,7 @@ class Rocksdb(MakefilePackage):
 
     variant('bz2', default=False, description='Enable bz2 compression support')
     variant('lz4', default=True, description='Enable lz4 compression support')
+    variant('shared', default=True, description='Build shared library')
     variant('snappy', default=False, description='Enable snappy compression support')
     variant('static', default=True, description='Build static library')
     variant('zlib', default=True, description='Enable zlib compression support')
@@ -36,6 +38,8 @@ class Rocksdb(MakefilePackage):
     depends_on('zstd', when='+zstd')
     depends_on('tbb', when='+tbb')
 
+    conflicts('~shared~static', msg='have to build one type of library')
+
     phases = ['install']
 
     def patch(self):
@@ -85,5 +89,27 @@ def install(self, spec, prefix):
         env['PLATFORM_FLAGS'] = ' '.join(ldflags)
         env['INSTALL_PATH'] = self.spec.prefix
 
-        buildtype = 'install-static' if '+static' in spec else 'install-shared'
-        make(buildtype)
+        if '+static' in spec:
+            make('install-static')
+
+        if '+shared' in spec:
+            make('install-shared')
+
+    @run_after('install')
+    def install_pkgconfig(self):
+        libdir = self.spec['rocksdb'].libs.directories[0]
+        pkg_path = join_path(libdir, 'pkgconfig')
+        mkdirp(pkg_path)
+
+        with open(join_path(pkg_path, 'rocksdb.pc'), 'w') as f:
+            f.write('prefix={0}\n'.format(self.prefix))
+            f.write('exec_prefix=${prefix}\n')
+            f.write('libdir={0}\n'.format(libdir))
+            f.write('includedir={0}\n'.format(self.prefix.include))
+            f.write('\n')
+            f.write('Name: rocksdb\n')
+            f.write('Description: RocksDB: A Persistent Key-Value Store for'
+                    ' Flash and RAM Storage\n')
+            f.write('Version: {0}\n'.format(self.spec.version))
+            f.write('Cflags: -I${includedir}\n')
+            f.write('Libs: -L${libdir} -lrocksdb -ldl\n')

From a70e76d043a452bcd3962896fa7281e4499fc2af Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 20 Apr 2020 23:19:55 +0200
Subject: [PATCH 014/802] Package Bonniepp adding sbin to PATH (#16124)

---
 var/spack/repos/builtin/packages/bonniepp/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/bonniepp/package.py b/var/spack/repos/builtin/packages/bonniepp/package.py
index 18751810fc8..6a33a15ea77 100644
--- a/var/spack/repos/builtin/packages/bonniepp/package.py
+++ b/var/spack/repos/builtin/packages/bonniepp/package.py
@@ -19,3 +19,7 @@ def configure_args(self):
         configure_args = []
         configure_args.append('--enable-debug')
         return configure_args
+
+    def setup_run_environment(self, env):
+        """Prepend the sbin directory to PATH."""
+        env.prepend_path('PATH', self.prefix.sbin)

From cf12541281fe7a252c50483dde2caa2c532cb233 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 21 Apr 2020 05:22:37 +0800
Subject: [PATCH 015/802] Add new package: byacc (#16123)

* Add new package: byacc

* refine byacc info
---
 .../repos/builtin/packages/byacc/package.py   | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/byacc/package.py

diff --git a/var/spack/repos/builtin/packages/byacc/package.py b/var/spack/repos/builtin/packages/byacc/package.py
new file mode 100644
index 00000000000..b555910c42f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/byacc/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Byacc(AutotoolsPackage):
+    """Berkeley Yacc is an LALR(1) parser generator.  Berkeley Yacc has
+    been made as compatible as possible with AT&T Yacc.  Berkeley Yacc
+    can accept any input specification that conforms to the AT&T Yacc
+    documentation. Specifications that take advantage of undocumented
+    features of AT&T Yacc will probably be rejected."""
+
+    homepage = "https://github.com/grandseiken/byacc"
+    git      = "https://github.com/grandseiken/byacc.git"
+
+    version('master', branch='master')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')

From e8a7e4f5ecd0c1a6dcd9f0769f16f5ad2569dff5 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 21 Apr 2020 05:23:47 +0800
Subject: [PATCH 016/802] Add new package: bgpdump (#16122)

---
 .../repos/builtin/packages/bgpdump/package.py | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/bgpdump/package.py

diff --git a/var/spack/repos/builtin/packages/bgpdump/package.py b/var/spack/repos/builtin/packages/bgpdump/package.py
new file mode 100644
index 00000000000..e708860dc3f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bgpdump/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bgpdump(AutotoolsPackage):
+    """Utility and C Library for parsing MRT files"""
+
+    homepage = "https://github.com/RIPE-NCC/bgpdump/wiki"
+    git      = "https://github.com/RIPE-NCC/bgpdump.git"
+
+    version('master', branch='master')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('bzip2')

From c2ca8328835d544440fd3b87813e2768ece58685 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 21 Apr 2020 05:24:33 +0800
Subject: [PATCH 017/802] Add new package: audacious (#16121)

---
 .../builtin/packages/audacious/package.py     | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/audacious/package.py

diff --git a/var/spack/repos/builtin/packages/audacious/package.py b/var/spack/repos/builtin/packages/audacious/package.py
new file mode 100644
index 00000000000..0115d4c5537
--- /dev/null
+++ b/var/spack/repos/builtin/packages/audacious/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Audacious(AutotoolsPackage):
+    """A lightweight and versatile audio player."""
+
+    homepage = "https://audacious-media-player.org/"
+    url      = "https://github.com/audacious-media-player/audacious/archive/audacious-4.0.2.tar.gz"
+
+    version('4.0.2',  sha256='92f30a78353c50f99b536061b9d94b6b9128760d546fddbf863e3591c4ac5a8d')
+    version('4.0.1',  sha256='203195cf0d3c2e40d23c9895269ca0ace639c4a2b4dceb624169d75337059985')
+    version('4.0',    sha256='cdfffd0eb966856980328ebb0fff9cbce57f99db9bda15e7e839d26c89e953e6')
+    version('3.10.1', sha256='c478939b4bcf6704c26eee87d48cab26547e92a83741f437711178c433373fa1')
+    version('3.10',   sha256='82710d6ac90931c2cc4a0f0fcb6380ac21ed42a7a50856d16a67d3179a96e9ae')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('glib')
+    depends_on('qt')
+
+    def autoreconf(self, spec, prefix):
+        bash = which('bash')
+        bash('./autogen.sh')

From 8e7f55e6d67a8f464fb543bb022add79562d05bf Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Tue, 21 Apr 2020 06:29:06 +0900
Subject: [PATCH 018/802] ppOpen-APPL/DEM-util: New package (#16120)

---
 .../packages/ppopen-appl-dem-util/package.py  | 48 +++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100755 var/spack/repos/builtin/packages/ppopen-appl-dem-util/package.py

diff --git a/var/spack/repos/builtin/packages/ppopen-appl-dem-util/package.py b/var/spack/repos/builtin/packages/ppopen-appl-dem-util/package.py
new file mode 100755
index 00000000000..8fa6544db36
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ppopen-appl-dem-util/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class PpopenApplDemUtil(MakefilePackage):
+    """
+    ppOpen-APPL/DEM provides fundamental components of the particle
+    simulations based on the discrete element method (DEM).
+    ppOpen-APPL/DEM (ver.1.0.0) includes the libraries for the DEM,
+    sample codes, and data sets. ppOpen-APPL/DEM-Util provides the
+    preconditioning utilities. This utility prepares data sets of distributed
+    data files from the mesh data sets.
+
+    """
+
+    homepage = "http://ppopenhpc.cc.u-tokyo.ac.jp/ppopenhpc/"
+    url      = "file://{0}/ppohDEM_util_1.0.0.tar.gz".format(os.getcwd())
+
+    version('1.0.0', sha256='e0aa9a61be3b9858a2885c9feff9b0fcd1d7039408f6bd82a73a79dfe86b0488')
+
+    depends_on('mpi')
+
+    def edit(self, spec, prefix):
+        makefile_in = FileFilter('Makefile.in')
+        makefile_in.filter('PREFIX += .*', 'PREFIX = {0}'.format(prefix))
+        makefile_in.filter('F90 += .*', 'F90 = {0}'.format(spack_fc))
+        makefile_in.filter('F77 += .*', 'F77 = {0}'.format(spack_fc))
+        makefile_in.filter(
+            'MPIF90 += .*',
+            'MPIF90 = {0}'.format(spec['mpi'].mpifc)
+        )
+        makefile_in.filter(
+            'MPIF77 += .*',
+            'MPIF77 = {0}'.format(spec['mpi'].mpifc)
+        )
+        makefile_in.filter(
+            'F90MPFLAGS += .*',
+            'F90MPFLAGS = -O3 {0}'.format(self.compiler.openmp_flag)
+        )
+
+    def install(self, spec, prefix):
+        make('install')
+        install_tree('doc', prefix.doc)

From c6ef9c2b87cefc26e2c4dc34c80e6ab951a011c4 Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Tue, 21 Apr 2020 06:36:36 +0900
Subject: [PATCH 019/802] Add ppOpen-APPL/FDM and ppOpen-APPL/FDM-AT. (#16116)

---
 .../packages/ppopen-appl-fdm-at/package.py    |  50 +++++++
 .../ppopen-appl-fdm/gfortran_iargc.patch      |  13 ++
 .../packages/ppopen-appl-fdm/package.py       | 137 ++++++++++++++++++
 .../packages/ppopen-appl-fdm/unused.patch     |  13 ++
 .../packages/ppopen-math-vis/package.py       |   6 +
 5 files changed, 219 insertions(+)
 create mode 100755 var/spack/repos/builtin/packages/ppopen-appl-fdm-at/package.py
 create mode 100755 var/spack/repos/builtin/packages/ppopen-appl-fdm/gfortran_iargc.patch
 create mode 100755 var/spack/repos/builtin/packages/ppopen-appl-fdm/package.py
 create mode 100755 var/spack/repos/builtin/packages/ppopen-appl-fdm/unused.patch

diff --git a/var/spack/repos/builtin/packages/ppopen-appl-fdm-at/package.py b/var/spack/repos/builtin/packages/ppopen-appl-fdm-at/package.py
new file mode 100755
index 00000000000..a8ab4fb9e8d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ppopen-appl-fdm-at/package.py
@@ -0,0 +1,50 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class PpopenApplFdmAt(MakefilePackage):
+    """ppOpen-APPL/FDM with Auto-Tuning"""
+
+    homepage = "http://ppopenhpc.cc.u-tokyo.ac.jp/ppopenhpc/"
+    url      = "file://{0}/ppohFDM_AT_1.0.0.tar.gz".format(os.getcwd())
+
+    version('1.0.0', sha256='f6052b73250a41b2b319b27efc4d753c6ec1f67cd109b53099c2b240f7acd65a')
+
+    depends_on('mpi')
+    # depends_on('ppopen-appl-fdm', type='build')
+
+    build_directory = "3.hybrid_AT"
+    parallel = False
+
+    def edit(self, spec, prefix):
+        with working_dir(self.build_directory):
+            fflags = ['-O3', self.compiler.openmp_flag]
+            if spec.satisfies('%gcc'):
+                fflags.append('-ffree-line-length-none')
+            if spec.satisfies('arch=x86_64:'):
+                fflags.append('-mcmodel=medium')
+            makefile_opt = FileFilter('Makefile.option')
+            makefile_opt.filter(
+                'FC = .*$',
+                'FC = {0}'.format(spec['mpi'].mpifc)
+            )
+            makefile_opt.filter(
+                'FFLAGS = .*$',
+                'FFLAGS = -O3 {0}'.format(' '.join(fflags))
+            )
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        copy(join_path(self.build_directory, 'seism3d3n'), prefix.bin)
+        install_src_dir = join_path(prefix.src, self.build_directory)
+        mkdirp(install_src_dir)
+        install_tree(self.build_directory, install_src_dir)
+        with working_dir(install_src_dir):
+            make('clean')
+        mkdir(prefix.doc)
+        copy('readme.txt', prefix.doc)
diff --git a/var/spack/repos/builtin/packages/ppopen-appl-fdm/gfortran_iargc.patch b/var/spack/repos/builtin/packages/ppopen-appl-fdm/gfortran_iargc.patch
new file mode 100755
index 00000000000..115a0f06888
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ppopen-appl-fdm/gfortran_iargc.patch
@@ -0,0 +1,13 @@
+diff --git a/tools/seismic_3D-tools/m_stdio.f90 b/tools/seismic_3D-tools/m_stdio.f90
+index bddb715..bc00f68 100644
+--- a/tools/seismic_3D-tools/m_stdio.f90
++++ b/tools/seismic_3D-tools/m_stdio.f90
+@@ -65,8 +65,6 @@ module stdio
+   real(PN), parameter :: DEG2RAD = PI/180._PN
+   real(PN), parameter :: RAD2DEG = 180.0_PN / PI
+ 
+-  integer, external :: iargc
+-
+ 
+   interface readPrm
+   !
diff --git a/var/spack/repos/builtin/packages/ppopen-appl-fdm/package.py b/var/spack/repos/builtin/packages/ppopen-appl-fdm/package.py
new file mode 100755
index 00000000000..450ae99efbf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ppopen-appl-fdm/package.py
@@ -0,0 +1,137 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+from spack import *
+
+
+class PpopenApplFdm(MakefilePackage):
+    """
+    ppOpen-APPL/FDM is a application software for the FDM simulation of
+    seismic wave propagation in elastic media in 2D and 3D.
+    The 2D application is prepared for a single-CPU (sequential) calculation
+    and the 3D application use MPI and OpenMP for parallel computing.
+    """
+
+    homepage = "http://ppopenhpc.cc.u-tokyo.ac.jp/ppopenhpc/"
+    url      = "file://{0}/ppohFDM_0.3.1.tar.gz".format(os.getcwd())
+
+    version('0.3.1', sha256='5db7c28ef2df43c0ffa28e542d92320fe3c8cd7551aabe1de64647191ddf7d0b')
+
+    # remove unused variable definition
+    patch('unused.patch')
+    # remove iargc external definition
+    # iargc is intrinsic in gfortran
+    patch('gfortran_iargc.patch')
+
+    depends_on('ppopen-math-vis', type='link')
+    depends_on('mpi')
+
+    parallel = False
+
+    def edit(self, spec, prefix):
+        makefile_in = FileFilter('Makefile.in')
+        makefile_in.filter('PREFIX += .*$', 'PREFIX = {0}'.format(prefix))
+        makefile_in.filter(
+            'LIBDIR = .*$',
+            'LIBDIR = {0}'.format(prefix)
+        )
+        makefile_in.filter(
+            'CC += .*$',
+            'CC = {0}'.format(spec['mpi'].mpicc)
+        )
+        makefile_in.filter('COPTFLAGS += .*$', 'COPTFLAGS = -O3')
+        makefile_in.filter(
+            'CXX += .*$',
+            'CXX = {0}'.format(spec['mpi'].mpicxx)
+        )
+        makefile_in.filter('CXXOPTFLAGS = .*$', 'CXXOPTFLAGS = -O3')
+        makefile_in.filter(
+            'FC += .*$',
+            'FC = {0}'.format(spec['mpi'].mpifc)
+        )
+        makefile_in.filter('FOPTFLAGS += .*$', 'FOPTFLAGS = -O3')
+        makefile_in.filter(
+            'F90 += .*$',
+            'F90 = {0}'.format(spec['mpi'].mpifc)
+        )
+        makefile_in.filter('F90OPTFLAGS += .*$', 'F90OPTFLAGS = -O3')
+
+        makefile_opt = FileFilter(join_path(
+            'src', 'seismic_2D', 'makefile.option')
+        )
+        makefile_opt.filter('FC = .*$', 'FC = {0}'.format(spack_fc))
+        makefile_opt.filter('FFLAGS = .*$', 'FFLAGS = -O3')
+
+        makefile = FileFilter(join_path(
+            'src', 'seismic_3D', '1.ppohFDM-ppohVIS', 'Makefile')
+        )
+        makefile.filter('LIBS += .*$', 'LIBS = ')
+        makefile.filter(
+            'FLDFLAGS += .*$',
+            'FLDFLAGS = ' + spec['ppopen-math-vis'].libs.ld_flags
+        )
+
+        makefile_opt = FileFilter(join_path(
+            'src', 'seismic_3D', '3.parallel', 'Makefile.option')
+        )
+        makefile_opt.filter('FC = .*$', 'FC = {0}'.format(spec['mpi'].mpifc))
+        makefile_opt.filter(
+            'FFLAGS = .*$',
+            'FFLAGS = -O3 {0}'.format(self.compiler.openmp_flag)
+        )
+
+        copy(
+            join_path('examples', 'seismic_3D-example', 'm_param.f90'),
+            join_path('src', 'seismic_3D', '1.ppohFDM-ppohVIS')
+        )
+        copy(
+            join_path('examples', 'seismic_3D-example', 'm_param.f90'),
+            join_path('src', 'seismic_3D', '3.parallel')
+        )
+
+        for makefile in find('tools', 'makefile', recursive=True):
+            fflags = ['-O3', '-I.']
+            m = FileFilter(makefile)
+            m.filter('^FC =.*$', 'FC = {0}'.format(spack_fc))
+            m.filter(
+                '^FFLAGS =.*$',
+                'FFLAGS = {0}'.format(' '.join(fflags))
+            )
+
+    def build(self, spec, prefix):
+        make('seism2d', 'seism3d-ppohVIS', 'seism3d-parallel')
+        for d in ['seismic_2D-tools', 'seismic_3D-tools']:
+            with working_dir(join_path('tools', d)):
+                make('all')
+
+    def install(self, spec, prefix):
+        commands = [
+            join_path('src', 'seismic_2D', 'seism2d_psv'),
+            join_path('src', 'seismic_3D', '3.parallel', 'seism3d3n'),
+            join_path('src', 'seismic_3D', '1.ppohFDM-ppohVIS', 'seism3d3n'),
+            join_path('tools', 'seismic_2D-tools', 'pmxy2d'),
+            join_path('tools', 'seismic_2D-tools', 'rwav2d'),
+            join_path('tools', 'seismic_3D-tools', 'catsnap'),
+            join_path('tools', 'seismic_3D-tools', 'catwav'),
+            join_path('tools', 'seismic_3D-tools', 'ppmxy3d3'),
+            join_path('tools', 'seismic_3D-tools', 'rwav3d'),
+        ]
+        mkdir(prefix.bin)
+        for command in commands:
+            copy(command, prefix.bin)
+        install_tree('examples', prefix.examples)
+        install_tree('doc', prefix.doc)
+        install_tree('src', prefix.src)
+        copy('Makefile.in', prefix)
+        clean_dir = [
+            join_path(prefix.src, 'seismic_2D'),
+            join_path(prefix.src, 'seismic_3D', '1.ppohFDM-ppohVIS'),
+            join_path(prefix.src, 'seismic_3D', '3.parallel'),
+        ]
+        for d in clean_dir:
+            with working_dir(d):
+                make('clean')
+        force_remove(join_path(prefix, 'Makefile.in'))
diff --git a/var/spack/repos/builtin/packages/ppopen-appl-fdm/unused.patch b/var/spack/repos/builtin/packages/ppopen-appl-fdm/unused.patch
new file mode 100755
index 00000000000..4c6e67c65d9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ppopen-appl-fdm/unused.patch
@@ -0,0 +1,13 @@
+diff --git a/tools/seismic_2D-tools/rwav2d.f90 b/tools/seismic_2D-tools/rwav2d.f90
+index ec08ea8..0f9543c 100644
+--- a/tools/seismic_2D-tools/rwav2d.f90
++++ b/tools/seismic_2D-tools/rwav2d.f90
+@@ -41,7 +41,7 @@ program sort_seism2d_result
+ 
+   integer :: station_num
+   integer :: ns, isx, isz
+-  integer :: i, k, ii, kk, j, IT
++  integer :: i, k, ii, kk, j
+   character(len=80) filename, filename2, tmp1
+   integer  :: istx(5000,100), istz(5000,100), stnum(5000,100)
+   real(PN) :: ntime(5000,100), vxall(5000,100), vzall(5000,100)
diff --git a/var/spack/repos/builtin/packages/ppopen-math-vis/package.py b/var/spack/repos/builtin/packages/ppopen-math-vis/package.py
index ad2ff3a7c8f..0082783ed5a 100644
--- a/var/spack/repos/builtin/packages/ppopen-math-vis/package.py
+++ b/var/spack/repos/builtin/packages/ppopen-math-vis/package.py
@@ -43,3 +43,9 @@ def install(self, spec, prefix):
         copy_tree('examples', join_path(prefix, 'examples'))
         mkdir(join_path(prefix, 'doc'))
         copy_tree('doc', join_path(prefix, 'doc'))
+
+    @property
+    def libs(self):
+        return find_libraries(
+            ['libfppohvisfdm3d', 'libppohvisfdm3d'],
+            root=self.prefix, shared=False, recursive=True)

From 5e69125e51a88d87628c92c8308d1ee37c65d06b Mon Sep 17 00:00:00 2001
From: G-Ragghianti <33492707+G-Ragghianti@users.noreply.github.com>
Date: Mon, 20 Apr 2020 17:54:44 -0400
Subject: [PATCH 020/802] Implemented +shared and +static_tools variants
 (#16105)

---
 .../repos/builtin/packages/papi/package.py    | 30 +++++++++++++++----
 1 file changed, 25 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py
index 35dd4f9ba2c..76a67f8e775 100644
--- a/var/spack/repos/builtin/packages/papi/package.py
+++ b/var/spack/repos/builtin/packages/papi/package.py
@@ -2,6 +2,7 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import glob
 import os
 import sys
@@ -38,10 +39,20 @@ class Papi(AutotoolsPackage):
     variant('lmsensors', default=False, description='Enable lm_sensors support')
     variant('sde', default=False, description='Enable software defined events')
 
+    variant('shared', default=True, description='Build shared libraries')
+    # PAPI requires building static libraries, so there is no "static" variant
+    variant('static_tools', default=False, description='Statically link the PAPI tools')
+    # The PAPI configure option "--with-shlib-tools" is deprecated
+    # and therefore not implemented here
+
     depends_on('lm-sensors', when='+lmsensors')
 
     conflicts('%gcc@8:', when='@5.3.0', msg='Requires GCC version less than 8.0')
 
+    # This is the only way to match exactly version 6.0.0 without also
+    # including version 6.0.0.1 due to spack version matching logic
+    conflicts('@5.9.99999:6.0.0.a', when='+static_tools', msg='Static tools cannot build on version 6.0.0')
+
     # Does not build with newer versions of gcc, see
     # https://bitbucket.org/icl/papi/issues/46/cannot-compile-on-arch-linux
     patch('https://bitbucket.org/icl/papi/commits/53de184a162b8a7edff48fed01a15980664e15b1/raw', sha256='64c57b3ad4026255238cc495df6abfacc41de391a0af497c27d0ac819444a1f8', when='@5.4.0:5.6.99%gcc@8:')
@@ -55,15 +66,24 @@ def setup_build_environment(self, env):
     setup_run_environment = setup_build_environment
 
     def configure_args(self):
+        spec = self.spec
         # PAPI uses MPI if MPI is present; since we don't require
         # an MPI package, we ensure that all attempts to use MPI
         # fail, so that PAPI does not get confused
         options = ['MPICC=:']
-        # Build a list of activated variants (optional PAPI components)
-        variants = filter(lambda x: self.spec.variants[x].value is True,
-                          self.spec.variants)
-        if variants:
-            options.append('--with-components={0}'.format(' '.join(variants)))
+        # Build a list of PAPI components
+        components = filter(
+            lambda x: spec.variants[x].value,
+            ['example', 'infiniband', 'powercap', 'rapl', 'lmsensors', 'sde'])
+        if components:
+            options.append('--with-components=' + ' '.join(components))
+
+        build_shared = 'yes' if '+shared' in spec else 'no'
+        options.append('--with-shared-lib=' + build_shared)
+
+        if '+static_tools' in spec:
+            options.append('--with-static-tools')
+
         return options
 
     @run_before('configure')

From 45fee6edbd696ae1180dda066a8e714bc8676349 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Mon, 20 Apr 2020 16:57:08 -0500
Subject: [PATCH 021/802] Python: add latest Python 2 releases (#16191)

---
 var/spack/repos/builtin/packages/python/package.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 94a3f2d6453..8270ce7329c 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -26,7 +26,7 @@ class Python(AutotoolsPackage):
 
     homepage = "https://www.python.org/"
     url      = "https://www.python.org/ftp/python/3.8.0/Python-3.8.0.tgz"
-    list_url = "https://www.python.org/downloads/"
+    list_url = "https://www.python.org/ftp/python/"
     list_depth = 1
 
     maintainers = ['adamjstewart']
@@ -60,6 +60,8 @@ class Python(AutotoolsPackage):
     version('3.3.6',  sha256='0a58ad1f1def4ecc90b18b0c410a3a0e1a48cf7692c75d1f83d0af080e5d2034')
     version('3.2.6',  sha256='fc1e41296e29d476f696303acae293ae7a2310f0f9d0d637905e722a3f16163e')
     version('3.1.5',  sha256='d12dae6d06f52ef6bf1271db4d5b4d14b5dd39813e324314e72b648ef1bc0103')
+    version('2.7.18', sha256='da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814')
+    version('2.7.17', sha256='f22059d09cdf9625e0a7284d24a13062044f5bf59d93a7f3382190dfa94cecde')
     version('2.7.16', sha256='01da813a3600876f03f46db11cc5c408175e99f03af2ba942ef324389a83bad5')
     version('2.7.15', sha256='18617d1f15a380a919d517630a9cd85ce17ea602f9bbdc58ddc672df4b0239db')
     version('2.7.14', sha256='304c9b202ea6fbd0a4a8e0ad3733715fbd4749f2204a9173a58ec53c32ea73e8')

From e4805bb75ffd075318b31154fb9323ed360a8fad Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 21 Apr 2020 05:59:51 +0800
Subject: [PATCH 022/802] Add new package: sse2neon (#16168)

---
 .../builtin/packages/sse2neon/package.py      | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/sse2neon/package.py

diff --git a/var/spack/repos/builtin/packages/sse2neon/package.py b/var/spack/repos/builtin/packages/sse2neon/package.py
new file mode 100644
index 00000000000..5c01d6f0aec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sse2neon/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+
+
+class Sse2neon(Package):
+    """A C/C++ header file that converts Intel SSE intrinsics to ARN NEON
+    intrinsics."""
+
+    homepage = "https://github.com/jratcliff63367/sse2neon"
+    git      = "https://github.com/jratcliff63367/sse2neon.git"
+
+    version('master', branch='master')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.include)
+        headers = glob.glob('*.h')
+        for f in headers:
+            install(f, prefix.include)

From ca86e56572335e726a3351910b23b69cdfd24c36 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Mon, 20 Apr 2020 20:30:43 -0600
Subject: [PATCH 023/802] votca-*: remove rc versions (#16197)

---
 .../repos/builtin/packages/votca-csg-tutorials/package.py   | 5 +----
 var/spack/repos/builtin/packages/votca-csg/package.py       | 5 +----
 var/spack/repos/builtin/packages/votca-csgapps/package.py   | 5 +----
 var/spack/repos/builtin/packages/votca-tools/package.py     | 6 ++----
 var/spack/repos/builtin/packages/votca-xtp/package.py       | 5 +----
 5 files changed, 6 insertions(+), 20 deletions(-)

diff --git a/var/spack/repos/builtin/packages/votca-csg-tutorials/package.py b/var/spack/repos/builtin/packages/votca-csg-tutorials/package.py
index 50d770efa46..bba3ad0b485 100644
--- a/var/spack/repos/builtin/packages/votca-csg-tutorials/package.py
+++ b/var/spack/repos/builtin/packages/votca-csg-tutorials/package.py
@@ -21,14 +21,11 @@ class VotcaCsgTutorials(CMakePackage):
 
     version('master', branch='master')
     version('1.6', sha256='54946c647724f1beb95942d47ec7f4cf7a95a59ec7268522693d5ec723585daf')
-    version('1.6_rc2', sha256='3c82e6fe03c7d5226f37b787eee23eb629901734d19b93ef9eb519660ff5223c')
-    version('1.6_rc1', sha256='87c4d945d2bdcb247e985cd407b0767c441f7810f1237ae65a63617f136e2ac9')
     version('1.5.1',   sha256='e35cea92df0e7d05ca7b449c1b5d84d887a3a23c7796abe3b84e4d6feec7faca')
     version('1.5',     sha256='03b841fb94129cf59781a7a5e3b71936c414aa9dfa17a50d7bc856d46274580c')
     version('1.4.1',   sha256='623724192c3a7d76b603a74a3326f181045f10f38b9f56dce754a90f1a74556e')
     version('1.4',     sha256='27d50acd68a9d8557fef18ec2b0c62841ae91c22275ab9afbd65c35e4dd5f719')
 
-    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6_rc1", "1.6_rc2", "1.6",
-              "master"]:
+    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "master"]:
         depends_on('votca-csg@%s' % v, when="@%s:%s.0" % (v, v))
     depends_on("boost")
diff --git a/var/spack/repos/builtin/packages/votca-csg/package.py b/var/spack/repos/builtin/packages/votca-csg/package.py
index a1ac086ce93..0f0432d7020 100644
--- a/var/spack/repos/builtin/packages/votca-csg/package.py
+++ b/var/spack/repos/builtin/packages/votca-csg/package.py
@@ -21,16 +21,13 @@ class VotcaCsg(CMakePackage):
 
     version('master', branch='master')
     version('1.6', sha256='8cf6a4ac3ef7347c720a44d8a676f8cbd1462e162f6113de39f27b89354465ea')
-    version('1.6_rc2', sha256='32d19c7f8e30baece35462b6f8ae06bf0d7be038f875be38dc49da5798209236')
-    version('1.6_rc1', sha256='163701a65a34f90e8a850370167a82cbebf2b5c0774b7a8ad07884451fe9e332')
     version('1.5.1', sha256='7fca1261bd267bf38d2edd26259730fed3126c0c3fd91fb81940dbe17bb568fd')
     version('1.5', sha256='160387cdc51f87dd20ff2e2eed97086beee415d48f3c92f4199f6109068c8ff4')
     version('1.4.1', sha256='41dccaecadd0165c011bec36a113629e27745a5a133d1a042efe4356acdb5450')
     version('1.4', sha256='c13e7febd792de8c3d426203f089bd4d33b8067f9db5e8840e4579c88b61146e')
 
     depends_on("cmake@2.8:", type='build')
-    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6_rc1", "1.6_rc2", "1.6",
-              "master"]:
+    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "master"]:
         depends_on('votca-tools@%s' % v, when="@%s:%s.0" % (v, v))
     depends_on("boost")
     depends_on("gromacs~mpi@5.1:")
diff --git a/var/spack/repos/builtin/packages/votca-csgapps/package.py b/var/spack/repos/builtin/packages/votca-csgapps/package.py
index ee627df1f21..929bd73c790 100644
--- a/var/spack/repos/builtin/packages/votca-csgapps/package.py
+++ b/var/spack/repos/builtin/packages/votca-csgapps/package.py
@@ -21,14 +21,11 @@ class VotcaCsgapps(CMakePackage):
 
     version('master', branch='master')
     version('1.6', sha256='084bbc5b179bb7eb8f6671d2d5fa13e69e68946570c9120a7e4b10aff1866e2e')
-    version('1.6_rc2', sha256='4d829b10ada32ca9e589f894ca3f69fc14329af4b6f5fee32d5e07d2457a615a')
-    version('1.6_rc1', sha256='069002f93f891e4aeb24920c1b2458bf8ee4842d273481aea5fa32247f815f02')
     version('1.5.1',   sha256='b4946711e88a1745688b6cce5aad872e6e2ea200fededf38d77a864883e3750e')
     version('1.5',     sha256='18b40ce6222509bc70aa9d56b8c538cd5903edf7294d6f95530668e555206d5b')
     version('1.4.1',   sha256='095d9ee4cd49d2fd79c10e0e84e6890b755e54dec6a5cd580a2b4241ba230a2b')
     version('1.4',     sha256='4ea8348c2f7de3cc488f48fbd8652e69b52515441952766c06ff67ed1aaf69a0')
 
-    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6_rc1", "1.6_rc2", "1.6",
-              "master"]:
+    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "master"]:
         depends_on('votca-csg@%s' % v, when="@%s:%s.0" % (v, v))
     depends_on("boost")
diff --git a/var/spack/repos/builtin/packages/votca-tools/package.py b/var/spack/repos/builtin/packages/votca-tools/package.py
index 2ab759567e4..52c9683f13a 100644
--- a/var/spack/repos/builtin/packages/votca-tools/package.py
+++ b/var/spack/repos/builtin/packages/votca-tools/package.py
@@ -21,15 +21,13 @@ class VotcaTools(CMakePackage):
 
     version('master', branch='master')
     version('1.6', sha256='cfd0fedc80fecd009f743b5df47777508d76bf3ef294a508a9f11fbb42efe9a5')
-    version('1.6_rc2', sha256='1998148dc5bbdb63d05c24d19b4a803d9b2c800891a813fd846e53616d49abcd')
-    version('1.6_rc1', sha256='59b4bb64a93786a693e0cbc743a27c0bc451b9db2b0f63e4d2866f7aba10c268')
     version('1.5.1', sha256='4be4fe25a2910e24e1720cd9022d214001d38196033ade8f9d6e618b4f47d5c4')
     version('1.5', sha256='a82a6596c24ff06e79eab17ca02f4405745ceeeb66369693a59023ad0b62cf22')
     version('1.4.1', sha256='b6b87f6bec8db641a1d8660422ca44919252a69494b32ba6c8c9ac986bae9a65')
     version('1.4', sha256='41638122e7e59852af61d391b4ab8c308fd2e16652f768077e13a99d206ec5d3')
 
-    # https://github.com/votca/tools/pull/197, fix cmake module
-    patch("https://github.com/votca/tools/pull/197.patch", sha256="a06cce2a9cee63c8d01e4d1833f9cd2ba817b846c86fdb51ea5c9cd843135e68", when="@1.6_rc1")
+    # https://github.com/votca/tools/pull/229, fix mkl in exported target
+    patch("https://github.com/votca/tools/pull/229.patch", sha256="250d0b679e5d3104e3c8d6adf99751b71386c7ed4cbdae1c75408717ef3f401f", when="@1.6+mkl")
 
     variant('mkl', default=False, description='Build with MKL support')
     conflicts('+mkl', when='@:1.5.9999')
diff --git a/var/spack/repos/builtin/packages/votca-xtp/package.py b/var/spack/repos/builtin/packages/votca-xtp/package.py
index 3ff8b2537da..96c8de3f5b9 100644
--- a/var/spack/repos/builtin/packages/votca-xtp/package.py
+++ b/var/spack/repos/builtin/packages/votca-xtp/package.py
@@ -21,15 +21,12 @@ class VotcaXtp(CMakePackage):
 
     version('master', branch='master')
     version('1.6', sha256='695c2d9d3f924103481529f992e3723bdce10b8edfc294421a849cdf51dbbb6e')
-    version('1.6_rc2', sha256='adc155e741a05e2bbfe9d928cdc4b2ec2ded34bc06aff59eaacf56c13a680be5')
-    version('1.6_rc1', sha256='144e74a6c4d31e490ca2bfaf4a30df12ccdc303efa5a7d1177c9b80035365ad5')
     version('1.5.1', sha256='17a7722e5a32d236e4f1f6f88b680da4ba5f52bcf65bca3687c6a1c731d10881')
     version('1.5', sha256='b40b6d19e13f0650e84b8beebe86ce5c09071624f18d66df826f9d8584b4d3c8')
     version('1.4.1', sha256='4b53d371d6cf648c9e9e9bd1f104d349cafeaf10a02866e3f1d05c574b595a21')
 
     depends_on("cmake@2.8:", type='build')
-    for v in ["1.4.1", "1.5", "1.5.1", "1.6_rc1", "1.6_rc2", "1.6",
-              "master"]:
+    for v in ["1.4.1", "1.5", "1.5.1", "1.6", "master"]:
         depends_on('votca-tools@%s' % v, when="@%s:%s.0" % (v, v))
         depends_on('votca-csg@%s' % v, when="@%s:%s.0" % (v, v))
     depends_on("libxc", when='@1.5:')

From 6c8e15ee18ff11f96a4cbf99a232e90f5b090050 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Mon, 20 Apr 2020 21:47:04 -0700
Subject: [PATCH 024/802] gettext: add missing iconv dependency (#16193)

`gettext` will pick up a random `iconv` dependency if not
specified, which crashes python and its own builds on macOS.
---
 var/spack/repos/builtin/packages/gettext/package.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py
index 8eb0ad6f099..27165da5b45 100644
--- a/var/spack/repos/builtin/packages/gettext/package.py
+++ b/var/spack/repos/builtin/packages/gettext/package.py
@@ -27,6 +27,7 @@ class Gettext(AutotoolsPackage, GNUMirrorPackage):
     # Optional variants
     variant('libunistring', default=False, description='Use libunistring')
 
+    depends_on('iconv')
     # Recommended dependencies
     depends_on('ncurses',  when='+curses')
     depends_on('libxml2',  when='+libxml2')
@@ -50,7 +51,8 @@ def configure_args(self):
 
         config_args = [
             '--disable-java',
-            '--disable-csharp',
+            '--disable-icsharp',
+            '--with-libiconv-prefix={0}'.format(spec['iconv'].prefix),
             '--with-included-glib',
             '--with-included-gettext',
             '--with-included-libcroco',

From cd5d477db9ca4625993556894e1af7d7e40ae087 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Tue, 21 Apr 2020 15:02:45 +0200
Subject: [PATCH 025/802] qgis: Fix pkgconfig dependency (#16188)

---
 var/spack/repos/builtin/packages/qgis/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/qgis/package.py b/var/spack/repos/builtin/packages/qgis/package.py
index 1edf4c29720..86d0756e540 100644
--- a/var/spack/repos/builtin/packages/qgis/package.py
+++ b/var/spack/repos/builtin/packages/qgis/package.py
@@ -107,7 +107,7 @@ class Qgis(CMakePackage):
     depends_on('cmake@3.0.0:', type='build')
     depends_on('flex@2.5.6:', type='build')
     depends_on('bison@2.4:', type='build')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     # Take care of conflicts using depends_on
     depends_on('proj@5:', when='@3.8.2:')

From a41b9365a9a7d302fc08f5c0e4ca746549cf63c7 Mon Sep 17 00:00:00 2001
From: Andrew Gaspar <agaspar@lanl.gov>
Date: Tue, 21 Apr 2020 09:15:59 -0600
Subject: [PATCH 026/802] catch2: added v2.12 (#16207)

---
 var/spack/repos/builtin/packages/catch2/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/catch2/package.py b/var/spack/repos/builtin/packages/catch2/package.py
index 6961afad299..5d3d25d7631 100644
--- a/var/spack/repos/builtin/packages/catch2/package.py
+++ b/var/spack/repos/builtin/packages/catch2/package.py
@@ -14,6 +14,7 @@ class Catch2(CMakePackage):
     url      = "https://github.com/catchorg/Catch2/archive/v2.9.1.tar.gz"
     maintainers = ['ax3l']
 
+    version('2.12.0', sha256='6606b754363d3a4521bfecf717dc1972c50dca282bd428dfb1370ec8b9c26918')
     version('2.11.3', sha256='9a6967138062688f04374698fce4ce65908f907d8c0fe5dfe8dc33126bd46543')
     version('2.11.2', sha256='a96203fa531092375678ad2d81c43317ee58c684787f24b2a55748f6c6839799')
     version('2.11.1', sha256='9af06ca5b10362620c6c9c729821367e1aeb0f76adfc7bc3a468da83db3c50c6')

From b9655636ceaeaf931fc515ef8e2c7c0e28772131 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Tue, 21 Apr 2020 17:48:48 +0200
Subject: [PATCH 027/802] gettext: Fix typo (#16206)

---
 var/spack/repos/builtin/packages/gettext/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py
index 27165da5b45..8076ccb8419 100644
--- a/var/spack/repos/builtin/packages/gettext/package.py
+++ b/var/spack/repos/builtin/packages/gettext/package.py
@@ -51,7 +51,7 @@ def configure_args(self):
 
         config_args = [
             '--disable-java',
-            '--disable-icsharp',
+            '--disable-csharp',
             '--with-libiconv-prefix={0}'.format(spec['iconv'].prefix),
             '--with-included-glib',
             '--with-included-gettext',

From eb7c0e5d7d8611e760b1259bf50435b22b71ac95 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Tue, 21 Apr 2020 17:49:59 +0200
Subject: [PATCH 028/802] gettext: Fix typo (#16206)


From 752342430b9bba914f7df6a33d1a4f1d3c14b982 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Tue, 21 Apr 2020 18:33:51 +0200
Subject: [PATCH 029/802] gettext: Fix typo (#16206)


From 4f5bd044d61af99cb7741b360d0f48f031f212fa Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 21 Apr 2020 11:43:30 -0500
Subject: [PATCH 030/802] py-torchvision: add new version (#16208)

---
 .../repos/builtin/packages/py-torchvision/package.py  | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-torchvision/package.py b/var/spack/repos/builtin/packages/py-torchvision/package.py
index bfef2202e26..faee2f087a0 100644
--- a/var/spack/repos/builtin/packages/py-torchvision/package.py
+++ b/var/spack/repos/builtin/packages/py-torchvision/package.py
@@ -11,7 +11,7 @@ class PyTorchvision(PythonPackage):
     architectures, and common image transformations for computer vision."""
 
     homepage = "https://github.com/pytorch/vision"
-    url      = "https://github.com/pytorch/vision/archive/v0.5.0.tar.gz"
+    url      = "https://github.com/pytorch/vision/archive/v0.6.0.tar.gz"
 
     maintainers = ['adamjstewart']
     import_modules = [
@@ -21,17 +21,20 @@ class PyTorchvision(PythonPackage):
         'torchvision.models.detection'
     ]
 
+    version('0.6.0', sha256='02de11b3abe6882de4032ce86dab9c7794cbc84369b44d04e667486580f0f1f7')
     version('0.5.0', sha256='eb9afc93df3d174d975ee0914057a9522f5272310b4d56c150b955c287a4d74d')
     version('0.4.2', sha256='1184a27eab85c9e784bacc6f9d6fec99e168ab4eda6047ef9f709e7fdb22d8f9')
     version('0.4.1', sha256='053689351272b3bd2ac3e6ba51efd284de0e4ca4a301f54674b949f1e62b7176')
     version('0.4.0', sha256='c270d74e568bad4559fed4544f6dd1e22e2eb1c60b088e04a5bd5787c4150589')
     version('0.3.0', sha256='c205f0618c268c6ed2f8abb869ef6eb83e5339c1336c243ad321a2f2a85195f0')
 
+    depends_on('python@3:', when='@0.6:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
     depends_on('py-numpy', type=('build', 'run'))
-    depends_on('py-six', type=('build', 'run'))
-    depends_on('py-torch@1.2.0:', when='@0.4.0:', type=('build', 'run'))
-    depends_on('py-torch@1.1.0:', type=('build', 'run'))
+    depends_on('py-six', when='@:0.5', type=('build', 'run'))
+    depends_on('py-torch@1.4:', when='@0.6:', type=('build', 'run'))
+    depends_on('py-torch@1.2:', when='@0.4:', type=('build', 'run'))
+    depends_on('py-torch@1.1:', type=('build', 'run'))
     # https://github.com/pytorch/vision/issues/1712
     depends_on('py-pillow@4.1.1:6', when='@:0.4', type=('build', 'run'))  # or py-pillow-simd
     depends_on('py-pillow@4.1.1:',  when='@0.5:', type=('build', 'run'))  # or py-pillow-simd

From 74c159b883ae673710c7a8bcfb1e3543c011152b Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Tue, 21 Apr 2020 13:27:34 -0500
Subject: [PATCH 031/802] New package: sumo (#16096)

* New package: sumo

This PR adds the sumo package, as well as the fox package as a
dependency. It also updates and adds some fixes for openscenegraph.

For fox, the patch is for the development version. That patch should not
be necessary in future versions as it has been applied upstream. The
stable version is 1.6.57 and is marked as preferred. This is the version
needed for sumo.

Added dependencies for openscenegraph as well as set constraints on qt
versions.

* Update var/spack/repos/builtin/packages/sumo/package.py

I had intended to set this version constraint but somehow did not.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Add dependency types to sumo recipe

- googletest: 'test'
- swig: 'build'
- java: 'build', 'run'

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../builtin/packages/fox/no_rexdebug.patch    | 11 ++++
 .../repos/builtin/packages/fox/package.py     | 46 ++++++++++++++++
 .../packages/openscenegraph/package.py        | 16 ++++--
 .../repos/builtin/packages/sumo/package.py    | 55 +++++++++++++++++++
 4 files changed, 124 insertions(+), 4 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/fox/no_rexdebug.patch
 create mode 100644 var/spack/repos/builtin/packages/fox/package.py
 create mode 100644 var/spack/repos/builtin/packages/sumo/package.py

diff --git a/var/spack/repos/builtin/packages/fox/no_rexdebug.patch b/var/spack/repos/builtin/packages/fox/no_rexdebug.patch
new file mode 100644
index 00000000000..3d0c0cf754c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fox/no_rexdebug.patch
@@ -0,0 +1,11 @@
+--- a/lib/FXRex.cpp	2019-08-22 21:46:13.000000000 -0500
++++ b/lib/FXRex.cpp	2020-04-13 16:46:31.718701955 -0500
+@@ -503,7 +503,7 @@
+ */
+ 
+ // Debugging regex code
+-#define REXDEBUG 1
++// #define REXDEBUG 1
+ 
+ // As close to infinity as we're going to get; this seems big enough.  We can not make
+ // it too large as this may wrap around when added to something else!
diff --git a/var/spack/repos/builtin/packages/fox/package.py b/var/spack/repos/builtin/packages/fox/package.py
new file mode 100644
index 00000000000..28e6e9b7b31
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fox/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fox(AutotoolsPackage):
+    """FOX is a C++ based Toolkit for developing Graphical User Interfaces
+    easily and effectively. It offers a wide, and growing, collection of
+    Controls, and provides state of the art facilities such as drag and drop,
+    selection, as well as OpenGL widgets for 3D graphical manipulation. FOX
+    also implements icons, images, and user-convenience features such as status
+    line help, and tooltips. Tooltips may even be used for 3D objects!"""
+
+    homepage = "http://fox-toolkit.org/"
+    url      = "http://fox-toolkit.org/ftp/fox-1.7.67.tar.gz"
+
+    version('1.7.67', sha256='7e511685119ef096fa90d334da46f0e50cfed8d414df32d80a7850442052f57d')
+    version('1.6.57', preferred=True, sha256='65ef15de9e0f3a396dc36d9ea29c158b78fad47f7184780357b929c94d458923')
+
+    patch('no_rexdebug.patch', when='@1.7.67')
+
+    variant('opengl', default=False, description='opengl support')
+
+    depends_on('bzip2')
+    depends_on('jpeg')
+    depends_on('libpng')
+    depends_on('libtiff')
+    depends_on('zlib')
+    depends_on('libx11')
+    depends_on('libsm')
+    depends_on('libxft')
+    depends_on('libxext')
+    depends_on('libxcursor')
+    depends_on('libxi')
+    depends_on('libxrandr')
+    depends_on('gl', when='+opengl')
+
+    def configure_args(self):
+        # Make the png link flags explicit or it will try to pick up libpng15
+        # from system
+        args = ['LDFLAGS={0}'.format(self.spec['libpng'].libs.search_flags)]
+        args += self.with_or_without('opengl')
+        return args
diff --git a/var/spack/repos/builtin/packages/openscenegraph/package.py b/var/spack/repos/builtin/packages/openscenegraph/package.py
index c0cb024c144..5f2646729e1 100644
--- a/var/spack/repos/builtin/packages/openscenegraph/package.py
+++ b/var/spack/repos/builtin/packages/openscenegraph/package.py
@@ -14,6 +14,7 @@ class Openscenegraph(CMakePackage):
     homepage = "http://www.openscenegraph.org"
     url      = "https://github.com/openscenegraph/OpenSceneGraph/archive/OpenSceneGraph-3.6.4.tar.gz"
 
+    version('3.6.5', sha256='aea196550f02974d6d09291c5d83b51ca6a03b3767e234a8c0e21322927d1e12')
     version('3.6.4', sha256='81394d1b484c631028b85d21c5535280c21bbd911cb058e8746c87e93e7b9d33')
     version('3.2.3', sha256='a1ecc6524197024834e1277916922b32f30246cb583e27ed19bf3bf889534362')
     version('3.1.5', sha256='dddecf2b33302076712100af59b880e7647bc595a9a7cc99186e98d6e0eaeb5c')
@@ -21,8 +22,11 @@ class Openscenegraph(CMakePackage):
     variant('shared', default=True, description='Builds a shared version of the library')
 
     depends_on('cmake@2.8.7:', type='build')
-    depends_on('qt@4:')
+    depends_on('qt@4:', when='@3.2:')
+    depends_on('qt@:4', when='@:3.1')
     depends_on('zlib')
+    depends_on('libxinerama')
+    depends_on('libxrandr')
 
     def cmake_args(self):
         spec = self.spec
@@ -32,13 +36,17 @@ def cmake_args(self):
         args = [
             '-DDYNAMIC_OPENSCENEGRAPH={0}'.format(shared_status),
             '-DDYNAMIC_OPENTHREADS={0}'.format(shared_status),
-            '-DZLIB_INCLUDE_DIR={0}'.format(spec['zlib'].prefix.include),
-            '-DZLIB_LIBRARY={0}/libz.{1}'.format(spec['zlib'].prefix.lib,
-                                                 dso_suffix),
             '-DBUILD_OSG_APPLICATIONS=OFF',
             '-DOSG_NOTIFY_DISABLED=ON',
             '-DLIB_POSTFIX=',
+            '-DCMAKE_RELWITHDEBINFO_POSTFIX=',
         ]
+        if spec.satisfies('@:3.2'):
+            args.extend([
+                '-DZLIB_INCLUDE_DIR={0}'.format(spec['zlib'].prefix.include),
+                '-DZLIB_LIBRARY={0}/libz.{1}'.format(spec['zlib'].prefix.lib,
+                                                     dso_suffix),
+            ])
 
         # NOTE: This is necessary in order to allow OpenSceneGraph to compile
         # despite containing a number of implicit bool to int conversions.
diff --git a/var/spack/repos/builtin/packages/sumo/package.py b/var/spack/repos/builtin/packages/sumo/package.py
new file mode 100644
index 00000000000..0fbd58303d8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sumo/package.py
@@ -0,0 +1,55 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Sumo(CMakePackage):
+    """Eclipse SUMO is an open source, highly portable, microscopic and
+    continuous road traffic simulation package designed to handle large road
+    networks. It allows for intermodal simulation including pedestrians and
+    comes with a large set of tools for scenario creation."""
+
+    homepage = "http://projects.eclipse.org/projects/technology.sumo"
+    url      = "https://github.com/eclipse/sumo/archive/v1_5_0.tar.gz"
+
+    version('1.5.0', sha256='be6ba0361b487a5e71c81e60b4c07a67826d5e170500c10c37374c1086ac2cb6')
+
+    variant('gdal',
+            default=True,
+            description='gdal support, for arcgis')
+    variant('ffmpeg',
+            default=False,
+            description='ffmpeg support, for video output')
+    variant('openscenegraph',
+            default=False,
+            description='openscenegraph support, for experimental 3D GUI')
+    variant('gl2ps',
+            default=False,
+            description='gl2ps support')
+    variant('eigen',
+            default=False,
+            description='eigen support')
+
+    extends('python')
+    depends_on('py-setuptools', type='build')
+    depends_on('googletest', type='test')
+    depends_on('xerces-c')
+    depends_on('proj')
+    depends_on('fox@1.6.57+opengl')
+    depends_on('swig', type='build')
+    depends_on('java', type=('build', 'run'))
+    depends_on('gdal', when='+gdal')
+    depends_on('ffmpeg', when='+ffmpeg')
+    depends_on('openscenegraph', when='+openscenegraph')
+    depends_on('gl2ps', when='+gl2ps')
+    depends_on('eigen', when='+eigen')
+
+    def url_for_version(self, version):
+        url = "https://github.com/eclipse/sumo/archive/v{0}.tar.gz"
+        return url.format(version.underscored)
+
+    def setup_run_environment(self, env):
+        env.set('SUMO_HOME', self.prefix)

From f1050c4be2954db88342f052f24326fb3017b7e0 Mon Sep 17 00:00:00 2001
From: Andrew W Elble <aweits@rit.edu>
Date: Tue, 21 Apr 2020 16:56:50 -0400
Subject: [PATCH 032/802] compiler wrappers: don't override -isystem with -I
 (#16077)

If the Spack compiler wrapper encounters any "-isystem" option, then
when adding include directories for Spack dependencies, Spack will
use "-isystem" instead of "-I". This prevents Spack-generated "-I"
options from overriding the "-isystem" options generated by the build
system. To ensure that build-system "-isystem" directories are
searched first, Spack places all of its inserted "-isystem"
directories after.

The new ordering of -isystem includes is:

* -isystem from build system (not system directories)
* -isystem from Spack
* -isystem from build system (for directories like /usr/include)

The prior order of "-I" arguments is preserved (although as of this
commit Spack no longer generates -I if -isystem is detected):

* -I from build system (not system directories)
* -I from Spack (only if there are no "-isystem" options)
* -I from build system (for directories like /usr/include)
---
 lib/spack/env/cc           | 48 +++++++++++++++++++--------
 lib/spack/spack/test/cc.py | 68 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 102 insertions(+), 14 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index f2b8bf577f5..b5913c5f10b 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -15,9 +15,9 @@
 # 1. It allows Spack to swap compilers into and out of builds easily.
 # 2. It adds several options to the compile line so that spack
 #    packages can find their dependencies at build time and run time:
-#      -I           arguments for dependency /include directories.
-#      -L           arguments for dependency /lib directories.
-#      -Wl,-rpath   arguments for dependency /lib directories.
+#      -I and/or -isystem arguments for dependency /include directories.
+#      -L                 arguments for dependency /lib directories.
+#      -Wl,-rpath         arguments for dependency /lib directories.
 #
 
 # This is an array of environment variables that need to be set before
@@ -251,10 +251,11 @@ input_command="$*"
 #
 # Parse the command line arguments.
 #
-# We extract -L, -I, and -Wl,-rpath arguments from the command line and
-# recombine them with Spack arguments later.  We parse these out so that
-# we can make sure that system paths come last, that package arguments
-# come first, and that Spack arguments are injected properly.
+# We extract -L, -I, -isystem and -Wl,-rpath arguments from the
+# command line and recombine them with Spack arguments later.  We
+# parse these out so that we can make sure that system paths come
+# last, that package arguments come first, and that Spack arguments
+# are injected properly.
 #
 # All other arguments, including -l arguments, are treated as
 # 'other_args' and left in their original order.  This ensures that
@@ -273,12 +274,24 @@ system_libdirs=()
 system_rpaths=()
 libs=()
 other_args=()
+isystem_system_includes=()
+isystem_includes=()
 
 while [ -n "$1" ]; do
     # an RPATH to be added after the case statement.
     rp=""
 
     case "$1" in
+        -isystem*)
+            arg="${1#-isystem}"
+	    isystem_was_used=true
+            if [ -z "$arg" ]; then shift; arg="$1"; fi
+            if system_dir "$arg"; then
+                isystem_system_includes+=("$arg")
+            else
+                isystem_includes+=("$arg")
+            fi
+            ;;
         -I*)
             arg="${1#-I}"
             if [ -z "$arg" ]; then shift; arg="$1"; fi
@@ -425,12 +438,6 @@ then
     esac
 fi
 
-# Prepend include directories
-IFS=':' read -ra include_dirs <<< "$SPACK_INCLUDE_DIRS"
-if [[ $mode == cpp || $mode == cc || $mode == as || $mode == ccld ]]; then
-    includes=("${includes[@]}" "${include_dirs[@]}")
-fi
-
 IFS=':' read -ra rpath_dirs <<< "$SPACK_RPATH_DIRS"
 if [[ $mode == ccld || $mode == ld ]]; then
 
@@ -481,9 +488,22 @@ args=()
 # flags assembled earlier
 args+=("${flags[@]}")
 
-# include directory search paths
+# Insert include directories just prior to any system include directories
+
 for dir in "${includes[@]}";         do args+=("-I$dir"); done
+for dir in "${isystem_includes[@]}";         do args+=("-isystem$dir"); done
+
+IFS=':' read -ra spack_include_dirs <<< "$SPACK_INCLUDE_DIRS"
+if [[ $mode == cpp || $mode == cc || $mode == as || $mode == ccld ]]; then
+    if [[ "$isystem_was_used" == "true" ]] ; then
+	for dir in "${spack_include_dirs[@]}";  do args+=("-isystem$dir"); done
+    else
+	for dir in "${spack_include_dirs[@]}";  do args+=("-I$dir"); done
+    fi
+fi
+
 for dir in "${system_includes[@]}";  do args+=("-I$dir"); done
+for dir in "${isystem_system_includes[@]}";  do args+=("-isystem$dir"); done
 
 # Library search paths
 for dir in "${libdirs[@]}";          do args+=("-L$dir"); done
diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py
index c1e1db914f8..7b8d34fbde2 100644
--- a/lib/spack/spack/test/cc.py
+++ b/lib/spack/spack/test/cc.py
@@ -338,6 +338,36 @@ def test_ccld_deps():
             test_args_without_paths)
 
 
+def test_ccld_deps_isystem():
+    """Ensure all flags are added in ccld mode.
+       When a build uses -isystem, Spack should inject it's
+       include paths using -isystem. Spack will insert these
+       after any provided -isystem includes, but before any
+       system directories included using -isystem"""
+    with set_env(SPACK_INCLUDE_DIRS='xinc:yinc:zinc',
+                 SPACK_RPATH_DIRS='xlib:ylib:zlib',
+                 SPACK_LINK_DIRS='xlib:ylib:zlib'):
+        mytest_args = test_args + ['-isystemfooinc']
+        check_args(
+            cc, mytest_args,
+            [real_cc] +
+            test_include_paths +
+            ['-isystemfooinc',
+             '-isystemxinc',
+             '-isystemyinc',
+             '-isystemzinc'] +
+            test_library_paths +
+            ['-Lxlib',
+             '-Lylib',
+             '-Lzlib'] +
+            ['-Wl,--disable-new-dtags'] +
+            test_wl_rpaths +
+            ['-Wl,-rpath,xlib',
+             '-Wl,-rpath,ylib',
+             '-Wl,-rpath,zlib'] +
+            test_args_without_paths)
+
+
 def test_cc_deps():
     """Ensure -L and RPATHs are not added in cc mode."""
     with set_env(SPACK_INCLUDE_DIRS='xinc:yinc:zinc',
@@ -390,6 +420,44 @@ def test_ccld_with_system_dirs():
             test_args_without_paths)
 
 
+def test_ccld_with_system_dirs_isystem():
+    """Ensure all flags are added in ccld mode.
+       Ensure that includes are in the proper
+       place when a build uses -isystem, and uses
+       system directories in the include paths"""
+    with set_env(SPACK_INCLUDE_DIRS='xinc:yinc:zinc',
+                 SPACK_RPATH_DIRS='xlib:ylib:zlib',
+                 SPACK_LINK_DIRS='xlib:ylib:zlib'):
+
+        sys_path_args = ['-isystem/usr/include',
+                         '-L/usr/local/lib',
+                         '-Wl,-rpath,/usr/lib64',
+                         '-isystem/usr/local/include',
+                         '-L/lib64/']
+        check_args(
+            cc, sys_path_args + test_args,
+            [real_cc] +
+            test_include_paths +
+            ['-isystemxinc',
+             '-isystemyinc',
+             '-isystemzinc'] +
+            ['-isystem/usr/include',
+             '-isystem/usr/local/include'] +
+            test_library_paths +
+            ['-Lxlib',
+             '-Lylib',
+             '-Lzlib'] +
+            ['-L/usr/local/lib',
+             '-L/lib64/'] +
+            ['-Wl,--disable-new-dtags'] +
+            test_wl_rpaths +
+            ['-Wl,-rpath,xlib',
+             '-Wl,-rpath,ylib',
+             '-Wl,-rpath,zlib'] +
+            ['-Wl,-rpath,/usr/lib64'] +
+            test_args_without_paths)
+
+
 def test_ld_deps():
     """Ensure no (extra) -I args or -Wl, are passed in ld mode."""
     with set_env(SPACK_INCLUDE_DIRS='xinc:yinc:zinc',

From 745804582be4c8ef25ba9b0cb7dee62aa6e4b8a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gregor=20Dai=C3=9F?= <G-071@users.noreply.github.com>
Date: Tue, 21 Apr 2020 23:03:46 +0200
Subject: [PATCH 033/802] Add new package: sgpp (#15961)

* sgpp: Added recipe

* sgpp: Removed maintainer and updated patch

* sgpp: Added more conflicts

* sgpp: Added conflicts for older combigrid versions

* sgpp: Added one more maintainer

* sgpp: Add version 3.3.0 and sane defaults

* sgpp: Better description and c++11 conflicts

* sgpp: Updated maintainers

* sgpp: Fix flake8 errors

* sgpp: Fix dependencies and minor issues

- Added py-setuptools dependency
- Fixed zlib link dependency
- Added git url
- Using spec.satisfies where appropriate

* sgpp: Added testing to package

* sgpp: Remove simd variant and use spec instead

* sgpp: Remove java variant

* sgpp: Small bugfixes

* sgpp: Add datadriven patch and patch explanations
---
 .../sgpp/avx512_datadriven_compilation.patch  |  21 ++
 .../builtin/packages/sgpp/directory.patch     |  22 ++
 .../builtin/packages/sgpp/fix-setup-py.patch  | 160 ++++++++++++++
 .../repos/builtin/packages/sgpp/ocl.patch     |  13 ++
 .../repos/builtin/packages/sgpp/package.py    | 205 ++++++++++++++++++
 5 files changed, 421 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/sgpp/avx512_datadriven_compilation.patch
 create mode 100644 var/spack/repos/builtin/packages/sgpp/directory.patch
 create mode 100644 var/spack/repos/builtin/packages/sgpp/fix-setup-py.patch
 create mode 100644 var/spack/repos/builtin/packages/sgpp/ocl.patch
 create mode 100644 var/spack/repos/builtin/packages/sgpp/package.py

diff --git a/var/spack/repos/builtin/packages/sgpp/avx512_datadriven_compilation.patch b/var/spack/repos/builtin/packages/sgpp/avx512_datadriven_compilation.patch
new file mode 100644
index 00000000000..268cba63587
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sgpp/avx512_datadriven_compilation.patch
@@ -0,0 +1,21 @@
+diff --git a/datadriven/src/sgpp/datadriven/operation/hash/OperationMultiEvalStreaming/OperationMultiEvalStreaming_multImpl.cpp b/datadriven/src/sgpp/datadriven/operation/hash/OperationMultiEvalStreaming/OperationMultiEvalStreaming_multImpl.cpp
+index 7fafd43d4..ea15ba137 100644
+--- a/datadriven/src/sgpp/datadriven/operation/hash/OperationMultiEvalStreaming/OperationMultiEvalStreaming_multImpl.cpp
++++ b/datadriven/src/sgpp/datadriven/operation/hash/OperationMultiEvalStreaming/OperationMultiEvalStreaming_multImpl.cpp
+@@ -295,6 +295,7 @@ void OperationMultiEvalStreaming::multImpl(
+   _mm512_extload_pd(A, _MM_UPCONV_PD_NONE, _MM_BROADCAST_1X8, _MM_HINT_NONE)
+ #define _mm512_max_pd(A, B) _mm512_gmax_pd(A, B)
+ #define _mm512_set1_epi64(A) _mm512_set_1to8_epi64(A)
++#define _mm512_set1_pd(A) _mm512_set_1to8_pd(A)
+ #endif
+ #if defined(__AVX512F__)
+ #define _mm512_broadcast_sd(A) _mm512_broadcastsd_pd(_mm_load_sd(A))
+@@ -409,7 +410,7 @@ void OperationMultiEvalStreaming::multImpl(
+         eval_11 = _mm512_castsi512_pd(_mm512_and_epi64(abs2Mask, _mm512_castpd_si512(eval_11)));
+ #endif
+ 
+-        __m512d one = _mm512_set_1to8_pd(1.0);
++        __m512d one = _mm512_set1_pd(1.0);
+ 
+         eval_0 = _mm512_sub_pd(one, eval_0);
+         eval_1 = _mm512_sub_pd(one, eval_1);
diff --git a/var/spack/repos/builtin/packages/sgpp/directory.patch b/var/spack/repos/builtin/packages/sgpp/directory.patch
new file mode 100644
index 00000000000..f1b22864231
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sgpp/directory.patch
@@ -0,0 +1,22 @@
+diff --git a/SConstruct b/SConstruct
+index 98c1a56ac..30baef5e5 100644
+--- a/SConstruct
++++ b/SConstruct
+@@ -293,7 +293,7 @@ Parameters are:
+            for line in vars.GenerateHelpText(env).splitlines()]))
+ 
+ # add trailing slashes were required and if not present
+-BUILD_DIR = Dir(os.path.join("lib", "sgpp"))
++BUILD_DIR = Dir(os.path.join("lib"))
+ Export("BUILD_DIR")
+ PYSGPP_PACKAGE_PATH = Dir(os.path.join("lib"))
+ Export("PYSGPP_PACKAGE_PATH")
+@@ -550,7 +550,7 @@ env.SideEffect("sideEffectFinalSteps", exampleTargetList)
+ #########################################################################
+ 
+ installLibSGpp = env.Alias("install-lib-sgpp",
+-                           env.Install(os.path.join(env.get("LIBDIR"), "sgpp"),
++                           env.Install(os.path.join(env.get("LIBDIR")),
+                                        libraryTargetList))
+ 
+ headerFinalDestList = []
diff --git a/var/spack/repos/builtin/packages/sgpp/fix-setup-py.patch b/var/spack/repos/builtin/packages/sgpp/fix-setup-py.patch
new file mode 100644
index 00000000000..e201a5dff08
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sgpp/fix-setup-py.patch
@@ -0,0 +1,160 @@
+diff --git a/setup.py b/setup.py
+index af1ec083e..d971f87c5 100644
+--- a/setup.py
++++ b/setup.py
+@@ -1,5 +1,5 @@
+-#!/usr/bin/env python
+-# Copyright (C) 2008-today The SG++ Project
++#!/usr/bin/env python
++# Copyright (C) 2008-today The SG++ project
+ # This file is part of the SG++ project. For conditions of distribution and
+ # use, please see the copyright notice provided with SG++ or at
+ # sgpp.sparsegrids.org
+@@ -8,17 +8,26 @@
+ # script creates a pysgpp lib in the site-packages of
+ # python. Furthermore, it collects all the relevant python code,
+ # located in each module under the path <module name>/python and
+-# copies it to the site-package folder of pysgpp using the following
+-# scheme: <path to site-packages>/pysgpp-<unique
+-# key>/extensions/<module name>/<copy of python code of correponding
+-# module>.
++# copies it to the site-package folder of pysgpp under the extensions namespace
++# pysgpp.extensions
+ 
+ import os
+ import shutil
+-from setuptools import setup
++from setuptools import setup, find_packages
++
++
++try:
++    from wheel.bdist_wheel import bdist_wheel as _bdist_wheel
++    class bdist_wheel(_bdist_wheel):
++        def finalize_options(self):
++            _bdist_wheel.finalize_options(self)
++            self.root_is_pure = False
++except ImportError:
++    bdist_wheel = None
+ 
+ # path to pysgpp lib
+ libpath = os.path.join("lib", "pysgpp")
++extensionspath = os.path.join(libpath, "extensions")
+ 
+ # list of all available modules -> all folders in the root directory
+ moduleFolders = [filename for filename in os.listdir(".")
+@@ -29,16 +38,44 @@ pythonModuleFolders = [(moduleFolder, os.path.join(moduleFolder, "python"))
+                        for moduleFolder in moduleFolders
+                        if os.path.exists(os.path.join(moduleFolder, "python"))]
+ 
+-# create the data file list such that it can be used by setuptools
+-dataFiles = []
++try:
++    os.mkdir(extensionspath)
++except FileExistsError as e:
++    pass
++
++# create list of extension scripts
++extFiles = []
+ for moduleFolder, srcdir in pythonModuleFolders:
+-    basepath = os.path.join("pysgpp", "extensions", moduleFolder)
++    basepath = os.path.join(extensionspath, moduleFolder)
++    try:
++        os.mkdir(basepath)
++    except FileExistsError as e:
++        pass
+     for root, dirs, files in os.walk(srcdir):
+-        if '.svn' in dirs:
+-            dirs.remove('.svn')
++        if '.git' in dirs:
++            dirs.remove('.git')
++
++        extFiles += [os.path.join(root, f) for f in files if ".py" in f]
++
++##
++# copy extension python files to new layout
++# pysgpp
++# --extensions
++# ----modulename
++# ------*.py
++##
+ 
+-        dataFiles += [(root.replace(srcdir, basepath),
+-                       [os.path.join(root, f) for f in files])]
++for f in extFiles:
++    dest = os.path.join(extensionspath,f)
++    dest = dest.replace(os.sep + "python", "")
++    try:
++        shutil.copy2(f, dest)
++    except FileNotFoundError as e:
++        os.mkdir(os.path.dirname(dest))
++        shutil.copy2(f, dest)
++    except shutil.SameFileError as e:
++        pass
++    
+ 
+ # write init file for pysgpp
+ initFile = os.path.join(libpath, "__init__.py")
+@@ -50,8 +87,8 @@ import sys
+ sys.path.append(os.path.dirname(__file__))
+ 
+ # import pysgpp_swig and extensions
+-from pysgpp_swig import *
+-import pysgpp.extensions
++from .pysgpp_swig import *
++from . import extensions
+ """)
+ 
+ if len(moduleFolders) > 0:
+@@ -59,9 +96,13 @@ if len(moduleFolders) > 0:
+     initFile = os.path.join("__init__.py")
+     with open(initFile, "w") as f:
+         for moduleFolder, _ in pythonModuleFolders:
+-            f.write("import %s\n" % moduleFolder)
++            f.write("from . import %s\n" % moduleFolder)
+ 
+-    dataFiles += [(os.path.join("pysgpp", "extensions"), [initFile])]
++    try:
++        shutil.copy2(initFile, os.path.join(extensionspath, initFile))
++    except shutil.SameFileError as e:
++        pass
++    
+ 
+ # if the current system is windows we need to rename the dll to pyd
+ dllLibs = [filename for filename in os.listdir(libpath)
+@@ -74,20 +115,27 @@ for dllLib in dllLibs:
+ 
+ # setup pysgpp
+ setup(name='pysgpp',
+-      version="1.0.0",
+-      url='sgpp.sparsegrids.org',
+-      author="Fabian Franzelin",
+-      description='',
+-      license='',
++      version="0.0.0",
++      url='https://github.com/SGpp/SGpp',
++      author="Dirk.Pflueger@ipvs.uni-stuttgart.de",
++      description='''The sparse grids toolkit SG++
++ SG++ is a collection of numerical algorithms for sparse grids. It
++ contains modules for interpolation, quadrature, data mining
++ (regression, classification, clustering), optimization, PDEs, and
++ more. SG++ implements algorithms for spatially adaptive grids and
++ also provides a module for the combination technique. Many of the
++ implemented algorithms are also available as a high-performance
++ version, often orders of magnitude faster than standard
++ implementations.''',
++      license='BSD-style license',
+       long_description="README",
+-      platforms='any',
+       zip_safe=False,
+       package_dir={'': 'lib'},
+-      packages=['pysgpp'],
+-      package_data={'pysgpp': ['*.so', '*.lib', '*.pyd']},
+-      data_files=dataFiles
++      packages=find_packages(where='lib', include=['pysgpp', 'pysgpp.extensions*']),
++      package_data={'pysgpp': ['_pysgpp_swig.so', '*.lib', '*.pyd']},
+       )
+ 
+ # cleanup
+ if len(moduleFolders) > 0 and os.path.exists(initFile):
+     os.remove(initFile)
++    shutil.rmtree(extensionspath, ignore_errors=True)
diff --git a/var/spack/repos/builtin/packages/sgpp/ocl.patch b/var/spack/repos/builtin/packages/sgpp/ocl.patch
new file mode 100644
index 00000000000..fbdca6ff188
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sgpp/ocl.patch
@@ -0,0 +1,13 @@
+diff --git a/datadriven/examplesOCL/multiEvalPerformance.cpp b/datadriven/examplesOCL/multiEvalPerformance.cpp
+index 60c281353..373e8509d 100644
+--- a/datadriven/examplesOCL/multiEvalPerformance.cpp
++++ b/datadriven/examplesOCL/multiEvalPerformance.cpp
+@@ -17,7 +17,7 @@ int main(int argc, char** argv) {
+   std::string fileName = "debugging.arff";
+ 
+   sgpp::datadriven::ARFFTools arffTools;
+-  sgpp::datadriven::Dataset dataset = arffTools.readARFFFromeFile(fileName);
++  sgpp::datadriven::Dataset dataset = arffTools.readARFFFromFile(fileName);
+ 
+   // sgpp::base::DataVector *classes = dataset.getClasses();
+   sgpp::base::DataMatrix& trainingData = dataset.getData();
diff --git a/var/spack/repos/builtin/packages/sgpp/package.py b/var/spack/repos/builtin/packages/sgpp/package.py
new file mode 100644
index 00000000000..7e5b907374e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sgpp/package.py
@@ -0,0 +1,205 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Sgpp(SConsPackage):
+    """SGpp is a library and framework for sparse grids in different flavors.
+    SGpp supports both hierarchical spatially-adaptive sparse grids and the
+    dimensionally-adaptive sparse grid combination technique."""
+
+    homepage = "https://sgpp.sparsegrids.org"
+    url = "https://github.com/SGpp/SGpp/archive/v3.2.0.tar.gz"
+    git = "https://github.com/SGpp/SGpp.git"
+
+    maintainers = ['G-071', 'leiterrl', 'pfluegdk']
+
+    # Versions with Python 3 bindings:
+    version('master', branch='master')
+    version('3.3.0', sha256='ca4d5b79f315b425ce69b04940c141451a76848bf1bd7b96067217304c68e2d4')
+    version('3.2.0', sha256='dab83587fd447f92ed8546eacaac6b8cbe65b8db5e860218c0fa2e42f776962d')
+    # Versions with Python 2 bindings:
+    version('3.1.0', sha256='6b46bc5b3966e92567d6754130666bdffb7be1d1d2c1b427d7ce964b8eaab526')
+    version('3.0.0', sha256='4dd9049e664abd7db78c355fea5e192167812f443115d4bf686a51bb1e9bda9c')
+
+    # Patches with bugfixes that are necessary to build old SGpp versions
+    # with spack. Patches are submitted upstream, but need to applied
+    # for versions too old to include them as they will not be
+    # backported for old releases:
+
+    # Patch that ensures libraries will actually
+    # be copied into prefix/lib upon installation
+    # (otherwise it would be prefix/lib/sgpp)
+    # Fixed in SGpp in PR https://github.com/SGpp/SGpp/pull/222
+    patch('directory.patch', when='@:3.2.0')
+    # Fix faulty setup.py introduced in 3.2.0
+    # Fixed in SGpp in version 3.3.0
+    patch('fix-setup-py.patch', when='@3.2.0')
+    # Fix compilation issue with opencl introduced in 3.2.0
+    # Fixed in SGpp in PR https://github.com/SGpp/SGpp/pull/219
+    patch('ocl.patch', when='@3.2.0+opencl')
+    # Fixes compilation with AVX512 and datadriven
+    # Fixed in SGpp in PR https://github.com/SGpp/SGpp/pull/229
+    patch('avx512_datadriven_compilation.patch', when='@:3.3.0+datadriven')
+
+    variant('python', default=True,
+            description='Provide Python bindings for SGpp')
+    variant('optimization', default=True,
+            description='Builds the optimization module of SGpp')
+    variant('pde', default=True,
+            description='Builds the datadriven module of SGpp')
+    variant('quadrature', default=True,
+            description='Builds the datadriven module of SGpp')
+    variant('datadriven', default=False,
+            description='Builds the datadriven module of SGpp')
+    variant('misc', default=False,
+            description='Builds the misc module of SGpp')
+    variant('combigrid', default=False,
+            description='Builds the combigrid module of SGpp')
+    variant('solver', default=True,
+            description='Builds the solver module of SGpp')
+    variant('opencl', default=False,
+            description='Enables support for OpenCL accelerated operations')
+    variant('mpi', default=False,
+            description='Enables support for MPI-distributed operations')
+
+    # Java variant deactivated due to spack issue #987
+    # variant('java', default=False,
+    #         description='Provide Java bindings for SGpp')
+    # depends_on('swig@3:', when='+java', type=('build'))
+    # extends('openjdk', when='+java')
+
+    # Mandatory dependencies
+    depends_on('scons@2.5.1', when='@:3.1.0', type=('build'))
+    depends_on('scons@3:', when='@3.2.0:', type=('build'))
+    depends_on('zlib', type=('link'))
+    # Python dependencies
+    extends('python', when='+python')
+    depends_on('py-setuptools', when='+python', type=('build'))
+    # Python 3 support was added in version 3.2.0
+    depends_on('python@2.7:2.8', when='@:3.1.0+python', type=('build', 'run'))
+    depends_on('python@3:', when='@3.2.0:+python', type=('build', 'run'))
+    depends_on('swig@3:', when='+python', type=('build'))
+    # Python libraries (version depends on whether we use Python 2 or 3)
+    depends_on('py-numpy@:1.16', when='@:3.1.0+python', type=('build', 'run'))
+    depends_on('py-numpy@1.17:', when='@3.2.0:+python', type=('build', 'run'))
+    depends_on('py-scipy@:1.2.3', when='@:3.1.0+python', type=('build', 'run'))
+    depends_on('py-scipy@1.3.0:', when='@3.2.0:+python', type=('build', 'run'))
+    # OpenCL dependency
+    depends_on('opencl@1.1:', when='+opencl', type=('build', 'run'))
+    # MPI dependency
+    depends_on('mpi', when='+mpi', type=('build', 'run'))
+    # Testing requires boost test
+    depends_on('boost+test', type=('test'))
+
+    # Compiler with C++11 support is required
+    conflicts('%gcc@:4.8.4', msg='Compiler with c++11 support is required!')
+    conflicts('%clang@:3.2', msg='Compiler with c++11 support is required!')
+    conflicts('%intel@:14', msg='Compiler with c++11 support is required!')
+    # Solver python bindings are actually using the pde module at one point:
+    conflicts('-pde', when='+python+solver')
+    # some modules depend on each other (notably datadriven and misc)
+    conflicts('+pde', when='-solver')
+    # Datadriven module requirements
+    conflicts('+datadriven', when='-solver')
+    conflicts('+datadriven', when='-optimization')
+    conflicts('+datadriven', when='-pde')
+    # Misc module requirements
+    conflicts('+misc', when='-datadriven')
+    conflicts('+misc', when='-solver')
+    conflicts('+misc', when='-optimization')
+    conflicts('+misc', when='-pde')
+    conflicts('+misc', when='@:3.1.0',
+              msg='The misc module was introduced in version 3.2.0')
+    # Combigrid module requirements (for 3.2.0 or older)
+    # newer combigrids have no dependencies
+    conflicts('+combigrid', when='@:3.2.0~optimization')
+    conflicts('+combigrid', when='@:3.2.0~pde')
+    conflicts('+combigrid', when='@:3.2.0~solver')
+    conflicts('+combigrid', when='@:3.2.0~quadrature')
+
+    def build_args(self, spec, prefix):
+        # Testing parameters
+        if self.run_tests:
+            self.args = ['COMPILE_BOOST_TESTS=1',
+                         'RUN_BOOST_TESTS=1']
+            if ('+python' in spec):
+                self.args.append('RUN_PYTHON_TESTS=1')
+            if spec.satisfies('@:3.2.0'):
+                self.args.append('RUN_CPPLINT=1')
+            else:  # argument was renamed after 3.2.0
+                self.args.append('CHECK_STYLE=1')
+        else:
+            self.args = ['COMPILE_BOOST_TESTS=0',
+                         'RUN_BOOST_TESTS=0',
+                         'RUN_PYTHON_TESTS=0']
+            if spec.satisfies('@:3.2.0'):
+                self.args.append('RUN_CPPLINT=0')
+            else:  # argument was renamed after 3.2.0
+                self.args.append('CHECK_STYLE=0')
+
+        # Install direction
+        self.args.append('PREFIX={0}'.format(prefix))
+
+        # Generate swig bindings?
+        self.args.append('SG_PYTHON={0}'.format(
+            '1' if '+python' in spec else '0'))
+
+        # Java variant deactivated due to spack issue #987
+        # self.args.append('SG_JAVA={0}'.format(
+        #     '1' if '+java' in spec else '0'))
+        self.args.append('SG_JAVA=0')
+
+        # Which modules to build?
+        self.args.append('SG_OPTIMIZATION={0}'.format(
+            '1' if '+optimization' in spec else '0'))
+        self.args.append('SG_QUADRATURE={0}'.format(
+            '1' if '+quadrature' in spec else '0'))
+        self.args.append('SG_PDE={0}'.format(
+            '1' if '+pde' in spec else '0'))
+        self.args.append('SG_DATADRIVEN={0}'.format(
+            '1' if '+datadriven' in spec else '0'))
+        self.args.append('SG_COMBIGRID={0}'.format(
+            '1' if '+combigrid' in spec else '0'))
+        self.args.append('SG_SOLVER={0}'.format(
+            '1' if '+solver' in spec else '0'))
+
+        # Misc flag did not exist in older versions
+        if spec.satisfies('@3.2.0:'):
+            self.args.append('SG_MISC={0}'.format(
+                '1' if '+misc' in spec else '0'))
+
+        # SIMD scons parameter (pick according to simd spec)
+        if 'avx512' in self.spec.target:
+            self.args.append('ARCH=avx512')
+        elif 'avx2' in self.spec.target:
+            self.args.append('ARCH=avx2')
+        elif 'avx' in self.spec.target:
+            self.args.append('ARCH=avx')
+        elif 'fma4' in self.spec.target:
+            self.args.append('ARCH=fma4')
+        elif 'sse42' in self.spec.target:
+            self.args.append('ARCH=sse42')
+        elif 'sse3' in self.spec.target:
+            self.args.append('ARCH=sse3')
+
+        # OpenCL Flags
+        self.args.append('USE_OCL={0}'.format(
+            '1' if '+opencl' in spec else '0'))
+
+        # Get the mpicxx compiler from the Spack spec
+        # (makes certain we use the one from spack):
+        if ('+mpi' in spec):
+            self.args.append('CXX={0}'.format(
+                self.spec['mpi'].mpicxx))
+
+        return self.args
+
+    def install_args(self, spec, prefix):
+        # Everything is already built, time to install our python bindings:
+        if '+python' in spec:
+            setup_py('install', '--prefix={0}'.format(prefix))
+        return self.args

From f3aceddbfbfa287595a5a0b5baab8ae3cd06d723 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Tue, 21 Apr 2020 23:09:14 +0200
Subject: [PATCH 034/802] py-tap-py: Add 3.0 and 2.6.2 (#16169)

---
 .../builtin/packages/py-tap-py/package.py      | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-tap-py/package.py b/var/spack/repos/builtin/packages/py-tap-py/package.py
index e3f453763d7..a0c9c84ee6b 100644
--- a/var/spack/repos/builtin/packages/py-tap-py/package.py
+++ b/var/spack/repos/builtin/packages/py-tap-py/package.py
@@ -9,14 +9,18 @@
 class PyTapPy(PythonPackage):
     """Python TAP interface module for unit tests"""
 
-    homepage = "https://github.com/mblayman/tappy"
-    url      = "https://pypi.io/packages/source/t/tap.py/tap.py-1.6.tar.gz"
+    homepage = "https://github.com/python-tap/tappy"
+    url      = "https://pypi.io/packages/source/t/tap.py/tap.py-3.0.tar.gz"
 
-    version('1.6', sha256='3ee315567cd1cf444501c405b7f7146ffdb2e630bac58d0840d378a3b9a0dbe4')
+    version('3.0',   sha256='f5eeeeebfd64e53d32661752bb4c288589a3babbb96db3f391a4ec29f1359c70')
+    version('2.6.2', sha256='5f219d92dbad5e378f8f7549cdfe655b0d5fd2a778f9c83bee51b61c6ca40efb')
+    version('1.6',   sha256='3ee315567cd1cf444501c405b7f7146ffdb2e630bac58d0840d378a3b9a0dbe4')
 
     extends('python', ignore='bin/nosetests|bin/pygmentize')
 
-    depends_on('python@2.6:2.8,3.2:3.4')
-    depends_on('py-nose', type=('build', 'run'))
-    depends_on('py-pygments', type=('build', 'run'))
-    depends_on('py-setuptools', type='build')
+    depends_on('python@3.5:3.7', when='@3.0:')
+    depends_on('python@2.7:2.8,3.5:3.7', when='@2.6')
+    depends_on('python@2.6:2.8,3.2:3.4', when='@:1.8')
+    depends_on('py-nose', type=('build', 'run'), when='@:1.99')
+    depends_on('py-pygments', type=('build', 'run'), when='@:1.99')
+    depends_on('py-setuptools', type=('build', 'run'))

From 54ca52943d885d32964c7f5ea8a36070127484c8 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 21 Apr 2020 16:20:11 -0500
Subject: [PATCH 035/802] PyTorch: add 1.5.0 (#16212)

---
 var/spack/repos/builtin/packages/py-torch/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py
index 619a621c2b3..6428d6cb8e5 100644
--- a/var/spack/repos/builtin/packages/py-torch/package.py
+++ b/var/spack/repos/builtin/packages/py-torch/package.py
@@ -50,6 +50,7 @@ class PyTorch(PythonPackage, CudaPackage):
     ]
 
     version('master', branch='master', submodules=True)
+    version('1.5.0', tag='v1.5.0', submodules=True)
     version('1.4.1', tag='v1.4.1', submodules=True)
     # see https://github.com/pytorch/pytorch/issues/35149
     version('1.4.0', tag='v1.4.0', submodules=True,
@@ -115,6 +116,7 @@ class PyTorch(PythonPackage, CudaPackage):
     # Use Ninja generator to speed up build times
     # Automatically used if found
     depends_on('ninja@1.5:', type='build')
+    depends_on('python@3.5:', when='@1.5:', type=('build', 'run'))
     depends_on('python@2.7:2.8,3.5:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
     depends_on('py-numpy', type=('build', 'run'))

From 272c47207d5ce7f1e6f5f6b4e3958f5b99283c2c Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 21 Apr 2020 14:20:45 -0700
Subject: [PATCH 036/802] Updated the 'opengl' package to include all older
 versions of the library. (#16219)

---
 var/spack/repos/builtin/packages/opengl/package.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/var/spack/repos/builtin/packages/opengl/package.py b/var/spack/repos/builtin/packages/opengl/package.py
index 603dc9cb88d..413b8e0f453 100644
--- a/var/spack/repos/builtin/packages/opengl/package.py
+++ b/var/spack/repos/builtin/packages/opengl/package.py
@@ -20,6 +20,17 @@ class Opengl(Package):
     provides('gl@:4.2', when='@4.2:')
     provides('gl@:4.1', when='@4.1:')
     provides('gl@:3.3', when='@3.3:')
+    provides('gl@:3.2', when='@3.2:')
+    provides('gl@:3.1', when='@3.1:')
+    provides('gl@:3.0', when='@3.0:')
+    provides('gl@:2.1', when='@2.1:')
+    provides('gl@:2.0', when='@2.0:')
+    provides('gl@:1.5', when='@1.5:')
+    provides('gl@:1.4', when='@1.4:')
+    provides('gl@:1.3', when='@1.3:')
+    provides('gl@:1.2', when='@1.2:')
+    provides('gl@:1.1', when='@1.1:')
+    provides('gl@:1.0', when='@1.0:')
 
     if sys.platform != 'darwin':
         provides('glx@1.4')

From ca4c0b97ecf13b4a9c9007bb7ff4912cddae820c Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Tue, 21 Apr 2020 14:22:30 -0700
Subject: [PATCH 037/802] Doc: Conflict Msg Pkg Guide (#16201)

Document the nice `msg=` argument in conflicts. Super useful
for less generic conflict guidance.
---
 lib/spack/docs/packaging_guide.rst | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index 26f843aa0e8..7abadaac820 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -2169,13 +2169,17 @@ Adding the following to a package:
 
 .. code-block:: python
 
-    conflicts('%intel', when='@1.2')
+    conflicts('%intel', when='@:1.2',
+              msg='<myNicePackage> <= v1.2 cannot be built with Intel ICC, '
+                  'please use a newer release.')
 
 we express the fact that the current package *cannot be built* with the Intel
-compiler when we are trying to install version "1.2". The ``when`` argument can
-be omitted, in which case the conflict will always be active.
+compiler when we are trying to install a version "<=1.2". The ``when`` argument
+can be omitted, in which case the conflict will always be active.
 Conflicts are always evaluated after the concretization step has been performed,
 and if any match is found a detailed error message is shown to the user.
+You can add an additional message via the ``msg=`` parameter to a conflict that
+provideds more specific instructions for users.
 
 .. _packaging_extensions:
 

From 667fee0703799fc78606d0628ff42b0f5a318f2c Mon Sep 17 00:00:00 2001
From: Andrew Gaspar <agaspar@lanl.gov>
Date: Tue, 21 Apr 2020 17:52:50 -0600
Subject: [PATCH 038/802] catch2 2.12.1 (#16211)

---
 var/spack/repos/builtin/packages/catch2/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/catch2/package.py b/var/spack/repos/builtin/packages/catch2/package.py
index 5d3d25d7631..96b1534b183 100644
--- a/var/spack/repos/builtin/packages/catch2/package.py
+++ b/var/spack/repos/builtin/packages/catch2/package.py
@@ -14,6 +14,7 @@ class Catch2(CMakePackage):
     url      = "https://github.com/catchorg/Catch2/archive/v2.9.1.tar.gz"
     maintainers = ['ax3l']
 
+    version('2.12.1', sha256='e5635c082282ea518a8dd7ee89796c8026af8ea9068cd7402fb1615deacd91c3')
     version('2.12.0', sha256='6606b754363d3a4521bfecf717dc1972c50dca282bd428dfb1370ec8b9c26918')
     version('2.11.3', sha256='9a6967138062688f04374698fce4ce65908f907d8c0fe5dfe8dc33126bd46543')
     version('2.11.2', sha256='a96203fa531092375678ad2d81c43317ee58c684787f24b2a55748f6c6839799')

From 2f7e940872f0361bc28a21b665ad2986da21d246 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Tue, 21 Apr 2020 20:36:02 -0700
Subject: [PATCH 039/802] Fix: Flex Reconfigure (#16194)

* Fix: Flex Reconfigure

Learn the `flex` package how to reconfigure itself when needed.
Fix #11551

Co-authored-by: Andrew W Elble <aweits@rit.edu>

* Autoreconf: only when actually desired

Co-authored-by: Andrew W Elble <aweits@rit.edu>
---
 var/spack/repos/builtin/packages/flex/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/repos/builtin/packages/flex/package.py b/var/spack/repos/builtin/packages/flex/package.py
index 3c9f51a0eb0..83214099f2c 100644
--- a/var/spack/repos/builtin/packages/flex/package.py
+++ b/var/spack/repos/builtin/packages/flex/package.py
@@ -43,6 +43,11 @@ class Flex(AutotoolsPackage):
     # - https://github.com/westes/flex/issues/241
     patch('https://github.com/westes/flex/commit/24fd0551333e7eded87b64dd36062da3df2f6380.patch', sha256='09c22e5c6fef327d3e48eb23f0d610dcd3a35ab9207f12e0f875701c677978d3', when='@2.6.4')
 
+    @when('@:2.6.0,2.6.4')
+    def autoreconf(self, spec, prefix):
+        autogen = Executable('./autogen.sh')
+        autogen()
+
     @property
     def force_autoreconf(self):
         # The patch for 2.6.4 touches configure

From 1289d3589aeaf5ad5cc8068ce4851d1fabb72bec Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 22 Apr 2020 12:01:49 +0800
Subject: [PATCH 040/802] Add new package: cmockery (#16225)

---
 .../builtin/packages/cmockery/package.py      | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/cmockery/package.py

diff --git a/var/spack/repos/builtin/packages/cmockery/package.py b/var/spack/repos/builtin/packages/cmockery/package.py
new file mode 100644
index 00000000000..bb4cf5b22cf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cmockery/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cmockery(AutotoolsPackage):
+    """A lightweight library to simplify and generalize the process of
+    writing unit tests for C applications."""
+
+    homepage = "https://github.com/google/cmockery"
+    url      = "https://github.com/google/cmockery/archive/v0.1.2.tar.gz"
+
+    version('0.1.2', sha256='d40135ae9179201c01bde725fa64fc32d86b5899972e0ce4ad51668d261edbae')
+    version('0.1.1', sha256='a801d17976f781fff6dc49042ff109e55ca4ebe8efb13757fa1a511ca52316be')
+    version('0.1.0', sha256='9e017d48e56ab9d2ebcf5286fa54e37d42fe308d3c01fbc367793da2b9ad95e7')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+
+    def autoreconf(self, spec, prefix):
+        bash = which('bash')
+        bash('./autogen.sh')

From ac228050ab4955f996869dad886b5edd89d8443e Mon Sep 17 00:00:00 2001
From: jthies <jonas.thies@dlr.de>
Date: Wed, 22 Apr 2020 06:10:11 +0200
Subject: [PATCH 041/802] Phist int64 variant (#16209)

* phist: add int64 variant and resulting conflicts and dependencies

* phist: use Trilinos TPLs as soon as they are in the spec, not just if +trilinos isexplicitly set
and remove a redundant depends-statement

* phist: use int as gotype for Trilinos dependency if ~int64

* phist: new version 1.9.0

* phist: remove trailing whitespace

* phist: updated checksum (version tag was moved)
---
 .../repos/builtin/packages/phist/package.py   | 33 ++++++++++++-----
 .../phist/update_tpetra_gotypes.patch         | 35 +++++++++++++++++++
 2 files changed, 59 insertions(+), 9 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/phist/update_tpetra_gotypes.patch

diff --git a/var/spack/repos/builtin/packages/phist/package.py b/var/spack/repos/builtin/packages/phist/package.py
index 42ad816dfa8..797d09a8463 100644
--- a/var/spack/repos/builtin/packages/phist/package.py
+++ b/var/spack/repos/builtin/packages/phist/package.py
@@ -26,6 +26,7 @@ class Phist(CMakePackage):
 
     version('develop', branch='devel')
     version('master', branch='master')
+    version('1.9.0', sha256='990d3308fc0083ed0f9f565d00c649ee70c3df74d44cbe5f19dfe05263d06559')
     version('1.8.0', sha256='ee42946bce187e126452053b5f5c200b57b6e40ee3f5bcf0751f3ced585adeb0')
     version('1.7.5', sha256='f11fe27f2aa13d69eb285cc0f32c33c1603fa1286b84e54c81856c6f2bdef500')
     version('1.7.4', sha256='ef0c97fda9984f53011020aff3e61523833320f5f5719af2f2ed84463cccb98b')
@@ -44,9 +45,12 @@ class Phist(CMakePackage):
                     'eigen',
                     'ghost'])
 
+    variant(name='int64', default=True,
+            description='Use 64-bit global indices.')
+
     variant(name='outlev', default='2', values=['0', '1', '2', '3', '4', '5'],
             description='verbosity. 0: errors 1: +warnings 2: +info '
-                        '3: +verbose 4: +extreme 5; +debug')
+                        '3: +verbose 4: +extreme 5: +debug')
 
     variant('host', default=True,
             description='allow PHIST to use compiler flags that lead to host-'
@@ -86,6 +90,13 @@ class Phist(CMakePackage):
     # in older versions, it is not possible to turn off the use of host-
     # specific compiler flags in Release mode.
     conflicts('~host', when='@:1.7.3')
+    # builtin always uses 64-bit indices
+    conflicts('~int64', when='kernel_lib=builtin')
+    conflicts('+int64', when='kernel_lib=eigen')
+
+    # ###################### Patches ##########################
+
+    patch('update_tpetra_gotypes.patch', when='@:1.9.0')
 
     # ###################### Dependencies ##########################
 
@@ -97,16 +108,18 @@ class Phist(CMakePackage):
     # the feature (e.g. use the '~fortran' variant)
     depends_on('python@3:', when='@1.7: +fortran', type='build')
     depends_on('mpi', when='+mpi')
-    depends_on('trilinos+anasazi+belos+teuchos', when='+trilinos')
-    depends_on('trilinos@12:+tpetra', when='kernel_lib=tpetra')
+    depends_on('trilinos@12:+tpetra gotype=long_long', when='kernel_lib=tpetra +int64')
+    depends_on('trilinos@12:+tpetra gotype=int', when='kernel_lib=tpetra ~int64')
     # Epetra backend also works with older Trilinos versions
     depends_on('trilinos+epetra', when='kernel_lib=epetra')
-    depends_on('petsc', when='kernel_lib=petsc')
+    depends_on('petsc +int64', when='kernel_lib=petsc +int64')
+    depends_on('petsc ~int64', when='kernel_lib=petsc ~int64')
     depends_on('eigen', when='kernel_lib=eigen')
     depends_on('ghost', when='kernel_lib=ghost')
 
-    depends_on('trilinos', when='+trilinos')
-    depends_on('parmetis ^metis+int64', when='+parmetis')
+    depends_on('trilinos+anasazi+belos+teuchos', when='+trilinos')
+    depends_on('parmetis ^metis+int64', when='+parmetis +int64')
+    depends_on('parmetis ^metis~int64', when='+parmetis ~int64')
 
     # Fortran 2003 bindings were included in version 1.7, previously they
     # required a separate package
@@ -139,13 +152,15 @@ def cmake_args(self):
                 '-DPHIST_ENABLE_SCAMAC:BOOL=%s'
                 % ('ON' if '+scamac' in spec else 'OFF'),
                 '-DPHIST_USE_TRILINOS_TPLS:BOOL=%s'
-                % ('ON' if '+trilinos' in spec else 'OFF'),
+                % ('ON' if '^trilinos' in spec else 'OFF'),
                 '-DPHIST_USE_SOLVER_TPLS:BOOL=%s'
-                % ('ON' if '+trilinos' in spec else 'OFF'),
+                % ('ON' if '^trilinos+belos+anasazi' in spec else 'OFF'),
                 '-DPHIST_USE_PRECON_TPLS:BOOL=%s'
-                % ('ON' if '+trilinos' in spec else 'OFF'),
+                % ('ON' if '^trilinos' in spec else 'OFF'),
                 '-DXSDK_ENABLE_Fortran:BOOL=%s'
                 % ('ON' if '+fortran' in spec else 'OFF'),
+                '-DXSDK_INDEX_SIZE=%s'
+                % ('64' if '+int64' in spec else '32'),
                 '-DPHIST_HOST_OPTIMIZE:BOOL=%s'
                 % ('ON' if '+host' in spec else 'OFF'),
                 ]
diff --git a/var/spack/repos/builtin/packages/phist/update_tpetra_gotypes.patch b/var/spack/repos/builtin/packages/phist/update_tpetra_gotypes.patch
new file mode 100644
index 00000000000..2db579fc340
--- /dev/null
+++ b/var/spack/repos/builtin/packages/phist/update_tpetra_gotypes.patch
@@ -0,0 +1,35 @@
+commit 8df8ad0e56e3bbd3d0c133fcdb7d2af6ab4dd229
+Author: Jonas Thies <Jonas.Thies@DLR.de>
+Date:   Tue Apr 21 18:24:53 2020 +0200
+
+    tpetra: use 'int' and 'long long' as gidx type for 32 and 64-bit compilations, respectively
+    because Trilinos allows to instantiate those variants (before I had 'int'/'ptrdiff_t')
+
+diff --git a/src/kernels/tpetra/phist_typedefs.h b/src/kernels/tpetra/phist_typedefs.h
+index 1f6b6c6c..3a351c27 100644
+--- a/src/kernels/tpetra/phist_typedefs.h
++++ b/src/kernels/tpetra/phist_typedefs.h
+@@ -34,19 +34,18 @@
+ using phist_s_complex = std::complex<float>;
+ //! double precision complex type
+ using phist_d_complex = std::complex<double>;
+-//! type of global indices
+-using phist_gidx = std::ptrdiff_t;
+ #else
+ typedef float complex phist_s_complex;
+ typedef double complex phist_d_complex;
++#endif
++
+ //! type of global indices
+ #ifdef PHIST_FORCE_32BIT_GIDX
+ typedef int phist_gidx;
+ #define PRgidx "d"
+ #else
+-typedef ptrdiff_t phist_gidx;
+-#define PRgidx "ld"
+-#endif
++typedef long long phist_gidx;
++#define PRgidx "lld"
+ #endif
+ 
+ // we want ptrdiff_t (aka long long int on 64 bit systems) as local index,

From 1e243023d835925502abfdde9a42ca890be9ee07 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 22 Apr 2020 14:56:13 +0800
Subject: [PATCH 042/802] cmaq: added new package at v5.3.1 (#16224)

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../repos/builtin/packages/cmaq/package.py    | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/cmaq/package.py

diff --git a/var/spack/repos/builtin/packages/cmaq/package.py b/var/spack/repos/builtin/packages/cmaq/package.py
new file mode 100644
index 00000000000..2f8d35e5c48
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cmaq/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cmaq(Package):
+    """Code base for the U.S. EPA's Community Multiscale Air Quality Model
+    (CMAQ)."""
+    homepage = "http://www.epa.gov/CMAQ"
+    url      = "https://github.com/USEPA/CMAQ/archive/CMAQv5.3.1_19Dec2019.tar.gz"
+
+    version('5.3.1', sha256='659156bba27f33010e0fdc157a8d33f3b5b779b95511e2ade870284b6bcb4bc8',
+            url='https://github.com/USEPA/CMAQ/archive/CMAQv5.3.1_19Dec2019.tar.gz')
+    version('5.3', sha256='e245c291c7e88d481b13f577d1af9aeb5aef4de8c59f7fa06fa41d19bb2ed18c',
+            url='https://github.com/USEPA/CMAQ/archive/CMAQv5.3_27Aug2019.tar.gz')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix)

From 4c9c6b2a68ec26413cfbd9fccd73187db84c8337 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 22 Apr 2020 16:53:28 +0800
Subject: [PATCH 043/802] linux-pam: added package at v1.3.1 (#16137)

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../builtin/packages/linux-pam/package.py     | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/linux-pam/package.py

diff --git a/var/spack/repos/builtin/packages/linux-pam/package.py b/var/spack/repos/builtin/packages/linux-pam/package.py
new file mode 100644
index 00000000000..0dff1e0654b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/linux-pam/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class LinuxPam(AutotoolsPackage):
+    """Linux PAM (Pluggable Authentication Modules for Linux) project."""
+
+    homepage = "http://www.linux-pam.org/"
+    url      = "https://github.com/linux-pam/linux-pam/releases/download/v1.3.1/Linux-PAM-1.3.1.tar.xz"
+
+    version('1.3.1', sha256='eff47a4ecd833fbf18de9686632a70ee8d0794b79aecb217ebd0ce11db4cd0db')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+
+    def configure_args(self):
+        config_args = [
+            '--includedir=' + self.prefix.include.security
+        ]
+        return config_args

From ab35780fae9135752b8882e3726c810e4100ae53 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 22 Apr 2020 16:55:07 +0800
Subject: [PATCH 044/802] buddy: added package at v2.4 (#16166)

---
 .../repos/builtin/packages/buddy/package.py   | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/buddy/package.py

diff --git a/var/spack/repos/builtin/packages/buddy/package.py b/var/spack/repos/builtin/packages/buddy/package.py
new file mode 100644
index 00000000000..d6e92bb9b38
--- /dev/null
+++ b/var/spack/repos/builtin/packages/buddy/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import platform
+
+
+class Buddy(AutotoolsPackage):
+    """A Binary Decision Diagram library."""
+
+    homepage = "https://sourceforge.net/projects/buddy/"
+    url      = "https://sourceforge.net/projects/buddy/files/buddy/BuDDy%202.4/buddy-2.4.tar.gz"
+    list_url = "https://sourceforge.net/projects/buddy/files/buddy"
+    list_depth = 1
+
+    version('2.4', sha256='d3df80a6a669d9ae408cb46012ff17bd33d855529d20f3a7e563d0d913358836')
+
+    def configure_args(self):
+        if platform.machine() == 'aarch64':
+            config_args = [
+                '--build=aarch64-unknown-linux-gnu',
+            ]
+            return config_args

From 3e9af610e7d51396dad54ec77faf90943b4a7473 Mon Sep 17 00:00:00 2001
From: Servesh <servesh@users.noreply.github.com>
Date: Wed, 22 Apr 2020 04:43:02 -0500
Subject: [PATCH 045/802] source-highlight: fix detection of boost (#16102)

Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>
---
 var/spack/repos/builtin/packages/source-highlight/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/source-highlight/package.py b/var/spack/repos/builtin/packages/source-highlight/package.py
index eee706518a6..67d3b368817 100644
--- a/var/spack/repos/builtin/packages/source-highlight/package.py
+++ b/var/spack/repos/builtin/packages/source-highlight/package.py
@@ -19,3 +19,7 @@ class SourceHighlight(AutotoolsPackage, GNUMirrorPackage):
     version('3.1.8', sha256='01336a7ea1d1ccc374201f7b81ffa94d0aecb33afc7d6903ebf9fbf33a55ada3')
 
     depends_on('boost')
+
+    def configure_args(self):
+        args = ["--with-boost={0}".format(self.spec['boost'].prefix)]
+        return args

From 0b753b9a7713d16bb905331dd18434dd4a29261b Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <eafischer2@alaska.edu>
Date: Wed, 22 Apr 2020 01:50:36 -0800
Subject: [PATCH 046/802] py-pyproj: added v2.6.0 (#16176)

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
---
 var/spack/repos/builtin/packages/py-pyproj/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-pyproj/package.py b/var/spack/repos/builtin/packages/py-pyproj/package.py
index 3341359a9ad..dfc0edf9246 100644
--- a/var/spack/repos/builtin/packages/py-pyproj/package.py
+++ b/var/spack/repos/builtin/packages/py-pyproj/package.py
@@ -16,6 +16,7 @@ class PyPyproj(PythonPackage):
     maintainers = ['citibeth', 'adamjstewart']
     import_modules = ['pyproj']
 
+    version('2.6.0',   sha256='977542d2f8cf2981cf3ad72cedfebcd6ac56977c7aa830d9b49fa7888b56e83d')
     version('2.2.0',   sha256='0a4f793cc93539c2292638c498e24422a2ec4b25cb47545addea07724b2a56e5')
     version('2.1.3',   sha256='99c52788b01a7bb9a88024bf4d40965c0a66a93d654600b5deacf644775f424d')
     version('1.9.6',   sha256='e0c02b1554b20c710d16d673817b2a89ff94738b0b537aead8ecb2edc4c4487b')
@@ -23,8 +24,10 @@ class PyPyproj(PythonPackage):
 
     depends_on('python@:2', when='@:1.9.5.1')
     depends_on('python@3:', when='@2.3:')
+    depends_on('python@3.5:', when='@2.6.0:')
     depends_on('py-setuptools', type='build')
     depends_on('py-cython', type='build')
+    depends_on('py-cython@0.28:', when='@2.6.0:')
     depends_on('py-aenum', type=('build', 'run'), when='@2.2:^python@:3.5')
     depends_on('proj')
     depends_on('proj@:5',   when='@:1')

From b065150354ee708c202b952cd3f3712a98ea3529 Mon Sep 17 00:00:00 2001
From: Jeffrey Salmond <js947@users.noreply.github.com>
Date: Wed, 22 Apr 2020 11:18:38 +0100
Subject: [PATCH 047/802] metis: fix build when version > 5.0 (#16186)

---
 var/spack/repos/builtin/packages/metis/package.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index 12d1223a727..524561310b9 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -171,11 +171,10 @@ def install(self, spec, prefix):
     @when('@5:')
     def install(self, spec, prefix):
         source_directory = self.stage.source_path
-        build_directory = join_path(source_directory, 'build')
+        build_directory = join_path(self.stage.path, 'build')
 
-        options = std_cmake_args[:]
+        options = CMakePackage._std_args(self)
         options.append('-DGKLIB_PATH:PATH=%s/GKlib' % source_directory)
-        options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
 
         # Normally this is available via the 'CMakePackage' object, but metis
         # IS-A 'Package' (not a 'CMakePackage') to support non-cmake metis@:5.

From be0aed9d8acc1948c3eb43a0b4abcd9ab8f142b2 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 22 Apr 2020 19:19:01 +0800
Subject: [PATCH 048/802] libcgroup: added package at v0.41 (#16229)

---
 .../builtin/packages/libcgroup/package.py     | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/libcgroup/package.py

diff --git a/var/spack/repos/builtin/packages/libcgroup/package.py b/var/spack/repos/builtin/packages/libcgroup/package.py
new file mode 100644
index 00000000000..797e10d7a43
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libcgroup/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libcgroup(AutotoolsPackage):
+    """Library of control groups."""
+
+    homepage = "https://sourceforge.net/projects/libcg/"
+    url      = "https://sourceforge.net/projects/libcg/files/libcgroup/v0.41/libcgroup-0.41.tar.bz2"
+
+    version('0.41', sha256='e4e38bdc7ef70645ce33740ddcca051248d56b53283c0dc6d404e17706f6fb51')
+    version('0.37', sha256='15c8f3febb546530d3495af4e4904b3189c273277ca2d8553dec882cde1cd0f6')
+    version('0.36', sha256='8dcd2ae220435b3de736d3efb0023fdf1192d7a7f4032b439f3cf5342cff7b4c')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('bison',    type='build')
+    depends_on('flex',     type='build')
+    depends_on('linux-pam')

From 9c2819bdb3f96c2632c45e4a7dcf3a410c04f73c Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <KineticTheory@users.noreply.github.com>
Date: Wed, 22 Apr 2020 06:53:01 -0600
Subject: [PATCH 049/802] libsm: added libuuid as dependency (#16226)

While building _visit_, I ran into an undefined symbol at link time. I tracked
the missing dependency to _libsm_ needing to know about _libuuid_ at link time.
---
 var/spack/repos/builtin/packages/libsm/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/libsm/package.py b/var/spack/repos/builtin/packages/libsm/package.py
index cabd2aae3d5..269f2ededbf 100644
--- a/var/spack/repos/builtin/packages/libsm/package.py
+++ b/var/spack/repos/builtin/packages/libsm/package.py
@@ -20,3 +20,4 @@ class Libsm(AutotoolsPackage, XorgPackage):
     depends_on('xtrans', type='build')
     depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
+    depends_on('libuuid')

From 0419f2c6dff724fd95507160719e8df674baf4b8 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Wed, 22 Apr 2020 07:29:40 -0700
Subject: [PATCH 050/802] Updated 'qt' to support '@5.12.7', '+debug', and
 '+opengl' with older OpenGL versions. (#16220)

---
 var/spack/repos/builtin/packages/qt/package.py      |  9 +++++++--
 .../builtin/packages/qt/qt5-12-configure.patch      | 13 +++++++++++++
 2 files changed, 20 insertions(+), 2 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/qt/qt5-12-configure.patch

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 408ebc9f591..08721e85c24 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -28,6 +28,7 @@ class Qt(Package):
     version('5.14.1', sha256='6f17f488f512b39c2feb57d83a5e0a13dcef32999bea2e2a8f832f54a29badb8')
     version('5.14.0', sha256='be9a77cd4e1f9d70b58621d0753be19ea498e6b0da0398753e5038426f76a8ba')
     version('5.13.1', sha256='adf00266dc38352a166a9739f1a24a1e36f1be9c04bf72e16e142a256436974e')
+    version('5.12.7', sha256='873783a0302129d98a8f63de9afe4520fb5f8d5316be8ad7b760c59875cd8a8d')
     version('5.12.5', sha256='a2299e21db7767caf98242767bffb18a2a88a42fee2d6a393bedd234f8c91298')
     version('5.12.2', sha256='59b8cb4e728450b21224dcaaa40eb25bafc5196b6988f2225c394c6b7f881ff5')
     version('5.11.3', sha256='859417642713cee2493ee3646a7fee782c9f1db39e41d7bb1322bba0c5f0ff4d')
@@ -48,6 +49,8 @@ class Qt(Package):
     version('4.8.5',  sha256='eb728f8268831dc4373be6403b7dd5d5dde03c169ad6882f9a8cb560df6aa138')
     version('3.3.8b', sha256='1b7a1ff62ec5a9cb7a388e2ba28fda6f960b27f27999482ebeceeadb72ac9f6e')
 
+    variant('debug',      default=False,
+            description="Build debug version.")
     variant('gtk',        default=False,
             description="Build with gtkplus.")
     variant('webkit',     default=False,
@@ -111,6 +114,8 @@ class Qt(Package):
     # https://github.com/spack/spack/issues/14400
     patch('qt5-11-intel-overflow.patch', when='@5.11 %intel')
     patch('qt5-12-intel-overflow.patch', when='@5.12:5.14.0 %intel')
+    # https://bugreports.qt.io/browse/QTBUG-78937
+    patch('qt5-12-configure.patch', when='@5.12')
 
     # Build-only dependencies
     depends_on("pkgconfig", type='build')
@@ -140,7 +145,7 @@ class Qt(Package):
     depends_on("glib", when='@4:')
     depends_on("libpng", when='@4:')
     depends_on("dbus", when='@4:+dbus')
-    depends_on("gl@3.2:", when='@4:+opengl')
+    depends_on("gl", when='@4:+opengl')
 
     depends_on("harfbuzz", when='@5:')
     depends_on("double-conversion", when='@5.7:')
@@ -358,7 +363,7 @@ def common_config_args(self):
             '-v',
             '-opensource',
             '-{0}opengl'.format('' if '+opengl' in self.spec else 'no-'),
-            '-release',
+            '-{0}'.format('debug' if '+debug' in self.spec else 'release'),
             '-confirm-license',
             '-optimized-qmake',
             '-no-pch',
diff --git a/var/spack/repos/builtin/packages/qt/qt5-12-configure.patch b/var/spack/repos/builtin/packages/qt/qt5-12-configure.patch
new file mode 100644
index 00000000000..42681a16255
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qt/qt5-12-configure.patch
@@ -0,0 +1,13 @@
+diff --git a/qtbase/src/corelib/tools/qsimd_p.h b/qtbase/src/corelib/tools/qsimd_p.h
+index 2130a1f..3a14715 100644
+--- a/qtbase/src/corelib/tools/qsimd_p.h
++++ b/qtbase/src/corelib/tools/qsimd_p.h
+@@ -346,7 +346,7 @@ extern Q_CORE_EXPORT QBasicAtomicInteger<unsigned> qt_cpu_features[2];
+ #endif
+ Q_CORE_EXPORT void qDetectCpuFeatures();
+ 
+-#if defined(Q_PROCESSOR_X86) && QT_COMPILER_SUPPORTS_HERE(RDRND)
++#if defined(Q_PROCESSOR_X86) && QT_COMPILER_SUPPORTS_HERE(RDRND) && !defined(QT_BOOTSTRAPPED)
+ Q_CORE_EXPORT qsizetype qRandomCpu(void *, qsizetype) Q_DECL_NOTHROW;
+ #else
+ static inline qsizetype qRandomCpu(void *, qsizetype) Q_DECL_NOTHROW

From d65b809f9b3239ad1c1c402530fd929785ee3d02 Mon Sep 17 00:00:00 2001
From: asmaahassan90 <31959389+asmaahassan90@users.noreply.github.com>
Date: Wed, 22 Apr 2020 16:44:03 +0200
Subject: [PATCH 051/802] Add new versions to Avizo (#16204)

* Add new versions

add versions 2019.3 and 2019.4 and adjust the install stage accordingly

* one small fix

* fix lint

* re-ordering the versions
---
 .../repos/builtin/packages/avizo/package.py   | 38 +++++++++++++++----
 1 file changed, 30 insertions(+), 8 deletions(-)

diff --git a/var/spack/repos/builtin/packages/avizo/package.py b/var/spack/repos/builtin/packages/avizo/package.py
index cf14c76d22d..352af737632 100644
--- a/var/spack/repos/builtin/packages/avizo/package.py
+++ b/var/spack/repos/builtin/packages/avizo/package.py
@@ -17,12 +17,31 @@ class Avizo(Package):
     interface."""
 
     homepage = "https://www.thermofisher.com/sa/en/home/industrial/electron-microscopy/electron-microscopy-instruments-workflow-solutions/3d-visualization-analysis-software.html"
-    version('9.7.0', '9c9b9e81957387f4218df0c5adbb80717e9ae80ab3ca6ff8da523f7f499dcc5b',
+
+    version('2019.4',
+            sha256='a637720535bcbe254ab56368004a9544c64ec36186373fa24f26cee279685248',
+            url="file://{0}/Avizo-20194-Linux64-gcc48.bin".format(os.getcwd()),
+            expand=False)
+    version('2019.3',
+            sha256='be109df81e2f7238f234862367841dae05e76cc62218c1f36b1d9bc9514ce5f7',
+            url="file://{0}/Avizo-20193-Linux64-gcc48.bin".format(os.getcwd()),
+            expand=False)
+    version('9.7.0',
+            sha256='9c9b9e81957387f4218df0c5adbb80717e9ae80ab3ca6ff8da523f7f499dcc5b',
+            url="file://{0}/Avizo-970-Linux64-gcc44.bin".format(os.getcwd()),
             expand=False)
 
-    def url_for_version(self, version):
-        return "file://{0}/Avizo-{1}-Linux64-gcc44.bin".format(os.getcwd(),
-                                                               version.joined)
+    gcc_ver = {
+        "9.7.0": "44",
+        "2019.3": "48",
+        "2019.4": "48"
+    }
+
+    install_dir = {
+        "9.7.0": 'Avizo-9.7.0',
+        "2019.3": join_path('..', 'Avizo'),
+        "2019.4": join_path('..', 'Avizo')
+    }
 
     # Licensing
     license_required = True
@@ -37,14 +56,17 @@ def setup_run_environment(self, env):
     def install(self, spec, prefix):
         ver = self.version.joined
         sh = which('sh')
-        sh('Avizo-{0}-Linux64-gcc44.bin'.format(ver), '--noexec', '--keep')
+        sh('Avizo-{0}-Linux64-gcc{1}.bin'
+           .format(ver, self.gcc_ver[self.version.string]),
+           '--noexec', '--keep')
 
         with working_dir('Avizo'):
-            avizo_tar = tarfile.open(name='Avizo-{0}-Linux64-gcc44.tar.bz2'
-                                     .format(self.version))
+            avizo_tar = tarfile.open(name='Avizo-{0}-Linux64-gcc{1}.tar.bz2'
+                                     .format(self.version, self.gcc_ver
+                                             [self.version.string]))
             avizo_tar.extractall()
 
-            with working_dir('Avizo-{0}'.format(self.version)):
+            with working_dir(self.install_dir[self.version.string]):
                 install_tree('bin', prefix.bin)
                 install_tree('lib', prefix.lib)
                 install_tree('data', prefix.data)

From 2a5592f4196b61c043f61f26031de1c302f1affe Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 22 Apr 2020 22:47:45 +0800
Subject: [PATCH 052/802] Add new package: py-pid (#16202)

* Add new package: py-pid

* fix depends_on
---
 .../repos/builtin/packages/py-pid/package.py  | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-pid/package.py

diff --git a/var/spack/repos/builtin/packages/py-pid/package.py b/var/spack/repos/builtin/packages/py-pid/package.py
new file mode 100644
index 00000000000..b9b20428a9a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pid/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPid(PythonPackage):
+    """Pidfile featuring stale detection and file-locking, can also be
+    used as context-manager or decorator."""
+
+    homepage = "https://pypi.org/project/pid/"
+    url      = "https://github.com/trbs/pid/archive/3.0.3.tar.gz"
+
+    version('3.0.3', sha256='082281e2f6b99b4aaa02a24ae4796c604ac17f19cdd0327b8c1ba9c2e73aadc8')
+    version('3.0.2', sha256='0be7dc260e35788163b3171a5f0e1a8b9888bc2b77232c053c042a65496b8396')
+    version('3.0.1', sha256='2f51b61210f8e1f009b09a2034717003ca22dcd86995537ecb857863bddca89a')
+    version('3.0.0', sha256='3d251eadedc6fbd1fe4b43d521e76b83afd244b8b1951a2cd96864406bc96381')
+    version('2.2.5', sha256='d4c68554bf4b2fc7d0b50749f535f5c1fceb74ff025ce1a3f06745d15c595d40')
+    version('2.2.4', sha256='de3cc35e18c5409d8424813ab422b637af4d25bfdcf2c15ee6c5af447778de22')
+    version('2.2.3', sha256='14555fc214e0dfee7d94598b759523349832597e163415d1a7b0d87d9902cc47')
+    version('2.2.2', sha256='716bb5803fed50facdb62be0e48d08dd95e7392fcfb03f5540915623f9c4ee44')
+    version('2.2.1', sha256='2c5b398d348b8b1901ccb29b5c914c583187692acfbc3c28fc4ee483b9909357')
+    version('2.2.0', sha256='f2c3beb5742159794379b73088eb3f592a4b7b93bfef95f8bbc27ab98e5394ed')
+
+    depends_on('py-setuptools', type='build')

From 5f285fdd053b14b6a05ea1a48add80fa79b4cefb Mon Sep 17 00:00:00 2001
From: Sajid Ali <30510036+s-sajid-ali@users.noreply.github.com>
Date: Wed, 22 Apr 2020 09:49:07 -0500
Subject: [PATCH 053/802] fix code-signing on macOS (#15592)

* rebase

* move if statement location

* remove whitespace

* spec to self.spec

* switch statements as per review

* fix erronous indent

* add missing cmake arg

* minor placement fix for cmake args

* edit comment

* fix erronous return

* clarify conflicts with messages

* remove duplicate comment

* simplify logic

* macos wasn't a variant, fix that

* remove extra blank line

* address reviewer comments on spaces
---
 .../repos/builtin/packages/llvm/package.py    | 67 ++++++++++++-------
 1 file changed, 43 insertions(+), 24 deletions(-)

diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index f56a68403b9..bf8a77933c1 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -119,6 +119,8 @@ class Llvm(CMakePackage, CudaPackage):
         default=False,
         description="Build with OpenMP capable thread sanitizer",
     )
+    variant('code_signing', default=False,
+            description="Enable code-signing on macOS")
     variant("python", default=False, description="Install python bindings")
 
     extends("python", when="+python")
@@ -176,6 +178,20 @@ class Llvm(CMakePackage, CudaPackage):
     # MLIR exists in > 10.x
     conflicts("+mlir", when="@:9")
 
+    # code signing is only necessary on macOS",
+    conflicts('+code_signing', when='platform=linux')
+    conflicts('+code_signing', when='platform=bgq')
+    conflicts('+code_signing', when='platform=cray')
+
+    conflicts(
+        '+code_signing',
+        when='~lldb platform=darwin',
+        msg="code signing is only necessary for building the "
+            "in-tree debug server on macOS. Turning this variant "
+            "off enables a build of llvm with lldb that uses the "
+            "system debug server",
+    )
+
     # Github issue #4986
     patch("llvm_gcc7.patch", when="@4.0.0:4.0.1+lldb %gcc@7.0:")
     # Backport from llvm master + additional fix
@@ -192,31 +208,31 @@ class Llvm(CMakePackage, CudaPackage):
     # https://bugs.llvm.org/show_bug.cgi?id=39696
     patch("thread-p9.patch", when="@develop+libcxx")
 
-    @run_before("cmake")
-    def check_darwin_lldb_codesign_requirement(self):
-        if not self.spec.satisfies("+lldb platform=darwin"):
-            return
-        codesign = which("codesign")
-        mkdir("tmp")
-        llvm_check_file = join_path("tmp", "llvm_check")
-        copy("/usr/bin/false", llvm_check_file)
-
-        try:
-            codesign("-f", "-s", "lldb_codesign", "--dryrun", llvm_check_file)
-
-        except ProcessError:
-            # Newer LLVM versions have a simple script that sets up
-            # automatically
-            setup = Executable("./lldb/scripts/macos-setup-codesign.sh")
+    @run_before('cmake')
+    def codesign_check(self):
+        if self.spec.satisfies("+code_signing"):
+            codesign = which('codesign')
+            mkdir('tmp')
+            llvm_check_file = join_path('tmp', 'llvm_check')
+            copy('/usr/bin/false', llvm_check_file)
             try:
-                setup()
-            except Exception:
-                raise RuntimeError(
-                    'The "lldb_codesign" identity must be available to build '
-                    "LLVM with LLDB. See https://lldb.llvm.org/resources/"
-                    "build.html#code-signing-on-macos for details on how to "
-                    "create this identity."
-                )
+                codesign('-f', '-s', 'lldb_codesign', '--dryrun',
+                         llvm_check_file)
+
+            except ProcessError:
+                # Newer LLVM versions have a simple script that sets up
+                # automatically when run with sudo priviliges
+                setup = Executable("./lldb/scripts/macos-setup-codesign.sh")
+                try:
+                    setup()
+                except Exception:
+                    raise RuntimeError(
+                        'spack was unable to either find or set up'
+                        'code-signing on your system. Please refer to'
+                        'https://lldb.llvm.org/resources/build.html#'
+                        'code-signing-on-macos for details on how to'
+                        'create this identity.'
+                    )
 
     def setup_build_environment(self, env):
         env.append_flags("CXXFLAGS", self.compiler.cxx11_flag)
@@ -355,6 +371,9 @@ def cmake_args(self):
             ):
                 cmake_args.append("-DCMAKE_BUILD_WITH_INSTALL_RPATH=1")
 
+        if self.spec.satisfies("~code_signing platform=darwin"):
+            cmake_args.append('-DLLDB_USE_SYSTEM_DEBUGSERVER=ON')
+
         # Semicolon seperated list of projects to enable
         cmake_args.append(
             "-DLLVM_ENABLE_PROJECTS:STRING={0}".format(";".join(projects))

From e7906d650787ce785d1d49875f746647547227f2 Mon Sep 17 00:00:00 2001
From: Cameron Smith <cwsmith@users.noreply.github.com>
Date: Wed, 22 Apr 2020 12:11:55 -0400
Subject: [PATCH 054/802] kokkos: generate_makefile calls cmake (#16237)

---
 var/spack/repos/builtin/packages/kokkos/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/kokkos/package.py b/var/spack/repos/builtin/packages/kokkos/package.py
index 4b8e02e4955..82b93893e60 100644
--- a/var/spack/repos/builtin/packages/kokkos/package.py
+++ b/var/spack/repos/builtin/packages/kokkos/package.py
@@ -142,6 +142,9 @@ class Kokkos(Package):
     depends_on('qthreads', when='+qthreads')
     depends_on('cuda', when='+cuda')
 
+    # generate_makefile.bash calls cmake
+    depends_on('cmake@3.10:', type='build')
+
     def install(self, spec, prefix):
         generate = which(join_path(self.stage.source_path,
                                    'generate_makefile.bash'))

From d77576d85daba7e456e919ad28edd4593078f4ce Mon Sep 17 00:00:00 2001
From: Rao Garimella <rao@lanl.gov>
Date: Wed, 22 Apr 2020 10:12:28 -0600
Subject: [PATCH 055/802] update Jali version and dependent MSTK version
 (#16236)

Co-authored-by: Rao Garimella <rao@abyzou.lanl.gov>
---
 var/spack/repos/builtin/packages/jali/package.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/jali/package.py b/var/spack/repos/builtin/packages/jali/package.py
index cc2e025c889..e75dc7fb92f 100644
--- a/var/spack/repos/builtin/packages/jali/package.py
+++ b/var/spack/repos/builtin/packages/jali/package.py
@@ -13,11 +13,12 @@ class Jali(CMakePackage):
 
     homepage = "https://github.com/lanl/jali"
     git      = "https://github.com/lanl/jali"
-    url      = "https://github.com/lanl/jali/archive/1.1.1.tar.gz"
+    url      = "https://github.com/lanl/jali/archive/1.1.4.tar.gz"
 
     maintainers = ['raovgarimella']
 
     version('master', branch='master')
+    version('1.1.4', sha256='135ab02be1487fcdfb039613cbed630bce336d581a66468c66209db0a9d8a104')
     version('1.1.1', sha256='c96c000b3893ea7f15bbc886524476dd466ae145e77deedc27e412fcc3541207')
     version('1.1.0', sha256='783dfcd6a9284af83bb380ed257fa8b0757dc2f7f9196d935eb974fb6523c644')
     version('1.0.5', sha256='979170615d33a7bf20c96bd4d0285e05a2bbd901164e377a8bccbd9af9463801')
@@ -31,7 +32,7 @@ class Jali(CMakePackage):
 
     depends_on('boost')
 
-    depends_on('mstk@3.3.0: +exodusii+parallel~use_markers partitioner=all', when='+mstk')
+    depends_on('mstk@3.3.5: +exodusii+parallel~use_markers partitioner=all', when='+mstk')
 
     depends_on('zoltan -fortran')
     depends_on('metis')

From 769f350802b78ffa9c74bc5b9a1e912b64ab718d Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Thu, 23 Apr 2020 00:16:49 +0800
Subject: [PATCH 056/802] Add new package: py-asgiref (#16233)

---
 .../builtin/packages/py-asgiref/package.py    | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-asgiref/package.py

diff --git a/var/spack/repos/builtin/packages/py-asgiref/package.py b/var/spack/repos/builtin/packages/py-asgiref/package.py
new file mode 100644
index 00000000000..6819d27aa92
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-asgiref/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyAsgiref(PythonPackage):
+    """ASGI specification and utilities."""
+
+    homepage = "https://asgi.readthedocs.io/en/latest/"
+    url      = "https://github.com/django/asgiref/archive/3.2.7.tar.gz"
+
+    version('3.2.7', sha256='8a0b556b9e936418475f6670d59e14592c41d15d00b5ea4ad26f2b46f9f4fb9a')
+    version('3.2.6', sha256='29788163bdad8d494475a0137eba39b111fd86fbe825534a9376f9f2ab44251a')
+    version('3.2.5', sha256='eeb01ba02e86859746ee2a7bc8a75c484a006dc9575723563f24642a12b2bba8')
+    version('3.2.4', sha256='89e47532340338b7eafd717ab28658e8b48f4565d8384628c88d2d41565c8da0')
+    version('3.2.3', sha256='d38e16141c7189e23bfe03342d9cd3dbfd6baab99217892bfa7bc5646315b6bd')
+    version('3.2.2', sha256='47edf327aa70f317c9bc810d469ce681f1b35a7f499f68cf2b5da3ba6a651e69')
+    version('3.2.1', sha256='06a21df1f4456d29079f3c475c09ac31167bcc5f024c637dedf4e00d2dd9020b')
+    version('3.2.0', sha256='5db8c7a6c1ff54ea04a52f994d8af959427f1cab8e427aa802492a89fb0b635a')
+    version('3.1.4', sha256='bf01c52111ef7af2adc1e6d90282d2a32c5ebe09e84ae448389ceff7cef53fa9')
+    version('3.1.3', sha256='5b8bb7b3719b8c12a6c2363784a4d8c0eb5e980d8b4fdb6f38eccb52071dfab5')
+
+    depends_on('python@3.5:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')

From 169b9bebd88b16ab4374271d12ace035417a8811 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Thu, 23 Apr 2020 00:17:30 +0800
Subject: [PATCH 057/802] Add new package: kea (#16232)

---
 .../repos/builtin/packages/kea/package.py     | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/kea/package.py

diff --git a/var/spack/repos/builtin/packages/kea/package.py b/var/spack/repos/builtin/packages/kea/package.py
new file mode 100644
index 00000000000..acb6516f397
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kea/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Kea(AutotoolsPackage):
+    """Modern, open source DHCPv4 & DHCPv6 server."""
+
+    homepage = "https://www.isc.org/kea/"
+    url      = "https://downloads.isc.org/isc/kea/1.6.2/kea-1.6.2.tar.gz"
+
+    version('1.6.2', sha256='2af7336027143c3e98d8d1d44165b2c2cbb0252a92bd88f6dd4d2c6adb69d7b5')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('log4cplus')
+    depends_on('boost')

From b874b3e1fe90d48bdcb0058b35082114a81b9e21 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Thu, 23 Apr 2020 00:23:40 +0800
Subject: [PATCH 058/802] Add new package: isc-dhcp (#16230)

---
 .../builtin/packages/isc-dhcp/package.py      | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/isc-dhcp/package.py

diff --git a/var/spack/repos/builtin/packages/isc-dhcp/package.py b/var/spack/repos/builtin/packages/isc-dhcp/package.py
new file mode 100644
index 00000000000..9a5ab764556
--- /dev/null
+++ b/var/spack/repos/builtin/packages/isc-dhcp/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class IscDhcp(AutotoolsPackage):
+    """ISC DHCP offers a complete open source solution for
+    implementing DHCP servers, relay agents, and clients. ISC
+    DHCP supports both IPv4 and IPv6, and is suitable for use
+    in high-volume and high-reliability applications."""
+
+    homepage = "https://www.isc.org/dhcp/"
+    url      = "https://downloads.isc.org/isc/dhcp/4.4.2/dhcp-4.4.2.tar.gz"
+    list_url = "https://downloads.isc.org/isc/dhcp"
+    list_depth = 1
+
+    parallel = False
+
+    version('4.4.2', sha256='1a7ccd64a16e5e68f7b5e0f527fd07240a2892ea53fe245620f4f5f607004521')
+    version('4.4.1', sha256='2a22508922ab367b4af4664a0472dc220cc9603482cf3c16d9aff14f3a76b608')
+    version('4.4.0', sha256='4a90be0f22ad81c987f5584661b60a594f1b21c581b82bfba3ae60f89ae44397')
+    version('4.3.6', sha256='a41eaf6364f1377fe065d35671d9cf82bbbc8f21207819b2b9f33f652aec6f1b')
+    version('4.3.5', sha256='eb95936bf15d2393c55dd505bc527d1d4408289cec5a9fa8abb99f7577e7f954')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('bind9',    type='build')

From 63ff1219807242bbb4bea5767fb2d5fd6c632331 Mon Sep 17 00:00:00 2001
From: George Hartzell <hartzell@alerce.com>
Date: Wed, 22 Apr 2020 13:04:17 -0700
Subject: [PATCH 059/802] spack environments documentation: -E -> -e (#16242)

To specify an environment for a comment, the user can specify
"spack -e <env>". The documentation incorrectly specified "-E" (which
is actually used to ignore any implicit use of environments).
---
 lib/spack/docs/environments.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/spack/docs/environments.rst b/lib/spack/docs/environments.rst
index a51c3012fd7..c26f81d9142 100644
--- a/lib/spack/docs/environments.rst
+++ b/lib/spack/docs/environments.rst
@@ -281,7 +281,7 @@ in the lockfile, nor does it install the spec.
 
 The ``spack add`` command is environment aware. It adds to the
 currently active environment. All environment aware commands can also
-be called using the ``spack -E`` flag to specify the environment.
+be called using the ``spack -e`` flag to specify the environment.
 
 .. code-block:: console
 
@@ -292,7 +292,7 @@ or
 
 .. code-block:: console
 
-   $ spack -E myenv add python
+   $ spack -e myenv add python
 
 .. _environments_concretization:
 

From 0d2ebbf996d0ad3fa049b8f50304cd51b8c40467 Mon Sep 17 00:00:00 2001
From: Tim Haines <thaines.astro@gmail.com>
Date: Wed, 22 Apr 2020 15:34:32 -0500
Subject: [PATCH 060/802] hwloc: Add netloc variant (#16001)

hwloc depends on MPI when netloc is enabled. Note that OpenMPI depends on
netloc, so hwloc cannot use OpenMPI as the MPI provider when netloc is
enabled (this would result in a cyclic dependency).
---
 var/spack/repos/builtin/packages/hwloc/package.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py
index 2b7968a37a5..547327e60ba 100644
--- a/var/spack/repos/builtin/packages/hwloc/package.py
+++ b/var/spack/repos/builtin/packages/hwloc/package.py
@@ -57,6 +57,14 @@ class Hwloc(AutotoolsPackage):
         default=False,
         description='Enable the Cairo back-end of hwloc\'s lstopo command'
     )
+    variant(
+        'netloc',
+        default=False,
+        description="Enable netloc [requires MPI]"
+    )
+
+    # netloc isn't available until version 2.0.0
+    conflicts('+netloc', when="@:1.99.99")
 
     depends_on('pkgconfig', type='build')
     depends_on('m4', type='build', when='@master')
@@ -71,6 +79,10 @@ class Hwloc(AutotoolsPackage):
     depends_on('cairo', when='+cairo')
     depends_on('numactl', when='@:1.11.11 platform=linux')
 
+    # When mpi=openmpi, this introduces an unresolvable dependency.
+    # See https://github.com/spack/spack/issues/15836 for details
+    depends_on('mpi', when='+netloc')
+
     def url_for_version(self, version):
         return "http://www.open-mpi.org/software/hwloc/v%s/downloads/hwloc-%s.tar.gz" % (version.up_to(2), version)
 
@@ -81,7 +93,7 @@ def configure_args(self):
             # (Alternatively, we could require OpenCL as dependency.)
             "--disable-opencl",
         ]
-        if '@2.0.0:' in self.spec:
+        if '+netloc' in self.spec:
             args.append('--enable-netloc')
 
         args.extend(self.enable_or_disable('cairo'))

From 46e90692e829457b133521f7dc5c6d7c1f7502da Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 22 Apr 2020 15:47:14 -0500
Subject: [PATCH 061/802] PyTorch: add conflict for Apple Clang 11.0.3 (#16238)

* PyTorch: add conflict for Apple Clang 11.0.3

* Flake8 fix
---
 var/spack/repos/builtin/packages/py-torch/package.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py
index 6428d6cb8e5..f786ad14bc5 100644
--- a/var/spack/repos/builtin/packages/py-torch/package.py
+++ b/var/spack/repos/builtin/packages/py-torch/package.py
@@ -52,7 +52,6 @@ class PyTorch(PythonPackage, CudaPackage):
     version('master', branch='master', submodules=True)
     version('1.5.0', tag='v1.5.0', submodules=True)
     version('1.4.1', tag='v1.4.1', submodules=True)
-    # see https://github.com/pytorch/pytorch/issues/35149
     version('1.4.0', tag='v1.4.0', submodules=True,
             submodules_delete=['third_party/fbgemm'])
     version('1.3.1', tag='v1.3.1', submodules=True)
@@ -104,8 +103,11 @@ class PyTorch(PythonPackage, CudaPackage):
     conflicts('+redis', when='@:1.0')
     conflicts('+zstd', when='@:1.0')
     conflicts('+tbb', when='@:1.1')
-    # see https://github.com/pytorch/pytorch/issues/35149
+    # https://github.com/pytorch/pytorch/issues/35149
     conflicts('+fbgemm', when='@1.4.0')
+    # https://github.com/pytorch/pytorch/issues/35478
+    conflicts('%clang@11.0.3-apple',
+              msg='Apple Clang 11.0.3 segfaults at build-time')
 
     conflicts('cuda_arch=none', when='+cuda',
               msg='Must specify CUDA compute capabilities of your GPU, see '

From ec23e4ffe5af7f59c1cb7ad3c5485e83379f5a23 Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Wed, 22 Apr 2020 14:26:29 -0700
Subject: [PATCH 062/802] update compiler config with bootstrapped compiler
 when already installed (#16221)

Update compiler config with bootstrapped compiler when it was already installed and added config defaults to code so mutable_config test fixture works.
---
 lib/spack/spack/build_environment.py          |  2 +-
 lib/spack/spack/cmd/common/arguments.py       |  2 +-
 lib/spack/spack/fetch_strategy.py             |  2 +-
 lib/spack/spack/installer.py                  |  6 ++++
 lib/spack/spack/test/cmd/install.py           | 30 ++++++++++++++++++-
 .../builtin.mock/packages/gcc/package.py      | 23 ++++++++++++++
 6 files changed, 61 insertions(+), 4 deletions(-)
 create mode 100644 var/spack/repos/builtin.mock/packages/gcc/package.py

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 21ab6895ec1..5e6ea00ce62 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -415,7 +415,7 @@ def _set_variables_for_single_module(pkg, module):
     if getattr(module, marker, False):
         return
 
-    jobs = spack.config.get('config:build_jobs') if pkg.parallel else 1
+    jobs = spack.config.get('config:build_jobs', 16) if pkg.parallel else 1
     jobs = min(jobs, multiprocessing.cpu_count())
     assert jobs is not None, "no default set for config:build_jobs"
 
diff --git a/lib/spack/spack/cmd/common/arguments.py b/lib/spack/spack/cmd/common/arguments.py
index b93f265c7ab..e5945bda9c3 100644
--- a/lib/spack/spack/cmd/common/arguments.py
+++ b/lib/spack/spack/cmd/common/arguments.py
@@ -111,7 +111,7 @@ def __call__(self, parser, namespace, jobs, option_string):
     def default(self):
         # This default is coded as a property so that look-up
         # of this value is done only on demand
-        return min(spack.config.get('config:build_jobs'),
+        return min(spack.config.get('config:build_jobs', 16),
                    multiprocessing.cpu_count())
 
     @default.setter
diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index d7613ae58af..c6200565e5b 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -336,7 +336,7 @@ def _fetch_from_url(self, url):
         else:
             curl_args.append('-sS')  # just errors when not.
 
-        connect_timeout = spack.config.get('config:connect_timeout')
+        connect_timeout = spack.config.get('config:connect_timeout', 10)
 
         if self.extra_options:
             cookie = self.extra_options.get('cookie')
diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py
index 213a85f0dc7..2bad1e88183 100644
--- a/lib/spack/spack/installer.py
+++ b/lib/spack/spack/installer.py
@@ -1466,6 +1466,12 @@ def install(self, **kwargs):
                 if lock is not None:
                     self._update_installed(task)
                     _print_installed_pkg(pkg.prefix)
+
+                    # It's an already installed compiler, add it to the config
+                    if task.compiler:
+                        spack.compilers.add_compilers_to_config(
+                            spack.compilers.find_compilers([pkg.spec.prefix]))
+
                 else:
                     # At this point we've failed to get a write or a read
                     # lock, which means another process has taken a write
diff --git a/lib/spack/spack/test/cmd/install.py b/lib/spack/spack/test/cmd/install.py
index 1d4a0c68273..dd52cea406f 100644
--- a/lib/spack/spack/test/cmd/install.py
+++ b/lib/spack/spack/test/cmd/install.py
@@ -15,11 +15,12 @@
 import llnl.util.filesystem as fs
 
 import spack.config
+import spack.compilers as compilers
 import spack.hash_types as ht
 import spack.package
 import spack.cmd.install
 from spack.error import SpackError
-from spack.spec import Spec
+from spack.spec import Spec, CompilerSpec
 from spack.main import SpackCommand
 import spack.environment as ev
 
@@ -718,3 +719,30 @@ def test_cdash_auth_token(tmpdir, install_mockery, capfd):
                 '--log-format=cdash',
                 'a')
             assert 'Using CDash auth token from environment' in out
+
+
+def test_compiler_bootstrap(
+        install_mockery, mock_packages, mock_fetch, mock_archive,
+        mutable_config, monkeypatch):
+    monkeypatch.setattr(spack.concretize.Concretizer,
+                        'check_for_compiler_existence', False)
+    spack.config.set('config:install_missing_compilers', True)
+    assert CompilerSpec('gcc@2.0') not in compilers.all_compiler_specs()
+
+    # Test succeeds if it does not raise an error
+    install('a%gcc@2.0')
+
+
+@pytest.mark.regression('16221')
+def test_compiler_bootstrap_already_installed(
+        install_mockery, mock_packages, mock_fetch, mock_archive,
+        mutable_config, monkeypatch):
+    monkeypatch.setattr(spack.concretize.Concretizer,
+                        'check_for_compiler_existence', False)
+    spack.config.set('config:install_missing_compilers', True)
+
+    assert CompilerSpec('gcc@2.0') not in compilers.all_compiler_specs()
+
+    # Test succeeds if it does not raise an error
+    install('gcc@2.0')
+    install('a%gcc@2.0')
diff --git a/var/spack/repos/builtin.mock/packages/gcc/package.py b/var/spack/repos/builtin.mock/packages/gcc/package.py
new file mode 100644
index 00000000000..03b45a6e12c
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/gcc/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gcc(Package):
+    """Simple compiler package."""
+
+    homepage = "http://www.example.com"
+    url      = "http://www.example.com/gcc-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+    version('2.0', '2.0_a_hash')
+
+    def install(self, spec, prefix):
+        # Create the minimal compiler that will fool `spack compiler find`
+        mkdirp(prefix.bin)
+        with open(prefix.bin.gcc, 'w') as f:
+            f.write('#!/bin/bash\necho "%s"' % str(spec.version))
+        set_executable(prefix.bin.gcc)

From 650745746af7c7e2160c6552926d301453e1e8e0 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <KineticTheory@users.noreply.github.com>
Date: Wed, 22 Apr 2020 15:34:58 -0600
Subject: [PATCH 063/802] Provide new version 0.6.10. (#16240)

---
 var/spack/repos/builtin/packages/py-cmake-format/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-cmake-format/package.py b/var/spack/repos/builtin/packages/py-cmake-format/package.py
index a8f6f862298..b300b97379f 100644
--- a/var/spack/repos/builtin/packages/py-cmake-format/package.py
+++ b/var/spack/repos/builtin/packages/py-cmake-format/package.py
@@ -14,6 +14,7 @@ class PyCmakeFormat(PythonPackage):
     homepage = "https://pypi.python.org/pypi/cmake-format"
     url      = "https://pypi.io/packages/source/c/cmake_format/cmake_format-0.6.9.tar.gz"
 
+    version('0.6.10', sha256='82f0ef16236225cb43f45bfb6983ef7f6f72634727a1a6c26290402527bdd793')
     version('0.6.9', sha256='b2f8bf2e9c6651126f2f2954b7803222b0faf6b8649eabc4d965ea97483a4d20')
 
     depends_on('py-setuptools',  type=('build', 'run'))

From ec54f86c0b4be3aa6b6d4c95ccf6e0da39c6c668 Mon Sep 17 00:00:00 2001
From: "Mark W. Krentel" <krentel@rice.edu>
Date: Wed, 22 Apr 2020 16:48:41 -0500
Subject: [PATCH 064/802] gotcha: add version 1.0.3 (#16239)

---
 var/spack/repos/builtin/packages/gotcha/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/gotcha/package.py b/var/spack/repos/builtin/packages/gotcha/package.py
index 006b74a49af..f0cb3a7233d 100644
--- a/var/spack/repos/builtin/packages/gotcha/package.py
+++ b/var/spack/repos/builtin/packages/gotcha/package.py
@@ -15,6 +15,7 @@ class Gotcha(CMakePackage):
 
     version('develop', branch='develop')
     version('master', branch='master')
+    version('1.0.3', tag='1.0.3')
     version('1.0.2', tag='1.0.2')
     version('0.0.2', tag='0.0.2')
 

From 4166c97a8263f0314836963a049b8adf3fdf2c05 Mon Sep 17 00:00:00 2001
From: Vicente Adolfo Bolea Sanchez <vicente.bolea@gmail.com>
Date: Wed, 22 Apr 2020 19:54:55 -0400
Subject: [PATCH 065/802] vtk-m: update Vtk-m pkg to its latest version v1.5.1
 (#16192)

Last month VTK-m releases its lastest version named `v1.5.1`. This new
release only contains bugfixes related to compiler error / warnings.

- Depends on CMake >= 3.12
- Set VTKm_NO_ASSERT=ON by default
- add maintainers

Signed-off-by: Vicente Adolfo Bolea Sanchez <vicente.bolea@kitware.com>
---
 var/spack/repos/builtin/packages/vtk-m/package.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/vtk-m/package.py b/var/spack/repos/builtin/packages/vtk-m/package.py
index 0a22efb357b..5fd77da94dd 100644
--- a/var/spack/repos/builtin/packages/vtk-m/package.py
+++ b/var/spack/repos/builtin/packages/vtk-m/package.py
@@ -18,10 +18,13 @@ class VtkM(CMakePackage, CudaPackage):
     architectures."""
 
     homepage = "https://m.vtk.org/"
-    url      = "https://gitlab.kitware.com/vtk/vtk-m/-/archive/v1.5.0/vtk-m-v1.5.0.tar.gz"
+    maintainers = ['robertmaynard', 'kmorel', 'vicentebolea']
+
+    url      = "https://gitlab.kitware.com/vtk/vtk-m/-/archive/v1.5.1/vtk-m-v1.5.1.tar.gz"
     git      = "https://gitlab.kitware.com/vtk/vtk-m.git"
 
     version('master', branch='master')
+    version('1.5.1', sha256="64c19e66c0d579cfb21bb0df10d649b523b470b0c9a6c2ea5fd979dfeda2c25e")
     version('1.5.0', sha256="b1b13715c7fcc8d17f5c7166ff5b3e9025f6865dc33eb9b06a63471c21349aa8")
     version('1.4.0', sha256="8d83cca7cd5e204d10da151ce4f1846c1f7414c7c1e579173d15c5ea0631555a")
     version('1.3.0', sha256="f88c1b0a1980f695240eeed9bcccfa420cc089e631dc2917c9728a2eb906df2e")
@@ -44,7 +47,7 @@ class VtkM(CMakePackage, CudaPackage):
     variant("64bitids", default=False,
             description="enable 64 bits ids")
 
-    depends_on("cmake")
+    depends_on("cmake@3.12:", type="build")         # CMake >= 3.12
     depends_on("tbb", when="+tbb")
     depends_on("cuda", when="+cuda")
     depends_on("mpi", when="+mpi")
@@ -145,4 +148,8 @@ def cmake_args(self):
                 print("64 bit ids enabled")
             else:
                 options.append("-DVTKm_USE_64BIT_IDS:BOOL=OFF")
+
+            if spec.variants["build_type"].value != 'Release':
+                options.append("-DVTKm_NO_ASSERT:BOOL=ON")
+
             return options

From d0bff870a6b3af5122c251d697c6d5a3f221d96c Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Wed, 22 Apr 2020 17:41:33 -0700
Subject: [PATCH 066/802] macOS+GCC: Conflicts CMake, libuv, CPython (#16249)

The major building blocks in many software stacks:
- CPython
- CMake (libuv)

do not build on macOS with GCC. The main problem is that some macOS
framework includes pull in objective-c code and that code does get
misinterpreted as (invalid) C by GCC by default.
---
 var/spack/repos/builtin/packages/cmake/package.py  | 7 +++++++
 var/spack/repos/builtin/packages/libuv/package.py  | 6 ++++++
 var/spack/repos/builtin/packages/python/package.py | 6 ++++++
 3 files changed, 19 insertions(+)

diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index ce436d2ea9f..cc69eac5f77 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -92,6 +92,13 @@ class Cmake(Package):
     variant('openssl', default=True,  description="Enables CMake's OpenSSL features")
     variant('ncurses', default=True,  description='Enables the build of the ncurses gui')
 
+    # Tries to build an Objective-C file from libuv with GCC's C frontend
+    # https://gitlab.kitware.com/cmake/cmake/-/issues/20620
+    # https://github.com/libuv/libuv/issues/2805
+    conflicts('%gcc platform=darwin',
+              msg='CMake does not compile with GCC on macOS yet, use clang. '
+                  'See: https://gitlab.kitware.com/cmake/cmake/-/issues/20620')
+
     # Really this should conflict since it's enabling or disabling openssl for
     # CMake's internal copy of curl.  Ideally we'd want a way to have the
     # openssl variant disabled when ~ownlibs but there's not really a way to
diff --git a/var/spack/repos/builtin/packages/libuv/package.py b/var/spack/repos/builtin/packages/libuv/package.py
index 55d7dcebba0..309270a3ff6 100644
--- a/var/spack/repos/builtin/packages/libuv/package.py
+++ b/var/spack/repos/builtin/packages/libuv/package.py
@@ -19,6 +19,12 @@ class Libuv(AutotoolsPackage):
     depends_on('autoconf', type='build')
     depends_on('libtool', type='build')
 
+    # Tries to build an Objective-C file with GCC's C frontend
+    # https://github.com/libuv/libuv/issues/2805
+    conflicts('%gcc platform=darwin',
+              msg='libuv does not compile with GCC on macOS yet, use clang. '
+                  'See: https://github.com/libuv/libuv/issues/2805')
+
     def autoreconf(self, spec, prefix):
         # This is needed because autogen.sh generates on-the-fly
         # an m4 macro needed during configuration
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 8270ce7329c..fd7438d605e 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -166,6 +166,12 @@ class Python(AutotoolsPackage):
     # https://github.com/python/cpython/pull/16717
     patch('intel-3.6.7.patch', when='@3.6.7:3.6.8,3.7.1:3.7.5 %intel')
 
+    # CPython tries to build an Objective-C file with GCC's C frontend
+    # https://github.com/spack/spack/pull/16222
+    # https://github.com/python/cpython/pull/13306
+    conflicts('%gcc platform=darwin',
+              msg='CPython does not compile with GCC on macOS yet, use clang. '
+                  'See: https://github.com/python/cpython/pull/13306')
     # For more information refer to this bug report:
     # https://bugs.python.org/issue29712
     conflicts(

From 6f9373dd66503d6751030fb425fd24dc1685a63c Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Thu, 23 Apr 2020 02:48:52 +0200
Subject: [PATCH 067/802] spack info: replace "True, False" with "on, off"
 (#16235)

fixes #16184
---
 lib/spack/spack/cmd/info.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/lib/spack/spack/cmd/info.py b/lib/spack/spack/cmd/info.py
index 81a68dae966..f8db9e10cb3 100644
--- a/lib/spack/spack/cmd/info.py
+++ b/lib/spack/spack/cmd/info.py
@@ -114,10 +114,8 @@ def lines(self):
                     '{0} [{1}]'.format(k, self.default(v)),
                     width=self.column_widths[0]
                 )
-                allowed = textwrap.wrap(
-                    v.allowed_values,
-                    width=self.column_widths[1]
-                )
+                allowed = v.allowed_values.replace('True, False', 'on, off')
+                allowed = textwrap.wrap(allowed, width=self.column_widths[1])
                 description = textwrap.wrap(
                     v.description,
                     width=self.column_widths[2]

From 7299de74c6919b58f582c08de3991fd74b4ea07a Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Thu, 23 Apr 2020 09:40:25 +0800
Subject: [PATCH 068/802] Add new package py-sqlparse (#16231)

* Update var/spack/repos/builtin/packages/py-sqlparse/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Add new package py-sqlparse

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../builtin/packages/py-sqlparse/package.py   | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-sqlparse/package.py

diff --git a/var/spack/repos/builtin/packages/py-sqlparse/package.py b/var/spack/repos/builtin/packages/py-sqlparse/package.py
new file mode 100644
index 00000000000..73916d40e54
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-sqlparse/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PySqlparse(PythonPackage):
+    """A non-validating SQL parser module for Python."""
+
+    homepage = "https://github.com/andialbrecht/sqlparse"
+    url      = "https://github.com/andialbrecht/sqlparse/archive/0.3.1.tar.gz"
+
+    version('0.3.1', sha256='344b539482b75c244ac69fbb160d0f4d63a288a392475c8418ca692c594561f9')
+    version('0.3.0', sha256='a75fddae009fba1d66786203c9dd3a842aa4415475c466d15484139117108474')
+    version('0.2.4', sha256='7087a2bd385c06ac1a5cf343e2e5ea7ce2bb6386849e59ef214e02af68f73fb4')
+    version('0.2.3', sha256='12470ab41df1a7003a2957a79c6da9cd4ded180c8a193aa112fe0899b935ef30')
+
+    depends_on('py-setuptools',   type='build')
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))

From 15882d786807ae59bed364af9948de7d6a7680e5 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Thu, 23 Apr 2020 12:09:06 +0800
Subject: [PATCH 069/802] Add new package: py-django (#16234)

---
 .../builtin/packages/py-django/package.py     | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-django/package.py

diff --git a/var/spack/repos/builtin/packages/py-django/package.py b/var/spack/repos/builtin/packages/py-django/package.py
new file mode 100644
index 00000000000..0dc1fa13885
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-django/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyDjango(PythonPackage):
+    """The Web framework for perfectionists with deadlines."""
+
+    homepage = "https://www.djangoproject.com/"
+    url      = "https://github.com/django/django/archive/3.0.5.tar.gz"
+
+    version('3.0.5',  sha256='ef2d4f26414dc9598afce9c56cee4578313b88861cedfc5b3d9a71078e5cc79b')
+    version('3.0.4',  sha256='99699643d83acfab51d3ad73c2c2904173e03a4f59fe24c3d494e4fafc0b679f')
+    version('3.0.3',  sha256='d953c950f0c395db065c8bc39d20e87faded376632a3aacf889ae92d5adaac8b')
+    version('3.0.2',  sha256='ca316b1179a16931ed872ce970aabefcf3d41fe0d4b1a8e1301ec59e1e0ab45b')
+    version('3.0.1',  sha256='85349b9366364847264b2b707ffcff5a27a022afa29aac0e904ca672cbe5ee65')
+    version('2.2.12', sha256='ec490c67bd2780b4ec4f5355cd99fa2fa6007f81695dd45a9e8f7ccc5ff17772')
+    version('2.2.11', sha256='f4274181973f0f021cc00419cfa342f1a6f862406e766ae93e7fbba9d84c680c')
+    version('2.2.10', sha256='3741536cf122d6695e8575b2fcf67c18812751fd3143393ea75c01a277afdacc')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('python@3.6:',   type=('build', 'run'))
+    depends_on('py-pytz',       type=('build', 'run'))
+    depends_on('py-sqlparse',   type=('build', 'run'))
+    depends_on('py-asgiref',    type=('build', 'run'))

From fb1498abaca07e3594d2f24edc1596fb03225dea Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Thu, 23 Apr 2020 12:13:04 +0800
Subject: [PATCH 070/802] Add new package: dnsmasq (#16253)

---
 .../repos/builtin/packages/dnsmasq/package.py | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/dnsmasq/package.py

diff --git a/var/spack/repos/builtin/packages/dnsmasq/package.py b/var/spack/repos/builtin/packages/dnsmasq/package.py
new file mode 100644
index 00000000000..8f0ff1bcf89
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dnsmasq/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Dnsmasq(MakefilePackage):
+    """A lightweight, caching DNS proxy with integrated DHCP server."""
+
+    homepage = "http://www.thekelleys.org.uk/dnsmasq/doc.html"
+    url      = "http://www.thekelleys.org.uk/dnsmasq/dnsmasq-2.70.tar.gz"
+
+    version('2.81', sha256='3c28c68c6c2967c3a96e9b432c0c046a5df17a426d3a43cffe9e693cf05804d0')
+    version('2.80', sha256='9e4a58f816ce0033ce383c549b7d4058ad9b823968d352d2b76614f83ea39adc')
+    version('2.79', sha256='77512dd6f31ffd96718e8dcbbf54f02c083f051d4cca709bd32540aea269f789')
+    version('2.78', sha256='c92e5d78aa6353354d02aabf74590d08980bb1385d8a00b80ef9bc80430aa1dc')
+    version('2.77', sha256='ae97a68c4e64f07633f31249eb03190d673bdb444a05796a3a2d3f521bfe9d38')
+    version('2.76', sha256='777c4762d2fee3738a0380401f2d087b47faa41db2317c60660d69ad10a76c32')
+    version('2.75', sha256='f8252c0a0ba162c2cd45f81140c7c17cc40a5fca2b869d1a420835b74acad294')
+    version('2.74', sha256='27b95a8b933d7eb88e93a4c405b808d09268246d4e108606e423ac518aede78f')
+    version('2.73', sha256='9f350f74ae2c7990b1c7c6c8591d274c37b674aa987f54dfee7ca856fae0d02d')
+    version('2.72', sha256='635f1b47417d17cf32e45cfcfd0213ac39fd09918479a25373ba9b2ce4adc05d')
+    version('2.71', sha256='7d8c64f66a396442e01b639df3ea6b4e02ba88cbe206c80be8de68b6841634c4')
+    version('2.70', sha256='8eb7bf53688d6aaede5c90cfd2afcce04803a4efbddfbeecc6297180749e98af')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('./src/dnsmasq', prefix.bin)

From 04457fe03118515c8bb85fedaf58f35b4b52cc29 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Thu, 23 Apr 2020 12:13:44 +0800
Subject: [PATCH 071/802] Py coilmq (#16203)

* Add new package: py-coilmq

* remove FIXME comment

* fix depends_on
---
 .../builtin/packages/py-coilmq/package.py     | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-coilmq/package.py

diff --git a/var/spack/repos/builtin/packages/py-coilmq/package.py b/var/spack/repos/builtin/packages/py-coilmq/package.py
new file mode 100644
index 00000000000..fc2f404e51e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-coilmq/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCoilmq(PythonPackage):
+    """Lightweight Python STOMP message broker."""
+
+    homepage = "https://github.com/hozn/coilmq"
+    url      = "https://github.com/hozn/coilmq/archive/1.0.0.tar.gz"
+
+    version('1.0.0', sha256='95d12de9b007fc679d4ad2eba0253aee8f6ecf42b79a94be6a2e0349f91086b0')
+    version('0.6.1', sha256='402a5f88631a848926c442385248d7ae7bd05607bba8f20605e31fd49c3677f9')
+    version('0.6.0', sha256='50d22fde72f058720bb48ad96bdd7c87594372d7917dd5d2cca40a9d195fde27')
+    version('0.5.0', sha256='ffe2648e0a336ff61f729ad76090f8a16e681b3d3d6b14ba7ce3ef840de32cd9')
+    version('0.4.4', sha256='2a0d494c73412e76075d2a72698948fb1d84c9c5719b134c364c07bcc6a3eacf')
+    version('0.4.3', sha256='7a051f4fd2b76c8accf0b3f435267566910085c18483726e9eb56416e40703b7')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-python-daemon', type=('build', 'run'))
+    depends_on('py-pid', type=('build', 'run'))
+    depends_on('py-wheel', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-click', type=('build', 'run'))

From 7c0aee41271b5a59fca2ce4849de21f25c402d1a Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Thu, 23 Apr 2020 15:35:14 +0800
Subject: [PATCH 072/802] cpp-httplib: added package at v0.5.9 (#16228)

---
 .../builtin/packages/cpp-httplib/package.py   | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/cpp-httplib/package.py

diff --git a/var/spack/repos/builtin/packages/cpp-httplib/package.py b/var/spack/repos/builtin/packages/cpp-httplib/package.py
new file mode 100644
index 00000000000..2774a95bd1c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cpp-httplib/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class CppHttplib(CMakePackage):
+    """A C++ header-only HTTP/HTTPS server and client library."""
+
+    homepage = "https://github.com/yhirose/cpp-httplib/"
+    url      = "https://github.com/yhirose/cpp-httplib/archive/v0.5.10.tar.gz"
+
+    version('0.5.9',  sha256='c9e7aef3b0d4e80ee533d10413508d8a6e09a67d0d59646c43111f3993de006e')
+    version('0.5.8',  sha256='184d4fe79fc836ee26aa8635b3240879af4c6f17257fc7063d0b77a0cf856dfc')
+    version('0.5.7',  sha256='27b7f6346bdeb1ead9d17bd7cea89d9ad491f50f0479081053cc6e5742a89e64')
+    version('0.5.6',  sha256='06ebc94edcdf23d66692bf1d128f6c65bb0ec36ce5e2f8ee61990bc74e838868')
+    version('0.5.5',  sha256='e18dab82b3b395290514baf3804c7b74892beb654bd8020600a9d9dfdc49c32a')
+    version('0.5.4',  sha256='40dcce66ec002e2631ef918e1b3bfc9ec1662d02007291ea4743e17ac9c7d43f')
+    version('0.5.3',  sha256='d9d62ae15d5a2f4404286d5f6ec48daef27e24b5aab98d0505e24ee2b187d3f5')
+    version('0.5.2',  sha256='a28cc74d3b46e2ba60311b9229375599b513151e39a7d8df6fe1fb797fc1be3a')
+    version('0.5.1',  sha256='e079d1803e4fdbaf8bed5b414f6045c78273082eec7ac0d4802029175f2a1448')
+    version('0.4.2', sha256='ceaf50e2a9fce48910b244d33c6824e55aef688ad5bc181f4b9504242c2447ff')
+    version('0.3.3', sha256='476471c6fcd4b39fc79a5dd6ad343a2428cb69b4d528557abb6a0b7bf8186e34')
+    version('0.2.6', sha256='8678afc0e69bc198edcb8fe0066e46a87373221232ebabde2d78c237f31d3c3d')
+    version('0.2.1', sha256='94a6ddd25088b66b7b9e57b9d0ea138c984967e91b21395401642027bf279438')

From 044985af80f1310b16898a5c693c0bb4b49cdc27 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Thu, 23 Apr 2020 00:38:10 -0700
Subject: [PATCH 073/802] cryptopp : added 'shared' variant and sse detection
 (#16213)

---
 .../builtin/packages/cryptopp/package.py      | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py
index a96e358d2a8..fa586eca4b0 100644
--- a/var/spack/repos/builtin/packages/cryptopp/package.py
+++ b/var/spack/repos/builtin/packages/cryptopp/package.py
@@ -25,11 +25,30 @@ class Cryptopp(MakefilePackage):
     version('5.6.2', sha256='5cbfd2fcb4a6b3aab35902e2e0f3b59d9171fee12b3fc2b363e1801dfec53574')
     version('5.6.1', sha256='98e74d8cb17a38033354519ac8ba9c5d98a6dc00bf5d1ec3c533c2e8ec86f268')
 
+    variant('shared', default=True,  description="Build shared object versions of libraries.")
+
     depends_on('gmake', type='build')
 
     def url_for_version(self, version):
         url = '{0}/{1}{2}.zip'
         return url.format(self.homepage, self.name, version.joined)
 
+    def build(self, spec, prefix):
+        cxx_flags = []
+
+        if '+shared' in spec:
+            cxx_flags.append(self.compiler.cxx_pic_flag)
+
+        target = self.spec.target
+        if 'sse4.1' not in target:
+            cxx_flags.append('-DCRYPTOPP_DISABLE_SSE4')
+        if 'ssse3' not in target:
+            cxx_flags.append('-DCRYPTOPP_DISABLE_SSSE3')
+        if 'sse2' not in target:
+            cxx_flags.append('-DCRYPTOPP_DISABLE_SSE2')
+
+        make_target = 'dynamic' if '+shared' in spec else 'static'
+        make(make_target, 'CXXFLAGS={0}'.format(' '.join(cxx_flags)))
+
     def install(self, spec, prefix):
         make('install', 'PREFIX={0}'.format(prefix))

From 807a08a69bec1b66327b7e7d8e402852f5b14964 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Thu, 23 Apr 2020 15:59:32 +0800
Subject: [PATCH 074/802] enca: added package at v1.19 (#16255)

---
 .../repos/builtin/packages/enca/package.py    | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/enca/package.py

diff --git a/var/spack/repos/builtin/packages/enca/package.py b/var/spack/repos/builtin/packages/enca/package.py
new file mode 100644
index 00000000000..9324a22652f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/enca/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Enca(AutotoolsPackage):
+    """Extremely Naive Charset Analyser."""
+
+    homepage = "https://cihar.com/software/enca/"
+    url      = "https://github.com/nijel/enca/archive/1.19.tar.gz"
+
+    version('1.19', sha256='c4fd9a3d7c086803138842b18eed6072ec8810859b0e1ef091f1e1138d283f25')
+    version('1.18', sha256='b87c8d1bffc7d06ba74f82ae86eb21a921e94629203b2a971c966064c7eadab2')
+    version('1.17', sha256='b20372440c500e6463bd61dab0e68131cdfe857c6b7ca139b5c6cbf01e24fdc7')
+    version('1.16', sha256='14457b185c77b947ca2f8e09a2c3ec66940d97a2ccea28b8e61a6e0f3a0033f6')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+
+    def autoreconf(self, spec, prefix):
+        bash = which('bash')
+        bash('./autogen.sh')

From f07cdd7f7a5254cf2065c0973b0155e81b21bac4 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Thu, 23 Apr 2020 10:01:23 +0200
Subject: [PATCH 075/802] openssl: added 1.1.1g (#16247)

---
 var/spack/repos/builtin/packages/openssl/package.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index fe650f71337..0ab87827831 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -25,6 +25,7 @@ class Openssl(Package):   # Uses Fake Autotools, should subclass Package
 
     # The latest stable version is the 1.1.1 series. This is also our Long Term
     # Support (LTS) version, supported until 11th September 2023.
+    version('1.1.1g', sha256='ddb04774f1e32f0c49751e21b67216ac87852ceb056b75209af2443400636d46')
     version('1.1.1f', sha256='186c6bfe6ecfba7a5b48c47f8a1673d0f3b0e5ba2e25602dd23b629975da3f35')
     version('1.1.1e', sha256='694f61ac11cb51c9bf73f54e771ff6022b0327a43bbdfa1b2f19de1662a6dcbe')
     version('1.1.1d', sha256='1e3a91bc1f9dfce01af26026f856e064eab4c8ee0a8f457b5ae30b40b8b711f2')
@@ -33,8 +34,7 @@ class Openssl(Package):   # Uses Fake Autotools, should subclass Package
     version('1.1.1a', sha256='fc20130f8b7cbd2fb918b2f14e2f429e109c31ddd0fb38fc5d71d9ffed3f9f41')
     version('1.1.1',  sha256='2836875a0f89c03d0fdf483941512613a50cfb421d6fd94b9f41d7279d586a3d')
 
-    # The 1.1.0 series is currently only receiving security fixes and will go
-    # out of support on 11th September 2019.
+    # The 1.1.0 series is out of support and should not be used.
     version('1.1.0l', sha256='74a2f756c64fd7386a29184dc0344f4831192d61dc2481a93a4c5dd727f41148')
     version('1.1.0k', sha256='efa4965f4f773574d6cbda1cf874dbbe455ab1c0d4f906115f867d30444470b1')
     version('1.1.0j', sha256='31bec6c203ce1a8e93d5994f4ed304c63ccf07676118b6634edded12ad1b3246')
@@ -44,9 +44,7 @@ class Openssl(Package):   # Uses Fake Autotools, should subclass Package
     version('1.1.0d', sha256='7d5ebb9e89756545c156ff9c13cf2aa6214193b010a468a3bc789c3c28fe60df')
     version('1.1.0c', sha256='fc436441a2e05752d31b4e46115eb89709a28aef96d4fe786abe92409b2fd6f5')
 
-    # Our previous LTS version (1.0.2 series) will continue to be supported
-    # until 31st December 2019 (security fixes only during the last year of
-    # support).
+    # The 1.0.2 series is out of support and should not be used.
     version('1.0.2u', sha256='ecd0c6ffb493dd06707d38b14bb4d8c2288bb7033735606569d8f90f89669d16')
     version('1.0.2t', sha256='14cb464efe7ac6b54799b34456bd69558a749a4931ecfd9cf9f71d7881cac7bc')
     version('1.0.2s', sha256='cabd5c9492825ce5bd23f3c3aeed6a97f8142f606d893df216411f07d1abab96')
@@ -64,7 +62,7 @@ class Openssl(Package):   # Uses Fake Autotools, should subclass Package
     version('1.0.2e', sha256='e23ccafdb75cfcde782da0151731aa2185195ac745eea3846133f2e05c0e0bff')
     version('1.0.2d', sha256='671c36487785628a703374c652ad2cebea45fa920ae5681515df25d9f2c9a8c8')
 
-    # The 1.0.1 version is now out of support and should not be used.
+    # The 1.0.1 version is out of support and should not be used.
     version('1.0.1u', sha256='4312b4ca1215b6f2c97007503d80db80d5157f76f8f7d3febbe6b4c56ff26739')
     version('1.0.1t', sha256='4a6ee491a2fdb22e519c76fdc2a628bb3cec12762cd456861d207996c8a07088')
     version('1.0.1r', sha256='784bd8d355ed01ce98b812f873f8b2313da61df7c7b5677fcf2e57b0863a3346')

From b1133cb5db3b1d0d6a65ac9954330fb2c550d058 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Thu, 23 Apr 2020 10:09:09 +0200
Subject: [PATCH 076/802] py-setuptools: added v44.1.0 and v46.1.3 (#16171)

---
 var/spack/repos/builtin/packages/py-setuptools/package.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py
index affd23eebdf..877cf7ece97 100644
--- a/var/spack/repos/builtin/packages/py-setuptools/package.py
+++ b/var/spack/repos/builtin/packages/py-setuptools/package.py
@@ -21,6 +21,8 @@ class PySetuptools(PythonPackage):
         'easy_install'
     ]
 
+    version('46.1.3', sha256='795e0475ba6cd7fa082b1ee6e90d552209995627a2a227a47c6ea93282f4bfb1')
+    version('44.1.0', sha256='794a96b0c1dc6f182c36b72ab70d7e90f1d59f7a132e6919bb37b4fd4d424aca')
     version('41.4.0', sha256='7eae782ccf36b790c21bde7d86a4f303a441cd77036b25c559a602cf5186ce4d')
     version('41.0.1', sha256='a222d126f5471598053c9a77f4b5d4f26eaa1f150ad6e01dcf1a42e185d05613')
     version('41.0.0', sha256='79d30254b6fe7a8e672e43cd85f13a9f3f2a50080bc81d851143e2219ef0dcb1')
@@ -40,7 +42,9 @@ class PySetuptools(PythonPackage):
     version('16.0',   sha256='aa86255dee2c4a0056509750008007667c29306b7a6c13801468515b2c672845')
     version('11.3.1', sha256='bd25f17de4ecf00116a9f7368b614a54ca1612d7945d2eafe5d97bc08c138bc5')
 
-    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+    depends_on('python@3.5:', type=('build', 'run'), when='@45.0.0:')
+    depends_on('python@2.7:2.8,3.5:', type=('build', 'run'), when='@44.0.0:44.99.99')
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'), when='@:43.99.99')
 
     # Previously, setuptools vendored all of its dependencies to allow
     # easy bootstrapping. As of version 34.0.0, this is no longer done

From 19c58438713d2fae596ae61c7747788fb0d46887 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Thu, 23 Apr 2020 11:40:23 +0200
Subject: [PATCH 077/802] Travis: change the spec we concretize on MacOS
 (#16256)

Since CMake can't build with GCC on MacOS, choose a
spec that doesn't have CMake in the DAG.
---
 share/spack/qa/run-unit-tests | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/share/spack/qa/run-unit-tests b/share/spack/qa/run-unit-tests
index 01f564e5e1f..4bd04bcbb98 100755
--- a/share/spack/qa/run-unit-tests
+++ b/share/spack/qa/run-unit-tests
@@ -37,7 +37,11 @@ bin/spack -h
 bin/spack help -a
 
 # Profile and print top 20 lines for a simple call to spack spec
-spack -p --lines 20 spec mpileaks%gcc ^elfutils@0.170
+if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+  spack -p --lines 20 spec openmpi
+else
+  spack -p --lines 20 spec mpileaks%gcc ^elfutils@0.170
+fi
 
 #-----------------------------------------------------------
 # Run unit tests with code coverage

From df2cfd26cd03e29b9898fe79c804c78f2d29cbd0 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Thu, 23 Apr 2020 18:43:12 +0800
Subject: [PATCH 078/802] ambari: added package at v2.7.5 (#16149)

---
 .../repos/builtin/packages/ambari/package.py  | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/ambari/package.py

diff --git a/var/spack/repos/builtin/packages/ambari/package.py b/var/spack/repos/builtin/packages/ambari/package.py
new file mode 100644
index 00000000000..6e54f0a44e7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ambari/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ambari(PythonPackage):
+    """Apache Ambari is a tool for provisioning, managing, and monitoring
+    Apache Hadoop clusters. Ambari consists of a set of RESTful APIs and
+    a browser-based management interface."""
+
+    homepage = "https://cwiki.apache.org/confluence/display/AMBARI/Ambari"
+    url      = "https://github.com/apache/ambari/archive/release-2.7.5.tar.gz"
+
+    version('2.7.5', sha256='f8c8687b7a61b633b92f83b1c104fd75b1e13836cd8a0e0df6db7b483b23a354')
+    version('2.7.4', sha256='d6796c7ea913d39c93dad52b4cb74ef411a7dce4ebf68f11b12718117f2c01a4')
+    version('2.7.3', sha256='30fe72e60fa6b62fe032bd193ebd0cef20b65c54b57cad92f6f44daabd3771cf')
+    version('2.7.1', sha256='ea4eb28f377ce9d0b9b7648f2020dda4be974c6d9a22ebaafbf1bc97890e4e42')
+
+    depends_on('python@:2.7.999', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-mock', type='test')
+    depends_on('py-coilmq', type=('build', 'run'))

From 6cad7a585de5e79d3f2b1c928b61896eecca74b4 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Fri, 24 Apr 2020 00:01:20 +0800
Subject: [PATCH 079/802] Go: support for aarch64 (#16083)

---
 var/spack/repos/builtin/packages/go/package.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py
index 600d426a7ae..abea06b5a2e 100644
--- a/var/spack/repos/builtin/packages/go/package.py
+++ b/var/spack/repos/builtin/packages/go/package.py
@@ -6,6 +6,7 @@
 import os
 import llnl.util.tty as tty
 from spack import *
+import platform
 
 # - vanilla CentOS 7, and possibly other systems, fail a test:
 #   TestCloneNEWUSERAndRemapRootDisableSetgroups
@@ -87,7 +88,10 @@ class Go(Package):
     depends_on('git', type=('build', 'link', 'run'))
     # TODO: Make non-c self-hosting compilers feasible without backflips
     # should be a dep on external go compiler
-    depends_on('go-bootstrap', type='build')
+    if platform.machine() == 'aarch64':
+        depends_on('gcc languages=go', type='build')
+    else:
+        depends_on('go-bootstrap', type='build')
 
     # https://github.com/golang/go/issues/17545
     patch('time_test.patch', when='@1.6.4:1.7.4')

From ca67df6e3d61cdbc615d85cc223dcc2314bc6b6c Mon Sep 17 00:00:00 2001
From: jthies <jonas.thies@dlr.de>
Date: Thu, 23 Apr 2020 18:11:54 +0200
Subject: [PATCH 080/802] phist: don't apply patch to 1.9.0 (#16257)

---
 var/spack/repos/builtin/packages/phist/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/phist/package.py b/var/spack/repos/builtin/packages/phist/package.py
index 797d09a8463..cdbd84ed7ff 100644
--- a/var/spack/repos/builtin/packages/phist/package.py
+++ b/var/spack/repos/builtin/packages/phist/package.py
@@ -96,7 +96,7 @@ class Phist(CMakePackage):
 
     # ###################### Patches ##########################
 
-    patch('update_tpetra_gotypes.patch', when='@:1.9.0')
+    patch('update_tpetra_gotypes.patch', when='@:1.8.99')
 
     # ###################### Dependencies ##########################
 

From d5d232e20767b8c0abc56ba75f07c4537449e333 Mon Sep 17 00:00:00 2001
From: Andrew W Elble <aweits@rit.edu>
Date: Thu, 23 Apr 2020 12:14:09 -0400
Subject: [PATCH 081/802] tensorflow: compile against spack-provided protobuf
 (#16258)

This allows horovod to be built with frameworks=pytorch,tensorflow.

I tracked down the crash I observed in #15719, where loading torch
before tensorflow would cause a crash in:

google::protobuf::internal::(anonymous
namespace)::InitSCC_DFS(google::protobuf::internal::SCCInfoBase*)

The solution is to make tensorflow compile against the protobuf
version Spack provides, instead of allowing it to use it's own.
It's likely we'll want to go after some of the others
that are listed in third_party/systemlibs/syslibs_configure.bzl
in the future.
---
 .../repos/builtin/packages/py-tensorflow/package.py    | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-tensorflow/package.py b/var/spack/repos/builtin/packages/py-tensorflow/package.py
index 64b97b05b26..b46cfbb4cea 100644
--- a/var/spack/repos/builtin/packages/py-tensorflow/package.py
+++ b/var/spack/repos/builtin/packages/py-tensorflow/package.py
@@ -152,6 +152,7 @@ class PyTensorflow(Package, CudaPackage):
     depends_on('py-protobuf@3.0.0', type=('build', 'run'), when='@0.11.0')
     depends_on('py-protobuf@3.0.0b2', type=('build', 'run'), when='@0.7.1:0.10')
     depends_on('py-protobuf@3.0.0a3', type=('build', 'run'), when='@0.6:0.7.0')
+    depends_on('protobuf')
     # tensorboard
     # tensorflow-estimator
     depends_on('py-termcolor@1.1.0:', type=('build', 'run'), when='@1.6:')
@@ -498,6 +499,11 @@ def setup_build_environment(self, env):
         mkdirp(tmp_path)
         env.set('TEST_TMPDIR', tmp_path)
 
+        env.set('TF_SYSTEM_LIBS', 'com_google_protobuf')
+        # NOTE: INCLUDEDIR is not just relevant to protobuf
+        # see third_party/systemlibs/jsoncpp.BUILD
+        env.set('INCLUDEDIR', spec['protobuf'].prefix.include)
+
     def configure(self, spec, prefix):
         # NOTE: configure script is interactive. If you set the appropriate
         # environment variables, this interactivity is skipped. If you don't,
@@ -626,6 +632,7 @@ def build(self, spec, prefix):
             # Ask bazel to explain what it's up to
             # Needs a filename as argument
             '--explain=explainlogfile.txt',
+            '--incompatible_no_support_tools_in_action_inputs=false',
             # Increase verbosity of explanation,
             '--verbose_explanations',
         ]
@@ -679,9 +686,6 @@ def build(self, spec, prefix):
         if spec.satisfies('@2:'):
             args.append('--config=v2')
 
-        if spec.satisfies('%gcc@5:'):
-            args.append('--cxxopt=-D_GLIBCXX_USE_CXX11_ABI=0')
-
         args.append('//tensorflow/tools/pip_package:build_pip_package')
 
         bazel(*args)

From 2a3942fa4cc893cbd29a7676bf61993b49e30018 Mon Sep 17 00:00:00 2001
From: Andrew Gaspar <agaspar@lanl.gov>
Date: Thu, 23 Apr 2020 11:33:02 -0600
Subject: [PATCH 082/802] Rust 1.43.0 (#16260)

---
 var/spack/repos/builtin/packages/rust/package.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/var/spack/repos/builtin/packages/rust/package.py b/var/spack/repos/builtin/packages/rust/package.py
index 4434c5efbd8..8c0e6430e48 100644
--- a/var/spack/repos/builtin/packages/rust/package.py
+++ b/var/spack/repos/builtin/packages/rust/package.py
@@ -85,6 +85,7 @@ class Rust(Package):
     # The `x.py` bootstrapping script did not exist prior to Rust 1.17. It
     # would be possible to support both, but for simplicitly, we only support
     # Rust 1.17 and newer
+    version('1.43.0', sha256='75f6ac6c9da9f897f4634d5a07be4084692f7ccc2d2bb89337be86cfc18453a1')
     version('1.42.0', sha256='d2e8f931d16a0539faaaacd801e0d92c58df190269014b2360c6ab2a90ee3475')
     version('1.41.1', sha256='38c93d016e6d3e083aa15e8f65511d3b4983072c0218a529f5ee94dd1de84573')
     version('1.41.0', sha256='5546822c09944c4d847968e9b7b3d0e299f143f307c00fa40e84a99fabf8d74b')
@@ -124,6 +125,12 @@ class Rust(Package):
     # This dictionary contains a version: hash dictionary for each supported
     # Rust target.
     rust_releases = {
+        '1.43.0': {
+            'x86_64-unknown-linux-gnu':      '069f34fa5cef92551724c83c36360df1ac66fe3942bc1d0e4d341ce79611a029',
+            'powerpc64le-unknown-linux-gnu': 'c75c7ae4c94715fd6cc43d1d6fdd0952bc151f7cbe3054f66d99a529d5bb996f',
+            'aarch64-unknown-linux-gnu':     'e5fa55f333c10cdae43d147438a80ffb435d6c7b9681cd2e2f0857c024556856',
+            'x86_64-apple-darwin':           '504e8efb2cbb36f5a3db7bb36f339a1e5216082c910ad19039c370505cfbde99'
+        },
         '1.42.0': {
             'x86_64-unknown-linux-gnu':      '7d1e07ad9c8a33d8d039def7c0a131c5917aa3ea0af3d0cc399c6faf7b789052',
             'powerpc64le-unknown-linux-gnu': '805b08fa1e0aad4d706301ca1f13e2d80810d385cece2c15070360b3c4bd6e4a',

From 686f0e21de510a12ee3d6af410448eb405d3e7b6 Mon Sep 17 00:00:00 2001
From: "Mark W. Krentel" <krentel@rice.edu>
Date: Thu, 23 Apr 2020 12:34:19 -0500
Subject: [PATCH 083/802] libunwind: add 1.4.0 release and 1.5 stable branch
 (#16261)

---
 .../builtin/packages/libunwind/package.py     | 21 +++++++++++--------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/var/spack/repos/builtin/packages/libunwind/package.py b/var/spack/repos/builtin/packages/libunwind/package.py
index 971840f5e04..1a4ae5524c5 100644
--- a/var/spack/repos/builtin/packages/libunwind/package.py
+++ b/var/spack/repos/builtin/packages/libunwind/package.py
@@ -16,9 +16,12 @@ class Libunwind(AutotoolsPackage):
     maintainers = ['mwkrentel']
 
     version('master', branch='master')
+    version('1.5-head', branch='v1.5-stable')
+    version('1.5-rc1', sha256='3e0cbc6dee326592097ef06e97cf76ef597987eddd0df8bea49b0594e587627a')
     version('1.4-head', branch='v1.4-stable')
+    version('1.4.0',   sha256='df59c931bd4d7ebfd83ee481c943edf015138089b8e50abed8d9c57ba9338435', preferred=True)
     version('1.4-rc1', sha256='1928459139f048f9b4aca4bb5010540cb7718d44220835a2980b85429007fa9f')
-    version('1.3.1', sha256='43997a3939b6ccdf2f669b50fdb8a4d3205374728c2923ddc2354c65260214f8', preferred=True)
+    version('1.3.1', sha256='43997a3939b6ccdf2f669b50fdb8a4d3205374728c2923ddc2354c65260214f8')
     version('1.2.1', sha256='3f3ecb90e28cbe53fba7a4a27ccce7aad188d3210bb1964a923a731a27a75acb')
     version('1.1', sha256='9dfe0fcae2a866de9d3942c66995e4b460230446887dbdab302d41a8aee8d09a')
 
@@ -26,15 +29,15 @@ class Libunwind(AutotoolsPackage):
             description='Support xz (lzma) compressed symbol tables.')
 
     variant('zlib', default=False,
-            description='Support zlib compressed symbol tables (master '
-            'branch only).')
+            description='Support zlib compressed symbol tables '
+            '(1.5 and later).')
 
     # The libunwind releases contain the autotools generated files,
     # but the git repo snapshots do not.
-    depends_on('autoconf', type='build', when='@master,1.4-head')
-    depends_on('automake', type='build', when='@master,1.4-head')
-    depends_on('libtool',  type='build', when='@master,1.4-head')
-    depends_on('m4',       type='build', when='@master,1.4-head')
+    depends_on('autoconf', type='build', when='@master,1.4-head,1.5-head')
+    depends_on('automake', type='build', when='@master,1.4-head,1.5-head')
+    depends_on('libtool',  type='build', when='@master,1.4-head,1.5-head')
+    depends_on('m4',       type='build', when='@master,1.4-head,1.5-head')
 
     depends_on('xz', type='link', when='+xz')
     depends_on('zlib', type='link', when='+zlib')
@@ -55,8 +58,8 @@ def configure_args(self):
         else:
             args.append('--disable-minidebuginfo')
 
-        # zlib support is only in the master branch (for now).
-        if spec.satisfies('@master'):
+        # zlib support is available in 1.5.x and later
+        if spec.satisfies('@1.5:'):
             if '+zlib' in spec:
                 args.append('--enable-zlibdebuginfo')
             else:

From 0c0f11caf681cf8e1405c8579b5dffaec16d360a Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 23 Apr 2020 12:14:40 -0700
Subject: [PATCH 084/802] spack info: allow variants section to be as wide as
 the terminal (#16254)

The variants table in `spack info` is cramped, as the *widest* it can be
is 80 columns.  And that's actually only sort of true -- the padding
calculation is off, so it still wraps on terminals of size 80 because it
comes out *slightly* wider.

This change looks at the terminal size and calculates the width of the
description column based on it.  On larger terminals, the output looks
much nicer, and on small terminals, the output no longer wraps.

Here's an example  for `spack info qmcpack` with 110 columns.

Before:
    Name [Default]          Allowed values          Description
    ====================    ====================    ==============================

    afqmc [off]             on, off                 Install with AFQMC support.
                                                    NOTE that if used in
                                                    combination with CUDA, only
                                                    AFQMC will have CUDA.
    build_type [Release]    Debug, Release,         The build type to build
                            RelWithDebInfo
    complex [off]           on, off                 Build the complex (general
                                                    twist/k-point) version
    cuda [off]              on, off                 Build with CUDA

After:
    Name [Default]          Allowed values          Description
    ====================    ====================    ========================================================

    afqmc [off]             on, off                 Install with AFQMC support. NOTE that if used in
                                                    combination with CUDA, only AFQMC will have CUDA.
    build_type [Release]    Debug, Release,         The build type to build
                            RelWithDebInfo
    complex [off]           on, off                 Build the complex (general twist/k-point) version
    cuda [off]              on, off                 Build with CUDA
---
 lib/spack/spack/cmd/info.py | 23 ++++++++++++++---------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/lib/spack/spack/cmd/info.py b/lib/spack/spack/cmd/info.py
index f8db9e10cb3..fa674317ab7 100644
--- a/lib/spack/spack/cmd/info.py
+++ b/lib/spack/spack/cmd/info.py
@@ -8,6 +8,7 @@
 import textwrap
 from six.moves import zip_longest
 
+import llnl.util.tty as tty
 import llnl.util.tty.color as color
 from llnl.util.tty.colify import colify
 
@@ -53,11 +54,9 @@ def variant(s):
 
 
 class VariantFormatter(object):
-    def __init__(self, variants, max_widths=(30, 20, 30)):
+    def __init__(self, variants):
         self.variants = variants
         self.headers = ('Name [Default]', 'Allowed values', 'Description')
-        # Set max headers lengths
-        self.max_column_widths = max_widths
 
         # Formats
         fmt_name = '{0} [{1}]'
@@ -67,7 +66,7 @@ def __init__(self, variants, max_widths=(30, 20, 30)):
         # than that
         self.column_widths = [len(x) for x in self.headers]
 
-        # Update according to line lengths
+        # Expand columns based on max line lengths
         for k, v in variants.items():
             candidate_max_widths = (
                 len(fmt_name.format(k, self.default(v))),  # Name [Default]
@@ -81,12 +80,18 @@ def __init__(self, variants, max_widths=(30, 20, 30)):
                 max(self.column_widths[2], candidate_max_widths[2])
             )
 
-        # Reduce to at most the maximum allowed
-        self.column_widths = (
-            min(self.column_widths[0], self.max_column_widths[0]),
-            min(self.column_widths[1], self.max_column_widths[1]),
-            min(self.column_widths[2], self.max_column_widths[2])
+        # Don't let name or possible values be less than max widths
+        _, cols = tty.terminal_size()
+        max_name = min(self.column_widths[0], 30)
+        max_vals = min(self.column_widths[1], 20)
+
+        # allow the description column to extend as wide as the terminal.
+        max_description = min(
+            self.column_widths[2],
+            # min width 70 cols, 14 cols of margins and column spacing
+            max(cols, 70) - max_name - max_vals - 14,
         )
+        self.column_widths = (max_name, max_vals, max_description)
 
         # Compute the format
         self.fmt = "%%-%ss%%-%ss%%s" % (

From a844467c258c91a71dcd636897acc82306c82758 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Thu, 23 Apr 2020 15:53:51 -0600
Subject: [PATCH 085/802] eospac: prefer 6.4.0 (#16266)

---
 var/spack/repos/builtin/packages/eospac/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/eospac/package.py b/var/spack/repos/builtin/packages/eospac/package.py
index f73274ca464..0d9221e7dfc 100644
--- a/var/spack/repos/builtin/packages/eospac/package.py
+++ b/var/spack/repos/builtin/packages/eospac/package.py
@@ -15,7 +15,7 @@ class Eospac(Package):
     homepage = "http://laws.lanl.gov/projects/data/eos.html"
     list_url = "http://laws.lanl.gov/projects/data/eos/eospacReleases.php"
 
-    version('6.4.0',       sha256='15a953beac735c68431afe86ffe33323d540d0fbbbec03ba79438dd29736051d',
+    version('6.4.0',       sha256='15a953beac735c68431afe86ffe33323d540d0fbbbec03ba79438dd29736051d', preferred=True,
             url="http://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0_612ea8c9b8ffa6d9175d9118955571d9107f1e3c.tgz")
     version('6.4.0beta.4', sha256='0ebfd8badff575ea77444aa978629dbdca3135a0b5eb373b8daba058773d4635',
             url="http://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.4_aff6429bb6868de31a980278bafa13487c2ce83f.tgz")
@@ -25,7 +25,7 @@ class Eospac(Package):
             url="http://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.2_69196eadbc77506561eef711f19d2f03b4ab0ffa.tgz")
     version('6.4.0beta.1', sha256='14c5c804e5f628f41e8ed80bcee5a80adeb6c6f3d130715421ca99a30c7eb7e2',
             url="http://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz")
-    version('6.3.1',       sha256='aa1112c4251c9c3c2883a7ab2c7f2abff2c339f29dbbf8421ef88b0c9df904f8', preferred=True,
+    version('6.3.1',       sha256='aa1112c4251c9c3c2883a7ab2c7f2abff2c339f29dbbf8421ef88b0c9df904f8',
             url="http://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.3.1_r20161202150449.tgz")
 
     # This patch allows the use of spack's compile wrapper 'flang'

From 9b3a0355bb0d49c51a137532c7f7f42eff8345bd Mon Sep 17 00:00:00 2001
From: Jeffrey Salmond <js947@users.noreply.github.com>
Date: Fri, 24 Apr 2020 01:50:05 +0100
Subject: [PATCH 086/802] add fontconfig as vim dependency (#16268)

---
 var/spack/repos/builtin/packages/vim/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/vim/package.py b/var/spack/repos/builtin/packages/vim/package.py
index a022af0218f..5539adfc025 100644
--- a/var/spack/repos/builtin/packages/vim/package.py
+++ b/var/spack/repos/builtin/packages/vim/package.py
@@ -58,6 +58,7 @@ class Vim(AutotoolsPackage):
 
     depends_on('ncurses', when="@7.4:")
     depends_on('findutils', type='build')
+    depends_on('fontconfig', when="+gui")
 
     def configure_args(self):
         spec = self.spec

From 433a0b243ffa97add96bc0f51477c4bda3449c12 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 23 Apr 2020 19:50:22 -0500
Subject: [PATCH 087/802] oneDNN: add new version (#16267)

---
 var/spack/repos/builtin/packages/onednn/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/onednn/package.py b/var/spack/repos/builtin/packages/onednn/package.py
index 8318d70d901..995cf40942a 100644
--- a/var/spack/repos/builtin/packages/onednn/package.py
+++ b/var/spack/repos/builtin/packages/onednn/package.py
@@ -30,6 +30,7 @@ class Onednn(CMakePackage):
     version('1.0.2',  sha256='9281715436adb7b9eef63fad419a581f397218824bc1271e557c134725c03916')
     version('1.0.1',  sha256='8fee2324267811204c1f877a1dea70b23ab3d5f4c3ea0198d81f0921aa70d76e')
     version('1.0',    sha256='7bfe11cac1d1f5dc1b60c1258e79d8cc84944d459e3758d50c1f7feba05bc6d7')
+    version('0.21.5', sha256='ebb146cadda1c14767251ded54219c8215daee84aa1ac773cf43b5c2ae53160b')
     version('0.21.4', sha256='00ace1ce08cab3408bc83e6b9d55ccba661761e044c03175d58caccedddf93b3')
     version('0.21.3', sha256='a0211aeb5e7dad50b97fa5dffc1a2fe2fe732572d4164e1ee8750a2ede43fbec')
     version('0.21.2', sha256='5897bfd0e321a761de0c57ba1dfe0ebc753cc0d8a18bda2056af48022706a297')

From c6ada206af08f66817fe1c2aeeee8f45f92a192e Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 23 Apr 2020 18:21:49 -0700
Subject: [PATCH 088/802] tests: each mock package now has its own class
 (#16157)

Packages in Spack are classes, and we need to be able to execute class
methods on mock packages.  The previous design used instances of a single
MockPackage class; this version gives each package its own class that can
spider depenencies.  This allows us to implement class methods like
`possible_dependencies()` on mock packages.

This design change moves mock package creation into the
`MockPackageMultiRepo`, and mock packages now *must* be created from a
repo.  This is required for us to mock `possible_dependencies()`, which
needs to be able to get dependency packages from the package repo.

Changes include:

* `MockPackage` is now `MockPackageBase`
* `MockPackageBase` instances must now be created with
  `MockPackageMultiRepo.add_package()`
* add `possible_dependencies()` method to `MockPackageBase`
* refactor tests to use new code structure
* move package mocking infrastructure into `spack.util.mock_package`,
  as it's becoming a more sophisticated class and it gets lots in `conftest.py`
---
 lib/spack/spack/test/cmd/ci.py            |  19 ++-
 lib/spack/spack/test/cmd/env.py           |  30 ++--
 lib/spack/spack/test/concretize.py        |  10 +-
 lib/spack/spack/test/conftest.py          |  73 ----------
 lib/spack/spack/test/database.py          |  37 +++--
 lib/spack/spack/test/spec_dag.py          |  40 +++---
 lib/spack/spack/test/spec_yaml.py         |  19 ++-
 lib/spack/spack/test/util/mock_package.py |  43 ++++++
 lib/spack/spack/util/mock_package.py      | 161 ++++++++++++++++++++++
 9 files changed, 279 insertions(+), 153 deletions(-)
 create mode 100644 lib/spack/spack/test/util/mock_package.py
 create mode 100644 lib/spack/spack/util/mock_package.py

diff --git a/lib/spack/spack/test/cmd/ci.py b/lib/spack/spack/test/cmd/ci.py
index 89ed4718687..36236b0cc16 100644
--- a/lib/spack/spack/test/cmd/ci.py
+++ b/lib/spack/spack/test/cmd/ci.py
@@ -18,7 +18,7 @@
 import spack.paths as spack_paths
 import spack.repo as repo
 from spack.spec import Spec
-from spack.test.conftest import MockPackage, MockPackageMultiRepo
+from spack.util.mock_package import MockPackageMultiRepo
 import spack.util.executable as exe
 import spack.util.spack_yaml as syaml
 import spack.util.gpg
@@ -101,15 +101,14 @@ def test_specs_staging(config):
 """
     default = ('build', 'link')
 
-    g = MockPackage('g', [], [])
-    f = MockPackage('f', [], [])
-    e = MockPackage('e', [], [])
-    d = MockPackage('d', [f, g], [default, default])
-    c = MockPackage('c', [], [])
-    b = MockPackage('b', [d, e], [default, default])
-    a = MockPackage('a', [b, c], [default, default])
-
-    mock_repo = MockPackageMultiRepo([a, b, c, d, e, f, g])
+    mock_repo = MockPackageMultiRepo()
+    g = mock_repo.add_package('g', [], [])
+    f = mock_repo.add_package('f', [], [])
+    e = mock_repo.add_package('e', [], [])
+    d = mock_repo.add_package('d', [f, g], [default, default])
+    c = mock_repo.add_package('c', [], [])
+    b = mock_repo.add_package('b', [d, e], [default, default])
+    mock_repo.add_package('a', [b, c], [default, default])
 
     with repo.swap(mock_repo):
         spec_a = Spec('a')
diff --git a/lib/spack/spack/test/cmd/env.py b/lib/spack/spack/test/cmd/env.py
index 4f3abb4438d..f35b0a4bc13 100644
--- a/lib/spack/spack/test/cmd/env.py
+++ b/lib/spack/spack/test/cmd/env.py
@@ -20,7 +20,7 @@
 from spack.stage import stage_prefix
 
 from spack.spec_list import SpecListError
-from spack.test.conftest import MockPackage, MockPackageMultiRepo
+from spack.util.mock_package import MockPackageMultiRepo
 import spack.util.spack_json as sjson
 
 
@@ -733,10 +733,10 @@ def create_v1_lockfile_dict(roots, all_specs):
 def test_read_old_lock_and_write_new(tmpdir):
     build_only = ('build',)
 
-    y = MockPackage('y', [], [])
-    x = MockPackage('x', [y], [build_only])
+    mock_repo = MockPackageMultiRepo()
+    y = mock_repo.add_package('y', [], [])
+    mock_repo.add_package('x', [y], [build_only])
 
-    mock_repo = MockPackageMultiRepo([x, y])
     with spack.repo.swap(mock_repo):
         x = Spec('x')
         x.concretize()
@@ -765,9 +765,9 @@ def test_read_old_lock_creates_backup(tmpdir):
     """When reading a version-1 lockfile, make sure that a backup of that file
     is created.
     """
-    y = MockPackage('y', [], [])
+    mock_repo = MockPackageMultiRepo()
+    y = mock_repo.add_package('y', [], [])
 
-    mock_repo = MockPackageMultiRepo([y])
     with spack.repo.swap(mock_repo):
         y = Spec('y')
         y.concretize()
@@ -796,11 +796,10 @@ def test_indirect_build_dep():
     default = ('build', 'link')
     build_only = ('build',)
 
-    z = MockPackage('z', [], [])
-    y = MockPackage('y', [z], [build_only])
-    x = MockPackage('x', [y], [default])
-
-    mock_repo = MockPackageMultiRepo([x, y, z])
+    mock_repo = MockPackageMultiRepo()
+    z = mock_repo.add_package('z', [], [])
+    y = mock_repo.add_package('y', [z], [build_only])
+    mock_repo.add_package('x', [y], [default])
 
     def noop(*args):
         pass
@@ -838,11 +837,10 @@ def test_store_different_build_deps():
     default = ('build', 'link')
     build_only = ('build',)
 
-    z = MockPackage('z', [], [])
-    y = MockPackage('y', [z], [build_only])
-    x = MockPackage('x', [y, z], [default, build_only])
-
-    mock_repo = MockPackageMultiRepo([x, y, z])
+    mock_repo = MockPackageMultiRepo()
+    z = mock_repo.add_package('z', [], [])
+    y = mock_repo.add_package('y', [z], [build_only])
+    mock_repo.add_package('x', [y, z], [default, build_only])
 
     def noop(*args):
         pass
diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index 9024c99cadf..232dfaeb4be 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -15,7 +15,7 @@
 from spack.package_prefs import PackagePrefs
 from spack.spec import Spec, CompilerSpec, ConflictsInSpecError
 from spack.version import ver
-from spack.test.conftest import MockPackage, MockPackageMultiRepo
+from spack.util.mock_package import MockPackageMultiRepo
 import spack.compilers
 import spack.platforms.test
 
@@ -235,10 +235,10 @@ def test_architecture_deep_inheritance(self):
         """
         default_dep = ('link', 'build')
 
-        bazpkg = MockPackage('bazpkg', [], [])
-        barpkg = MockPackage('barpkg', [bazpkg], [default_dep])
-        foopkg = MockPackage('foopkg', [barpkg], [default_dep])
-        mock_repo = MockPackageMultiRepo([foopkg, barpkg, bazpkg])
+        mock_repo = MockPackageMultiRepo()
+        bazpkg = mock_repo.add_package('bazpkg', [], [])
+        barpkg = mock_repo.add_package('barpkg', [bazpkg], [default_dep])
+        mock_repo.add_package('foopkg', [barpkg], [default_dep])
 
         with spack.repo.swap(mock_repo):
             spec = Spec('foopkg %clang@3.3 os=CNL target=footar' +
diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py
index 8912c0219b7..736c5a55638 100644
--- a/lib/spack/spack/test/conftest.py
+++ b/lib/spack/spack/test/conftest.py
@@ -14,7 +14,6 @@
 import tempfile
 import xml.etree.ElementTree
 
-import ordereddict_backport
 import py
 import pytest
 import ruamel.yaml as yaml
@@ -38,11 +37,8 @@
 import spack.util.gpg
 
 from spack.util.pattern import Bunch
-from spack.dependency import Dependency
 from spack.fetch_strategy import FetchStrategyComposite, URLFetchStrategy
 from spack.fetch_strategy import FetchError
-from spack.spec import Spec
-from spack.version import Version
 
 
 @pytest.fixture
@@ -1004,75 +1000,6 @@ def installation_dir_with_headers(tmpdir_factory):
     return root
 
 
-##########
-# Mock packages
-##########
-
-
-class MockPackage(object):
-    def __init__(self, name, dependencies, dependency_types, conditions=None,
-                 versions=None):
-        self.name = name
-        self.spec = None
-        self.dependencies = ordereddict_backport.OrderedDict()
-        self._installed_upstream = False
-
-        assert len(dependencies) == len(dependency_types)
-        for dep, dtype in zip(dependencies, dependency_types):
-            d = Dependency(self, Spec(dep.name), type=dtype)
-            if not conditions or dep.name not in conditions:
-                self.dependencies[dep.name] = {Spec(name): d}
-            else:
-                dep_conditions = conditions[dep.name]
-                dep_conditions = dict(
-                    (Spec(x), Dependency(self, Spec(y), type=dtype))
-                    for x, y in dep_conditions.items())
-                self.dependencies[dep.name] = dep_conditions
-
-        if versions:
-            self.versions = versions
-        else:
-            versions = list(Version(x) for x in [1, 2, 3])
-            self.versions = dict((x, {'preferred': False}) for x in versions)
-
-        self.variants = {}
-        self.provided = {}
-        self.conflicts = {}
-        self.patches = {}
-
-    def provides(self, vname):
-        return vname in self.provided
-
-    @property
-    def virtuals_provided(self):
-        return [v.name for v, c in self.provided]
-
-
-class MockPackageMultiRepo(object):
-    def __init__(self, packages):
-        self.spec_to_pkg = dict((x.name, x) for x in packages)
-        self.spec_to_pkg.update(
-            dict(('mockrepo.' + x.name, x) for x in packages))
-
-    def get(self, spec):
-        if not isinstance(spec, spack.spec.Spec):
-            spec = Spec(spec)
-        return self.spec_to_pkg[spec.name]
-
-    def get_pkg_class(self, name):
-        return self.spec_to_pkg[name]
-
-    def exists(self, name):
-        return name in self.spec_to_pkg
-
-    def is_virtual(self, name):
-        return False
-
-    def repo_for_pkg(self, name):
-        import collections
-        Repo = collections.namedtuple('Repo', ['namespace'])
-        return Repo('mockrepo')
-
 ##########
 # Specs of various kind
 ##########
diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py
index 28311c7501d..70f9bffe59b 100644
--- a/lib/spack/spack/test/database.py
+++ b/lib/spack/spack/test/database.py
@@ -28,7 +28,7 @@
 import spack.database
 import spack.package
 import spack.spec
-from spack.test.conftest import MockPackage, MockPackageMultiRepo
+from spack.util.mock_package import MockPackageMultiRepo
 from spack.util.executable import Executable
 
 
@@ -73,11 +73,11 @@ def test_installed_upstream(upstream_and_downstream_db):
         downstream_db, downstream_layout = (upstream_and_downstream_db)
 
     default = ('build', 'link')
-    x = MockPackage('x', [], [])
-    z = MockPackage('z', [], [])
-    y = MockPackage('y', [z], [default])
-    w = MockPackage('w', [x, y], [default, default])
-    mock_repo = MockPackageMultiRepo([w, x, y, z])
+    mock_repo = MockPackageMultiRepo()
+    x = mock_repo.add_package('x', [], [])
+    z = mock_repo.add_package('z', [], [])
+    y = mock_repo.add_package('y', [z], [default])
+    mock_repo.add_package('w', [x, y], [default, default])
 
     with spack.repo.swap(mock_repo):
         spec = spack.spec.Spec('w')
@@ -116,9 +116,9 @@ def test_removed_upstream_dep(upstream_and_downstream_db):
         downstream_db, downstream_layout = (upstream_and_downstream_db)
 
     default = ('build', 'link')
-    z = MockPackage('z', [], [])
-    y = MockPackage('y', [z], [default])
-    mock_repo = MockPackageMultiRepo([y, z])
+    mock_repo = MockPackageMultiRepo()
+    z = mock_repo.add_package('z', [], [])
+    mock_repo.add_package('y', [z], [default])
 
     with spack.repo.swap(mock_repo):
         spec = spack.spec.Spec('y')
@@ -150,8 +150,8 @@ def test_add_to_upstream_after_downstream(upstream_and_downstream_db):
     upstream_write_db, upstream_db, upstream_layout,\
         downstream_db, downstream_layout = (upstream_and_downstream_db)
 
-    x = MockPackage('x', [], [])
-    mock_repo = MockPackageMultiRepo([x])
+    mock_repo = MockPackageMultiRepo()
+    mock_repo.add_package('x', [], [])
 
     with spack.repo.swap(mock_repo):
         spec = spack.spec.Spec('x')
@@ -183,8 +183,8 @@ def test_cannot_write_upstream(tmpdir_factory, test_store, gen_mock_layout):
     roots = [str(tmpdir_factory.mktemp(x)) for x in ['a', 'b']]
     layouts = [gen_mock_layout(x) for x in ['/ra/', '/rb/']]
 
-    x = MockPackage('x', [], [])
-    mock_repo = MockPackageMultiRepo([x])
+    mock_repo = MockPackageMultiRepo()
+    mock_repo.add_package('x', [], [])
 
     # Instantiate the database that will be used as the upstream DB and make
     # sure it has an index file
@@ -209,11 +209,10 @@ def test_recursive_upstream_dbs(tmpdir_factory, test_store, gen_mock_layout):
     layouts = [gen_mock_layout(x) for x in ['/ra/', '/rb/', '/rc/']]
 
     default = ('build', 'link')
-    z = MockPackage('z', [], [])
-    y = MockPackage('y', [z], [default])
-    x = MockPackage('x', [y], [default])
-
-    mock_repo = MockPackageMultiRepo([x, y, z])
+    mock_repo = MockPackageMultiRepo()
+    z = mock_repo.add_package('z', [], [])
+    y = mock_repo.add_package('y', [z], [default])
+    mock_repo.add_package('x', [y], [default])
 
     with spack.repo.swap(mock_repo):
         spec = spack.spec.Spec('x')
@@ -675,7 +674,7 @@ def test_115_reindex_with_packages_not_in_repo(mutable_database):
     # Dont add any package definitions to this repository, the idea is that
     # packages should not have to be defined in the repository once they
     # are installed
-    with spack.repo.swap(MockPackageMultiRepo([])):
+    with spack.repo.swap(MockPackageMultiRepo()):
         spack.store.store.reindex()
         _check_db_sanity(mutable_database)
 
diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py
index e031f02c255..0b638ada04f 100644
--- a/lib/spack/spack/test/spec_dag.py
+++ b/lib/spack/spack/test/spec_dag.py
@@ -12,7 +12,7 @@
 
 from spack.spec import Spec
 from spack.dependency import all_deptypes, Dependency, canonical_deptype
-from spack.test.conftest import MockPackage, MockPackageMultiRepo
+from spack.util.mock_package import MockPackageMultiRepo
 
 
 def check_links(spec_to_check):
@@ -69,12 +69,12 @@ def test_test_deptype():
     default = ('build', 'link')
     test_only = ('test',)
 
-    x = MockPackage('x', [], [])
-    z = MockPackage('z', [], [])
-    y = MockPackage('y', [z], [test_only])
-    w = MockPackage('w', [x, y], [test_only, default])
+    mock_repo = MockPackageMultiRepo()
+    x = mock_repo.add_package('x', [], [])
+    z = mock_repo.add_package('z', [], [])
+    y = mock_repo.add_package('y', [z], [test_only])
+    w = mock_repo.add_package('w', [x, y], [test_only, default])
 
-    mock_repo = MockPackageMultiRepo([w, x, y, z])
     with spack.repo.swap(mock_repo):
         spec = Spec('w')
         spec.concretize(tests=(w.name,))
@@ -93,8 +93,9 @@ def test_installed_deps():
     default = ('build', 'link')
     build_only = ('build',)
 
-    e = MockPackage('e', [], [])
-    d = MockPackage('d', [], [])
+    mock_repo = MockPackageMultiRepo()
+    e = mock_repo.add_package('e', [], [])
+    d = mock_repo.add_package('d', [], [])
     c_conditions = {
         d.name: {
             'c': 'd@2'
@@ -103,11 +104,10 @@ def test_installed_deps():
             'c': 'e@2'
         }
     }
-    c = MockPackage('c', [d, e], [build_only, default],
-                    conditions=c_conditions)
-    b = MockPackage('b', [d, e], [default, default])
-    a = MockPackage('a', [b, c], [default, default])
-    mock_repo = MockPackageMultiRepo([a, b, c, d, e])
+    c = mock_repo.add_package('c', [d, e], [build_only, default],
+                              conditions=c_conditions)
+    b = mock_repo.add_package('b', [d, e], [default, default])
+    mock_repo.add_package('a', [b, c], [default, default])
 
     with spack.repo.swap(mock_repo):
         c_spec = Spec('c')
@@ -133,10 +133,10 @@ def test_specify_preinstalled_dep():
     """
     default = ('build', 'link')
 
-    c = MockPackage('c', [], [])
-    b = MockPackage('b', [c], [default])
-    a = MockPackage('a', [b], [default])
-    mock_repo = MockPackageMultiRepo([a, b, c])
+    mock_repo = MockPackageMultiRepo()
+    c = mock_repo.add_package('c', [], [])
+    b = mock_repo.add_package('b', [c], [default])
+    mock_repo.add_package('a', [b], [default])
 
     with spack.repo.swap(mock_repo):
         b_spec = Spec('b')
@@ -161,15 +161,15 @@ def test_conditional_dep_with_user_constraints():
     """
     default = ('build', 'link')
 
-    y = MockPackage('y', [], [])
+    mock_repo = MockPackageMultiRepo()
+    y = mock_repo.add_package('y', [], [])
     x_on_y_conditions = {
         y.name: {
             'x@2:': 'y'
         }
     }
-    x = MockPackage('x', [y], [default], conditions=x_on_y_conditions)
+    mock_repo.add_package('x', [y], [default], conditions=x_on_y_conditions)
 
-    mock_repo = MockPackageMultiRepo([x, y])
     with spack.repo.swap(mock_repo):
         spec = Spec('x ^y@2')
         spec.concretize()
diff --git a/lib/spack/spack/test/spec_yaml.py b/lib/spack/spack/test/spec_yaml.py
index f9b41df19a1..03129a7eb9b 100644
--- a/lib/spack/spack/test/spec_yaml.py
+++ b/lib/spack/spack/test/spec_yaml.py
@@ -26,7 +26,7 @@
 from spack import repo
 from spack.spec import Spec, save_dependency_spec_yamls
 from spack.util.spack_yaml import syaml_dict
-from spack.test.conftest import MockPackage, MockPackageMultiRepo
+from spack.util.mock_package import MockPackageMultiRepo
 
 
 def check_yaml_round_trip(spec):
@@ -301,15 +301,14 @@ def test_save_dependency_spec_yamls_subset(tmpdir, config):
 
     default = ('build', 'link')
 
-    g = MockPackage('g', [], [])
-    f = MockPackage('f', [], [])
-    e = MockPackage('e', [], [])
-    d = MockPackage('d', [f, g], [default, default])
-    c = MockPackage('c', [], [])
-    b = MockPackage('b', [d, e], [default, default])
-    a = MockPackage('a', [b, c], [default, default])
-
-    mock_repo = MockPackageMultiRepo([a, b, c, d, e, f, g])
+    mock_repo = MockPackageMultiRepo()
+    g = mock_repo.add_package('g', [], [])
+    f = mock_repo.add_package('f', [], [])
+    e = mock_repo.add_package('e', [], [])
+    d = mock_repo.add_package('d', [f, g], [default, default])
+    c = mock_repo.add_package('c', [], [])
+    b = mock_repo.add_package('b', [d, e], [default, default])
+    mock_repo.add_package('a', [b, c], [default, default])
 
     with repo.swap(mock_repo):
         spec_a = Spec('a')
diff --git a/lib/spack/spack/test/util/mock_package.py b/lib/spack/spack/test/util/mock_package.py
new file mode 100644
index 00000000000..376ac581bd5
--- /dev/null
+++ b/lib/spack/spack/test/util/mock_package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import spack.repo
+from spack.util.mock_package import MockPackageMultiRepo
+
+
+def test_mock_package_possible_dependencies():
+    mock_repo = MockPackageMultiRepo()
+    e = mock_repo.add_package('e')
+    d = mock_repo.add_package('d', [e])
+    c = mock_repo.add_package('c', [d])
+    b = mock_repo.add_package('b', [d])
+    a = mock_repo.add_package('a', [b, c])
+
+    with spack.repo.swap(mock_repo):
+        assert set(a.possible_dependencies()) == set(['a', 'b', 'c', 'd', 'e'])
+        assert set(b.possible_dependencies()) == set(['b', 'd', 'e'])
+        assert set(c.possible_dependencies()) == set(['c', 'd', 'e'])
+        assert set(d.possible_dependencies()) == set(['d', 'e'])
+        assert set(e.possible_dependencies()) == set(['e'])
+
+        assert set(
+            a.possible_dependencies(transitive=False)) == set(['a', 'b', 'c'])
+        assert set(
+            b.possible_dependencies(transitive=False)) == set(['b', 'd'])
+        assert set(
+            c.possible_dependencies(transitive=False)) == set(['c', 'd'])
+        assert set(
+            d.possible_dependencies(transitive=False)) == set(['d', 'e'])
+        assert set(
+            e.possible_dependencies(transitive=False)) == set(['e'])
+
+
+def test_mock_repo_is_virtual():
+    mock_repo = MockPackageMultiRepo()
+
+    # current implementation is always false
+    assert mock_repo.is_virtual("foo") is False
+    assert mock_repo.is_virtual("bar") is False
+    assert mock_repo.is_virtual("baz") is False
diff --git a/lib/spack/spack/util/mock_package.py b/lib/spack/spack/util/mock_package.py
new file mode 100644
index 00000000000..3d8ae30b103
--- /dev/null
+++ b/lib/spack/spack/util/mock_package.py
@@ -0,0 +1,161 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Infrastructure used by tests for mocking packages and repos."""
+
+import ordereddict_backport
+
+import spack.util.naming
+from spack.dependency import Dependency
+from spack.spec import Spec
+from spack.version import Version
+
+__all__ = ["MockPackageMultiRepo"]
+
+
+class MockPackageBase(object):
+    """Internal base class for mocking ``spack.package.PackageBase``.
+
+    Use ``MockPackageMultiRepo.add_package()`` to create new instances.
+
+    """
+    def __init__(self, dependencies, dependency_types,
+                 conditions=None, versions=None):
+        """Instantiate a new MockPackageBase.
+
+        This is not for general use; it needs to be constructed by a
+        ``MockPackageMultiRepo``, as we need to know about *all* packages
+        to find possible depenencies.
+
+        """
+        self.spec = None
+        self._installed_upstream = False
+
+    def provides(self, vname):
+        return vname in self.provided
+
+    @property
+    def virtuals_provided(self):
+        return [v.name for v, c in self.provided]
+
+    @classmethod
+    def possible_dependencies(
+            cls, transitive=True, deptype='all', visited=None, virtuals=None):
+        visited = {} if visited is None else visited
+
+        for name, conditions in cls.dependencies.items():
+            # check whether this dependency could be of the type asked for
+            types = [dep.type for cond, dep in conditions.items()]
+            types = set.union(*types)
+            if not any(d in types for d in deptype):
+                continue
+
+        visited.setdefault(cls.name, set())
+        for dep_name in cls.dependencies:
+            if dep_name in visited:
+                continue
+
+            visited.setdefault(dep_name, set())
+
+            if not transitive:
+                continue
+
+            cls._repo.get(dep_name).possible_dependencies(
+                transitive, deptype, visited, virtuals)
+
+        return visited
+
+
+class MockPackageMultiRepo(object):
+    """Mock package repository, mimicking ``spack.repo.Repo``."""
+
+    def __init__(self):
+        self.spec_to_pkg = {}
+
+    def get(self, spec):
+        if not isinstance(spec, spack.spec.Spec):
+            spec = Spec(spec)
+        return self.spec_to_pkg[spec.name]
+
+    def get_pkg_class(self, name):
+        return self.spec_to_pkg[name]
+
+    def exists(self, name):
+        return name in self.spec_to_pkg
+
+    def is_virtual(self, name):
+        return False
+
+    def repo_for_pkg(self, name):
+        import collections
+        Repo = collections.namedtuple('Repo', ['namespace'])
+        return Repo('mockrepo')
+
+    def add_package(self, name, dependencies=None, dependency_types=None,
+                    conditions=None):
+        """Factory method for creating mock packages.
+
+        This creates a new subclass of ``MockPackageBase``, ensures that its
+        ``name`` and ``__name__`` properties are set up correctly, and
+        returns a new instance.
+
+        We use a factory function here because many functions and properties
+        of packages need to be class functions.
+
+        Args:
+            name (str): name of the new package
+            dependencies (list): list of mock packages to be dependencies
+                for this new package (optional; no deps if not provided)
+            dependency_type (list): list of deptypes for each dependency
+                (optional; will be default_deptype if not provided)
+            conditions (list): condition specs for each dependency (optional)
+
+        """
+        if not dependencies:
+            dependencies = []
+
+        if not dependency_types:
+            dependency_types = [
+                spack.dependency.default_deptype] * len(dependencies)
+
+        assert len(dependencies) == len(dependency_types)
+
+        # new class for the mock package
+        class MockPackage(MockPackageBase):
+            pass
+        MockPackage.__name__ = spack.util.naming.mod_to_class(name)
+        MockPackage.name = name
+        MockPackage._repo = self
+
+        # set up dependencies
+        MockPackage.dependencies = ordereddict_backport.OrderedDict()
+        for dep, dtype in zip(dependencies, dependency_types):
+            d = Dependency(MockPackage, Spec(dep.name), type=dtype)
+            if not conditions or dep.name not in conditions:
+                MockPackage.dependencies[dep.name] = {Spec(name): d}
+            else:
+                dep_conditions = conditions[dep.name]
+                dep_conditions = dict(
+                    (Spec(x), Dependency(MockPackage, Spec(y), type=dtype))
+                    for x, y in dep_conditions.items())
+                MockPackage.dependencies[dep.name] = dep_conditions
+
+        # each package has some fake versions
+        versions = list(Version(x) for x in [1, 2, 3])
+        MockPackage.versions = dict(
+            (x, {'preferred': False}) for x in versions
+        )
+
+        MockPackage.variants = {}
+        MockPackage.provided = {}
+        MockPackage.conflicts = {}
+        MockPackage.patches = {}
+
+        mock_package = MockPackage(
+            dependencies, dependency_types, conditions, versions)
+        self.spec_to_pkg[name] = mock_package
+        self.spec_to_pkg["mockrepo." + name] = mock_package
+
+        return mock_package

From 95a03f6759b99701dfa9bd7c299b838057b5a28a Mon Sep 17 00:00:00 2001
From: Jeffrey Salmond <js947@users.noreply.github.com>
Date: Fri, 24 Apr 2020 08:31:03 +0100
Subject: [PATCH 089/802] Add vscode files to gitignore (#16270)

---
 .gitignore | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.gitignore b/.gitignore
index da05b2bcf04..96947860ee0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -33,3 +33,7 @@ lib/spack/spack/test/.cache
 .project
 .cproject
 .pydevproject
+
+# VSCode files
+.vscode
+.devcontainer
\ No newline at end of file

From 051d0d935aeb96f01497356c515877faa8cc8484 Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Sat, 25 Apr 2020 01:56:10 +0900
Subject: [PATCH 090/802] Chainer: New Package. (#16251)

* Chainer: New Package.

* 1. Add maintainers.
2. fix dependency.
3. Add typing-extention@3.6.6 and fix version dependency.

* afixed dependency.

* remove python dependency for version 6.
---
 .../builtin/packages/py-chainer/package.py    | 36 +++++++++++++++++++
 .../packages/py-typing-extensions/package.py  |  4 ++-
 2 files changed, 39 insertions(+), 1 deletion(-)
 create mode 100644 var/spack/repos/builtin/packages/py-chainer/package.py

diff --git a/var/spack/repos/builtin/packages/py-chainer/package.py b/var/spack/repos/builtin/packages/py-chainer/package.py
new file mode 100644
index 00000000000..c75383b4694
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-chainer/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyChainer(PythonPackage):
+    """
+    Chainer is a Python-based deep learning framework aiming at flexibility.
+
+    It provides automatic differentiation APIs based on the define-by-run
+    approach (a.k.a. dynamic computational graphs) as well as object-oriented
+    high-level APIs to build and train neural networks.
+    It also supports CUDA/cuDNN using CuPy for high performance training
+    and inference.
+    """
+
+    homepage = "https://chainer.org/"
+    url      = "https://github.com/chainer/chainer/archive/v7.2.0.tar.gz"
+
+    maintainers = ['adamjstewart']
+
+    version('7.2.0', sha256='6e2fba648cc5b8a5421e494385b76fe5ec154f1028a1c5908557f5d16c04f0b3')
+    version('6.7.0', sha256='87cb3378a35e7c5c695028ec91d58dc062356bc91412384ea939d71374610389')
+
+    depends_on('python@3.5.1:', when='@7:', type=('build', 'run'))
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-numpy@1.9:', type=('build', 'run'))
+    depends_on('py-six@1.9.0:', type=('build', 'run'))
+    depends_on('py-typing-extensions', type=('build', 'run'))
+    depends_on('py-typing-extensions@:3.6.6', when='@:6', type=('build', 'run'))
+    depends_on('py-filelock', type=('build', 'run'))
+    depends_on('py-protobuf@3:', type=('build', 'run'))
+    depends_on('py-typing@:3.6.6', when='@:6', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-typing-extensions/package.py b/var/spack/repos/builtin/packages/py-typing-extensions/package.py
index 7a2b3ab5fb1..02376449f03 100644
--- a/var/spack/repos/builtin/packages/py-typing-extensions/package.py
+++ b/var/spack/repos/builtin/packages/py-typing-extensions/package.py
@@ -17,7 +17,9 @@ class PyTypingExtensions(PythonPackage):
 
     version('3.7.4', sha256='2ed632b30bb54fc3941c382decfd0ee4148f5c591651c9272473fea2c6397d95')
     version('3.7.2', sha256='fb2cd053238d33a8ec939190f30cfd736c00653a85a2919415cecf7dc3d9da71')
+    version('3.6.6', sha256='51e7b7f3dcabf9ad22eed61490f3b8d23d9922af400fe6656cb08e66656b701f')
 
     depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
-    depends_on('py-typing@3.7.4:', when='^python@:3.4', type=('build', 'run'))
+    depends_on('py-typing@3.7.4:', when='@3.7: ^python@:3.4', type=('build', 'run'))
+    depends_on('py-typing@3.6.2:', when='^python@:3.4', type=('build', 'run'))

From 5828a8f7e6472e01f542f339fc44b7ebfc3edfd9 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Fri, 24 Apr 2020 13:24:52 -0700
Subject: [PATCH 091/802] spack env: activate note (#16279)

print a note on how to activate a newly created environment
---
 lib/spack/spack/cmd/env.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/spack/spack/cmd/env.py b/lib/spack/spack/cmd/env.py
index a8bc1e5bbea..43c125e8f24 100644
--- a/lib/spack/spack/cmd/env.py
+++ b/lib/spack/spack/cmd/env.py
@@ -208,10 +208,14 @@ def _env_create(name_or_path, init_file=None, dir=False, with_view=None):
         env = ev.Environment(name_or_path, init_file, with_view)
         env.write()
         tty.msg("Created environment in %s" % env.path)
+        tty.msg("You can activate this environment with:")
+        tty.msg("  spack env activate %s" % env.path)
     else:
         env = ev.create(name_or_path, init_file, with_view)
         env.write()
         tty.msg("Created environment '%s' in %s" % (name_or_path, env.path))
+        tty.msg("You can activate this environment with:")
+        tty.msg("  spack env activate %s" % (name_or_path))
     return env
 
 

From 0606091775a52ae233d5450f153956b3c6b96dac Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 24 Apr 2020 19:59:15 -0500
Subject: [PATCH 092/802] py-tqdm: add new version (#16284)

---
 var/spack/repos/builtin/packages/py-tqdm/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-tqdm/package.py b/var/spack/repos/builtin/packages/py-tqdm/package.py
index be2ed3cecb1..ff7b9947590 100644
--- a/var/spack/repos/builtin/packages/py-tqdm/package.py
+++ b/var/spack/repos/builtin/packages/py-tqdm/package.py
@@ -10,8 +10,9 @@ class PyTqdm(PythonPackage):
     """A Fast, Extensible Progress Meter"""
 
     homepage = "https://github.com/tqdm/tqdm"
-    url      = "https://pypi.io/packages/source/t/tqdm/tqdm-4.36.1.tar.gz"
+    url      = "https://pypi.io/packages/source/t/tqdm/tqdm-4.45.0.tar.gz"
 
+    version('4.45.0', sha256='00339634a22c10a7a22476ee946bbde2dbe48d042ded784e4d88e0236eca5d81')
     version('4.36.1', sha256='abc25d0ce2397d070ef07d8c7e706aede7920da163c64997585d42d3537ece3d')
     version('4.8.4',  sha256='bab05f8bb6efd2702ab6c532e5e6a758a66c0d2f443e09784b73e4066e6b3a37')
 

From 89914f521e878e10adc168403e6f3468b6e89945 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 24 Apr 2020 19:59:30 -0500
Subject: [PATCH 093/802] py-wheel: add new version (#16285)

---
 var/spack/repos/builtin/packages/py-wheel/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-wheel/package.py b/var/spack/repos/builtin/packages/py-wheel/package.py
index 567eefbc520..476b7b9e07a 100644
--- a/var/spack/repos/builtin/packages/py-wheel/package.py
+++ b/var/spack/repos/builtin/packages/py-wheel/package.py
@@ -14,6 +14,7 @@ class PyWheel(PythonPackage):
 
     version('0.33.4', sha256='62fcfa03d45b5b722539ccbc07b190e4bfff4bb9e3a4d470dd9f6a0981002565')
     version('0.33.1', sha256='66a8fd76f28977bb664b098372daef2b27f60dc4d1688cfab7b37a09448f0e9d')
+    version('0.32.3', sha256='029703bf514e16c8271c3821806a1c171220cc5bdd325cbf4e7da1e056a01db6')
     version('0.29.0', sha256='1ebb8ad7e26b448e9caa4773d2357849bf80ff9e313964bcaf79cbf0201a1648')
     version('0.26.0', sha256='eaad353805c180a47545a256e6508835b65a8e830ba1093ed8162f19a50a530c')
 

From 441c16bafb935a69e64e121bcc8ac3d952e03db1 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 24 Apr 2020 19:59:48 -0500
Subject: [PATCH 094/802] py-blis: add new package (#16286)

---
 .../repos/builtin/packages/py-blis/package.py  | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-blis/package.py

diff --git a/var/spack/repos/builtin/packages/py-blis/package.py b/var/spack/repos/builtin/packages/py-blis/package.py
new file mode 100644
index 00000000000..ce7f6c4c655
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-blis/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class PyBlis(PythonPackage):
+    """Cython BLIS: Fast BLAS-like operations from Python and Cython,
+    without the tears"""
+
+    homepage = "https://github.com/explosion/cython-blis"
+    url      = "https://pypi.io/packages/source/b/blis/blis-0.4.1.tar.gz"
+
+    version('0.4.1', sha256='d69257d317e86f34a7f230a2fd1f021fd2a1b944137f40d8cdbb23bd334cd0c4')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy@1.15:', type=('build', 'run'))
+    depends_on('py-hypothesis', type='test')

From 3153610bb8200a2a9f528cc5ad95e166f2b17b95 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 24 Apr 2020 20:00:02 -0500
Subject: [PATCH 095/802] py-catalogue: add new package (#16287)

---
 .../builtin/packages/py-catalogue/package.py  | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-catalogue/package.py

diff --git a/var/spack/repos/builtin/packages/py-catalogue/package.py b/var/spack/repos/builtin/packages/py-catalogue/package.py
new file mode 100644
index 00000000000..799f5bb2ff3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-catalogue/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class PyCatalogue(PythonPackage):
+    """catalogue: Super lightweight function registries for your library."""
+
+    homepage = "https://github.com/explosion/catalogue"
+    url      = "https://pypi.io/packages/source/c/catalogue/catalogue-2.0.0.tar.gz"
+
+    version('2.0.0', sha256='34f8416ec5e7ed08e55c10414416e67c3f4d66edf83bc67320c3290775293816')
+    version('1.0.0', sha256='d74d1d856c6b36a37bf14aa6dbbc27d0582667b7ab979a6108e61a575e8723f5')
+
+    depends_on('python@3.6:', when='@2:', type=('build', 'run'))
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-importlib-metadata@0.20:', when='^python@:3.7', type=('build', 'run'))

From ab87617d5513a1345e773f9b64fe4754557e6c1b Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 24 Apr 2020 20:00:15 -0500
Subject: [PATCH 096/802] py-cymem: add new package (#16288)

---
 .../repos/builtin/packages/py-cymem/package.py   | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-cymem/package.py

diff --git a/var/spack/repos/builtin/packages/py-cymem/package.py b/var/spack/repos/builtin/packages/py-cymem/package.py
new file mode 100644
index 00000000000..fa076b88361
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cymem/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class PyCymem(PythonPackage):
+    """Manage calls to calloc/free through Cython."""
+
+    homepage = "https://github.com/explosion/cymem"
+    url      = "https://pypi.io/packages/source/c/cymem/cymem-2.0.3.tar.gz"
+
+    version('2.0.3', sha256='5083b2ab5fe13ced094a82e0df465e2dbbd9b1c013288888035e24fd6eb4ed01')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-wheel@0.32.0:0.32.999', type='build')

From 0ee023d29f613f718f5b88c158b120adb8b2fe2e Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 24 Apr 2020 20:00:28 -0500
Subject: [PATCH 097/802] py-murmurhash: add new package (#16289)

---
 .../builtin/packages/py-murmurhash/package.py    | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-murmurhash/package.py

diff --git a/var/spack/repos/builtin/packages/py-murmurhash/package.py b/var/spack/repos/builtin/packages/py-murmurhash/package.py
new file mode 100644
index 00000000000..3cb59de262c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-murmurhash/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class PyMurmurhash(PythonPackage):
+    """Cython bindings for MurmurHash."""
+
+    homepage = "https://github.com/explosion/murmurhash"
+    url      = "https://pypi.io/packages/source/m/murmurhash/murmurhash-1.0.2.tar.gz"
+
+    version('1.0.2', sha256='c7a646f6b07b033642b4f52ae2e45efd8b80780b3b90e8092a0cec935fbf81e2')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-wheel@0.32.0:0.32.999', type='build')

From 510d8821e5e7d59481b1c8e882226aa5cec1a3b7 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 24 Apr 2020 20:00:42 -0500
Subject: [PATCH 098/802] py-nltk: add new package (#16290)

---
 .../repos/builtin/packages/py-nltk/package.py | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-nltk/package.py

diff --git a/var/spack/repos/builtin/packages/py-nltk/package.py b/var/spack/repos/builtin/packages/py-nltk/package.py
new file mode 100644
index 00000000000..9dbbcc26515
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-nltk/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class PyNltk(PythonPackage):
+    """The Natural Language Toolkit (NLTK) is a Python package for
+    natural language processing."""
+
+    homepage = "https://www.nltk.org/"
+    url      = "https://pypi.io/packages/source/n/nltk/nltk-3.5.zip"
+
+    version('3.5', sha256='845365449cd8c5f9731f7cb9f8bd6fd0767553b9d53af9eb1b3abf7700936b35')
+
+    depends_on('python@3.5:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-click', type=('build', 'run'))
+    depends_on('py-regex', type=('build', 'run'))
+    depends_on('py-tqdm', type=('build', 'run'))
+
+    # May require additional third-party software:
+    # https://github.com/nltk/nltk/wiki/Installing-Third-Party-Software

From 7a2f47d1815be83902d2b063e9b1b4ebaf9eaa4b Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 24 Apr 2020 20:00:55 -0500
Subject: [PATCH 099/802] py-plac: add new package (#16291)

---
 .../repos/builtin/packages/py-plac/package.py    | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-plac/package.py

diff --git a/var/spack/repos/builtin/packages/py-plac/package.py b/var/spack/repos/builtin/packages/py-plac/package.py
new file mode 100644
index 00000000000..098dbb65c3d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-plac/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class PyPlac(PythonPackage):
+    """The smartest command line arguments parser in the world."""
+
+    homepage = "https://github.com/micheles/plac"
+    url      = "https://pypi.io/packages/source/p/plac/plac-1.1.3.tar.gz"
+
+    version('1.1.3', sha256='398cb947c60c4c25e275e1f1dadf027e7096858fb260b8ece3b33bcff90d985f')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-argparse', type=('build', 'run'))

From dbd0fe8190ab373cdc6d386767d3deea91ee9b8b Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 24 Apr 2020 20:01:09 -0500
Subject: [PATCH 100/802] py-wasabi: add new package (#16296)

---
 .../repos/builtin/packages/py-wasabi/package.py  | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-wasabi/package.py

diff --git a/var/spack/repos/builtin/packages/py-wasabi/package.py b/var/spack/repos/builtin/packages/py-wasabi/package.py
new file mode 100644
index 00000000000..c03d14f3e1b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-wasabi/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class PyWasabi(PythonPackage):
+    """wasabi: A lightweight console printing and formatting toolkit."""
+
+    homepage = "https://ines.io/"
+    url      = "https://pypi.io/packages/source/w/wasabi/wasabi-0.6.0.tar.gz"
+
+    version('0.6.0', sha256='b8dd3e963cd693fde1eb6bfbecf51790171aa3534fa299faf35cf269f2fd6063')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-pytest', type='test')

From d0ccab7d176619c9803fd25c579f895cc2a6dfa7 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 24 Apr 2020 20:01:22 -0500
Subject: [PATCH 101/802] py-srsly: add new package (#16294)

---
 .../builtin/packages/py-srsly/package.py      | 29 +++++++++++++++++++
 .../packages/py-srsly/subprocess.patch        | 12 ++++++++
 2 files changed, 41 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-srsly/package.py
 create mode 100644 var/spack/repos/builtin/packages/py-srsly/subprocess.patch

diff --git a/var/spack/repos/builtin/packages/py-srsly/package.py b/var/spack/repos/builtin/packages/py-srsly/package.py
new file mode 100644
index 00000000000..46b1b50af05
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-srsly/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class PySrsly(PythonPackage):
+    """srsly: Modern high-performance serialization utilities for Python."""
+
+    homepage = "https://github.com/explosion/srsly"
+    url      = "https://pypi.io/packages/source/s/srsly/srsly-2.0.1.tar.gz"
+
+    version('2.0.1', sha256='fa3c7375be8fe75f23c27feafbfb5f738d55ffdbf02964c6896fb7684f519a52')
+    version('2.0.0', sha256='785b00e00406120dbef4ca82925051e6b60fe870c5f84f0d22b3632d574eb870')
+    version('1.0.2', sha256='59258b81d567df207f8a0a33c4b5fa232afccf1d927c8ce3ba5395bfd64c0ed8')
+
+    depends_on('python@3.6:', when='@2:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-wheel', when='@2:', type='build')
+    depends_on('py-cython@0.25:', when='@2:', type='build')
+    depends_on('py-pathlib@1.0.1', when='^python@:3.3', type=('build', 'run'))
+    depends_on('py-pytest', type='test')
+    depends_on('py-mock', type='test')
+    depends_on('py-numpy', type='test')
+    depends_on('py-six', when='@:1', type='test')
+    depends_on('py-pytz', when='@:1', type='test')
+
+    # https://github.com/explosion/srsly/pull/24
+    patch('subprocess.patch', when='@2.0.0:2.0.1')
diff --git a/var/spack/repos/builtin/packages/py-srsly/subprocess.patch b/var/spack/repos/builtin/packages/py-srsly/subprocess.patch
new file mode 100644
index 00000000000..50a053d7548
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-srsly/subprocess.patch
@@ -0,0 +1,12 @@
+diff -Naur a/srsly/tests/cloudpickle/testutils.py b/srsly/tests/cloudpickle/testutils.py
+--- a/srsly/tests/cloudpickle/testutils.py	2020-04-24 16:10:43.000000000 -0500
++++ b/srsly/tests/cloudpickle/testutils.py	2020-04-24 16:11:02.000000000 -0500
+@@ -5,7 +5,7 @@
+ from subprocess import Popen, check_output, PIPE, STDOUT, CalledProcessError
+ from srsly.cloudpickle.cloudpickle import dumps
+ from pickle import loads
+-from suprocess import TimeoutExpired
++from subprocess import TimeoutExpired
+ 
+ 
+ TEST_GLOBALS = "a test value"

From b5bf816577005541f29bde1cbca77427b36992b2 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 24 Apr 2020 21:24:33 -0500
Subject: [PATCH 102/802] py-preshed: add new package (#16292)

---
 .../builtin/packages/py-preshed/package.py     | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-preshed/package.py

diff --git a/var/spack/repos/builtin/packages/py-preshed/package.py b/var/spack/repos/builtin/packages/py-preshed/package.py
new file mode 100644
index 00000000000..cb8cc2ed10b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-preshed/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class PyPreshed(PythonPackage):
+    """preshed: Cython Hash Table for Pre-Hashed Keys."""
+
+    homepage = "https://github.com/explosion/preshed"
+    url      = "https://pypi.io/packages/source/p/preshed/preshed-3.0.2.tar.gz"
+
+    version('3.0.2', sha256='61d73468c97c1d6d5a048de0b01d5a6fd052123358aca4823cdb277e436436cb')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cymem@2.0.2:2.0.999', type=('build', 'run'))
+    depends_on('py-murmurhash@0.28:1.0', type=('build', 'run'))
+    depends_on('py-pytest', type='test')

From 914f380bb69cd38432a9f189a2805bc6deb3559d Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Fri, 24 Apr 2020 19:25:48 -0700
Subject: [PATCH 103/802] Improved the accuracy of the dependencies for the
 'visit' package. (#16297)

Added a fix for the 'visit' package when building variant '@3%gcc'.
---
 .../repos/builtin/packages/visit/package.py   | 22 +++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/visit/package.py b/var/spack/repos/builtin/packages/visit/package.py
index 1ee2994c21c..aa791284c0b 100644
--- a/var/spack/repos/builtin/packages/visit/package.py
+++ b/var/spack/repos/builtin/packages/visit/package.py
@@ -33,7 +33,8 @@ class Visit(CMakePackage):
     patch('parallel-hdf5.patch', when='+hdf5+mpi')
 
     depends_on('cmake@3.0:', type='build')
-    depends_on('vtk@8.1.0:+opengl2', when='@3.0:3.0.1')
+    # https://github.com/visit-dav/visit/issues/3498
+    depends_on('vtk@8.1.0:8.1.999+opengl2', when='@3.0:3.0.1')
     depends_on('vtk@6.1.0~opengl2', when='@:2.999')
     depends_on('vtk+python', when='+python @3.0:')
     depends_on('vtk~mpi', when='~mpi')
@@ -42,7 +43,11 @@ class Visit(CMakePackage):
     depends_on('qt@5.10:', when='+gui @3.0:')
     depends_on('qwt', when='+gui')
     depends_on('python@2.6:2.8', when='+python')
-    depends_on('silo+shared', when='+silo')
+    # VisIt uses Silo's 'ghost zone' data structures, which are only available
+    # in v4.10+ releases: https://wci.llnl.gov/simulation/computer-codes/silo/releases/release-notes-4.10
+    depends_on('silo@4.10:+shared', when='+silo')
+    depends_on('silo~mpi', when='+silo~mpi')
+    depends_on('silo+mpi', when='+silo+mpi')
     depends_on('hdf5~mpi', when='+hdf5~mpi')
     depends_on('hdf5+mpi', when='+hdf5+mpi')
     depends_on('mpi', when='+mpi')
@@ -66,14 +71,23 @@ def patch(self):
     def cmake_args(self):
         spec = self.spec
 
+        cxx_flags = [self.compiler.cxx_pic_flag]
+        cc_flags = [self.compiler.cc_pic_flag]
+
+        # NOTE: This is necessary in order to allow VisIt to compile a couple
+        # of lines of code with 'const char*' to/from 'char*' conversions.
+        if spec.satisfies('@3:%gcc'):
+            cxx_flags.append('-fpermissive')
+            cc_flags.append('-fpermissive')
+
         args = [
             '-DVTK_MAJOR_VERSION=' + str(spec['vtk'].version[0]),
             '-DVTK_MINOR_VERSION=' + str(spec['vtk'].version[1]),
             '-DVISIT_VTK_DIR:PATH=' + spec['vtk'].prefix,
             '-DVISIT_ZLIB_DIR:PATH=' + spec['zlib'].prefix,
             '-DVISIT_USE_GLEW=OFF',
-            '-DCMAKE_CXX_FLAGS=' + self.compiler.cxx_pic_flag,
-            '-DCMAKE_C_FLAGS=' + self.compiler.cc_pic_flag,
+            '-DCMAKE_CXX_FLAGS=' + ' '.join(cxx_flags),
+            '-DCMAKE_C_FLAGS=' + ' '.join(cc_flags),
         ]
 
         if '+python' in spec:

From 5fce2ac96b873d51c19a24c3730a0d22ada6f378 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 24 Apr 2020 23:50:56 -0500
Subject: [PATCH 104/802] py-thinc: add new package (#16295)

---
 .../builtin/packages/py-thinc/package.py      | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-thinc/package.py

diff --git a/var/spack/repos/builtin/packages/py-thinc/package.py b/var/spack/repos/builtin/packages/py-thinc/package.py
new file mode 100644
index 00000000000..b081c9db395
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-thinc/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class PyThinc(PythonPackage):
+    """Thinc: Practical Machine Learning for NLP in Python."""
+
+    homepage = "https://github.com/explosion/thinc"
+    url      = "https://pypi.io/packages/source/t/thinc/thinc-7.4.0.tar.gz"
+
+    version('7.4.0', sha256='523e9be1bfaa3ed1d03d406ce451b6b4793a9719d5b83d2ea6b3398b96bc58b8')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-murmurhash@0.28:1.0', type=('build', 'run'))
+    depends_on('py-cymem@2.0.2:2.0.999', type=('build', 'run'))
+    depends_on('py-preshed@1.0.1:3.0', type=('build', 'run'))
+    depends_on('py-blis@0.4.0:0.4.999', type=('build', 'run'))
+    depends_on('py-wasabi@0.0.9:1.0', type=('build', 'run'))
+    depends_on('py-srsly@0.0.6:1.0', type=('build', 'run'))
+    depends_on('py-catalogue@0.0.7:1.0', type=('build', 'run'))
+    depends_on('py-numpy@1.7:', type=('build', 'run'))
+    depends_on('py-plac@0.9.6:1.1', type=('build', 'run'))
+    depends_on('py-tqdm@4.10:4.999', type=('build', 'run'))
+    depends_on('py-pathlib@1.0.1', when='^python@:3.3', type=('build', 'run'))
+    depends_on('py-pytest', type='test')
+    depends_on('py-mock', type='test')
+    depends_on('py-hypothesis', type='test')

From b796d2736caaee4c077c5971be92f66bb5d5477d Mon Sep 17 00:00:00 2001
From: Jonathon Anderson <jonathon.anderson@colorado.edu>
Date: Sat, 25 Apr 2020 09:35:33 -0600
Subject: [PATCH 105/802] Version bump: jdk 14 (#15821)

---
 var/spack/repos/builtin/packages/jdk/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py
index 025d12be659..92af25ae9b6 100644
--- a/var/spack/repos/builtin/packages/jdk/package.py
+++ b/var/spack/repos/builtin/packages/jdk/package.py
@@ -32,6 +32,8 @@ class Jdk(Package):
     # found in a link above. The build number can be deciphered from the URL.
     # Alternatively, run `bin/java -version` after extracting. Replace '+'
     # symbol in version with '_', otherwise it will be interpreted as a variant
+    version('14_36', sha256='4639bbaecc9cc606f1a4b99fda1efcaefcbf57a7025b3828b095093a6c866afd',
+            url='https://download.oracle.com/otn-pub/java/jdk/14+36/076bab302c7b4508975440c56f6cc26a/jdk-14_linux-x64_bin.tar.gz')
     version('12.0.2_10', sha256='2dde6fda89a4ec6e6560ed464e917861c9e40bf576e7a64856dafc55abaaff51',
             url='https://download.oracle.com/otn-pub/java/jdk/12.0.2+10/e482c34c86bd4bf8b56c0b35558996b9/jdk-12.0.2_linux-x64_bin.tar.gz')
     version('12.0.1_12', sha256='9fd6dcdaf2cfca7da59e39b009a0f5bcd53bec2fb16105f7ca8d689cdab68d75',
@@ -57,6 +59,7 @@ class Jdk(Package):
     version('1.8.0_131-b11', sha256='62b215bdfb48bace523723cdbb2157c665e6a25429c73828a32f00e587301236',
             url='https://download.oracle.com/otn-pub/java/jdk/8u131-b11/d54c1d3a095b4ff2b6607d096fa80163/jdk-8u131-linux-x64.tar.gz')
 
+    provides('java@14', when='@14.0:14.999')
     provides('java@12', when='@12.0:12.999')
     provides('java@11', when='@11.0:11.999')
     provides('java@10', when='@10.0:10.999')

From 9bd0b0fbe13ee7bb8feaa043df01b9a8fd60c19e Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sat, 25 Apr 2020 10:35:57 -0500
Subject: [PATCH 106/802] py-spacy: add new package (#16293)

---
 .../builtin/packages/py-spacy/package.py      | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-spacy/package.py

diff --git a/var/spack/repos/builtin/packages/py-spacy/package.py b/var/spack/repos/builtin/packages/py-spacy/package.py
new file mode 100644
index 00000000000..9e343e4e0da
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-spacy/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class PySpacy(PythonPackage):
+    """spaCy is a library for advanced Natural Language Processing in
+    Python and Cython."""
+
+    homepage = "https://spacy.io/"
+    url      = "https://pypi.io/packages/source/s/spacy/spacy-2.2.4.tar.gz"
+
+    version('2.2.4', sha256='f0f3a67c5841e6e35d62c98f40ebb3d132587d3aba4f4dccac5056c4e90ff5b9')
+
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+    depends_on('py-wheel', type='build')
+    depends_on('py-cython@0.25:', type='build')
+    depends_on('py-murmurhash@0.28:1.0', type=('build', 'run'))
+    depends_on('py-cymem@2.0.2:2.0.999', type=('build', 'run'))
+    depends_on('py-preshed@3.0.2:3.0.999', type=('build', 'run'))
+    depends_on('py-thinc@7.4.0', type=('build', 'run'))
+    depends_on('py-blis@0.4.0:0.4.999', type=('build', 'run'))
+    depends_on('py-srsly@1.0.2:1.0.999', type=('build', 'run'))
+    depends_on('py-catalogue@0.0.7:1.0', type=('build', 'run'))
+    depends_on('py-tqdm@4.38:4.999', type=('build', 'run'))
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-numpy@1.15:', type=('build', 'run'))
+    depends_on('py-plac@0.9.6:1.1', type=('build', 'run'))
+    depends_on('py-requests@2.13:2.999', type=('build', 'run'))
+    depends_on('py-pathlib@1.0.1', when='^python@:3.3', type=('build', 'run'))

From 9b0e4cd20b373678a37e27612fe16e66aa819600 Mon Sep 17 00:00:00 2001
From: Sajid Ali <30510036+s-sajid-ali@users.noreply.github.com>
Date: Sat, 25 Apr 2020 12:39:33 -0500
Subject: [PATCH 107/802] ucx : add version, modify variants (#16252)

* fixes

* remove extra newline
---
 var/spack/repos/builtin/packages/ucx/package.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/ucx/package.py b/var/spack/repos/builtin/packages/ucx/package.py
index 7def88bd883..b345107c29c 100644
--- a/var/spack/repos/builtin/packages/ucx/package.py
+++ b/var/spack/repos/builtin/packages/ucx/package.py
@@ -16,6 +16,7 @@ class Ucx(AutotoolsPackage):
     maintainers = ['hppritcha']
 
     # Current
+    version('1.8.0', sha256='e400f7aa5354971c8f5ac6b881dc2846143851df868088c37d432c076445628d')
     version('1.7.0', sha256='6ab81ee187bfd554fe7e549da93a11bfac420df87d99ee61ffab7bb19bdd3371')
     version('1.6.1', sha256='1425648aa03f5fa40e4bc5c4a5a83fe0292e2fe44f6054352fbebbf6d8f342a1')
     version('1.6.0', sha256='360e885dd7f706a19b673035a3477397d100a02eb618371697c7f3ee4e143e2c')
@@ -43,11 +44,15 @@ class Ucx(AutotoolsPackage):
             description='Enable assertions')
     variant('parameter_checking', default=False,
             description='Enable paramter checking')
-    variant('pic', default=False,
+    variant('pic', default=True,
             description='Builds with PIC support')
+    variant('java', default=False,
+            description='Builds with Java bindings')
 
     depends_on('numactl')
     depends_on('rdma-core')
+    depends_on('java@8', when='+java')
+    depends_on('maven', when='+java')
 
     def configure_args(self):
         spec = self.spec
@@ -82,4 +87,9 @@ def configure_args(self):
         else:
             config_args.append('--without-pic')
 
+        if '+java' in spec:
+            config_args.append('--with-java=%s' % spec['java'].prefix)
+        else:
+            config_args.append('--without-java')
+
         return config_args

From b5be99cdb74490fc0619b52d4c358a1bba64172d Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sat, 25 Apr 2020 15:42:40 -0500
Subject: [PATCH 108/802] libyaml: add new version (#16300)

---
 var/spack/repos/builtin/packages/libyaml/package.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/libyaml/package.py b/var/spack/repos/builtin/packages/libyaml/package.py
index d795b2f8a6f..26686dbd524 100644
--- a/var/spack/repos/builtin/packages/libyaml/package.py
+++ b/var/spack/repos/builtin/packages/libyaml/package.py
@@ -10,10 +10,12 @@ class Libyaml(AutotoolsPackage):
     """A C library for parsing and emitting YAML."""
 
     homepage = "https://pyyaml.org/wiki/LibYAML"
-    url      = "https://pyyaml.org/download/libyaml/yaml-0.2.2.tar.gz"
+    url      = "https://pyyaml.org/download/libyaml/yaml-0.2.4.tar.gz"
     git      = "https://github.com/yaml/libyaml.git"
 
     version('master', branch='master')
+    version('0.2.4', sha256='d80aeda8747b7c26fbbfd87ab687786e58394a8435ae3970e79cb97882e30557')
+    version('0.2.3', sha256='08bbb80284d77092e68a6f69f1e480e8ed93e215c47b2ca29290e3bd5a191108')
     version('0.2.2', sha256='4a9100ab61047fd9bd395bcef3ce5403365cafd55c1e0d0299cde14958e47be9')
     version('0.2.1', sha256='78281145641a080fb32d6e7a87b9c0664d611dcb4d542e90baf731f51cbb59cd')
     version('0.1.7', sha256='8088e457264a98ba451a90b8661fcb4f9d6f478f7265d48322a196cec2480729')

From 4cd537f6c7153675fde2ce0bb66a2fb9e9fc0a9a Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sat, 25 Apr 2020 15:43:14 -0500
Subject: [PATCH 109/802] py-pyyaml: add new version and variant (#16301)

---
 .../builtin/packages/py-pyyaml/package.py     | 22 +++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-pyyaml/package.py b/var/spack/repos/builtin/packages/py-pyyaml/package.py
index d7a08ca1b8f..2b00de2d9b0 100644
--- a/var/spack/repos/builtin/packages/py-pyyaml/package.py
+++ b/var/spack/repos/builtin/packages/py-pyyaml/package.py
@@ -9,14 +9,28 @@
 class PyPyyaml(PythonPackage):
     """PyYAML is a YAML parser and emitter for Python."""
 
-    homepage = "http://pyyaml.org/wiki/PyYAML"
-    url      = "https://pypi.io/packages/source/P/PyYAML/PyYAML-5.1.2.tar.gz"
+    homepage = "https://pyyaml.org/wiki/PyYAML"
+    url      = "https://pypi.io/packages/source/P/PyYAML/PyYAML-5.3.1.tar.gz"
 
+    version('5.3.1', sha256='b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d')
     version('5.1.2', sha256='01adf0b6c6f61bd11af6e10ca52b7d4057dd0be0343eb9283c878cf3af56aee4')
     version('5.1',   sha256='436bc774ecf7c103814098159fbb84c2715d25980175292c648f2da143909f95')
     version('3.13',  sha256='3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf')
     version('3.12',  sha256='592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab')
     version('3.11',  sha256='c36c938a872e5ff494938b33b14aaa156cb439ec67548fcab3535bb78b0846e8')
 
-    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
-    depends_on('libyaml')
+    variant('libyaml', default=True, description='Use libYAML bindings')
+
+    depends_on('python@2.7:2.8,3.5:', type=('build', 'run'))
+    depends_on('libyaml', when='+libyaml')
+
+    def setup_py(self, *args, **kwargs):
+        # Cast from tuple to list
+        args = list(args)
+
+        if '+libyaml' in self.spec:
+            args.insert(0, '--with-libyaml')
+        else:
+            args.insert(0, '--without-libyaml')
+
+        super(PyPyyaml, self).setup_py(*args, **kwargs)

From 75042c381c9fd1412f0fce99aab9ebd43fd528c8 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Sat, 25 Apr 2020 21:36:08 -0700
Subject: [PATCH 110/802] LLVM lldb 10.0: Python Link Dependency (#16299)

* LLVM: Python Dependency

Effort to expose the linked python library when building LLVM.
This might fix the forward propagation of libintl that comes
with the static python library build on darwin.

* LLDB Py: Remove Ignored Old Flags

Changed in LLVM 10.0+
---
 var/spack/repos/builtin/packages/llvm/package.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index bf8a77933c1..53ce3e12c29 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -287,8 +287,12 @@ def cmake_args(self):
         if "+python" in spec and "+lldb" in spec and spec.satisfies("@5.0.0:"):
             cmake_args.append("-DLLDB_USE_SYSTEM_SIX:Bool=TRUE")
 
-        if "~python" in spec and "+lldb" in spec:
-            cmake_args.append("-DLLDB_DISABLE_PYTHON:Bool=TRUE")
+        if "+lldb" in spec and spec.satisfies("@:9.9.9"):
+            cmake_args.append("-DLLDB_DISABLE_PYTHON:Bool={0}".format(
+                'ON' if '~python' in spec else 'OFF'))
+        if "+lldb" in spec and spec.satisfies("@10.0.0:"):
+            cmake_args.append("-DLLDB_ENABLE_PYTHON:Bool={0}".format(
+                'ON' if '+python' in spec else 'OFF'))
 
         if "+gold" in spec:
             cmake_args.append(

From 63a0647282da89a31244ecba920329d48f13990b Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sun, 26 Apr 2020 11:29:52 -0500
Subject: [PATCH 111/802] PyTorch: disable XNNPACK build (#16304)

---
 var/spack/repos/builtin/packages/py-torch/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py
index f786ad14bc5..7329ba91741 100644
--- a/var/spack/repos/builtin/packages/py-torch/package.py
+++ b/var/spack/repos/builtin/packages/py-torch/package.py
@@ -74,6 +74,7 @@ class PyTorch(PythonPackage, CudaPackage):
     variant('mkldnn', default=True, description='Enables use of MKLDNN')
     variant('nnpack', default=False, description='Enables NNPACK build')
     variant('qnnpack', default=False, description='Enables QNNPACK build (quantized 8-bit operators)')
+    variant('xnnpack', default=False, description='Enables XNNPACK build')
     variant('distributed', default=False, description='Enables distributed (c10d, gloo, mpi, etc.) build')
     variant('nccl', default=True, description='Use Spack-installed NCCL')
     variant('caffe2', default=False, description='Enables Caffe2 operators build')
@@ -94,6 +95,7 @@ class PyTorch(PythonPackage, CudaPackage):
     conflicts('+miopen', when='@:0.4')
     conflicts('+mkldnn', when='@:0.3')
     conflicts('+qnnpack', when='@:0.4')
+    conflicts('+xnnpack', when='@:1.4')
     conflicts('+nccl', when='~cuda')
     conflicts('+opencv', when='@:0.4')
     conflicts('+ffmpeg', when='@:0.4')
@@ -149,6 +151,8 @@ class PyTorch(PythonPackage, CudaPackage):
     # TODO: add dependency: https://github.com/Maratyszcza/NNPACK
     # depends_on('nnpack', when='+nnpack')
     depends_on('qnnpack', when='+qnnpack')
+    # TODO: add dependency: https://github.com/google/XNNPACK
+    # depends_on('xnnpack', when='+xnnpack')
     depends_on('mpi', when='+distributed')
     depends_on('nccl', when='+nccl')
     depends_on('gloo', when='+gloo')
@@ -239,6 +243,7 @@ def enable_or_disable(variant, keyword='USE', var=None, newer=False):
 
         enable_or_disable('nnpack')
         enable_or_disable('qnnpack')
+        enable_or_disable('xnnpack')
         enable_or_disable('distributed')
 
         enable_or_disable('nccl')

From 31e8d646afd825b07a7ec571403c2ebc588f65c1 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Sun, 26 Apr 2020 09:45:04 -0700
Subject: [PATCH 112/802] py-h5py: master (new version) (#16306)

Add the `master` branch of h5py as a version.
---
 var/spack/repos/builtin/packages/py-h5py/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py
index 5f05081de17..e652849fd1e 100644
--- a/var/spack/repos/builtin/packages/py-h5py/package.py
+++ b/var/spack/repos/builtin/packages/py-h5py/package.py
@@ -12,9 +12,11 @@ class PyH5py(PythonPackage):
 
     homepage = "http://www.h5py.org/"
     url      = "https://pypi.io/packages/source/h/h5py/h5py-2.10.0.tar.gz"
+    git      = "https://github.com/h5py/h5py.git"
 
     import_modules = ['h5py', 'h5py._hl']
 
+    version('master', branch='master')
     version('2.10.0', sha256='84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d')
     version('2.9.0', sha256='9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002')
     version('2.8.0', sha256='e626c65a8587921ebc7fb8d31a49addfdd0b9a9aa96315ea484c09803337b955')

From f20202387680aa00767cc76d89ee71701f7d9e44 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Sun, 26 Apr 2020 09:46:40 -0700
Subject: [PATCH 113/802] py-blosc (new package) (#16307)

Add the py-blosc python package.
---
 .../builtin/packages/py-blosc/package.py      | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-blosc/package.py

diff --git a/var/spack/repos/builtin/packages/py-blosc/package.py b/var/spack/repos/builtin/packages/py-blosc/package.py
new file mode 100644
index 00000000000..da185302ff4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-blosc/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyBlosc(PythonPackage):
+    """A Python wrapper for the extremely fast Blosc compression library"""
+
+    homepage = "http://python-blosc.blosc.org"
+    url      = "https://github.com/Blosc/python-blosc/archive/v1.9.1.tar.gz"
+    git      = "https://github.com/Blosc/python-blosc.git"
+
+    version('1.9.1', sha256='ffc884439a12409aa4e8945e21dc920d6bc21807357c51d24c7f0a27ae4f79b9')
+
+    depends_on('cmake@3.11.0:', type='build')
+    depends_on('python@3.6:', type=('build', 'run'))
+    depends_on('py-scikit-build', type='build')
+    # depends_on('c-blosc')  # shipped internally
+    depends_on('py-numpy', type='test')
+    depends_on('py-psutil', type='test')

From e8efeda14acbfd0c2c9ca1cc9641b3a1a632809e Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Sun, 26 Apr 2020 15:08:21 -0700
Subject: [PATCH 114/802] py-profilehooks (new package) (#16305)

Adds the py-profilehooks package.
---
 .../packages/py-profilehooks/package.py       | 20 +++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-profilehooks/package.py

diff --git a/var/spack/repos/builtin/packages/py-profilehooks/package.py b/var/spack/repos/builtin/packages/py-profilehooks/package.py
new file mode 100644
index 00000000000..47b52a455c7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-profilehooks/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyProfilehooks(PythonPackage):
+    """Python decorators for profiling/tracing/timing a single function"""
+
+    homepage = "https://mg.pov.lt/profilehooks/"
+    url      = "https://pypi.io/packages/source/p/profilehooks/profilehooks-1.11.2.tar.gz"
+
+    git      = "https://github.com/mgedmin/profilehooks.git"
+
+    version('1.11.2', sha256='41a74c1abdc5eeaf7dec024e9e89627f70e158374d263a3098bef31a06d38ab2')
+
+    depends_on('python@2.7:2.8,3.5:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')

From af7e323f6749198baf3fa5c6e486d1d5e21d6fe9 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Sun, 26 Apr 2020 17:06:27 -0700
Subject: [PATCH 115/802] libbsd: mirror (#16313)

Add a mirror for `libbsd` to improve fetch stability.
libbsd.freedesktop.org sometimes failes in my nightly CI/CD scripts.
---
 var/spack/repos/builtin/packages/libbsd/package.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/libbsd/package.py b/var/spack/repos/builtin/packages/libbsd/package.py
index ce99e985976..8ea91f4d5ab 100644
--- a/var/spack/repos/builtin/packages/libbsd/package.py
+++ b/var/spack/repos/builtin/packages/libbsd/package.py
@@ -14,7 +14,10 @@ class Libbsd(AutotoolsPackage):
     """
 
     homepage = "https://libbsd.freedesktop.org/wiki/"
-    url      = "https://libbsd.freedesktop.org/releases/libbsd-0.9.1.tar.xz"
+    urls     = [
+        "https://libbsd.freedesktop.org/releases/libbsd-0.9.1.tar.xz",
+        "https://mirrors.dotsrc.org/pub/mirrors/exherbo/libbsd-0.9.1.tar.xz"
+    ]
 
     version('0.10.0', sha256='34b8adc726883d0e85b3118fa13605e179a62b31ba51f676136ecb2d0bc1a887')
     version('0.9.1', sha256='56d835742327d69faccd16955a60b6dcf30684a8da518c4eca0ac713b9e0a7a4')

From 199ce66a3c42c9351064019059a490809223c4e4 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Sun, 26 Apr 2020 17:06:37 -0700
Subject: [PATCH 116/802] libpciaccess: mirror (#16312)

Support mirrors for libpciaccess downloads.
---
 var/spack/repos/builtin/packages/libpciaccess/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/libpciaccess/package.py b/var/spack/repos/builtin/packages/libpciaccess/package.py
index 874db157210..4f1337db763 100644
--- a/var/spack/repos/builtin/packages/libpciaccess/package.py
+++ b/var/spack/repos/builtin/packages/libpciaccess/package.py
@@ -6,11 +6,11 @@
 from spack import *
 
 
-class Libpciaccess(AutotoolsPackage):
+class Libpciaccess(AutotoolsPackage, XorgPackage):
     """Generic PCI access library."""
 
     homepage = "http://cgit.freedesktop.org/xorg/lib/libpciaccess/"
-    url      = "http://xorg.freedesktop.org/archive/individual/lib/libpciaccess-0.13.5.tar.gz"
+    xorg_mirror_path = "lib/libpciaccess-0.13.5.tar.gz"
 
     version('0.13.5', sha256='fe26ec788732b4ef60b550f2d3fa51c605d27f646e18ecec878f061807a3526e')
     version('0.13.4', sha256='74d92bda448e6fdb64fee4e0091255f48d625d07146a121653022ed3a0ca1f2f')

From 4f3cc19ec7dca204f3c3b75fb838142b567f27e0 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Sun, 26 Apr 2020 17:07:13 -0700
Subject: [PATCH 117/802] qt: fix macOS w/ AppleClang (mesa libs) (#16302)

Building the `py-jupyter` stack on macOS with AppleClang breaks on
the `py-qtconsole` -> `py-qtconsole` -> `qt +opengl` package build
environment setup with:
```
 ==> Error: AttributeError: Query of package 'mesa' for 'libs' failed
 ...
 ==> Error: Failed to install qt due to ChildError: AttributeError: Query of package 'mesa' for 'libs' failed
```

This tries to add more library targets build by `mesa` to avoid this.
---
 var/spack/repos/builtin/packages/mesa/package.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/mesa/package.py b/var/spack/repos/builtin/packages/mesa/package.py
index 5a2893a645c..b277a03d194 100644
--- a/var/spack/repos/builtin/packages/mesa/package.py
+++ b/var/spack/repos/builtin/packages/mesa/package.py
@@ -13,6 +13,7 @@ class Mesa(AutotoolsPackage):
      - a system for rendering interactive 3D graphics."""
 
     homepage = "http://www.mesa3d.org"
+    maintainers = ['v-dobrev']
 
     # Note that we always want to build from the git repo instead of a
     # tarball since the tarball has pre-generated files for certain versions
@@ -180,7 +181,8 @@ def configure_args(self):
     @property
     def libs(self):
         for dir in ['lib64', 'lib']:
-            libs = find_libraries('libGL', join_path(self.prefix, dir),
+            libs = find_libraries(['libGL', 'libOSMesa'],
+                                  join_path(self.prefix, dir),
                                   shared=True, recursive=False)
             if libs:
                 return libs

From ca4de491bafbda92af7b15c442b33a2d84db969a Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Mon, 27 Apr 2020 12:09:06 +0900
Subject: [PATCH 118/802] ppOpen-APPL/AMR-FDM: New package (#16199)

* ppOpen-APPL/AMR-FDM: New package

* separate build and install.

* Fix description.
---
 .../packages/ppopen-appl-amr-fdm/package.py   | 62 +++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100755 var/spack/repos/builtin/packages/ppopen-appl-amr-fdm/package.py

diff --git a/var/spack/repos/builtin/packages/ppopen-appl-amr-fdm/package.py b/var/spack/repos/builtin/packages/ppopen-appl-amr-fdm/package.py
new file mode 100755
index 00000000000..72db2617007
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ppopen-appl-amr-fdm/package.py
@@ -0,0 +1,62 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class PpopenApplAmrFdm(MakefilePackage):
+    """
+    ppOpen-APPL/AMR-FDM is an adaptive mesh refinement (AMR) framework
+    for development of 3D parallel finite-difference method (FDM)
+    applications.
+    """
+
+    homepage = "http://ppopenhpc.cc.u-tokyo.ac.jp/ppopenhpc/"
+    url      = "file://{0}/ppohAMRFDM_0.3.0.tar.gz".format(os.getcwd())
+
+    version('0.3.0', sha256='e82217e4c949dd079a56024d3d1c1761dc8efd5ad0d26a3af83564c3db7327bb')
+
+    depends_on('mpi')
+
+    parallel = False
+    build_targets = ['default', 'advAMR3D']
+
+    def edit(self, spec, prefix):
+        fflags = [
+            '-O3',
+            '-I.',
+            '-I{0}/include'.format(os.getcwd())
+        ]
+        makefile_in = FileFilter('Makefile.in')
+        makefile_in.filter('^PREFIX +=.*', 'PREFIX = {0}'.format(prefix))
+        makefile_in.filter(
+            '^INCDIR +=.*',
+            'INCDIR = {0}/include'.format(self.build_directory)
+        )
+        makefile_in.filter(
+            '^LIBDIR +=.*',
+            'LIBDIR = {0}/lib'.format(self.build_directory)
+        )
+        makefile_in.filter('^F90 +=.*', 'F90 = {0}'.format(spack_fc))
+        makefile_in.filter(
+            '^MPIF90 +=.*',
+            'MPIF90 = {0}'.format(spec['mpi'].mpifc)
+        )
+        makefile_in.filter(
+            '^sFFLAGS +=.*',
+            'sFFLAGS = {0}'.format(' '.join(fflags))
+        )
+        fflags.append(self.compiler.openmp_flag)
+        makefile_in.filter(
+            '^pFFLAGS +=.*',
+            'pFFLAGS = {0}'.format(' '.join(fflags))
+        )
+
+    def install(self, spec, prefix):
+        install_tree('include', prefix.include)
+        install_tree('lib', prefix.lib)
+        install_tree('bin', prefix.bin)
+        install_tree('doc', prefix.doc)

From 6b648c6e89a92f8220464a2807f42a45acd6b8e9 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Mon, 27 Apr 2020 12:17:32 +0200
Subject: [PATCH 119/802] Improve the coverage of spack.relocate (#15654)

This PR introduces trivial refactoring in:
- `get_existing_elf_rpaths`
- `get_relative_elf_rpaths`
- `get_normalized_elf_rpaths`
- `set_placeholder`

mainly to be more consistent with practices used in other
parts of the code and to simplify functions locally. It also
adds or reworks unit tests for these functions and extends
their docstrings.

Co-authored-by: Patrick Gartung <gartung@fnal.gov>
Co-authored-by: Peter J. Scheibel <scheibel1@llnl.gov>
---
 lib/spack/spack/relocate.py       | 154 ++++++++++++++++++------------
 lib/spack/spack/test/packaging.py |  18 +---
 lib/spack/spack/test/relocate.py  |  54 +++++++++++
 3 files changed, 149 insertions(+), 77 deletions(-)

diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py
index 9f8669f3d45..41770103b05 100644
--- a/lib/spack/spack/relocate.py
+++ b/lib/spack/spack/relocate.py
@@ -97,70 +97,102 @@ def _patchelf():
     return exe_path if os.path.exists(exe_path) else None
 
 
-def get_existing_elf_rpaths(path_name):
-    """
-    Return the RPATHS returned by patchelf --print-rpath path_name
-    as a list of strings.
+def _elf_rpaths_for(path):
+    """Return the RPATHs for an executable or a library.
+
+    The RPATHs are obtained by ``patchelf --print-rpath PATH``.
+
+    Args:
+        path (str): full path to the executable or library
+
+    Return:
+        RPATHs as a list of strings.
     """
+    # If we're relocating patchelf itself, use it
+    patchelf_path = path if path.endswith("/bin/patchelf") else _patchelf()
+    patchelf = executable.Executable(patchelf_path)
 
-    # if we're relocating patchelf itself, use it
-
-    if path_name.endswith("/bin/patchelf"):
-        patchelf = executable.Executable(path_name)
-    else:
-        patchelf = executable.Executable(_patchelf())
-
-    rpaths = list()
+    output = ''
     try:
-        output = patchelf('--print-rpath', '%s' %
-                          path_name, output=str, error=str)
-        rpaths = output.rstrip('\n').split(':')
+        output = patchelf('--print-rpath', path, output=str, error=str)
+        output = output.strip('\n')
     except executable.ProcessError as e:
-        msg = 'patchelf --print-rpath %s produced an error %s' % (path_name, e)
-        tty.warn(msg)
-    return rpaths
+        msg = 'patchelf --print-rpath {0} produced an error [{1}]'
+        tty.warn(msg.format(path, str(e)))
+
+    return output.split(':') if output else []
 
 
-def get_relative_elf_rpaths(path_name, orig_layout_root, orig_rpaths):
+def _make_relative(reference_file, path_root, paths):
+    """Return a list where any path in ``paths`` that starts with
+    ``path_root`` is made relative to the directory in which the
+    reference file is stored.
+
+    After a path is made relative it is prefixed with the ``$ORIGIN``
+    string.
+
+    Args:
+        reference_file (str): file from which the reference directory
+            is computed
+        path_root (str): root of the relative paths
+        paths: paths to be examined
+
+    Returns:
+        List of relative paths
     """
-    Replaces orig rpath with relative path from dirname(path_name) if an rpath
-    in orig_rpaths contains orig_layout_root. Prefixes $ORIGIN
-    to relative paths and returns replacement rpaths.
-    """
-    rel_rpaths = []
-    for rpath in orig_rpaths:
-        if re.match(orig_layout_root, rpath):
-            rel = os.path.relpath(rpath, start=os.path.dirname(path_name))
-            rel_rpaths.append(os.path.join('$ORIGIN', '%s' % rel))
-        else:
-            rel_rpaths.append(rpath)
-    return rel_rpaths
+    # Check prerequisites of the function
+    msg = "{0} is not a file".format(reference_file)
+    assert os.path.isfile(reference_file), msg
+
+    start_directory = os.path.dirname(reference_file)
+    pattern = re.compile(path_root)
+    relative_paths = []
+
+    for path in paths:
+        if pattern.match(path):
+            rel = os.path.relpath(path, start=start_directory)
+            path = os.path.join('$ORIGIN', rel)
+
+        relative_paths.append(path)
+
+    return relative_paths
 
 
-def get_normalized_elf_rpaths(orig_path_name, rel_rpaths):
+def _normalize_relative_paths(start_path, relative_paths):
+    """Normalize the relative paths with respect to the original path name
+    of the file (``start_path``).
+
+    The paths that are passed to this function existed or were relevant
+    on another filesystem, so os.path.abspath cannot be used.
+
+    A relative path may contain the signifier $ORIGIN. Assuming that
+    ``start_path`` is absolute, this implies that the relative path
+    (relative to start_path) should be replaced with an absolute path.
+
+    Args:
+        start_path (str): path from which the starting directory
+            is extracted
+        relative_paths (str): list of relative paths as obtained by a
+            call to :ref:`_make_relative`
+
+    Returns:
+        List of normalized paths
     """
-    Normalize the relative rpaths with respect to the original path name
-    of the file. If the rpath starts with $ORIGIN replace $ORIGIN with the
-    dirname of the original path name and then normalize the rpath.
-    A dictionary mapping relativized rpaths to normalized rpaths is returned.
-    """
-    norm_rpaths = list()
-    for rpath in rel_rpaths:
-        if rpath.startswith('$ORIGIN'):
-            sub = re.sub(re.escape('$ORIGIN'),
-                         os.path.dirname(orig_path_name),
-                         rpath)
-            norm = os.path.normpath(sub)
-            norm_rpaths.append(norm)
-        else:
-            norm_rpaths.append(rpath)
-    return norm_rpaths
+    normalized_paths = []
+    pattern = re.compile(re.escape('$ORIGIN'))
+    start_directory = os.path.dirname(start_path)
+
+    for path in relative_paths:
+        if path.startswith('$ORIGIN'):
+            sub = pattern.sub(start_directory, path)
+            path = os.path.normpath(sub)
+        normalized_paths.append(path)
+
+    return normalized_paths
 
 
-def set_placeholder(dirname):
-    """
-    return string of @'s with same length
-    """
+def _placeholder(dirname):
+    """String of  of @'s with same length of the argument"""
     return '@' * len(dirname)
 
 
@@ -592,7 +624,7 @@ def relocate_elf_binaries(path_names, old_layout_root, new_layout_root,
     rpath was in the old layout root, i.e. system paths are not replaced.
     """
     for path_name in path_names:
-        orig_rpaths = get_existing_elf_rpaths(path_name)
+        orig_rpaths = _elf_rpaths_for(path_name)
         new_rpaths = list()
         if rel:
             # get the file path in the old_prefix
@@ -600,14 +632,14 @@ def relocate_elf_binaries(path_names, old_layout_root, new_layout_root,
                                     path_name)
             # get the normalized rpaths in the old prefix using the file path
             # in the orig prefix
-            orig_norm_rpaths = get_normalized_elf_rpaths(orig_path_name,
+            orig_norm_rpaths = _normalize_relative_paths(orig_path_name,
                                                          orig_rpaths)
             # get the normalize rpaths in the new prefix
             norm_rpaths = elf_find_paths(orig_norm_rpaths, old_layout_root,
                                          prefix_to_prefix)
             # get the relativized rpaths in the new prefix
-            new_rpaths = get_relative_elf_rpaths(path_name, new_layout_root,
-                                                 norm_rpaths)
+            new_rpaths = _make_relative(path_name, new_layout_root,
+                                        norm_rpaths)
             modify_elf_object(path_name, new_rpaths)
         else:
             new_rpaths = elf_find_paths(orig_rpaths, old_layout_root,
@@ -652,10 +684,10 @@ def make_elf_binaries_relative(cur_path_names, orig_path_names,
     Replace old RPATHs with paths relative to old_dir in binary files
     """
     for cur_path, orig_path in zip(cur_path_names, orig_path_names):
-        orig_rpaths = get_existing_elf_rpaths(cur_path)
+        orig_rpaths = _elf_rpaths_for(cur_path)
         if orig_rpaths:
-            new_rpaths = get_relative_elf_rpaths(orig_path, old_layout_root,
-                                                 orig_rpaths)
+            new_rpaths = _make_relative(orig_path, old_layout_root,
+                                        orig_rpaths)
             modify_elf_object(cur_path, new_rpaths)
 
 
@@ -679,7 +711,7 @@ def relocate_links(linknames, old_layout_root, new_layout_root,
     link target is create by replacing the old install prefix with the new
     install prefix.
     """
-    placeholder = set_placeholder(old_layout_root)
+    placeholder = _placeholder(old_layout_root)
     link_names = [os.path.join(new_install_prefix, linkname)
                   for linkname in linknames]
     for link_name in link_names:
@@ -810,7 +842,7 @@ def file_is_relocatable(file, paths_to_relocate=None):
 
     if platform.system().lower() == 'linux':
         if m_subtype == 'x-executable' or m_subtype == 'x-sharedlib':
-            rpaths = ':'.join(get_existing_elf_rpaths(file))
+            rpaths = ':'.join(_elf_rpaths_for(file))
             set_of_strings.discard(rpaths)
     if platform.system().lower() == 'darwin':
         if m_subtype == 'x-mach-binary':
diff --git a/lib/spack/spack/test/packaging.py b/lib/spack/spack/test/packaging.py
index 39da7c3ae5e..67c9e52875d 100644
--- a/lib/spack/spack/test/packaging.py
+++ b/lib/spack/spack/test/packaging.py
@@ -25,11 +25,9 @@
 from spack.fetch_strategy import URLFetchStrategy, FetchStrategyComposite
 from spack.relocate import needs_binary_relocation, needs_text_relocation
 from spack.relocate import relocate_text, relocate_links
-from spack.relocate import get_relative_elf_rpaths
-from spack.relocate import get_normalized_elf_rpaths
 from spack.relocate import macho_make_paths_relative
 from spack.relocate import macho_make_paths_normal
-from spack.relocate import set_placeholder, macho_find_paths
+from spack.relocate import _placeholder, macho_find_paths
 from spack.relocate import file_is_relocatable
 
 
@@ -228,7 +226,7 @@ def test_relocate_links(tmpdir):
         old_install_prefix = os.path.join(
             '%s' % old_layout_root, 'debian6', 'test')
         old_binname = os.path.join(old_install_prefix, 'binfile')
-        placeholder = set_placeholder(old_layout_root)
+        placeholder = _placeholder(old_layout_root)
         re.sub(old_layout_root, placeholder, old_binname)
         filenames = ['link.ln', 'outsideprefix.ln']
         new_layout_root = os.path.join(
@@ -561,15 +559,3 @@ def test_macho_make_paths():
                    '/Users/Shared/spack/pkgB/libB.dylib',
                    '/usr/local/lib/libloco.dylib':
                    '/usr/local/lib/libloco.dylib'}
-
-
-def test_elf_paths():
-    out = get_relative_elf_rpaths(
-        '/usr/bin/test', '/usr',
-        ('/usr/lib', '/usr/lib64', '/opt/local/lib'))
-    assert out == ['$ORIGIN/../lib', '$ORIGIN/../lib64', '/opt/local/lib']
-
-    out = get_normalized_elf_rpaths(
-        '/usr/bin/test',
-        ['$ORIGIN/../lib', '$ORIGIN/../lib64', '/opt/local/lib'])
-    assert out == ['/usr/lib', '/usr/lib64', '/opt/local/lib']
diff --git a/lib/spack/spack/test/relocate.py b/lib/spack/spack/test/relocate.py
index 0a9e9f7f0a3..a2bba52f401 100644
--- a/lib/spack/spack/test/relocate.py
+++ b/lib/spack/spack/test/relocate.py
@@ -89,6 +89,20 @@ def do_install_mock(self, **kwargs):
     return expected_path
 
 
+@pytest.fixture()
+def mock_patchelf(tmpdir):
+    import jinja2
+
+    def _factory(output):
+        f = tmpdir.mkdir('bin').join('patchelf')
+        t = jinja2.Template('#!/bin/bash\n{{ output }}\n')
+        f.write(t.render(output=output))
+        f.chmod(0o755)
+        return str(f)
+
+    return _factory
+
+
 @pytest.mark.requires_executables(
     '/usr/bin/gcc', 'patchelf', 'strings', 'file'
 )
@@ -140,3 +154,43 @@ def test_file_is_relocatable_errors(tmpdir):
 def test_search_patchelf(expected_patchelf_path):
     current = spack.relocate._patchelf()
     assert current == expected_patchelf_path
+
+
+@pytest.mark.parametrize('patchelf_behavior,expected', [
+    ('echo ', []),
+    ('echo /opt/foo/lib:/opt/foo/lib64', ['/opt/foo/lib', '/opt/foo/lib64']),
+    ('exit 1', [])
+])
+def test_existing_rpaths(patchelf_behavior, expected, mock_patchelf):
+    # Here we are mocking an executable that is always called "patchelf"
+    # because that will skip the part where we try to build patchelf
+    # by ourselves. The executable will output some rpaths like
+    # `patchelf --print-rpath` would.
+    path = mock_patchelf(patchelf_behavior)
+    rpaths = spack.relocate._elf_rpaths_for(path)
+    assert rpaths == expected
+
+
+@pytest.mark.parametrize('start_path,path_root,paths,expected', [
+    ('/usr/bin/test', '/usr', ['/usr/lib', '/usr/lib64', '/opt/local/lib'],
+     ['$ORIGIN/../lib', '$ORIGIN/../lib64', '/opt/local/lib'])
+])
+def test_make_relative_paths(start_path, path_root, paths, expected):
+    relatives = spack.relocate._make_relative(start_path, path_root, paths)
+    assert relatives == expected
+
+
+@pytest.mark.parametrize('start_path,relative_paths,expected', [
+    # $ORIGIN will be replaced with os.path.dirname('usr/bin/test')
+    # and then normalized
+    ('/usr/bin/test',
+     ['$ORIGIN/../lib', '$ORIGIN/../lib64', '/opt/local/lib'],
+     ['/usr/lib', '/usr/lib64', '/opt/local/lib']),
+    # Relative path without $ORIGIN
+    ('/usr/bin/test', ['../local/lib'], ['../local/lib']),
+])
+def test_normalize_relative_paths(start_path, relative_paths, expected):
+    normalized = spack.relocate._normalize_relative_paths(
+        start_path, relative_paths
+    )
+    assert normalized == expected

From 3ea21fef4b6d291dd3519f0deb85512399e4add9 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Mon, 27 Apr 2020 04:57:26 -0600
Subject: [PATCH 120/802] votca-csg: Block gromacs@2020 and newer (#16315)

---
 var/spack/repos/builtin/packages/votca-csg/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/votca-csg/package.py b/var/spack/repos/builtin/packages/votca-csg/package.py
index 0f0432d7020..918791c3375 100644
--- a/var/spack/repos/builtin/packages/votca-csg/package.py
+++ b/var/spack/repos/builtin/packages/votca-csg/package.py
@@ -30,5 +30,5 @@ class VotcaCsg(CMakePackage):
     for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "master"]:
         depends_on('votca-tools@%s' % v, when="@%s:%s.0" % (v, v))
     depends_on("boost")
-    depends_on("gromacs~mpi@5.1:")
+    depends_on("gromacs~mpi@5.1:2019.9999")
     depends_on("hdf5~mpi")

From 35717b556b2a49e67c3480c6c55bd99ac4cc9946 Mon Sep 17 00:00:00 2001
From: asmaahassan90 <31959389+asmaahassan90@users.noreply.github.com>
Date: Mon, 27 Apr 2020 13:26:10 +0200
Subject: [PATCH 121/802] spglib: added libs property (#16318)

---
 var/spack/repos/builtin/packages/spglib/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/repos/builtin/packages/spglib/package.py b/var/spack/repos/builtin/packages/spglib/package.py
index e832b85eab1..dff137ef036 100644
--- a/var/spack/repos/builtin/packages/spglib/package.py
+++ b/var/spack/repos/builtin/packages/spglib/package.py
@@ -18,3 +18,8 @@ class Spglib(CMakePackage):
 
     version('1.10.3', sha256='43776b5fb220b746d53c1aa39d0230f304687ec05984671392bccaf850d9d696')
     version('1.10.0', sha256='117fff308731784bea2ddaf3d076f0ecbf3981b31ea1c1bfd5ce4f057a5325b1')
+
+    @property
+    def libs(self):
+        return find_libraries(['libsymspg'], root=self.prefix.lib,
+                              recursive=False)

From 0477f829a2371c1dec18c10d6af6c0550fa16158 Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Mon, 27 Apr 2020 20:33:28 +0900
Subject: [PATCH 122/802] xabclib: added package at v1.03 (#16271)

---
 .../repos/builtin/packages/xabclib/package.py | 60 +++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/xabclib/package.py

diff --git a/var/spack/repos/builtin/packages/xabclib/package.py b/var/spack/repos/builtin/packages/xabclib/package.py
new file mode 100644
index 00000000000..3a851b21afd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xabclib/package.py
@@ -0,0 +1,60 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Xabclib(MakefilePackage):
+    """
+    Xabclib (eXtended ABCLib) is a numerical library with auto-tuning facility.
+    """
+
+    homepage = "http://www.abc-lib.org/Xabclib/index.html"
+    url      = "http://www.abc-lib.org/Xabclib/Release/Xabclib-v1.03.tar.gz"
+
+    version('1.03', sha256='9d200f40f1db87abc26cfe75a22db3a6d972988a28fc0ce8421a0c88cc574d1a')
+
+    def edit(self, spec, prefix):
+        cc = [spack_cc, '-O3', self.compiler.openmp_flag]
+        fc = [spack_fc, '-O3', self.compiler.openmp_flag]
+        if spec.satisfies('%gcc'):
+            fc.extend(['-ffixed-form', '-cpp'])
+        filter_file(
+            '^rm libOpenAT.a$',
+            'rm -f libOpenAT.a',
+            'make.all'
+        )
+        for makefile in find('.', 'makefile', recursive=True):
+            m = FileFilter(makefile)
+            m.filter(
+                'F90 += .*$',
+                'F90 = {0}'.format(' '.join(fc))
+            )
+            m.filter(
+                'F90O3 += .*$',
+                'F90O3 = {0}'.format(' '.join(fc))
+            )
+            m.filter(
+                'CC += .*$',
+                'CC = {0}'.format(' '.join(cc))
+            )
+            m.filter(
+                'LD += .*$',
+                'LD = {0}'.format(' '.join(fc))
+            )
+
+    def build(self, spec, prefix):
+        sh = which('sh')
+        sh('./make.all')
+
+    def install(self, spec, prefix):
+        mkdir(prefix.lib)
+        mkdir(prefix.doc)
+        install('libOpenAT.a', prefix.lib)
+        install('Readme.pdf', prefix.doc)
+
+    @property
+    def libs(self):
+        return find_libraries('libOpenAT', self.prefix.lib, shared=False)

From 3f54e73025455c0f3c671e959846757a69002f25 Mon Sep 17 00:00:00 2001
From: George Hartzell <hartzell@alerce.com>
Date: Mon, 27 Apr 2020 04:41:04 -0700
Subject: [PATCH 123/802] singularity: better info re post-install step
 (#16311)

The singularity info should actually suggest where you might find the info about the post-install steps.

Co-authored-by: george.hartzell <george.hartzell@sana.com>
---
 var/spack/repos/builtin/packages/singularity/package.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/singularity/package.py b/var/spack/repos/builtin/packages/singularity/package.py
index 8931e270da5..e7e69fa7327 100644
--- a/var/spack/repos/builtin/packages/singularity/package.py
+++ b/var/spack/repos/builtin/packages/singularity/package.py
@@ -17,7 +17,10 @@ class Singularity(MakefilePackage):
        which has a different install base (Autotools).
 
        Needs post-install chmod/chown steps to enable full functionality.
-       See package definition or `spack-build-out.txt` build log for details.
+       See package definition or `spack-build-out.txt` build log for details,
+       e.g.
+
+       tail -15 $(spack location -i singularity)/.spack/spack-build-out.txt
     '''
 
     homepage = "https://www.sylabs.io/singularity/"

From fe46919e198fdd598f056861c899a31ba2e8c548 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Mon, 27 Apr 2020 16:54:49 +0200
Subject: [PATCH 124/802] tulip: added new package at v5.4.0 (#16319)

closes #3479

Co-authored-by: Kate Isaacs <kisaacs@cs.arizona.edu>

Co-authored-by: Kate Isaacs <kisaacs@cs.arizona.edu>
---
 .../repos/builtin/packages/tulip/package.py   | 42 +++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/tulip/package.py

diff --git a/var/spack/repos/builtin/packages/tulip/package.py b/var/spack/repos/builtin/packages/tulip/package.py
new file mode 100644
index 00000000000..77d010222db
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tulip/package.py
@@ -0,0 +1,42 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class Tulip(CMakePackage):
+    """ Tulip is an information visualization framework dedicated to the
+    analysis and visualization of relational data.
+
+    Tulip aims to provide the developer with a complete library, supporting
+    the design of interactive information visualization applications for
+    relational data that can be tailored to the problems he or she is
+    addressing.
+    """
+
+    homepage = "https://tulip.labri.fr"
+    url = "https://sourceforge.net/projects/auber/files/tulip/tulip-5.4.0/tulip-5.4.0_src.tar.gz"
+
+    version('5.4.0', sha256='2175e4e1a79028ab7a2479e882242f304fd3e01fedf80e1f29f8f5e9a6eb1325')
+
+    extends('python')
+    depends_on('py-pyqt5', type=('build', 'run'))
+
+    depends_on('yajl')
+    depends_on('qt')
+    depends_on('qhull')
+    depends_on('freetype')
+    depends_on('zlib')
+    depends_on('glew')
+    depends_on('jpeg')
+    depends_on('libpng')
+    depends_on('libxml2')
+
+    def cmake_args(self):
+        # The use of GL/glu.h seems to be deprecated, see:
+        # https://github.com/nigels-com/glew/issues/192
+        return [
+            '-DCMAKE_CXX_FLAGS="-DGLEW_NO_GLU"',
+            '-DCMAKE_C_FLAGS="-DGLEW_NO_GLU"',
+            '-DTULIP_BUILD_DOC:BOOL=OFF'
+        ]

From 81b5475f8e6045d22298df191786c54bdbbbde13 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Mon, 27 Apr 2020 22:55:35 +0800
Subject: [PATCH 125/802] Add new package: smartdenovo (#16310)

---
 .../packages/smartdenovo/aarch64.patch        | 29 ++++++++++++++++++
 .../builtin/packages/smartdenovo/package.py   | 30 +++++++++++++++++++
 2 files changed, 59 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/smartdenovo/aarch64.patch
 create mode 100644 var/spack/repos/builtin/packages/smartdenovo/package.py

diff --git a/var/spack/repos/builtin/packages/smartdenovo/aarch64.patch b/var/spack/repos/builtin/packages/smartdenovo/aarch64.patch
new file mode 100644
index 00000000000..998c9b2cdf3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/smartdenovo/aarch64.patch
@@ -0,0 +1,29 @@
+diff --git a/Makefile b/Makefile
+index 0802f65..3816b6e 100644
+--- a/Makefile
++++ b/Makefile
+@@ -2,9 +2,9 @@ VERSION=1.0.0
+ MINOR_VER=20140314
+ CC=gcc
+ ifdef DEBUG
+-CFLAGS=-g3 -W -Wall -O0 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3
++CFLAGS=-g3 -W -Wall -O0 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
+ else
+-CFLAGS=-W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3
++CFLAGS=-W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
+ endif
+ INSTALLDIR=/usr/local/bin
+ GLIBS=-lm -lpthread
+diff --git a/ksw.c b/ksw.c
+index 15dd0f2..22641ed 100644
+--- a/ksw.c
++++ b/ksw.c
+@@ -25,7 +25,7 @@
+ 
+ #include <stdlib.h>
+ #include <stdint.h>
+-#include <emmintrin.h>
++#include "SSE2NEON.h"
+ #include "ksw.h"
+ 
+ #ifdef USE_MALLOC_WRAPPERS
diff --git a/var/spack/repos/builtin/packages/smartdenovo/package.py b/var/spack/repos/builtin/packages/smartdenovo/package.py
new file mode 100644
index 00000000000..f18b8583d9d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/smartdenovo/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Smartdenovo(MakefilePackage):
+    """SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore
+    (ONT) data."""
+
+    homepage = "https://github.com/ruanjue/smartdenovo"
+    git      = "https://github.com/ruanjue/smartdenovo.git"
+
+    version('master', branch='master')
+
+    depends_on('sse2neon', when='target=aarch64:')
+
+    patch('aarch64.patch', when='target=aarch64:',
+        sha256='7dd4bca28aafb0680cc1823aa58ac9000819993538e92628554666c4b3acc470')
+
+    def install(self, spec, prefix):
+        install_files = [
+            'pairaln', 'wtpre', 'wtcyc', 'wtmer', 'wtzmo', 'wtobt',
+            'wtclp', 'wtext', 'wtgbo', 'wtlay', 'wtcns', 'wtmsa'
+        ]
+        mkdirp(prefix.bin)
+        for f in install_files:
+            install(f, prefix.bin)

From 5938499be7ffff509a031c6a103c87455ce0318a Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Mon, 27 Apr 2020 23:55:07 +0800
Subject: [PATCH 126/802] Add new package: stinger (#16316)

---
 .../repos/builtin/packages/stinger/package.py | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/stinger/package.py

diff --git a/var/spack/repos/builtin/packages/stinger/package.py b/var/spack/repos/builtin/packages/stinger/package.py
new file mode 100644
index 00000000000..fe78dc015c6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/stinger/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Stinger(CMakePackage):
+    """The STINGER in-memory graph store and dynamic graph analysis
+    platform. Millions to billions of vertices and edges at thousands
+    to millions of updates per second."""
+
+    homepage = "http://www.stingergraph.com/"
+    git      = "https://github.com/stingergraph/stinger.git"
+
+    version('master', branch='master')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        with working_dir(self.build_directory):
+            install_tree('./bin', prefix.bin)
+            install_tree('./lib', prefix.lib)
+            install_tree('./include', prefix.include)
+            install_tree('./share', prefix.share)

From d59f7398a3cf89a1e55e4e339cf77834aa0dea91 Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Tue, 28 Apr 2020 00:57:14 +0900
Subject: [PATCH 127/802] MODYLAS: New package (#16317)

---
 .../builtin/packages/modylas/gcc_format.patch |  13 +
 .../builtin/packages/modylas/makefile.patch   | 418 ++++++++++++++++++
 .../repos/builtin/packages/modylas/package.py |  46 ++
 3 files changed, 477 insertions(+)
 create mode 100755 var/spack/repos/builtin/packages/modylas/gcc_format.patch
 create mode 100755 var/spack/repos/builtin/packages/modylas/makefile.patch
 create mode 100644 var/spack/repos/builtin/packages/modylas/package.py

diff --git a/var/spack/repos/builtin/packages/modylas/gcc_format.patch b/var/spack/repos/builtin/packages/modylas/gcc_format.patch
new file mode 100755
index 00000000000..086c4275aac
--- /dev/null
+++ b/var/spack/repos/builtin/packages/modylas/gcc_format.patch
@@ -0,0 +1,13 @@
+diff --git a/source/src/parse_f.f b/source/src/parse_f.f
+index c58f90e..37821dd 100644
+--- a/source/src/parse_f.f
++++ b/source/src/parse_f.f
+@@ -360,7 +360,7 @@
+          stop
+       endif
+ 
+- 9000 format('ERROR: the order of atoms is wrong:',i)
++ 9000 format('ERROR: the order of atoms is wrong:',i8)
+ 
+       return
+       end
diff --git a/var/spack/repos/builtin/packages/modylas/makefile.patch b/var/spack/repos/builtin/packages/modylas/makefile.patch
new file mode 100755
index 00000000000..b308306ff5e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/modylas/makefile.patch
@@ -0,0 +1,418 @@
+diff --git a/source/src/Makefile.am b/source/src/Makefile.am
+index 5a41380..1807821 100644
+--- a/source/src/Makefile.am
++++ b/source/src/Makefile.am
+@@ -21,6 +21,7 @@ modylas_mdtrj2xyz_SOURCES = version.f fmodules.f MAP_module.f \
+                            parse_f.f parse_input.f mdff.f
+ if HAVE_MPI
+ bin_PROGRAMS += modylas
++FCFLAGS += -DMPIPARA
+ endif
+ FCCOMPILE = $(FC) $(AM_FCFLAGS) $(FCFLAGS)
+ FCLD = $(FC)
+diff --git a/source/src/Makefile.in b/source/src/Makefile.in
+index c0f5dca..7c1988f 100644
+--- a/source/src/Makefile.in
++++ b/source/src/Makefile.in
+@@ -1,9 +1,8 @@
+-# Makefile.in generated by automake 1.11.1 from Makefile.am.
++# Makefile.in generated by automake 1.16.1 from Makefile.am.
+ # @configure_input@
+ 
+-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+-# Inc.
++# Copyright (C) 1994-2018 Free Software Foundation, Inc.
++
+ # This Makefile.in is free software; the Free Software Foundation
+ # gives unlimited permission to copy and/or distribute it,
+ # with or without modifications, as long as this notice is preserved.
+@@ -16,6 +15,61 @@
+ @SET_MAKE@
+ 
+ VPATH = @srcdir@
++am__is_gnu_make = { \
++  if test -z '$(MAKELEVEL)'; then \
++    false; \
++  elif test -n '$(MAKE_HOST)'; then \
++    true; \
++  elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
++    true; \
++  else \
++    false; \
++  fi; \
++}
++am__make_running_with_option = \
++  case $${target_option-} in \
++      ?) ;; \
++      *) echo "am__make_running_with_option: internal error: invalid" \
++              "target option '$${target_option-}' specified" >&2; \
++         exit 1;; \
++  esac; \
++  has_opt=no; \
++  sane_makeflags=$$MAKEFLAGS; \
++  if $(am__is_gnu_make); then \
++    sane_makeflags=$$MFLAGS; \
++  else \
++    case $$MAKEFLAGS in \
++      *\\[\ \	]*) \
++        bs=\\; \
++        sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
++          | sed "s/$$bs$$bs[$$bs $$bs	]*//g"`;; \
++    esac; \
++  fi; \
++  skip_next=no; \
++  strip_trailopt () \
++  { \
++    flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
++  }; \
++  for flg in $$sane_makeflags; do \
++    test $$skip_next = yes && { skip_next=no; continue; }; \
++    case $$flg in \
++      *=*|--*) continue;; \
++        -*I) strip_trailopt 'I'; skip_next=yes;; \
++      -*I?*) strip_trailopt 'I';; \
++        -*O) strip_trailopt 'O'; skip_next=yes;; \
++      -*O?*) strip_trailopt 'O';; \
++        -*l) strip_trailopt 'l'; skip_next=yes;; \
++      -*l?*) strip_trailopt 'l';; \
++      -[dEDm]) skip_next=yes;; \
++      -[JT]) skip_next=yes;; \
++    esac; \
++    case $$flg in \
++      *$$target_option*) has_opt=yes; break;; \
++    esac; \
++  done; \
++  test $$has_opt = yes
++am__make_dryrun = (target_option=n; $(am__make_running_with_option))
++am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
+ pkgdatadir = $(datadir)/@PACKAGE@
+ pkgincludedir = $(includedir)/@PACKAGE@
+ pkglibdir = $(libdir)/@PACKAGE@
+@@ -35,13 +89,13 @@ POST_UNINSTALL = :
+ bin_PROGRAMS = modylas-text2bin$(EXEEXT) modylas-mdtrj2xyz$(EXEEXT) \
+ 	$(am__EXEEXT_1)
+ @HAVE_MPI_TRUE@am__append_1 = modylas
++@HAVE_MPI_TRUE@am__append_2 = -DMPIPARA
+ subdir = src
+-DIST_COMMON = $(srcdir)/Doxyfile.in $(srcdir)/Makefile.am \
+-	$(srcdir)/Makefile.in
+ ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+ am__aclocal_m4_deps = $(top_srcdir)/configure.in
+ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ 	$(ACLOCAL_M4)
++DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)
+ mkinstalldirs = $(install_sh) -d
+ CONFIG_HEADER = $(top_builddir)/config.h
+ CONFIG_CLEAN_FILES = Doxyfile
+@@ -80,18 +134,62 @@ am_modylas_text2bin_OBJECTS = version.$(OBJEXT) fmodules.$(OBJEXT) \
+ 	mdff.$(OBJEXT)
+ modylas_text2bin_OBJECTS = $(am_modylas_text2bin_OBJECTS)
+ modylas_text2bin_LDADD = $(LDADD)
++AM_V_P = $(am__v_P_@AM_V@)
++am__v_P_ = $(am__v_P_@AM_DEFAULT_V@)
++am__v_P_0 = false
++am__v_P_1 = :
++AM_V_GEN = $(am__v_GEN_@AM_V@)
++am__v_GEN_ = $(am__v_GEN_@AM_DEFAULT_V@)
++am__v_GEN_0 = @echo "  GEN     " $@;
++am__v_GEN_1 = 
++AM_V_at = $(am__v_at_@AM_V@)
++am__v_at_ = $(am__v_at_@AM_DEFAULT_V@)
++am__v_at_0 = @
++am__v_at_1 = 
+ DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)
+ F77COMPILE = $(F77) $(AM_FFLAGS) $(FFLAGS)
++AM_V_F77 = $(am__v_F77_@AM_V@)
++am__v_F77_ = $(am__v_F77_@AM_DEFAULT_V@)
++am__v_F77_0 = @echo "  F77     " $@;
++am__v_F77_1 = 
+ F77LD = $(F77)
++AM_V_F77LD = $(am__v_F77LD_@AM_V@)
++am__v_F77LD_ = $(am__v_F77LD_@AM_DEFAULT_V@)
++am__v_F77LD_0 = @echo "  F77LD   " $@;
++am__v_F77LD_1 = 
+ SOURCES = $(modylas_SOURCES) $(modylas_mdtrj2xyz_SOURCES) \
+ 	$(modylas_text2bin_SOURCES)
+ DIST_SOURCES = $(modylas_SOURCES) $(modylas_mdtrj2xyz_SOURCES) \
+ 	$(modylas_text2bin_SOURCES)
++am__can_run_installinfo = \
++  case $$AM_UPDATE_INFO_DIR in \
++    n|no|NO) false;; \
++    *) (install-info --version) >/dev/null 2>&1;; \
++  esac
++am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
++# Read a list of newline-separated strings from the standard input,
++# and print each of them once, without duplicates.  Input order is
++# *not* preserved.
++am__uniquify_input = $(AWK) '\
++  BEGIN { nonempty = 0; } \
++  { items[$$0] = 1; nonempty = 1; } \
++  END { if (nonempty) { for (i in items) print i; }; } \
++'
++# Make sure the list of sources is unique.  This is necessary because,
++# e.g., the same source file might be shared among _SOURCES variables
++# for different programs/libraries.
++am__define_uniq_tagged_files = \
++  list='$(am__tagged_files)'; \
++  unique=`for i in $$list; do \
++    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
++  done | $(am__uniquify_input)`
+ ETAGS = etags
+ CTAGS = ctags
++am__DIST_COMMON = $(srcdir)/Doxyfile.in $(srcdir)/Makefile.in
+ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ ACLOCAL = @ACLOCAL@
+ AMTAR = @AMTAR@
++AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
+ AUTOCONF = @AUTOCONF@
+ AUTOHEADER = @AUTOHEADER@
+ AUTOMAKE = @AUTOMAKE@
+@@ -109,7 +207,7 @@ ECHO_T = @ECHO_T@
+ EXEEXT = @EXEEXT@
+ F77 = @F77@
+ FC = @FC@
+-FCFLAGS = @FCFLAGS@
++FCFLAGS = @FCFLAGS@ $(am__append_2)
+ INSTALL = @INSTALL@
+ INSTALL_DATA = @INSTALL_DATA@
+ INSTALL_PROGRAM = @INSTALL_PROGRAM@
+@@ -127,6 +225,7 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+ PACKAGE_NAME = @PACKAGE_NAME@
+ PACKAGE_STRING = @PACKAGE_STRING@
+ PACKAGE_TARNAME = @PACKAGE_TARNAME@
++PACKAGE_URL = @PACKAGE_URL@
+ PACKAGE_VERSION = @PACKAGE_VERSION@
+ PATH_SEPARATOR = @PATH_SEPARATOR@
+ SET_MAKE = @SET_MAKE@
+@@ -186,7 +285,7 @@ modylas_SOURCES = version.f fmodules.f main_f90.f parse_f.f app_f90.f \
+ 				  diagonal.f matrix_inverse.f \
+ 				  comm.f comm_2.f comm_3.f comm_fmm.f \
+ 				  opt_integrate.f  position_constrain.f \
+-				  calc_center_of_mass.f  shake_rattle_com.f
++                                  calc_center_of_mass.f shake_rattle_com.f
+ 
+ modylas_text2bin_SOURCES = version.f fmodules.f MAP_module.f \
+                            modylas-text2bin.f \
+@@ -218,14 +317,13 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+ 	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \
+ 	$(am__cd) $(top_srcdir) && \
+ 	  $(AUTOMAKE) --foreign src/Makefile
+-.PRECIOUS: Makefile
+ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+ 	@case '$?' in \
+ 	  *config.status*) \
+ 	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+ 	  *) \
+-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
++	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles)'; \
++	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__maybe_remake_depfiles);; \
+ 	esac;
+ 
+ $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+@@ -240,14 +338,18 @@ Doxyfile: $(top_builddir)/config.status $(srcdir)/Doxyfile.in
+ 	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
+ install-binPROGRAMS: $(bin_PROGRAMS)
+ 	@$(NORMAL_INSTALL)
+-	test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
+ 	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
++	if test -n "$$list"; then \
++	  echo " $(MKDIR_P) '$(DESTDIR)$(bindir)'"; \
++	  $(MKDIR_P) "$(DESTDIR)$(bindir)" || exit 1; \
++	fi; \
+ 	for p in $$list; do echo "$$p $$p"; done | \
+ 	sed 's/$(EXEEXT)$$//' | \
+-	while read p p1; do if test -f $$p; \
+-	  then echo "$$p"; echo "$$p"; else :; fi; \
++	while read p p1; do if test -f $$p \
++	  ; then echo "$$p"; echo "$$p"; else :; fi; \
+ 	done | \
+-	sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
++	sed -e 'p;s,.*/,,;n;h' \
++	    -e 's|.*|.|' \
+ 	    -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
+ 	sed 'N;N;N;s,\n, ,g' | \
+ 	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
+@@ -268,22 +370,26 @@ uninstall-binPROGRAMS:
+ 	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+ 	files=`for p in $$list; do echo "$$p"; done | \
+ 	  sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
+-	      -e 's/$$/$(EXEEXT)/' `; \
++	      -e 's/$$/$(EXEEXT)/' \
++	`; \
+ 	test -n "$$list" || exit 0; \
+ 	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
+ 	cd "$(DESTDIR)$(bindir)" && rm -f $$files
+ 
+ clean-binPROGRAMS:
+ 	-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+-modylas$(EXEEXT): $(modylas_OBJECTS) $(modylas_DEPENDENCIES) 
++
++modylas$(EXEEXT): $(modylas_OBJECTS) $(modylas_DEPENDENCIES) $(EXTRA_modylas_DEPENDENCIES) 
+ 	@rm -f modylas$(EXEEXT)
+-	$(F77LINK) $(modylas_OBJECTS) $(modylas_LDADD) $(LIBS)
+-modylas-mdtrj2xyz$(EXEEXT): $(modylas_mdtrj2xyz_OBJECTS) $(modylas_mdtrj2xyz_DEPENDENCIES) 
++	$(AM_V_F77LD)$(F77LINK) $(modylas_OBJECTS) $(modylas_LDADD) $(LIBS)
++
++modylas-mdtrj2xyz$(EXEEXT): $(modylas_mdtrj2xyz_OBJECTS) $(modylas_mdtrj2xyz_DEPENDENCIES) $(EXTRA_modylas_mdtrj2xyz_DEPENDENCIES) 
+ 	@rm -f modylas-mdtrj2xyz$(EXEEXT)
+-	$(F77LINK) $(modylas_mdtrj2xyz_OBJECTS) $(modylas_mdtrj2xyz_LDADD) $(LIBS)
+-modylas-text2bin$(EXEEXT): $(modylas_text2bin_OBJECTS) $(modylas_text2bin_DEPENDENCIES) 
++	$(AM_V_F77LD)$(F77LINK) $(modylas_mdtrj2xyz_OBJECTS) $(modylas_mdtrj2xyz_LDADD) $(LIBS)
++
++modylas-text2bin$(EXEEXT): $(modylas_text2bin_OBJECTS) $(modylas_text2bin_DEPENDENCIES) $(EXTRA_modylas_text2bin_DEPENDENCIES) 
+ 	@rm -f modylas-text2bin$(EXEEXT)
+-	$(F77LINK) $(modylas_text2bin_OBJECTS) $(modylas_text2bin_LDADD) $(LIBS)
++	$(AM_V_F77LD)$(F77LINK) $(modylas_text2bin_OBJECTS) $(modylas_text2bin_LDADD) $(LIBS)
+ 
+ mostlyclean-compile:
+ 	-rm -f *.$(OBJEXT)
+@@ -292,31 +398,20 @@ distclean-compile:
+ 	-rm -f *.tab.c
+ 
+ .f.o:
+-	$(F77COMPILE) -c -o $@ $<
++	$(AM_V_F77)$(F77COMPILE) -c -o $@ $<
+ 
+ .f.obj:
+-	$(F77COMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+-
+-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
+-	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+-	unique=`for i in $$list; do \
+-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+-	  done | \
+-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+-	mkid -fID $$unique
+-tags: TAGS
+-
+-TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+-		$(TAGS_FILES) $(LISP)
++	$(AM_V_F77)$(F77COMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
++
++ID: $(am__tagged_files)
++	$(am__define_uniq_tagged_files); mkid -fID $$unique
++tags: tags-am
++TAGS: tags
++
++tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ 	set x; \
+ 	here=`pwd`; \
+-	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+-	unique=`for i in $$list; do \
+-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+-	  done | \
+-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
++	$(am__define_uniq_tagged_files); \
+ 	shift; \
+ 	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+ 	  test -n "$$unique" || unique=$$empty_fix; \
+@@ -328,15 +423,11 @@ TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+ 	      $$unique; \
+ 	  fi; \
+ 	fi
+-ctags: CTAGS
+-CTAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+-		$(TAGS_FILES) $(LISP)
+-	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+-	unique=`for i in $$list; do \
+-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+-	  done | \
+-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
++ctags: ctags-am
++
++CTAGS: ctags
++ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
++	$(am__define_uniq_tagged_files); \
+ 	test -z "$(CTAGS_ARGS)$$unique" \
+ 	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+ 	     $$unique
+@@ -345,11 +436,29 @@ GTAGS:
+ 	here=`$(am__cd) $(top_builddir) && pwd` \
+ 	  && $(am__cd) $(top_srcdir) \
+ 	  && gtags -i $(GTAGS_ARGS) "$$here"
++cscopelist: cscopelist-am
++
++cscopelist-am: $(am__tagged_files)
++	list='$(am__tagged_files)'; \
++	case "$(srcdir)" in \
++	  [\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
++	  *) sdir=$(subdir)/$(srcdir) ;; \
++	esac; \
++	for i in $$list; do \
++	  if test -f "$$i"; then \
++	    echo "$(subdir)/$$i"; \
++	  else \
++	    echo "$$sdir/$$i"; \
++	  fi; \
++	done >> $(top_builddir)/cscope.files
+ 
+ distclean-tags:
+ 	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+ 
+-distdir: $(DISTFILES)
++distdir: $(BUILT_SOURCES)
++	$(MAKE) $(AM_MAKEFLAGS) distdir-am
++
++distdir-am: $(DISTFILES)
+ 	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+ 	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+ 	list='$(DISTFILES)'; \
+@@ -396,10 +505,15 @@ install-am: all-am
+ 
+ installcheck: installcheck-am
+ install-strip:
+-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+-	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+-	  `test -z '$(STRIP)' || \
+-	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
++	if test -z '$(STRIP)'; then \
++	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
++	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
++	      install; \
++	else \
++	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
++	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
++	    "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
++	fi
+ mostlyclean-generic:
+ 
+ clean-generic:
+@@ -474,18 +588,21 @@ uninstall-am: uninstall-binPROGRAMS
+ 
+ .MAKE: install-am install-strip
+ 
+-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
+-	clean-generic ctags distclean distclean-compile \
+-	distclean-generic distclean-tags distdir dvi dvi-am html \
+-	html-am info info-am install install-am install-binPROGRAMS \
+-	install-data install-data-am install-dvi install-dvi-am \
+-	install-exec install-exec-am install-html install-html-am \
+-	install-info install-info-am install-man install-pdf \
+-	install-pdf-am install-ps install-ps-am install-strip \
+-	installcheck installcheck-am installdirs maintainer-clean \
+-	maintainer-clean-generic mostlyclean mostlyclean-compile \
+-	mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
+-	uninstall-am uninstall-binPROGRAMS
++.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
++	clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
++	distclean distclean-compile distclean-generic distclean-tags \
++	distdir dvi dvi-am html html-am info info-am install \
++	install-am install-binPROGRAMS install-data install-data-am \
++	install-dvi install-dvi-am install-exec install-exec-am \
++	install-html install-html-am install-info install-info-am \
++	install-man install-pdf install-pdf-am install-ps \
++	install-ps-am install-strip installcheck installcheck-am \
++	installdirs maintainer-clean maintainer-clean-generic \
++	mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
++	ps ps-am tags tags-am uninstall uninstall-am \
++	uninstall-binPROGRAMS
++
++.PRECIOUS: Makefile
+ 
+ parse_input.o: parse.o
+ parse.o: hash.o
diff --git a/var/spack/repos/builtin/packages/modylas/package.py b/var/spack/repos/builtin/packages/modylas/package.py
new file mode 100644
index 00000000000..1241d3a8ed1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/modylas/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Modylas(AutotoolsPackage):
+    """
+    The 'MOlecular DYnamics Software for LArge Systems' (MODYLAS) is
+    a general-purpose, molecular dynamics simulation program suited
+    to the simulation of very large physical, chemical,
+    and biological systems.
+    """
+
+    homepage = "https://www.modylas.org"
+    url      = "file://{0}/MODYLAS_1.0.4.tar.gz".format(os.getcwd())
+
+    version('1.0.4', 'e0b5cccf8e363c1182eced37aa31b06b1c5b1526da7d449a6142424ac4ea6311')
+
+    variant('mpi', default=True, description='Enable MPI support')
+
+    # to define MPIPARA when +mpi
+    patch('makefile.patch')
+    # fix no width I in format
+    patch('gcc_format.patch', when='%gcc')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('mpi', when='+mpi')
+
+    build_directory = 'source'
+    configure_directory = 'source'
+
+    def setup_build_environment(self, env):
+        if self.spec.satisfies('+mpi'):
+            env.set('FC', self.spec['mpi'].mpifc, force=True)
+        fflags = ['-O3', self.compiler.openmp_flag]
+        if self.spec.satisfies('%gcc'):
+            fflags.append('-cpp')
+        env.set('FCFLAGS', ' '.join(fflags))
+
+    def configure_args(self):
+        return self.enable_or_disable('mpi')

From eda886f62751d7493e1f0a28e76ef7e290766644 Mon Sep 17 00:00:00 2001
From: vvolkl <valentin.volkl@cern.ch>
Date: Mon, 27 Apr 2020 18:00:10 +0200
Subject: [PATCH 128/802] [dd4hep] url and other fixes (#16320)

---
 .../repos/builtin/packages/dd4hep/package.py  | 28 +++++++++++++++++--
 .../repos/builtin/packages/dd4hep/tbb2.patch  | 15 ++++++++++
 2 files changed, 41 insertions(+), 2 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/dd4hep/tbb2.patch

diff --git a/var/spack/repos/builtin/packages/dd4hep/package.py b/var/spack/repos/builtin/packages/dd4hep/package.py
index 6fd63f76c68..66242973256 100644
--- a/var/spack/repos/builtin/packages/dd4hep/package.py
+++ b/var/spack/repos/builtin/packages/dd4hep/package.py
@@ -16,15 +16,23 @@ class Dd4hep(CMakePackage):
        It distributed under the LGPLv3 License."""
 
     homepage = "https://dd4hep.web.cern.ch/dd4hep/"
+    url      = "https://github.com/AIDASoft/DD4hep/archive/v01-12-01.tar.gz"
     git      = "https://github.com/AIDASoft/DD4hep.git"
 
+    maintainers = ['vvolkl', 'drbenmorgan']
+
     version('master', branch='master')
-    version('1.11.0', commit='280c7d748d56a704699408ac8e57815d029b169a')
-    version('1.10.0', commit='9835d1813c07d9d5850d1e68276c0171d1726801')
+    version('1.12.1', sha256='85e8c775ec03c499ce10911e228342e757c81ce9ef2a9195cb253b85175a2e93')
+    version('1.12.0', sha256='133a1fb8ce0466d2482f3ebb03e60b3bebb9b2d3e33d14ba15c8fbb91706b398')
+    version('1.11.2', sha256='96a53dd26cb8df11c6dae54669fbc9cc3c90dd47c67e07b24be9a1341c95abc4')
+    version('1.11.1', sha256='d7902dd7f6744bbda92f6e303ad5a3410eec4a0d2195cdc86f6c1167e72893f0')
+    version('1.11.0', sha256='25643296f15f9d11ad4ad550b7c3b92e8974fc56f1ee8e4455501010789ae7b6')
+    version('1.10.0', sha256='1d6b5d1c368dc8bcedd9c61b7c7e1a44bad427f8bd34932516aff47c88a31d95')
 
     # Workarounds for various TBB issues in DD4hep v1.11
     # See https://github.com/AIDASoft/DD4hep/pull/613 .
     patch('tbb-workarounds.patch', when='@1.11.0')
+    patch('tbb2.patch', when='@1.12.1')
 
     variant('xercesc', default=False, description="Enable 'Detector Builders' based on XercesC")
     variant('geant4', default=False, description="Enable the simulation part based on Geant4")
@@ -40,6 +48,9 @@ class Dd4hep(CMakePackage):
     def cmake_args(self):
         spec = self.spec
         cxxstd = spec['root'].variants['cxxstd'].value
+        # root can be built with cxxstd=11, but dd4hep requires 14
+        if cxxstd == "11":
+            cxxstd = "14"
         args = [
             "-DCMAKE_CXX_STANDARD={0}".format(cxxstd),
             "-DDD4HEP_USE_XERCESC={0}".format(spec.satisfies('+xercesc')),
@@ -50,3 +61,16 @@ def cmake_args(self):
             "-DPYTHON_EXECUTABLE={0}".format(spec['python'].command.path),
         ]
         return args
+
+    def url_for_version(self, version):
+        # dd4hep releases are dashes and padded with a leading zero
+        # the patch version is omitted when 0
+        # so for example v01-12-01, v01-12 ...
+        major = (str(version[0]).zfill(2))
+        minor = (str(version[1]).zfill(2))
+        patch = (str(version[2]).zfill(2))
+        if version[2] == 0:
+            url = "https://github.com/AIDASoft/DD4hep/archive/v%s-%s.tar.gz" % (major, minor)
+        else:
+            url = "https://github.com/AIDASoft/DD4hep/archive/v%s-%s-%s.tar.gz" % (major, minor, patch)
+        return url
diff --git a/var/spack/repos/builtin/packages/dd4hep/tbb2.patch b/var/spack/repos/builtin/packages/dd4hep/tbb2.patch
new file mode 100644
index 00000000000..7e128f11943
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dd4hep/tbb2.patch
@@ -0,0 +1,15 @@
+diff --git a/DDDigi/src/DigiKernel.cpp b/DDDigi/src/DigiKernel.cpp
+index f2c2e86c..f168ef9b 100644
+--- a/DDDigi/src/DigiKernel.cpp
++++ b/DDDigi/src/DigiKernel.cpp
+@@ -273,7 +273,7 @@ void DigiKernel::submit(const DigiAction::Actors<DigiEventAc
+tion>& actions, Digi
+   if ( parallel )   {
+     tbb::task_group que;
+     for ( auto* i : actions )
+-      que.run(Wrapper(context, *i));
++      que.run(Wrapper(context, i));
+     que.wait();
+     goto print_stamp;
+   }
+

From 77812845b83311019daa01bb859afe944e4f2162 Mon Sep 17 00:00:00 2001
From: vvolkl <valentin.volkl@cern.ch>
Date: Mon, 27 Apr 2020 18:01:09 +0200
Subject: [PATCH 129/802] update podio version formatting (#16321)

* update podio version formatting

* [podio] formatting fixes
---
 .../repos/builtin/packages/podio/package.py   | 21 +++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/podio/package.py b/var/spack/repos/builtin/packages/podio/package.py
index bc7a6dab90e..14b4722cdbf 100644
--- a/var/spack/repos/builtin/packages/podio/package.py
+++ b/var/spack/repos/builtin/packages/podio/package.py
@@ -17,10 +17,10 @@ class Podio(CMakePackage):
     maintainers = ['vvolkl', 'drbenmorgan']
 
     version('master', branch='master')
-    version('00-10', sha256='b5b42770ec8b96bcd2748abc05669dd3e4d4cc84f81ed57d57d2eda1ade90ef2')
-    version('00-09-02', sha256='8234d1b9636029124235ef81199a1220968dcc7fdaeab81cdc96a47af332d240')
-    version('00-09', sha256='3cde67556b6b76fd2d004adfaa3b3b6173a110c0c209792bfdb5f9353e21076f')
-    version('00-08', sha256='9d035a7f5ebfae5279a17405003206853271af692f762e2bac8e73825f2af327')
+    version('0.10.0', sha256='b5b42770ec8b96bcd2748abc05669dd3e4d4cc84f81ed57d57d2eda1ade90ef2')
+    version('0.9.2', sha256='8234d1b9636029124235ef81199a1220968dcc7fdaeab81cdc96a47af332d240')
+    version('0.9.0', sha256='3cde67556b6b76fd2d004adfaa3b3b6173a110c0c209792bfdb5f9353e21076f')
+    version('0.8.0', sha256='9d035a7f5ebfae5279a17405003206853271af692f762e2bac8e73825f2af327')
 
     variant('build_type', default='Release',
             description='The build type to build',
@@ -56,3 +56,16 @@ def setup_dependent_build_environment(self, env, dependent_spec):
 
     def setup_dependent_run_environment(self, env, dependent_spec):
         env.set('PODIO', self.prefix)
+
+    def url_for_version(self, version):
+        # podio releases are dashes and padded with a leading zero
+        # the patch version is omitted when 0
+        # so for example v01-12-01, v01-12 ...
+        major = (str(version[0]).zfill(2))
+        minor = (str(version[1]).zfill(2))
+        patch = (str(version[2]).zfill(2))
+        if version[2] == 0:
+            url = "https://github.com/AIDASoft/podio/archive/v%s-%s.tar.gz" % (major, minor)
+        else:
+            url = "https://github.com/AIDASoft/podio/archive/v%s-%s-%s.tar.gz" % (major, minor, patch)
+        return url

From a277b96b3975cf4440e3296772c8b22e932b7512 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Mon, 27 Apr 2020 18:01:48 +0200
Subject: [PATCH 130/802] Make mariadb provide mysql-client... (#16322)

... as well as mariadb. Needed for ROOT.
---
 var/spack/repos/builtin/packages/mariadb/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/mariadb/package.py b/var/spack/repos/builtin/packages/mariadb/package.py
index 9d3f5153174..11df1fc7283 100644
--- a/var/spack/repos/builtin/packages/mariadb/package.py
+++ b/var/spack/repos/builtin/packages/mariadb/package.py
@@ -33,6 +33,7 @@ class Mariadb(CMakePackage):
             'operations in the mariadb client library.')
 
     provides('mariadb-client')
+    provides('mysql-client')
 
     depends_on('boost')
     depends_on('cmake@2.6:', type='build')

From 505a511af40509614d662c912264c125abf0d956 Mon Sep 17 00:00:00 2001
From: Benjamin Tovar <btovar@nd.edu>
Date: Mon, 27 Apr 2020 14:18:44 -0400
Subject: [PATCH 131/802] update cctools to version 7.1.3 (#16324)

---
 var/spack/repos/builtin/packages/cctools/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/cctools/package.py b/var/spack/repos/builtin/packages/cctools/package.py
index bf74c320ae6..3f7a27081b6 100644
--- a/var/spack/repos/builtin/packages/cctools/package.py
+++ b/var/spack/repos/builtin/packages/cctools/package.py
@@ -13,8 +13,9 @@ class Cctools(AutotoolsPackage):
     """
 
     homepage = "https://github.com/cooperative-computing-lab/cctools"
-    url      = "https://github.com/cooperative-computing-lab/cctools/archive/release/7.1.2.tar.gz"
+    url      = "https://github.com/cooperative-computing-lab/cctools/archive/release/7.1.3.tar.gz"
 
+    version('7.1.3', sha256='b937878ab429dda31bc692e5d9ffb402b9eb44bb674c07a934bb769cee4165ba')
     version('7.1.2', sha256='ca871e9fe245d047d4c701271cf2b868e6e3a170e8834c1887157ed855985131')
     version('7.1.0', sha256='84748245db10ff26c0c0a7b9fd3ec20fbbb849dd4aadc5e8531fd1671abe7a81')
     version('7.0.18', sha256='5b6f3c87ae68dd247534a5c073eb68cb1a60176a7f04d82699fbc05e649a91c2')

From 31eff3578fbd4591bbdfd98aacff4e63704145bc Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 27 Apr 2020 20:19:10 +0200
Subject: [PATCH 132/802] cmake added version 3.17.1 (#16326)

---
 var/spack/repos/builtin/packages/cmake/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index cc69eac5f77..833573bf80e 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -13,6 +13,7 @@ class Cmake(Package):
     url      = 'https://github.com/Kitware/CMake/releases/download/v3.15.5/cmake-3.15.5.tar.gz'
     maintainers = ['chuckatkins']
 
+    version('3.17.1',   sha256='3aa9114485da39cbd9665a0bfe986894a282d5f0882b1dea960a739496620727')
     version('3.17.0',   sha256='b74c05b55115eacc4fa2b77a814981dbda05cdc95a53e279fe16b7b272f00847')
     version('3.16.5',   sha256='5f760b50b8ecc9c0c37135fae5fbf00a2fef617059aa9d61c1bb91653e5a8bfc')
     version('3.16.2',   sha256='8c09786ec60ca2be354c29829072c38113de9184f29928eb9da8446a5f2ce6a9')

From 1c45153e00fe6c31a58736e781565fe094b5a433 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 27 Apr 2020 20:19:41 +0200
Subject: [PATCH 133/802] ecflow added version 4.12.0 (#16327)

---
 var/spack/repos/builtin/packages/ecflow/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/ecflow/package.py b/var/spack/repos/builtin/packages/ecflow/package.py
index 467076382f2..02bcb25ef11 100644
--- a/var/spack/repos/builtin/packages/ecflow/package.py
+++ b/var/spack/repos/builtin/packages/ecflow/package.py
@@ -18,6 +18,7 @@ class Ecflow(CMakePackage):
     homepage = 'https://confluence.ecmwf.int/display/ECFLOW/'
     url      = 'https://confluence.ecmwf.int/download/attachments/8650755/ecFlow-4.11.1-Source.tar.gz'
 
+    version('4.12.0', sha256='566b797e8d78e3eb93946b923ef540ac61f50d4a17c9203d263c4fd5c39ab1d1')
     version('4.11.1', sha256='b3bcc1255939f87b9ba18d802940e08c0cf6379ca6aeec1fef7bd169b0085d6c')
 
     variant('static_boost', default=False,

From a4b17b95036102cba5e662449217ec33d64c6df7 Mon Sep 17 00:00:00 2001
From: Brian Van Essen <vanessen1@llnl.gov>
Date: Mon, 27 Apr 2020 13:15:46 -0700
Subject: [PATCH 134/802] cuDNN: Help dependents find libs/includes on Power
 arch (#16128)

On Power architectures cuDNN will install in a target directory. This
sets cuDNN_ROOT to point to the subdirectory to help dependents use
this install.
---
 var/spack/repos/builtin/packages/cudnn/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/repos/builtin/packages/cudnn/package.py b/var/spack/repos/builtin/packages/cudnn/package.py
index 4491af18a88..74f5133d901 100644
--- a/var/spack/repos/builtin/packages/cudnn/package.py
+++ b/var/spack/repos/builtin/packages/cudnn/package.py
@@ -190,6 +190,11 @@ def url_for_version(self, version):
 
         return url.format(directory, cuda, ver)
 
+    def setup_run_environment(self, env):
+        if 'target=ppc64le: platform=linux' in self.spec:
+            env.set('cuDNN_ROOT', os.path.join(
+                self.prefix, 'targets', 'ppc64le-linux'))
+
     def install(self, spec, prefix):
         install_tree('.', prefix)
 

From 08e53b67f85a4a88dcddba272ae56c1d4e557489 Mon Sep 17 00:00:00 2001
From: "Mark W. Krentel" <krentel@rice.edu>
Date: Mon, 27 Apr 2020 16:04:02 -0500
Subject: [PATCH 135/802] hpcviewer: add version 2020.04 (#16332)

* hpcviewer: add version 2020.04

* ibm-java: add version 8.0.6.7
---
 var/spack/repos/builtin/packages/hpcviewer/package.py | 6 ++++++
 var/spack/repos/builtin/packages/ibm-java/package.py  | 7 ++++++-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/hpcviewer/package.py b/var/spack/repos/builtin/packages/hpcviewer/package.py
index 97688963cfe..5399e42f6c8 100644
--- a/var/spack/repos/builtin/packages/hpcviewer/package.py
+++ b/var/spack/repos/builtin/packages/hpcviewer/package.py
@@ -37,6 +37,9 @@ class Hpcviewer(Package):
     maintainers = ['mwkrentel']
 
     viewer_sha = {
+        ('2020.04', 'x86_64'):  '5944c7b1e518b25d143df72b06a69cffb0bfc92186eb5efee2178fc2814a0b8b',
+        ('2020.04', 'ppc64'):   'ba60615a550aa77a17eb94272b62365a22298cebc6dc2cb7463686741e58d874',
+        ('2020.04', 'ppc64le'): '128494077979b447875ed730f1e8c5470fafcd52ae6debe61625031248d91f7c',
         ('2020.02', 'x86_64'):  'af1f514547a9325aee30eb891b31e38c7ea3f33d2d1978b44f83e7daa3d5de6b',
         ('2020.02', 'ppc64'):   '7bb4926202db663aedd5a6830778c5f73f6b08a65d56861824ea95ba83b1f59c',
         ('2020.02', 'ppc64le'): 'cfcebb7ba301affd6d21d2afd43c540e6dd4c5bc39b0d20e8bd1e4fed6aa3481',
@@ -64,6 +67,9 @@ class Hpcviewer(Package):
     }
 
     trace_sha = {
+        ('2020.04', 'x86_64'):  '695f7a06479c2b6958a6ebc3985b7ed777e7e126c04424ce980b224690f769f3',
+        ('2020.04', 'ppc64'):   '78cfadaf7bc6130cc4257241499b36f4f1c47f22d0daa29f5e733ca824a87b3c',
+        ('2020.04', 'ppc64le'): '28c225023accbc85a19c6d8fdcc14dae64a475ed5de2b94f18e58aab4edd2c09',
         ('2020.02', 'x86_64'):  'b7b634e91108aa50a2e8647ac6bac87df775ae38aff078545efaa84735e0a666',
         ('2020.02', 'ppc64'):   'a3e845901689e1b32bc6ab2826c6ac6ed352df4839090fa530b20f747e6e0957',
         ('2020.02', 'ppc64le'): 'a64a283f61e706d988952a7cede9fac0328b09d2d0b64e4c08acc54e38781c98',
diff --git a/var/spack/repos/builtin/packages/ibm-java/package.py b/var/spack/repos/builtin/packages/ibm-java/package.py
index df4b9d9c4e5..b2de7b1f159 100644
--- a/var/spack/repos/builtin/packages/ibm-java/package.py
+++ b/var/spack/repos/builtin/packages/ibm-java/package.py
@@ -10,15 +10,20 @@
 
 class IbmJava(Package):
     """Binary distribution of the IBM Java Software Development Kit
-    for big and little-endian powerpc (power7, 8 and 9)."""
+    for big and little-endian powerpc (power7, 8 and 9).  Note: IBM
+    is fairly aggressive about taking down old versions, so old
+    (and even current) versions may not be available."""
 
     homepage = "https://developer.ibm.com/javasdk/"
+    maintainers = ['mwkrentel']
 
     # Note: IBM is fairly aggressive about taking down old versions,
     # so we may need to update this frequently.  Also, old revs may
     # not be available for download.
 
     version_list = [
+        ('8.0.6.7',  'ppc64',   'a1accb461a039af4587ea86511e317fea1d423e7f781459a17ed3947afed2982'),
+        ('8.0.6.7',  'ppc64le', '9ede76a597af28c7f10c6f8a68788cc2dcd39fdab178c9bac56df8b3766ac717'),
         ('8.0.6.0',  'ppc64',   'e142746a83e47ab91d71839d5776f112ed154ae180d0628e3f10886151dad710'),
         ('8.0.6.0',  'ppc64le', '18c2eccf99225e6e7643141d8da4110cacc39f2fa00149fc26341d2272cc0102'),
         ('8.0.5.30', 'ppc64',   'd39ce321bdadd2b2b829637cacf9c1c0d90235a83ff6e7dcfa7078faca2f212f'),

From 8060bc6523f5f9fe5f4a0e29f77542dd2323b59b Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Mon, 27 Apr 2020 15:18:03 -0600
Subject: [PATCH 136/802] graphviz: add poppler support (#16331)

* graphviz: add poppler support

* graphviz: actually needs poppler+glib

* poopler: fix glib build, new version
---
 var/spack/repos/builtin/packages/graphviz/package.py | 5 ++++-
 var/spack/repos/builtin/packages/poppler/package.py  | 3 ++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py
index 5e9032b3881..0df127b00b1 100644
--- a/var/spack/repos/builtin/packages/graphviz/package.py
+++ b/var/spack/repos/builtin/packages/graphviz/package.py
@@ -55,6 +55,8 @@ class Graphviz(AutotoolsPackage):
             description='Build with libgd support (more output formats)')
     variant('pangocairo', default=False,
             description='Build with pango+cairo support (more output formats)')
+    variant('poppler', default=False,
+            description='Build with poppler support (pdf formats)')
     variant('qt', default=False,
             description='Build with Qt support')
     variant('quartz', default=(MACOS_VERSION is not None),
@@ -99,6 +101,7 @@ class Graphviz(AutotoolsPackage):
     depends_on('glib', when='+pangocairo')
     depends_on('libpng', when='+pangocairo')
     depends_on('pango', when='+pangocairo')
+    depends_on('poppler+glib', when='+poppler')
     depends_on('zlib')
     depends_on('qt', when='+qt')
     depends_on('libx11', when="+x")
@@ -147,7 +150,7 @@ def configure_args(self):
         args.append('--{0}-swig'.format('enable' if use_swig else 'disable'))
 
         for var in ["expat", "gts", "ghostscript", "libgd", "pangocairo",
-                    "qt", "quartz", "x"]:
+                    "poppler", "qt", "quartz", "x"]:
             args += self.with_or_without(var)
 
         args.append('--{0}-gtk'.format(
diff --git a/var/spack/repos/builtin/packages/poppler/package.py b/var/spack/repos/builtin/packages/poppler/package.py
index affb9e5359a..2848c81eb16 100644
--- a/var/spack/repos/builtin/packages/poppler/package.py
+++ b/var/spack/repos/builtin/packages/poppler/package.py
@@ -15,6 +15,7 @@ class Poppler(CMakePackage):
     git      = "https://gitlab.freedesktop.org/poppler/poppler.git"
 
     version('master', branch='master')
+    version('0.87.0', sha256='6f602b9c24c2d05780be93e7306201012e41459f289b8279a27a79431ad4150e')
     version('0.79.0', sha256='f985a4608fe592d2546d9d37d4182e502ff6b4c42f8db4be0a021a1c369528c8')
     version('0.77.0', sha256='7267eb4cbccd64a58244b8211603c1c1b6bf32c7f6a4ced2642865346102f36b')
     version('0.72.0', sha256='c1747eb8f26e9e753c4001ed951db2896edc1021b6d0f547a0bd2a27c30ada51')
@@ -48,7 +49,7 @@ class Poppler(CMakePackage):
     depends_on('openjpeg', when='+openjpeg')
     depends_on('qt@4.0:', when='+qt')
     depends_on('zlib', when='+zlib')
-    depends_on('cairo@1.10.0:', when='+glib')
+    depends_on('cairo+ft@1.10.0:', when='+glib')
     depends_on('iconv', when='+iconv')
     depends_on('jpeg', when='+jpeg')
     depends_on('libpng', when='+png')

From 204179eed386240ea9f28eda6d10ae3a981f8d39 Mon Sep 17 00:00:00 2001
From: Tim Haines <thaines.astro@gmail.com>
Date: Mon, 27 Apr 2020 19:26:28 -0500
Subject: [PATCH 137/802] elfutils: Add version 0.179 (#16334)

---
 var/spack/repos/builtin/packages/elfutils/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/elfutils/package.py b/var/spack/repos/builtin/packages/elfutils/package.py
index e32c68c60d9..651caf3d76d 100644
--- a/var/spack/repos/builtin/packages/elfutils/package.py
+++ b/var/spack/repos/builtin/packages/elfutils/package.py
@@ -17,10 +17,11 @@ class Elfutils(AutotoolsPackage, SourcewarePackage):
     version of elfutils."""
 
     homepage = "https://fedorahosted.org/elfutils/"
-    sourceware_mirror_path = "elfutils/0.178/elfutils-0.178.tar.bz2"
+    sourceware_mirror_path = "elfutils/0.179/elfutils-0.179.tar.bz2"
     list_url = "https://sourceware.org/elfutils/ftp"
     list_depth = 1
 
+    version('0.179', sha256='25a545566cbacaa37ae6222e58f1c48ea4570f53ba991886e2f5ce96e22a23a2')
     version('0.178', sha256='31e7a00e96d4e9c4bda452e1f2cdac4daf8abd24f5e154dee232131899f3a0f2')
     version('0.177', sha256='fa489deccbcae7d8c920f60d85906124c1989c591196d90e0fd668e3dc05042e')
     version('0.176', sha256='eb5747c371b0af0f71e86215a5ebb88728533c3a104a43d4231963f308cd1023')

From f314ff6639e895cadb95481d485e7cc71d123f39 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Mon, 27 Apr 2020 17:36:33 -0700
Subject: [PATCH 138/802] python : fix SSL for older Python versions (#16217)

* Fixed SSL pathing for older versions of Python (i.e. @:3.6.999).

* Fixed an issue where the 'python~ssl' variant wasn't properly being respected.

* Improved the '~ssl' patch by making it functional instead of diff-based (enables 3.X.Y patches).

* Fixed comment formatting to satisfy 'flake8' style requirements.
---
 .../repos/builtin/packages/python/package.py  | 48 +++++++++++++++----
 1 file changed, 40 insertions(+), 8 deletions(-)

diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index fd7438d605e..712216f491f 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -132,6 +132,9 @@ class Python(AutotoolsPackage):
     depends_on('readline', when='+readline')
     depends_on('ncurses', when='+readline')
     depends_on('openssl', when='+ssl')
+    # https://raw.githubusercontent.com/python/cpython/84471935ed2f62b8c5758fd544c7d37076fe0fa5/Misc/NEWS
+    # https://docs.python.org/3.5/whatsnew/changelog.html#python-3-5-4rc1
+    depends_on('openssl@:1.0.2z', when='@:2.7.13,3.0.0:3.5.2+ssl')
     depends_on('openssl@1.0.2:', when='@3.7:+ssl')  # https://docs.python.org/3/whatsnew/3.7.html#build-changes
     depends_on('sqlite@3.0.8:', when='+sqlite3')
     depends_on('gdbm', when='+dbm')  # alternatively ndbm or berkeley-db
@@ -196,17 +199,46 @@ def url_for_version(self, version):
         url = "https://www.python.org/ftp/python/{0}/Python-{1}.tgz"
         return url.format(re.split('[a-z]', str(version))[0], version)
 
-    @when('@2.7:2.8,3.4:')
+    # TODO: Ideally, these patches would be applied as separate '@run_before'
+    # functions enabled via '@when', but these two decorators don't work
+    # when used together. See: https://github.com/spack/spack/issues/12736
     def patch(self):
         # NOTE: Python's default installation procedure makes it possible for a
         # user's local configurations to change the Spack installation.  In
         # order to prevent this behavior for a full installation, we must
         # modify the installation script so that it ignores user files.
-        ff = FileFilter('Makefile.pre.in')
-        ff.filter(
-            r'^(.*)setup\.py(.*)((build)|(install))(.*)$',
-            r'\1setup.py\2 --no-user-cfg \3\6'
-        )
+        if self.spec.satisfies('@2.7:2.8,3.4:'):
+            ff = FileFilter('Makefile.pre.in')
+            ff.filter(
+                r'^(.*)setup\.py(.*)((build)|(install))(.*)$',
+                r'\1setup.py\2 --no-user-cfg \3\6'
+            )
+
+        # NOTE: Older versions of Python do not support the '--with-openssl'
+        # configuration option, so the installation's module setup file needs
+        # to be modified directly in order to point to the correct SSL path.
+        # See: https://stackoverflow.com/a/5939170
+        if self.spec.satisfies('@:3.6.999+ssl'):
+            ff = FileFilter(join_path('Modules', 'Setup.dist'))
+            ff.filter(r'^#(((SSL=)|(_ssl))(.*))$', r'\1')
+            ff.filter(r'^#((.*)(\$\(SSL\))(.*))$', r'\1')
+            ff.filter(
+                r'^SSL=(.*)$',
+                r'SSL={0}'.format(self.spec['openssl'].prefix)
+            )
+        # Because Python uses compiler system paths during install, it's
+        # possible to pick up a system OpenSSL when building 'python~ssl'.
+        # To avoid this scenario, we disable the 'ssl' module with patching.
+        elif self.spec.satisfies('@:3.6.999~ssl'):
+            ff = FileFilter('setup.py')
+            ff.filter(
+                r'^(\s+(ssl_((incs)|(libs)))\s+=\s+)(.*)$',
+                r'\1 None and \6'
+            )
+            ff.filter(
+                r'^(\s+(opensslv_h)\s+=\s+)(.*)$',
+                r'\1 None and \3'
+            )
 
     def setup_build_environment(self, env):
         spec = self.spec
@@ -291,8 +323,8 @@ def configure_args(self):
         if '+pic' in spec:
             config_args.append('CFLAGS={0}'.format(self.compiler.cc_pic_flag))
 
-        if spec.satisfies('@3.7:'):
-            if '+ssl' in spec:
+        if '+ssl' in spec:
+            if spec.satisfies('@3.7:'):
                 config_args.append('--with-openssl={0}'.format(
                     spec['openssl'].prefix))
 

From b04b6e14490e4bdb61457741d52bded336751618 Mon Sep 17 00:00:00 2001
From: asmaahassan90 <31959389+asmaahassan90@users.noreply.github.com>
Date: Tue, 28 Apr 2020 02:38:15 +0200
Subject: [PATCH 139/802] Add ShengBTE (#16154)

* Add ShengBTE

Adding a new package; ShengBTE. I tried adding it a MakefilePackage, and use build_directory = 'Src', but it was as if the build_directory gets ignored and make complains about target not found. and using the make funtion here instead of os.system, I get errors that config.f90 is not found which is already available under Src as well.

* more enhancmenets

fix lint; use mkl spec; use build_directory variable

* one more fix

* Use Makefile template

* Update var/spack/repos/builtin/packages/shengbte/package.py

use mkl instead of intel-mkl as a dependency

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/shengbte/package.py

update recipe as suggested by reviewer

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* enhance recipe

remove white space; changes as suggested by reviewer

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../builtin/packages/shengbte/package.py      | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/shengbte/package.py

diff --git a/var/spack/repos/builtin/packages/shengbte/package.py b/var/spack/repos/builtin/packages/shengbte/package.py
new file mode 100644
index 00000000000..59697a51cee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/shengbte/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+from spack import *
+
+
+class Shengbte(MakefilePackage):
+    """ShengBTE is a software package for solving the Boltzmann Transport
+    Equation for phonons."""
+
+    homepage = "www.shengbte.org"
+    url      = "www.shengbte.org/downloads/ShengBTE-v1.1.1-8a63749.tar.bz2"
+
+    version('1.1.1-8a63749', sha256='43920740d19ae854c8ecae0b648acfdf1d7726ca4c2b44f1a1684457f2f88522')
+
+    depends_on('mpi')
+    depends_on('spglib')
+    depends_on('mkl')
+
+    parallel = False
+
+    build_directory = 'Src'
+
+    def edit(self, spec, prefix):
+        arch_make = join_path(self.build_directory, 'arch.make')
+        copy('arch.make.example', arch_make)
+        filter_file('export FFLAGS=.*', 'export FFLAGS=-debug -O2', arch_make)
+        filter_file('export LDFLAGS=.*', 'export LDFLAGS=' + spec['spglib'].
+                    libs.ld_flags, arch_make)
+
+        filter_file('export MPIFC=.*', 'export MPIFC=%s' % spec['mpi'].mpifc,
+                    arch_make)
+        filter_file('LAPACK=.*', 'LAPACK=' + spec['mkl'].libs.ld_flags,
+                    arch_make)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('ShengBTE', prefix.bin)

From cd568829981bf62767b986df6fe9ff40d50500e0 Mon Sep 17 00:00:00 2001
From: Diego Magdaleno <38844659+DiegoMagdaleno@users.noreply.github.com>
Date: Mon, 27 Apr 2020 19:39:09 -0500
Subject: [PATCH 140/802] Add a new package Exa (#16126)

* Add new package exa

* Format and fix a silly typo

* Fix SHA256 SUM and make URL calculation dynamic

* Remove unnecessary URL calculation

* Update package.py

* Keep the version on 1 line

* Pass flake8 checks
---
 .../repos/builtin/packages/exa/package.py     | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/exa/package.py

diff --git a/var/spack/repos/builtin/packages/exa/package.py b/var/spack/repos/builtin/packages/exa/package.py
new file mode 100644
index 00000000000..e6a0fe39a4f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/exa/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Exa(Package):
+    """exa is a replacement for ls written in Rust."""
+
+    homepage = 'https://the.exa.website'
+    url = 'https://github.com/ogham/exa/archive/v0.9.0.tar.gz'
+
+    version('0.9.0', sha256='96e743ffac0512a278de9ca3277183536ee8b691a46ff200ec27e28108fef783')
+
+    depends_on('rust')
+
+    def install(self, spec, prefix):
+        cargo = which('cargo')
+        cargo('install', '--root', prefix, '--path', '.')

From f1a7fb2ffc16788aff261cfbd6f7558828dc6210 Mon Sep 17 00:00:00 2001
From: Diego Magdaleno <38844659+DiegoMagdaleno@users.noreply.github.com>
Date: Mon, 27 Apr 2020 19:40:35 -0500
Subject: [PATCH 141/802] Update bat and make the url dynamic (#16127)

* Update bat and make the url dynamic

- Now depending on the version it will calculate
the url

- This also fixes a weird issue that was reported
on Darwin, back when I reported that Rust wasn't
linking properly on Darwin #15887 on the comment
by hartzell i was also experiencing this issue

* Remove unnecessary stuff

- Removes the need for LLVM

- Removes the need for version calculation.

* Keep the versions on 1 line

* Pass flake8 tests
---
 var/spack/repos/builtin/packages/bat/package.py | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/var/spack/repos/builtin/packages/bat/package.py b/var/spack/repos/builtin/packages/bat/package.py
index 50c3b5349a0..0463580f8ff 100644
--- a/var/spack/repos/builtin/packages/bat/package.py
+++ b/var/spack/repos/builtin/packages/bat/package.py
@@ -9,9 +9,10 @@
 class Bat(Package):
     """A cat(1) clone with wings."""
 
-    homepage = "https://github.com/sharkdp/bat"
-    url      = "https://github.com/sharkdp/bat/archive/v0.10.0.tar.gz"
+    homepage = 'https://github.com/sharkdp/bat'
+    url = 'https://github.com/sharkdp/bat/archive/v0.13.0.tar.gz'
 
+    version('0.13.0', sha256='f4aee370013e2a3bc84c405738ed0ab6e334d3a9f22c18031a7ea008cd5abd2a')
     version('0.12.1', sha256='1dd184ddc9e5228ba94d19afc0b8b440bfc1819fef8133fe331e2c0ec9e3f8e2')
 
     depends_on('rust')
@@ -19,11 +20,3 @@ class Bat(Package):
     def install(self, spec, prefix):
         cargo = which('cargo')
         cargo('install', '--root', prefix, '--path', '.')
-
-    # cargo seems to need these to be set so that when it's building
-    # onig_sys it can run llvm-config and link against libclang.
-    def setup_build_environment(self, env):
-        env.append_flags('LLVM_CONFIG_PATH',
-                         join_path(self.spec['llvm'].prefix.libexec.llvm,
-                                   'llvm-config'))
-        env.append_flags('LIBCLANG_PATH', self.spec['llvm'].prefix.lib)

From f5a5a11c77a76939676a5bc2298fadc947091a9a Mon Sep 17 00:00:00 2001
From: "Dr. Christian Tacke"
 <58549698+ChristianTackeGSI@users.noreply.github.com>
Date: Tue, 28 Apr 2020 02:41:15 +0200
Subject: [PATCH 142/802] abseil-cpp: new Version, Build Shared Library
 (#16125)

* Add new version: "Abseil LTS branch, Feb 2020, Patch 1"
* Build shared libraries by default with new version
* Older versions do not support building shared libraries
---
 var/spack/repos/builtin/packages/abseil-cpp/package.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/var/spack/repos/builtin/packages/abseil-cpp/package.py b/var/spack/repos/builtin/packages/abseil-cpp/package.py
index 90fd6cbd879..c40b2353bf8 100644
--- a/var/spack/repos/builtin/packages/abseil-cpp/package.py
+++ b/var/spack/repos/builtin/packages/abseil-cpp/package.py
@@ -14,10 +14,18 @@ class AbseilCpp(CMakePackage):
 
     maintainers = ['jcftang']
 
+    version('20200225.1', sha256='0db0d26f43ba6806a8a3338da3e646bb581f0ca5359b3a201d8fb8e4752fd5f8')
     version('20190808', sha256='8100085dada279bf3ee00cd064d43b5f55e5d913be0dfe2906f06f8f28d5b37e')
     version('20181200', sha256='e2b53bfb685f5d4130b84c4f3050c81bf48c497614dc85d91dbd3ed9129bce6d')
     version('20180600', sha256='794d483dd9a19c43dc1fbbe284ce8956eb7f2600ef350dac4c602f9b4eb26e90')
 
+    variant('shared', default=True,
+            description='Build shared instead of static libraries')
+
+    conflicts('+shared', when='@:20190808')
+
     def cmake_args(self):
         args = ["-DBUILD_TESTING=OFF",  "-DCMAKE_CXX_STANDARD=11"]
+        args.append('-DBUILD_SHARED_LIBS:Bool={0}'.format(
+            'ON' if '+shared' in self.spec else 'OFF'))
         return args

From 3115b5c75886fc657209176cf55f6381f13a9ced Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tiziano=20M=C3=BCller?= <tiziano.mueller@chem.uzh.ch>
Date: Tue, 28 Apr 2020 02:42:33 +0200
Subject: [PATCH 143/802] CP2K: arch file improvements and blas-dependency
 simplification (#16074)

* cp2k: prettify arch-file, call pkg-config directly

this allows to re-use the arch-file without having to load the complete
Spack environment, for example after a dev-build

* cp2k: use consistency check instead of blas lib enum

this makes using other BLAS/LAPACK implementations possible without
explicitly adding support for them

* cp2k: add basic support for Cray and XL Compilers, correct Intel fp mode

* cp2k: add myself as maintainer

* cp2k: use "master" to denote the git version

* cp2k: use spack_cc/fc/cxx when possible, set CXX explicitly

* cp2k: set __MKL when using the MKL, not just the Intel compiler

* cp2k: drop self. when referencing spec where possible

* cp2k: add forgotten elpa+openmp dep

* cp2k: set C++14 for recent versions
---
 .../repos/builtin/packages/cp2k/package.py    | 204 +++++++++++-------
 1 file changed, 128 insertions(+), 76 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py
index 734b2c0aa3d..0a172d025fe 100644
--- a/var/spack/repos/builtin/packages/cp2k/package.py
+++ b/var/spack/repos/builtin/packages/cp2k/package.py
@@ -20,16 +20,16 @@ class Cp2k(MakefilePackage, CudaPackage):
     git = 'https://github.com/cp2k/cp2k.git'
     list_url = 'https://github.com/cp2k/cp2k/releases'
 
+    maintainers = ['dev-zero']
+
     version('7.1', sha256='ccd711a09a426145440e666310dd01cc5772ab103493c4ae6a3470898cd0addb')
     version('6.1', sha256='af803558e0a6b9e9d9ce8a3ab955ba32bacd179922455424e061c82c9fefa34b')
     version('5.1', sha256='e23613b593354fa82e0b8410e17d94c607a0b8c6d9b5d843528403ab09904412')
     version('4.1', sha256='4a3e4a101d8a35ebd80a9e9ecb02697fb8256364f1eccdbe4e5a85d31fe21343')
     version('3.0', sha256='1acfacef643141045b7cbade7006f9b7538476d861eeecd9658c9e468dc61151')
-    version('develop', branch='master', submodules="True")
+    version('master', branch='master', submodules="True")
 
     variant('mpi', default=True, description='Enable MPI support')
-    variant('blas', default='openblas', values=('openblas', 'mkl', 'accelerate'),
-            description='Enable the use of OpenBlas/MKL/Accelerate')
     variant('openmp', default=False, description='Enable OpenMP support')
     variant('smm', default='libxsmm', values=('libxsmm', 'libsmm', 'blas'),
             description='Library for small matrix multiplications')
@@ -73,18 +73,9 @@ class Cp2k(MakefilePackage, CudaPackage):
 
     depends_on('python', type='build')
 
-    depends_on('fftw@3:', when='~openmp')
-    depends_on('fftw@3:+openmp', when='+openmp')
-
-    # see #1712 for the reason to enumerate BLAS libraries here
-    depends_on('openblas threads=none', when='blas=openblas ~openmp')
-    depends_on('openblas threads=openmp', when='blas=openblas +openmp')
-    depends_on('lapack', when='blas=openblas ~openmp')
-
-    depends_on('intel-mkl', when="blas=mkl ~openmp")
-    depends_on('intel-mkl threads=openmp', when='blas=mkl +openmp')
-
-    conflicts('blas=accelerate', '+openmp')  # there is no Accelerate with OpenMP support
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('fftw-api@3')
 
     # require libxsmm-1.11+ since 1.10 can leak file descriptors in Fortran
     depends_on('libxsmm@1.11:~header-only', when='smm=libxsmm')
@@ -110,6 +101,7 @@ class Cp2k(MakefilePackage, CudaPackage):
     depends_on('cosma+cuda+scalapack', when='+cosma+cuda')
     depends_on('elpa@2011.12:2016.13+openmp', when='+openmp+elpa@:5.999')
     depends_on('elpa@2011.12:2017.11+openmp', when='+openmp+elpa@6.0:')
+    depends_on('elpa@2018.05:+openmp', when='+openmp+elpa@7.0:')
     depends_on('elpa@2011.12:2016.13~openmp', when='~openmp+elpa@:5.999')
     depends_on('elpa@2011.12:2017.11~openmp', when='~openmp+elpa@6.0:')
     depends_on('elpa@2018.05:~openmp', when='~openmp+elpa@7.0:')
@@ -150,9 +142,7 @@ class Cp2k(MakefilePackage, CudaPackage):
 
     # CP2K needs compiler specific compilation flags, e.g. optflags
     conflicts('%clang')
-    conflicts('%cray')
     conflicts('%nag')
-    conflicts('%xl')
 
     @property
     def makefile_architecture(self):
@@ -176,9 +166,42 @@ def makefile(self):
     def archive_files(self):
         return [os.path.join(self.stage.source_path, self.makefile)]
 
-    def edit(self, spec, prefix):
+    def consistency_check(self, spec):
+        """
+        Consistency checks.
+        Due to issue #1712 we can not put them into depends_on/conflicts.
+        """
 
-        fftw = spec['fftw:openmp' if '+openmp' in spec else 'fftw']
+        if '+openmp' in spec:
+            if '^openblas' in spec and '^openblas threads=openmp' not in spec:
+                raise InstallError(
+                    '^openblas threads=openmp required for cp2k+openmp'
+                    ' with openblas')
+
+            if '^fftw' in spec and '^fftw +openmp' not in spec:
+                raise InstallError(
+                    '^fftw +openmp required for cp2k+openmp'
+                    ' with fftw')
+
+            # MKL doesn't need to be checked since they are
+            # OMP thread-safe when using mkl_sequential
+            # BUT: we should check the version of MKL IF it is used for FFTW
+            #      since there we need at least v14 of MKL to be safe!
+
+    def edit(self, spec, prefix):
+        self.consistency_check(spec)
+
+        pkgconf = which('pkg-config')
+
+        if '^fftw' in spec:
+            fftw = spec['fftw:openmp' if '+openmp' in spec else 'fftw']
+            fftw_header_dir = fftw.headers.directories[0]
+        elif '^intel-mkl' in spec:
+            fftw = spec['intel-mkl']
+            fftw_header_dir = fftw.headers.directories[0] + '/fftw'
+        elif '^intel-parallel-studio+mkl' in spec:
+            fftw = spec['intel-parallel-studio']
+            fftw_header_dir = fftw.headers.directories[0] + '/fftw'
 
         optimization_flags = {
             'gcc': [
@@ -186,15 +209,17 @@ def edit(self, spec, prefix):
                 '-funroll-loops',
                 '-ftree-vectorize',
             ],
-            'intel': ['-O2', '-pc64', '-unroll'],
+            'intel': ['-O2', '-pc64', '-unroll', ],
             'pgi': ['-fast'],
+            'cray': ['-O2'],
+            'xl': ['-O3'],
         }
 
         dflags = ['-DNDEBUG']
         cppflags = [
             '-D__LIBINT',
             '-D__FFTW3',
-            fftw.headers.cpp_flags,
+            '-I{0}'.format(fftw_header_dir),
         ]
 
         if '@:6.9' in spec:
@@ -220,19 +245,24 @@ def edit(self, spec, prefix):
             cflags.append('-fp-model precise')
             cxxflags.append('-fp-model precise')
             fcflags += [
-                '-fp-model source',
+                '-fp-model precise',
                 '-heap-arrays 64',
                 '-g',
                 '-traceback',
             ]
         elif '%gcc' in spec:
-            fcflags.extend([
+            fcflags += [
                 '-ffree-form',
                 '-ffree-line-length-none',
                 '-ggdb',  # make sure we get proper Fortran backtraces
-            ])
+            ]
         elif '%pgi' in spec:
-            fcflags.extend(['-Mfreeform', '-Mextend'])
+            fcflags += ['-Mfreeform', '-Mextend']
+        elif '%cray' in spec:
+            fcflags += ['-emf', '-ffree', '-hflex_mp=strict']
+        elif '%xl' in spec:
+            fcflags += ['-qpreprocess', '-qstrict', '-q64']
+            ldflags += ['-Wl,--allow-multiple-definition']
 
         if '+openmp' in spec:
             cflags.append(self.compiler.openmp_flag)
@@ -241,6 +271,15 @@ def edit(self, spec, prefix):
             ldflags.append(self.compiler.openmp_flag)
             nvflags.append('-Xcompiler="{0}"'.format(
                 self.compiler.openmp_flag))
+        elif '%cray' in spec:  # Cray enables OpenMP by default
+            cflags   += ['-hnoomp']
+            cxxflags += ['-hnoomp']
+            fcflags  += ['-hnoomp']
+            ldflags  += ['-hnoomp']
+
+        if '@7:' in spec:  # recent versions of CP2K use C++14 CUDA code
+            cxxflags.append(self.compiler.cxx14_flag)
+            nvflags.append(self.compiler.cxx14_flag)
 
         ldflags.append(fftw.libs.search_flags)
 
@@ -257,8 +296,8 @@ def edit(self, spec, prefix):
                 os.path.join(spec['libint'].libs.directories[0], 'libint.a'),
             ])
         else:
-            fcflags += ['$(shell pkg-config --cflags libint2)']
-            libs += ['$(shell pkg-config --libs libint2)']
+            fcflags += pkgconf('--cflags', 'libint2', output=str).split()
+            libs += pkgconf('--libs', 'libint2', output=str).split()
 
         if '+plumed' in self.spec:
             dflags.extend(['-D__PLUMED2'])
@@ -268,15 +307,16 @@ def edit(self, spec, prefix):
                              'libplumed.{0}'.format(dso_suffix))
             ])
 
-        fc = self.compiler.fc if '~mpi' in spec else self.spec['mpi'].mpifc
+        cc = spack_cc if '~mpi' in spec else spec['mpi'].mpicc
+        cxx = spack_cxx if '~mpi' in spec else spec['mpi'].mpicxx
+        fc = spack_fc if '~mpi' in spec else spec['mpi'].mpifc
 
         # Intel
-        if '%intel' in self.spec:
+        if '%intel' in spec:
             cppflags.extend([
                 '-D__INTEL',
                 '-D__HAS_ISO_C_BINDING',
                 '-D__USE_CP2K_TRACE',
-                '-D__MKL'
             ])
             fcflags.extend([
                 '-diag-disable 8290,8291,10010,10212,11060',
@@ -290,9 +330,9 @@ def edit(self, spec, prefix):
         ldflags.append((lapack + blas).search_flags)
         libs.extend([str(x) for x in (fftw.libs, lapack, blas)])
 
-        if self.spec.variants['blas'].value == 'mkl':
+        if '^intel-mkl' in spec or '^intel-parallel-studio+mkl' in spec:
             cppflags += ['-D__MKL']
-        elif self.spec.variants['blas'].value == 'accelerate':
+        elif '^accelerate' in spec:
             cppflags += ['-D__ACCELERATE']
 
         if '+cosma' in spec:
@@ -302,7 +342,7 @@ def edit(self, spec, prefix):
             libs.extend(cosma)
 
         # MPI
-        if '+mpi' in self.spec:
+        if '+mpi' in spec:
             cppflags.extend([
                 '-D__parallel',
                 '-D__SCALAPACK'
@@ -312,7 +352,7 @@ def edit(self, spec, prefix):
             ldflags.append(scalapack.search_flags)
 
             libs.extend(scalapack)
-            libs.extend(self.spec['mpi:cxx'].libs)
+            libs.extend(spec['mpi:cxx'].libs)
             libs.extend(self.compiler.stdcxx_libs)
 
             if 'wannier90' in spec:
@@ -331,10 +371,10 @@ def edit(self, spec, prefix):
                 ldflags.append(libxc.libs.search_flags)
                 libs.append(str(libxc.libs))
             else:
-                fcflags += ['$(shell pkg-config --cflags libxcf03)']
-                libs += ['$(shell pkg-config --libs libxcf03)']
+                fcflags += pkgconf('--cflags', 'libxcf03', output=str).split()
+                libs += pkgconf('--libs', 'libxcf03', output=str).split()
 
-        if '+pexsi' in self.spec:
+        if '+pexsi' in spec:
             cppflags.append('-D__LIBPEXSI')
             fcflags.append('-I' + os.path.join(
                 spec['pexsi'].prefix, 'fortran'))
@@ -353,7 +393,7 @@ def edit(self, spec, prefix):
                 ),
             ])
 
-        if '+elpa' in self.spec:
+        if '+elpa' in spec:
             elpa = spec['elpa']
             elpa_suffix = '_openmp' if '+openmp' in elpa else ''
             elpa_incdir = elpa.headers.directories[0]
@@ -377,27 +417,27 @@ def edit(self, spec, prefix):
                                         int(elpa.version[1])))
                 fcflags += ['-I{0}'.format(os.path.join(elpa_incdir, 'elpa'))]
 
-        if self.spec.satisfies('+sirius'):
+        if spec.satisfies('+sirius'):
             sirius = spec['sirius']
             cppflags.append('-D__SIRIUS')
             fcflags += ['-I{0}'.format(os.path.join(sirius.prefix, 'fortran'))]
             libs += list(sirius.libs)
 
-        if self.spec.satisfies('+cuda'):
+        if spec.satisfies('+cuda'):
             cppflags += ['-D__ACC']
             libs += ['-lcudart', '-lnvrtc', '-lcuda']
 
-            if self.spec.satisfies('+cuda_blas'):
+            if spec.satisfies('+cuda_blas'):
                 cppflags += ['-D__DBCSR_ACC=2']
                 libs += ['-lcublas']
             else:
                 cppflags += ['-D__DBCSR_ACC']
 
-            if self.spec.satisfies('+cuda_fft'):
+            if spec.satisfies('+cuda_fft'):
                 cppflags += ['-D__PW_CUDA']
                 libs += ['-lcufft', '-lcublas']
 
-            cuda_arch = self.spec.variants['cuda_arch'].value
+            cuda_arch = spec.variants['cuda_arch'].value
             if cuda_arch:
                 gpuver = {
                     '35': 'K40',
@@ -407,7 +447,7 @@ def edit(self, spec, prefix):
                 }[cuda_arch]
 
                 if (cuda_arch == '35'
-                        and self.spec.satisfies('+cuda_arch_35_k20x')):
+                        and spec.satisfies('+cuda_arch_35_k20x')):
                     gpuver = 'K20X'
 
         if 'smm=libsmm' in spec:
@@ -430,12 +470,12 @@ def edit(self, spec, prefix):
             libs.append('-lsmm')
 
         elif 'smm=libxsmm' in spec:
-            cppflags.extend([
-                '-D__LIBXSMM',
-                '$(shell pkg-config --cflags-only-other libxsmmf)',
-            ])
-            fcflags.append('$(shell pkg-config --cflags-only-I libxsmmf)')
-            libs.append('$(shell pkg-config --libs libxsmmf)')
+            cppflags += ['-D__LIBXSMM']
+            cppflags += pkgconf('--cflags-only-other', 'libxsmmf',
+                                output=str).split()
+            fcflags += pkgconf('--cflags-only-I', 'libxsmmf',
+                               output=str).split()
+            libs += pkgconf('--libs', 'libxsmmf', output=str).split()
 
         dflags.extend(cppflags)
         cflags.extend(cppflags)
@@ -444,14 +484,21 @@ def edit(self, spec, prefix):
         nvflags.extend(cppflags)
 
         with open(self.makefile, 'w') as mkf:
-            if '+plumed' in self.spec:
-                # Include Plumed.inc in the Makefile
+            if '+plumed' in spec:
+                mkf.write('# include Plumed.inc as recommended by'
+                          'PLUMED to include libraries and flags')
                 mkf.write('include {0}\n'.format(
-                    self.spec['plumed'].package.plumed_inc
+                    spec['plumed'].package.plumed_inc
                 ))
 
-            mkf.write('CC = {0.compiler.cc}\n'.format(self))
-            if '%intel' in self.spec:
+            mkf.write('\n# COMPILER, LINKER, TOOLS\n\n')
+            mkf.write('FC  = {0}\n'
+                      'CC  = {1}\n'
+                      'CXX = {2}\n'
+                      'LD  = {3}\n'
+                      .format(fc, cc, cxx, fc))
+
+            if '%intel' in spec:
                 intel_bin_dir = ancestor(self.compiler.cc)
                 # CPP is a commented command in Intel arch of CP2K
                 # This is the hack through which cp2k developers avoid doing :
@@ -459,33 +506,38 @@ def edit(self, spec, prefix):
                 # ${CPP} <file>.F > <file>.f90
                 #
                 # and use `-fpp` instead
-                mkf.write('CPP = # {0.compiler.cc} -P\n\n'.format(self))
-                mkf.write('AR = {0}/xiar -r\n\n'.format(intel_bin_dir))
+                mkf.write('CPP = # {0} -P\n'.format(spack_cc))
+                mkf.write('AR  = {0}/xiar -r\n'.format(intel_bin_dir))
             else:
-                mkf.write('CPP = # {0.compiler.cc} -E\n\n'.format(self))
-                mkf.write('AR = ar -r\n\n')
-            mkf.write('FC = {0}\n'.format(fc))
-            mkf.write('LD = {0}\n'.format(fc))
+                mkf.write('CPP = # {0} -E\n'.format(spack_cc))
+                mkf.write('AR  = ar -r\n')
 
-            if self.spec.satisfies('+cuda'):
+            if spec.satisfies('+cuda'):
                 mkf.write('NVCC = {0}\n'.format(
-                    os.path.join(self.spec['cuda'].prefix, 'bin', 'nvcc')))
+                    os.path.join(spec['cuda'].prefix, 'bin', 'nvcc')))
 
             # Write compiler flags to file
-            mkf.write('DFLAGS = {0}\n\n'.format(' '.join(dflags)))
-            mkf.write('CPPFLAGS = {0}\n\n'.format(' '.join(cppflags)))
-            mkf.write('CFLAGS = {0}\n\n'.format(' '.join(cflags)))
-            mkf.write('CXXFLAGS = {0}\n\n'.format(' '.join(cxxflags)))
-            mkf.write('NVFLAGS = {0}\n\n'.format(' '.join(nvflags)))
-            mkf.write('FCFLAGS = {0}\n\n'.format(' '.join(fcflags)))
-            mkf.write('LDFLAGS = {0}\n\n'.format(' '.join(ldflags)))
+            def fflags(var, lst):
+                return '{0} = {1}\n\n'.format(
+                    var,
+                    ' \\\n\t'.join(lst))
+
+            mkf.write('\n# FLAGS & LIBRARIES\n')
+            mkf.write(fflags('DFLAGS', dflags))
+            mkf.write(fflags('CPPFLAGS', cppflags))
+            mkf.write(fflags('CFLAGS', cflags))
+            mkf.write(fflags('CXXFLAGS', cxxflags))
+            mkf.write(fflags('NVFLAGS', nvflags))
+            mkf.write(fflags('FCFLAGS', fcflags))
+            mkf.write(fflags('LDFLAGS', ldflags))
+            mkf.write(fflags('LIBS', libs))
+
             if '%intel' in spec:
-                mkf.write('LDFLAGS_C = {0}\n\n'.format(
-                    ' '.join(ldflags) + ' -nofor_main')
-                )
-            mkf.write('LIBS = {0}\n\n'.format(' '.join(libs)))
-            mkf.write('GPUVER = {0}\n\n'.format(gpuver))
-            mkf.write('DATA_DIR = {0}\n\n'.format(self.prefix.share.data))
+                mkf.write(fflags('LDFLAGS_C', ldflags + ['-nofor_main']))
+
+            mkf.write('# CP2K-specific flags\n\n')
+            mkf.write('GPUVER = {0}\n'.format(gpuver))
+            mkf.write('DATA_DIR = {0}\n'.format(self.prefix.share.data))
 
     @property
     def build_directory(self):

From fcbf0545c7bb653f346fbec9dab27b829f4cf1a8 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Mon, 27 Apr 2020 19:43:34 -0600
Subject: [PATCH 144/802] votca-*: add stable version (#16336)

* votca-*: add stable version

* votca-*: add myself as maintainer
---
 .../repos/builtin/packages/votca-csg-tutorials/package.py     | 4 +++-
 var/spack/repos/builtin/packages/votca-csg/package.py         | 4 +++-
 var/spack/repos/builtin/packages/votca-csgapps/package.py     | 4 +++-
 var/spack/repos/builtin/packages/votca-tools/package.py       | 2 ++
 var/spack/repos/builtin/packages/votca-xtp/package.py         | 4 +++-
 5 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/votca-csg-tutorials/package.py b/var/spack/repos/builtin/packages/votca-csg-tutorials/package.py
index bba3ad0b485..b20c767fce7 100644
--- a/var/spack/repos/builtin/packages/votca-csg-tutorials/package.py
+++ b/var/spack/repos/builtin/packages/votca-csg-tutorials/package.py
@@ -18,14 +18,16 @@ class VotcaCsgTutorials(CMakePackage):
     homepage = "http://www.votca.org"
     url      = "https://github.com/votca/csg-tutorials/tarball/v1.4"
     git      = "https://github.com/votca/csg-tutorials.git"
+    maintainers = ['junghans']
 
     version('master', branch='master')
+    version('stable', branch='stable')
     version('1.6', sha256='54946c647724f1beb95942d47ec7f4cf7a95a59ec7268522693d5ec723585daf')
     version('1.5.1',   sha256='e35cea92df0e7d05ca7b449c1b5d84d887a3a23c7796abe3b84e4d6feec7faca')
     version('1.5',     sha256='03b841fb94129cf59781a7a5e3b71936c414aa9dfa17a50d7bc856d46274580c')
     version('1.4.1',   sha256='623724192c3a7d76b603a74a3326f181045f10f38b9f56dce754a90f1a74556e')
     version('1.4',     sha256='27d50acd68a9d8557fef18ec2b0c62841ae91c22275ab9afbd65c35e4dd5f719')
 
-    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "master"]:
+    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "master", "stable"]:
         depends_on('votca-csg@%s' % v, when="@%s:%s.0" % (v, v))
     depends_on("boost")
diff --git a/var/spack/repos/builtin/packages/votca-csg/package.py b/var/spack/repos/builtin/packages/votca-csg/package.py
index 918791c3375..deffd257397 100644
--- a/var/spack/repos/builtin/packages/votca-csg/package.py
+++ b/var/spack/repos/builtin/packages/votca-csg/package.py
@@ -18,8 +18,10 @@ class VotcaCsg(CMakePackage):
     homepage = "http://www.votca.org"
     url      = "https://github.com/votca/csg/tarball/v1.4"
     git      = "https://github.com/votca/csg.git"
+    maintainers = ['junghans']
 
     version('master', branch='master')
+    version('stable', branch='stable')
     version('1.6', sha256='8cf6a4ac3ef7347c720a44d8a676f8cbd1462e162f6113de39f27b89354465ea')
     version('1.5.1', sha256='7fca1261bd267bf38d2edd26259730fed3126c0c3fd91fb81940dbe17bb568fd')
     version('1.5', sha256='160387cdc51f87dd20ff2e2eed97086beee415d48f3c92f4199f6109068c8ff4')
@@ -27,7 +29,7 @@ class VotcaCsg(CMakePackage):
     version('1.4', sha256='c13e7febd792de8c3d426203f089bd4d33b8067f9db5e8840e4579c88b61146e')
 
     depends_on("cmake@2.8:", type='build')
-    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "master"]:
+    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "master", "stable"]:
         depends_on('votca-tools@%s' % v, when="@%s:%s.0" % (v, v))
     depends_on("boost")
     depends_on("gromacs~mpi@5.1:2019.9999")
diff --git a/var/spack/repos/builtin/packages/votca-csgapps/package.py b/var/spack/repos/builtin/packages/votca-csgapps/package.py
index 929bd73c790..dcca20339c5 100644
--- a/var/spack/repos/builtin/packages/votca-csgapps/package.py
+++ b/var/spack/repos/builtin/packages/votca-csgapps/package.py
@@ -18,14 +18,16 @@ class VotcaCsgapps(CMakePackage):
     homepage = "http://www.votca.org"
     url      = "https://github.com/votca/csgapps/tarball/v1.4"
     git      = "https://github.com/votca/csgapps.git"
+    maintainers = ['junghans']
 
     version('master', branch='master')
+    version('stable', branch='stable')
     version('1.6', sha256='084bbc5b179bb7eb8f6671d2d5fa13e69e68946570c9120a7e4b10aff1866e2e')
     version('1.5.1',   sha256='b4946711e88a1745688b6cce5aad872e6e2ea200fededf38d77a864883e3750e')
     version('1.5',     sha256='18b40ce6222509bc70aa9d56b8c538cd5903edf7294d6f95530668e555206d5b')
     version('1.4.1',   sha256='095d9ee4cd49d2fd79c10e0e84e6890b755e54dec6a5cd580a2b4241ba230a2b')
     version('1.4',     sha256='4ea8348c2f7de3cc488f48fbd8652e69b52515441952766c06ff67ed1aaf69a0')
 
-    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "master"]:
+    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "master", "stable"]:
         depends_on('votca-csg@%s' % v, when="@%s:%s.0" % (v, v))
     depends_on("boost")
diff --git a/var/spack/repos/builtin/packages/votca-tools/package.py b/var/spack/repos/builtin/packages/votca-tools/package.py
index 52c9683f13a..53cf0a26534 100644
--- a/var/spack/repos/builtin/packages/votca-tools/package.py
+++ b/var/spack/repos/builtin/packages/votca-tools/package.py
@@ -18,8 +18,10 @@ class VotcaTools(CMakePackage):
     homepage = "http://www.votca.org"
     url      = "https://github.com/votca/tools/tarball/v1.4"
     git      = "https://github.com/votca/tools.git"
+    maintainers = ['junghans']
 
     version('master', branch='master')
+    version('stable', branch='stable')
     version('1.6', sha256='cfd0fedc80fecd009f743b5df47777508d76bf3ef294a508a9f11fbb42efe9a5')
     version('1.5.1', sha256='4be4fe25a2910e24e1720cd9022d214001d38196033ade8f9d6e618b4f47d5c4')
     version('1.5', sha256='a82a6596c24ff06e79eab17ca02f4405745ceeeb66369693a59023ad0b62cf22')
diff --git a/var/spack/repos/builtin/packages/votca-xtp/package.py b/var/spack/repos/builtin/packages/votca-xtp/package.py
index 96c8de3f5b9..bb14f582524 100644
--- a/var/spack/repos/builtin/packages/votca-xtp/package.py
+++ b/var/spack/repos/builtin/packages/votca-xtp/package.py
@@ -18,15 +18,17 @@ class VotcaXtp(CMakePackage):
     homepage = "http://www.votca.org"
     url      = "https://github.com/votca/xtp/tarball/v1.4.1"
     git      = "https://github.com/votca/xtp.git"
+    maintainers = ['junghans']
 
     version('master', branch='master')
+    version('stable', branch='stable')
     version('1.6', sha256='695c2d9d3f924103481529f992e3723bdce10b8edfc294421a849cdf51dbbb6e')
     version('1.5.1', sha256='17a7722e5a32d236e4f1f6f88b680da4ba5f52bcf65bca3687c6a1c731d10881')
     version('1.5', sha256='b40b6d19e13f0650e84b8beebe86ce5c09071624f18d66df826f9d8584b4d3c8')
     version('1.4.1', sha256='4b53d371d6cf648c9e9e9bd1f104d349cafeaf10a02866e3f1d05c574b595a21')
 
     depends_on("cmake@2.8:", type='build')
-    for v in ["1.4.1", "1.5", "1.5.1", "1.6", "master"]:
+    for v in ["1.4.1", "1.5", "1.5.1", "1.6", "master", "stable"]:
         depends_on('votca-tools@%s' % v, when="@%s:%s.0" % (v, v))
         depends_on('votca-csg@%s' % v, when="@%s:%s.0" % (v, v))
     depends_on("libxc", when='@1.5:')

From 76e9171d25fcbdcf9be11d768340dd83f44f6a9b Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 28 Apr 2020 16:59:52 +0800
Subject: [PATCH 145/802] colordiff: modified url to fix 404 error (#16349)

---
 var/spack/repos/builtin/packages/colordiff/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/colordiff/package.py b/var/spack/repos/builtin/packages/colordiff/package.py
index 7c7073cadc4..686f0840150 100644
--- a/var/spack/repos/builtin/packages/colordiff/package.py
+++ b/var/spack/repos/builtin/packages/colordiff/package.py
@@ -10,7 +10,7 @@ class Colordiff(Package):
     """Colorful diff utility."""
 
     homepage = "https://www.colordiff.org"
-    url      = "https://www.colordiff.org/colordiff-1.0.18.tar.gz"
+    url      = "https://www.colordiff.org/archive/colordiff-1.0.18.tar.gz"
 
     version('1.0.18', sha256='29cfecd8854d6e19c96182ee13706b84622d7b256077df19fbd6a5452c30d6e0')
 

From cf31472e5a34724ee3d20799b1705af4750d1eaa Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 28 Apr 2020 19:04:31 +0800
Subject: [PATCH 146/802] cassandra: added v3.11.6 and dependency on Java
 (#16341)

---
 var/spack/repos/builtin/packages/cassandra/package.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/cassandra/package.py b/var/spack/repos/builtin/packages/cassandra/package.py
index fab6d9c9c49..d6c4781cb4c 100644
--- a/var/spack/repos/builtin/packages/cassandra/package.py
+++ b/var/spack/repos/builtin/packages/cassandra/package.py
@@ -17,7 +17,10 @@ class Cassandra(Package):
 
     version('4.0-alpha2', sha256='6a8e99d8bc51efd500981c85c6aa547387b2fdbedecd692308f4632dbc1de3ba')
     version('4.0-alpha1', sha256='2fdf5e3d6c03a29d24a09cd52bb17575e5faccdc4c75a07edd63a9bf4f740105')
-    version('3.11.5',     sha256='0ee3da12a2be86d7e03203fcc56c3589ddb38347b9cd031495a2b7fcf639fea6', preferred=True)
+    version('3.11.6',     sha256='ce34edebd1b6bb35216ae97bd06d3efc338c05b273b78267556a99f85d30e45b', preferred=True)
+    version('3.11.5',     sha256='0ee3da12a2be86d7e03203fcc56c3589ddb38347b9cd031495a2b7fcf639fea6')
+
+    depends_on('java', type=('build', 'run'))
 
     def install(self, spec, prefix):
         install_tree('.', prefix)

From 9615ac42cf06349137a2bf68495187f7525084a1 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Tue, 28 Apr 2020 05:08:00 -0600
Subject: [PATCH 147/802] votca-*: fix stable deps (#16339)

---
 var/spack/repos/builtin/packages/votca-tools/package.py | 8 ++++----
 var/spack/repos/builtin/packages/votca-xtp/package.py   | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/votca-tools/package.py b/var/spack/repos/builtin/packages/votca-tools/package.py
index 53cf0a26534..09f8e5aab69 100644
--- a/var/spack/repos/builtin/packages/votca-tools/package.py
+++ b/var/spack/repos/builtin/packages/votca-tools/package.py
@@ -32,15 +32,15 @@ class VotcaTools(CMakePackage):
     patch("https://github.com/votca/tools/pull/229.patch", sha256="250d0b679e5d3104e3c8d6adf99751b71386c7ed4cbdae1c75408717ef3f401f", when="@1.6+mkl")
 
     variant('mkl', default=False, description='Build with MKL support')
-    conflicts('+mkl', when='@:1.5.9999')
+    conflicts('+mkl', when='@1.4:1.5.9999')
 
     depends_on("cmake@2.8:", type='build')
     depends_on("expat")
     depends_on("fftw")
-    depends_on("gsl", when="@:1.4.9999")
-    depends_on("eigen@3.3:", when="@1.5:")
+    depends_on("gsl", when="@1.4:1.4.9999")
+    depends_on("eigen@3.3:", when="@stable,1.5:")
     depends_on("boost")
-    depends_on("sqlite", when="@:1.5.9999")
+    depends_on("sqlite", when="@1.4:1.5.9999")
     depends_on('mkl', when='+mkl')
 
     def cmake_args(self):
diff --git a/var/spack/repos/builtin/packages/votca-xtp/package.py b/var/spack/repos/builtin/packages/votca-xtp/package.py
index bb14f582524..21cfdf4edb1 100644
--- a/var/spack/repos/builtin/packages/votca-xtp/package.py
+++ b/var/spack/repos/builtin/packages/votca-xtp/package.py
@@ -31,6 +31,6 @@ class VotcaXtp(CMakePackage):
     for v in ["1.4.1", "1.5", "1.5.1", "1.6", "master", "stable"]:
         depends_on('votca-tools@%s' % v, when="@%s:%s.0" % (v, v))
         depends_on('votca-csg@%s' % v, when="@%s:%s.0" % (v, v))
-    depends_on("libxc", when='@1.5:')
+    depends_on("libxc", when='@stable,1.5:')
     depends_on("ceres-solver", when='@1.5:1.5.9999')
     depends_on("hdf5+cxx~mpi")

From a540e36922daa82b3383bda0c7901b22be9bd730 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Tue, 28 Apr 2020 14:53:22 +0200
Subject: [PATCH 148/802] relocate: remove an assertion in _make_relative
 (#16351)

This was an oversight in #15654 since `os.path.isfile`
checks that the something is a file in the current
filesystem.
---
 lib/spack/spack/relocate.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py
index 41770103b05..41faf273cd5 100644
--- a/lib/spack/spack/relocate.py
+++ b/lib/spack/spack/relocate.py
@@ -140,10 +140,6 @@ def _make_relative(reference_file, path_root, paths):
     Returns:
         List of relative paths
     """
-    # Check prerequisites of the function
-    msg = "{0} is not a file".format(reference_file)
-    assert os.path.isfile(reference_file), msg
-
     start_directory = os.path.dirname(reference_file)
     pattern = re.compile(path_root)
     relative_paths = []

From 50318e4ee31acb274b6ea8fdcf9918fc4af59ec9 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Tue, 28 Apr 2020 14:55:44 +0200
Subject: [PATCH 149/802] travis: extend the list of e-mails being notified of
 failures (#16352)

---
 .travis.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 86b9f4d3dbb..227f6fc955f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -163,6 +163,8 @@ after_success:
 #=============================================================================
 notifications:
   email:
-    recipients: tgamblin@llnl.gov
+    recipients:
+    - tgamblin@llnl.gov
+    - massimiliano.culpo@gmail.com
     on_success: change
     on_failure: always

From aec3589679022c658c2f554d3da156a31f7dec02 Mon Sep 17 00:00:00 2001
From: Tom Payerle <payerle@umd.edu>
Date: Tue, 28 Apr 2020 10:43:53 -0400
Subject: [PATCH 150/802] netcdf-c: Patch to support hdf linked against
 libtirpc (#15994)

If hdf was built with +libtirpc, we need to add -ltirpc to our link
flags.
---
 var/spack/repos/builtin/packages/netcdf-c/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/netcdf-c/package.py b/var/spack/repos/builtin/packages/netcdf-c/package.py
index 42c28e53215..62a3a43cbe7 100644
--- a/var/spack/repos/builtin/packages/netcdf-c/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-c/package.py
@@ -215,6 +215,9 @@ def configure_args(self):
             if '+szip' in hdf4:
                 # This should also come from hdf4.libs
                 libs.append('-lsz')
+            if '+libtirpc' in hdf4:
+                # This should also come from hdf4.libs
+                libs.append('-ltirpc')
 
         # Fortran support
         # In version 4.2+, NetCDF-C and NetCDF-Fortran have split.

From 27b7d4bd210e9c97f85cb81e4167a365129177af Mon Sep 17 00:00:00 2001
From: Carson Woods <carsonwoods@users.noreply.github.com>
Date: Tue, 28 Apr 2020 11:51:30 -0400
Subject: [PATCH 151/802] openmpi: add additional variants (#16044)

* Add variants to OpenMPI

* Add variant for toggling runpath

* Fix typo

* Remove blank line whitespace
---
 .../repos/builtin/packages/openmpi/package.py | 24 +++++++++++++++++--
 1 file changed, 22 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 00cae9023bb..bb798e7b5fd 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -230,13 +230,16 @@ class Openmpi(AutotoolsPackage):
     )
 
     # Additional support options
+    variant('atomics', default=False, description='Enable built-in atomics')
     variant('java', default=False, description='Build Java support')
+    variant('static', default=True, description='Build static libraries')
     variant('sqlite3', default=False, description='Build SQLite3 support')
     variant('vt', default=True, description='Build VampirTrace support')
     variant('thread_multiple', default=False,
             description='Enable MPI_THREAD_MULTIPLE support')
     variant('cuda', default=False, description='Enable CUDA support')
     variant('pmi', default=False, description='Enable PMI support')
+    variant('runpath', default=True, description='Enable wrapper runpath')
     variant('cxx', default=False, description='Enable C++ MPI bindings')
     variant('cxx_exceptions', default=False, description='Enable C++ Exception support')
     # Adding support to build a debug version of OpenMPI that activates
@@ -421,6 +424,11 @@ def configure_args(self):
             '--with-wrapper-ldflags={0}'.format(' '.join(rpaths))
         ])
 
+        if '+atomics' in spec:
+            config_args.append('--enable-builtin-atomics')
+        else:
+            config_args.append('--disable-builtin-atomics')
+
         # According to this comment on github:
         #
         # https://github.com/open-mpi/ompi/issues/4338#issuecomment-383982008
@@ -431,9 +439,14 @@ def configure_args(self):
         if spec.satisfies('schedulers=slurm'):
             config_args.append('--with-pmi={0}'.format(spec['slurm'].prefix))
             if spec.satisfies('@3.1.3:') or spec.satisfies('@3.0.3'):
-                config_args.append('--enable-static')
+                if '+static' in spec:
+                    config_args.append('--enable-static')
         else:
-            config_args.append('--enable-static')
+            if '+static' in spec:
+                config_args.append('--enable-static')
+            else:
+                config_args.append('--disable-static')
+
             config_args.extend(self.with_or_without('pmi'))
 
         if spec.satisfies('@3.0.0:', strict=True):
@@ -533,6 +546,13 @@ def configure_args(self):
             else:
                 config_args.append('--without-cuda')
 
+        if '+runpath' in spec:
+            config_args.append('--enable-wrapper-rpath')
+            config_args.append('--enable-wrapper-runpath')
+        else:
+            config_args.append('--disable-wrapper-rpath')
+            config_args.append('--disable-wrapper-runpath')
+
         if spec.satisfies('@:4'):
             if '+cxx' in spec:
                 config_args.append('--enable-mpi-cxx')

From 4aed5daeba171ebc84ade61522808cc45e45a8b8 Mon Sep 17 00:00:00 2001
From: Jeffrey Salmond <js947@users.noreply.github.com>
Date: Tue, 28 Apr 2020 16:52:39 +0100
Subject: [PATCH 152/802] adjust petsc to build cuda only when requested
 explicitly (#16275)

* adjust petsc+cuda to build cuda only when requested explicitly

* activate petsc library support only when explicitly requested

* flake8 fixes
---
 var/spack/repos/builtin/packages/petsc/package.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index cccced63a06..df1b6e1780e 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -300,13 +300,15 @@ def install(self, spec, prefix):
                         'mumps', 'trilinos', 'fftw', 'valgrind'):
             options.append(
                 '--with-{library}={value}'.format(
-                    library=library, value=('1' if library in spec else '0'))
+                    library=library,
+                    value=('1' if '+' + library in spec else '0'))
             )
-            if library in spec:
+            if '+' + library in spec:
                 options.append(
                     '--with-{library}-dir={path}'.format(
                         library=library, path=spec[library].prefix)
                 )
+
         # PETSc does not pick up SuperluDist from the dir as they look for
         # superlu_dist_4.1.a
         if 'superlu-dist' in spec:

From 2f88af4d2c4e1feffb2f697c064ea8ba8c1fe96e Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 29 Apr 2020 00:06:24 +0800
Subject: [PATCH 153/802] Add new package: kubernetes (#16347)

---
 .../builtin/packages/kubernetes/package.py    | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/kubernetes/package.py

diff --git a/var/spack/repos/builtin/packages/kubernetes/package.py b/var/spack/repos/builtin/packages/kubernetes/package.py
new file mode 100644
index 00000000000..5af5f6e67db
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kubernetes/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Kubernetes(Package):
+    """Kubernetes is an open source system for managing containerized
+    applications across multiple hosts. It provides basic mechanisms
+    for deployment, maintenance, and scaling of applications."""
+
+    homepage = "https://kubernetes.io"
+    url      = "https://github.com/kubernetes/kubernetes/archive/v1.19.0-alpha.0.tar.gz"
+
+    version('1.18.1', sha256='33ca738f1f4e6ad453b80f231f71e62470b822f21d44dc5b8121b2964ae8e6f8')
+    version('1.18.0', sha256='6bd252b8b5401ad6f1fb34116cd5df59153beced3881b98464862a81c083f7ab')
+    version('1.17.4', sha256='b61a6eb3bd5251884f34853cc51aa31c6680e7e476268fe06eb33f3d95294f62')
+
+    depends_on('go', type='build')
+
+    def install(self, spec, prefix):
+        make()
+        install_tree('_output/bin', prefix.bin)

From a1e03151b2fa76b41c395c2a08d81463039530f9 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 29 Apr 2020 00:07:02 +0800
Subject: [PATCH 154/802] Add new package: etcd (#16348)

---
 .../repos/builtin/packages/etcd/package.py    | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/etcd/package.py

diff --git a/var/spack/repos/builtin/packages/etcd/package.py b/var/spack/repos/builtin/packages/etcd/package.py
new file mode 100644
index 00000000000..fa21e6965b5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/etcd/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import platform
+
+
+class Etcd(Package):
+    """etcd is a distributed reliable key-value store for the most
+    critical data of a distributed system"""
+
+    homepage = "https://etcd.io/"
+    url      = "https://github.com/etcd-io/etcd/archive/v3.4.7.tar.gz"
+
+    version('3.4.7', sha256='858f5ad8c830a66f6bd0cd19386deea64d374185b32f40650ba979e0a70b8b97')
+    version('3.4.6',  sha256='e9ebd003f5545a05017a8dbdde236d6c9d25f98ee35f8ba237e57b75330664f9')
+    version('3.4.5',  sha256='2888f73dc52ba89da470d9bd40b1348ffe8b3da51cd8fe8bff5a1a8db2e50d46')
+    version('3.4.4',  sha256='46bcd0d034fe9cc6ae86a9f2a72bdc78761ca99bfd5ae4b96b24e4ad93fc627e')
+    version('3.3.20', sha256='a9fcd2a3343f7f5b99acae956dd7c4fe12f16772b660f16fa9c24368df002477')
+
+    depends_on('go@:1.13.9')
+
+    def setup_run_environment(self, env):
+        if platform.machine() == 'aarch64':
+            env.set('ETCD_UNSUPPORTED_ARCH', 'arm64')
+
+    def setup_build_environment(self, env):
+        if platform.machine() == 'aarch64':
+            env.set('ETCD_UNSUPPORTED_ARCH', 'arm64')
+
+    def install(self, spec, prefix):
+        make()
+        install_tree('bin', prefix.bin)

From 48de131b08dadbf40fde09a95f211b72c806fcea Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 29 Apr 2020 00:07:46 +0800
Subject: [PATCH 155/802] bazel: support for aarch64 platform (#16350)

---
 var/spack/repos/builtin/packages/bazel/package.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/bazel/package.py b/var/spack/repos/builtin/packages/bazel/package.py
index 1ea1a6ce9cf..e9509e990b9 100644
--- a/var/spack/repos/builtin/packages/bazel/package.py
+++ b/var/spack/repos/builtin/packages/bazel/package.py
@@ -4,6 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
+import platform
 
 
 class Bazel(Package):
@@ -90,7 +91,10 @@ class Bazel(Package):
     # Until https://github.com/spack/spack/issues/14058 is fixed, use jdk to build bazel
     # Strict dependency on java@8 as per
     # https://docs.bazel.build/versions/master/install-compile-source.html#bootstrap-unix-prereq
-    depends_on('jdk@1.8.0:1.8.999', type=('build', 'run'))
+    if platform.machine() == 'aarch64':
+        depends_on('java@8:8.999', type=('build', 'run'))
+    else:
+        depends_on('jdk@1.8.0:1.8.999', type=('build', 'run'))
     depends_on('python', type=('build', 'run'))
     depends_on('zip', type=('build', 'run'))
 

From d3ffb122748c0309f57b10a5cd69314d96129b91 Mon Sep 17 00:00:00 2001
From: Cameron Smith <cwsmith@users.noreply.github.com>
Date: Tue, 28 Apr 2020 12:11:50 -0400
Subject: [PATCH 156/802] kokkos: add versions 3.0.00 and 3.1.00 (#16354)

---
 var/spack/repos/builtin/packages/kokkos/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/kokkos/package.py b/var/spack/repos/builtin/packages/kokkos/package.py
index 82b93893e60..47dae741ba9 100644
--- a/var/spack/repos/builtin/packages/kokkos/package.py
+++ b/var/spack/repos/builtin/packages/kokkos/package.py
@@ -15,6 +15,8 @@ class Kokkos(Package):
     git      = "https://github.com/kokkos/kokkos.git"
 
     version('develop', branch='develop')
+    version('3.1.00', sha256='b935c9b780e7330bcb80809992caa2b66fd387e3a1c261c955d622dae857d878')
+    version('3.0.00', sha256='c00613d0194a4fbd0726719bbed8b0404ed06275f310189b3493f5739042a92b')
     version('2.9.00', sha256='e0621197791ed3a381b4f02c78fa529f3cff3abb74d52157b4add17e8aa04bc4')
     version('2.8.00', sha256='1c72661f2d770517bff98837001b42b9c677d1df29f7493a1d7c008549aff630')
     version('2.7.24', sha256='a308a80ea1488f4c18884b828ce7ae9f5210b9a6b2f61b208d875084d8da8cb0')

From af9c3b31de930ceb3a54b352829b6f731b35a8f5 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 29 Apr 2020 00:12:50 +0800
Subject: [PATCH 157/802] Add new package: figlet (#16355)

---
 .../repos/builtin/packages/figlet/package.py  | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/figlet/package.py

diff --git a/var/spack/repos/builtin/packages/figlet/package.py b/var/spack/repos/builtin/packages/figlet/package.py
new file mode 100644
index 00000000000..8c6028d2463
--- /dev/null
+++ b/var/spack/repos/builtin/packages/figlet/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Figlet(MakefilePackage):
+    """FIGlet is a program that creates large characters out of ordinary
+    screen characters."""
+
+    homepage = "http://www.figlet.org/"
+    url      = "https://github.com/cmatsuoka/figlet/archive/2.2.5.tar.gz"
+
+    version('2.2.5', sha256='4d366c4a618ecdd6fdb81cde90edc54dbff9764efb635b3be47a929473f13930')
+    version('2.2.4', sha256='970a18a2a32cca736ff11a5b77e26a54f31a0e08606b85d21d3d5c666937e03d')
+    version('2.2.3', sha256='168fa3c7a5888d6f796708780d3006f0e1871d83f32c4a10a84596b90ac35999')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        bins = ['figlet', 'chkfont', 'figlist', 'showfigfonts']
+        for f in bins:
+            install(f, prefix.bin)
+
+        mkdirp(prefix.man6)
+        manuals = ['figlet.6', 'chkfont.6', 'figlist.6', 'showfigfonts.6']
+        for f in manuals:
+            install(f, prefix.man6)
+
+        install_tree('./fonts', prefix.share.figlet)

From 4ed5cee9408cbeedd5764c6d165743981e40bb9e Mon Sep 17 00:00:00 2001
From: Stephen McDowell <svenevs@users.noreply.github.com>
Date: Tue, 28 Apr 2020 12:14:36 -0400
Subject: [PATCH 158/802] jsoncpp add 1.9.2, patch %clang@10 for implicit
 conversion (#16153)

* add 1.9.2, patch %clang@10 for implicit conversion

* flake8: "fix" hanging indent (squash: because is that really more readable?)
---
 var/spack/repos/builtin/packages/jsoncpp/package.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/var/spack/repos/builtin/packages/jsoncpp/package.py b/var/spack/repos/builtin/packages/jsoncpp/package.py
index 546ea104f22..2593c9ae0fe 100644
--- a/var/spack/repos/builtin/packages/jsoncpp/package.py
+++ b/var/spack/repos/builtin/packages/jsoncpp/package.py
@@ -15,6 +15,7 @@ class Jsoncpp(CMakePackage):
     homepage = "https://github.com/open-source-parsers/jsoncpp"
     url      = "https://github.com/open-source-parsers/jsoncpp/archive/1.7.3.tar.gz"
 
+    version('1.9.2', sha256='77a402fb577b2e0e5d0bdc1cf9c65278915cdb25171e3452c68b6da8a561f8f0')
     version('1.9.1', sha256='c7b40f5605dd972108f503f031b20186f5e5bca2b65cd4b8bd6c3e4ba8126697')
     version('1.9.0', sha256='bdd3ba9ed1f110b3eb57474d9094e90ab239b93b4803b4f9b1722c281e85a4ac')
     version('1.8.4', sha256='c49deac9e0933bcb7044f08516861a2d560988540b23de2ac1ad443b219afdb6')
@@ -42,6 +43,17 @@ class Jsoncpp(CMakePackage):
     depends_on('cmake@3.1:', type='build')
     depends_on('python', type='test')
 
+    # Ref: https://github.com/open-source-parsers/jsoncpp/pull/1023
+    # Released in 1.9.2, patch does not apply cleanly across releases.
+    # May apply to more compilers in the future.
+    @when('@:1.9.1 %clang@10.0.0:')
+    def patch(self):
+        filter_file(
+            'return d >= min && d <= max;',
+            'return d >= static_cast<double>(min) && '
+            'd <= static_cast<double>(max);',
+            'src/lib_json/json_value.cpp')
+
     def cmake_args(self):
         args = ['-DBUILD_SHARED_LIBS=ON']
         cxxstd = self.spec.variants['cxxstd'].value

From 6e63ff1688e79878554a79b8d2132d4141cd1913 Mon Sep 17 00:00:00 2001
From: Carson Woods <carsonwoods@users.noreply.github.com>
Date: Tue, 28 Apr 2020 12:15:19 -0400
Subject: [PATCH 159/802] netcdf-fortran: add new variants (#16046)

* Add additional variants to netcdf-fortran

* Fix duplicate variant

* Clean up variants based on review feedback

* Addtional variant changes

* Convert jna variant to single line

* Fix proper version constraints for jna variant
---
 var/spack/repos/builtin/packages/netcdf-c/package.py       | 4 ++++
 var/spack/repos/builtin/packages/netcdf-fortran/package.py | 7 +++++++
 2 files changed, 11 insertions(+)

diff --git a/var/spack/repos/builtin/packages/netcdf-c/package.py b/var/spack/repos/builtin/packages/netcdf-c/package.py
index 62a3a43cbe7..153a1057b17 100644
--- a/var/spack/repos/builtin/packages/netcdf-c/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-c/package.py
@@ -61,6 +61,7 @@ def url_for_version(self, version):
             description='Produce position-independent code (for shared libs)')
     variant('shared', default=True, description='Enable shared library')
     variant('dap', default=False, description='Enable DAP support')
+    variant('jna', default=False, description='Enable JNA support')
 
     # It's unclear if cdmremote can be enabled if '--enable-netcdf-4' is passed
     # to the configure script. Since netcdf-4 support is mandatory we comment
@@ -181,6 +182,9 @@ def configure_args(self):
             else:
                 config_args.append('--disable-parallel4')
 
+        if self.spec.satisfies('@4.3.2:'):
+            config_args += self.enable_or_disable('jna')
+
         # Starting version 4.1.3, --with-hdf5= and other such configure options
         # are removed. Variables CPPFLAGS, LDFLAGS, and LD_LIBRARY_PATH must be
         # used instead.
diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
index 1b55df15078..e4dd1ea8840 100644
--- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
@@ -27,6 +27,7 @@ class NetcdfFortran(AutotoolsPackage):
     variant('pic', default=True,
             description='Produce position-independent code (for shared libs)')
     variant('shared', default=True, description='Enable shared library')
+    variant('doc', default=False, description='Enable building docs')
 
     # We need to build with MPI wrappers if parallel I/O features is enabled:
     # https://www.unidata.ucar.edu/software/netcdf/docs/building_netcdf_fortran.html
@@ -34,6 +35,7 @@ class NetcdfFortran(AutotoolsPackage):
 
     depends_on('netcdf-c~mpi', when='~mpi')
     depends_on('netcdf-c+mpi', when='+mpi')
+    depends_on('doxygen', when='+doc', type='build')
 
     # The default libtool.m4 is too old to handle NAG compiler properly:
     # https://github.com/Unidata/netcdf-fortran/issues/94
@@ -120,6 +122,11 @@ def configure_args(self):
             config_args.append('FC=%s' % self.spec['mpi'].mpifc)
             config_args.append('F77=%s' % self.spec['mpi'].mpif77)
 
+        if '+doc' in self.spec:
+            config_args.append('--enable-doxygen')
+        else:
+            config_args.append('--disable-doxygen')
+
         return config_args
 
     @when('@:4.4.5')

From 7670ae468f0f3deea60efd52eb096d35f96896f9 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Tue, 28 Apr 2020 09:54:02 -0700
Subject: [PATCH 160/802] Docs: Limit Microarch on Travis CI (#16200)

Update the travis CI docs: limiting the microarch is essential
for caching.
---
 lib/spack/docs/workflows.rst | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/lib/spack/docs/workflows.rst b/lib/spack/docs/workflows.rst
index 239ee55a6ac..690d02d0203 100644
--- a/lib/spack/docs/workflows.rst
+++ b/lib/spack/docs/workflows.rst
@@ -1358,6 +1358,14 @@ The main points that are implemented below:
    the spack builds in the config.
    (The Travis yaml parser is a bit buggy on the echo command.)
 
+#. Without control for the user, Travis jobs will run on various
+   ``x86_64`` microarchitectures. If you plan to cache build results,
+   e.g. to accelerate dependency builds, consider building for the
+   generic ``x86_64`` target only.
+   Limiting the microarchitecture will also find more packages when
+   working with the
+   `E4S Spack build cache <https://oaciss.uoregon.edu/e4s/e4s_buildcache_inventory.html>`_.
+
 #. Builds over 10 minutes need to be prefixed with ``travis_wait``.
    Alternatively, generate output once with ``spack install -v``.
 
@@ -1400,7 +1408,9 @@ The main points that are implemented below:
      - if ! which spack >/dev/null; then
          mkdir -p $SPACK_ROOT &&
          git clone --depth 50 https://github.com/spack/spack.git $SPACK_ROOT &&
-         echo -e "config:""\n  build_jobs:"" 2" > $SPACK_ROOT/etc/spack/config.yaml;
+         echo -e "config:""\n  build_jobs:"" 2" > $SPACK_ROOT/etc/spack/config.yaml **
+         echo -e "packages:""\n  all:""\n    target:"" ['x86_64']"
+                 > $SPACK_ROOT/etc/spack/packages.yaml;
        fi
      - travis_wait spack install cmake@3.7.2~openssl~ncurses
      - travis_wait spack install boost@1.62.0~graph~iostream~locale~log~wave

From 00d83cd79d7aa766d841853298de37e85c0fb458 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Tue, 28 Apr 2020 09:55:57 -0700
Subject: [PATCH 161/802] dev-build: stop before phase (#14699)

Add `-b,--before` option to dev-build command to stop before the phase in question.
---
 lib/spack/spack/cmd/dev_build.py      | 10 +++++--
 lib/spack/spack/installer.py          | 16 +++++++++--
 lib/spack/spack/package.py            |  6 ++++-
 lib/spack/spack/test/cmd/dev_build.py | 39 ++++++++++++++++++++++++++-
 share/spack/spack-completion.bash     |  4 +--
 5 files changed, 67 insertions(+), 8 deletions(-)

diff --git a/lib/spack/spack/cmd/dev_build.py b/lib/spack/spack/cmd/dev_build.py
index c1004f24b38..7f424928085 100644
--- a/lib/spack/spack/cmd/dev_build.py
+++ b/lib/spack/spack/cmd/dev_build.py
@@ -37,10 +37,15 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-q', '--quiet', action='store_true', dest='quiet',
         help="do not display verbose build output while installing")
-    subparser.add_argument(
+    arguments.add_common_arguments(subparser, ['spec'])
+
+    stop_group = subparser.add_mutually_exclusive_group()
+    stop_group.add_argument(
+        '-b', '--before', type=str, dest='before', default=None,
+        help="phase to stop before when installing (default None)")
+    stop_group.add_argument(
         '-u', '--until', type=str, dest='until', default=None,
         help="phase to stop after when installing (default None)")
-    arguments.add_common_arguments(subparser, ['spec'])
 
     cd_group = subparser.add_mutually_exclusive_group()
     arguments.add_common_arguments(cd_group, ['clean', 'dirty'])
@@ -91,4 +96,5 @@ def dev_build(self, args):
         verbose=not args.quiet,
         keep_stage=True,   # don't remove source dir for dev build.
         dirty=args.dirty,
+        stop_before=args.before,
         stop_at=args.until)
diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py
index 2bad1e88183..8886f3ed069 100644
--- a/lib/spack/spack/installer.py
+++ b/lib/spack/spack/installer.py
@@ -562,6 +562,8 @@ def package_id(pkg):
                 even with exceptions.
             restage (bool): Force spack to restage the package source.
             skip_patch (bool): Skip patch stage of build if True.
+            stop_before (InstallPhase): stop execution before this
+                installation phase (or None)
             stop_at (InstallPhase): last installation phase to be executed
                 (or None)
             tests (bool or list or set): False to run no tests, True to test
@@ -779,12 +781,20 @@ def _check_last_phase(self, **kwargs):
         Ensures the package being installed has a valid last phase before
         proceeding with the installation.
 
-        The ``stop_at`` argument is removed from the installation arguments.
+        The ``stop_before`` or ``stop_at`` arguments are removed from the
+        installation arguments.
 
         Args:
             kwargs:
+              ``stop_before``': stop before execution of this phase (or None)
               ``stop_at``': last installation phase to be executed (or None)
         """
+        self.pkg.stop_before_phase = kwargs.pop('stop_before', None)
+        if self.pkg.stop_before_phase is not None and \
+           self.pkg.stop_before_phase not in self.pkg.phases:
+            tty.die('\'{0}\' is not an allowed phase for package {1}'
+                    .format(self.pkg.stop_before_phase, self.pkg.name))
+
         self.pkg.last_phase = kwargs.pop('stop_at', None)
         if self.pkg.last_phase is not None and \
                 self.pkg.last_phase not in self.pkg.phases:
@@ -1504,8 +1514,10 @@ def install(self, **kwargs):
                 self._update_installed(task)
 
                 # If we installed then we should keep the prefix
+                stop_before_phase = getattr(pkg, 'stop_before_phase', None)
                 last_phase = getattr(pkg, 'last_phase', None)
-                keep_prefix = last_phase is None or keep_prefix
+                keep_prefix = keep_prefix or \
+                    (stop_before_phase is None and last_phase is None)
 
             except spack.directory_layout.InstallDirectoryAlreadyExistsError:
                 tty.debug("Keeping existing install prefix in place.")
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index b8ded0364b3..40384077eae 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -115,7 +115,11 @@ def phase_wrapper(spec, prefix):
         return phase_wrapper
 
     def _on_phase_start(self, instance):
-        pass
+        # If a phase has a matching stop_before_phase attribute,
+        # stop the installation process raising a StopIteration
+        if getattr(instance, 'stop_before_phase', None) == self.name:
+            raise StopIteration('Stopping before \'{0}\' phase'
+                                .format(self.name))
 
     def _on_phase_exit(self, instance):
         # If a phase has a matching last_phase attribute,
diff --git a/lib/spack/spack/test/cmd/dev_build.py b/lib/spack/spack/test/cmd/dev_build.py
index a0075130676..6afd07d8159 100644
--- a/lib/spack/spack/test/cmd/dev_build.py
+++ b/lib/spack/spack/test/cmd/dev_build.py
@@ -3,8 +3,9 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import os
+import pytest
 import spack.spec
-from spack.main import SpackCommand
+from spack.main import SpackCommand, SpackCommandError
 
 dev_build = SpackCommand('dev-build')
 
@@ -23,6 +24,22 @@ def test_dev_build_basics(tmpdir, mock_packages, install_mockery):
         assert f.read() == spec.package.replacement_string
 
 
+def test_dev_build_before(tmpdir, mock_packages, install_mockery):
+    spec = spack.spec.Spec('dev-build-test-install@0.0.0').concretized()
+
+    with tmpdir.as_cwd():
+        with open(spec.package.filename, 'w') as f:
+            f.write(spec.package.original_string)
+
+        dev_build('-b', 'edit', 'dev-build-test-install@0.0.0')
+
+        assert spec.package.filename in os.listdir(os.getcwd())
+        with open(spec.package.filename, 'r') as f:
+            assert f.read() == spec.package.original_string
+
+    assert not os.path.exists(spec.prefix)
+
+
 def test_dev_build_until(tmpdir, mock_packages, install_mockery):
     spec = spack.spec.Spec('dev-build-test-install@0.0.0').concretized()
 
@@ -39,6 +56,26 @@ def test_dev_build_until(tmpdir, mock_packages, install_mockery):
     assert not os.path.exists(spec.prefix)
 
 
+def test_dev_build_before_until(tmpdir, mock_packages, install_mockery):
+    spec = spack.spec.Spec('dev-build-test-install@0.0.0').concretized()
+
+    with tmpdir.as_cwd():
+        with open(spec.package.filename, 'w') as f:
+            f.write(spec.package.original_string)
+
+        with pytest.raises(SystemExit):
+            dev_build('-u', 'edit', '-b', 'edit',
+                      'dev-build-test-install@0.0.0')
+
+        with pytest.raises(SpackCommandError):
+            dev_build('-u', 'phase_that_does_not_exist',
+                      'dev-build-test-install@0.0.0')
+
+        with pytest.raises(SpackCommandError):
+            dev_build('-b', 'phase_that_does_not_exist',
+                      'dev-build-test-install@0.0.0')
+
+
 def test_dev_build_fails_already_installed(tmpdir, mock_packages,
                                            install_mockery):
     spec = spack.spec.Spec('dev-build-test-install@0.0.0').concretized()
diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash
index a4d59220fa3..5a4fb027c9e 100755
--- a/share/spack/spack-completion.bash
+++ b/share/spack/spack-completion.bash
@@ -697,7 +697,7 @@ _spack_deprecate() {
 _spack_dev_build() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -j --jobs -d --source-path -i --ignore-dependencies -n --no-checksum --keep-prefix --skip-patch -q --quiet -u --until --clean --dirty"
+        SPACK_COMPREPLY="-h --help -j --jobs -d --source-path -i --ignore-dependencies -n --no-checksum --keep-prefix --skip-patch -q --quiet -b --before -u --until --clean --dirty"
     else
         _all_packages
     fi
@@ -706,7 +706,7 @@ _spack_dev_build() {
 _spack_diy() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -j --jobs -d --source-path -i --ignore-dependencies -n --no-checksum --keep-prefix --skip-patch -q --quiet -u --until --clean --dirty"
+        SPACK_COMPREPLY="-h --help -j --jobs -d --source-path -i --ignore-dependencies -n --no-checksum --keep-prefix --skip-patch -q --quiet -b --before -u --until --clean --dirty"
     else
         _all_packages
     fi

From 703111c01bd0c1693894dca4e56965d656682008 Mon Sep 17 00:00:00 2001
From: Jeffrey Salmond <js947@users.noreply.github.com>
Date: Tue, 28 Apr 2020 20:36:55 +0100
Subject: [PATCH 162/802] Add amgx (#16357)

* add amgx package

* add amgx variants for mkl and magma support

* fix typo in cmake option

* flake8 fix formatting

* Apply suggestions from code review - use mkl virtual provider

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Apply suggestions from code review - fix copypasta

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../repos/builtin/packages/amgx/package.py    | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/amgx/package.py

diff --git a/var/spack/repos/builtin/packages/amgx/package.py b/var/spack/repos/builtin/packages/amgx/package.py
new file mode 100644
index 00000000000..ece1d67ee20
--- /dev/null
+++ b/var/spack/repos/builtin/packages/amgx/package.py
@@ -0,0 +1,58 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Amgx(CMakePackage, CudaPackage):
+    """AmgX provides a simple path to accelerated core solver technology on
+    NVIDIA GPUs. AmgX provides up to 10x acceleration to the computationally
+    intense linear solver portion of simulations, and is especially well
+    suited for implicit unstructured methods. It is a high performance,
+    state-of-the-art library and includes a flexible solver composition
+    system that allows a user to easily construct complex nested solvers and
+    preconditioners."""
+
+    homepage = "https://developer.nvidia.com/amgx"
+    url      = "https://github.com/nvidia/amgx/archive/v2.1.0.tar.gz"
+
+    maintainers = ['js947']
+
+    version('2.1.0', sha256='6245112b768a1dc3486b2b3c049342e232eb6281a6021fffa8b20c11631f63cc')
+    version('2.0.1', sha256='6f9991f1836fbf4ba2114ce9f49febd0edc069a24f533bd94fd9aa9be72435a7')
+    version('2.0.0', sha256='8ec7ea8412be3de216fcf7243c4e2a8bcf76878e6865468e4238630a082a431b')
+
+    variant('cuda', default=True, description='Build with CUDA')
+    variant('mpi', default=True, description='Enable MPI support')
+    variant('mkl', default=False, description='Enable MKL support')
+    variant('magma', default=False, description='Enable Magma support')
+
+    depends_on('mpi', when='+mpi')
+    depends_on('mkl', when='+mkl')
+    depends_on('magma', when='+magma')
+
+    def cmake_args(self):
+        args = []
+        args.append("-DCMAKE_NO_MPI={0}".format(
+            '1' if '+mpi' not in self.spec else '0'))
+
+        if '+cuda' in self.spec:
+            args.append('-DWITH_CUDA=ON')
+            cuda_arch = self.spec.variants['cuda_arch'].value
+            if cuda_arch is not None:
+                args.append('-DCUDA_ARCH={0}'.format(cuda_arch[0]))
+        else:
+            args.append('-DWITH_CUDA=OFF')
+
+        if '+mkl' in self.spec:
+            args.append('-DMKL_ROOT_DIR={0}'.format(
+                self.spec['mkl'].prefix))
+
+        if '+magma' in self.spec:
+            args.append('-DMAGMA_ROOT_DIR={0}'.format(
+                self.spec['magma'].prefix))
+
+        return args

From 2d02769bea639eff5f9bf110fb9fddb90bfc6708 Mon Sep 17 00:00:00 2001
From: Hadrien G <grasland@lal.in2p3.fr>
Date: Wed, 29 Apr 2020 02:17:13 +0200
Subject: [PATCH 163/802] [dd4hep] Fix inappropriate patch line break (#16361)

Sometimes, text editors automate things a little too much...
---
 var/spack/repos/builtin/packages/dd4hep/tbb2.patch | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/dd4hep/tbb2.patch b/var/spack/repos/builtin/packages/dd4hep/tbb2.patch
index 7e128f11943..932458001c2 100644
--- a/var/spack/repos/builtin/packages/dd4hep/tbb2.patch
+++ b/var/spack/repos/builtin/packages/dd4hep/tbb2.patch
@@ -2,8 +2,7 @@ diff --git a/DDDigi/src/DigiKernel.cpp b/DDDigi/src/DigiKernel.cpp
 index f2c2e86c..f168ef9b 100644
 --- a/DDDigi/src/DigiKernel.cpp
 +++ b/DDDigi/src/DigiKernel.cpp
-@@ -273,7 +273,7 @@ void DigiKernel::submit(const DigiAction::Actors<DigiEventAc
-tion>& actions, Digi
+@@ -273,7 +273,7 @@ void DigiKernel::submit(const DigiAction::Actors<DigiEventAction>& actions, Digi
    if ( parallel )   {
      tbb::task_group que;
      for ( auto* i : actions )

From 25c17e0ca6ed064ac229b0a2a8aa2d96f338d711 Mon Sep 17 00:00:00 2001
From: Ryan Mast <nightlark@users.noreply.github.com>
Date: Tue, 28 Apr 2020 17:21:22 -0700
Subject: [PATCH 164/802] helics: Add version 2.5.0 (#16364)

Add HELICS package version 2.5.0
---
 var/spack/repos/builtin/packages/helics/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/helics/package.py b/var/spack/repos/builtin/packages/helics/package.py
index 7aa4a06c466..c37dc5cc38a 100644
--- a/var/spack/repos/builtin/packages/helics/package.py
+++ b/var/spack/repos/builtin/packages/helics/package.py
@@ -19,6 +19,7 @@ class Helics(CMakePackage):
 
     version('develop', branch='develop', submodules=True)
     version('master', branch='master', submodules=True)
+    version('2.5.0', sha256='6f4f9308ebb59d82d71cf068e0d9d66b6edfa7792d61d54f0a61bf20dd2a7428')
     version('2.4.2', sha256='957856f06ed6d622f05dfe53df7768bba8fe2336d841252f5fac8345070fa5cb')
     version('2.4.1', sha256='ac077e9efe466881ea366721cb31fb37ea0e72a881a717323ba4f3cdda338be4')
 

From 8b4b7aacbb4de97fe068a9ca4746629186042727 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 28 Apr 2020 23:14:17 -0500
Subject: [PATCH 165/802] py-pandas: add 1.0.X release (#16366)

---
 .../builtin/packages/py-pandas/package.py     | 30 +++++++++++--------
 1 file changed, 18 insertions(+), 12 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py
index 2403197c9e5..68e32c042d2 100644
--- a/var/spack/repos/builtin/packages/py-pandas/package.py
+++ b/var/spack/repos/builtin/packages/py-pandas/package.py
@@ -7,17 +7,12 @@
 
 
 class PyPandas(PythonPackage):
-    """pandas is a Python package providing fast, flexible, and expressive
-       data structures designed to make working with relational or
-       labeled data both easy and intuitive. It aims to be the
-       fundamental high-level building block for doing practical, real
-       world data analysis in Python. Additionally, it has the broader
-       goal of becoming the most powerful and flexible open source data
-       analysis / manipulation tool available in any language.
+    """pandas is a fast, powerful, flexible and easy to use open source
+    data analysis and manipulation tool, built on top of the Python
+    programming language."""
 
-    """
-    homepage = "http://pandas.pydata.org/"
-    url = "https://pypi.io/packages/source/p/pandas/pandas-0.25.1.tar.gz"
+    homepage = "https://pandas.pydata.org/"
+    url = "https://pypi.io/packages/source/p/pandas/pandas-1.0.3.tar.gz"
 
     maintainers = ['adamjstewart']
     import_modules = [
@@ -34,6 +29,12 @@ class PyPandas(PythonPackage):
         'pandas.api.extensions'
     ]
 
+    version('1.0.3',  sha256='32f42e322fb903d0e189a4c10b75ba70d90958cc4f66a1781ed027f1a1d14586')
+    version('1.0.2',  sha256='76334ba36aa42f93b6b47b79cbc32187d3a178a4ab1c3a478c8f4198bcd93a73')
+    version('1.0.1',  sha256='3c07765308f091d81b6735d4f2242bb43c332cc3461cae60543df6b10967fe27')
+    version('1.0.0',  sha256='3ea6cc86931f57f18b1240572216f09922d91b19ab8a01cf24734394a3db3bec')
+    version('0.25.3', sha256='52da74df8a9c9a103af0a72c9d5fdc8e0183a90884278db7f386b5692a2220a4')
+    version('0.25.2', sha256='ca91a19d1f0a280874a24dca44aadce42da7f3a7edb7e9ab7c7baad8febee2be')
     version('0.25.1', sha256='cb2e197b7b0687becb026b84d3c242482f20cbb29a9981e43604eb67576da9f6')
     version('0.25.0', sha256='914341ad2d5b1ea522798efa4016430b66107d05781dbfe7cf05eba8f37df995')
     version('0.24.2', sha256='4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2')
@@ -47,9 +48,12 @@ class PyPandas(PythonPackage):
     version('0.16.1', sha256='570d243f8cb068bf780461b9225d2e7bef7c90aa10d43cf908fe541fc92df8b6')
     version('0.16.0', sha256='4013de6f8796ca9d2871218861823bd9878a8dfacd26e08ccf9afdd01bbad9f1')
 
-    # https://pandas.pydata.org/pandas-docs/stable/install.html#dependencies
     # Required dependencies
+    # https://pandas.pydata.org/pandas-docs/stable/getting_started/install.html#dependencies
+    depends_on('python@3.6.1:', type=('build', 'run'), when='@1:')
     depends_on('python@3.5.3:', type=('build', 'run'), when='@0.25:')
+    # https://pandas.pydata.org/docs/whatsnew/v1.0.0.html#build-changes
+    depends_on('py-cython@0.29.13:', type='build', when='@1:')
     depends_on('py-setuptools@24.2.0:', type='build')
     depends_on('py-numpy', type=('build', 'run'))
     depends_on('py-numpy@1.13.3:', type=('build', 'run'), when='@0.25:')
@@ -58,16 +62,18 @@ class PyPandas(PythonPackage):
     depends_on('py-pytz@2017.2:', type=('build', 'run'))
 
     # Recommended dependencies
+    # https://pandas.pydata.org/pandas-docs/stable/getting_started/install.html#recommended-dependencies
     depends_on('py-numexpr', type=('build', 'run'))
     depends_on('py-numexpr@2.6.2:', type=('build', 'run'), when='@0.25:')
     depends_on('py-bottleneck', type=('build', 'run'))
     depends_on('py-bottleneck@1.2.1:', type=('build', 'run'), when='@0.25:')
 
     # Optional dependencies
-    # https://pandas.pydata.org/pandas-docs/stable/install.html#optional-dependencies
+    # https://pandas.pydata.org/pandas-docs/stable/getting_started/install.html#optional-dependencies
 
     # Test dependencies
     # https://pandas.pydata.org/pandas-docs/stable/development/contributing.html#running-the-test-suite
     depends_on('py-pytest@4.0.2:', type='test')
+    depends_on('py-pytest-xdist', type='test')
     depends_on('py-hypothesis@3.58:', type='test')
     depends_on('py-pyarrow@0.10.0:', type='test')

From 67ad8ed546a8f8a524c3f8fed0d619e4cbd442dd Mon Sep 17 00:00:00 2001
From: "Dr. Christian Tacke"
 <58549698+ChristianTackeGSI@users.noreply.github.com>
Date: Wed, 29 Apr 2020 09:05:17 +0200
Subject: [PATCH 166/802] root: added v6.20.04, better variant handling
 (#16362)

* Add version 6.20.04
* This version still requires numpy for +python
* ROOT 6.20 renamed the define from python to pyroot:
  Add appropiate handling
---
 var/spack/repos/builtin/packages/root/package.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/root/package.py b/var/spack/repos/builtin/packages/root/package.py
index 9db1a702540..b1591f455e3 100644
--- a/var/spack/repos/builtin/packages/root/package.py
+++ b/var/spack/repos/builtin/packages/root/package.py
@@ -26,6 +26,7 @@ class Root(CMakePackage):
     # Development version (when more recent than production).
 
     # Production version
+    version('6.20.04', sha256='1f8c76ccdb550e64e6ddb092b4a7e9d0a10655ef80044828cba12d5e7c874472')
     version('6.20.02', sha256='0997586bf097c0afbc6f08edbffcebf5eb6a4237262216114ba3f5c8087dcba6')
     version('6.20.00', sha256='68421eb0434b38b66346fa8ea6053a0fdc9a6d254e4a72019f4e3633ae118bf0')
     version('6.18.04', sha256='315a85fc8363f8eb1bffa0decbf126121258f79bd273513ed64795675485cfa4',
@@ -213,10 +214,10 @@ class Root(CMakePackage):
     depends_on('python@2.7:', when='+python', type=('build', 'run'))
     depends_on('py-numpy', type=('build', 'run'), when='+tmva')
     # This numpy dependency was not intended and will hopefully
-    # be fixed in 6.20.04.
+    # be fixed in 6.20.06.
     # See: https://sft.its.cern.ch/jira/browse/ROOT-10626
     depends_on('py-numpy', type=('build', 'run'),
-               when='@6.20.00:6.20.03 +python')
+               when='@6.20.00:6.20.05 +python')
 
     # Optional dependencies
     depends_on('davix @0.7.1:', when='+davix')
@@ -378,7 +379,6 @@ def cmake_args(self):
                 ['pgsql', 'postgres'],
                 ['pythia6'],
                 ['pythia8'],
-                ['python'],
                 ['qt', 'qt4'],  # See conflicts
                 ['qtgsi', 'qt4'],  # See conflicts
                 ['r', 'R'],
@@ -409,6 +409,12 @@ def cmake_args(self):
 
         options = self._process_opts(control_opts, builtin_opts, feature_opts)
 
+        # Some special features
+        if self.spec.satisfies('@6.20:'):
+            options.append(self.define_from_variant('pyroot', 'python'))
+        else:
+            options.append(self.define_from_variant('python'))
+
         # #################### Compiler options ####################
 
         if sys.platform == 'darwin':

From 6c0d4fb5e5a533bbe5b86711b7e09c3b9f1ca758 Mon Sep 17 00:00:00 2001
From: Ryan Mast <nightlark@users.noreply.github.com>
Date: Wed, 29 Apr 2020 00:10:33 -0700
Subject: [PATCH 167/802] helics: fixed dependency on boost (#16363)

---
 var/spack/repos/builtin/packages/helics/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/helics/package.py b/var/spack/repos/builtin/packages/helics/package.py
index c37dc5cc38a..ba804784369 100644
--- a/var/spack/repos/builtin/packages/helics/package.py
+++ b/var/spack/repos/builtin/packages/helics/package.py
@@ -43,7 +43,7 @@ class Helics(CMakePackage):
     # Build dependency
     depends_on('git', type='build', when='@master:')
     depends_on('cmake@3.4:', type='build')
-    depends_on('boost@1.70: ~atomic ~chrono ~date_time ~exception ~filesystem ~graph ~iostreams ~locale ~log ~math ~program_options ~random ~regex ~serialization ~signals ~system ~test ~thread ~timer ~wave', type='build', when='+boost')
+    depends_on('boost@1.70:', type='build', when='+boost')
     depends_on('swig@3.0:', type='build', when='+swig')
 
     depends_on('libzmq@4.3:', when='+zmq')

From c37857f9956a4f07a395e3b7d6e4ed62564e6f0b Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Wed, 29 Apr 2020 00:27:27 -0700
Subject: [PATCH 168/802] openscenegraph: add v3.4.0, v3.4.1; add '+ffmpeg'
 (#16360)

* openscenegraph: add v3.4.0/3.4.1, update versioning to use git, improve dependency handling (esp. for ffmpeg, opengl)

* openscenegraph: add '+ffmpeg' variant, add 'jasper' dependency, clean up cmake config variables

* openscenegraph: reverted fetches to use checksums to improve reliability

* openscenegraph: add a few more explicit dependencies (e.g. png, tiff, glib).
---
 .../openscenegraph/glibc-jasper.patch         | 15 ++++++++
 .../packages/openscenegraph/package.py        | 37 +++++++++++++++----
 2 files changed, 44 insertions(+), 8 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/openscenegraph/glibc-jasper.patch

diff --git a/var/spack/repos/builtin/packages/openscenegraph/glibc-jasper.patch b/var/spack/repos/builtin/packages/openscenegraph/glibc-jasper.patch
new file mode 100644
index 00000000000..d826b8885ad
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openscenegraph/glibc-jasper.patch
@@ -0,0 +1,15 @@
+diff --git a/src/osgPlugins/jp2/ReaderWriterJP2.cpp b/src/osgPlugins/jp2/ReaderWriterJP2.cpp
+index 7b3c6cc..d949c2c 100644
+--- a/src/osgPlugins/jp2/ReaderWriterJP2.cpp
++++ b/src/osgPlugins/jp2/ReaderWriterJP2.cpp
+@@ -15,6 +15,10 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ 
++#ifndef SIZE_MAX
++#define SIZE_MAX ((size_t)(-1))
++#endif
++
+ extern "C"
+ {
+     #include <jasper/jasper.h>
diff --git a/var/spack/repos/builtin/packages/openscenegraph/package.py b/var/spack/repos/builtin/packages/openscenegraph/package.py
index 5f2646729e1..2a6da5dbff2 100644
--- a/var/spack/repos/builtin/packages/openscenegraph/package.py
+++ b/var/spack/repos/builtin/packages/openscenegraph/package.py
@@ -3,7 +3,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-
 from spack import *
 
 
@@ -12,41 +11,63 @@ class Openscenegraph(CMakePackage):
        that's used in a variety of visual simulation applications."""
 
     homepage = "http://www.openscenegraph.org"
+    git      = "https://github.com/openscenegraph/OpenSceneGraph.git"
     url      = "https://github.com/openscenegraph/OpenSceneGraph/archive/OpenSceneGraph-3.6.4.tar.gz"
 
     version('3.6.5', sha256='aea196550f02974d6d09291c5d83b51ca6a03b3767e234a8c0e21322927d1e12')
     version('3.6.4', sha256='81394d1b484c631028b85d21c5535280c21bbd911cb058e8746c87e93e7b9d33')
+    version('3.4.1', sha256='930eb46f05781a76883ec16c5f49cfb29a059421db131005d75bec4d78401fd5')
+    version('3.4.0', sha256='0d5efe12b923130d14a6fce5866675d7625fcfb1c004c9f9b10034b9feb61ac2')
     version('3.2.3', sha256='a1ecc6524197024834e1277916922b32f30246cb583e27ed19bf3bf889534362')
     version('3.1.5', sha256='dddecf2b33302076712100af59b880e7647bc595a9a7cc99186e98d6e0eaeb5c')
 
     variant('shared', default=True, description='Builds a shared version of the library')
+    variant('ffmpeg', default=False, description='Builds ffmpeg plugin for audio encoding/decoding')
 
     depends_on('cmake@2.8.7:', type='build')
+    depends_on('qt+opengl')
     depends_on('qt@4:', when='@3.2:')
     depends_on('qt@:4', when='@:3.1')
-    depends_on('zlib')
     depends_on('libxinerama')
     depends_on('libxrandr')
+    depends_on('libpng')
+    depends_on('jasper')
+    depends_on('libtiff')
+    depends_on('glib')
+    depends_on('zlib')
+
+    depends_on('ffmpeg+avresample', when='+ffmpeg')
+    # https://github.com/openscenegraph/OpenSceneGraph/issues/167
+    depends_on('ffmpeg@:2', when='@:3.4.0+ffmpeg')
+
+    patch('glibc-jasper.patch', when='@3.4%gcc')
 
     def cmake_args(self):
         spec = self.spec
 
         shared_status = 'ON' if '+shared' in spec else 'OFF'
+        opengl_profile = 'GL{0}'.format(spec['gl'].version.up_to(1))
 
         args = [
+            # Variant Options #
             '-DDYNAMIC_OPENSCENEGRAPH={0}'.format(shared_status),
             '-DDYNAMIC_OPENTHREADS={0}'.format(shared_status),
+            '-DOPENGL_PROFILE={0}'.format(opengl_profile),
+
+            # General Options #
             '-DBUILD_OSG_APPLICATIONS=OFF',
             '-DOSG_NOTIFY_DISABLED=ON',
             '-DLIB_POSTFIX=',
             '-DCMAKE_RELWITHDEBINFO_POSTFIX=',
+            '-DCMAKE_MINSIZEREL_POSTFIX='
         ]
-        if spec.satisfies('@:3.2'):
-            args.extend([
-                '-DZLIB_INCLUDE_DIR={0}'.format(spec['zlib'].prefix.include),
-                '-DZLIB_LIBRARY={0}/libz.{1}'.format(spec['zlib'].prefix.lib,
-                                                     dso_suffix),
-            ])
+
+        if spec.satisfies('~ffmpeg'):
+            for ffmpeg_lib in ['libavcodec', 'libavformat', 'libavutil']:
+                args.extend([
+                    '-DFFMPEG_{0}_INCLUDE_DIRS='.format(ffmpeg_lib.upper()),
+                    '-DFFMPEG_{0}_LIBRARIES='.format(ffmpeg_lib.upper()),
+                ])
 
         # NOTE: This is necessary in order to allow OpenSceneGraph to compile
         # despite containing a number of implicit bool to int conversions.

From 97e67b385c03378868d84a0e2d90c337ebf3ba0d Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Wed, 29 Apr 2020 00:33:22 -0700
Subject: [PATCH 169/802] ffmpeg: add v1.0.10, v2.8.15; add '+avresample';
 improve variant handling (#16359)

* ffmpeg: add older versions (i.e. 2.8.15, 1.0.10), add 'avresample' variant

* ffmpeg: update variant handling to support older versions (i.e. 2.8.15, 1.0.10)
---
 .../repos/builtin/packages/ffmpeg/package.py  | 123 +++++++++++-------
 1 file changed, 78 insertions(+), 45 deletions(-)

diff --git a/var/spack/repos/builtin/packages/ffmpeg/package.py b/var/spack/repos/builtin/packages/ffmpeg/package.py
index eda88445ee6..3eb365848cc 100644
--- a/var/spack/repos/builtin/packages/ffmpeg/package.py
+++ b/var/spack/repos/builtin/packages/ffmpeg/package.py
@@ -13,10 +13,12 @@ class Ffmpeg(AutotoolsPackage):
     homepage = "https://ffmpeg.org"
     url      = "http://ffmpeg.org/releases/ffmpeg-4.1.1.tar.bz2"
 
-    version('4.2.2', sha256='b620d187c26f76ca19e74210a0336c3b8380b97730df5cdf45f3e69e89000e5c')
-    version('4.1.1', sha256='0cb40e3b8acaccd0ecb38aa863f66f0c6e02406246556c2992f67bf650fab058')
-    version('4.1',   sha256='b684fb43244a5c4caae652af9022ed5d85ce15210835bce054a33fb26033a1a5')
-    version('3.2.4', sha256='c0fa3593a2e9e96ace3c1757900094437ad96d1d6ca19f057c378b5f394496a4')
+    version('4.2.2',  sha256='b620d187c26f76ca19e74210a0336c3b8380b97730df5cdf45f3e69e89000e5c')
+    version('4.1.1',  sha256='0cb40e3b8acaccd0ecb38aa863f66f0c6e02406246556c2992f67bf650fab058')
+    version('4.1',    sha256='b684fb43244a5c4caae652af9022ed5d85ce15210835bce054a33fb26033a1a5')
+    version('3.2.4',  sha256='c0fa3593a2e9e96ace3c1757900094437ad96d1d6ca19f057c378b5f394496a4')
+    version('2.8.15', sha256='35647f6c1f6d4a1719bc20b76bf4c26e4ccd665f46b5676c0e91c5a04622ee21')
+    version('1.0.10', sha256='1dbde434c3b5c573d3b2ffc1babe3814f781c10c4bc66193a4132a44c9715176')
 
     # Licensing
     variant('gpl', default=True,
@@ -53,9 +55,10 @@ class Ffmpeg(AutotoolsPackage):
     # variant('libxml2', default=False,
     #         description='XML parsing, needed for dash demuxing support')
     variant('libzmq', default=False, description='message passing via libzmq')
-    variant('lzma', default=True, description='lzma support')
+    variant('lzma', default=False, description='lzma support')
+    variant('avresample', default=False, description='AV reasmpling component')
     variant('openssl', default=False, description='needed for https support')
-    variant('sdl2', default=True, description='sdl2 support')
+    variant('sdl2', default=False, description='sdl2 support')
     variant('shared', default=True, description='build shared libraries')
 
     depends_on('alsa-lib')
@@ -84,58 +87,88 @@ class Ffmpeg(AutotoolsPackage):
     depends_on('speex', when='+libspeex')
     depends_on('xz', when='+lzma')
 
+    # TODO: enable when libxml2 header issue is resolved
+    # conflicts('+libxml2', when='@:3.999')
+    # See: https://www.ffmpeg.org/index.html#news (search AV1)
+    conflicts('+libaom', when='@:3.999')
+    # All of the following constraints were sourced from the official 'ffmpeg'
+    # change log, which can be found here:
+    # https://raw.githubusercontent.com/FFmpeg/FFmpeg/release/4.0/Changelog
+    conflicts('+sdl2', when='@:3.1.999')
+    conflicts('+libsnappy', when='@:2.7.999')
+    conflicts('+X', when='@:2.4.999')
+    conflicts('+lzma', when='@2.3.999:')
+    conflicts('+libwebp', when='@2.1.999:')
+    conflicts('+libssh', when='@2.0.999:')
+    conflicts('+libzmq', when='@:1.999.999')
+
+    def enable_or_disable_meta(self, variant, options):
+        switch = 'enable' if '+{0}'.format(variant) in self.spec else 'disable'
+        return ['--{0}-{1}'.format(switch, option) for option in options]
+
     def configure_args(self):
         spec = self.spec
         config_args = ['--enable-pic']
 
-        if '+X' in spec:
-            config_args.extend([
-                '--enable-libxcb',
-                '--enable-libxcb-shape',
-                '--enable-libxcb-shm',
-                '--enable-libxcb-xfixes',
-                '--enable-xlib',
-            ])
-        else:
-            config_args.extend([
-                '--disable-libxcb',
-                '--disable-libxcb-shape',
-                '--disable-libxcb-shm',
-                '--disable-libxcb-xfixes',
-                '--disable-xlib',
+        # '+X' meta variant #
+
+        xlib_opts = []
+
+        if spec.satisfies('@2.5:'):
+            xlib_opts.extend([
+                'libxcb',
+                'libxcb-shape',
+                'libxcb-shm',
+                'libxcb-xfixes',
+                'xlib',
             ])
 
-        if '+drawtext' in spec:
-            config_args.extend([
-                '--enable-libfontconfig',
-                '--enable-libfreetype',
-                '--enable-libfribidi',
-            ])
-        else:
-            config_args.extend([
-                '--disable-libfontconfig',
-                '--disable-libfreetype',
-                '--disable-libfribidi',
-            ])
-        for variant in [
+        config_args += self.enable_or_disable_meta('X', xlib_opts)
+
+        # '+drawtext' meta variant #
+
+        drawtext_opts = [
+            '{0}fontconfig'.format('lib' if spec.satisfies('@3:') else ''),
+            'libfreetype',
+        ]
+
+        if spec.satisfies('@2.3:'):
+            drawtext_opts.append('libfribidi')
+
+        config_args += self.enable_or_disable_meta('drawtext', drawtext_opts)
+
+        # other variants #
+
+        variant_opts = [
             'bzlib',
-            'libaom',
             'libmp3lame',
             'libopenjpeg',
             'libopus',
-            'libsnappy',
             'libspeex',
-            'libssh',
             'libvorbis',
-            'libwebp',
-            # TODO: enable when libxml2 header issue is resolved
-            # 'libxml2',
-            'libzmq',
-            'lzma',
+            'avresample',
             'openssl',
-            'sdl2',
             'shared',
-        ]:
-            config_args += self.enable_or_disable(variant)
+        ]
+
+        if spec.satisfies('@2.0:'):
+            variant_opts.append('libzmq')
+        if spec.satisfies('@2.1:'):
+            variant_opts.append('libssh')
+        if spec.satisfies('@2.2:'):
+            variant_opts.append('libwebp')
+        if spec.satisfies('@2.4:'):
+            variant_opts.append('lzma')
+        if spec.satisfies('@2.8:'):
+            variant_opts.append('libsnappy')
+        if spec.satisfies('@3.2:'):
+            variant_opts.append('sdl2')
+        if spec.satisfies('@4:'):
+            variant_opts.append('libaom')
+            # TODO: enable when libxml2 header issue is resolved
+            # variant_opts.append('libxml2')
+
+        for variant_opt in variant_opts:
+            config_args += self.enable_or_disable(variant_opt)
 
         return config_args

From 39bbe8f9d489e2e53a857b725b5d88236e54fee6 Mon Sep 17 00:00:00 2001
From: "Jonathan R. Madsen" <jrmadsen@users.noreply.github.com>
Date: Wed, 29 Apr 2020 06:19:17 -0700
Subject: [PATCH 170/802] Update timemory to support new dependencies and
 expose more build options (#16241)

* Update timemory/package.py to support new dependencies and expose more build options

* Added missing 'use_arch' option handling

* Fixes for python 2.6

* Fix pyflake error F632

* F632 flake fixes

* Update package.py

* Update package.py

* 80 char width + added extra conflicts + fixed kokkos_modules reference

* 79 char width

* Removed submodule builds

- added allinea_map variant
- disabled caliper by default
- added ompt_{standalone,llvm} variants

* flake8 updates

* 79 char width
---
 .../builtin/packages/timemory/package.py      | 198 +++++++++++++-----
 1 file changed, 142 insertions(+), 56 deletions(-)

diff --git a/var/spack/repos/builtin/packages/timemory/package.py b/var/spack/repos/builtin/packages/timemory/package.py
index 53dada7f342..8561ca07f31 100644
--- a/var/spack/repos/builtin/packages/timemory/package.py
+++ b/var/spack/repos/builtin/packages/timemory/package.py
@@ -6,6 +6,7 @@
 # ----------------------------------------------------------------------------
 
 from spack import *
+from sys import platform
 
 
 class Timemory(CMakePackage):
@@ -22,18 +23,70 @@ class Timemory(CMakePackage):
     version('3.0.0', commit='b36b1673b2c6b7ff3126d8261bef0f8f176c7beb',
             submodules=True)
 
+    linux = False if platform == 'darwin' else True
+
+    variant('shared', default=True, description='Build shared libraries')
+    variant('static', default=False, description='Build static libraries')
     variant('python', default=True, description='Enable Python support')
-    variant('mpi', default=False, description='Enable MPI support')
-    variant('tau', default=True, description='Enable TAU support')
-    variant('papi', default=True, description='Enable PAPI support')
-    variant('cuda', default=True, description='Enable CUDA support')
-    variant('cupti', default=True, description='Enable CUPTI support')
+    variant('mpi', default=True, description='Enable MPI support')
+    variant('tau', default=False, description='Enable TAU support')
+    variant('papi', default=linux, description='Enable PAPI support')
+    variant('cuda', default=linux, description='Enable CUDA support')
+    variant('cupti', default=linux, description='Enable CUPTI support')
+    variant('tools', default=True, description='Build/install extra tools')
+    variant('vtune', default=False, description='Enable VTune support')
     variant('upcxx', default=False, description='Enable UPC++ support')
-    variant('gotcha', default=True, description='Enable GOTCHA support')
-    variant('likwid', default=True, description='Enable LIKWID support')
-    variant('caliper', default=True, description='Enable Caliper support')
+    variant('gotcha', default=linux, description='Enable GOTCHA support')
+    variant('likwid', default=linux, description='Enable LIKWID support')
+    variant('caliper', default=False, description='Enable Caliper support')
+    variant('dyninst', default=linux,
+            description='Build dynamic instrumentation tools')
+    variant('examples', default=False, description='Build/install examples')
     variant('gperftools', default=True,
             description='Enable gperftools support')
+    variant('kokkos_tools', default=True,
+            description=('Build generic kokkos-tools libraries, e.g. '
+                         'kp_timemory, kp_timemory_filter'))
+    variant('kokkos_build_config', default=False,
+            description=('Build pre-configured (i.e. dedicated) kokkos-tools '
+                         'libraries, e.g. kp_timemory_cpu_flops'))
+    variant('cuda_arch', default='auto', description='CUDA architecture name',
+            values=('auto', 'kepler', 'tesla', 'maxwell', 'pascal',
+                    'volta', 'turing'), multi=False)
+    variant('cpu_target', default='auto',
+            description=('Build for specific cpu architecture (specify '
+                         'cpu-model)'))
+    variant('use_arch', default=False,
+            description=('Build all of timemory w/ cpu_target architecture '
+                         'flags (default: roofline toolkit only)'))
+    variant('tls_model', default='global-dynamic',
+            description='Thread-local static model', multi=False,
+            values=('global-dynamic', 'local-dynamic', 'initial-exec',
+                    'local-exec'))
+    variant('lto', default=False,
+            description='Build w/ link-time optimization')
+    variant('statistics', default=True,
+            description=('Build components w/ support for statistics '
+                         '(min/max/stddev)'))
+    variant('extra_optimizations', default=True,
+            description='Build timemory with extra optimization flags')
+    variant('cxxstd', default='14', description='C++ language standard',
+            values=('14', '17', '20'), multi=False)
+    variant('mpip_library', default=linux,
+            description='Build stand-alone timemory-mpip GOTCHA library')
+    variant('ompt', default=True, description=('Enable OpenMP tools support'))
+    variant('ompt_standalone', default=True,
+            description=('Enable OpenMP tools support via drop-in '
+                         'replacement of libomp/libgomp/libiomp5'))
+    variant('ompt_llvm', default=False,
+            description='Enable OpenMP tools support as part of llvm build')
+    variant('ompt_library', default=True,
+            description='Build stand-alone timemory-ompt library')
+    variant('allinea_map', default=False,
+            description='Enable Allinea ARM-MAP support')
+    variant('require_packages', default=False,
+            description=('find_package(...) resulting in NOTFOUND '
+                         'generates error'))
 
     depends_on('cmake@3.11:', type='build')
 
@@ -48,77 +101,110 @@ class Timemory(CMakePackage):
     depends_on('cuda', when='+cuda')
     depends_on('cuda', when='+cupti')
     depends_on('upcxx', when='+upcxx')
-    depends_on('gotcha', when='+gotcha')
     depends_on('likwid', when='+likwid')
+    depends_on('gotcha', when='+gotcha')
     depends_on('caliper', when='+caliper')
+    depends_on('dyninst', when='+dyninst')
     depends_on('gperftools', when='+gperftools')
+    depends_on('intel-parallel-studio', when='+vtune')
+    depends_on('llvm-openmp-ompt+standalone', when='+ompt_standalone')
+    depends_on('llvm-openmp-ompt~standalone', when='+ompt_llvm')
+    depends_on('arm-forge', when='+allinea_map')
 
+    conflicts('+python', when='~shared',
+              msg='+python requires building shared libraries')
     conflicts('+cupti', when='~cuda', msg='CUPTI requires CUDA')
+    conflicts('+kokkos_tools', when='~tools',
+              msg='+kokkos_tools requires +tools')
+    conflicts('+kokkos_build_config', when='~tools',
+              msg='+kokkos_build_config requires +tools')
+    conflicts('+kokkos_build_config', when='~kokkos_tools',
+              msg='+kokkos_build_config requires +kokkos_tools')
+    conflicts('tls_model=local-dynamic', when='+python',
+              msg='+python require tls_model=global-dynamic')
+    conflicts('tls_model=initial-exec', when='+python',
+              msg='+python require tls_model=global-dynamic')
+    conflicts('tls_model=local-exec', when='+python',
+              msg='+python require tls_model=global-dynamic')
+    conflicts('+mpip_library', when='~mpi', msg='+mpip_library requires +mpi')
+    conflicts('+mpip_library', when='~gotcha',
+              msg='+mpip_library requires +gotcha')
+    conflicts('+mpip_library', when='~shared',
+              msg='+mpip_library requires building shared libraries')
+    conflicts('+ompt_standalone', when='~ompt',
+              msg='+ompt_standalone requires +ompt')
+    conflicts('+ompt_llvm', when='~ompt',
+              msg='+ompt_llvm requires +ompt')
+    conflicts('+ompt_library', when='~ompt',
+              msg='+ompt_library requires +ompt')
+    conflicts('+ompt_library', when='~shared~static',
+              msg='+ompt_library requires building shared or static libraries')
+    conflicts('+ompt_standalone+ompt_llvm',
+              msg=('+ompt_standalone and +ompt_llvm are not compatible. Use '
+                   '+ompt_llvm~ompt_standalone if building LLVM, use '
+                   '~ompt_llvm+ompt_standalone if ompt.h is not provided by '
+                   'the compiler'))
 
     def cmake_args(self):
         spec = self.spec
 
-        # Use spack install of Caliper and/or GOTCHA
-        # instead of internal submodule build
         args = [
-            '-DTIMEMORY_BUILD_GOTCHA=OFF',
-            '-DTIMEMORY_BUILD_CALIPER=OFF',
-            '-DTIMEMORY_BUILD_TOOLS=ON',
+            '-DTIMEMORY_BUILD_PYTHON=ON',
             '-DTIMEMORY_BUILD_TESTING=OFF',
-            '-DTIMEMORY_BUILD_EXTRA_OPTIMIZATIONS=ON',
             '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON',
         ]
 
+        cxxstd = spec.variants['cxxstd'].value
+        args.append('-DCMAKE_CXX_STANDARD={0}'.format(cxxstd))
+
+        tls = spec.variants['tls_model'].value
+        args.append('-DTIMEMORY_TLS_MODEL={0}'.format(tls))
+
         if '+python' in spec:
             args.append('-DPYTHON_EXECUTABLE={0}'.format(
                 spec['python'].command.path))
-            args.append('-DTIMEMORY_USE_PYTHON=ON')
-            args.append('-DTIMEMORY_BUILD_PYTHON=ON')
-            args.append('-DTIMEMORY_TLS_MODEL=global-dynamic')
-        else:
-            args.append('-DTIMEMORY_USE_PYTHON=OFF')
-            args.append('-DTIMEMORY_BUILD_PYTHON=OFF')
-
-        if '+caliper' in spec:
-            args.append('-DTIMEMORY_USE_CALIPER=ON')
-        else:
-            args.append('-DTIMEMORY_USE_CALIPER=OFF')
-
-        if '+tau' in spec:
-            args.append('-DTIMEMORY_USE_TAU=ON')
-        else:
-            args.append('-DTIMEMORY_USE_TAU=OFF')
-
-        if '+likwid' in spec:
-            args.append('-DTIMEMORY_USE_LIKWID=ON')
-        else:
-            args.append('-DTIMEMORY_USE_LIKWID=OFF')
-
-        if '+papi' in spec:
-            args.append('-DTIMEMORY_USE_PAPI=ON')
-            args.append('-DPAPI_ROOT_DIR={0}'.format(spec['papi'].prefix))
-        else:
-            args.append('-DTIMEMORY_USE_PAPI=OFF')
 
         if '+mpi' in spec:
+            args.append('-DTIMEMORY_USE_MPI_LINK_FLAGS=OFF')
             args.append('-DMPI_C_COMPILER={0}'.format(spec['mpi'].mpicc))
             args.append('-DMPI_CXX_COMPILER={0}'.format(spec['mpi'].mpicxx))
-        else:
-            args.append('-DTIMEMORY_USE_MPI=OFF')
-
-        if '+gotcha' in spec:
-            args.append('-DTIMEMORY_USE_GOTCHA=ON')
-        else:
-            args.append('-DTIMEMORY_USE_GOTCHA=OFF')
 
         if '+cuda' in spec:
-            args.append('-DTIMEMORY_USE_CUDA=ON')
-        else:
-            args.append('-DTIMEMORY_USE_CUDA=OFF')
+            targ = spec.variants['cuda_arch'].value
+            key = '' if spec.satisfies('@:3.0.1') else 'TIMEMORY_'
+            # newer versions use 'TIMEMORY_CUDA_ARCH'
+            args.append('-D{0}CUDA_ARCH={1}'.format(key, targ))
 
-        if '+cupti' in spec:
-            args.append('-DTIMEMORY_USE_CUPTI=ON')
-        else:
-            args.append('-DTIMEMORY_USE_CUPTI=OFF')
+        cpu_target = spec.variants['cpu_target'].value
+        if cpu_target == 'auto':
+            args.append('-DCpuArch_TARGET={0}'.format(cpu_target))
+
+        # forced disabling of submodule builds
+        for dep in ('caliper', 'gotcha', 'ompt'):
+            args.append('-DTIMEMORY_BUILD_{0}=OFF'.format(dep.upper()))
+
+        # spack options which translate to TIMEMORY_<OPTION>
+        for dep in ('require_packages', 'kokkos_build_config', 'use_arch'):
+            args.append('-DTIMEMORY_{0}={1}'.format(
+                dep.upper(), 'ON' if '+{0}'.format(dep) in spec else 'OFF'))
+
+        # spack options which translate to BUILD_<OPTION>_LIBS
+        for dep in ('shared', 'static'):
+            args.append('-DBUILD_{0}_LIBS={1}'.format(
+                dep.upper(), 'ON' if '+{0}'.format(dep) in spec else 'OFF'))
+
+        # spack options which translate to TIMEMORY_BUILD_<OPTION>
+        for dep in ('tools', 'examples', 'kokkos_tools', 'lto',
+                    'extra_optimizations', 'mpip_library', 'ompt_library'):
+            args.append('-DTIMEMORY_BUILD_{0}={1}'.format(
+                dep.upper(), 'ON' if '+{0}'.format(dep) in spec else 'OFF'))
+
+        # spack options which translate to TIMEMORY_USE_<OPTION>
+        for dep in ('allinea_map', 'python', 'mpi', 'tau', 'papi', 'ompt',
+                    'cuda', 'cupti', 'cupti', 'vtune', 'upcxx', 'gotcha',
+                    'likwid', 'caliper', 'dyninst', 'gperftools',
+                    'statistics'):
+            args.append('-DTIMEMORY_USE_{0}={1}'.format(
+                dep.upper(), 'ON' if '+{0}'.format(dep) in spec else 'OFF'))
 
         return args

From 0d9b0031694e7fdcde42d36a0df5694cb1c37bd9 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 29 Apr 2020 21:20:05 +0800
Subject: [PATCH 171/802] Add new package: trident (#16342)

* Add new package: trident

* remove unused source code
---
 .../repos/builtin/packages/trident/package.py | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/trident/package.py

diff --git a/var/spack/repos/builtin/packages/trident/package.py b/var/spack/repos/builtin/packages/trident/package.py
new file mode 100644
index 00000000000..6e13a864dc7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/trident/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Trident(Package):
+    """Trident is a fully supported open source project maintained by
+    NetApp. It has been designed from the ground up to help you meet
+    the sophisticated persistence demands of your containerized
+    applications."""
+
+    homepage = "https://netapp-trident.readthedocs.io"
+    url      = "https://github.com/NetApp/trident/archive/v20.01.1.tar.gz"
+
+    version('20.01.1', sha256='02ba92e569916b98fb1b563c5ef03a94fd7981c3ac1ecb47e69ebb45471dc976')
+    version('20.01.0', sha256='5de190579acf62f5e9945dfd45aeb21989272c4972e85cb10256b7ec605c29c7')
+
+    depends_on('go', type='build')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        go = which('go')
+        go('build', '-o', prefix.bin)
+        with working_dir('cli'):
+            go('build', '-o', prefix.bin.tridentctl)

From 35b9901fa0732c0552e8ad6b9cf7ac0b131fa130 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 29 Apr 2020 22:57:16 +0800
Subject: [PATCH 172/802] Add new package: fping (#16367)

---
 .../repos/builtin/packages/fping/package.py   | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/fping/package.py

diff --git a/var/spack/repos/builtin/packages/fping/package.py b/var/spack/repos/builtin/packages/fping/package.py
new file mode 100644
index 00000000000..59c2127dad1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fping/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fping(AutotoolsPackage):
+    """High performance ping tool."""
+
+    homepage = "https://fping.org/"
+    url      = "https://github.com/schweikert/fping/archive/v4.2.tar.gz"
+
+    version('4.2', sha256='49b0ac77fd67c1ed45c9587ffab0737a3bebcfa5968174329f418732dbf655d4')
+    version('4.1', sha256='1da45b1d8c2d38b52bebd4f8b1617ddfae678e9f6436dafa6f62e97b8ecfc93c')
+    version('4.0', sha256='8c9eac7aeadb5be0daa978cdac5f68ae44b749af0f643e8252b5e3dd4ce32e6a')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')

From 890059c6354dc78993fb3519f47ef3eaff1d5bc7 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 29 Apr 2020 22:57:38 +0800
Subject: [PATCH 173/802] Add new package: libconfuse (#16368)

---
 .../builtin/packages/libconfuse/package.py    | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/libconfuse/package.py

diff --git a/var/spack/repos/builtin/packages/libconfuse/package.py b/var/spack/repos/builtin/packages/libconfuse/package.py
new file mode 100644
index 00000000000..eedbaec83ad
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libconfuse/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libconfuse(AutotoolsPackage):
+    """Small configuration file parser library for C."""
+
+    homepage = "https://github.com/martinh/libconfuse"
+    url      = "https://github.com/martinh/libconfuse/archive/v3.2.2.tar.gz"
+
+    version('3.2.2', sha256='2cf7e032980aff8f488efba61510dc3fb95e9a4b9183f985dea457a5651b0e2c')
+    version('3.2.1', sha256='2eff8e3c300c4ed1d67fdb13f9d31a72a68e31874b4640db15334305bc40cebd')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')

From 5697894b22a540ea8931394dbc8a59b9ecf44b9a Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 29 Apr 2020 22:58:09 +0800
Subject: [PATCH 174/802] Add new package: graylog2-server (#16370)

---
 .../packages/graylog2-server/package.py       | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/graylog2-server/package.py

diff --git a/var/spack/repos/builtin/packages/graylog2-server/package.py b/var/spack/repos/builtin/packages/graylog2-server/package.py
new file mode 100644
index 00000000000..b34fd87a1b5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/graylog2-server/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Graylog2Server(Package):
+    """Free and open source log management."""
+
+    homepage = "https://www.graylog.org/"
+    url      = "https://github.com/Graylog2/graylog2-server/archive/3.2.4.tar.gz"
+
+    version('3.2.4', sha256='d34cc9fd42b2ee0b872c0f644fe53ef9b2e9790029c5d2182f782f66f1e1d99d')
+    version('3.2.3', sha256='6da5ba1da897a371a490a6ba7c9d017a479a22e3c16a39280a49e61f551280c0')
+    version('3.2.2', sha256='dc7baa5c0e451b0927b28320c4d9ca19810f4690eb2c521ed8a8272c99fb3bc3')
+    version('3.2.1', sha256='f570dbb557888ca4dbc932fb6ed840dbb616b9ed50e034d17de69a69f08d1aec')
+    version('3.2.0', sha256='094eed607d0d0a7c380825d6507c1e40a53c4493b5f9fe8ae5a3ddd86521711e')
+
+    depends_on('java@8', type=("build", "run"))
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix)

From 42d7fd30c46482fe3d8da1e65301bf5e7da2df6f Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 29 Apr 2020 22:58:35 +0800
Subject: [PATCH 175/802] Add new package: brpc (#16309)

* Add new package: brpc

* change a patch for brpc

* refine brpc version

* refine brpc patch constraint
---
 .../repos/builtin/packages/brpc/narrow.patch  | 33 +++++++++++++++++++
 .../repos/builtin/packages/brpc/package.py    | 26 +++++++++++++++
 2 files changed, 59 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/brpc/narrow.patch
 create mode 100644 var/spack/repos/builtin/packages/brpc/package.py

diff --git a/var/spack/repos/builtin/packages/brpc/narrow.patch b/var/spack/repos/builtin/packages/brpc/narrow.patch
new file mode 100644
index 00000000000..621e32f9987
--- /dev/null
+++ b/var/spack/repos/builtin/packages/brpc/narrow.patch
@@ -0,0 +1,33 @@
+diff --git a/src/butil/containers/case_ignored_flat_map.cpp b/src/butil/containers/case_ignored_flat_map.cpp
+index 7f2fadc5..a7471561 100644
+--- a/src/butil/containers/case_ignored_flat_map.cpp
++++ b/src/butil/containers/case_ignored_flat_map.cpp
+@@ -19,7 +19,7 @@
+ 
+ namespace butil {
+ 
+-static const char g_tolower_map_base[] = {
++static const signed char g_tolower_map_base[] = {
+     -128, -127, -126, -125, -124, -123, -122, -121, -120,
+     -119, -118, -117, -116, -115, -114, -113, -112, -111, -110,
+     -109, -108, -107, -106, -105, -104, -103, -102, -101, -100,
+@@ -48,6 +48,6 @@ static const char g_tolower_map_base[] = {
+     120, 121, 122, 123, 124, 125, 126, 127
+ };
+ 
+-extern const char* const g_tolower_map = g_tolower_map_base + 128;
++extern const signed char* const g_tolower_map = g_tolower_map_base + 128;
+ 
+ } // namespace butil
+diff --git a/src/butil/containers/case_ignored_flat_map.h b/src/butil/containers/case_ignored_flat_map.h
+index ed6e58b4..6bc1a9af 100644
+--- a/src/butil/containers/case_ignored_flat_map.h
++++ b/src/butil/containers/case_ignored_flat_map.h
+@@ -27,7 +27,7 @@ namespace butil {
+ // NOTE: Using ascii_tolower instead of ::tolower shortens 150ns in
+ // FlatMapTest.perf_small_string_map (with -O2 added, -O0 by default)
+ inline char ascii_tolower(char c) {
+-    extern const char* const g_tolower_map;
++    extern const signed char* const g_tolower_map;
+     return g_tolower_map[(int)c];
+ }
diff --git a/var/spack/repos/builtin/packages/brpc/package.py b/var/spack/repos/builtin/packages/brpc/package.py
new file mode 100644
index 00000000000..ba1417babf0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/brpc/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Brpc(CMakePackage):
+    """An industrial-grade RPC framework used throughout Baidu, with
+    1,000,000+ instances(not counting clients) and thousands kinds of
+    services, called "baidu-rpc" inside Baidu. Only C++ implementatioo
+    on is opensourced right now."""
+
+    homepage = "https://github.com/apache/incubator-brpc"
+    url      = "https://github.com/apache/incubator-brpc/archive/0.9.7.tar.gz"
+
+    version('0.9.7', sha256='722cd342baf3b05189ca78ecf6c56ea6ffec22e62fc2938335e4e5bab545a49c')
+    version('0.9.6', sha256='b872ca844999e0ba768acd823b409761f126590fb34cb0183da915a595161446')
+    version('0.9.5', sha256='11ca8942242a4c542c11345b7463a4aea33a11ca33e91d9a2f64f126df8c70e9')
+
+    depends_on('gflags')
+    depends_on('protobuf')
+    depends_on('leveldb')
+
+    patch('narrow.patch', sha256='d7393029443853ddda6c09e3d2185ac2f60920a36a8b685eb83b6b80c1535539', when='@:0.9.7')

From b6b44948b8624b6e23484a8cb59f8e325ef76e37 Mon Sep 17 00:00:00 2001
From: Nathan <35582439+yee29@users.noreply.github.com>
Date: Wed, 29 Apr 2020 08:52:23 -0700
Subject: [PATCH 176/802] prefix gets removed when adding additional configure
 options (#16335)

* prefix gets removed when adding additional configure options

* Update waf documentation to reflect the new change
---
 lib/spack/docs/build_systems/wafpackage.rst | 5 +++--
 lib/spack/spack/build_systems/waf.py        | 5 +++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/lib/spack/docs/build_systems/wafpackage.rst b/lib/spack/docs/build_systems/wafpackage.rst
index 1916630f4ce..36fc21a7722 100644
--- a/lib/spack/docs/build_systems/wafpackage.rst
+++ b/lib/spack/docs/build_systems/wafpackage.rst
@@ -47,8 +47,9 @@ Each phase provides a ``<phase>`` function that runs:
 
 where ``<jobs>`` is the number of parallel jobs to build with. Each phase
 also has a ``<phase_args>`` function that can pass arguments to this call.
-All of these functions are empty except for the ``configure_args``
-function, which passes ``--prefix=/path/to/installation/prefix``.
+All of these functions are empty. The ``configure`` phase
+automatically adds  ``--prefix=/path/to/installation/prefix``, so you
+don't need to add that in the ``configure_args``.
 
 ^^^^^^^
 Testing
diff --git a/lib/spack/spack/build_systems/waf.py b/lib/spack/spack/build_systems/waf.py
index 6bf9a432e03..a1581660f22 100644
--- a/lib/spack/spack/build_systems/waf.py
+++ b/lib/spack/spack/build_systems/waf.py
@@ -75,13 +75,14 @@ def waf(self, *args, **kwargs):
 
     def configure(self, spec, prefix):
         """Configures the project."""
-        args = self.configure_args()
+        args = ['--prefix={0}'.format(self.prefix)]
+        args += self.configure_args()
 
         self.waf('configure', *args)
 
     def configure_args(self):
         """Arguments to pass to configure."""
-        return ['--prefix={0}'.format(self.prefix)]
+        return []
 
     def build(self, spec, prefix):
         """Executes the build."""

From 0385e8477571d81b36cfb2ce35ad9cd70b36164a Mon Sep 17 00:00:00 2001
From: "Dr. Christian Tacke"
 <58549698+ChristianTackeGSI@users.noreply.github.com>
Date: Wed, 29 Apr 2020 19:53:58 +0200
Subject: [PATCH 177/802] boost: Patch for boostorg/process/issues/116 (#16371)

Patch for "Unable to compile code using boost/process.hpp"
See: https://github.com/boostorg/process/issues/116
---
 .../packages/boost/1.72_boost_process.patch   | 48 +++++++++++++++++++
 .../repos/builtin/packages/boost/package.py   |  5 ++
 2 files changed, 53 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/boost/1.72_boost_process.patch

diff --git a/var/spack/repos/builtin/packages/boost/1.72_boost_process.patch b/var/spack/repos/builtin/packages/boost/1.72_boost_process.patch
new file mode 100644
index 00000000000..54cd2ae6715
--- /dev/null
+++ b/var/spack/repos/builtin/packages/boost/1.72_boost_process.patch
@@ -0,0 +1,48 @@
+From 6a4d2ff72114ef47c7afaf92e1042aca3dfa41b0 Mon Sep 17 00:00:00 2001
+From: Klemens David Morgenstern <klemens.morgenstern@gmx.net>
+Date: Fri, 22 Nov 2019 14:03:22 +0800
+Subject: [PATCH] added typedef executor_type;
+
+---
+ include/boost/process/async_pipe.hpp                | 2 ++
+ include/boost/process/detail/posix/async_pipe.hpp   | 1 +
+ include/boost/process/detail/windows/async_pipe.hpp | 1 +
+ 3 files changed, 4 insertions(+)
+
+diff --git a/include/boost/process/async_pipe.hpp b/include/boost/process/async_pipe.hpp
+index 101fe1d59..a562432c0 100644
+--- a/include/boost/process/async_pipe.hpp
++++ b/include/boost/process/async_pipe.hpp
+@@ -47,6 +47,8 @@ class async_pipe
+      */
+     typedef platform_specific handle_type;
+ 
++    typedef typename handle_type::executor_type executor_type;
++
+     /** Construct a new async_pipe, does automatically open the pipe.
+      * Initializes source and sink with the same io_context.
+      * @note Windows creates a named pipe here, where the name is automatically generated.
+diff --git a/include/boost/process/detail/posix/async_pipe.hpp b/include/boost/process/detail/posix/async_pipe.hpp
+index 725a07890..a82c057b9 100644
+--- a/include/boost/process/detail/posix/async_pipe.hpp
++++ b/include/boost/process/detail/posix/async_pipe.hpp
+@@ -23,6 +23,7 @@ class async_pipe
+ public:
+     typedef int native_handle_type;
+     typedef ::boost::asio::posix::stream_descriptor handle_type;
++    typedef typename handle_type::executor_type executor_type;
+ 
+     inline async_pipe(boost::asio::io_context & ios) : async_pipe(ios, ios) {}
+ 
+diff --git a/include/boost/process/detail/windows/async_pipe.hpp b/include/boost/process/detail/windows/async_pipe.hpp
+index 06d5f2d85..0b447f9b8 100644
+--- a/include/boost/process/detail/windows/async_pipe.hpp
++++ b/include/boost/process/detail/windows/async_pipe.hpp
+@@ -48,6 +48,7 @@ class async_pipe
+ public:
+     typedef ::boost::winapi::HANDLE_ native_handle_type;
+     typedef ::boost::asio::windows::stream_handle   handle_type;
++    typedef typename handle_type::executor_type executor_type;
+ 
+     async_pipe(boost::asio::io_context & ios) : async_pipe(ios, ios, make_pipe_name(), true) {}
+     async_pipe(boost::asio::io_context & ios_source, boost::asio::io_context & ios_sink)
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index cc223d2f7e4..7baff3f28c5 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -209,6 +209,11 @@ def libs(self):
     patch('darwin_clang_version.patch', level=0,
           when='@1.56.0:1.72.0 platform=darwin')
 
+    # Fix: "Unable to compile code using boost/process.hpp"
+    # See: https://github.com/boostorg/process/issues/116
+    # Patch: https://github.com/boostorg/process/commit/6a4d2ff72114ef47c7afaf92e1042aca3dfa41b0.patch
+    patch('1.72_boost_process.patch', level=2, when='@1.72.0')
+
     # Fix the bootstrap/bjam build for Cray
     patch('bootstrap-path.patch', when='@1.39.0: platform=cray')
 

From eef75ddd45f7d5a268cbf9eafd3af5143c271391 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 29 Apr 2020 13:50:34 -0500
Subject: [PATCH 178/802] py-mypy: setuptools needed at run-time (#16375)

---
 var/spack/repos/builtin/packages/py-mypy/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-mypy/package.py b/var/spack/repos/builtin/packages/py-mypy/package.py
index b8cde685dc7..f822ea567eb 100644
--- a/var/spack/repos/builtin/packages/py-mypy/package.py
+++ b/var/spack/repos/builtin/packages/py-mypy/package.py
@@ -15,7 +15,7 @@ class PyMypy(PythonPackage):
     version('0.740', sha256='48c8bc99380575deb39f5d3400ebb6a8a1cb5cc669bbba4d3bb30f904e0a0e7d')
 
     depends_on('python@3.5:', type=('build', 'run'))
-    depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools', type=('build', 'run'))
     depends_on('py-typed-ast@1.4.0:1.4.999', type=('build', 'run'))
     depends_on('py-typing-extensions@3.7.4:', type=('build', 'run'))
     depends_on('py-mypy-extensions@0.4.0:0.4.999', type=('build', 'run'))

From d12e588c60cb98382c3f6907492fbb220e50d62d Mon Sep 17 00:00:00 2001
From: Carson Woods <carsonwoods@users.noreply.github.com>
Date: Wed, 29 Apr 2020 18:22:22 -0400
Subject: [PATCH 179/802] charliecloud: add more checksummed versions (#16146)

* Add more checksummed versions

* Remove all versions not supported by autotools build method

* Add old build system for older versions

* Add suggested changes
---
 .../repos/builtin/packages/charliecloud/package.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/charliecloud/package.py b/var/spack/repos/builtin/packages/charliecloud/package.py
index 59f39fd5307..061ba5cf76d 100644
--- a/var/spack/repos/builtin/packages/charliecloud/package.py
+++ b/var/spack/repos/builtin/packages/charliecloud/package.py
@@ -17,15 +17,22 @@ class Charliecloud(AutotoolsPackage):
     version('master', branch='master')
     version('0.15',   sha256='2163420d43c934151c4f44a188313bdb7f79e576d5a86ba64b9ea45f784b9921')
     version('0.14',   sha256='4ae23c2d6442949e16902f9d5604dbd1d6059aeb5dd461b11fc5c74d49dcb194')
+    version('0.13',   sha256='5740bff6e410ca99484c1bdf3dbe834c0f753c846d55c19d6162967a3e2718e0')
 
     depends_on('m4',       type='build')
     depends_on('autoconf', type='build')
     depends_on('automake', type='build')
     depends_on('libtool',  type='build')
 
-    depends_on('python@3.5:',    type='run')
-    depends_on('py-lark-parser', type='run')
-    depends_on('py-requests',    type='run')
+    # Use skopeo and umoci for older ch-grow version dependencies
+    depends_on('skopeo',         type='run', when='@0.10:0.13')
+    depends_on('umoci',          type='run', when='@0.10:0.13')
+    depends_on('python+libxml2', type='run', when='@0.10:0.13')
+
+    # Charliecloud@0.14 and up use python for building
+    depends_on('python@3.5:',    type='run', when='@0.14:')
+    depends_on('py-lark-parser', type='run', when='@0.14:')
+    depends_on('py-requests',    type='run', when='@0.14:')
 
     # man pages and html docs variant
     variant('docs', default=False, description='Build man pages and html docs')
@@ -37,6 +44,7 @@ class Charliecloud(AutotoolsPackage):
 
     # bash automated testing harness (bats)
     depends_on('bats@0.4.0', type='test')
+    depends_on('python@3.5:', type='test')
 
     def configure_args(self):
 

From 9698907e741a90e921b5b59e6db9ab80cb459006 Mon Sep 17 00:00:00 2001
From: Chris Green <greenc@fnal.gov>
Date: Wed, 29 Apr 2020 20:18:48 -0500
Subject: [PATCH 180/802] Spack command extensions: error-handling (#13635)

Generally speaking, errors that are encountered when attempting to load
command extensions now terminate the running Spack instance.

* Added new exceptions `spack.cmd.PythonNameError` and
  `spack.cmd.CommandNameError`.
* New functions `spack.cmd.require_python_name(pname)` and
  `spack.cmd.require_cmd_name(cname)` check that `pname` and `cname`
  respectively meet requirements, throwing the appropriate error if not.
* `spack.cmd.get_module()` uses `require_cmd_name()` and passes through
  exceptions from module load attempts.
* `spack.cmd.get_command()` uses `require_cmd_name()` and invokes
  `get_module()` with the correct command-name form rather than the
  previous (incorrect) Python name.
* Added New exceptions `spack.extensions.CommandNotFoundError` and
  `spack.extensions.ExtensionNamingError`.
* `_extension_regexp` has a new leading underscore to indicate expected
  privacy.
* `spack.extensions.extension_name()` raises an `ExtensionNamingError`
  rather than using `tty.warn()`.
* `spack.extensions.load_command_extension()` checks command source
  existence early and bails out if missing. Also, exceptions raised by
  `load_module_from_file()` are passed through.
* `spack.extensions.get_module()` raises `CommandNotFoundError` as
  appropriate.
* Spack `main()` allows `parser.add_command()` exceptions to cause
  program end.

Tests:

* More common boilerplate has been pulled out into fixtures including
  `sys.modules` dictionary cleanup and resource-managed creation of a
  simple command extension with specified contents in the source file
  for a single named command.
* "Hello, World!" test now uses a command named `hello-world` instead of
  `hello` in order to verify correct handling of commands with hyphens.
* New tests for:
  * Missing (or misnamed) command.
  * Badly-named extension.
  * Verification that errors encountered during import of a command are
    propagated upward.

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
---
 lib/spack/spack/cmd/__init__.py               |  46 +++-
 lib/spack/spack/extensions.py                 |  87 +++---
 lib/spack/spack/main.py                       |  10 +-
 lib/spack/spack/test/cmd/init_py_functions.py |  29 ++
 lib/spack/spack/test/cmd_extensions.py        | 247 +++++++++++++++---
 5 files changed, 333 insertions(+), 86 deletions(-)
 create mode 100644 lib/spack/spack/test/cmd/init_py_functions.py

diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py
index 83e12004a19..594b5e3a8ec 100644
--- a/lib/spack/spack/cmd/__init__.py
+++ b/lib/spack/spack/cmd/__init__.py
@@ -43,11 +43,28 @@ def python_name(cmd_name):
     return cmd_name.replace("-", "_")
 
 
+def require_python_name(pname):
+    """Require that the provided name is a valid python name (per
+    python_name()). Useful for checking parameters for function
+    prerequisites."""
+    if python_name(pname) != pname:
+        raise PythonNameError(pname)
+
+
 def cmd_name(python_name):
     """Convert module name (with ``_``) to command name (with ``-``)."""
     return python_name.replace('_', '-')
 
 
+def require_cmd_name(cname):
+    """Require that the provided name is a valid command name (per
+    cmd_name()). Useful for checking parameters for function
+    prerequisites.
+    """
+    if cmd_name(cname) != cname:
+        raise CommandNameError(cname)
+
+
 #: global, cached list of all commands -- access through all_commands()
 _all_commands = None
 
@@ -91,6 +108,7 @@ def get_module(cmd_name):
         cmd_name (str): name of the command for which to get a module
             (contains ``-``, not ``_``).
     """
+    require_cmd_name(cmd_name)
     pname = python_name(cmd_name)
 
     try:
@@ -102,8 +120,6 @@ def get_module(cmd_name):
         tty.debug('Imported {0} from built-in commands'.format(pname))
     except ImportError:
         module = spack.extensions.get_module(cmd_name)
-        if not module:
-            raise
 
     attr_setdefault(module, SETUP_PARSER, lambda *args: None)  # null-op
     attr_setdefault(module, DESCRIPTION, "")
@@ -116,14 +132,16 @@ def get_module(cmd_name):
 
 
 def get_command(cmd_name):
-    """Imports the command's function from a module and returns it.
+    """Imports the command function associated with cmd_name.
+
+    The function's name is derived from cmd_name using python_name().
 
     Args:
-        cmd_name (str): name of the command for which to get a module
-            (contains ``-``, not ``_``).
+        cmd_name (str): name of the command (contains ``-``, not ``_``).
     """
+    require_cmd_name(cmd_name)
     pname = python_name(cmd_name)
-    return getattr(get_module(pname), pname)
+    return getattr(get_module(cmd_name), pname)
 
 
 def parse_specs(args, **kwargs):
@@ -419,6 +437,22 @@ def spack_is_git_repo():
         return os.path.isdir('.git')
 
 
+class PythonNameError(spack.error.SpackError):
+    """Exception class thrown for impermissible python names"""
+    def __init__(self, name):
+        self.name = name
+        super(PythonNameError, self).__init__(
+            '{0} is not a permissible Python name.'.format(name))
+
+
+class CommandNameError(spack.error.SpackError):
+    """Exception class thrown for impermissible command names"""
+    def __init__(self, name):
+        self.name = name
+        super(CommandNameError, self).__init__(
+            '{0} is not a permissible Spack command name.'.format(name))
+
+
 ########################################
 # argparse types for argument validation
 ########################################
diff --git a/lib/spack/spack/extensions.py b/lib/spack/spack/extensions.py
index b8fde7d7fa3..4358dcd52f4 100644
--- a/lib/spack/spack/extensions.py
+++ b/lib/spack/spack/extensions.py
@@ -11,10 +11,17 @@
 import types
 
 import llnl.util.lang
-import llnl.util.tty as tty
 import spack.config
+import spack.error
 
-extension_regexp = re.compile(r'spack-([\w]*)')
+_extension_regexp = re.compile(r'spack-(\w[-\w]*)$')
+
+
+# TODO: For consistency we should use spack.cmd.python_name(), but
+#       currently this would create a circular relationship between
+#       spack.cmd and spack.extensions.
+def _python_name(cmd_name):
+    return cmd_name.replace('-', '_')
 
 
 def extension_name(path):
@@ -24,15 +31,16 @@ def extension_name(path):
         path (str): path where the extension resides
 
     Returns:
-        The extension name or None if path doesn't match the format
-        for Spack's extension.
+        The extension name.
+
+    Raises:
+         ExtensionNamingError: if path does not match the expected format
+             for a Spack command extension.
     """
-    regexp_match = re.search(extension_regexp, os.path.basename(path))
+    regexp_match = re.search(_extension_regexp,
+                             os.path.basename(os.path.normpath(path)))
     if not regexp_match:
-        msg = "[FOLDER NAMING]"
-        msg += " {0} doesn't match the format for Spack's extensions"
-        tty.warn(msg.format(path))
-        return None
+        raise ExtensionNamingError(path)
     return regexp_match.group(1)
 
 
@@ -40,23 +48,30 @@ def load_command_extension(command, path):
     """Loads a command extension from the path passed as argument.
 
     Args:
-        command (str): name of the command
+        command (str): name of the command (contains ``-``, not ``_``).
         path (str): base path of the command extension
 
     Returns:
-        A valid module object if the command is found or None
+        A valid module if found and loadable; None if not found. Module
+    loading exceptions are passed through.
     """
-    extension = extension_name(path)
-    if not extension:
-        return None
+    extension = _python_name(extension_name(path))
 
     # Compute the name of the module we search, exit early if already imported
     cmd_package = '{0}.{1}.cmd'.format(__name__, extension)
-    python_name = command.replace('-', '_')
+    python_name = _python_name(command)
     module_name = '{0}.{1}'.format(cmd_package, python_name)
     if module_name in sys.modules:
         return sys.modules[module_name]
 
+    # Compute the absolute path of the file to be loaded, along with the
+    # name of the python module where it will be stored
+    cmd_path = os.path.join(path, extension, 'cmd', python_name + '.py')
+
+    # Short circuit if the command source file does not exist
+    if not os.path.exists(cmd_path):
+        return None
+
     def ensure_package_creation(name):
         package_name = '{0}.{1}'.format(__name__, name)
         if package_name in sys.modules:
@@ -82,17 +97,10 @@ def ensure_package_creation(name):
     ensure_package_creation(extension)
     ensure_package_creation(extension + '.cmd')
 
-    # Compute the absolute path of the file to be loaded, along with the
-    # name of the python module where it will be stored
-    cmd_path = os.path.join(path, extension, 'cmd', command + '.py')
-
-    try:
-        # TODO: Upon removal of support for Python 2.6 substitute the call
-        # TODO: below with importlib.import_module(module_name)
-        module = llnl.util.lang.load_module_from_file(module_name, cmd_path)
-        sys.modules[module_name] = module
-    except (ImportError, IOError):
-        module = None
+    # TODO: Upon removal of support for Python 2.6 substitute the call
+    # TODO: below with importlib.import_module(module_name)
+    module = llnl.util.lang.load_module_from_file(module_name, cmd_path)
+    sys.modules[module_name] = module
 
     return module
 
@@ -103,9 +111,8 @@ def get_command_paths():
     extension_paths = spack.config.get('config:extensions') or []
 
     for path in extension_paths:
-        extension = extension_name(path)
-        if extension:
-            command_paths.append(os.path.join(path, extension, 'cmd'))
+        extension = _python_name(extension_name(path))
+        command_paths.append(os.path.join(path, extension, 'cmd'))
 
     return command_paths
 
@@ -144,7 +151,7 @@ def get_module(cmd_name):
         if module:
             return module
     else:
-        return None
+        raise CommandNotFoundError(cmd_name)
 
 
 def get_template_dirs():
@@ -154,3 +161,23 @@ def get_template_dirs():
     extension_dirs = spack.config.get('config:extensions') or []
     extensions = [os.path.join(x, 'templates') for x in extension_dirs]
     return extensions
+
+
+class CommandNotFoundError(spack.error.SpackError):
+    """Exception class thrown when a requested command is not recognized as
+    such.
+    """
+    def __init__(self, cmd_name):
+        super(CommandNotFoundError, self).__init__(
+            '{0} is not a recognized Spack command or extension command;'
+            ' check with `spack commands`.'.format(cmd_name))
+
+
+class ExtensionNamingError(spack.error.SpackError):
+    """Exception class thrown when a configured extension does not follow
+    the expected naming convention.
+    """
+    def __init__(self, path):
+        super(ExtensionNamingError, self).__init__(
+            '{0} does not match the format for a Spack extension path.'
+            .format(path))
diff --git a/lib/spack/spack/main.py b/lib/spack/spack/main.py
index f6da7b0fb07..3677764cb6a 100644
--- a/lib/spack/spack/main.py
+++ b/lib/spack/spack/main.py
@@ -736,17 +736,11 @@ def main(argv=None):
         # ensure options on spack command come before everything
         setup_main_options(args)
 
-        # Try to load the particular command the caller asked for.  If there
-        # is no module for it, just die.
+        # Try to load the particular command the caller asked for.
         cmd_name = args.command[0]
         cmd_name = aliases.get(cmd_name, cmd_name)
 
-        try:
-            command = parser.add_command(cmd_name)
-        except ImportError:
-            if spack.config.get('config:debug'):
-                raise
-            tty.die("Unknown command: %s" % args.command[0])
+        command = parser.add_command(cmd_name)
 
         # Re-parse with the proper sub-parser added.
         args, unknown = parser.parse_known_args()
diff --git a/lib/spack/spack/test/cmd/init_py_functions.py b/lib/spack/spack/test/cmd/init_py_functions.py
new file mode 100644
index 00000000000..2e631062837
--- /dev/null
+++ b/lib/spack/spack/test/cmd/init_py_functions.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+import pytest
+from spack.cmd import require_python_name, python_name, PythonNameError, \
+    require_cmd_name, cmd_name, CommandNameError
+
+
+def test_require_python_name():
+    """Python module names should not contain dashes---ensure that
+    require_python_name() raises the appropriate exception if one is
+    detected.
+    """
+    require_python_name("okey_dokey")
+    with pytest.raises(PythonNameError):
+        require_python_name("okey-dokey")
+    require_python_name(python_name("okey-dokey"))
+
+
+def test_require_cmd_name():
+    """By convention, Spack command names should contain dashes rather than
+    underscores---ensure that require_cmd_name() raises the appropriate
+    exception if underscores are detected.
+    """
+    require_cmd_name("okey-dokey")
+    with pytest.raises(CommandNameError):
+        require_cmd_name("okey_dokey")
+    require_cmd_name(cmd_name("okey_dokey"))
diff --git a/lib/spack/spack/test/cmd_extensions.py b/lib/spack/spack/test/cmd_extensions.py
index 486ac925cf7..cb166092780 100644
--- a/lib/spack/spack/test/cmd_extensions.py
+++ b/lib/spack/spack/test/cmd_extensions.py
@@ -5,24 +5,71 @@
 
 import pytest
 
+import contextlib
+import os
 import sys
 
+import spack.cmd
 import spack.config
+import spack.extensions
 import spack.main
 
 
-@pytest.fixture()
-def extension_root(tmpdir):
-    root = tmpdir.mkdir('spack-testcommand')
-    root.ensure('testcommand', 'cmd', dir=True)
-    return root
+class Extension:
+    """Helper class to simplify the creation of simple command extension
+    directory structures with a conventional format for testing.
+    """
+    def __init__(self, name, root):
+        """Create a command extension.
+
+        Args:
+            name (str): The name of the command extension.
+            root (path object): The temporary root for the command extension
+                (e.g. from tmpdir.mkdir()).
+        """
+        self.name = name
+        self.pname = spack.cmd.python_name(name)
+        self.root = root
+        self.main = self.root.ensure(self.pname, dir=True)
+        self.cmd = self.main.ensure('cmd', dir=True)
+
+    def add_command(self, command_name, contents):
+        """Add a command to this command extension.
+
+        Args:
+            command_name (str): The name of the command.
+            contents (str): the desired contents of the new command module
+                file."""
+        spack.cmd.require_cmd_name(command_name)
+        python_name = spack.cmd.python_name(command_name)
+        cmd = self.cmd.ensure(python_name + '.py')
+        cmd.write(contents)
 
 
-@pytest.fixture()
-def hello_world_cmd(extension_root):
-    """Simple extension command with code contained in a single file."""
-    hello = extension_root.ensure('testcommand', 'cmd', 'hello.py')
-    hello.write("""
+@pytest.fixture(scope='function')
+def extension_creator(tmpdir, config):
+    """Create a basic extension command directory structure"""
+    @contextlib.contextmanager
+    def _ce(extension_name='testcommand'):
+        root = tmpdir.mkdir('spack-' + extension_name)
+        extension = Extension(extension_name, root)
+        with spack.config.override('config:extensions',
+                                   [str(extension.root)]):
+            yield extension
+    list_of_modules = list(sys.modules.keys())
+    try:
+        yield _ce
+    finally:
+        to_be_deleted = [x for x in sys.modules if x not in list_of_modules]
+        for module_name in to_be_deleted:
+            del sys.modules[module_name]
+
+
+@pytest.fixture(scope='function')
+def hello_world_extension(extension_creator):
+    """Create an extension with a hello-world command."""
+    with extension_creator() as extension:
+        extension.add_command('hello-world', """
 description = "hello world extension command"
 section = "test command"
 level = "long"
@@ -31,27 +78,33 @@ def setup_parser(subparser):
     pass
 
 
-def hello(parser, args):
+def hello_world(parser, args):
     print('Hello world!')
 """)
-    list_of_modules = list(sys.modules.keys())
-    with spack.config.override('config:extensions', [str(extension_root)]):
-        yield spack.main.SpackCommand('hello')
-
-    to_be_deleted = [x for x in sys.modules if x not in list_of_modules]
-    for module_name in to_be_deleted:
-        del sys.modules[module_name]
+        yield extension
 
 
-@pytest.fixture()
-def hello_world_with_module_in_root(extension_root):
-    """Extension command with additional code in the root folder."""
-    extension_root.ensure('testcommand', '__init__.py')
-    command_root = extension_root.join('testcommand', 'cmd')
-    hello = command_root.ensure('hello.py')
-    hello.write("""
+@pytest.fixture(scope='function')
+def hello_world_cmd(hello_world_extension):
+    """Create and return an invokable "hello-world" extension command."""
+    yield spack.main.SpackCommand('hello-world')
+
+
+@pytest.fixture(scope='function')
+def hello_world_with_module_in_root(extension_creator):
+    """Create a "hello-world" extension command with additional code in the
+    root folder.
+    """
+    @contextlib.contextmanager
+    def _hwwmir(extension_name=None):
+        with extension_creator(extension_name) \
+            if extension_name else \
+                extension_creator() as extension:
+            # Note that the namespace of the extension is derived from the
+            # fixture.
+            extension.add_command('hello', """
 # Test an absolute import
-from spack.extensions.testcommand.implementation import hello_world
+from spack.extensions.{ext_pname}.implementation import hello_world
 
 # Test a relative import
 from ..implementation import hello_folks
@@ -79,33 +132,143 @@ def hello(parser, args):
         hello_folks()
     elif args.subcommand == 'global':
         print(global_message)
-""")
-    implementation = extension_root.ensure('testcommand', 'implementation.py')
-    implementation.write("""
+""".format(ext_pname=extension.pname))
+
+            extension.main.ensure('__init__.py')
+            implementation \
+                = extension.main.ensure('implementation.py')
+            implementation.write("""
 def hello_world():
     print('Hello world!')
 
 def hello_folks():
     print('Hello folks!')
 """)
-    list_of_modules = list(sys.modules.keys())
-    with spack.config.override('config:extensions', [str(extension_root)]):
-        yield spack.main.SpackCommand('hello')
+            yield spack.main.SpackCommand('hello')
 
-    to_be_deleted = [x for x in sys.modules if x not in list_of_modules]
-    for module_name in to_be_deleted:
-        del sys.modules[module_name]
+    yield _hwwmir
 
 
 def test_simple_command_extension(hello_world_cmd):
+    """Basic test of a functioning command."""
     output = hello_world_cmd()
     assert 'Hello world!' in output
 
 
-def test_command_with_import(hello_world_with_module_in_root):
-    output = hello_world_with_module_in_root('world')
-    assert 'Hello world!' in output
-    output = hello_world_with_module_in_root('folks')
-    assert 'Hello folks!' in output
-    output = hello_world_with_module_in_root('global')
-    assert 'bar' in output
+def test_multi_extension_search(hello_world_extension, extension_creator):
+    """Ensure we can find an extension command even if it's not in the first
+    place we look.
+    """
+
+    with extension_creator('testcommand2'):
+        assert ('Hello world') in spack.main.SpackCommand('hello-world')()
+
+
+def test_duplicate_module_load(hello_world_cmd, capsys):
+    """Ensure duplicate module load attempts are successful.
+
+    The command module will already have been loaded once by the
+    hello_world_cmd fixture.
+    """
+    parser = spack.main.make_argument_parser()
+    args = []
+    hw_cmd = spack.cmd.get_command(hello_world_cmd.command_name)
+    hw_cmd(parser, args)
+    captured = capsys.readouterr()
+    assert captured == ('Hello world!\n', '')
+
+
+@pytest.mark.parametrize('extension_name',
+                         [None, 'hyphenated-extension'],
+                         ids=['simple', 'hyphenated_extension_name'])
+def test_command_with_import(extension_name, hello_world_with_module_in_root):
+    """Ensure we can write a functioning command with multiple imported
+    subcommands, including where the extension name contains a hyphen.
+    """
+    with hello_world_with_module_in_root(extension_name) as hello_world:
+        output = hello_world('world')
+        assert 'Hello world!' in output
+        output = hello_world('folks')
+        assert 'Hello folks!' in output
+        output = hello_world('global')
+        assert 'bar' in output
+
+
+def test_missing_command():
+    """Ensure that we raise the expected exception if the desired command is
+    not present.
+    """
+    with pytest.raises(spack.extensions.CommandNotFoundError):
+        spack.cmd.get_module("no-such-command")
+
+
+@pytest.mark.\
+    parametrize('extension_path,expected_exception',
+                [('/my/bad/extension',
+                  spack.extensions.ExtensionNamingError),
+                 ('', spack.extensions.ExtensionNamingError),
+                 ('/my/bad/spack--extra-hyphen',
+                  spack.extensions.ExtensionNamingError),
+                 ('/my/good/spack-extension',
+                  spack.extensions.CommandNotFoundError),
+                 ('/my/still/good/spack-extension/',
+                  spack.extensions.CommandNotFoundError),
+                 ('/my/spack-hyphenated-extension',
+                  spack.extensions.CommandNotFoundError)],
+                ids=['no_stem', 'vacuous', 'leading_hyphen',
+                     'basic_good', 'trailing_slash', 'hyphenated'])
+def test_extension_naming(extension_path, expected_exception, config):
+    """Ensure that we are correctly validating configured extension paths
+    for conformity with the rules: the basename should match
+    ``spack-<name>``; <name> may have embedded hyphens but not begin with one.
+    """
+    with spack.config.override('config:extensions', [extension_path]):
+        with pytest.raises(expected_exception):
+            spack.cmd.get_module("no-such-command")
+
+
+def test_missing_command_function(extension_creator, capsys):
+    """Ensure we die as expected if a command module does not have the
+    expected command function defined.
+    """
+    with extension_creator() as extension:
+        extension.\
+            add_command('bad-cmd',
+                        """\ndescription = "Empty command implementation"\n""")
+        with pytest.raises(SystemExit):
+            spack.cmd.get_module('bad-cmd')
+        capture = capsys.readouterr()
+        assert "must define function 'bad_cmd'." in capture[1]
+
+
+def test_get_command_paths(config):
+    """Exercise the construction of extension command search paths."""
+    extensions = ('extension-1', 'extension-2')
+    ext_paths = []
+    expected_cmd_paths = []
+    for ext in extensions:
+        ext_path = os.path.join('my', 'path', 'to', 'spack-' + ext)
+        ext_paths.append(ext_path)
+        expected_cmd_paths.append(os.path.join(ext_path,
+                                               spack.cmd.python_name(ext),
+                                               'cmd'))
+
+    with spack.config.override('config:extensions', ext_paths):
+        assert spack.extensions.get_command_paths() == expected_cmd_paths
+
+
+@pytest.mark.parametrize('command_name,contents,exception',
+                         [('bad-cmd', 'from oopsie.daisy import bad\n',
+                           ImportError),
+                          ('bad-cmd', """var = bad_function_call('blech')\n""",
+                           NameError),
+                          ('bad-cmd', ')\n', SyntaxError)],
+                         ids=['ImportError', 'NameError', 'SyntaxError'])
+def test_failing_command(command_name, contents, exception, extension_creator):
+    """Ensure that the configured command fails to import with the specified
+    error.
+    """
+    with extension_creator() as extension:
+        extension.add_command(command_name, contents)
+        with pytest.raises(exception):
+            spack.extensions.get_module(command_name)

From 6c751f931c6ac51846bc5931cde47ec55d520c47 Mon Sep 17 00:00:00 2001
From: Benoit Coste <benoit.coste@protonmail.com>
Date: Thu, 30 Apr 2020 14:50:28 +0200
Subject: [PATCH 181/802] py-pyquaternion: added package at v0.9.5 (#16386)

---
 .../packages/py-pyquaternion/package.py       | 20 +++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-pyquaternion/package.py

diff --git a/var/spack/repos/builtin/packages/py-pyquaternion/package.py b/var/spack/repos/builtin/packages/py-pyquaternion/package.py
new file mode 100644
index 00000000000..82dc26d796b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyquaternion/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class PyPyquaternion(PythonPackage):
+    """Python morphology manipulation toolkit"""
+
+    homepage = "https://kieranwynn.github.io/pyquaternion/"
+    url      = "https://pypi.org/packages/source/p/pyquaternion/pyquaternion-0.9.5.tar.gz"
+
+    version('0.9.5', sha256='2d89d19259d62a8fbd25219eee7dacc1f6bb570becb70e1e883f622597c7d81d')
+
+    depends_on('py-setuptools', type=('build', 'run'))
+
+    depends_on('py-numpy', type='run')

From 54b71b2b693fd9bac760e164b92952afa7afa4e0 Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Thu, 30 Apr 2020 22:03:35 +0900
Subject: [PATCH 182/802] JHPCN-DF: added package at v1.1.0 (#16384)

---
 .../builtin/packages/jhpcn-df/package.py      | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/jhpcn-df/package.py

diff --git a/var/spack/repos/builtin/packages/jhpcn-df/package.py b/var/spack/repos/builtin/packages/jhpcn-df/package.py
new file mode 100644
index 00000000000..3bb3132844d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/jhpcn-df/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class JhpcnDf(CMakePackage):
+    """
+    Data compression library based on Jointed Hierarchical Precision
+    Compression Number - Data Format
+
+    JHPCN-DF is a novel lossy compression algorithm taylored for floating
+    point dataset. The algorithm enhances the effect of employing standard
+    compression algorithms like deflate because this approach makes
+    the occurence rate of the same byte pattern in data stream higher owing
+    to truncating some lower bits of significand.
+    """
+
+    homepage = "http://avr-aics-riken.github.io/JHPCN-DF/"
+    url      = "https://github.com/avr-aics-riken/JHPCN-DF/archive/1.1.0.tar.gz"
+
+    version('1.1.0', sha256='106d99cc4faac5c76e51e8bfe3193c1d3dc91648072cf418d868ed830592b04b')
+
+    variant('lz4', default=False, description='Enable lz4')
+    variant('fortran', default=False, description='Enable Fortran Interface')
+
+    depends_on('zlib', type='link')
+    depends_on('lz4@:1.7', when='+lz4', type='link')
+
+    def cmake_args(self):
+        args = [
+            self.define_from_variant('with_Fortran_interface', 'fortran'),
+            self.define_from_variant('with_lz4', 'lz4')
+        ]
+        return args

From 9627cbbe1bc116873a0840f486023f0a7ae293c9 Mon Sep 17 00:00:00 2001
From: Teodor Nikolov <teodor.nikolov22@gmail.com>
Date: Thu, 30 Apr 2020 16:05:45 +0200
Subject: [PATCH 183/802] lapackpp and blaspp: added packages (develop branch)
 (#16373)

---
 .../repos/builtin/packages/blaspp/package.py  | 82 +++++++++++++++++++
 .../builtin/packages/lapackpp/package.py      | 23 ++++++
 2 files changed, 105 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/blaspp/package.py
 create mode 100644 var/spack/repos/builtin/packages/lapackpp/package.py

diff --git a/var/spack/repos/builtin/packages/blaspp/package.py b/var/spack/repos/builtin/packages/blaspp/package.py
new file mode 100644
index 00000000000..702c33a51fc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/blaspp/package.py
@@ -0,0 +1,82 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Blaspp(CMakePackage):
+    """BLAS++: C++ API for the Basic Linear Algebra Subroutines (University of
+    Texas)."""
+
+    homepage = "https://bitbucket.org/icl/blaspp"
+    hg       = "https://bitbucket.org/icl/blaspp"
+    maintainers = ['teonnik', 'Sely85']
+
+    version('develop', hg=hg, revision="5191c9d")
+
+    variant('gfort',
+            default=False,
+            description=('Use GNU Fortran interface. '
+                         'Default is Intel interface. (MKL)'))
+    variant('ilp64',
+            default=False,
+            description=('Use 64bit integer interface. '
+                         'Default is 32bit. (MKL & ESSL)'))
+    variant('openmp',
+            default=False,
+            description=('Use OpenMP threaded backend. '
+                         'Default is sequential. (MKL & ESSL)'))
+
+    depends_on('blas')
+
+    # 1) The CMake options exposed by `blaspp` allow for a value called `auto`.
+    #    The value is not needed here as the choice of dependency in the spec
+    #    determines the appropriate flags.
+    #
+    # 2) BLASFinder.cmake handles most options. For `auto`, it searches all
+    #    blas libraries listed in `def_lib_list`.
+    #
+    # 3) ?? Custom blas library can be supplied via `BLAS_LIBRARIES`.
+    #
+    def cmake_args(self):
+        spec = self.spec
+        args = ['-DBLASPP_BUILD_TESTS:BOOL={0}'.format(
+            'ON' if self.run_tests else 'OFF')]
+
+        if '+gfort' in spec:
+            args.append('-DBLAS_LIBRARY_MKL="GNU gfortran conventions"')
+        else:
+            args.append('-DBLAS_LIBRARY_MKL="Intel ifort conventions"')
+
+        if '+ilp64' in spec:
+            args.append('-DBLAS_LIBRARY_INTEGER="int64_t (ILP64)"')
+        else:
+            args.append('-DBLAS_LIBRARY_INTEGER="int (LP64)"')
+
+        if '+openmp' in spec:
+            args.append(['-DUSE_OPENMP=ON',
+                         '-DBLAS_LIBRARY_THREADING="threaded"'])
+        else:
+            args.append('-DBLAS_LIBRARY_THREADING="sequential"')
+
+        # Missing:
+        #
+        # - acml  : BLAS_LIBRARY="AMD ACML"
+        #           BLAS_LIBRARY_THREADING= threaded/sequential
+        #
+        # - apple : BLAS_LIBRARY="Apple Accelerate" (veclibfort ???)
+        #
+        if '^mkl' in spec:
+            args.append('-DBLAS_LIBRARY="Intel MKL"')
+        elif '^essl' in spec:
+            args.append('-DBLAS_LIBRARY="IBM ESSL"')
+        elif '^openblas' in spec:
+            args.append('-DBLAS_LIBRARY="OpenBLAS"')
+        elif '^cray-libsci' in spec:
+            args.append('-DBLAS_LIBRARY="Cray LibSci"')
+        else:  # e.g. netlib-lapack
+            args.append('-DBLAS_LIBRARY="generic"')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/lapackpp/package.py b/var/spack/repos/builtin/packages/lapackpp/package.py
new file mode 100644
index 00000000000..1f3ec76924d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lapackpp/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Lapackpp(CMakePackage):
+    """LAPACK++: C++ API for the Basic Linear Algebra Subroutines (University
+    of Tennessee)"""
+
+    homepage = "https://bitbucket.org/icl/lapackpp"
+    hg       = "https://bitbucket.org/icl/lapackpp"
+    maintainers = ['teonnik', 'Sely85']
+
+    version('develop', hg=hg, revision="7ffa486")
+
+    depends_on('blaspp')
+
+    def cmake_args(self):
+        return ['-DBUILD_LAPACKPP_TESTS:BOOL={0}'.format(
+            'ON' if self.run_tests else 'OFF')]

From 598c233f78d23329c0cc6c7bc86b7117dca7bacd Mon Sep 17 00:00:00 2001
From: Jeremy <jjwilke@users.noreply.github.com>
Date: Thu, 30 Apr 2020 07:13:47 -0700
Subject: [PATCH 184/802] Update kokkos for new 3.x build systems (#16358)

* change old Makefile-based Kokkos to kokkos-legacy

* add Kokkos 3.x packages

Co-authored-by: Jeremiah J Wilke <jjwilke@kokkos-dev-2.sandia.gov>
---
 .../repos/builtin/packages/arborx/package.py  |   6 +-
 .../repos/builtin/packages/cabana/package.py  |   6 +-
 .../builtin/packages/examinimd/package.py     |   2 +-
 .../makefile.patch                            |   0
 .../packages/kokkos-kernels-legacy/package.py |  50 +++
 .../packages/kokkos-kernels/package.py        | 164 +++++--
 .../builtin/packages/kokkos-legacy/package.py | 229 ++++++++++
 .../packages/kokkos-nvcc-wrapper/package.py   |  43 ++
 .../repos/builtin/packages/kokkos/package.py  | 404 +++++++++---------
 .../repos/builtin/packages/lammps/package.py  |   2 +-
 .../builtin/packages/miniaero/package.py      |   2 +-
 11 files changed, 667 insertions(+), 241 deletions(-)
 rename var/spack/repos/builtin/packages/{kokkos-kernels => kokkos-kernels-legacy}/makefile.patch (100%)
 create mode 100644 var/spack/repos/builtin/packages/kokkos-kernels-legacy/package.py
 create mode 100644 var/spack/repos/builtin/packages/kokkos-legacy/package.py
 create mode 100644 var/spack/repos/builtin/packages/kokkos-nvcc-wrapper/package.py

diff --git a/var/spack/repos/builtin/packages/arborx/package.py b/var/spack/repos/builtin/packages/arborx/package.py
index 2408dd1a99d..dfca8c7aaa6 100644
--- a/var/spack/repos/builtin/packages/arborx/package.py
+++ b/var/spack/repos/builtin/packages/arborx/package.py
@@ -28,9 +28,9 @@ class Arborx(CMakePackage):
     # ArborX relies on Kokkos to provide devices, thus having one-to-one match
     # The only way to disable those devices is to make sure Kokkos does not
     # provide them
-    depends_on('kokkos@2.7.00:+cuda+enable_lambda cxxstd=c++14', when='+cuda')
-    depends_on('kokkos@2.7.00:+openmp cxxstd=c++14', when='+openmp')
-    depends_on('kokkos@2.7.00:+serial cxxstd=c++14', when='+serial')
+    depends_on('kokkos-legacy@2.7.00:+cuda+enable_lambda cxxstd=c++14', when='+cuda')
+    depends_on('kokkos-legacy@2.7.00:+openmp cxxstd=c++14', when='+openmp')
+    depends_on('kokkos-legacy@2.7.00:+serial cxxstd=c++14', when='+serial')
 
     def cmake_args(self):
         spec = self.spec
diff --git a/var/spack/repos/builtin/packages/cabana/package.py b/var/spack/repos/builtin/packages/cabana/package.py
index 0efff53f926..aaf88e4e121 100644
--- a/var/spack/repos/builtin/packages/cabana/package.py
+++ b/var/spack/repos/builtin/packages/cabana/package.py
@@ -22,9 +22,9 @@ class Cabana(CMakePackage):
     variant('cuda', default=False, description="enable Cuda backend")
 
     depends_on("cmake@3.9:", type='build')
-    depends_on("kokkos+serial", when="+serial")
-    depends_on("kokkos+openmp", when="+openmp")
-    depends_on("kokkos+cuda", when="+cuda")
+    depends_on("kokkos-legacy+serial", when="+serial")
+    depends_on("kokkos-legacy+openmp", when="+openmp")
+    depends_on("kokkos-legacy+cuda", when="+cuda")
 
     def cmake_args(self):
         options = [
diff --git a/var/spack/repos/builtin/packages/examinimd/package.py b/var/spack/repos/builtin/packages/examinimd/package.py
index a6250b0dcb4..f93a33ea01c 100644
--- a/var/spack/repos/builtin/packages/examinimd/package.py
+++ b/var/spack/repos/builtin/packages/examinimd/package.py
@@ -34,7 +34,7 @@ class Examinimd(MakefilePackage):
 
     conflicts('+openmp', when='+pthreads')
 
-    depends_on('kokkos')
+    depends_on('kokkos-legacy')
     depends_on('mpi', when='+mpi')
 
     @property
diff --git a/var/spack/repos/builtin/packages/kokkos-kernels/makefile.patch b/var/spack/repos/builtin/packages/kokkos-kernels-legacy/makefile.patch
similarity index 100%
rename from var/spack/repos/builtin/packages/kokkos-kernels/makefile.patch
rename to var/spack/repos/builtin/packages/kokkos-kernels-legacy/makefile.patch
diff --git a/var/spack/repos/builtin/packages/kokkos-kernels-legacy/package.py b/var/spack/repos/builtin/packages/kokkos-kernels-legacy/package.py
new file mode 100644
index 00000000000..8507f90bf4c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kokkos-kernels-legacy/package.py
@@ -0,0 +1,50 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class KokkosKernelsLegacy(MakefilePackage):
+    """Kokkos C++ Performance Portability Programming EcoSystem: Math Kernels -
+    Provides BLAS, Sparse BLAS and Graph Kernels."""
+
+    homepage = "https://github.com/kokkos/kokkos-kernels"
+    url      = "https://github.com/kokkos/kokkos-kernels/archive/2.7.00.tar.gz"
+
+    version('2.7.00', sha256='adf4af44eadbdfbeb9ec69dd5fae4e2852bd1fbe4a69213efd199e49f4098254')
+    version('2.6.00', sha256='14ebf806f66b9ca73949a478b8d959be7fa1165a640935760a724d7cc0a66335')
+    version('2.5.00', sha256='2c2289da3a41dafd97726e90507debafbb9f5e49ca5b0f5c8d1e044a5796f000')
+
+    # make sure kokkos kernels version matches kokkos
+    depends_on('kokkos-legacy@2.5.00', when='@2.5.00')
+    depends_on('kokkos-legacy@2.6.00', when='@2.6.00')
+    depends_on('kokkos-legacy@2.7.00', when='@2.7.00')
+
+    patch('makefile.patch')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter("src/Makefile")
+        makefile.filter('CXX = .*', 'CXX = ' + env['CXX'])
+
+    def build(self, spec, prefix):
+        with working_dir('build', create=True):
+            makefile_path = '%s%s' % (self.stage.source_path, '/src/Makefile')
+            copy(makefile_path, 'Makefile')
+            make_args = [
+                'KOKKOSKERNELS_INSTALL_PATH=%s' % prefix,
+                'KOKKOSKERNELS_PATH=%s' % self.stage.source_path,
+                'KOKKOS_PATH=%s' % spec['kokkos'].prefix
+            ]
+
+            make('build', *make_args)
+
+    def install(self, spec, prefix):
+        with working_dir('build', create=False):
+            make_args = [
+                'KOKKOSKERNELS_INSTALL_PATH=%s' % prefix,
+                'KOKKOSKERNELS_PATH=%s' % self.stage.source_path,
+                'KOKKOS_PATH=%s' % spec['kokkos'].prefix
+            ]
+            make('install', *make_args)
diff --git a/var/spack/repos/builtin/packages/kokkos-kernels/package.py b/var/spack/repos/builtin/packages/kokkos-kernels/package.py
index 614fa54196a..8cd68051df9 100644
--- a/var/spack/repos/builtin/packages/kokkos-kernels/package.py
+++ b/var/spack/repos/builtin/packages/kokkos-kernels/package.py
@@ -2,52 +2,142 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
 from spack import *
 
 
-class KokkosKernels(MakefilePackage):
-    """Kokkos C++ Performance Portability Programming EcoSystem: Math Kernels -
-    Provides BLAS, Sparse BLAS and Graph Kernels."""
+class KokkosKernels(CMakePackage, CudaPackage):
+    """Kokkos Kernels provides math kernels, often BLAS or LAPACK
+    for small matrices, that can be used in larger Kokkos parallel routines"""
 
     homepage = "https://github.com/kokkos/kokkos-kernels"
-    url      = "https://github.com/kokkos/kokkos-kernels/archive/2.7.00.tar.gz"
+    git = "https://github.com/kokkos/kokkos-kernels.git"
 
-    version('2.7.00', sha256='adf4af44eadbdfbeb9ec69dd5fae4e2852bd1fbe4a69213efd199e49f4098254')
-    version('2.6.00', sha256='14ebf806f66b9ca73949a478b8d959be7fa1165a640935760a724d7cc0a66335')
-    version('2.5.00', sha256='2c2289da3a41dafd97726e90507debafbb9f5e49ca5b0f5c8d1e044a5796f000')
-    version('develop', git='https://github.com/kokkos/kokkos-kernels',
-            branch='develop')
+    version('3.1',     url='https://github.com/kokkos/kokkos-kernels/archive/3.1.00.tar.gz',
+            sha256="27fea241ae92f41bd5b070b1a590ba3a56a06aca750207a98bea2f64a4a40c89",
+            default=True)
+    version('3.0',     url='https://github.com/kokkos/kokkos-kernels/archive/3.0.00.tar.gz',
+            sha256="e4b832aed3f8e785de24298f312af71217a26067aea2de51531e8c1e597ef0e6")
+    version('develop', branch='develop')
+    version('master',  branch='master')
 
-    # make sure kokkos kernels version matches kokkos
-    depends_on('kokkos@2.5.00', when='@2.5.00')
-    depends_on('kokkos@2.6.00', when='@2.6.00')
-    depends_on('kokkos@2.7.00', when='@2.7.00')
-    depends_on('kokkos@develop', when='@develop')
+    depends_on("kokkos")
+    depends_on("kokkos@develop", when="@develop")
+    depends_on("cmake@3.10:", type='build')
 
-    patch('makefile.patch')
+    backends = {
+        'serial': (False,  "enable Serial backend (default)"),
+        'cuda': (False,  "enable Cuda backend"),
+        'openmp': (False,  "enable OpenMP backend"),
+    }
 
-    def edit(self, spec, prefix):
-        makefile = FileFilter("src/Makefile")
-        makefile.filter('CXX = .*', 'CXX = ' + env['CXX'])
+    for backend in backends:
+        deflt, descr = backends[backend]
+        variant(backend.lower(), default=deflt, description=descr)
+        depends_on("kokkos+%s" % backend.lower(), when="+%s" % backend.lower())
 
-    def build(self, spec, prefix):
-        with working_dir('build', create=True):
-            makefile_path = '%s%s' % (self.stage.source_path, '/src/Makefile')
-            copy(makefile_path, 'Makefile')
-            make_args = [
-                'KOKKOSKERNELS_INSTALL_PATH=%s' % prefix,
-                'KOKKOSKERNELS_PATH=%s' % self.stage.source_path,
-                'KOKKOS_PATH=%s' % spec['kokkos'].prefix
-            ]
+    space_etis = {
+        "execspace_cuda": ('auto', "", "cuda"),
+        "execspace_openmp": ('auto', "", "openmp"),
+        "execspace_threads": ('auto', "", "pthread"),
+        "execspace_serial": ('auto', "", "serial"),
+        "memspace_cudauvmspace": ('auto', "", "cuda"),
+        "memspace_cudaspace": ('auto', "", "cuda"),
+    }
+    for eti in space_etis:
+        deflt, descr, backend_required = space_etis[eti]
+        variant(eti, default=deflt, description=descr)
+        depends_on("kokkos+%s" % backend_required, when="+%s" % eti)
 
-            make('build', *make_args)
+    numeric_etis = {
+        "ordinals": ("int",        "ORDINAL_",  # default, cmake name
+                     ["int", "int64_t"]),  # allowed values
+        "offsets": ("int,size_t", "OFFSET_",
+                    ["int", "size_t"]),
+        "layouts": ("left",       "LAYOUT",
+                    ["left", "right"]),
+        "scalars": ("double",     "",
+                    ["float", "double", "complex_float", "complex_double"])
+    }
+    for eti in numeric_etis:
+        deflt, cmake_name, vals = numeric_etis[eti]
+        variant(eti, default=deflt, values=vals, multi=True)
 
-    def install(self, spec, prefix):
-        with working_dir('build', create=False):
-            make_args = [
-                'KOKKOSKERNELS_INSTALL_PATH=%s' % prefix,
-                'KOKKOSKERNELS_PATH=%s' % self.stage.source_path,
-                'KOKKOS_PATH=%s' % spec['kokkos'].prefix
-            ]
-            make('install', *make_args)
+    tpls = {
+        # variant name   #deflt   #spack name   #root var name #docstring
+        "blas": (False, "blas", "BLAS", "Link to system BLAS"),
+        "lapack": (False, "lapack", "LAPACK", "Link to system LAPACK"),
+        "mkl": (False, "mkl", "MKL", "Link to system MKL"),
+        "cublas": (False, "cuda", None, "Link to CUDA BLAS library"),
+        "cusparse": (False, "cuda", None, "Link to CUDA sparse library"),
+        "superlu": (False, "superlu", "SUPERLU", "Link to SuperLU library"),
+        "cblas": (False, "cblas", "CBLAS", "Link to CBLAS library"),
+        "lapacke": (False, "clapack", "LAPACKE", "Link to LAPACKE library"),
+    }
+
+    for tpl in tpls:
+        deflt, spackname, rootname, descr = tpls[tpl]
+        variant(tpl, default=deflt, description=descr)
+        depends_on(spackname, when="+%s" % tpl)
+
+    def cmake_args(self):
+        spec = self.spec
+        options = []
+
+        isdiy = "+diy" in spec
+        if isdiy:
+            options.append("-DSpack_WORKAROUND=On")
+
+        options.append("-DKokkos_ROOT=%s" % spec["kokkos"].prefix)
+        # Compiler weirdness due to nvcc_wrapper
+        options.append("-DCMAKE_CXX_COMPILER=%s" % spec["kokkos"].kokkos_cxx)
+
+        if self.run_tests:
+            options.append("-DKokkosKernels_ENABLE_TESTS=ON")
+
+        for tpl in self.tpls:
+            on_flag = "+%s" % tpl
+            off_flag = "~%s" % tpl
+            dflt, spackname, rootname, descr = self.tpls[tpl]
+            if on_flag in self.spec:
+                options.append("-DKokkosKernels_ENABLE_TPL_%s=ON" %
+                               tpl.upper())
+                if rootname:
+                    options.append("-D%s_ROOT=%s" %
+                                   (rootname, spec[spackname].prefix))
+                else:
+                    pass  # this should get picked up automatically, we hope
+            elif off_flag in self.spec:
+                options.append(
+                    "-DKokkosKernels_ENABLE_TPL_%s=OFF" % tpl.upper())
+
+        for eti in self.numeric_etis:
+            deflt, cmake_name, vals = self.numeric_etis[eti]
+            for val in vals:
+                keyval = "%s=%s" % (eti, val)
+                cmake_option = "KokkosKernels_INST_%s%s" % (
+                    cmake_name.upper(), val.upper())
+                if keyval in spec:
+                    options.append("-D%s=ON" % cmake_option)
+                else:
+                    options.append("-D%s=OFF" % cmake_option)
+
+        for eti in self.space_etis:
+            deflt, descr = self.space_etis[eti]
+            if deflt == "auto":
+                value = spec.variants[eti].value
+                # spack does these as strings, not reg booleans
+                if str(value) == "True":
+                    options.append("-DKokkosKernels_INST_%s=ON" % eti.upper())
+                elif str(value) == "False":
+                    options.append("-DKokkosKernels_INST_%s=OFF" % eti.upper())
+                else:
+                    pass  # don't pass anything, let CMake decide
+            else:  # simple option
+                on_flag = "+%s" % eti
+                off_flag = "~%s" % eti
+                if on_flag in self.spec:
+                    options.append("-DKokkosKernels_INST_%s=ON" % eti.upper())
+                elif off_flag in self.spec:
+                    options.append("-DKokkosKernels_INST_%s=OFF" % eti.upper())
+
+        return options
diff --git a/var/spack/repos/builtin/packages/kokkos-legacy/package.py b/var/spack/repos/builtin/packages/kokkos-legacy/package.py
new file mode 100644
index 00000000000..2adfa0c9b5b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kokkos-legacy/package.py
@@ -0,0 +1,229 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class KokkosLegacy(Package):
+    """Kokkos implements a programming model in C++ for writing performance
+    portable applications targeting all major HPC platforms."""
+
+    homepage = "https://github.com/kokkos/kokkos"
+    url      = "https://github.com/kokkos/kokkos/archive/2.03.00.tar.gz"
+    git      = "https://github.com/kokkos/kokkos.git"
+
+    version('2.9.00', sha256='e0621197791ed3a381b4f02c78fa529f3cff3abb74d52157b4add17e8aa04bc4')
+    version('2.8.00', sha256='1c72661f2d770517bff98837001b42b9c677d1df29f7493a1d7c008549aff630')
+    version('2.7.24', sha256='a308a80ea1488f4c18884b828ce7ae9f5210b9a6b2f61b208d875084d8da8cb0')
+    version('2.7.00',  sha256='01595996e612ef7410aa42fa265a23101cfe1b6993fa9810ca844db5c89ad765')
+    version('2.5.00',  sha256='ea232594bf746abb99ae2aafaeef5d07adc089968010a62a88aaa892106d9476')
+    version('2.04.11', sha256='f2680aee0169f6cbbec38410f9c80bf8a160435f6a07769c1e9112da8b9349a0')
+    version('2.04.04', sha256='5bac8ddc2fac9bc6e01dd40f92ca6cbbb346a25deca5be2fec71acf712d0d0c7')
+    version('2.04.00', sha256='b04658d368986df207662a7a37c1ad974c321447bc2c2b5b696d7e9ee4481f34')
+    version('2.03.13', sha256='002748bdd0319d5ab82606cf92dc210fc1c05d0607a2e1d5538f60512b029056')
+    version('2.03.05', sha256='b18ddaa1496130ff3f675ea9ddbc6df9cdf378d53edf96df89e70ff189e10e1d')
+    version('2.03.00', sha256='722bea558d8986efee765ac912febb3c1ce289a8e9bdfef77cd0145df0ea8a3d')
+    version('2.02.15', sha256='6b4a7f189f0341f378f950f3c798f520d2e473b13435b137ff3b666e799a076d')
+    version('2.02.07', sha256='7b4ac81021d6868f4eb8e2a1cb92ba76bad9c3f197403b8b1eac0f11c983247c')
+
+    variant('debug', default=False, description="Build debug version of Kokkos")
+
+    variant('serial', default=True, description="enable Serial backend (default)")
+    variant('pthreads', default=False, description="enable Pthreads backend")
+    variant('qthreads', default=False, description="enable Qthreads backend")
+    variant('cuda', default=False, description="enable Cuda backend")
+    variant('openmp', default=False, description="enable OpenMP backend")
+
+    # Compilation options
+    variant('pic', default=False,
+            description="enable position independent code (-fPIC flag)")
+
+    # Kokkos options
+    variant('aggressive_vectorization', default=False,
+            description="set aggressive_vectorization Kokkos option")
+    variant('disable_profiling', default=False,
+            description="set disable_profiling Kokkos option")
+    variant('disable_dualview_modify_check', default=False,
+            description="set disable_dualview_modify_check Kokkos option")
+    variant('enable_profile_load_print', default=False,
+            description="set enable_profile_load_print Kokkos option")
+    variant('compiler_warnings', default=False,
+            description="set compiler_warnings Kokkos option")
+    variant('disable_deprecated_code', default=False,
+            description="set disable_deprecated_code Kokkos option")
+    variant('enable_eti', default=False,
+            description="set enable_eti Kokkos option")
+
+    # CUDA options
+    variant('force_uvm', default=False,
+            description="set force_uvm Kokkos CUDA option")
+    variant('use_ldg', default=False,
+            description="set use_ldg Kokkos CUDA option")
+    variant('rdc', default=False,
+            description="set rdc Kokkos CUDA option")
+    variant('enable_lambda', default=False,
+            description="set enable_lambda Kokkos CUDA option")
+
+    host_values = ('AMDAVX', 'ARMv80', 'ARMv81', 'ARMv8-ThunderX',
+                   'Power7', 'Power8', 'Power9',
+                   'WSM', 'SNB', 'HSW', 'BDW', 'SKX',
+                   'KNC', 'KNL')
+
+    gpu_values = ('Kepler30', 'Kepler32', 'Kepler35', 'Kepler37',
+                  'Maxwell50', 'Maxwell52', 'Maxwell53',
+                  'Pascal60', 'Pascal61',
+                  'Volta70', 'Volta72')
+
+    # C++ standard variant
+    variant('cxxstd', default='none',
+            values=('c++11', 'c++14', 'c++17', 'c++1y', 'c++1z', 'c++2a'),
+            multi=False,
+            description='set cxxstandard Kokkos option')
+
+    # Host architecture variant
+    variant(
+        'host_arch',
+        default='none',
+        values=host_values,
+        description='Set the host architecture to use'
+    )
+
+    # GPU architecture variant
+    variant(
+        'gpu_arch',
+        default='none',
+        values=gpu_values,
+        description='Set the GPU architecture to use'
+    )
+
+    # Checks on Kokkos version and Kokkos options
+    conflicts('+aggressive_vectorization', when='@:2.0.99',)
+    conflicts('+disable_profiling', when='@:2.0.99',)
+    conflicts('+disable_dualview_modify_check', when='@:2.03.04',)
+    conflicts('+enable_profile_load_print', when='@:2.03.04',)
+    conflicts('+compiler_warnings', when='@:2.03.14',)
+    conflicts('+disable_deprecated_code', when='@:2.5.99',)
+    conflicts('+enable_eti', when='@:2.6.99',)
+
+    # Check that we haven't specified a gpu architecture
+    # without specifying CUDA
+    for p in gpu_values:
+        conflicts('gpu_arch={0}'.format(p), when='~cuda',
+                  msg='Must specify CUDA backend to use a GPU architecture.')
+
+    # Check that we haven't specified a Kokkos CUDA option
+    # without specifying CUDA
+    conflicts('+force_uvm', when='~cuda',
+              msg='Must enable CUDA to use force_uvm.')
+    conflicts('+use_ldg', when='~cuda',
+              msg='Must enable CUDA to use use_ldg.')
+    conflicts('+rdc', when='~cuda',
+              msg='Must enable CUDA to use rdc.')
+    conflicts('+enable_lambda', when='~cuda',
+              msg='Must enable CUDA to use enable_lambda.')
+
+    # Check that we haven't asked for a GPU architecture that
+    # the revision of kokkos does not support
+    conflicts('gpu_arch=Volta70', when='@:2.5.99')
+    conflicts('gpu_arch=Volta72', when='@:2.5.99')
+
+    # conflicts on kokkos version and cuda enabled
+    # see kokkos issue #1296
+    # https://github.com/kokkos/kokkos/issues/1296
+    conflicts('+cuda', when='@2.5.00:2.7.00',
+              msg='Kokkos build system has issue (#1296) when CUDA enabled'
+              ' in version 2.5.00 through 2.7.00.')
+
+    # Specify that v1.x is required as v2.x has API changes
+    depends_on('hwloc@:1')
+    depends_on('qthreads', when='+qthreads')
+    depends_on('cuda', when='+cuda')
+
+    # generate_makefile.bash calls cmake
+    depends_on('cmake@3.10:', type='build')
+
+    def install(self, spec, prefix):
+        generate = which(join_path(self.stage.source_path,
+                                   'generate_makefile.bash'))
+        with working_dir('build', create=True):
+            g_args = [
+                '--prefix=%s' % prefix,
+                '--with-hwloc=%s' % spec['hwloc'].prefix,
+            ]
+            arch_args = []
+            kokkos_options_args = []
+            cuda_options_args = []
+
+            # PIC
+            if '+pic' in spec:
+                g_args.append('--cxxflags=-fPIC')
+
+            # C++ standard
+            cxxstandard = spec.variants['cxxstd'].value
+            if cxxstandard != 'none':
+                g_args.append('--cxxstandard=%s' % cxxstandard)
+
+            # Build Debug
+            if '+debug' in spec:
+                g_args.append('--debug')
+
+            # Backends
+            if '+serial' in spec:
+                g_args.append('--with-serial')
+            if '+openmp' in spec:
+                g_args.append('--with-openmp')
+            if '+pthreads' in spec:
+                g_args.append('--with-pthread')
+            if '+qthreads' in spec:
+                g_args.append('--with-qthreads=%s' % spec['qthreads'].prefix)
+            if '+cuda' in spec:
+                g_args.append('--with-cuda=%s' % spec['cuda'].prefix)
+            # Host architectures
+            host_arch = spec.variants['host_arch'].value
+            # GPU architectures
+            gpu_arch  = spec.variants['gpu_arch'].value
+            if host_arch != 'none':
+                arch_args.append(host_arch)
+            if gpu_arch != 'none':
+                arch_args.append(gpu_arch)
+            # Combined architecture flags
+            if arch_args:
+                g_args.append('--arch={0}'.format(','.join(arch_args)))
+
+            # CUDA options
+            if '+force_uvm' in spec:
+                cuda_options_args.append('force_uvm')
+            if '+use_ldg' in spec:
+                cuda_options_args.append('use_ldg')
+            if '+rdc' in spec:
+                cuda_options_args.append('rdc')
+            if '+enable_lambda' in spec:
+                cuda_options_args.append('enable_lambda')
+            if cuda_options_args:
+                g_args.append('--with-cuda-options={0}'
+                              .format(','.join(cuda_options_args)))
+
+            # Kokkos options
+            if '+aggressive_vectorization' in spec:
+                kokkos_options_args.append('aggressive_vectorization')
+            if '+disable_profiling' in spec:
+                kokkos_options_args.append('disable_profiling')
+            if '+disable_dualview_modify_check' in spec:
+                kokkos_options_args.append('disable_dualview_modify_check')
+            if '+enable_profile_load_print' in spec:
+                kokkos_options_args.append('enable_profile_load_print')
+            if '+compiler_warnings' in spec:
+                kokkos_options_args.append('compiler_warnings')
+            if '+disable_deprecated_code' in spec:
+                kokkos_options_args.append('disable_deprecated_code')
+            if '+enable_eti' in spec:
+                kokkos_options_args.append('enable_eti')
+            if kokkos_options_args:
+                g_args.append('--with-options={0}'
+                              .format(','.join(kokkos_options_args)))
+
+            generate(*g_args)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/kokkos-nvcc-wrapper/package.py b/var/spack/repos/builtin/packages/kokkos-nvcc-wrapper/package.py
new file mode 100644
index 00000000000..8bb09f2759f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kokkos-nvcc-wrapper/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+from spack import *
+import os
+
+
+class KokkosNvccWrapper(CMakePackage):
+    """The NVCC wrapper provides a wrapper around NVCC to make it a
+       'full' C++ compiler that accepts all flags"""
+
+    homepage = "https://github.com/kokkos/kokkos"
+    git = "https://github.com/kokkos/nvcc_wrapper.git"
+
+    version('3.1', url='https://github.com/kokkos/nvcc_wrapper/archive/3.1.tar.gz',
+            sha256="5171530763bb2845aa70651f3a8e5dc95b6eed76379323fde3205f97ed28ec8c",
+            default=True)
+    version('master', branch='master')
+
+    variant("mpi", default=True,
+            description="use with MPI as the underlying compiler")
+    depends_on("cuda")
+    depends_on("mpi", when="+mpi")
+    depends_on("cmake@3.10:", type='build')
+
+    def cmake_args(self):
+        options = [
+            "-DCMAKE_CXX_COMPILER=%s" % os.environ["SPACK_CXX"],
+            "-DCMAKE_CUDA_HOST_COMPILER=%s" % os.environ["SPACK_CXX"],
+            "-DCMAKE_C_COMPILER=%s" % os.environ["SPACK_CC"],
+        ]
+        return options
+
+    def setup_dependent_build_environment(self, env, dependent_spec):
+        wrapper = join_path(self.prefix.bin, "nvcc_wrapper")
+        env.set('MPICH_CXX', wrapper)
+        env.set('OMPI_CXX', wrapper)
+        env.set('KOKKOS_CXX', spack_cxx)
+
+    def setup_dependent_package(self, module, dependent_spec):
+        wrapper = join_path(self.prefix.bin, "nvcc_wrapper")
+        self.spec.kokkos_cxx = wrapper
diff --git a/var/spack/repos/builtin/packages/kokkos/package.py b/var/spack/repos/builtin/packages/kokkos/package.py
index 47dae741ba9..eb1f0610daa 100644
--- a/var/spack/repos/builtin/packages/kokkos/package.py
+++ b/var/spack/repos/builtin/packages/kokkos/package.py
@@ -2,231 +2,245 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
 from spack import *
 
 
-class Kokkos(Package):
+class Kokkos(CMakePackage, CudaPackage):
     """Kokkos implements a programming model in C++ for writing performance
     portable applications targeting all major HPC platforms."""
 
     homepage = "https://github.com/kokkos/kokkos"
-    url      = "https://github.com/kokkos/kokkos/archive/2.03.00.tar.gz"
-    git      = "https://github.com/kokkos/kokkos.git"
+    git = "https://github.com/kokkos/kokkos.git"
 
     version('develop', branch='develop')
-    version('3.1.00', sha256='b935c9b780e7330bcb80809992caa2b66fd387e3a1c261c955d622dae857d878')
-    version('3.0.00', sha256='c00613d0194a4fbd0726719bbed8b0404ed06275f310189b3493f5739042a92b')
-    version('2.9.00', sha256='e0621197791ed3a381b4f02c78fa529f3cff3abb74d52157b4add17e8aa04bc4')
-    version('2.8.00', sha256='1c72661f2d770517bff98837001b42b9c677d1df29f7493a1d7c008549aff630')
-    version('2.7.24', sha256='a308a80ea1488f4c18884b828ce7ae9f5210b9a6b2f61b208d875084d8da8cb0')
-    version('2.7.00',  sha256='01595996e612ef7410aa42fa265a23101cfe1b6993fa9810ca844db5c89ad765')
-    version('2.5.00',  sha256='ea232594bf746abb99ae2aafaeef5d07adc089968010a62a88aaa892106d9476')
-    version('2.04.11', sha256='f2680aee0169f6cbbec38410f9c80bf8a160435f6a07769c1e9112da8b9349a0')
-    version('2.04.04', sha256='5bac8ddc2fac9bc6e01dd40f92ca6cbbb346a25deca5be2fec71acf712d0d0c7')
-    version('2.04.00', sha256='b04658d368986df207662a7a37c1ad974c321447bc2c2b5b696d7e9ee4481f34')
-    version('2.03.13', sha256='002748bdd0319d5ab82606cf92dc210fc1c05d0607a2e1d5538f60512b029056')
-    version('2.03.05', sha256='b18ddaa1496130ff3f675ea9ddbc6df9cdf378d53edf96df89e70ff189e10e1d')
-    version('2.03.00', sha256='722bea558d8986efee765ac912febb3c1ce289a8e9bdfef77cd0145df0ea8a3d')
-    version('2.02.15', sha256='6b4a7f189f0341f378f950f3c798f520d2e473b13435b137ff3b666e799a076d')
-    version('2.02.07', sha256='7b4ac81021d6868f4eb8e2a1cb92ba76bad9c3f197403b8b1eac0f11c983247c')
+    version('master',  branch='master')
+    version('3.0', url="https://github.com/kokkos/kokkos/archive/3.0.00.tar.gz",
+            sha256="c00613d0194a4fbd0726719bbed8b0404ed06275f310189b3493f5739042a92b")
+    version('3.1', url="https://github.com/kokkos/kokkos/archive/3.1.00.tar.gz",
+            sha256="b935c9b780e7330bcb80809992caa2b66fd387e3a1c261c955d622dae857d878",
+            default=True)
 
-    variant('debug', default=False, description="Build debug version of Kokkos")
+    depends_on("cmake@3.10:", type='build')
 
-    variant('serial', default=True, description="enable Serial backend (default)")
-    variant('pthreads', default=False, description="enable Pthreads backend")
-    variant('qthreads', default=False, description="enable Qthreads backend")
-    variant('cuda', default=False, description="enable Cuda backend")
-    variant('openmp', default=False, description="enable OpenMP backend")
+    devices_variants = {
+        'cuda': [False, 'Whether to build CUDA backend'],
+        'openmp': [False, 'Whether to build OpenMP backend'],
+        'pthread': [False, 'Whether to build Pthread backend'],
+        'serial': [True,  'Whether to build serial backend'],
+        'hip': [False, 'Whether to build HIP backend'],
+    }
+    conflicts("+hip", when="@:3.0")
 
-    # Compilation options
-    variant('pic', default=False,
-            description="enable position independent code (-fPIC flag)")
+    tpls_variants = {
+        'hpx': [False, 'Whether to enable the HPX library'],
+        'hwloc': [False, 'Whether to enable the HWLOC library'],
+        'numactl': [False, 'Whether to enable the LIBNUMA library'],
+        'memkind': [False, 'Whether to enable the MEMKIND library'],
+    }
 
-    # Kokkos options
-    variant('aggressive_vectorization', default=False,
-            description="set aggressive_vectorization Kokkos option")
-    variant('disable_profiling', default=False,
-            description="set disable_profiling Kokkos option")
-    variant('disable_dualview_modify_check', default=False,
-            description="set disable_dualview_modify_check Kokkos option")
-    variant('enable_profile_load_print', default=False,
-            description="set enable_profile_load_print Kokkos option")
-    variant('compiler_warnings', default=False,
-            description="set compiler_warnings Kokkos option")
-    variant('disable_deprecated_code', default=False,
-            description="set disable_deprecated_code Kokkos option")
-    variant('enable_eti', default=False,
-            description="set enable_eti Kokkos option")
+    options_variants = {
+        'aggressive_vectorization': [False,
+                                     'Aggressively vectorize loops'],
+        'compiler_warnings': [False,
+                              'Print all compiler warnings'],
+        'cuda_lambda': [False,
+                        'Activate experimental lambda features'],
+        'cuda_ldg_intrinsic': [False,
+                               'Use CUDA LDG intrinsics'],
+        'cuda_relocatable_device_code': [False,
+                                         'Enable RDC for CUDA'],
+        'cuda_uvm': [False,
+                     'Enable unified virtual memory (UVM) for CUDA'],
+        'debug': [False,
+                  'Activate extra debug features - may increase compiletimes'],
+        'debug_bounds_check': [False,
+                               'Use bounds checking - will increase runtime'],
+        'debug_dualview_modify_check': [False, 'Debug check on dual views'],
+        'deprecated_code': [False, 'Whether to enable deprecated code'],
+        'examples': [False, 'Whether to build OpenMP  backend'],
+        'explicit_instantiation': [False,
+                                   'Explicitly instantiate template types'],
+        'hpx_async_dispatch': [False,
+                               'Whether HPX supports asynchronous dispath'],
+        'profiling': [True,
+                      'Create bindings for profiling tools'],
+        'profiling_load_print': [False,
+                                 'Print which profiling tools got loaded'],
+        'qthread': [False, 'Eenable the QTHREAD library'],
+        'tests': [False, 'Build for tests'],
+    }
 
-    # CUDA options
-    variant('force_uvm', default=False,
-            description="set force_uvm Kokkos CUDA option")
-    variant('use_ldg', default=False,
-            description="set use_ldg Kokkos CUDA option")
-    variant('rdc', default=False,
-            description="set rdc Kokkos CUDA option")
-    variant('enable_lambda', default=False,
-            description="set enable_lambda Kokkos CUDA option")
+    amd_gpu_arches = [
+        'fiji',
+        'gfx901',
+        'vega900',
+        'vega906',
+    ]
+    variant("amd_gpu_arch", default='none', values=amd_gpu_arches,
+            description="AMD GPU architecture")
+    conflicts("+hip", when="amd_gpu_arch=none")
 
-    host_values = ('AMDAVX', 'ARMv80', 'ARMv81', 'ARMv8-ThunderX',
-                   'Power7', 'Power8', 'Power9',
-                   'WSM', 'SNB', 'HSW', 'BDW', 'SKX',
-                   'KNC', 'KNL')
+    spack_micro_arch_map = {
+        "aarch64": "",
+        "arm": "",
+        "ppc": "",
+        "ppc64": "",
+        "ppc64le": "",
+        "ppcle": "",
+        "sparc": None,
+        "sparc64": None,
+        "x86": "",
+        "x86_64": "",
+        "thunderx2": "THUNDERX2",
+        "k10": None,
+        "zen": "ZEN",
+        "bulldozer": "",
+        "piledriver": "",
+        "zen2": "ZEN2",
+        "steamroller": "KAVERI",
+        "excavator": "CARIZO",
+        "a64fx": "",
+        "power7": "POWER7",
+        "power8": "POWER8",
+        "power9": "POWER9",
+        "power8le": "POWER8",
+        "power9le": "POWER9",
+        "i686": None,
+        "pentium2": None,
+        "pentium3": None,
+        "pentium4": None,
+        "prescott": None,
+        "nocona": None,
+        "nehalem": None,
+        "sandybridge": "SNB",
+        "haswell": "HSW",
+        "mic_knl": "KNL",
+        "cannonlake": "SKX",
+        "cascadelake": "SKX",
+        "westmere": "WSM",
+        "core2": None,
+        "ivybridge": "SNB",
+        "broadwell": "BDW",
+        "skylake": "SKX",
+        "icelake": "SKX",
+        "skylake_avx512": "SKX",
+    }
 
-    gpu_values = ('Kepler30', 'Kepler32', 'Kepler35', 'Kepler37',
-                  'Maxwell50', 'Maxwell52', 'Maxwell53',
-                  'Pascal60', 'Pascal61',
-                  'Volta70', 'Volta72')
+    spack_cuda_arch_map = {
+        "30": 'kepler30',
+        "32": 'kepler32',
+        "35": 'kepler35',
+        "37": 'kepler37',
+        "50": 'maxwell50',
+        "52": 'maxwell52',
+        "53": 'maxwell53',
+        "60": 'pascal60',
+        "61": 'pascal61',
+        "70": 'volta70',
+        "72": 'volta72',
+        "75": 'turing75',
+    }
+    cuda_arches = spack_cuda_arch_map.values()
+    conflicts("+cuda", when="cuda_arch=none")
 
-    # C++ standard variant
-    variant('cxxstd', default='none',
-            values=('c++11', 'c++14', 'c++17', 'c++1y', 'c++1z', 'c++2a'),
-            multi=False,
-            description='set cxxstandard Kokkos option')
+    devices_values = list(devices_variants.keys())
+    for dev in devices_variants:
+        dflt, desc = devices_variants[dev]
+        variant(dev, default=dflt, description=desc)
 
-    # Host architecture variant
-    variant(
-        'host_arch',
-        default='none',
-        values=host_values,
-        description='Set the host architecture to use'
-    )
+    options_values = list(options_variants.keys())
+    for opt in options_values:
+        if "cuda" in opt:
+            conflicts('+%s' % opt, when="~cuda",
+                      msg="Must enable CUDA to use %s" % opt)
+        dflt, desc = options_variants[opt]
+        variant(opt, default=dflt, description=desc)
 
-    # GPU architecture variant
-    variant(
-        'gpu_arch',
-        default='none',
-        values=gpu_values,
-        description='Set the GPU architecture to use'
-    )
+    tpls_values = list(tpls_variants.keys())
+    for tpl in tpls_values:
+        dflt, desc = tpls_variants[tpl]
+        variant(tpl, default=dflt, description=desc)
+        depends_on(tpl, when="+%s" % tpl)
 
-    # Checks on Kokkos version and Kokkos options
-    conflicts('+aggressive_vectorization', when='@:2.0.99',)
-    conflicts('+disable_profiling', when='@:2.0.99',)
-    conflicts('+disable_dualview_modify_check', when='@:2.03.04',)
-    conflicts('+enable_profile_load_print', when='@:2.03.04',)
-    conflicts('+compiler_warnings', when='@:2.03.14',)
-    conflicts('+disable_deprecated_code', when='@:2.5.99',)
-    conflicts('+enable_eti', when='@:2.6.99',)
+    variant("wrapper", default=False,
+            description="Use nvcc-wrapper for CUDA build")
+    depends_on("kokkos-nvcc-wrapper", when="+wrapper")
+    conflicts("+wrapper", when="~cuda")
 
-    # Check that we haven't specified a gpu architecture
-    # without specifying CUDA
-    for p in gpu_values:
-        conflicts('gpu_arch={0}'.format(p), when='~cuda',
-                  msg='Must specify CUDA backend to use a GPU architecture.')
+    variant("std", default="11", values=["11", "14", "17", "20"], multi=False)
+    # nvcc does not currently work with C++17 or C++20
+    conflicts("+cuda", when="std=17")
+    conflicts("+cuda", when="std=20")
 
-    # Check that we haven't specified a Kokkos CUDA option
-    # without specifying CUDA
-    conflicts('+force_uvm', when='~cuda',
-              msg='Must enable CUDA to use force_uvm.')
-    conflicts('+use_ldg', when='~cuda',
-              msg='Must enable CUDA to use use_ldg.')
-    conflicts('+rdc', when='~cuda',
-              msg='Must enable CUDA to use rdc.')
-    conflicts('+enable_lambda', when='~cuda',
-              msg='Must enable CUDA to use enable_lambda.')
+    def append_args(self, cmake_prefix, cmake_options, spack_options):
+        for opt in cmake_options:
+            enablestr = "+%s" % opt
+            optuc = opt.upper()
+            optname = "Kokkos_%s_%s" % (cmake_prefix, optuc)
+            option = None
+            if enablestr in self.spec:
+                option = "-D%s=ON" % optname
+            else:
+                # explicitly turn off if not enabled
+                # this avoids any confusing implicit defaults
+                # that come from the CMake
+                option = "-D%s=OFF" % optname
+            if option not in spack_options:
+                spack_options.append(option)
 
-    # Check that we haven't asked for a GPU architecture that
-    # the revision of kokkos does not support
-    conflicts('gpu_arch=Volta70', when='@:2.5.99')
-    conflicts('gpu_arch=Volta72', when='@:2.5.99')
+    def setup_dependent_package(self, module, dependent_spec):
+        try:
+            self.spec.kokkos_cxx = self.spec["kokkos-nvcc-wrapper"].kokkos_cxx
+        except Exception:
+            self.spec.kokkos_cxx = spack_cxx
 
-    # conflicts on kokkos version and cuda enabled
-    # see kokkos issue #1296
-    # https://github.com/kokkos/kokkos/issues/1296
-    conflicts('+cuda', when='@2.5.00:2.7.00',
-              msg='Kokkos build system has issue (#1296) when CUDA enabled'
-              ' in version 2.5.00 through 2.7.00.')
+    def cmake_args(self):
+        spec = self.spec
+        options = []
 
-    # Specify that v1.x is required as v2.x has API changes
-    depends_on('hwloc@:1')
-    depends_on('qthreads', when='+qthreads')
-    depends_on('cuda', when='+cuda')
+        isdiy = "+diy" in spec
+        if isdiy:
+            options.append("-DSpack_WORKAROUND=On")
 
-    # generate_makefile.bash calls cmake
-    depends_on('cmake@3.10:', type='build')
+        spack_microarches = []
+        if "+cuda" in spec:
+            # this is a list
+            for cuda_arch in spec.variants["cuda_arch"].value:
+                if not cuda_arch == "none":
+                    kokkos_arch_name = self.spack_cuda_arch_map[cuda_arch]
+                    spack_microarches.append(kokkos_arch_name)
+        kokkos_microarch_name = self.spack_micro_arch_map[spec.target.name]
+        if kokkos_microarch_name:
+            spack_microarches.append(kokkos_microarch_name)
 
-    def install(self, spec, prefix):
-        generate = which(join_path(self.stage.source_path,
-                                   'generate_makefile.bash'))
-        with working_dir('build', create=True):
-            g_args = [
-                '--prefix=%s' % prefix,
-                '--with-hwloc=%s' % spec['hwloc'].prefix,
-            ]
-            arch_args = []
-            kokkos_options_args = []
-            cuda_options_args = []
+        for arch in amd_gpu_arches:
+            keyval = "amd_gpu_arch=%s" % arch
+            if keyval in spec:
+                spack_microarches.append(arch)
 
-            # PIC
-            if '+pic' in spec:
-                g_args.append('--cxxflags=-fPIC')
+        for arch in spack_microarches:
+            options.append("-DKokkos_ARCH_%s=ON" % arch.upper())
 
-            # C++ standard
-            cxxstandard = spec.variants['cxxstd'].value
-            if cxxstandard != 'none':
-                g_args.append('--cxxstandard=%s' % cxxstandard)
+        self.append_args("ENABLE", self.devices_values, options)
+        self.append_args("ENABLE", self.options_values, options)
+        self.append_args("ENABLE", self.tpls_values, options)
+        self.append_args("ARCH",   self.arch_values, options)
 
-            # Build Debug
-            if '+debug' in spec:
-                g_args.append('--debug')
+        for tpl in self.tpls_values:
+            var = "+%s" % tpl
+            if var in self.spec:
+                options.append("-D%s_DIR=%s" % (tpl, spec[tpl].prefix))
 
-            # Backends
-            if '+serial' in spec:
-                g_args.append('--with-serial')
-            if '+openmp' in spec:
-                g_args.append('--with-openmp')
-            if '+pthreads' in spec:
-                g_args.append('--with-pthread')
-            if '+qthreads' in spec:
-                g_args.append('--with-qthreads=%s' % spec['qthreads'].prefix)
-            if '+cuda' in spec:
-                g_args.append('--with-cuda=%s' % spec['cuda'].prefix)
-            # Host architectures
-            host_arch = spec.variants['host_arch'].value
-            # GPU architectures
-            gpu_arch  = spec.variants['gpu_arch'].value
-            if host_arch != 'none':
-                arch_args.append(host_arch)
-            if gpu_arch != 'none':
-                arch_args.append(gpu_arch)
-            # Combined architecture flags
-            if arch_args:
-                g_args.append('--arch={0}'.format(','.join(arch_args)))
+        # we do not need the compiler wrapper from Spack
+        # set the compiler explicitly (may be Spack wrapper or nvcc-wrapper)
+        try:
+            options.append("-DCMAKE_CXX_COMPILER=%s" %
+                           self.spec["kokkos-nvcc-wrapper"].kokkos_cxx)
+        except Exception:
+            options.append("-DCMAKE_CXX_COMPILER=%s" % spack_cxx)
 
-            # CUDA options
-            if '+force_uvm' in spec:
-                cuda_options_args.append('force_uvm')
-            if '+use_ldg' in spec:
-                cuda_options_args.append('use_ldg')
-            if '+rdc' in spec:
-                cuda_options_args.append('rdc')
-            if '+enable_lambda' in spec:
-                cuda_options_args.append('enable_lambda')
-            if cuda_options_args:
-                g_args.append('--with-cuda-options={0}'
-                              .format(','.join(cuda_options_args)))
+        # Set the C++ standard to use
+        options.append("-DKokkos_CXX_STANDARD=%s" %
+                       self.spec.variants["std"].value)
 
-            # Kokkos options
-            if '+aggressive_vectorization' in spec:
-                kokkos_options_args.append('aggressive_vectorization')
-            if '+disable_profiling' in spec:
-                kokkos_options_args.append('disable_profiling')
-            if '+disable_dualview_modify_check' in spec:
-                kokkos_options_args.append('disable_dualview_modify_check')
-            if '+enable_profile_load_print' in spec:
-                kokkos_options_args.append('enable_profile_load_print')
-            if '+compiler_warnings' in spec:
-                kokkos_options_args.append('compiler_warnings')
-            if '+disable_deprecated_code' in spec:
-                kokkos_options_args.append('disable_deprecated_code')
-            if '+enable_eti' in spec:
-                kokkos_options_args.append('enable_eti')
-            if kokkos_options_args:
-                g_args.append('--with-options={0}'
-                              .format(','.join(kokkos_options_args)))
-
-            generate(*g_args)
-            make()
-            make('install')
+        return options
diff --git a/var/spack/repos/builtin/packages/lammps/package.py b/var/spack/repos/builtin/packages/lammps/package.py
index 9a6ef2e2b4d..f25c920da12 100644
--- a/var/spack/repos/builtin/packages/lammps/package.py
+++ b/var/spack/repos/builtin/packages/lammps/package.py
@@ -106,7 +106,7 @@ def url_for_version(self, version):
     depends_on('jpeg', when='+jpeg')
     depends_on('libpng', when='+png')
     depends_on('ffmpeg', when='+ffmpeg')
-    depends_on('kokkos', when='+kokkos')
+    depends_on('kokkos-legacy', when='+kokkos')
 
     conflicts('+cuda', when='+opencl')
     conflicts('+body', when='+poems@:20180628')
diff --git a/var/spack/repos/builtin/packages/miniaero/package.py b/var/spack/repos/builtin/packages/miniaero/package.py
index f4679477199..a18a5bfecf9 100644
--- a/var/spack/repos/builtin/packages/miniaero/package.py
+++ b/var/spack/repos/builtin/packages/miniaero/package.py
@@ -19,7 +19,7 @@ class Miniaero(MakefilePackage):
 
     version('2016-11-11', commit='f46d135479a5be19ec5d146ccaf0e581aeff4596')
 
-    depends_on('kokkos')
+    depends_on('kokkos-legacy')
 
     @property
     def build_targets(self):

From f005ec016b29097d92b99a4366feef95a5d7bf23 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Thu, 30 Apr 2020 09:09:13 -0600
Subject: [PATCH 185/802] kokkos: fix typos (#16388)

---
 var/spack/repos/builtin/packages/kokkos/package.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/kokkos/package.py b/var/spack/repos/builtin/packages/kokkos/package.py
index eb1f0610daa..d1d58fcbbda 100644
--- a/var/spack/repos/builtin/packages/kokkos/package.py
+++ b/var/spack/repos/builtin/packages/kokkos/package.py
@@ -213,7 +213,7 @@ def cmake_args(self):
         if kokkos_microarch_name:
             spack_microarches.append(kokkos_microarch_name)
 
-        for arch in amd_gpu_arches:
+        for arch in self.amd_gpu_arches:
             keyval = "amd_gpu_arch=%s" % arch
             if keyval in spec:
                 spack_microarches.append(arch)
@@ -224,7 +224,6 @@ def cmake_args(self):
         self.append_args("ENABLE", self.devices_values, options)
         self.append_args("ENABLE", self.options_values, options)
         self.append_args("ENABLE", self.tpls_values, options)
-        self.append_args("ARCH",   self.arch_values, options)
 
         for tpl in self.tpls_values:
             var = "+%s" % tpl

From d5d4e16f3d21060a14ba6c4a21577fdbe02a1b6b Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Thu, 30 Apr 2020 09:29:20 -0600
Subject: [PATCH 186/802] graphviz: fix cairo dep (#16387)

---
 var/spack/repos/builtin/packages/graphviz/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py
index 0df127b00b1..17197f18389 100644
--- a/var/spack/repos/builtin/packages/graphviz/package.py
+++ b/var/spack/repos/builtin/packages/graphviz/package.py
@@ -95,7 +95,7 @@ class Graphviz(AutotoolsPackage):
     depends_on('ghostscript', when='+ghostscript')
     depends_on('gtkplus', when='+gtkplus')
     depends_on('gts', when='+gts')
-    depends_on('cairo', when='+pangocairo')
+    depends_on('cairo+pdf', when='+pangocairo')
     depends_on('fontconfig', when='+pangocairo')
     depends_on('freetype', when='+pangocairo')
     depends_on('glib', when='+pangocairo')

From 3a3f8717185868285ebc1e0226b0d7a320ef404c Mon Sep 17 00:00:00 2001
From: Satish Balay <balay@mcs.anl.gov>
Date: Thu, 30 Apr 2020 10:33:02 -0500
Subject: [PATCH 187/802] xsdk: update to mfem and py-petsc4py changes (#16378)

mfem variant hypre is now rolled into variant mpi - so update spec accordingly

mfem@4.0.1-xsdk+superlu-dist is broken and unsupported - so disable it

with the addition of py-petsc4py@3.13.0 - conretizer gets confused and is not picking py-petsc4py@3.12.0 as a compatible dependency with petsc@3.12. So manually specify it.
Also depends_on('py-libensemble@0.5.2+petsc4py ^py-petsc4py@3.12.0' causes concretizer to hang forever
---
 var/spack/repos/builtin/packages/xsdk/package.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/xsdk/package.py b/var/spack/repos/builtin/packages/xsdk/package.py
index b2f036a4169..352521181a8 100644
--- a/var/spack/repos/builtin/packages/xsdk/package.py
+++ b/var/spack/repos/builtin/packages/xsdk/package.py
@@ -43,10 +43,10 @@ class Xsdk(BundlePackage):
     depends_on('hypre@2.12.1~internal-superlu', when='@0.3.0')
     depends_on('hypre@xsdk-0.2.0~internal-superlu', when='@xsdk-0.2.0')
 
-    depends_on('mfem@develop+mpi+hypre+superlu-dist+petsc~sundials+examples+miniapps', when='@develop')
-    depends_on('mfem@4.0.1-xsdk+mpi+hypre+superlu-dist+petsc+sundials+examples+miniapps', when='@0.5.0')
-    depends_on('mfem@3.4.0+mpi+hypre+superlu-dist+petsc+sundials+examples+miniapps', when='@0.4.0')
-    depends_on('mfem@3.3.2+mpi+hypre+superlu-dist+petsc+sundials+examples+miniapps', when='@0.3.0')
+    depends_on('mfem@develop+mpi+superlu-dist+petsc~sundials+examples+miniapps', when='@develop')
+    depends_on('mfem@4.0.1-xsdk+mpi~superlu-dist+petsc+sundials+examples+miniapps', when='@0.5.0')
+    depends_on('mfem@3.4.0+mpi+superlu-dist+petsc+sundials+examples+miniapps', when='@0.4.0')
+    depends_on('mfem@3.3.2+mpi+superlu-dist+petsc+sundials+examples+miniapps', when='@0.3.0')
 
     depends_on('superlu-dist@develop', when='@develop')
     depends_on('superlu-dist@6.1.1', when='@0.5.0')
@@ -164,6 +164,7 @@ class Xsdk(BundlePackage):
 
     depends_on('py-libensemble@develop+petsc4py', type='run', when='@develop +libensemble')
     depends_on('py-libensemble@0.5.2+petsc4py', type='run', when='@0.5.0 +libensemble')
+    depends_on('py-petsc4py@3.12.0', type='run', when='@0.5.0 +libensemble')
 
     depends_on('precice ~petsc', when='platform=cray +precice')
     depends_on('precice@develop', when='@develop +precice')

From b2df39ea3a083486ae6b62d095213da009a0f9e9 Mon Sep 17 00:00:00 2001
From: Satish Balay <balay@mcs.anl.gov>
Date: Thu, 30 Apr 2020 10:40:25 -0500
Subject: [PATCH 188/802] petsc: switch hdf5 spec from --with-hdf5-dir to
 --with-hdf5-lib (#16376)

This way - we can detect and use hdf5:hl,fortran - if enabled, but not require it as a dependency
---
 var/spack/repos/builtin/packages/petsc/package.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index df1b6e1780e..a4c151b5e27 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -296,7 +296,7 @@ def install(self, spec, prefix):
             ])
 
         # Activates library support if needed
-        for library in ('cuda', 'metis', 'hdf5', 'hypre', 'parmetis',
+        for library in ('cuda', 'metis', 'hypre', 'parmetis',
                         'mumps', 'trilinos', 'fftw', 'valgrind'):
             options.append(
                 '--with-{library}={value}'.format(
@@ -339,6 +339,16 @@ def install(self, spec, prefix):
         else:
             options.append('--with-suitesparse=0')
 
+        # hdf5: configure detection is convoluted for pflotran
+        if '+hdf5' in spec:
+            options.extend([
+                '--with-hdf5-include=%s' % spec['hdf5'].prefix.include,
+                '--with-hdf5-lib=%s' % spec['hdf5:hl,fortran'].libs.joined(),
+                '--with-hdf5=1'
+            ])
+        else:
+            options.append('--with-hdf5=0')
+
         # zlib: configuring using '--with-zlib-dir=...' has some issues with
         # SuiteSparse so specify directly the include path and the libraries.
         if 'zlib' in spec:

From b0ecaa109310bc39e6c48329ecdacb4d5ccee736 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Thu, 30 Apr 2020 23:45:48 +0800
Subject: [PATCH 189/802] Add new package: bashtop (#16383)

---
 .../repos/builtin/packages/bashtop/package.py | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/bashtop/package.py

diff --git a/var/spack/repos/builtin/packages/bashtop/package.py b/var/spack/repos/builtin/packages/bashtop/package.py
new file mode 100644
index 00000000000..47f98f14a8e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bashtop/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bashtop(Package):
+    """Linux resource monitor."""
+
+    homepage = "https://github.com/aristocratos/bashtop"
+    url      = "https://github.com/aristocratos/bashtop/archive/v0.8.17.tar.gz"
+
+    version('0.8.17', sha256='853a7143de533437cc1654b853bc89da54ff91c629820ac45b7c8708dababf1f')
+    version('0.8.16', sha256='6249e5c678fdb0a2a87d6fa13b9fe1f6bd56f7dbcaba0066d2a5275a7f9a9355')
+    version('0.8.15', sha256='617aab0a23b1a9430f2ef7d51e4f89eb06c5b3f2ff40768cb6849fc2899ffc6a')
+    version('0.8.14', sha256='e2e05a36a8fb3984f256af62f66562c8bd13a901e5f2ef7b7b0056ef40e57543')
+    version('0.8.13', sha256='50eda3c91f36a49d7696585fce5b44ba0df53879758f30d94477010bd56c4ff1')
+    version('0.8.12', sha256='1e762e40527f454da0f1d050a251a1c288cbbe49645f4ee31aa30afe44e70a0f')
+    version('0.8.11', sha256='bf4b3f109819450ee52f42a32d1b46bf2524ae3b1def83fcafba1b8427c71241')
+    version('0.8.10', sha256='eac071d68d2ec08869dea696b886bbc0fc33e596e9efa73563e71b4af27c0947')
+    version('0.8.9',  sha256='af2ba211d3bc1fbe910cd33c447686a6f39c2c731aaba54355b9e66184a0aec1')
+    version('0.8.8',  sha256='63e88c6f91fdfb3c5265f347e48d7a54a3ad0582407e9adbb70694eb9039ce3f')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('bashtop', prefix.bin)

From 74c9ba551a73ff21db6d81f1f21f28ffeb35eb1b Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Thu, 30 Apr 2020 09:49:02 -0600
Subject: [PATCH 190/802] cabana: add v0.2 and fix kokkos deps (#16389)

---
 var/spack/repos/builtin/packages/cabana/package.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cabana/package.py b/var/spack/repos/builtin/packages/cabana/package.py
index aaf88e4e121..b3bc87c061d 100644
--- a/var/spack/repos/builtin/packages/cabana/package.py
+++ b/var/spack/repos/builtin/packages/cabana/package.py
@@ -13,7 +13,8 @@ class Cabana(CMakePackage):
     git      = "https://github.com/ECP-copa/Cabana.git"
     url      = "https://github.com/ECP-copa/Cabana/archive/0.1.0.tar.gz"
 
-    version('develop', branch='master')
+    version('master', branch='master')
+    version('0.2.0', sha256='3e0c0e224e90f4997f6c7e2b92f00ffa18f8bcff72f789e0908cea0828afc2cb')
     version('0.1.0', sha256='3280712facf6932b9d1aff375b24c932abb9f60a8addb0c0a1950afd0cb9b9cf')
     version('0.1.0-rc0', sha256='73754d38aaa0c2a1e012be6959787108fec142294774c23f70292f59c1bdc6c5')
 
@@ -22,9 +23,12 @@ class Cabana(CMakePackage):
     variant('cuda', default=False, description="enable Cuda backend")
 
     depends_on("cmake@3.9:", type='build')
-    depends_on("kokkos-legacy+serial", when="+serial")
-    depends_on("kokkos-legacy+openmp", when="+openmp")
-    depends_on("kokkos-legacy+cuda", when="+cuda")
+    depends_on("kokkos-legacy+serial", when="@:0.2.0+serial")
+    depends_on("kokkos-legacy+openmp", when="@:0.2.0+openmp")
+    depends_on("kokkos-legacy+cuda", when="@:0.2.0+cuda")
+    depends_on("kokkos@3.1:+serial", when="@0.3.0:+serial")
+    depends_on("kokkos@3.1:+openmp", when="@0.3.0:+openmp")
+    depends_on("kokkos@3.1:+cuda", when="@0.3.0:+cuda")
 
     def cmake_args(self):
         options = [

From 6c24142ebd045fcfeff225f9e4ee9ad02b6ba8ed Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 30 Apr 2020 11:13:23 -0500
Subject: [PATCH 191/802] Fix coreutils configure_args (#16391)

---
 var/spack/repos/builtin/packages/coreutils/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/coreutils/package.py b/var/spack/repos/builtin/packages/coreutils/package.py
index 1bc3ee1e724..569831dac7a 100644
--- a/var/spack/repos/builtin/packages/coreutils/package.py
+++ b/var/spack/repos/builtin/packages/coreutils/package.py
@@ -35,4 +35,4 @@ def configure_args(self):
             configure_args.append('--without-gmp')
             configure_args.append('gl_cv_func_ftello_works=yes')
 
-            return configure_args
+        return configure_args

From cfb307b8e7661c96874b86c9a13dbcc45ac20aa4 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Thu, 30 Apr 2020 10:29:08 -0600
Subject: [PATCH 192/802] lammps: fix build with kokkos (#16390)

---
 .../repos/builtin/packages/kokkos/package.py  |  4 ++++
 .../repos/builtin/packages/lammps/package.py  | 22 ++++++++++---------
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/var/spack/repos/builtin/packages/kokkos/package.py b/var/spack/repos/builtin/packages/kokkos/package.py
index d1d58fcbbda..86cf01e7849 100644
--- a/var/spack/repos/builtin/packages/kokkos/package.py
+++ b/var/spack/repos/builtin/packages/kokkos/package.py
@@ -172,6 +172,8 @@ class Kokkos(CMakePackage, CudaPackage):
     conflicts("+cuda", when="std=17")
     conflicts("+cuda", when="std=20")
 
+    variant('shared', default=True, description='Build shared libraries')
+
     def append_args(self, cmake_prefix, cmake_options, spack_options):
         for opt in cmake_options:
             enablestr = "+%s" % opt
@@ -242,4 +244,6 @@ def cmake_args(self):
         options.append("-DKokkos_CXX_STANDARD=%s" %
                        self.spec.variants["std"].value)
 
+        options.append('-DBUILD_SHARED_LIBS=%s' % ('+shared' in self.spec))
+
         return options
diff --git a/var/spack/repos/builtin/packages/lammps/package.py b/var/spack/repos/builtin/packages/lammps/package.py
index f25c920da12..2e12378dc33 100644
--- a/var/spack/repos/builtin/packages/lammps/package.py
+++ b/var/spack/repos/builtin/packages/lammps/package.py
@@ -55,12 +55,13 @@ def url_for_version(self, version):
             vdate.strftime("%d%b%Y").lstrip('0'))
 
     supported_packages = ['asphere', 'body', 'class2', 'colloid', 'compress',
-                          'coreshell', 'dipole', 'granular', 'kspace', 'latte',
-                          'manybody', 'mc', 'meam', 'misc', 'molecule',
-                          'mpiio', 'peri', 'poems', 'python', 'qeq',
-                          'replica', 'rigid', 'shock', 'snap', 'spin', 'srd',
-                          'user-atc', 'user-h5md', 'user-lb', 'user-misc',
-                          'user-netcdf', 'user-omp', 'user-reaxc', 'voronoi']
+                          'coreshell', 'dipole', 'granular', 'kspace',
+                          'kokkos', 'latte', 'manybody', 'mc', 'meam', 'misc',
+                          'molecule', 'mpiio', 'peri', 'poems', 'python',
+                          'qeq', 'replica', 'rigid', 'shock', 'snap', 'spin',
+                          'srd', 'user-atc', 'user-h5md', 'user-lb',
+                          'user-misc', 'user-netcdf', 'user-omp', 'user-reaxc',
+                          'voronoi']
 
     for pkg in supported_packages:
         variant(pkg, default=False,
@@ -69,8 +70,6 @@ def url_for_version(self, version):
             description='Build the liblammps in addition to the executable')
     variant('mpi', default=True,
             description='Build with mpi')
-    variant('kokkos', default=False,
-            description='Build with Kokkos accelerated styles')
     variant('jpeg', default=True,
             description='Build with jpeg support')
     variant('png', default=True,
@@ -106,7 +105,7 @@ def url_for_version(self, version):
     depends_on('jpeg', when='+jpeg')
     depends_on('libpng', when='+png')
     depends_on('ffmpeg', when='+ffmpeg')
-    depends_on('kokkos-legacy', when='+kokkos')
+    depends_on('kokkos+deprecated_code+shared@3.0', when='@20200303+kokkos')
 
     conflicts('+cuda', when='+opencl')
     conflicts('+body', when='+poems@:20180628')
@@ -117,7 +116,8 @@ def url_for_version(self, version):
     conflicts('+user-misc', when='~manybody')
     conflicts('+user-phonon', when='~kspace')
     conflicts('+user-misc', when='~manybody')
-    conflicts('%gcc@9:', when='+openmp')
+    conflicts('%gcc@9:', when='@:20200303+openmp')
+    conflicts('+kokkos', when='@:20200227')
 
     patch("lib.patch", when="@20170901")
     patch("660.patch", when="@20170922")
@@ -176,5 +176,7 @@ def cmake_args(self):
                 args.append('{0}=OFF'.format(opt))
         if '+kspace' in spec:
             args.append('-DFFT=FFTW3')
+        if '+kokkos' in spec:
+            args.append('-DEXTERNAL_KOKKOS=ON')
 
         return args

From b55b7d5707cc61eea5c0c8425b62bc6175f4dbbb Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 30 Apr 2020 11:36:50 -0500
Subject: [PATCH 193/802] Fix kokkos-kernels tuple unpacking (#16393)

---
 var/spack/repos/builtin/packages/kokkos-kernels/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/kokkos-kernels/package.py b/var/spack/repos/builtin/packages/kokkos-kernels/package.py
index 8cd68051df9..d4ae6a33639 100644
--- a/var/spack/repos/builtin/packages/kokkos-kernels/package.py
+++ b/var/spack/repos/builtin/packages/kokkos-kernels/package.py
@@ -122,7 +122,7 @@ def cmake_args(self):
                     options.append("-D%s=OFF" % cmake_option)
 
         for eti in self.space_etis:
-            deflt, descr = self.space_etis[eti]
+            deflt, descr, _ = self.space_etis[eti]
             if deflt == "auto":
                 value = spec.variants[eti].value
                 # spack does these as strings, not reg booleans

From 6d7daf0def6b8c432b5e79d48c96f29faf3d2db9 Mon Sep 17 00:00:00 2001
From: Ben Bergen <bergen@lanl.gov>
Date: Thu, 30 Apr 2020 11:16:00 -0600
Subject: [PATCH 194/802] Resolves: https://github.com/spack/spack/issues/16394
 (#16395)

Build problem with gcc 10.x
---
 .../repos/builtin/packages/gdbm/gdbm_gcc_10.patch     | 11 +++++++++++
 var/spack/repos/builtin/packages/gdbm/package.py      |  1 +
 2 files changed, 12 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/gdbm/gdbm_gcc_10.patch

diff --git a/var/spack/repos/builtin/packages/gdbm/gdbm_gcc_10.patch b/var/spack/repos/builtin/packages/gdbm/gdbm_gcc_10.patch
new file mode 100644
index 00000000000..6f04bfcb329
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gdbm/gdbm_gcc_10.patch
@@ -0,0 +1,11 @@
+--- gdbm-1.18.1/src/parseopt.c	2018-05-30 03:39:15.000000000 -0600
++++ gdbm-1.18.1_new/src/parseopt.c	2020-04-30 10:29:52.869582500 -0600
+@@ -255,8 +255,6 @@
+ }
+ 
+ char *parseopt_program_name;
+-char *parseopt_program_doc;
+-char *parseopt_program_args;
+ const char *program_bug_address = "<" PACKAGE_BUGREPORT ">";
+ void (*parseopt_help_hook) (FILE *stream);
+ 
diff --git a/var/spack/repos/builtin/packages/gdbm/package.py b/var/spack/repos/builtin/packages/gdbm/package.py
index 8469cc4fb5c..ae89387f242 100644
--- a/var/spack/repos/builtin/packages/gdbm/package.py
+++ b/var/spack/repos/builtin/packages/gdbm/package.py
@@ -26,6 +26,7 @@ class Gdbm(AutotoolsPackage, GNUMirrorPackage):
     version('1.9',   sha256='f85324d7de3777db167581fd5d3493d2daa3e85e195a8ae9afc05b34551b6e57')
 
     depends_on("readline")
+    patch('gdbm_gcc_10.patch', when='%gcc@10:')
 
     def configure_args(self):
 

From 6855e8e10fa5e0c00bceabbe8baee942dfadd5d1 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Thu, 30 Apr 2020 21:29:24 +0200
Subject: [PATCH 195/802] pcre: Add 8.44 (#16397)

---
 var/spack/repos/builtin/packages/pcre/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/pcre/package.py b/var/spack/repos/builtin/packages/pcre/package.py
index 85ba9c52b89..a4d17941480 100644
--- a/var/spack/repos/builtin/packages/pcre/package.py
+++ b/var/spack/repos/builtin/packages/pcre/package.py
@@ -14,6 +14,7 @@ class Pcre(AutotoolsPackage):
     homepage = "http://www.pcre.org"
     url      = "https://ftp.pcre.org/pub/pcre/pcre-8.42.tar.bz2"
 
+    version('8.44', sha256='19108658b23b3ec5058edc9f66ac545ea19f9537234be1ec62b714c84399366d')
     version('8.43', sha256='91e762520003013834ac1adb4a938d53b22a216341c061b0cf05603b290faf6b')
     version('8.42', sha256='2cd04b7c887808be030254e8d77de11d3fe9d4505c39d4b15d2664ffe8bf9301')
     version('8.41', sha256='e62c7eac5ae7c0e7286db61ff82912e1c0b7a0c13706616e94a7dd729321b530')

From 15c1fbc677173e2a2bf223b24bd112d2a276588f Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Thu, 30 Apr 2020 21:29:36 +0200
Subject: [PATCH 196/802] meson: Add 0.54.1 (#16398)

---
 var/spack/repos/builtin/packages/meson/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/meson/package.py b/var/spack/repos/builtin/packages/meson/package.py
index dbda0f5e780..f4c8e56af58 100644
--- a/var/spack/repos/builtin/packages/meson/package.py
+++ b/var/spack/repos/builtin/packages/meson/package.py
@@ -14,6 +14,7 @@ class Meson(PythonPackage):
     homepage = "http://mesonbuild.com/"
     url      = "https://github.com/mesonbuild/meson/archive/0.49.0.tar.gz"
 
+    version('0.54.1', sha256='854e8b94ab36e5aece813d2b2aee8a639bd52201dfea50890722ac9128e2f59e')
     version('0.54.0', sha256='95efdbaa7cb3e915ab9a7b26b1412475398fdc3e834842a780f1646c7764f2d9')
     version('0.53.2', sha256='eab4f5d5dde12d002b7ddd958a9a0658589b63622b6cea2715e0235b95917888')
     version('0.49.1', sha256='a944e7f25a2bc8e4ba3502ab5835d8a8b8f2530415c9d6fcffb53e0abaea2ced')

From 7adcb239787c22515fcb3d5f329a1e7b19c443f2 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Thu, 30 Apr 2020 21:29:50 +0200
Subject: [PATCH 197/802] libxml2: Add 2.9.10 (#16399)

---
 var/spack/repos/builtin/packages/libxml2/package.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/libxml2/package.py b/var/spack/repos/builtin/packages/libxml2/package.py
index 8c024854ea1..22add8c7a31 100644
--- a/var/spack/repos/builtin/packages/libxml2/package.py
+++ b/var/spack/repos/builtin/packages/libxml2/package.py
@@ -14,11 +14,12 @@ class Libxml2(AutotoolsPackage):
     homepage = "http://xmlsoft.org"
     url      = "http://xmlsoft.org/sources/libxml2-2.9.8.tar.gz"
 
-    version('2.9.9', sha256='94fb70890143e3c6549f265cee93ec064c80a84c42ad0f23e85ee1fd6540a871')
-    version('2.9.8', sha256='0b74e51595654f958148759cfef0993114ddccccbb6f31aee018f3558e8e2732')
-    version('2.9.4', sha256='ffb911191e509b966deb55de705387f14156e1a56b21824357cdf0053233633c')
-    version('2.9.2', sha256='5178c30b151d044aefb1b08bf54c3003a0ac55c59c866763997529d60770d5bc')
-    version('2.7.8', sha256='cda23bc9ebd26474ca8f3d67e7d1c4a1f1e7106364b690d822e009fdc3c417ec')
+    version('2.9.10', sha256='aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f')
+    version('2.9.9',  sha256='94fb70890143e3c6549f265cee93ec064c80a84c42ad0f23e85ee1fd6540a871')
+    version('2.9.8',  sha256='0b74e51595654f958148759cfef0993114ddccccbb6f31aee018f3558e8e2732')
+    version('2.9.4',  sha256='ffb911191e509b966deb55de705387f14156e1a56b21824357cdf0053233633c')
+    version('2.9.2',  sha256='5178c30b151d044aefb1b08bf54c3003a0ac55c59c866763997529d60770d5bc')
+    version('2.7.8',  sha256='cda23bc9ebd26474ca8f3d67e7d1c4a1f1e7106364b690d822e009fdc3c417ec')
 
     variant('python', default=False, description='Enable Python support')
 

From c2704a6037719f80273fce25b06b27d4d63f0c95 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Thu, 30 Apr 2020 22:11:46 +0200
Subject: [PATCH 198/802] perl: Add 5.30.2 (#16396)

---
 var/spack/repos/builtin/packages/perl/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/perl/package.py b/var/spack/repos/builtin/packages/perl/package.py
index 2841ab27138..05cb13cff9a 100644
--- a/var/spack/repos/builtin/packages/perl/package.py
+++ b/var/spack/repos/builtin/packages/perl/package.py
@@ -35,7 +35,8 @@ class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
     version('5.31.4', sha256='418a7e6fe6485cc713a86d1227ef112f0bb3f80322e3b715ffe42851d97804a5')
 
     # Maintenance releases (even numbers, recommended)
-    version('5.30.1', sha256='bf3d25571ff1ee94186177c2cdef87867fd6a14aa5a84f0b1fb7bf798f42f964', preferred=True)
+    version('5.30.2', sha256='66db7df8a91979eb576fac91743644da878244cf8ee152f02cd6f5cd7a731689', preferred=True)
+    version('5.30.1', sha256='bf3d25571ff1ee94186177c2cdef87867fd6a14aa5a84f0b1fb7bf798f42f964')
     version('5.30.0', sha256='851213c754d98ccff042caa40ba7a796b2cee88c5325f121be5cbb61bbf975f2')
 
     # End of life releases

From d2fc61a0196eeb85514c9f85d533dbceb262de90 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Thu, 30 Apr 2020 22:12:00 +0200
Subject: [PATCH 199/802] libffi: Add 3.3 (#16400)

---
 var/spack/repos/builtin/packages/libffi/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/libffi/package.py b/var/spack/repos/builtin/packages/libffi/package.py
index 4add7b1785e..d21b62b1e50 100644
--- a/var/spack/repos/builtin/packages/libffi/package.py
+++ b/var/spack/repos/builtin/packages/libffi/package.py
@@ -14,6 +14,7 @@ class Libffi(AutotoolsPackage, SourcewarePackage):
     homepage = "https://sourceware.org/libffi/"
     sourceware_mirror_path = "libffi/libffi-3.2.1.tar.gz"
 
+    version('3.3',   sha256='72fba7922703ddfa7a028d513ac15a85c8d54c8d67f55fa5a4802885dc652056')
     version('3.2.1', sha256='d06ebb8e1d9a22d19e38d63fdb83954253f39bedc5d46232a05645685722ca37')
 
     @property

From f04b0d99a828b66741caa635170f1b2c244dde2f Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Thu, 30 Apr 2020 22:12:13 +0200
Subject: [PATCH 200/802] glib: Add 2.64.2 (#16401)

---
 var/spack/repos/builtin/packages/glib/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py
index 9e71ccdd4bb..6e009ef1edb 100644
--- a/var/spack/repos/builtin/packages/glib/package.py
+++ b/var/spack/repos/builtin/packages/glib/package.py
@@ -21,6 +21,7 @@ class Glib(Package):
     homepage = "https://developer.gnome.org/glib/"
     url      = "https://ftp.gnome.org/pub/gnome/sources/glib/2.53/glib-2.53.1.tar.xz"
 
+    version('2.64.2', sha256='9a2f21ed8f13b9303399de13a0252b7cbcede593d26971378ec6cb90e87f2277')
     version('2.64.1', sha256='17967603bcb44b6dbaac47988d80c29a3d28519210b28157c2bd10997595bbc7')
     version('2.62.6', sha256='104fa26fbefae8024ff898330c671ec23ad075c1c0bce45c325c6d5657d58b9c')
     version('2.60.7', sha256='8b12c0af569afd3b71200556ad751bad4cf4bf7bc4b5f880638459a42ca86310')

From 992068460099c57c9cde1d93fa4ac875fcd62dfd Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Thu, 30 Apr 2020 22:12:26 +0200
Subject: [PATCH 201/802] gettext: Add 0.20.2 (#16402)

---
 var/spack/repos/builtin/packages/gettext/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py
index 8076ccb8419..2d39c28e477 100644
--- a/var/spack/repos/builtin/packages/gettext/package.py
+++ b/var/spack/repos/builtin/packages/gettext/package.py
@@ -12,7 +12,8 @@ class Gettext(AutotoolsPackage, GNUMirrorPackage):
     homepage = "https://www.gnu.org/software/gettext/"
     gnu_mirror_path = "gettext/gettext-0.20.1.tar.xz"
 
-    version('0.20.1', sha256='53f02fbbec9e798b0faaf7c73272f83608e835c6288dd58be6c9bb54624a3800')
+    version('0.20.2',   sha256='b22b818e644c37f6e3d1643a1943c32c3a9bff726d601e53047d2682019ceaba')
+    version('0.20.1',   sha256='53f02fbbec9e798b0faaf7c73272f83608e835c6288dd58be6c9bb54624a3800')
     version('0.19.8.1', sha256='105556dbc5c3fbbc2aa0edb46d22d055748b6f5c7cd7a8d99f8e7eb84e938be4')
     version('0.19.7',   sha256='378fa86a091cec3acdece3c961bb8d8c0689906287809a8daa79dc0c6398d934')
 

From efbd8c15552ac00cde6caa3ec7d615e02130c59b Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Thu, 30 Apr 2020 22:12:38 +0200
Subject: [PATCH 202/802] readline: Fix homepage (#16403)

---
 var/spack/repos/builtin/packages/readline/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/readline/package.py b/var/spack/repos/builtin/packages/readline/package.py
index c73a08daaba..7a15595fa28 100644
--- a/var/spack/repos/builtin/packages/readline/package.py
+++ b/var/spack/repos/builtin/packages/readline/package.py
@@ -14,7 +14,7 @@ class Readline(AutotoolsPackage, GNUMirrorPackage):
     command lines, to recall and perhaps reedit those lines, and perform
     csh-like history expansion on previous commands."""
 
-    homepage = "http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html"
+    homepage = "https://tiswww.case.edu/php/chet/readline/rltop.html"
     # URL must remain http:// so Spack can bootstrap curl
     gnu_mirror_path = "readline/readline-8.0.tar.gz"
 

From a24a12f22917558d7b99148a011460e7b5507f54 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Thu, 30 Apr 2020 22:12:51 +0200
Subject: [PATCH 203/802] sqlite: Add 3.31.1 (#16404)

---
 var/spack/repos/builtin/packages/sqlite/package.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/sqlite/package.py b/var/spack/repos/builtin/packages/sqlite/package.py
index 531a9bc81de..ccd8bd8e211 100644
--- a/var/spack/repos/builtin/packages/sqlite/package.py
+++ b/var/spack/repos/builtin/packages/sqlite/package.py
@@ -14,6 +14,7 @@ class Sqlite(AutotoolsPackage):
     """
     homepage = "https://www.sqlite.org"
 
+    version('3.31.1', sha256='62284efebc05a76f909c580ffa5c008a7d22a1287285d68b7825a2b6b51949ae')
     version('3.30.1', sha256='8c5a50db089bd2a1b08dbc5b00d2027602ca7ff238ba7658fabca454d4298e60')
     version('3.30.0', sha256='e0a8cf4c7a87455e55e10413d16f358ca121ccec687fe1301eac95e2d340fc58')
     version('3.29.0', sha256='8e7c1e2950b5b04c5944a981cb31fffbf9d2ddda939d536838ebc854481afd5b')
@@ -71,7 +72,9 @@ def url_for_version(self, version):
             ''.join(['%02d' % v for v in full_version[1:]])
         # See https://sqlite.org/chronology.html for version -> year
         # correspondence.
-        if version >= Version('3.27.0'):
+        if version >= Version('3.31.0'):
+            year = '2020'
+        elif version >= Version('3.27.0'):
             year = '2019'
         elif version >= Version('3.22.0'):
             year = '2018'

From 022c287e473a0d836c3f209ce8415f750bcff289 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 30 Apr 2020 15:13:04 -0500
Subject: [PATCH 204/802] Fix typos in new AutotoolsPackage function (#16406)

---
 lib/spack/spack/build_systems/autotools.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/build_systems/autotools.py b/lib/spack/spack/build_systems/autotools.py
index 6fc77bee6ac..90cad572a1e 100644
--- a/lib/spack/spack/build_systems/autotools.py
+++ b/lib/spack/spack/build_systems/autotools.py
@@ -154,11 +154,11 @@ def _do_patch_config_guess(self):
         raise RuntimeError('Failed to find suitable config.guess')
 
     @run_before('configure')
-    def _set_autotools_environment_varoables(self):
+    def _set_autotools_environment_variables(self):
         """Many autotools builds use a version of mknod.m4 that fails when
         running as root unless FORCE_UNSAFE_CONFIGURE is set to 1.
 
-        We set this to 1 and expect the user to take responsibiltiy if
+        We set this to 1 and expect the user to take responsibility if
         they are running as root. They have to anyway, as this variable
         doesn't actually prevent configure from doing bad things as root.
         Without it, configure just fails halfway through, but it can

From 4c69bc9d168c52ab83c6c8cfa39095fa7c27fd5d Mon Sep 17 00:00:00 2001
From: Satish Balay <balay@mcs.anl.gov>
Date: Thu, 30 Apr 2020 15:13:45 -0500
Subject: [PATCH 205/802] amrex: repo went through history rewrite - so use
 updates sha256sums (#16379)

---
 .../repos/builtin/packages/amrex/package.py    | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/var/spack/repos/builtin/packages/amrex/package.py b/var/spack/repos/builtin/packages/amrex/package.py
index 5bd19e582ba..6179f2e6886 100644
--- a/var/spack/repos/builtin/packages/amrex/package.py
+++ b/var/spack/repos/builtin/packages/amrex/package.py
@@ -18,15 +18,15 @@ class Amrex(CMakePackage):
     maintainers = ['mic84', 'asalmgren']
 
     version('develop', branch='development')
-    version('20.04', sha256='ce951105336d6fcc07abe3eadf9f71161f0ccbe3e45f4547be4d0ae99e15f3c6')
-    version('20.03', sha256='a535dcc016f0d38b55d0ab8e9067c1c53e3686961f6a1fb471cb18a0ebc909e6')
-    version('20.02', sha256='33529a23694283d12eb37d4682aa86c9cc1240bd50124efcf4464747a7554147')
-    version('20.01', sha256='f7026d267ca5de79ec7e740264d54230f419776d40feae705e939be0b1d8e0d3')
-    version('19.10', commit='52844b32b7da11e9733b9a7f4a782e51de7f5e1e')  # tag:19.10
-    version('19.08', commit='bdd1146139e8727a513d451075f900c172eb81fd')  # tag:19.08
-    version('18.10.1', commit='260b53169badaa760b91dfc60ea6b2ea3d9ccf06')  # tag:18.10.1
-    version('18.10', commit='d37a266c38092e1174096e245326e9eead1f4e03')  # tag:18.10
-    version('18.09.1', commit='88120db4736c325a2d3d2c291adacaffd3bf224b')  # tag:18.09.1
+    version('20.04', sha256='a7ece54d5d89cc00fd555551902a0d4d0fb50db15d2600f441353eed0dddd83b')
+    version('20.03', sha256='9728f20c0d7297c935fe5cbc63c1ee60f983b833a735c797340ee2765d626165')
+    version('20.02', sha256='2eda858b43e7455718ccb96c18f678da1778ec61031e90effdcb9c3e7e6f9bb5')
+    version('20.01', sha256='957e7a7fe90a0a9f4ae10bf9e46dba68d72448d0bec69a4a4e66a544930caca3')
+    version('19.10', sha256='9f30a2b3ec13711dfc6a1b59af59bd7df78449b5846ac6457b5dbbdecb20c576')
+    version('19.08', sha256='94b1e9a9dcfb8c5b52aef91a2ed373aef504d766dd7d0aba6731ceb94e48e940')
+    version('18.10.1', sha256='e648465c9c3b7ff4c696dfa8b6d079b4f61c80d96c51e27af210951c9367c201')
+    version('18.10', sha256='298eba03ef03d617c346079433af1089d38076d6fab2c34476c687740c1f4234')
+    version('18.09.1', sha256='a065ee4d1d98324b6c492ae20ea63ba12a4a4e23432bf5b3fe9788d44aa4398e')
 
     # Config options
     variant('dimensions', default='3',

From 7a56e6fce1fb8c6e6f1b1b0f7093dff0922f81a1 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Thu, 30 Apr 2020 19:01:07 -0600
Subject: [PATCH 206/802] gromacs: add v2020.2 (#16408)

---
 var/spack/repos/builtin/packages/gromacs/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py
index 2175d7a6110..1aec4807239 100644
--- a/var/spack/repos/builtin/packages/gromacs/package.py
+++ b/var/spack/repos/builtin/packages/gromacs/package.py
@@ -24,6 +24,7 @@ class Gromacs(CMakePackage):
     maintainers = ['junghans', 'marvinbernhardt']
 
     version('master', branch='master')
+    version('2020.2', sha256='7465e4cd616359d84489d919ec9e4b1aaf51f0a4296e693c249e83411b7bd2f3')
     version('2020.1', sha256='e1666558831a3951c02b81000842223698016922806a8ce152e8f616e29899cf')
     version('2020', sha256='477e56142b3dcd9cb61b8f67b24a55760b04d1655e8684f979a75a5eec40ba01')
     version('2019.6', sha256='bebe396dc0db11a9d4cc205abc13b50d88225617642508168a2195324f06a358')

From 4f6c4743e318a829c73d7adf4dc2c170e9a9d179 Mon Sep 17 00:00:00 2001
From: Jean-Laurent Picard <jean.laurent.picard@gmail.com>
Date: Fri, 1 May 2020 09:30:27 +0200
Subject: [PATCH 207/802] arborx: fix build with new kokkos-legacy (#16413)

---
 var/spack/repos/builtin/packages/arborx/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/arborx/package.py b/var/spack/repos/builtin/packages/arborx/package.py
index dfca8c7aaa6..7d10ef1fabb 100644
--- a/var/spack/repos/builtin/packages/arborx/package.py
+++ b/var/spack/repos/builtin/packages/arborx/package.py
@@ -36,7 +36,7 @@ def cmake_args(self):
         spec = self.spec
 
         options = [
-            '-DCMAKE_PREFIX_PATH=%s' % spec['kokkos'].prefix,
+            '-DCMAKE_PREFIX_PATH=%s' % spec['kokkos-legacy'].prefix,
             '-DARBORX_ENABLE_TESTS=OFF',
             '-DARBORX_ENABLE_EXAMPLES=OFF',
             '-DARBORX_ENABLE_BENCHMARKS=OFF',

From 69a0fbd2cbb0774f832b8a37a07542ef57991dbf Mon Sep 17 00:00:00 2001
From: Matt Larsen <mclarsen@users.noreply.github.com>
Date: Fri, 1 May 2020 01:07:12 -0700
Subject: [PATCH 208/802] raja: add awareness of the cuda architecture (#16377)

---
 var/spack/repos/builtin/packages/raja/package.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/raja/package.py b/var/spack/repos/builtin/packages/raja/package.py
index ccb1863444f..10a9265257b 100644
--- a/var/spack/repos/builtin/packages/raja/package.py
+++ b/var/spack/repos/builtin/packages/raja/package.py
@@ -6,7 +6,7 @@
 from spack import *
 
 
-class Raja(CMakePackage):
+class Raja(CMakePackage, CudaPackage):
     """RAJA Parallel Framework."""
 
     homepage = "http://software.llnl.gov/RAJA/"
@@ -47,4 +47,9 @@ def cmake_args(self):
                 '-DENABLE_CUDA=On',
                 '-DCUDA_TOOLKIT_ROOT_DIR=%s' % (spec['cuda'].prefix)])
 
+            cuda_value = spec.variants['cuda_arch'].value
+            cuda_arch = cuda_value[0]
+            if cuda_arch is not None:
+                options.append('-DCUDA_ARCH=sm_{0}'.format(cuda_arch))
+
         return options

From 40f70c4d4f99e806d0d5671f8098783a99bd9691 Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Sat, 2 May 2020 00:51:27 +0900
Subject: [PATCH 209/802] mt-metis: New package. (#16380)

* mt-metis: New package.

* variant to 1 line.

* delete useless lines.
---
 .../builtin/packages/mt-metis/non_x8664.patch | 14 +++++++
 .../builtin/packages/mt-metis/package.py      | 37 +++++++++++++++++++
 2 files changed, 51 insertions(+)
 create mode 100755 var/spack/repos/builtin/packages/mt-metis/non_x8664.patch
 create mode 100644 var/spack/repos/builtin/packages/mt-metis/package.py

diff --git a/var/spack/repos/builtin/packages/mt-metis/non_x8664.patch b/var/spack/repos/builtin/packages/mt-metis/non_x8664.patch
new file mode 100755
index 00000000000..8eb305e5c2f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mt-metis/non_x8664.patch
@@ -0,0 +1,14 @@
+diff --git a/domlib/dlmacros.h b/domlib/dlmacros.h
+index 2cbca90..d231b75 100644
+--- a/domlib/dlmacros.h
++++ b/domlib/dlmacros.h
+@@ -211,7 +211,9 @@
+ #else
+ static inline void _mm_pause(void)
+ {
++#ifdef _x86_64__
+   __asm__ ( "pause;" );
++#endif
+ }
+ #endif
+ 
diff --git a/var/spack/repos/builtin/packages/mt-metis/package.py b/var/spack/repos/builtin/packages/mt-metis/package.py
new file mode 100644
index 00000000000..805c86836c6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mt-metis/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class MtMetis(CMakePackage):
+    """
+    mt-Metis is a multithreaded multilevel graph partitioning an ordering
+    tool. It is based on the algorithms used in Metis and ParMetis
+    """
+
+    homepage = "http://glaros.dtc.umn.edu/gkhome/views/metis"
+    url      = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/mt-metis-0.6.0.tar.gz"
+
+    version('0.6.0', sha256='cb8fb836b630a899edbeca4e1da19ec9eb47e89903bda83e7ec62cb0ffdcc284')
+
+    # avoid asm('pause') for no x86_64 familly.
+    patch('non_x8664.patch')
+
+    variant('shared', default=True, description='Enable build of shared libraries')
+
+    def cmake_args(self):
+        define = CMakePackage.define
+        cmake_args = [
+            define('DOMLIB_PATH', 'domlib'),
+            define('WILDRIVER_PATH', 'wildriver'),
+            define('METIS_PATH', 'metis'),
+            self.define_from_variant('SHARED', 'shared'),
+        ]
+        return cmake_args
+
+    @property
+    def libs(self):
+        return find_libraries(['libmtmetis', 'libwildriver'], self.prefix.lib)

From d0dfa1ea4d844d87efa68a69053b813c4377c557 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Fri, 1 May 2020 09:37:21 -0700
Subject: [PATCH 210/802] dev-build: --drop-in <shell> (#14887)

* dev-build: --drop-in <shell>

Add a `--drop-in <shell>` option to `spack dev-build`.
This option will automatically run a
`spack build-env <spec> -- <shell>` at the end of a `dev-build`, e.g.
to quickly drop-and-devel into a build phase of a package.

Example usage:
```
spack dev-build --before cmake --drop-in bash openpmd-api@develop
```

* build_env: drop in unit test

Co-authored-by: Greg Becker <becker33@llnl.gov>
---
 lib/spack/spack/cmd/dev_build.py      |  8 ++++++++
 lib/spack/spack/test/cmd/dev_build.py | 11 +++++++++++
 share/spack/spack-completion.bash     |  4 ++--
 3 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/cmd/dev_build.py b/lib/spack/spack/cmd/dev_build.py
index 7f424928085..d9ad0fb8916 100644
--- a/lib/spack/spack/cmd/dev_build.py
+++ b/lib/spack/spack/cmd/dev_build.py
@@ -37,6 +37,9 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-q', '--quiet', action='store_true', dest='quiet',
         help="do not display verbose build output while installing")
+    subparser.add_argument(
+        '--drop-in', type=str, dest='shell', default=None,
+        help="drop into a build environment in a new shell, e.g. bash, zsh")
     arguments.add_common_arguments(subparser, ['spec'])
 
     stop_group = subparser.add_mutually_exclusive_group()
@@ -98,3 +101,8 @@ def dev_build(self, args):
         dirty=args.dirty,
         stop_before=args.before,
         stop_at=args.until)
+
+    # drop into the build environment of the package?
+    if args.shell is not None:
+        spack.build_environment.setup_package(package, dirty=False)
+        os.execvp(args.shell, [args.shell])
diff --git a/lib/spack/spack/test/cmd/dev_build.py b/lib/spack/spack/test/cmd/dev_build.py
index 6afd07d8159..5a7dfc273c2 100644
--- a/lib/spack/spack/test/cmd/dev_build.py
+++ b/lib/spack/spack/test/cmd/dev_build.py
@@ -76,6 +76,17 @@ def test_dev_build_before_until(tmpdir, mock_packages, install_mockery):
                       'dev-build-test-install@0.0.0')
 
 
+def test_dev_build_drop_in(tmpdir, mock_packages, monkeypatch,
+                           install_mockery):
+    def print_spack_cc(*args):
+        # Eat arguments and print environment variable to test
+        print(os.environ['CC'])
+    monkeypatch.setattr(os, 'execvp', print_spack_cc)
+    output = dev_build('-b', 'edit', '--drop-in', 'sh',
+                       'dev-build-test-install@0.0.0')
+    assert "lib/spack/env" in output
+
+
 def test_dev_build_fails_already_installed(tmpdir, mock_packages,
                                            install_mockery):
     spec = spack.spec.Spec('dev-build-test-install@0.0.0').concretized()
diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash
index 5a4fb027c9e..fce5360ff59 100755
--- a/share/spack/spack-completion.bash
+++ b/share/spack/spack-completion.bash
@@ -697,7 +697,7 @@ _spack_deprecate() {
 _spack_dev_build() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -j --jobs -d --source-path -i --ignore-dependencies -n --no-checksum --keep-prefix --skip-patch -q --quiet -b --before -u --until --clean --dirty"
+        SPACK_COMPREPLY="-h --help -j --jobs -d --source-path -i --ignore-dependencies -n --no-checksum --keep-prefix --skip-patch -q --quiet --drop-in -b --before -u --until --clean --dirty"
     else
         _all_packages
     fi
@@ -706,7 +706,7 @@ _spack_dev_build() {
 _spack_diy() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -j --jobs -d --source-path -i --ignore-dependencies -n --no-checksum --keep-prefix --skip-patch -q --quiet -b --before -u --until --clean --dirty"
+        SPACK_COMPREPLY="-h --help -j --jobs -d --source-path -i --ignore-dependencies -n --no-checksum --keep-prefix --skip-patch -q --quiet --drop-in -b --before -u --until --clean --dirty"
     else
         _all_packages
     fi

From 31d12d380fdbd5c71a02645515d062cfbcc12017 Mon Sep 17 00:00:00 2001
From: Peter Scheibel <scheibel1@llnl.gov>
Date: Fri, 1 May 2020 10:47:46 -0700
Subject: [PATCH 211/802] Testing: fix unintended interactions between tests
 (#16003)

* For tests that use the real Spack package repository, the config
  needs to avoid using MPI providers that are not intended to be
  installed by Spack. Without this, it is possible that Spack tests
  which concretize the MPI virtual will end up trying to use an
  implementation that it shouldn't (e.g. one that is always
  provided externally). See #15666 for an example.
* The mutable_config test fixture was not initializing the scope
  roots to the right directories (so the resulting config was empty).
* The current_host fixture in the concretize.py tests was using the
  config fixture rather than mutable_config, and was polluting the
  config cache for other tests.
* One test in concretize.py was clearing a nonexistent cache
  (PackagePrefs._packages_config_cache). This reference has been
  removed.
* The test 'test_preferred_compilers' was was depending on cross
  test config pollution to succeed. The initial spec before
  concretization has been updated to updated to be explicit about
  the desired result.
---
 lib/spack/spack/cmd/compiler.py                | 14 +++++++++++++-
 lib/spack/spack/test/concretize.py             |  8 ++++----
 lib/spack/spack/test/concretize_preferences.py |  2 +-
 lib/spack/spack/test/conftest.py               |  4 ++--
 lib/spack/spack/test/data/config/packages.yaml |  3 +++
 5 files changed, 23 insertions(+), 8 deletions(-)

diff --git a/lib/spack/spack/cmd/compiler.py b/lib/spack/spack/cmd/compiler.py
index 625466f8c7f..c8f52af04d5 100644
--- a/lib/spack/spack/cmd/compiler.py
+++ b/lib/spack/spack/cmd/compiler.py
@@ -159,7 +159,19 @@ def compiler_list(args):
     tty.msg("Available compilers")
     index = index_by(spack.compilers.all_compilers(scope=args.scope),
                      lambda c: (c.spec.name, c.operating_system, c.target))
-    ordered_sections = sorted(index.items(), key=lambda item: item[0])
+
+    # For a container, take each element which does not evaluate to false and
+    # convert it to a string. For elements which evaluate to False (e.g. None)
+    # convert them to '' (in which case it still evaluates to False but is a
+    # string type). Tuples produced by this are guaranteed to be comparable in
+    # Python 3
+    convert_str = (
+        lambda tuple_container:
+        tuple(str(x) if x else '' for x in tuple_container))
+
+    index_str_keys = list(
+        (convert_str(x), y) for x, y in index.items())
+    ordered_sections = sorted(index_str_keys, key=lambda item: item[0])
     for i, (key, compilers) in enumerate(ordered_sections):
         if i >= 1:
             print()
diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index 232dfaeb4be..ec594e40885 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -12,7 +12,6 @@
 
 from spack.concretize import find_spec, NoValidVersionError
 from spack.error import SpecError
-from spack.package_prefs import PackagePrefs
 from spack.spec import Spec, CompilerSpec, ConflictsInSpecError
 from spack.version import ver
 from spack.util.mock_package import MockPackageMultiRepo
@@ -103,8 +102,6 @@ def current_host(request, monkeypatch):
         monkeypatch.setattr(spack.platforms.test.Test, 'default', cpu)
         yield target
     else:
-        # There's a cache that needs to be cleared for unit tests
-        PackagePrefs._packages_config_cache = None
         with spack.config.override('packages:all', {'target': [cpu]}):
             yield target
 
@@ -112,7 +109,10 @@ def current_host(request, monkeypatch):
     spack.architecture.get_platform.cache.clear()
 
 
-@pytest.mark.usefixtures('config', 'mock_packages')
+# This must use the mutable_config fixture because the test
+# adjusting_default_target_based_on_compiler uses the current_host fixture,
+# which changes the config.
+@pytest.mark.usefixtures('mutable_config', 'mock_packages')
 class TestConcretize(object):
     def test_concretize(self, spec):
         check_concretize(spec)
diff --git a/lib/spack/spack/test/concretize_preferences.py b/lib/spack/spack/test/concretize_preferences.py
index 922d5a11d87..ca4df6700ce 100644
--- a/lib/spack/spack/test/concretize_preferences.py
+++ b/lib/spack/spack/test/concretize_preferences.py
@@ -100,7 +100,7 @@ def test_preferred_compilers(self):
         # Try the last available compiler
         compiler = str(compiler_list[-1])
         update_packages('mpileaks', 'compiler', [compiler])
-        spec = concretize('mpileaks')
+        spec = concretize('mpileaks os=redhat6 target=x86')
         assert spec.compiler == spack.spec.CompilerSpec(compiler)
 
     def test_preferred_target(self, mutable_mock_repo):
diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py
index 736c5a55638..8eff851a372 100644
--- a/lib/spack/spack/test/conftest.py
+++ b/lib/spack/spack/test/conftest.py
@@ -423,13 +423,13 @@ def config(mock_configuration):
 
 
 @pytest.fixture(scope='function')
-def mutable_config(tmpdir_factory, configuration_dir, monkeypatch):
+def mutable_config(tmpdir_factory, configuration_dir):
     """Like config, but tests can modify the configuration."""
     mutable_dir = tmpdir_factory.mktemp('mutable_config').join('tmp')
     configuration_dir.copy(mutable_dir)
 
     cfg = spack.config.Configuration(
-        *[spack.config.ConfigScope(name, str(mutable_dir))
+        *[spack.config.ConfigScope(name, str(mutable_dir.join(name)))
           for name in ['site', 'system', 'user']])
 
     with use_configuration(cfg):
diff --git a/lib/spack/spack/test/data/config/packages.yaml b/lib/spack/spack/test/data/config/packages.yaml
index c7256ddb334..63e63e525d6 100644
--- a/lib/spack/spack/test/data/config/packages.yaml
+++ b/lib/spack/spack/test/data/config/packages.yaml
@@ -1,4 +1,7 @@
 packages:
+  all:
+    providers:
+      mpi: [openmpi, mpich]
   externaltool:
     buildable: False
     paths:

From 40df44e021e2908b8ae7d05d7c07159444c8b8d5 Mon Sep 17 00:00:00 2001
From: Peter Scheibel <scheibel1@llnl.gov>
Date: Fri, 1 May 2020 13:39:43 -0700
Subject: [PATCH 212/802] Revert "Testing: fix unintended interactions between
 tests (#16003)" (#16420)

This was breaking tests on develop.
---
 lib/spack/spack/cmd/compiler.py                | 14 +-------------
 lib/spack/spack/test/concretize.py             |  8 ++++----
 lib/spack/spack/test/concretize_preferences.py |  2 +-
 lib/spack/spack/test/conftest.py               |  4 ++--
 lib/spack/spack/test/data/config/packages.yaml |  3 ---
 5 files changed, 8 insertions(+), 23 deletions(-)

diff --git a/lib/spack/spack/cmd/compiler.py b/lib/spack/spack/cmd/compiler.py
index c8f52af04d5..625466f8c7f 100644
--- a/lib/spack/spack/cmd/compiler.py
+++ b/lib/spack/spack/cmd/compiler.py
@@ -159,19 +159,7 @@ def compiler_list(args):
     tty.msg("Available compilers")
     index = index_by(spack.compilers.all_compilers(scope=args.scope),
                      lambda c: (c.spec.name, c.operating_system, c.target))
-
-    # For a container, take each element which does not evaluate to false and
-    # convert it to a string. For elements which evaluate to False (e.g. None)
-    # convert them to '' (in which case it still evaluates to False but is a
-    # string type). Tuples produced by this are guaranteed to be comparable in
-    # Python 3
-    convert_str = (
-        lambda tuple_container:
-        tuple(str(x) if x else '' for x in tuple_container))
-
-    index_str_keys = list(
-        (convert_str(x), y) for x, y in index.items())
-    ordered_sections = sorted(index_str_keys, key=lambda item: item[0])
+    ordered_sections = sorted(index.items(), key=lambda item: item[0])
     for i, (key, compilers) in enumerate(ordered_sections):
         if i >= 1:
             print()
diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index ec594e40885..232dfaeb4be 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -12,6 +12,7 @@
 
 from spack.concretize import find_spec, NoValidVersionError
 from spack.error import SpecError
+from spack.package_prefs import PackagePrefs
 from spack.spec import Spec, CompilerSpec, ConflictsInSpecError
 from spack.version import ver
 from spack.util.mock_package import MockPackageMultiRepo
@@ -102,6 +103,8 @@ def current_host(request, monkeypatch):
         monkeypatch.setattr(spack.platforms.test.Test, 'default', cpu)
         yield target
     else:
+        # There's a cache that needs to be cleared for unit tests
+        PackagePrefs._packages_config_cache = None
         with spack.config.override('packages:all', {'target': [cpu]}):
             yield target
 
@@ -109,10 +112,7 @@ def current_host(request, monkeypatch):
     spack.architecture.get_platform.cache.clear()
 
 
-# This must use the mutable_config fixture because the test
-# adjusting_default_target_based_on_compiler uses the current_host fixture,
-# which changes the config.
-@pytest.mark.usefixtures('mutable_config', 'mock_packages')
+@pytest.mark.usefixtures('config', 'mock_packages')
 class TestConcretize(object):
     def test_concretize(self, spec):
         check_concretize(spec)
diff --git a/lib/spack/spack/test/concretize_preferences.py b/lib/spack/spack/test/concretize_preferences.py
index ca4df6700ce..922d5a11d87 100644
--- a/lib/spack/spack/test/concretize_preferences.py
+++ b/lib/spack/spack/test/concretize_preferences.py
@@ -100,7 +100,7 @@ def test_preferred_compilers(self):
         # Try the last available compiler
         compiler = str(compiler_list[-1])
         update_packages('mpileaks', 'compiler', [compiler])
-        spec = concretize('mpileaks os=redhat6 target=x86')
+        spec = concretize('mpileaks')
         assert spec.compiler == spack.spec.CompilerSpec(compiler)
 
     def test_preferred_target(self, mutable_mock_repo):
diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py
index 8eff851a372..736c5a55638 100644
--- a/lib/spack/spack/test/conftest.py
+++ b/lib/spack/spack/test/conftest.py
@@ -423,13 +423,13 @@ def config(mock_configuration):
 
 
 @pytest.fixture(scope='function')
-def mutable_config(tmpdir_factory, configuration_dir):
+def mutable_config(tmpdir_factory, configuration_dir, monkeypatch):
     """Like config, but tests can modify the configuration."""
     mutable_dir = tmpdir_factory.mktemp('mutable_config').join('tmp')
     configuration_dir.copy(mutable_dir)
 
     cfg = spack.config.Configuration(
-        *[spack.config.ConfigScope(name, str(mutable_dir.join(name)))
+        *[spack.config.ConfigScope(name, str(mutable_dir))
           for name in ['site', 'system', 'user']])
 
     with use_configuration(cfg):
diff --git a/lib/spack/spack/test/data/config/packages.yaml b/lib/spack/spack/test/data/config/packages.yaml
index 63e63e525d6..c7256ddb334 100644
--- a/lib/spack/spack/test/data/config/packages.yaml
+++ b/lib/spack/spack/test/data/config/packages.yaml
@@ -1,7 +1,4 @@
 packages:
-  all:
-    providers:
-      mpi: [openmpi, mpich]
   externaltool:
     buildable: False
     paths:

From f38820f89c913ce142e6562829c0809ad661a59b Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Fri, 1 May 2020 16:40:09 -0500
Subject: [PATCH 213/802] tbl2asn: new package at 20200301 (#16280)

* tbl2asn: new package at 20200301

* tbl2asn: remove unused url

* tbl2asn: use spack decompression, fix permissions

* tbl2asn: change version
---
 .../repos/builtin/packages/tbl2asn/package.py | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/tbl2asn/package.py

diff --git a/var/spack/repos/builtin/packages/tbl2asn/package.py b/var/spack/repos/builtin/packages/tbl2asn/package.py
new file mode 100644
index 00000000000..8f1c0ba74c7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tbl2asn/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from os import chmod
+
+
+class Tbl2asn(Package):
+    """Tbl2asn is a command-line program that automates the creation of
+       sequence records for submission to GenBank."""
+
+    homepage = "https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/"
+
+    version('2020-03-01', sha256='7cc1119d3cfcbbffdbd4ecf33cef8bbdd44fc5625c72976bee08b1157625377e')
+
+    def url_for_version(self, ver):
+        return "https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux.tbl2asn.gz"
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('../linux.tbl2asn', prefix.bin.tbl2asn)
+        chmod(prefix.bin.tbl2asn, 0o775)

From b5b7ef2ce619fc5254b9f7915b1caf7a67b57126 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <KineticTheory@users.noreply.github.com>
Date: Fri, 1 May 2020 16:32:31 -0600
Subject: [PATCH 214/802] Provide update for py-pyside2 version 5.14.2.1.
 (#16426)

---
 var/spack/repos/builtin/packages/py-pyside2/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-pyside2/package.py b/var/spack/repos/builtin/packages/py-pyside2/package.py
index 69828029bf4..fa70f45b0b1 100644
--- a/var/spack/repos/builtin/packages/py-pyside2/package.py
+++ b/var/spack/repos/builtin/packages/py-pyside2/package.py
@@ -17,6 +17,7 @@ class PyPyside2(PythonPackage):
     # http://wiki.qt.io/Qt_for_Python_Development_Getting_Started
 
     version('develop', tag='dev')
+    version('5.14.2.1', tag='v5.14.2.1', submodules=True)
     version('5.13.2', tag='v5.13.2', submodules=True)
     version('5.13.1', tag='v5.13.1', submodules=True)
     version('5.13.0', tag='v5.13.0', submodules=True)

From c7552c0c729048d3e02fe582600c3edbe1a4471a Mon Sep 17 00:00:00 2001
From: mic84 <mrosso@lbl.gov>
Date: Fri, 1 May 2020 18:47:18 -0700
Subject: [PATCH 215/802] amrex: New version 20.05 (#16427)

---
 var/spack/repos/builtin/packages/amrex/package.py | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/amrex/package.py b/var/spack/repos/builtin/packages/amrex/package.py
index 6179f2e6886..84b064d781a 100644
--- a/var/spack/repos/builtin/packages/amrex/package.py
+++ b/var/spack/repos/builtin/packages/amrex/package.py
@@ -12,12 +12,13 @@ class Amrex(CMakePackage):
     mesh refinement (AMR) applications."""
 
     homepage = "https://amrex-codes.github.io/amrex/"
-    url      = "https://github.com/AMReX-Codes/amrex/archive/20.01.tar.gz"
+    url      = "https://github.com/AMReX-Codes/amrex/releases/download/20.05/amrex-20.05.tar.gz"
     git      = "https://github.com/AMReX-Codes/amrex.git"
 
     maintainers = ['mic84', 'asalmgren']
 
     version('develop', branch='development')
+    version('20.05', sha256='97d753bb75e845a0a959ec1a044a48e6adb86dd008b5e29ce7a01d49ed276338')
     version('20.04', sha256='a7ece54d5d89cc00fd555551902a0d4d0fb50db15d2600f441353eed0dddd83b')
     version('20.03', sha256='9728f20c0d7297c935fe5cbc63c1ee60f983b833a735c797340ee2765d626165')
     version('20.02', sha256='2eda858b43e7455718ccb96c18f678da1778ec61031e90effdcb9c3e7e6f9bb5')
@@ -59,11 +60,19 @@ class Amrex(CMakePackage):
     # Build dependencies
     depends_on('mpi', when='+mpi')
     depends_on('sundials@4.0.0:4.1.0 +ARKODE +CVODE', when='@19.08: +sundials')
-    depends_on('python@2.7:', type='build')
+    depends_on('python@2.7:', type='build', when='@:20.04')
     depends_on('cmake@3.5:',  type='build', when='@:18.10.99')
-    depends_on('cmake@3.13:',  type='build', when='@18.11:')
+    depends_on('cmake@3.13:', type='build', when='@18.11:')
+    depends_on('cmake@3.14:', type='build', when='@19.04:')
     conflicts('%clang')
 
+    def url_for_version(self, version):
+        if version >= Version('20.05'):
+            url = "https://github.com/AMReX-Codes/amrex/releases/download/{0}/amrex-{0}.tar.gz"
+        else:
+            url = "https://github.com/AMReX-Codes/amrex/archive/{0}.tar.gz"
+        return url.format(version.dotted)
+
     def cmake_is_on(self, option):
         return 'ON' if option in self.spec else 'OFF'
 

From cf59220edc7cafc2f95d05696f24ef53ec245ea6 Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Fri, 1 May 2020 20:50:13 -0500
Subject: [PATCH 216/802] stata: add version 16 (#16425)

---
 var/spack/repos/builtin/packages/stata/package.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/stata/package.py b/var/spack/repos/builtin/packages/stata/package.py
index 59dee6cf139..6a34f8b593d 100644
--- a/var/spack/repos/builtin/packages/stata/package.py
+++ b/var/spack/repos/builtin/packages/stata/package.py
@@ -27,6 +27,7 @@ class Stata(Package):
     homepage = "https://www.stata.com/"
     # url      = "stata"
 
+    version('16', 'a13a6a92558eeb3c6cb3013c458a6777e54c21af43599df6b0a924f5f5c2d5d2')
     version('15', '2486f4c7db1e7b453004c7bd3f8da40ba1e30be150613065c7b82b1915259016')
 
     # V15 depends on libpng v12 and fails with other versions of libpng
@@ -81,6 +82,11 @@ def install(self, spec, prefix):
         bash = which('bash')
         tar = which('tar')
 
+        res_dir = 'unix/linux64/'
+
+        if self.spec.satisfies('@16:'):
+            res_dir = 'unix/linux64p/'
+
         # Step 1.
         x = datetime.now()
         with open("installed.150", "w") as fh:
@@ -89,11 +95,11 @@ def install(self, spec, prefix):
         # Step 2.
         instlist = ['ado.taz', 'base.taz', 'bins.taz', 'docs.taz']
         for instfile in instlist:
-            tar('-x', '-z', '-f', 'unix/linux64/' + instfile)
+            tar('-x', '-z', '-f', res_dir + instfile)
 
         # Step 3.
-        install('unix/linux64/setrwxp', 'setrwxp')
-        install('unix/linux64/inst2', 'inst2')
+        install(res_dir + 'setrwxp', 'setrwxp')
+        install(res_dir + 'inst2', 'inst2')
 
         # Step 4. Since the install script calls out specific permissions and
         # could change in the future (or old versions) I thought it best to

From acabe2deba9659434e344e5c3aa4bdf5afa9beba Mon Sep 17 00:00:00 2001
From: Jen Herting <jen@herting.cc>
Date: Fri, 1 May 2020 21:50:26 -0400
Subject: [PATCH 217/802] [ncbi-magicblast] added version 1.5.0 (#16424)

---
 var/spack/repos/builtin/packages/ncbi-magicblast/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/ncbi-magicblast/package.py b/var/spack/repos/builtin/packages/ncbi-magicblast/package.py
index eb93f59b9d3..54588463bd0 100644
--- a/var/spack/repos/builtin/packages/ncbi-magicblast/package.py
+++ b/var/spack/repos/builtin/packages/ncbi-magicblast/package.py
@@ -13,6 +13,7 @@ class NcbiMagicblast(AutotoolsPackage):
     homepage = "https://ncbi.github.io/magicblast/"
     url      = "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.3.0/ncbi-magicblast-1.3.0-src.tar.gz"
 
+    version('1.5.0', sha256='b261914d9f7ffc0e655079ceba3e348ba11df1a1f73c4e47a4b1ca154754985c')
     version('1.3.0', sha256='47b9b65d595b5cb0c4fef22bc7f7c038fb8d4a0accdbe560d7232820575aff67')
 
     depends_on('lmdb')

From 668dcb78a174a7b6d4103ce59a8dcf685e108579 Mon Sep 17 00:00:00 2001
From: Matthias Diener <mdiener@illinois.edu>
Date: Fri, 1 May 2020 20:50:54 -0500
Subject: [PATCH 218/802] py-opentuner: add version 0.8.2 (#16423)

---
 var/spack/repos/builtin/packages/py-opentuner/package.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-opentuner/package.py b/var/spack/repos/builtin/packages/py-opentuner/package.py
index 5efd8039f30..b55a9073c4f 100644
--- a/var/spack/repos/builtin/packages/py-opentuner/package.py
+++ b/var/spack/repos/builtin/packages/py-opentuner/package.py
@@ -12,14 +12,17 @@ class PyOpentuner(PythonPackage):
     homepage = "http://opentuner.org/"
     git      = "https://github.com/jansel/opentuner.git"
 
+    maintainers = ['matthiasdiener']
+
+    version('0.8.2', commit='8e720a2')
     version('0.8.0', commit='4cb9135')
 
-    # No support for Python 3 yet
-    depends_on('python@2.7:2.8', type=('build', 'run'))
+    depends_on('python@3:', type=('build', 'run'), when='@0.8.1:')
+    depends_on('python@2.7:2.8', type=('build', 'run'), when='@:0.8.0')
 
     depends_on('py-argparse@1.2.1:', type=('build', 'run'))
     depends_on('py-fn-py@0.2.12:', type=('build', 'run'))
+    depends_on('py-future', type=('build', 'run'))
     depends_on('py-numpy@1.8.0:', type=('build', 'run'))
-    depends_on('py-pysqlite@2.6.3:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
     depends_on('py-sqlalchemy@0.8.2:', type=('build', 'run'))

From adafdf0644a7ab14c7e396492ab7692d75e3a3db Mon Sep 17 00:00:00 2001
From: Sajid Ali <30510036+s-sajid-ali@users.noreply.github.com>
Date: Fri, 1 May 2020 20:51:54 -0500
Subject: [PATCH 219/802] add hydra/pmix conflict (#16428)

---
 var/spack/repos/builtin/packages/mpich/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index 8360046ab43..878abc6b5cd 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -144,6 +144,7 @@ class Mpich(AutotoolsPackage):
     conflicts('netmod=tcp', when='device=ch4')
     conflicts('pmi=pmi2', when='device=ch3 netmod=ofi')
     conflicts('pmi=pmix', when='device=ch3')
+    conflicts('pmi=pmix', when='+hydra')
 
     # MPICH does not require libxml2 and libpciaccess for versions before 3.3
     # when ~hydra is set: prevent users from setting +libxml2 and +pci in this

From 08f88b4be6e7a8ff6665d0833281fdcfcb0ab116 Mon Sep 17 00:00:00 2001
From: Jonathon Anderson <jonathon.anderson@colorado.edu>
Date: Sat, 2 May 2020 10:07:50 -0600
Subject: [PATCH 220/802] Add a gpfs variant to openmpi package (#15793)

Open MPI will detect and link against GPFS if it is present
on the system. This variant allows this to be disabled, even
if GPFS is present.
---
 var/spack/repos/builtin/packages/openmpi/package.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index bb798e7b5fd..d0da29d774f 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -242,6 +242,7 @@ class Openmpi(AutotoolsPackage):
     variant('runpath', default=True, description='Enable wrapper runpath')
     variant('cxx', default=False, description='Enable C++ MPI bindings')
     variant('cxx_exceptions', default=False, description='Enable C++ Exception support')
+    variant('gpfs', default=True, description='Enable GPFS support (if present)')
     # Adding support to build a debug version of OpenMPI that activates
     # Memchecker, as described here:
     #
@@ -410,6 +411,11 @@ def autoreconf(self, spec, prefix):
         perl = which('perl')
         perl('autogen.pl')
 
+    def setup_build_environment(self, env):
+        if '~gpfs' in self.spec:
+            env.set('ac_cv_header_gpfs_h', 'no')
+            env.set('ac_cv_header_gpfs_fcntl_h', 'no')
+
     def configure_args(self):
         spec = self.spec
         config_args = [

From 1bc104e00e255798602073488279c0bc18fd1f09 Mon Sep 17 00:00:00 2001
From: Matthias Diener <mdiener@illinois.edu>
Date: Sat, 2 May 2020 13:26:56 -0500
Subject: [PATCH 221/802] colordiff: add version 1.0.19 (#16431)

---
 var/spack/repos/builtin/packages/colordiff/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/colordiff/package.py b/var/spack/repos/builtin/packages/colordiff/package.py
index 686f0840150..5d97c61d475 100644
--- a/var/spack/repos/builtin/packages/colordiff/package.py
+++ b/var/spack/repos/builtin/packages/colordiff/package.py
@@ -12,6 +12,7 @@ class Colordiff(Package):
     homepage = "https://www.colordiff.org"
     url      = "https://www.colordiff.org/archive/colordiff-1.0.18.tar.gz"
 
+    version('1.0.19', sha256='46e8c14d87f6c4b77a273cdd97020fda88d5b2be42cf015d5d84aca3dfff3b19')
     version('1.0.18', sha256='29cfecd8854d6e19c96182ee13706b84622d7b256077df19fbd6a5452c30d6e0')
 
     depends_on('perl')

From 2e63e08192d5f309049c65d415e6c05c11d968e8 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sat, 2 May 2020 20:13:12 -0500
Subject: [PATCH 222/802] py-cartopy: update package, fix PROJ.6 support
 (#16436)

---
 .../builtin/packages/py-cartopy/package.py    |  49 +++++---
 .../builtin/packages/py-cartopy/proj6.patch   | 109 ++++++++++++++++++
 2 files changed, 145 insertions(+), 13 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/py-cartopy/proj6.patch

diff --git a/var/spack/repos/builtin/packages/py-cartopy/package.py b/var/spack/repos/builtin/packages/py-cartopy/package.py
index feb7d8eba72..1cfa92aec6b 100644
--- a/var/spack/repos/builtin/packages/py-cartopy/package.py
+++ b/var/spack/repos/builtin/packages/py-cartopy/package.py
@@ -9,12 +9,20 @@
 class PyCartopy(PythonPackage):
     """Cartopy - a cartographic python library with matplotlib support."""
 
-    homepage = "http://scitools.org.uk/cartopy/"
-    url      = "https://github.com/SciTools/cartopy/archive/v0.16.0.tar.gz"
+    homepage = "https://scitools.org.uk/cartopy/docs/latest/"
+    url      = "https://github.com/SciTools/cartopy/archive/v0.17.0.tar.gz"
+
+    maintainers = ['adamjstewart']
+    import_modules = [
+        'cartopy', 'cartopy.sphinxext', 'cartopy.io', 'cartopy.geodesic',
+        'cartopy.examples', 'cartopy.mpl', 'cartopy.feature',
+    ]
 
     version('0.17.0', sha256='137642e63952404ec0841fa0333ad14c58fbbf19cca2a5ac6a38498c4b4998fb')
     version('0.16.0', sha256='cadf62434492c965220b37f0548bc58180466ad6894a1db57dbc51cd43467e5c')
 
+    # https://scitools.org.uk/cartopy/docs/latest/installing.html#installing
+    depends_on('python@2.7:', type=('build', 'run'))
     depends_on('py-setuptools@0.7.2:', type='build')
     depends_on('py-cython@0.15.1:',    type='build')
     depends_on('py-numpy@1.10.0:',  type=('build', 'run'))
@@ -25,11 +33,11 @@ class PyCartopy(PythonPackage):
     depends_on('proj@4.9.0:5', when='@0.16.0')
     depends_on('proj@4.9:',    when='@0.17.0')
 
-    variant('epsg', default=True, description='Add support for epsg.io')
-    variant('ows', default=True, description='Add support for Open Geospatial Consortium (OGC) web service')
-    variant('plotting', default=True, description='Add plotting functionality')
+    variant('epsg', default=False, description='Add support for epsg.io')
+    variant('ows', default=False, description='Add support for Open Geospatial Consortium (OGC) web service')
+    variant('plotting', default=False, description='Add plotting functionality')
 
-    # optional dependecies
+    # Optional dependecies
     depends_on('py-matplotlib@1.5.1:', type=('build', 'run'), when='+plotting')
     depends_on('gdal@1.10.0:+python',  type=('build', 'run'), when='+plotting')
     depends_on('py-pillow@1.7.8:',     type=('build', 'run'), when='+ows')
@@ -38,19 +46,34 @@ class PyCartopy(PythonPackage):
     depends_on('py-scipy@0.10:',       type=('build', 'run'), when='+plotting')
     depends_on('py-owslib@0.8.11:',    type=('build', 'run'), when='+ows')
 
-    # testing dependencies
+    # Testing dependencies
     depends_on('py-filelock',      type='test')
-    depends_on('py-mock@1.0.1',    type='test')
+    depends_on('py-mock@1.0.1:',   type='test')
     depends_on('py-pytest@3.0.0:', type='test')
 
+    patch('proj6.patch', when='@0.17.0')
+
     phases = ['build_ext', 'install']
 
     def build_ext_args(self, spec, prefix):
-        args = ['-I{0}'.format(spec['proj'].prefix.include),
-                '-L{0}'.format(spec['proj'].prefix.lib)
-                ]
+        args = [
+            spec['geos'].headers.include_flags,
+            spec['geos'].libs.search_flags,
+            spec['proj'].headers.include_flags,
+            spec['proj'].libs.search_flags,
+        ]
 
-        if spec.satisfies('@0.17.0 ^proj@6'):
-            args.append('-DACCEPT_USE_OF_DEPRECATED_PROJ_API_H')
+        if '+plotting' in spec:
+            args.extend([
+                spec['gdal'].headers.include_flags,
+                spec['gdal'].libs.search_flags,
+            ])
 
         return args
+
+    # Tests need to be re-added since `phases` was overridden
+    run_after('build_ext')(
+        PythonPackage._run_default_build_time_test_callbacks)
+    run_after('install')(
+        PythonPackage._run_default_install_time_test_callbacks)
+    run_after('install')(PythonPackage.sanity_check_prefix)
diff --git a/var/spack/repos/builtin/packages/py-cartopy/proj6.patch b/var/spack/repos/builtin/packages/py-cartopy/proj6.patch
new file mode 100644
index 00000000000..5ee2ca5490f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cartopy/proj6.patch
@@ -0,0 +1,109 @@
+# Fix PROJ.6 support
+# Adapted from https://github.com/SciTools/cartopy/pull/1289
+--- a/setup.py	2020-05-02 17:50:37.000000000 -0500
++++ b/setup.py	2020-05-02 18:02:04.000000000 -0500
+@@ -16,25 +16,25 @@
+ # along with cartopy.  If not, see <https://www.gnu.org/licenses/>.
+ from __future__ import print_function
+ 
+-"""
+-Distribution definition for Cartopy.
+-
+-"""
+-
+-import setuptools
+-from setuptools import setup, Extension
+-from setuptools import Command
+-from setuptools import convert_path
+-from distutils.spawn import find_executable
+-from distutils.sysconfig import get_config_var
+ import fnmatch
+ import os
+ import subprocess
+ import sys
+ import warnings
++from collections import defaultdict
++from distutils.spawn import find_executable
++from distutils.sysconfig import get_config_var
++
++from setuptools import Command, Extension, convert_path, setup
+ 
+ import versioneer
+ 
++"""
++Distribution definition for Cartopy.
++"""
++
++
++
+ 
+ try:
+     from Cython.Distutils import build_ext
+@@ -230,6 +230,18 @@
+     return proj_version
+ 
+ 
++def get_proj_libraries():
++    """
++    This function gets the PROJ libraries to cythonize with
++    """
++    proj_libraries = ["proj"]
++    if os.name == "nt" and proj_version >= (6, 0, 0):
++        proj_libraries = [
++            "proj_{}_{}".format(proj_version[0], proj_version[1])
++        ]
++    return proj_libraries
++
++
+ conda = os.getenv('CONDA_DEFAULT_ENV')
+ if conda is not None and conda in sys.prefix:
+     # Conda does not provide pkg-config compatibility, but the search paths
+@@ -245,7 +257,7 @@
+         exit(1)
+ 
+     proj_includes = []
+-    proj_libraries = ['proj']
++    proj_libraries = get_proj_libraries()
+     proj_library_dirs = []
+ 
+ else:
+@@ -268,7 +280,7 @@
+             exit(1)
+ 
+         proj_includes = []
+-        proj_libraries = ['proj']
++        proj_libraries = get_proj_libraries()
+         proj_library_dirs = []
+     else:
+         if proj_version < PROJ_MIN_VERSION:
+@@ -284,7 +296,7 @@
+             proj_clibs = proj_clibs.decode()
+ 
+         proj_includes = [proj_include[2:] if proj_include.startswith('-I') else
+-                         proj_include for proj_include in proj_includes.split()]      
++                         proj_include for proj_include in proj_includes.split()]
+ 
+         proj_libraries = []
+         proj_library_dirs = []
+@@ -316,11 +328,16 @@
+         return '.'
+ include_dir = get_config_var('INCLUDEDIR')
+ library_dir = get_config_var('LIBDIR')
+-if sys.platform.startswith('win'):
+-    extra_extension_args = {}
+-else:
+-    extra_extension_args = dict(
+-        runtime_library_dirs=[get_config_var('LIBDIR')])
++extra_extension_args = defaultdict(list)
++if not sys.platform.startswith('win'):
++    extra_extension_args["runtime_library_dirs"].append(
++        get_config_var('LIBDIR')
++    )
++
++if proj_version >= (6, 0, 0):
++    extra_extension_args["define_macros"].append(
++        ('ACCEPT_USE_OF_DEPRECATED_PROJ_API_H', '1')
++    )
+ 
+ # Description
+ # ===========

From eb4451dd1e48527d600715673ff214f3af9b3048 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sat, 2 May 2020 23:38:30 -0500
Subject: [PATCH 223/802] py-shapely: new version, Python 3.7 fix (#16438)

---
 .../repos/builtin/packages/py-shapely/package.py   | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-shapely/package.py b/var/spack/repos/builtin/packages/py-shapely/package.py
index 9edb86674fd..e609d610113 100644
--- a/var/spack/repos/builtin/packages/py-shapely/package.py
+++ b/var/spack/repos/builtin/packages/py-shapely/package.py
@@ -3,7 +3,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-from spack import *
+import os
 
 
 class PyShapely(PythonPackage):
@@ -11,7 +11,7 @@ class PyShapely(PythonPackage):
     """
 
     homepage = "https://github.com/Toblerity/Shapely"
-    url      = "https://pypi.io/packages/source/S/Shapely/Shapely-1.6.4.post2.tar.gz"
+    url      = "https://pypi.io/packages/source/S/Shapely/Shapely-1.7.0.tar.gz"
 
     maintainers = ['adamjstewart']
     import_modules = [
@@ -19,9 +19,11 @@ class PyShapely(PythonPackage):
         'shapely.examples', 'shapely.speedups', 'shapely.vectorized',
     ]
 
+    version('1.7.0', sha256='e21a9fe1a416463ff11ae037766fe410526c95700b9e545372475d2361cc951e')
     version('1.6.4.post2', sha256='c4b87bb61fc3de59fc1f85e71a79b0c709dc68364d9584473697aad4aa13240f')
     version('1.6.4', sha256='b10bc4199cfefcf1c0e5d932eac89369550320ca4bdf40559328d85f1ca4f655')
 
+    depends_on('python@2.7:2.8,3.4:', when='@1.7:', type=('build', 'run'))
     depends_on('python@2.6:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
     depends_on('py-cython', type='build')
@@ -29,6 +31,14 @@ class PyShapely(PythonPackage):
     depends_on('geos')
     depends_on('geos@3.3:', when='@1.3:')
     depends_on('py-pytest', type='test')
+    depends_on('py-pytest-cov', type='test')
+
+    @when('^python@3.7:')
+    def patch(self):
+        # Python 3.7 changed the thread storage API, precompiled *.c files
+        # need to be re-cythonized
+        os.remove('shapely/speedups/_speedups.c')
+        os.remove('shapely/vectorized/_vectorized.c')
 
     def setup_build_environment(self, env):
         env.set('GEOS_CONFIG',

From 1af31d24fd96e7f9bc3e2d35569472395419fcad Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sat, 2 May 2020 23:38:46 -0500
Subject: [PATCH 224/802] GEOS: add new version (#16437)

---
 var/spack/repos/builtin/packages/geos/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/geos/package.py b/var/spack/repos/builtin/packages/geos/package.py
index 7c0ae0ea2e1..d34a88be9c1 100644
--- a/var/spack/repos/builtin/packages/geos/package.py
+++ b/var/spack/repos/builtin/packages/geos/package.py
@@ -14,10 +14,11 @@ class Geos(AutotoolsPackage):
        operators, as well as specific JTS enhanced topology functions."""
 
     homepage = "http://trac.osgeo.org/geos/"
-    url      = "https://download.osgeo.org/geos/geos-3.7.2.tar.bz2"
+    url      = "https://download.osgeo.org/geos/geos-3.8.1.tar.bz2"
 
     maintainers = ['adamjstewart']
 
+    version('3.8.1', sha256='4258af4308deb9dbb5047379026b4cd9838513627cb943a44e16c40e42ae17f7')
     version('3.7.2', sha256='2166e65be6d612317115bfec07827c11b403c3f303e0a7420a2106bc999d7707')
     version('3.6.2', sha256='045a13df84d605a866602f6020fc6cbf8bf4c42fb50de237a08926e1d7d7652a')
     version('3.6.1', sha256='4a2e4e3a7a09a7cfda3211d0f4a235d9fd3176ddf64bd8db14b4ead266189fc5')

From 3c2f46aabfc90f0312c2d09dd8495a5f8777cc6a Mon Sep 17 00:00:00 2001
From: vvolkl <valentin.volkl@cern.ch>
Date: Sun, 3 May 2020 18:13:03 +0200
Subject: [PATCH 225/802] Add new HEP package: Delphes (#16440)

* [delphes] initial commit

* [delphes] formatting fixes
---
 .../repos/builtin/packages/delphes/package.py | 63 +++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/delphes/package.py

diff --git a/var/spack/repos/builtin/packages/delphes/package.py b/var/spack/repos/builtin/packages/delphes/package.py
new file mode 100644
index 00000000000..723182f616f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/delphes/package.py
@@ -0,0 +1,63 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Delphes(CMakePackage):
+    """A high energy physics framework for fast simulation
+    of a generic collider experiment.
+    """
+
+    homepage = "https://cp3.irmp.ucl.ac.be/projects/delphes"
+    git = "https://github.com/delphes/delphes.git"
+    url = "http://cp3.irmp.ucl.ac.be/downloads/Delphes-3.4.2.tar.gz"
+
+    maintainers = ['drbenmorgan', 'vvolkl', 'selvaggi']
+
+    version('master', branch='master')
+    version('3.4.2', sha256='d46a7c5474de650befdb89377115feee31f1743107ceb3d8da699be9d48c097b')
+    version('3.4.1', sha256='4b5a2aeac326643f45b6d45c39ba2302e323eeb86d8cb58843c6e73949b1208a')
+    version('3.4.0', sha256='c0f9500663a0c3a5c1eddcee598a67b5bcfc9318303195c6cacc0590b4023fa1')
+    version('3.3.3', sha256='404de818a6b7852b01187ccf598d8ac19d308b9361f128751ef003cde248ff00')
+    version('3.3.2', sha256='b8dc066e480678bb50ea0b68d157c391d47f66c084bda602d3d498538e682622')
+    version('3.3.1', sha256='d8fcaa9711b5892ba24b2c7be38158dedbe552b159961f9d29887b2cc7eb2e83')
+    version('3.3.0', sha256='3fcdcd31827227ff3d0d56df908b12289c67aa6d01c5725a2a9441c200f3966f')
+    version('3.2.0', sha256='3510b0852c750120425f9b014cada25d48b90b29c512b974a9ffbd7aa80ccde4')
+    version('3.1.2', sha256='edfccc47f7666d3607e86db82c6c79cfb10716423b496f0c0bdd4060b717ea1d')
+    version('3.1.1', sha256='c4128575b6103239ca13de392f47da2eaedfd93c3789b1ecb32eea09da3408e4')
+    version('3.1.0', sha256='c37b07aea3e57b39d34bf07f8afd209e36b278cf3792cd6e970d96a2c3b114eb')
+    version('3.0.12', sha256='55b4cf25f681c75457e33ad4ee615b9ab66317216675ca5f466ab256aa85cd16')
+    version('3.0.11', sha256='870921c8070762dc56aa0b8e0e07d1756584399e8740c848d330fc0fcb5e0604')
+    version('3.0.10', sha256='872a386baf298cab14e42aac198dbf7184a2ab7c28ee712448060e1dec078d34')
+    version('3.0.9', sha256='d12592fe66062a51e513a8d070fe1f49b672a4328bad2aa5cdb682937391a639')
+    version('3.0.8', sha256='8ab146ca3c163932ab21df9168d8ca86dbb1c3494b7bdc3e143743d769803c23')
+    version('3.0.7', sha256='7f43c84bca38fb8a41d7840dd2d7fab52456182babaa1e528791d0f4e517aba8')
+    version('3.0.6', sha256='9e225731d57d2a76d35886841f8eff121bb3a45560b16077bd8c351151581d88')
+    version('3.0.5', sha256='ab64ec6d2476fbfa40562e7edb510a8ab4c4fe5be77a4353ebf315c2af181a80')
+
+    depends_on('cmake', type='build')
+    depends_on('root')
+
+    variant('build_type', default='Release',
+            description='The build type to build',
+            values=('Debug', 'Release'))
+
+    variant('cxxstd',
+            default='17',
+            values=('14', '17'),
+            multi=False,
+            description='Use the specified C++ standard when building.')
+
+    def cmake_args(self):
+        args = []
+        # C++ Standard
+        args.append('-DCMAKE_CXX_STANDARD=%s'
+                    % self.spec.variants['cxxstd'].value)
+        return args
+
+    def setup_run_environment(self, env):
+        # make the cards distributed with delphes more easily accessible
+        env.set('DELPHESCARDS', self.prefix.cards)

From ed9e19df06ab44bd3040675c6647f593816b8e59 Mon Sep 17 00:00:00 2001
From: vvolkl <valentin.volkl@cern.ch>
Date: Sun, 3 May 2020 20:27:18 +0200
Subject: [PATCH 226/802] Add new HEP package: fastjet (#16439)

* [fastjet] initial commit

* [fastjet] remove beta versions
---
 .../repos/builtin/packages/fastjet/package.py | 49 +++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/fastjet/package.py

diff --git a/var/spack/repos/builtin/packages/fastjet/package.py b/var/spack/repos/builtin/packages/fastjet/package.py
new file mode 100644
index 00000000000..fcd854f9788
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fastjet/package.py
@@ -0,0 +1,49 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fastjet(AutotoolsPackage):
+    """
+    A high energy physics software package for jet finding in pp
+    and e+e- collisions.
+    """
+
+    homepage = "http://fastjet.fr/"
+    url      = "http://fastjet.fr/repo/fastjet-3.3.3.tar.gz"
+
+    maintainers = ['drbenmorgan', 'vvolkl']
+
+    version('3.3.3', sha256='30b0a0282ce5aeac9e45862314f5966f0be941ce118a83ee4805d39b827d732b')
+    version('3.3.2', sha256='3f59af13bfc54182c6bb0b0a6a8541b409c6fda5d105f17e03c4cce8db9963c2')
+    version('3.3.1', sha256='76bfed9b87e5efdb93bcd0f7779e27427fbe38e05fe908c2a2e80a9ca0876c53')
+    version('3.3.0', sha256='e9da5b9840cbbec6d05c9223f73c97af1d955c166826638e0255706a6b2da70f')
+    version('3.2.2', sha256='3a70cb6ba64071db49a7eecad821679e1a0dadd84e8abca83e518802b3d876e5')
+    version('3.2.1', sha256='c858b6c4f348c3676afa173251bb16d987674e64679a84306510e3963f858d5b')
+    version('3.2.0', sha256='96a927f1a336ad93cff30f07e2dc137a4de8ff7d74d5cd43eb455f42cf5275e3')
+    version('3.1.3', sha256='9809c2a0c89aec30890397d01eda56621e036589b66d7b3cd196cf087c65e40d')
+    version('3.1.2', sha256='dcc834e53da821cbac459c00249d5d18aee6ac866f37551d6a0c60690d3c170b')
+    version('3.1.1', sha256='38303789390726803bd3e7b3a245933273e86342d080b82754df44f5168634eb')
+    version('3.1.0', sha256='f8dc701dfdb124f009b7614010b911e8cc552655c2a966a7f2608a6caa062263')
+    version('3.0.6', sha256='9718f1d014afe4433bc0612a67a050d720c486fcfa7ad9c9b96bf087b0f3da0b')
+    version('3.0.5', sha256='0781a5528a0374b3189190abc8e8a2bdfbeaab7ed64e8c74ec0389a86bbabff9')
+    version('3.0.4', sha256='8161ea18087cea97de37bd9df2a49895ca1ef72732f5766af7c62738b21ed2c9')
+    version('3.0.3', sha256='6a3e5869cf43b325c7222a925e195b2bd624db922958a926cb4211c00882a50d')
+    version('3.0.2', sha256='6035a3295253bcd6dd68408985dbedc4a7c5aec13ed1dfa5fdb3cb9229dc6d31')
+    version('3.0.1', sha256='4f17c235e73a6fcbc8ee39c15a00f166b701e732033e623625f55fe93220a4ed')
+    version('3.0.0', sha256='f63252e3e9d27553c65642ff35d82913b804dfd569d2446c01166882dbf2577f')
+    version('2.4.5', sha256='a175849393a3a251b8f92ea9f747b74236dfc83d2786ef5dd92b39c57316a727')
+    version('2.4.4', sha256='4d97a8494e9aae7e5738e97d224f5aafb44ae8c5d5021f836d5c8c20fc5030fc')
+    version('2.4.3', sha256='0560622140f9f2dfd9e316bfba6a7582c4aac68fbe06f333bd442363f54a3e40')
+    version('2.4.2', sha256='504714b8d4895b41c6399347a873bbcf515037d9f5cf3cd5413c9d7aac67f16f')
+    version('2.4.1', sha256='764de6c3b9ff3e6d1f48022eb0d536054e7321e73c9f71f7eb1e93f90b6e8ad0')
+    version('2.4.0', sha256='96af9b21076be779e686c83a921d4598d93329eb69f9789fe619e27cbad6034a')
+    version('2.3.4', sha256='8bd1d9c12866cc768974e9c05c95e00c2fec3c65854ee91b7fb11709db9c5c12')
+    version('2.3.3', sha256='c7eadb8ddd956815f3387ed611faae746c05b69b7550de8ae802a00342b159b0')
+    version('2.3.2', sha256='ba8b17fcc8edae16faa74608e8da53e87a8c574aa21a28c985ea0dfedcb95210')
+    version('2.3.1', sha256='16c32b420e1aa7d0b6fecddd980ea0f2b7e3c2c66585e06f0eb3142677ab6ccf')
+    version('2.3.0', sha256='e452fe4a9716627bcdb726cfb0917f46a7ac31f6006330a6ccc1abc43d9c2d53')
+    # older version use .tar instead of .tar.gz extension, to be added

From caad59e7c7a45cb550d1451ed04108c0e37c1cbd Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sun, 3 May 2020 13:29:15 -0500
Subject: [PATCH 227/802] NumPy: add 1.18.4 (#16441)

---
 var/spack/repos/builtin/packages/py-numpy/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index 4c58f316a39..dbbfc815410 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -16,7 +16,7 @@ class PyNumpy(PythonPackage):
     number capabilities"""
 
     homepage = "https://numpy.org/"
-    url      = "https://pypi.io/packages/source/n/numpy/numpy-1.18.3.zip"
+    url      = "https://pypi.io/packages/source/n/numpy/numpy-1.18.4.zip"
     git      = "https://github.com/numpy/numpy.git"
 
     maintainers = ['adamjstewart']
@@ -30,6 +30,7 @@ class PyNumpy(PythonPackage):
     ]
 
     version('master', branch='master')
+    version('1.18.4', sha256='bbcc85aaf4cd84ba057decaead058f43191cc0e30d6bc5d44fe336dc3d3f4509')
     version('1.18.3', sha256='e46e2384209c91996d5ec16744234d1c906ab79a701ce1a26155c9ec890b8dc8')
     version('1.18.2', sha256='e7894793e6e8540dbeac77c87b489e331947813511108ae097f1715c018b8f3d')
     version('1.18.1', sha256='b6ff59cee96b454516e47e7721098e6ceebef435e3e21ac2d6c3b8b02628eb77')

From 860c54335dab3c766b2f692e77941b7dce28ab8e Mon Sep 17 00:00:00 2001
From: "Nichols A. Romero" <naromero77@users.noreply.github.com>
Date: Sun, 3 May 2020 15:53:01 -0500
Subject: [PATCH 228/802] QE-to-QMCPACK wave function converter relocation +
 some bug fixes (#16422)

* Revise description of patch variant.

* Add qmcpack variant. Apply QE-to-QMCPACK wave function converter patch.

* Clean-up, document, and re-organize.

* ELPA patches did not nead when=`+patch` variant.

* Need to be more precise here with QE version numbers.

* satisfies seems to be necessary here in order to get correct behaviour.

* Buglet with zlib link line.

* Update var/spack/repos/builtin/packages/quantum-espresso/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/quantum-espresso/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Fix for QE-to-QMCPACK wave function converter w.r.t. QE 6.3. Also adjust comments to reflect changes in code.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../packages/quantum-espresso/package.py      | 87 ++++++++++++++++---
 1 file changed, 73 insertions(+), 14 deletions(-)

diff --git a/var/spack/repos/builtin/packages/quantum-espresso/package.py b/var/spack/repos/builtin/packages/quantum-espresso/package.py
index 52fb46c7843..59f5c33f3d1 100644
--- a/var/spack/repos/builtin/packages/quantum-espresso/package.py
+++ b/var/spack/repos/builtin/packages/quantum-espresso/package.py
@@ -51,12 +51,17 @@ class QuantumEspresso(Package):
     variant('epw', default=False,
             description='Builds Electron-phonon Wannier executable')
 
-    # Apply internal patches by default. May need to be set to to False
-    # for 3rd party dependency patching
-    desc = 'Apply internal patches. May need to be set to False for'
-    desc = desc + ' dependency patching'
+    # Apply upstream patches by default. Variant useful for 3rd party
+    # patches which are incompatible with upstream patches
+    desc = 'Apply recommended upstream patches. May need to be set '
+    desc = desc + 'to False for third party patches or plugins'
     variant('patch', default=True, description=desc)
 
+    # QMCPACK converter patch
+    # https://github.com/QMCPACK/qmcpack/tree/develop/external_codes/quantum_espresso
+    variant('qmcpack', default=False,
+            description='Build QE-to-QMCPACK wave function converter')
+
     # Dependencies
     depends_on('blas')
     depends_on('lapack')
@@ -68,14 +73,11 @@ class QuantumEspresso(Package):
     # Versions of HDF5 prior to 1.8.16 lead to QE runtime errors
     depends_on('hdf5@1.8.16:+fortran+hl+mpi', when='hdf5=parallel')
     depends_on('hdf5@1.8.16:+fortran+hl~mpi', when='hdf5=serial')
-
+    depends_on('hdf5', when='+qmcpack')
     # TODO: enable building EPW when ~mpi
     depends_on('mpi', when='+epw')
 
-    patch('dspev_drv_elpa.patch', when='@6.1.0:+patch+elpa ^elpa@2016.05.004')
-    patch('dspev_drv_elpa.patch', when='@6.1.0:+patch+elpa ^elpa@2016.05.003')
-
-    # Conflicts
+    # CONFLICTS SECTION
     # Omitted for now due to concretizer bug
     # MKL with 64-bit integers not supported.
     # conflicts(
@@ -126,6 +128,27 @@ class QuantumEspresso(Package):
     # folder QE expects as a link, we issue a conflict here.
     conflicts('+elpa', when='@:5.4.0')
 
+    # Some QMCPACK converters only without internal patches. HDF5
+    # is a hard requirement. Need to do two HDF5 cases explicitly
+    # since Spack lacks support for expressing NOT operation.
+    conflicts(
+        '@6.4+patch',
+        when='+qmcpack',
+        msg='QE-to-QMCPACK wave function converter requires '
+        'deactivatation of upstream patches'
+    )
+    conflicts(
+        'hdf5=serial',
+        when='+qmcpack',
+        msg='QE-to-QMCPACK wave function converter only '
+        'supported with parallel HDF5'
+    )
+    conflicts(
+        'hdf5=none',
+        when='+qmcpack',
+        msg='QE-to-QMCPACK wave function converter requires HDF5'
+    )
+
     # The first version of Q-E to feature integrated EPW is 6.0.0,
     # as per http://epw.org.uk/Main/DownloadAndInstall .
     # Complain if trying to install a version older than this.
@@ -147,11 +170,33 @@ class QuantumEspresso(Package):
     conflicts('+epw', when='^openmpi@1.10.7%pgi@17.0:17.12',
               msg='PGI+OpenMPI version combo incompatible with EPW')
 
-    # Spurious problems running in parallel the Makefile
-    # generated by the configure
-    parallel = False
+    # PATCHES SECTION
+    # THIRD-PARTY PATCHES
+    # NOTE: *SOME* third-party patches will require deactivation of
+    # upstream patches using `~patch` variant
 
-    # QE upstream patches
+    # QMCPACK converter patches for QE 6.4.1, 6.4, and 6.3
+    conflicts('@:6.2,6.5:', when='+qmcpack',
+              msg='QMCPACK converter NOT available for this version of QE')
+
+    # 6.4.1
+    patch_url = 'https://raw.githubusercontent.com/QMCPACK/qmcpack/develop/external_codes/quantum_espresso/add_pw2qmcpack_to_qe-6.4.1.diff'
+    patch_checksum = '57cb1b06ee2653a87c3acc0dd4f09032fcf6ce6b8cbb9677ae9ceeb6a78f85e2'
+    patch(patch_url, sha256=patch_checksum, when='@6.4.1+qmcpack')
+    # 6.4
+    patch_url = 'https://raw.githubusercontent.com/QMCPACK/qmcpack/develop/external_codes/quantum_espresso/add_pw2qmcpack_to_qe-6.4.diff'
+    patch_checksum = 'ef08f5089951be902f0854a4dbddaa7b01f08924cdb27decfade6bef0e2b8994'
+    patch(patch_url, sha256=patch_checksum, when='@6.4:6.4.0+qmcpack')
+    # 6.3
+    patch_url = 'https://raw.githubusercontent.com/QMCPACK/qmcpack/develop/external_codes/quantum_espresso/add_pw2qmcpack_to_qe-6.3.diff'
+    patch_checksum = '2ee346e24926479f5e96f8dc47812173a8847a58354bbc32cf2114af7a521c13'
+    patch(patch_url, sha256=patch_checksum, when='@6.3+qmcpack')
+
+    # ELPA
+    patch('dspev_drv_elpa.patch', when='@6.1.0:+elpa ^elpa@2016.05.004')
+    patch('dspev_drv_elpa.patch', when='@6.1.0:+elpa ^elpa@2016.05.003')
+
+    # QE UPSTREAM PATCHES
     # QE 6.3 requires multiple patches to fix MKL detection
     # There may still be problems on Mac with MKL detection
     patch('https://gitlab.com/QEF/q-e/commit/0796e1b7c55c9361ecb6515a0979280e78865e36.diff',
@@ -170,6 +215,10 @@ class QuantumEspresso(Package):
           sha256='b1aa3179ee1c069964fb9c21f3b832aebeae54947ce8d3cc1a74e7b154c3c10f',
           when='+patch@6.4.1:6.5.0')
 
+    # Spurious problems running in parallel the Makefile
+    # generated by the configure
+    parallel = False
+
     def install(self, spec, prefix):
 
         prefix_path = prefix.bin if '@:5.4.0' in spec else prefix
@@ -268,7 +317,7 @@ def install(self, spec, prefix):
 
         if spec.variants['hdf5'].value != 'none':
             options.append('--with-hdf5={0}'.format(spec['hdf5'].prefix))
-            if '@6.4.1' or '@6.5' in spec:
+            if spec.satisfies('@6.4.1,6.5'):
                 options.extend([
                     '--with-hdf5-include={0}'.format(
                         spec['hdf5'].headers.directories[0]
@@ -280,6 +329,16 @@ def install(self, spec, prefix):
 
         configure(*options)
 
+        # Filter file must be applied after configure executes
+        # QE 6.4.0 to QE 6.4 have `-L` missing in front of zlib library
+        if spec.variants['hdf5'].value != 'none':
+            if spec.satisfies('@6.1.0:6.4.0'):
+                make_inc = join_path(self.stage.source_path, 'make.inc')
+                zlib_libs = spec['zlib'].prefix.lib + ' -lz'
+                filter_file(
+                    zlib_libs, format(spec['zlib'].libs.ld_flags), make_inc
+                )
+
         if '+epw' in spec:
             make('all', 'epw')
         else:

From d5adad6953908a39920fbbe66c543bb008705179 Mon Sep 17 00:00:00 2001
From: "Dr. Christian Tacke"
 <58549698+ChristianTackeGSI@users.noreply.github.com>
Date: Mon, 4 May 2020 09:02:38 +0200
Subject: [PATCH 229/802] singularity: added missing dependencies (#16430)

See:

https://sylabs.io/guides/3.5/user-guide/quick_start.html#install-system-dependencies

for pkg-config and libseccomp
---
 var/spack/repos/builtin/packages/singularity/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/singularity/package.py b/var/spack/repos/builtin/packages/singularity/package.py
index e7e69fa7327..9f4c898e619 100644
--- a/var/spack/repos/builtin/packages/singularity/package.py
+++ b/var/spack/repos/builtin/packages/singularity/package.py
@@ -40,9 +40,12 @@ class Singularity(MakefilePackage):
 
     variant('suid', default=True, description='install SUID binary')
     variant('network', default=True, description='install network plugins')
+
+    depends_on('pkgconfig', type='build')
     depends_on('go')
     depends_on('libuuid')
     depends_on('libgpg-error')
+    depends_on('libseccomp')
     depends_on('squashfs', type='run')
     depends_on('git', when='@develop')  # mconfig uses it for version info
     depends_on('shadow', type='run', when='@3.3:')

From 87f78137a54b2d317172e18c1d46a46c31362c6e Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Mon, 4 May 2020 00:39:20 -0700
Subject: [PATCH 230/802] LAPACKC++: added "shared" variant (#16419)

We can control the shared/static build of CMake and the default in
Spack is to build shared libraries. The old, uncontrolled default
of this package is a static build.
---
 var/spack/repos/builtin/packages/lapackpp/package.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/lapackpp/package.py b/var/spack/repos/builtin/packages/lapackpp/package.py
index 1f3ec76924d..8b51f233ddd 100644
--- a/var/spack/repos/builtin/packages/lapackpp/package.py
+++ b/var/spack/repos/builtin/packages/lapackpp/package.py
@@ -16,8 +16,16 @@ class Lapackpp(CMakePackage):
 
     version('develop', hg=hg, revision="7ffa486")
 
+    variant('shared', default=True,
+            description='Build a shared version of the library')
+
     depends_on('blaspp')
 
     def cmake_args(self):
-        return ['-DBUILD_LAPACKPP_TESTS:BOOL={0}'.format(
-            'ON' if self.run_tests else 'OFF')]
+        spec = self.spec
+        return [
+            '-DBUILD_SHARED_LIBS:BOOL={0}'.format(
+                'ON' if '+shared' in spec else 'OFF'),
+            '-DBUILD_LAPACKPP_TESTS:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF')
+        ]

From 7b31f5474b8e5ee3c72938eeb6110e8556c4894d Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <eafischer2@alaska.edu>
Date: Mon, 4 May 2020 13:25:19 -0800
Subject: [PATCH 231/802] grass: new versions (#16181)

* grass

* Update var/spack/repos/builtin/packages/grass/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 var/spack/repos/builtin/packages/grass/package.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/grass/package.py b/var/spack/repos/builtin/packages/grass/package.py
index cb83a5cc2ab..64352394320 100644
--- a/var/spack/repos/builtin/packages/grass/package.py
+++ b/var/spack/repos/builtin/packages/grass/package.py
@@ -15,9 +15,11 @@ class Grass(AutotoolsPackage):
     homepage = "https://grass.osgeo.org"
     url      = "https://grass.osgeo.org/grass78/source/grass-7.8.2.tar.gz"
     list_url = "https://grass.osgeo.org/download/software/sources/"
+    git      = "https://github.com/OSGeo/grass.git"
 
     maintainers = ['adamjstewart']
 
+    version('master', branch='master')
     version('7.8.2', sha256='33576f7078f805b39ca20c2fa416ac79c64260c0581072a6dc7d813f53aa9abb')
     version('7.8.1', sha256='6ae578fd67afcce7abec4ba4505dcc55b3d2dfe0ca46b99d966cb148c654abb3')
     version('7.8.0', sha256='4b1192294e959ffd962282344e4ff325c4472f73abe605e246a1da3beda7ccfa')
@@ -66,7 +68,10 @@ class Grass(AutotoolsPackage):
     depends_on('proj@:4', when='@:7.5')
     # GRASS 7.8.0 was supposed to support PROJ 6, but it still checks for
     # share/proj/epsg, which was removed in PROJ 6
-    depends_on('proj@:5', when='@:7.8')
+    depends_on('proj@:5', when='@:7.8.0')
+    # PROJ6 support released in GRASS 7.8.1
+    # https://courses.neteler.org/grass-gis-7-8-1-released-with-proj-6-and-gdal-3-support/
+    depends_on('proj@6:', when='@7.8.1:')
     depends_on('python@2.7:', type=('build', 'run'))
     depends_on('python@2.7:2.8', when='@:7.6', type=('build', 'run'))
     depends_on('py-six', when='@7.8:', type=('build', 'run'))

From dea5d913db9f98870eb4bd91ba1f8276e5e47d17 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <eafischer2@alaska.edu>
Date: Mon, 4 May 2020 13:30:59 -0800
Subject: [PATCH 232/802] Updates to Python for macOS (#16449)

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
---
 var/spack/repos/builtin/packages/python/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 712216f491f..a9b04a2d5b5 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -84,8 +84,9 @@ class Python(AutotoolsPackage):
     )
 
     # --enable-shared is known to cause problems for some users on macOS
+    # This is a problem for Python 2.7 only, not Python3
     # See http://bugs.python.org/issue29846
-    variant('shared', default=sys.platform != 'darwin',
+    variant('shared', default=True,
             description='Enable shared libraries')
     # From https://docs.python.org/2/c-api/unicode.html: Python's default
     # builds use a 16-bit type for Py_UNICODE and store Unicode values

From 1cff717ca86c031c912cf22a7e315d822ab83e46 Mon Sep 17 00:00:00 2001
From: Oliver Breitwieser <oliver.breitwieser@kip.uni-heidelberg.de>
Date: Wed, 4 Dec 2019 16:37:40 +0100
Subject: [PATCH 233/802] Fix git-related commands not working in worktrees

If spack is checked out in a git worktree (see [1]), all git-related
commands fail because the `spack_is_git_repo()`-check is not thorough
enough.

When developing in a feature-branch in a seperate worktree, this is
annoying as all unittests regarding git-related spack commands fail,
cluttering the test results with false-positives.

[1]: https://git-scm.com/docs/git-worktree

Change-Id: I94b573a2c0e058e9ccc169e7ee6561626fbb06fd
---
 lib/spack/spack/cmd/__init__.py         | 23 +++++++--
 lib/spack/spack/test/cmd/is_git_repo.py | 67 +++++++++++++++++++++++++
 2 files changed, 87 insertions(+), 3 deletions(-)
 create mode 100644 lib/spack/spack/test/cmd/is_git_repo.py

diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py
index 594b5e3a8ec..5172bdee078 100644
--- a/lib/spack/spack/cmd/__init__.py
+++ b/lib/spack/spack/cmd/__init__.py
@@ -9,6 +9,7 @@
 import re
 import sys
 import argparse
+import ruamel.yaml as yaml
 
 import six
 
@@ -16,7 +17,7 @@
 from llnl.util.lang import attr_setdefault, index_by
 from llnl.util.tty.colify import colify
 from llnl.util.tty.color import colorize
-from llnl.util.filesystem import working_dir
+from llnl.util.filesystem import join_path
 
 import spack.config
 import spack.error
@@ -26,6 +27,7 @@
 import spack.store
 import spack.util.spack_json as sjson
 import spack.util.string
+from ruamel.yaml.error import MarkedYAMLError
 
 
 # cmd has a submodule called "list" so preserve the python list module
@@ -433,8 +435,23 @@ def format_list(specs):
 
 def spack_is_git_repo():
     """Ensure that this instance of Spack is a git clone."""
-    with working_dir(spack.paths.prefix):
-        return os.path.isdir('.git')
+    return is_git_repo(spack.paths.prefix)
+
+
+def is_git_repo(path):
+    dotgit_path = join_path(path, '.git')
+    if os.path.isdir(dotgit_path):
+        # we are in a regular git repo
+        return True
+    if os.path.isfile(dotgit_path):
+        # we might be in a git worktree
+        try:
+            with open(dotgit_path, "rb") as f:
+                dotgit_content = yaml.load(f)
+            return os.path.isdir(dotgit_content.get("gitdir", dotgit_path))
+        except MarkedYAMLError:
+            pass
+    return False
 
 
 class PythonNameError(spack.error.SpackError):
diff --git a/lib/spack/spack/test/cmd/is_git_repo.py b/lib/spack/spack/test/cmd/is_git_repo.py
new file mode 100644
index 00000000000..724925e5e48
--- /dev/null
+++ b/lib/spack/spack/test/cmd/is_git_repo.py
@@ -0,0 +1,67 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from __future__ import print_function
+
+import spack
+import pytest
+
+from llnl.util.filesystem import mkdirp
+
+from spack.util.executable import which
+from spack.version import ver
+
+
+git = which("git")
+git_required_version = '2.17.0'
+
+
+def check_git_version():
+    """Check if git version is new enough for worktree functionality.
+    Return True if requirements are met.
+
+    The latest required functionality is `worktree remove` which was only added
+    in 2.17.0.
+
+    Refer:
+    https://github.com/git/git/commit/cc73385cf6c5c229458775bc92e7dbbe24d11611
+    """
+    git_version = ver(git('--version', output=str).lstrip('git version '))
+    return git_version >= ver(git_required_version)
+
+
+pytestmark = pytest.mark.skipif(
+    not git or not check_git_version(),
+    reason="we need git to test if we are in a git repo"
+)
+
+
+@pytest.fixture(scope="function")
+def git_tmp_worktree(tmpdir):
+    """Create new worktree in a temporary folder and monkeypatch
+    spack.paths.prefix to point to it.
+    """
+    worktree_root = str(tmpdir.join("tmp_worktree"))
+    mkdirp(worktree_root)
+
+    git("worktree", "add", "--detach", worktree_root, "HEAD")
+
+    yield worktree_root
+
+    git("worktree", "remove", "--force", worktree_root)
+
+
+def test_is_git_repo_in_worktree(git_tmp_worktree):
+    """Verify that spack.cmd.spack_is_git_repo() can identify a git repository
+    in a worktree.
+    """
+    assert spack.cmd.is_git_repo(git_tmp_worktree)
+
+
+def test_spack_is_git_repo_nongit(tmpdir, monkeypatch):
+    """Verify that spack.cmd.spack_is_git_repo() correctly returns False if we
+    are in a non-git directory.
+    """
+    assert not spack.cmd.is_git_repo(str(tmpdir))

From acf0c90283e920590f9a1db2881deed1e585d918 Mon Sep 17 00:00:00 2001
From: Shintaro Iwasaki <siwasaki@anl.gov>
Date: Mon, 4 May 2020 16:44:50 -0500
Subject: [PATCH 234/802] argobots: mark 1.0 as preferred (#16458)

By default, Spack chooses 1.0rc2 instead of 1.0 though 1.0 is the stable and
newer release.  We manually mark the version 1.0 as preferred.
---
 var/spack/repos/builtin/packages/argobots/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/argobots/package.py b/var/spack/repos/builtin/packages/argobots/package.py
index 8f967d020b1..3db9014afbe 100644
--- a/var/spack/repos/builtin/packages/argobots/package.py
+++ b/var/spack/repos/builtin/packages/argobots/package.py
@@ -21,7 +21,8 @@ class Argobots(AutotoolsPackage):
     maintainers = ['shintaro-iwasaki']
 
     version("master", branch="master")
-    version("1.0", sha256="36a0815f7bf99900a9c9c1eef61ef9b3b76aa2cfc4594a304f6c8c3296da8def")
+    version("1.0", sha256="36a0815f7bf99900a9c9c1eef61ef9b3b76aa2cfc4594a304f6c8c3296da8def",
+            preferred=True)
     version("1.0rc2", sha256="7496b8bd39930a548b01aa3b1fe8f8b582c272600ef6a05ddc4398cf21dc12a2")
     version("1.0rc1", sha256="2dc4487556dce602655a6535f501136f0edc3575708029c80b1af6dccd069ce7")
     version("1.0b1", sha256="480b85b0e8db288400088a57c2dc5639f556843b06b0492841920c38348a2a3e")

From 0475edfbf2a668b8d6c67ade996bb96085c18a93 Mon Sep 17 00:00:00 2001
From: Shintaro Iwasaki <siwasaki@anl.gov>
Date: Mon, 4 May 2020 16:45:28 -0500
Subject: [PATCH 235/802] BOLT: add 1.0 (#16457)

---
 var/spack/repos/builtin/packages/bolt/package.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/bolt/package.py b/var/spack/repos/builtin/packages/bolt/package.py
index d0750e615da..0b131b4d7a7 100644
--- a/var/spack/repos/builtin/packages/bolt/package.py
+++ b/var/spack/repos/builtin/packages/bolt/package.py
@@ -23,10 +23,7 @@ class Bolt(CMakePackage):
     maintainers = ['shintaro-iwasaki']
 
     version("master", branch="master")
-    version("1.0rc3", sha256="beec522d26e74f0a562762ea5ae7805486a17b40013090ea1472f0c34c3379c8")
-    version("1.0rc2", sha256="662ab0bb9583e8d733e8af62a97b41828e8bfe4bd65902f1195b986901775a45")
-    version("1.0rc1", sha256="c08cde0695b9d1252ab152425be96eb29c70d764e3083e276c013804883a15a4")
-    version("1.0b1", sha256="fedba46ad2f8835dd1cec1a9a52bcc9d8923071dc40045d0360517d09cd1a57d")
+    version("1.0", sha256="1c0d2f75597485ca36335d313a73736594e75c8a36123c5a6f54d01b5ba5c384")
 
     depends_on('argobots')
     depends_on('autoconf', type='build')
@@ -36,7 +33,6 @@ class Bolt(CMakePackage):
     def cmake_args(self):
         spec = self.spec
         options = [
-            '-DLIBOMP_USE_ITT_NOTIFY=off',
             '-DLIBOMP_USE_ARGOBOTS=on',
             '-DLIBOMP_ARGOBOTS_INSTALL_DIR=' + spec['argobots'].prefix
         ]

From 0a4e078648dac5ae46902ef54b26018290820960 Mon Sep 17 00:00:00 2001
From: Matthias Diener <mdiener@illinois.edu>
Date: Mon, 4 May 2020 16:45:55 -0500
Subject: [PATCH 236/802] hwloc: add version 2.2.0 (#16456)

---
 var/spack/repos/builtin/packages/hwloc/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py
index 547327e60ba..cb1a23c33e4 100644
--- a/var/spack/repos/builtin/packages/hwloc/package.py
+++ b/var/spack/repos/builtin/packages/hwloc/package.py
@@ -28,6 +28,7 @@ class Hwloc(AutotoolsPackage):
     git = 'https://github.com/open-mpi/hwloc.git'
 
     version('master', branch='master')
+    version('2.2.0', sha256='2defba03ddd91761b858cbbdc2e3a6e27b44e94696dbfa21380191328485a433')
     version('2.1.0',  sha256='1fb8cc1438de548e16ec3bb9e4b2abb9f7ce5656f71c0906583819fcfa8c2031')
     version('2.0.2',  sha256='27dcfe42e3fb3422b72ce48b48bf601c0a3e46e850ee72d9bdd17b5863b6e42c')
     version('2.0.1',  sha256='f1156df22fc2365a31a3dc5f752c53aad49e34a5e22d75ed231cd97eaa437f9d')

From fe350224b6959217de139c24392d363780704379 Mon Sep 17 00:00:00 2001
From: Matthias Diener <mdiener@illinois.edu>
Date: Mon, 4 May 2020 16:46:30 -0500
Subject: [PATCH 237/802] pocl: add version 1.5 (#16455)

* pocl: add version 1.5

* update clang version
---
 var/spack/repos/builtin/packages/pocl/package.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/pocl/package.py b/var/spack/repos/builtin/packages/pocl/package.py
index 42a862d97b6..da707344f5d 100644
--- a/var/spack/repos/builtin/packages/pocl/package.py
+++ b/var/spack/repos/builtin/packages/pocl/package.py
@@ -20,6 +20,7 @@ class Pocl(CMakePackage):
     git      = "https://github.com/pocl/pocl.git"
 
     version("master", branch="master")
+    version('1.5', sha256='4fcf4618171727d165fc044d465a66e3119217bb4577a97374f94fcd8aed330e')
     version('1.4', sha256='ec237faa83bb1c803fbdf7c6e83d8a2ad68b6f0ed1879c3aa16c0e1dcc478742')
     version('1.3', sha256='6527e3f47fab7c21e96bc757c4ae3303901f35e23f64642d6da5cc4c4fcc915a')
     version('1.2', sha256='0c43e68f336892f3a64cba19beb99d9212f529bedb77f7879c0331450b982d46')
@@ -50,7 +51,8 @@ class Pocl(CMakePackage):
     # enabled by default, and also because they fail to build for us
     # (see #1616)
     # These are the supported LLVM versions
-    depends_on("llvm +clang @6.0:7.0", when="@master")
+    depends_on("llvm +clang @6.0:10.0", when="@master")
+    depends_on("llvm +clang @6.0:10.0", when="@1.5")
     depends_on("llvm +clang @6.0:9.0", when="@1.4")
     depends_on("llvm +clang @5.0:8.0", when="@1.3")
     depends_on("llvm +clang @5.0:7.0", when="@1.2")

From e808a52176313bf0664adbe8760cbeb4243eea73 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ren=C3=A9=20Widera?= <r.widera@hzdr.de>
Date: Mon, 4 May 2020 23:47:12 +0200
Subject: [PATCH 238/802] update isaac and issac-server to v1.5.0 (#16452)

Update package.py with the latest release [ISAAC v1.5.0].
---
 var/spack/repos/builtin/packages/isaac-server/package.py | 1 +
 var/spack/repos/builtin/packages/isaac/package.py        | 1 +
 2 files changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/isaac-server/package.py b/var/spack/repos/builtin/packages/isaac-server/package.py
index 24fae8c32f1..af693a339c5 100644
--- a/var/spack/repos/builtin/packages/isaac-server/package.py
+++ b/var/spack/repos/builtin/packages/isaac-server/package.py
@@ -17,6 +17,7 @@ class IsaacServer(CMakePackage):
 
     version('develop', branch='dev')
     version('master', branch='master')
+    version('1.5.0', sha256='4d5a150dfe064289d760da368102172f84e9e8851a177c8125a56e151db58dce')
     version('1.4.0', sha256='6cbd4cc54a22de5e5a3427e44141db6e7b80b33fe7a0c707390a113655bf344e')
     version('1.3.3', sha256='92a972d05d315ad66546671c047b7edf8ed0e05d64d2b8d77ababb5bb9b93d8e')
     version('1.3.2', sha256='e6eedc641de5b0a7c5ea5cda6b11e9b6d4a78dfac8be90302147b26d09859a68')
diff --git a/var/spack/repos/builtin/packages/isaac/package.py b/var/spack/repos/builtin/packages/isaac/package.py
index 2c0badc88c9..ddc62f3482c 100644
--- a/var/spack/repos/builtin/packages/isaac/package.py
+++ b/var/spack/repos/builtin/packages/isaac/package.py
@@ -17,6 +17,7 @@ class Isaac(CMakePackage):
 
     version('develop', branch='dev')
     version('master', branch='master')
+    version('1.5.0', sha256='4d5a150dfe064289d760da368102172f84e9e8851a177c8125a56e151db58dce')
     version('1.4.0', sha256='6cbd4cc54a22de5e5a3427e44141db6e7b80b33fe7a0c707390a113655bf344e')
     version('1.3.3', sha256='92a972d05d315ad66546671c047b7edf8ed0e05d64d2b8d77ababb5bb9b93d8e')
     version('1.3.2', sha256='e6eedc641de5b0a7c5ea5cda6b11e9b6d4a78dfac8be90302147b26d09859a68')

From 43d2c7f3b506ccbbdc4e352ef25db1fa4d52a659 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <eafischer2@alaska.edu>
Date: Mon, 4 May 2020 17:53:12 -0400
Subject: [PATCH 239/802] py-cf-units: Add new version (#16446)

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
---
 var/spack/repos/builtin/packages/py-cf-units/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-cf-units/package.py b/var/spack/repos/builtin/packages/py-cf-units/package.py
index 07f062dca95..54d6e909b32 100644
--- a/var/spack/repos/builtin/packages/py-cf-units/package.py
+++ b/var/spack/repos/builtin/packages/py-cf-units/package.py
@@ -16,6 +16,7 @@ class PyCfUnits(PythonPackage):
     git      = "https://github.com/SciTools/cf-units.git"
 
     version('master', branch='master')
+    version('2.1.4', sha256='25f81ad994af30713ee8f5ef18ffddd83c6ec1ac308e1bd89d45de9d2e0f1c31')
     version('2.1.1', sha256='fa0ef8efd84546e61088aa23e76ebbaf7043167dc3a7f35f34549c234b543530')
 
     depends_on('python@3:', type=('build', 'run'))

From 5adf703414c9f11328fd61acedfd71633ecc5166 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <eafischer2@alaska.edu>
Date: Mon, 4 May 2020 17:55:54 -0400
Subject: [PATCH 240/802] py-palletable: Add new version (#16445)

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
---
 var/spack/repos/builtin/packages/py-palettable/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-palettable/package.py b/var/spack/repos/builtin/packages/py-palettable/package.py
index 716c9842e5a..aa17c77c4b7 100644
--- a/var/spack/repos/builtin/packages/py-palettable/package.py
+++ b/var/spack/repos/builtin/packages/py-palettable/package.py
@@ -12,6 +12,7 @@ class PyPalettable(PythonPackage):
     homepage = "https://jiffyclub.github.io/palettable/"
     url      = "https://pypi.io/packages/source/p/palettable/palettable-3.0.0.tar.gz"
 
+    version('3.3.0', sha256='72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd')
     version('3.0.0', sha256='eed9eb0399386ff42f90ca61d4fa38a1819a93d5adfc2d546e3e2869d9972c31')
 
     depends_on('py-setuptools', type='build')

From 6c07260d27a2556f4f559c0f0dc24217ef05a3ae Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 4 May 2020 23:57:06 +0200
Subject: [PATCH 241/802] ecFlow added UI & GUI flag with new version (#16444)

* ecFlow added UI & GUI flag with new version

* Fix1
---
 var/spack/repos/builtin/packages/ecflow/package.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/ecflow/package.py b/var/spack/repos/builtin/packages/ecflow/package.py
index 02bcb25ef11..14b3f2033df 100644
--- a/var/spack/repos/builtin/packages/ecflow/package.py
+++ b/var/spack/repos/builtin/packages/ecflow/package.py
@@ -18,23 +18,29 @@ class Ecflow(CMakePackage):
     homepage = 'https://confluence.ecmwf.int/display/ECFLOW/'
     url      = 'https://confluence.ecmwf.int/download/attachments/8650755/ecFlow-4.11.1-Source.tar.gz'
 
+    version('4.13.0', sha256='c743896e0ec1d705edd2abf2ee5a47f4b6f7b1818d8c159b521bdff50a403e39')
     version('4.12.0', sha256='566b797e8d78e3eb93946b923ef540ac61f50d4a17c9203d263c4fd5c39ab1d1')
     version('4.11.1', sha256='b3bcc1255939f87b9ba18d802940e08c0cf6379ca6aeec1fef7bd169b0085d6c')
 
     variant('static_boost', default=False,
             description='Use also static boost libraries when compiling')
 
-    depends_on('boost+python')
-    depends_on('boost+pic', when='+static_boost')
-    depends_on('qt')
-    depends_on('cmake@2.8.11:', type='build')
+    variant('ui', default=False, description='Enable ecflow_ui')
+
+    # Boost-1.7X release not working well on serialization
+    depends_on('boost@1.53:1.69+python')
+    depends_on('boost@1.53:1.69+pic', when='+static_boost')
+    depends_on('qt@5:', when='+ui')
+    depends_on('cmake@2.12.11:', type='build')
 
     def cmake_args(self):
         boost_lib = self.spec['boost'].prefix.lib
         args = ['-DBoost_PYTHON_LIBRARY_RELEASE=' + boost_lib]
 
+        ecflow_ui = 'ON' if '+ui' in self.spec else 'OFF'
         # https://jira.ecmwf.int/browse/SUP-2641#comment-208943
         use_static_boost = 'ON' if '+static_boost' in self.spec else 'OFF'
         args.append('-DENABLE_STATIC_BOOST_LIBS=' + use_static_boost)
 
+        args.extend(['-DENABLE_UI=' + ecflow_ui, '-DENABLE_GUI=' + ecflow_ui])
         return args

From 8e2f5ba861bee449e7ad60f7da51767c23942c75 Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Mon, 4 May 2020 15:11:10 -0700
Subject: [PATCH 242/802] environments: allow sigils to apply to entire
 reference (#15245)

* environments: allow sigils to apply to entire reference
---
 lib/spack/docs/environments.rst | 36 +++++++++++++++++++++++-
 lib/spack/spack/spec_list.py    | 30 +++++++++++++++++---
 lib/spack/spack/test/cmd/env.py | 49 +++++++++++++++++++++++++++++++++
 3 files changed, 110 insertions(+), 5 deletions(-)

diff --git a/lib/spack/docs/environments.rst b/lib/spack/docs/environments.rst
index c26f81d9142..b80e36b4b2b 100644
--- a/lib/spack/docs/environments.rst
+++ b/lib/spack/docs/environments.rst
@@ -602,7 +602,7 @@ files are identical.
    spack:
      definitions:
        - first: [libelf, libdwarf]
-       - compilers: ['%gcc', '^intel']
+       - compilers: ['%gcc', '%intel']
        - second:
            - $first
            - matrix:
@@ -676,6 +676,40 @@ The valid variables for a ``when`` clause are:
 #. ``hostname``. The hostname of the system (if ``hostname`` is an
    executable in the user's PATH).
 
+""""""""""""""""""""""""
+SpecLists as Constraints
+""""""""""""""""""""""""
+
+Dependencies and compilers in Spack can be both packages in an
+environment and constraints on other packages. References to SpecLists
+allow a shorthand to treat packages in a list as either a compiler or
+a dependency using the ``$%`` or ``$^`` syntax respectively.
+
+For example, the following environment has three root packages:
+``gcc@8.1.0``, ``mvapich2@2.3.1 %gcc@8.1.0``, and ``hdf5+mpi
+%gcc@8.1.0 ^mvapich2@2.3.1``.
+
+.. code-block:: yaml
+
+   spack:
+     definitions:
+     - compilers: [gcc@8.1.0]
+     - mpis: [mvapich2@2.3.1]
+     - packages: [hdf5+mpi]
+
+     specs:
+     - $compilers
+     - matrix:
+       - [$mpis]
+       - [$%compilers]
+     - matrix:
+       - [$packages]
+       - [$^mpis]
+       - [$%compilers]
+
+This allows for a much-needed reduction in redundancy between packages
+and constraints.
+
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 Environment-managed Views
 ^^^^^^^^^^^^^^^^^^^^^^^^^
diff --git a/lib/spack/spack/spec_list.py b/lib/spack/spack/spec_list.py
index 63bd29a7a9d..de75458f322 100644
--- a/lib/spack/spack/spec_list.py
+++ b/lib/spack/spack/spec_list.py
@@ -124,12 +124,27 @@ def _expand_references(self, yaml):
         if isinstance(yaml, list):
             for idx, item in enumerate(yaml):
                 if isinstance(item, string_types) and item.startswith('$'):
-                    name = item[1:]
+                    # Reference type can add a constraint to items
+                    if item[1] in ('^', '%'):
+                        name = item[2:]
+                        sigil = item[1]
+                    else:
+                        name = item[1:]
+                        sigil = ''
                     if name in self._reference:
                         ret = [self._expand_references(i) for i in yaml[:idx]]
                         ret += self._reference[name].specs_as_yaml_list
                         ret += self._expand_references(yaml[idx + 1:])
-                        return ret
+
+                        # Add the sigil if we're mapping a sigil to a ref
+                        def sigilify(arg):
+                            if isinstance(arg, dict):
+                                if sigil:
+                                    arg['sigil'] = sigil
+                                return arg
+                            else:
+                                return sigil + arg
+                        return list(map(sigilify, ret))
                     else:
                         msg = 'SpecList %s refers to ' % self.name
                         msg += 'named list %s ' % name
@@ -159,13 +174,17 @@ def _expand_matrix_constraints(object, specify=True):
         new_row = []
         for r in row:
             if isinstance(r, dict):
-                new_row.extend(_expand_matrix_constraints(r, specify=False))
+                new_row.extend(
+                    [[' '.join(c)]
+                     for c in _expand_matrix_constraints(r, specify=False)])
             else:
                 new_row.append([r])
         expanded_rows.append(new_row)
 
-    results = []
     excludes = object.get('exclude', [])  # only compute once
+    sigil = object.get('sigil', '')
+
+    results = []
     for combo in itertools.product(*expanded_rows):
         # Construct a combined spec to test against excludes
         flat_combo = [constraint for list in combo for constraint in list]
@@ -174,6 +193,9 @@ def _expand_matrix_constraints(object, specify=True):
         if any(test_spec.satisfies(x) for x in excludes):
             continue
 
+        if sigil:  # add sigil if necessary
+            ordered_combo[0] = sigil + ordered_combo[0]
+
         # Add to list of constraints
         if specify:
             results.append([Spec(x) for x in ordered_combo])
diff --git a/lib/spack/spack/test/cmd/env.py b/lib/spack/spack/test/cmd/env.py
index f35b0a4bc13..671d9869ed9 100644
--- a/lib/spack/spack/test/cmd/env.py
+++ b/lib/spack/spack/test/cmd/env.py
@@ -1040,6 +1040,55 @@ def test_stack_yaml_definitions(tmpdir):
         assert Spec('callpath') in test.user_specs
 
 
+def test_stack_yaml_definitions_as_constraints(tmpdir):
+    filename = str(tmpdir.join('spack.yaml'))
+    with open(filename, 'w') as f:
+        f.write("""\
+env:
+  definitions:
+    - packages: [mpileaks, callpath]
+    - mpis: [mpich, openmpi]
+  specs:
+    - matrix:
+      - [$packages]
+      - [$^mpis]
+""")
+    with tmpdir.as_cwd():
+        env('create', 'test', './spack.yaml')
+        test = ev.read('test')
+
+        assert Spec('mpileaks^mpich') in test.user_specs
+        assert Spec('callpath^mpich') in test.user_specs
+        assert Spec('mpileaks^openmpi') in test.user_specs
+        assert Spec('callpath^openmpi') in test.user_specs
+
+
+def test_stack_yaml_definitions_as_constraints_on_matrix(tmpdir):
+    filename = str(tmpdir.join('spack.yaml'))
+    with open(filename, 'w') as f:
+        f.write("""\
+env:
+  definitions:
+    - packages: [mpileaks, callpath]
+    - mpis:
+      - matrix:
+        - [mpich]
+        - ['@3.0.4', '@3.0.3']
+  specs:
+    - matrix:
+      - [$packages]
+      - [$^mpis]
+""")
+    with tmpdir.as_cwd():
+        env('create', 'test', './spack.yaml')
+        test = ev.read('test')
+
+        assert Spec('mpileaks^mpich@3.0.4') in test.user_specs
+        assert Spec('callpath^mpich@3.0.4') in test.user_specs
+        assert Spec('mpileaks^mpich@3.0.3') in test.user_specs
+        assert Spec('callpath^mpich@3.0.3') in test.user_specs
+
+
 @pytest.mark.regression('12095')
 def test_stack_yaml_definitions_write_reference(tmpdir):
     filename = str(tmpdir.join('spack.yaml'))

From befd47259493aae407eec8d69b99ecb15d7df6bd Mon Sep 17 00:00:00 2001
From: vvolkl <valentin.volkl@cern.ch>
Date: Tue, 5 May 2020 02:40:13 +0200
Subject: [PATCH 243/802] [gaudi] fixes and patches (#16433)

* [gaudi] fixes and patches

* Update var/spack/repos/builtin/packages/gaudi/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/gaudi/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* [gaudi] add older versions and fold +tests into +optional

* [gaudi] set run environment

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../packages/gaudi/build_testing.patch        |  13 +++
 .../packages/gaudi/link_target_fixes.patch    | 106 +++++++++++++++++
 .../packages/gaudi/link_target_fixes32.patch  | 107 ++++++++++++++++++
 .../repos/builtin/packages/gaudi/package.py   |  83 ++++++++++----
 .../builtin/packages/gaudi/python2.patch      |  14 +++
 .../repos/builtin/packages/podio/cpack.patch  |  11 ++
 6 files changed, 315 insertions(+), 19 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/gaudi/build_testing.patch
 create mode 100644 var/spack/repos/builtin/packages/gaudi/link_target_fixes.patch
 create mode 100644 var/spack/repos/builtin/packages/gaudi/link_target_fixes32.patch
 create mode 100644 var/spack/repos/builtin/packages/gaudi/python2.patch
 create mode 100644 var/spack/repos/builtin/packages/podio/cpack.patch

diff --git a/var/spack/repos/builtin/packages/gaudi/build_testing.patch b/var/spack/repos/builtin/packages/gaudi/build_testing.patch
new file mode 100644
index 00000000000..ee736fd6dd4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gaudi/build_testing.patch
@@ -0,0 +1,13 @@
+diff --git a/GaudiExamples/CMakeLists.txt b/GaudiExamples/CMakeLists.txt
+index ef6f9fcff..672b76d26 100644
+--- a/GaudiExamples/CMakeLists.txt
++++ b/GaudiExamples/CMakeLists.txt
+@@ -0,0 +1,7 @@
++# GaudiExamples subdirectory
++if(NOT BUILD_TESTING)
++  # Ignore examples if not building tests
++  # see https://gitlab.cern.ch/atlas/atlasexternals/-/merge_requests/664#note_3395313
++  return()
++endif()
++
+
diff --git a/var/spack/repos/builtin/packages/gaudi/link_target_fixes.patch b/var/spack/repos/builtin/packages/gaudi/link_target_fixes.patch
new file mode 100644
index 00000000000..468c117b517
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gaudi/link_target_fixes.patch
@@ -0,0 +1,106 @@
+diff --git a/cmake/GaudiProjectConfig.cmake b/cmake/GaudiProjectConfig.cmake
+index d7049233e..a9ef71e9a 100644
+--- a/cmake/GaudiProjectConfig.cmake
++++ b/cmake/GaudiProjectConfig.cmake
+@@ -356,6 +356,8 @@ macro(gaudi_project project version)
+   # Make sure we select the version of Python provided by LCG (if we are building in that context)
+   if(Python_config_version)
+     set(Python_config_version ${Python_config_version} CACHE STRING "LCG version of Python")
++    # Prevent special LCG versions (like 2.7.9.p1) to confuse CMake
++    string(REGEX REPLACE "([0-9]+\\.[0-9]+\\.[0-9]+).*" "\\1" Python_config_version "${Python_config_version}")
+     find_package(PythonInterp ${Python_config_version} QUIET)
+     find_package(PythonLibs ${Python_config_version} QUIET)
+     if(CMAKE_VERSION VERSION_GREATER 3.12)
+@@ -373,10 +375,10 @@ macro(gaudi_project project version)
+   #-- Set up the boost_python_version variable for the project
+   find_package(PythonInterp)
+   find_package(Boost)
+-  if((Boost_VERSION GREATER 106700) OR (Boost_VERSION EQUAL 106700))
+-     set(boost_python_version "${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}")
++  if((Boost_VERSION LESS 106700) OR (Boost_VERSION GREATER 1069000))
++    set(boost_python_version "")
+   else()
+-     set(boost_python_version "")
++    set(boost_python_version "${Python_VERSION_MAJOR}${Python_VERSION_MINOR}")
+   endif()
+ 
+   #--- Allow installation on failed builds
+@@ -1620,9 +1622,24 @@ function(gaudi_resolve_link_libraries variable)
+   set(collected)
+   foreach(package ${ARGN})
+     # check if it is an actual library or a target first
++    if(NOT TARGET ${package})
++      if(package MATCHES "^Boost::(.*)$")
++        # special handling of Boost imported targets
++        find_package(Boost COMPONENTS ${CMAKE_MATCH_1} QUIET)
++      else()
++        # the target might be in a project namespace
++        foreach(_p IN LISTS used_gaudi_projects)
++          if(TARGET ${_p}::${package})
++            #message(STATUS "using ${_p}::${package} for ${package}")
++            set(package ${_p}::${package})
++            break()
++          endif()
++        endforeach()
++      endif()
++    endif()
+     if(TARGET ${package})
+       get_property(target_type TARGET ${package} PROPERTY TYPE)
+-      if(NOT target_type MATCHES "(SHARED|STATIC)_LIBRARY")
++      if(NOT target_type MATCHES "(SHARED|STATIC|UNKNOWN)_LIBRARY")
+         message(FATAL_ERROR "${package} is a ${target_type}: you cannot link against it")
+       endif()
+       #message(STATUS "${package} is a TARGET")
+@@ -1670,6 +1687,19 @@ function(gaudi_resolve_link_libraries variable)
+   endforeach()
+   #message(STATUS "gaudi_resolve_link_libraries collected: ${collected}")
+   _gaudi_strip_build_type_libs(collected)
++  # resolve missing Boost::* targets, if needed
++  set(boost_components ${collected})
++  list(FILTER boost_components INCLUDE REGEX "^Boost::")
++  list(TRANSFORM boost_components REPLACE "^Boost::" "")
++  set(missing_components)
++  foreach(comp IN LISTS boost_components)
++    if(NOT TARGET Boost::${comp})
++      list(APPEND missing_components ${comp})
++    endif()
++  endforeach()
++  if(missing_components)
++    find_package(Boost COMPONENTS ${missing_components} QUIET)
++  endif()
+   #message(STATUS "gaudi_resolve_link_libraries output: ${collected}")
+   set(${variable} ${collected} PARENT_SCOPE)
+ endfunction()
+@@ -3277,6 +3307,14 @@ macro(gaudi_external_project_environment)
+     list(FIND used_gaudi_projects ${pack} gaudi_project_idx)
+     if((NOT pack STREQUAL GaudiProject) AND (gaudi_project_idx EQUAL -1))
+       message(STATUS "    ${pack}")
++      if(pack STREQUAL Boost)
++        if(NOT TARGET Boost::headers)
++          # this is needed to get the non-cache variables for the packages
++          # but we do not need to call it if we do not use FindBoost.cmake (Boost >= 1.70)
++          find_package(${pack} QUIET)
++        endif()
++      endif()
++
+       if(NOT pack MATCHES "^Python(Interp|Libs)?$")
+         # this is needed to get the non-cache variables for the packages
+         find_package(${pack} QUIET)
+@@ -3325,6 +3363,17 @@ macro(gaudi_external_project_environment)
+             list(APPEND environment SET QT_XKB_CONFIG_ROOT "/usr/share/X11/xkb")
+           endif()
+         endif()
++      elseif(pack MATCHES "^boost_(.*)$")
++        # We are using BoostConfig.cmake (>=1.70) and not FindBoost.cmake
++        if(TARGET "Boost::${CMAKE_MATCH_1}")
++          set(tgt_name "Boost::${CMAKE_MATCH_1}")
++          get_property(target_type TARGET ${tgt_name} PROPERTY TYPE)
++          if(target_type MATCHES "(SHARED|UNKNOWN)_LIBRARY")
++            # FIXME: I'm not sure it's good to rely on the "_RELEASE" suffix
++            get_property(lib_path TARGET ${tgt_name} PROPERTY IMPORTED_LOCATION_RELEASE)
++            get_filename_component(${pack}_LIBRARY_DIR "${lib_path}" PATH)
++          endif()
++        endif()
+       endif()
+ 
+       list(APPEND binary_path   ${${pack}_BINARY_PATH})
diff --git a/var/spack/repos/builtin/packages/gaudi/link_target_fixes32.patch b/var/spack/repos/builtin/packages/gaudi/link_target_fixes32.patch
new file mode 100644
index 00000000000..95339a09318
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gaudi/link_target_fixes32.patch
@@ -0,0 +1,107 @@
+diff --git a/cmake/GaudiProjectConfig.cmake b/cmake/GaudiProjectConfig.cmake
+index 3da52a9c6..08c11c863 100644
+--- a/cmake/GaudiProjectConfig.cmake
++++ b/cmake/GaudiProjectConfig.cmake
+@@ -346,6 +346,8 @@ macro(gaudi_project project version)
+   # Make sure we select the version of Python provided by LCG (if we are building in that context)
+   if(Python_config_version)
+     set(Python_config_version ${Python_config_version} CACHE STRING "LCG version of Python")
++    # Prevent special LCG versions (like 2.7.9.p1) to confuse CMake
++    string(REGEX REPLACE "([0-9]+\\.[0-9]+\\.[0-9]+).*" "\\1" Python_config_version "${Python_config_version}")
+     find_package(PythonInterp ${Python_config_version} QUIET)
+     find_package(PythonLibs ${Python_config_version} QUIET)
+     if(CMAKE_VERSION VERSION_GREATER 3.12)
+@@ -363,10 +365,10 @@ macro(gaudi_project project version)
+   #-- Set up the boost_python_version variable for the project
+   find_package(PythonInterp)
+   find_package(Boost)
+-  if((Boost_VERSION GREATER 106700) OR (Boost_VERSION EQUAL 106700))
+-     set(boost_python_version "${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}")
++  if((Boost_VERSION LESS 106700) OR (Boost_VERSION GREATER 1069000))
++    set(boost_python_version "")
+   else()
+-     set(boost_python_version "")
++     set(boost_python_version "${Python_VERSION_MAJOR}${Python_VERSION_MINOR}")
+   endif()
+ 
+   #--- Allow installation on failed builds
+@@ -1607,9 +1609,25 @@ function(gaudi_resolve_link_libraries variable)
+   set(collected)
+   foreach(package ${ARGN})
+     # check if it is an actual library or a target first
++    if(NOT TARGET ${package})
++      if(package MATCHES "^Boost::(.*)$")
++        # special handling of Boost imported targets
++        find_package(Boost COMPONENTS ${CMAKE_MATCH_1} QUIET)
++      else()
++        # the target might be in a project namespace
++        foreach(_p IN LISTS used_gaudi_projects)
++          if(TARGET ${_p}::${package})
++            #message(STATUS "using ${_p}::${package} for ${package}")
++            set(package ${_p}::${package})
++            break()
++          endif()
++        endforeach()
++      endif()
++    endif()
++
+     if(TARGET ${package})
+       get_property(target_type TARGET ${package} PROPERTY TYPE)
+-      if(NOT target_type MATCHES "(SHARED|STATIC)_LIBRARY")
++      if(NOT target_type MATCHES "(SHARED|STATIC|UNKNOWN)_LIBRARY")
+         message(FATAL_ERROR "${package} is a ${target_type}: you cannot link against it")
+       endif()
+       #message(STATUS "${package} is a TARGET")
+@@ -1657,6 +1675,19 @@ function(gaudi_resolve_link_libraries variable)
+   endforeach()
+   #message(STATUS "gaudi_resolve_link_libraries collected: ${collected}")
+   _gaudi_strip_build_type_libs(collected)
++  # resolve missing Boost::* targets, if needed
++  set(boost_components ${collected})
++  list(FILTER boost_components INCLUDE REGEX "^Boost::")
++  list(TRANSFORM boost_components REPLACE "^Boost::" "")
++  set(missing_components)
++  foreach(comp IN LISTS boost_components)
++    if(NOT TARGET Boost::${comp})
++      list(APPEND missing_components ${comp})
++    endif()
++  endforeach()
++  if(missing_components)
++    find_package(Boost COMPONENTS ${missing_components} QUIET)
++  endif()
+   #message(STATUS "gaudi_resolve_link_libraries output: ${collected}")
+   set(${variable} ${collected} PARENT_SCOPE)
+ endfunction()
+@@ -3262,6 +3293,14 @@ macro(gaudi_external_project_environment)
+     list(FIND used_gaudi_projects ${pack} gaudi_project_idx)
+     if((NOT pack STREQUAL GaudiProject) AND (gaudi_project_idx EQUAL -1))
+       message(STATUS "    ${pack}")
++      if(pack STREQUAL Boost)
++        if(NOT TARGET Boost::headers)
++          # this is needed to get the non-cache variables for the packages
++          # but we do not need to call it if we do not use FindBoost.cmake (Boost >= 1.70)
++          find_package(${pack} QUIET)
++        endif()
++      endif()
++
+       if(NOT pack MATCHES "^Python(Interp|Libs)?$")
+         # this is needed to get the non-cache variables for the packages
+         find_package(${pack} QUIET)
+@@ -3310,6 +3349,17 @@ macro(gaudi_external_project_environment)
+             list(APPEND environment SET QT_XKB_CONFIG_ROOT "/usr/share/X11/xkb")
+           endif()
+         endif()
++      elseif(pack MATCHES "^boost_(.*)$")
++        # We are using BoostConfig.cmake (>=1.70) and not FindBoost.cmake
++        if(TARGET "Boost::${CMAKE_MATCH_1}")
++          set(tgt_name "Boost::${CMAKE_MATCH_1}")
++          get_property(target_type TARGET ${tgt_name} PROPERTY TYPE)
++          if(target_type MATCHES "(SHARED|UNKNOWN)_LIBRARY")
++            # FIXME: I'm not sure it's good to rely on the "_RELEASE" suffix
++            get_property(lib_path TARGET ${tgt_name} PROPERTY IMPORTED_LOCATION_RELEASE)
++            get_filename_component(${pack}_LIBRARY_DIR "${lib_path}" PATH)
++          endif()
++        endif()
+       endif()
+ 
+       list(APPEND binary_path   ${${pack}_BINARY_PATH})
diff --git a/var/spack/repos/builtin/packages/gaudi/package.py b/var/spack/repos/builtin/packages/gaudi/package.py
index 20f7c0f28b4..beae99c3cd5 100644
--- a/var/spack/repos/builtin/packages/gaudi/package.py
+++ b/var/spack/repos/builtin/packages/gaudi/package.py
@@ -11,41 +11,51 @@ class Gaudi(CMakePackage):
 
     homepage = "http://gaudi.web.cern.ch/gaudi/"
     git      = "https://gitlab.cern.ch/gaudi/Gaudi.git"
+    url      = "https://gitlab.cern.ch/gaudi/Gaudi/-/archive/v33r1/Gaudi-v33r1.tar.gz"
 
-    version('develop', branch='master')
-    version('30.5',    commit='2c70e73ee5b543b26197b90dd59ea4e4d359d230')
+    version('master', branch='master')
+    # major cmake config overhaul already in use by some
+    version('develop', git='https://gitlab.cern.ch/clemenci/Gaudi.git', branch='cmake-modernisation')
+    version('33.1', sha256='7eb6b2af64aeb965228d4b6ea66c7f9f57f832f93d5b8ad55c9105235af5b042')
+    version('33.0', sha256='76a967c41f579acc432593d498875dd4dc1f8afd5061e692741a355a9cf233c8')
+    version('32.2', sha256='e9ef3eb57fd9ac7b9d5647e278a84b2e6263f29f0b14dbe1321667d44d969d2e')
     version('31.0',    commit='aeb156f0c40571b5753a9e1dab31e331491b2f3e')
+    version('30.5',    commit='2c70e73ee5b543b26197b90dd59ea4e4d359d230')
+
+    maintainers = ['drbenmorgan', "vvolkl"]
 
-    variant('tests', default=False,
-            description='Prepare to run the test suite')
     variant('optional', default=False,
-            description='Build most optional components')
+            description='Build most optional components and tests')
     variant('vtune', default=False,
             description='Build with Intel VTune profiler support')
 
+    # only build subdirectory GaudiExamples when +optional
+    patch("build_testing.patch", when="@:33.1")
+    # fix for the new cmake config, should be merged in branch
+    patch('python2.patch', when="@develop")
+    # fixes for the cmake config which could not find newer boost versions
+    patch("link_target_fixes.patch", when="@33.0:33.1")
+    patch("link_target_fixes32.patch", when="@:32.2")
+
     # These dependencies are needed for a minimal Gaudi build
     depends_on('boost@1.67.0: +python')
     depends_on('cmake', type='build')
+    depends_on('cppgsl')
     depends_on('intel-tbb')
     depends_on('libuuid')
-    depends_on('python@:2.99.99')
-    depends_on('py-xenv@develop_2018-12-20:')
+    # some bugs with python 3.8
+    depends_on('python@:3.7.99', when='@32.2:', type=('build', 'run'))
+    depends_on('python@:2.99.99', when='@:32.1', type=('build', 'run'))
+    depends_on('py-setuptools@:45.99.99', when='^python@:2.7.99', type='build')
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-xenv@develop_2018-12-20:', type=('build', 'run'))
     depends_on('range-v3')
     depends_on('root +python +root7 +ssl +tbb +threads')
     depends_on('zlib')
 
-    # These dependencies are required by the Gaudi test suite
-    depends_on('aida', when='+tests')
-    depends_on('clhep', when='+tests')
-    depends_on('cppunit', when='+tests')
-    depends_on('gdb', when='+tests')
-    depends_on('gperftools', when='+tests')
-    depends_on('heppdt@:2.99.99', when='+tests')
-    depends_on('py-networkx', when='+tests')
-    depends_on('py-nose', when='+tests')
-    depends_on('py-setuptools', when='+tests')
-    depends_on('relax', when='+tests')
-    depends_on('xerces-c', when='+tests')
+    # todo: this should be a test dependency only,
+    # should be fixed in the cmake-modernisation branch
+    depends_on('py-nose', when="@develop", type=('build', 'run'))
 
     # Adding these dependencies triggers the build of most optional components
     depends_on('aida', when='+optional')
@@ -54,11 +64,16 @@ class Gaudi(CMakePackage):
     depends_on('cppunit', when='+optional')
     depends_on('doxygen +graphviz', when='+optional')
     depends_on('gperftools', when='+optional')
+    depends_on('gdb', when='+optional')
     depends_on('gsl', when='+optional')
     depends_on('heppdt@:2.99.99', when='+optional')
     depends_on('jemalloc', when='+optional')
     depends_on('libpng', when='+optional')
     depends_on('libunwind', when='+optional')
+    depends_on('py-networkx@:2.2', when='+optional ^python@:2.7.99')
+    depends_on('py-networkx', when='+optional ^python@3.0.0:')
+    depends_on('py-setuptools', when='+optional')
+    depends_on('py-nose', when='+optional')
     depends_on('relax', when='+optional')
     depends_on('xerces-c', when='+optional')
     # NOTE: pocl cannot be added as a minimal OpenCL implementation because
@@ -66,3 +81,33 @@ class Gaudi(CMakePackage):
 
     # The Intel VTune dependency is taken aside because it requires a license
     depends_on('intel-parallel-studio -mpi +vtune', when='+vtune')
+
+    def cmake_args(self):
+        args = [
+            self.define_from_variant("BUILD_TESTING", "optional"),
+            self.define_from_variant("GAUDI_USE_AIDA", "optional"),
+            self.define_from_variant("GAUDI_USE_XERCESC", "optional"),
+            self.define_from_variant("GAUDI_USE_CLHEP", "optional"),
+            self.define_from_variant("GAUDI_USE_HEPPDT", "optional"),
+            self.define_from_variant("GAUDI_USE_CPPUNIT", "optional"),
+            self.define_from_variant("GAUDI_USE_UNWIND", "optional"),
+            self.define_from_variant("GAUDI_USE_GPERFTOOLS", "optional"),
+            self.define_from_variant("GAUDI_USE_DOXYGEN", "optional"),
+            self.define_from_variant("GAUDI_USE_INTELAMPLIFIER", "optional"),
+            self.define_from_variant("GAUDI_USE_JEMALLOC", "optional"),
+            # this is not really used in spack builds, but needs to be set
+            "-DHOST_BINARY_TAG=x86_64-linux-gcc9-opt",
+        ]
+        return args
+
+    def setup_run_environment(self, env):
+        # environment as in Gaudi.xenv
+        env.prepend.path('PATH', self.prefix.scripts)
+        env.prepend.path('PYTHONPATH', self.prefix.python)
+        env.prepend.path('ROOT_INCLUDE_PATH', self.prefix.include)
+
+    def url_for_version(self, version):
+        major = str(version[0])
+        minor = str(version[1])
+        url = "https://gitlab.cern.ch/gaudi/Gaudi/-/archive/v{0}r{1}/Gaudi-v{0}r{1}.tar.gz".format(major, minor)
+        return url
diff --git a/var/spack/repos/builtin/packages/gaudi/python2.patch b/var/spack/repos/builtin/packages/gaudi/python2.patch
new file mode 100644
index 00000000000..8afcebc9291
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gaudi/python2.patch
@@ -0,0 +1,14 @@
+diff --git a/cmake/GaudiDependencies.cmake b/cmake/GaudiDependencies.cmake
+index 7fc224cef..0323f8e5c 100644
+--- a/cmake/GaudiDependencies.cmake
++++ b/cmake/GaudiDependencies.cmake
+@@ -97,7 +97,7 @@ foreach(component IN ITEMS system filesystem regex thread python unit_test_frame
+ endforeach()
+ 
+ set(Python_FIND_STRATEGY VERSION) # Find latest version available
+-find_package(Python 2.7.15 ${__quiet} COMPONENTS Interpreter Development)
++find_package(Python ${__quiet} COMPONENTS Interpreter Development)
+ set_package_properties(Python PROPERTIES TYPE REQUIRED)
+ 
+ find_package(ROOT 6.18 ${__quiet} CONFIG COMPONENTS Core RIO Hist Thread Matrix
+`
diff --git a/var/spack/repos/builtin/packages/podio/cpack.patch b/var/spack/repos/builtin/packages/podio/cpack.patch
new file mode 100644
index 00000000000..e685f9bc13d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/podio/cpack.patch
@@ -0,0 +1,11 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -86,7 +86,7 @@ include(cmake/podioMacros.cmake)
+ include(CTest)
+ 
+ #--- enable CPack --------------------------------------------------------------
+-include(cmake/podioCPack.cmake)
++#include(cmake/podioCPack.cmake)
+ 
+ #--- target for Doxygen documentation ------------------------------------------
+ if(CREATE_DOC)

From e575ba277314164870f5f562e1abde5f07731a26 Mon Sep 17 00:00:00 2001
From: vvolkl <valentin.volkl@cern.ch>
Date: Tue, 5 May 2020 02:41:19 +0200
Subject: [PATCH 244/802] bugfix: Update run-time dependencies of py-xenv
 (#16460)

Otherwise, if I run `xenv` after `spack load py-xenv` it fails with:
```
Traceback (most recent call last):
  File "/home/vavolkl/spack/opt/spack/linux-centos7-broadwell/gcc-8.3.0/py-xenv-develop_2018-12-20-lqbxakapsepqo5w3sjhhokj5o7c5jei2/bin/xenv", line 6, in <module>
    from pkg_resources import load_entry_point
ModuleNotFoundError: No module named 'pkg_resources'
```
---
 var/spack/repos/builtin/packages/py-xenv/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-xenv/package.py b/var/spack/repos/builtin/packages/py-xenv/package.py
index c52b71098a4..5047691cbd0 100644
--- a/var/spack/repos/builtin/packages/py-xenv/package.py
+++ b/var/spack/repos/builtin/packages/py-xenv/package.py
@@ -18,4 +18,4 @@ class PyXenv(PythonPackage):
     version('develop',            branch='master')
     version('develop_2018-12-20', commit='ddc3bf5e65e1689da499f639af7a27c5c4242841')
 
-    depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools', type=('build', 'run'))

From 76bd143c30759f7d510a4f646f5cba19e9c1b937 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <eafischer2@alaska.edu>
Date: Mon, 4 May 2020 20:44:23 -0400
Subject: [PATCH 245/802] libsecret (#16174)

* libsecret

* Update package.py

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
---
 var/spack/repos/builtin/packages/libsecret/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/libsecret/package.py b/var/spack/repos/builtin/packages/libsecret/package.py
index 8c41caf1c37..6302b9c69d3 100644
--- a/var/spack/repos/builtin/packages/libsecret/package.py
+++ b/var/spack/repos/builtin/packages/libsecret/package.py
@@ -25,6 +25,8 @@ class Libsecret(AutotoolsPackage):
     # Optional Vala support is not implemented yet
     # variant('vala', default=False, descript='Build with Vala support')
 
+    depends_on('pkgconfig', type='build')
+#    depends_on('mesa')
     # https://gitlab.gnome.org/GNOME/libsecret/blob/master/meson.build
     depends_on('glib@2.44:')
     depends_on('libgcrypt@1.2.2:', when='+gcrypt')

From 4c323e49bfa934d7103c2390ba3c313ef3d5bd93 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <eafischer2@alaska.edu>
Date: Mon, 4 May 2020 20:44:54 -0400
Subject: [PATCH 246/802] libspatialite: Update for proj@6 (#16173)

* libspatialite

* flake8

* Added proper version constrain

* Update var/spack/repos/builtin/packages/libspatialite/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/libspatialite/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../builtin/packages/libspatialite/package.py  | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/libspatialite/package.py b/var/spack/repos/builtin/packages/libspatialite/package.py
index 45fe1f6109c..2eb9b9df2f5 100644
--- a/var/spack/repos/builtin/packages/libspatialite/package.py
+++ b/var/spack/repos/builtin/packages/libspatialite/package.py
@@ -3,6 +3,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import os
 from spack import *
 
 
@@ -13,12 +14,25 @@ class Libspatialite(AutotoolsPackage):
     homepage = "http://www.gaia-gis.it"
     url      = "http://www.gaia-gis.it/gaia-sins/libspatialite-sources/libspatialite-4.3.0a.tar.gz"
 
-    version('4.3.0a', sha256='88900030a4762904a7880273f292e5e8ca6b15b7c6c3fb88ffa9e67ee8a5a499')
+    # Must download manually from:
+    #     https://www.gaia-gis.it/fossil/libspatialite/info/c7f67038bf06d98d
+    # For instructions on the file:// below..
+    #     https://github.com/spack/spack/issues/2489
+    version('5.0.0.2.c7f67038bf',
+        sha256='f8100f71b769c7db066c6f938af6b00e920e4b90ac14c00a4f3ed7171565caab',
+        url="file://%s/SpatiaLite-c7f67038bf.tar.gz" % os.getcwd())
+
+    version('5.0.0-beta0', sha256='caacf5378a5cfab9b8e98bb361e2b592e714e21f5c152b795df80d0ab1da1c42')
+    version('4.3.0a', preferred=True,
+            sha256='88900030a4762904a7880273f292e5e8ca6b15b7c6c3fb88ffa9e67ee8a5a499')
     version('3.0.1', sha256='4983d6584069fd5ff0cfcccccee1015088dab2db177c0dc7050ce8306b68f8e6')
 
     depends_on('pkgconfig', type='build')
     depends_on('sqlite+rtree')
-    depends_on('proj@:5')
+    depends_on('proj@:5', when='@:4.999.999')
+    # PROJ.6 is OK w/ newer versions
+    # https://www.gaia-gis.it/fossil/libspatialite/wiki?name=PROJ.6
+    depends_on('proj')
     depends_on('geos')
     depends_on('freexl')
     depends_on('iconv')

From b9ed788589d98f1c65f1659045439660ab5acafa Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Mon, 4 May 2020 23:42:17 -0500
Subject: [PATCH 247/802] py-shapely: add master version (#16465)

---
 .../builtin/packages/py-shapely/package.py     | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-shapely/package.py b/var/spack/repos/builtin/packages/py-shapely/package.py
index e609d610113..a6b2e8ceee1 100644
--- a/var/spack/repos/builtin/packages/py-shapely/package.py
+++ b/var/spack/repos/builtin/packages/py-shapely/package.py
@@ -12,6 +12,7 @@ class PyShapely(PythonPackage):
 
     homepage = "https://github.com/Toblerity/Shapely"
     url      = "https://pypi.io/packages/source/S/Shapely/Shapely-1.7.0.tar.gz"
+    git      = "https://github.com/Toblerity/Shapely.git"
 
     maintainers = ['adamjstewart']
     import_modules = [
@@ -19,10 +20,12 @@ class PyShapely(PythonPackage):
         'shapely.examples', 'shapely.speedups', 'shapely.vectorized',
     ]
 
+    version('master', branch='master')
     version('1.7.0', sha256='e21a9fe1a416463ff11ae037766fe410526c95700b9e545372475d2361cc951e')
     version('1.6.4.post2', sha256='c4b87bb61fc3de59fc1f85e71a79b0c709dc68364d9584473697aad4aa13240f')
     version('1.6.4', sha256='b10bc4199cfefcf1c0e5d932eac89369550320ca4bdf40559328d85f1ca4f655')
 
+    depends_on('python@3.5:', when='@1.8:', type=('build', 'run'))
     depends_on('python@2.7:2.8,3.4:', when='@1.7:', type=('build', 'run'))
     depends_on('python@2.6:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
@@ -33,13 +36,24 @@ class PyShapely(PythonPackage):
     depends_on('py-pytest', type='test')
     depends_on('py-pytest-cov', type='test')
 
+    # https://github.com/Toblerity/Shapely/pull/891
+    patch('https://github.com/Toblerity/Shapely/commit/98f6b36710bbe05b4ab59231cb0e08b06fe8b69c.patch',
+          sha256='4984cd0590beb5091f213948a953f70cea08ea11c5db1de07ba98c19e3d13f06')
+
     @when('^python@3.7:')
     def patch(self):
         # Python 3.7 changed the thread storage API, precompiled *.c files
         # need to be re-cythonized
-        os.remove('shapely/speedups/_speedups.c')
-        os.remove('shapely/vectorized/_vectorized.c')
+        if os.path.exists('shapely/speedups/_speedups.c'):
+            os.remove('shapely/speedups/_speedups.c')
+        if os.path.exists('shapely/vectorized/_vectorized.c'):
+            os.remove('shapely/vectorized/_vectorized.c')
 
     def setup_build_environment(self, env):
         env.set('GEOS_CONFIG',
                 join_path(self.spec['geos'].prefix.bin, 'geos-config'))
+
+    def test(self):
+        # Tests fail when 'geos' library not found in usual search directories
+        # python('-m', 'pytest')
+        pass

From 3ae76d8c1e7ca0cbe09af8bb98c67751b4e0572a Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Mon, 4 May 2020 23:10:25 -0700
Subject: [PATCH 248/802] bugfix: config:install_hash_length ignored (#15919)

---
 lib/spack/spack/directory_layout.py   |  1 +
 lib/spack/spack/test/config_values.py | 41 +++++++++++++++++++++++++++
 2 files changed, 42 insertions(+)
 create mode 100644 lib/spack/spack/test/config_values.py

diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index a2e871ee1a3..0f4c9663bae 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -190,6 +190,7 @@ def __init__(self, root, **kwargs):
             "{architecture}/"
             "{compiler.name}-{compiler.version}/"
             "{name}-{version}-{hash}")
+        self.path_scheme = self.path_scheme.lower()
         if self.hash_len is not None:
             if re.search(r'{hash:\d+}', self.path_scheme):
                 raise InvalidDirectoryLayoutParametersError(
diff --git a/lib/spack/spack/test/config_values.py b/lib/spack/spack/test/config_values.py
new file mode 100644
index 00000000000..ff97f26db42
--- /dev/null
+++ b/lib/spack/spack/test/config_values.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import spack.spec
+
+
+def test_set_install_hash_length(mock_packages, mutable_config, monkeypatch):
+    # spack.store.layout caches initial config values, so we monkeypatch
+    mutable_config.set('config:install_hash_length', 5)
+    monkeypatch.setattr(spack.store, 'store', spack.store._store())
+
+    spec = spack.spec.Spec('libelf').concretized()
+    prefix = spec.prefix
+    hash = prefix.rsplit('-')[-1]
+
+    assert len(hash) == 5
+
+    mutable_config.set('config:install_hash_length', 9)
+    monkeypatch.setattr(spack.store, 'store', spack.store._store())
+
+    spec = spack.spec.Spec('libelf').concretized()
+    prefix = spec.prefix
+    hash = prefix.rsplit('-')[-1]
+
+    assert len(hash) == 9
+
+
+def test_set_install_hash_length_upper_case(mock_packages, mutable_config,
+                                            monkeypatch):
+    # spack.store.layout caches initial config values, so we monkeypatch
+    mutable_config.set('config:install_path_scheme', '{name}-{HASH}')
+    mutable_config.set('config:install_hash_length', 5)
+    monkeypatch.setattr(spack.store, 'store', spack.store._store())
+
+    spec = spack.spec.Spec('libelf').concretized()
+    prefix = spec.prefix
+    hash = prefix.rsplit('-')[-1]
+
+    assert len(hash) == 5

From 04cb1800a69436c752c8479cf169c7eb47b606f4 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Tue, 5 May 2020 01:54:30 -0600
Subject: [PATCH 249/802] lammps: added v20200505 (#16463)

---
 var/spack/repos/builtin/packages/lammps/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/lammps/package.py b/var/spack/repos/builtin/packages/lammps/package.py
index 2e12378dc33..2320cf00504 100644
--- a/var/spack/repos/builtin/packages/lammps/package.py
+++ b/var/spack/repos/builtin/packages/lammps/package.py
@@ -21,6 +21,7 @@ class Lammps(CMakePackage, CudaPackage):
     tags = ['ecp', 'ecp-apps']
 
     version('master', branch='master')
+    version('20200505', sha256='c49d77fd602d28ebd8cf10f7359b9fc4d14668c72039028ed7792453d416de73')
     version('20200303', sha256='9aa56dfb8673a06e6c88588505ec1dfc01dd94f9d60e719ed0c605e48cc06c58')
     version('20200227', sha256='1aabcf38bc72285797c710b648e906151a912c36b634a9c88ac383aacf85516e')
     version('20200218', sha256='73bcf146660804ced954f6a0a8dce937482677778d46018ca5a688127bf97211')
@@ -106,6 +107,7 @@ def url_for_version(self, version):
     depends_on('libpng', when='+png')
     depends_on('ffmpeg', when='+ffmpeg')
     depends_on('kokkos+deprecated_code+shared@3.0', when='@20200303+kokkos')
+    depends_on('kokkos+shared@3.1:', when='@20200505:+kokkos')
 
     conflicts('+cuda', when='+opencl')
     conflicts('+body', when='+poems@:20180628')

From f1bb0f8aad511177c05f1b8c35c3e21521beaccf Mon Sep 17 00:00:00 2001
From: Benjamin Tovar <btovar@nd.edu>
Date: Tue, 5 May 2020 09:24:42 -0400
Subject: [PATCH 250/802] cctools to 7.1.5 (#16450)

* change homepage to readthedocs

* update cctools version to 7.1.5

* change http to https
---
 var/spack/repos/builtin/packages/cctools/package.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cctools/package.py b/var/spack/repos/builtin/packages/cctools/package.py
index 3f7a27081b6..ade997bbb89 100644
--- a/var/spack/repos/builtin/packages/cctools/package.py
+++ b/var/spack/repos/builtin/packages/cctools/package.py
@@ -12,9 +12,10 @@ class Cctools(AutotoolsPackage):
        machines from clusters, clouds, and grids.
     """
 
-    homepage = "https://github.com/cooperative-computing-lab/cctools"
-    url      = "https://github.com/cooperative-computing-lab/cctools/archive/release/7.1.3.tar.gz"
+    homepage = "https://cctools.readthedocs.io"
+    url      = "https://ccl.cse.nd.edu/software/files/cctools-7.1.5-source.tar.gz"
 
+    version('7.1.5', sha256='c01415fd47a1d9626b6c556e0dc0a6b0d3cd67224fa060cabd44ff78eede1d8a')
     version('7.1.3', sha256='b937878ab429dda31bc692e5d9ffb402b9eb44bb674c07a934bb769cee4165ba')
     version('7.1.2', sha256='ca871e9fe245d047d4c701271cf2b868e6e3a170e8834c1887157ed855985131')
     version('7.1.0', sha256='84748245db10ff26c0c0a7b9fd3ec20fbbb849dd4aadc5e8531fd1671abe7a81')

From c2791a4baa1bb7a46a1bd4448e7fe29ef827e082 Mon Sep 17 00:00:00 2001
From: vvolkl <valentin.volkl@cern.ch>
Date: Tue, 5 May 2020 15:25:26 +0200
Subject: [PATCH 251/802] [dd4hep] fix python setup (#16461)

---
 var/spack/repos/builtin/packages/dd4hep/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/dd4hep/package.py b/var/spack/repos/builtin/packages/dd4hep/package.py
index 66242973256..abfdb5d19c0 100644
--- a/var/spack/repos/builtin/packages/dd4hep/package.py
+++ b/var/spack/repos/builtin/packages/dd4hep/package.py
@@ -41,7 +41,7 @@ class Dd4hep(CMakePackage):
     depends_on('cmake @3.12:', type='build')
     depends_on('boost @1.49:')
     depends_on('root @6.08: +gdml +math +opengl +python +x')
-    depends_on('python')
+    extends('python')
     depends_on('xerces-c', when='+xercesc')
     depends_on('geant4@10.2.2:', when='+geant4')
 

From 33b129b919777623670d05592a8fc9704c02e1ee Mon Sep 17 00:00:00 2001
From: Tim Haines <thaines.astro@gmail.com>
Date: Tue, 5 May 2020 08:26:11 -0500
Subject: [PATCH 252/802] Boost: Add version 1.73.0 (#16442)

---
 .../repos/builtin/packages/boost/package.py    | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index 7baff3f28c5..aa4768e9548 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -25,6 +25,7 @@ class Boost(Package):
     maintainers = ['hainest']
 
     version('develop', branch='develop', submodules=True)
+    version('1.73.0', sha256='4eb3b8d442b426dc35346235c8733b5ae35ba431690e38c6a8263dce9fcbb402')
     version('1.72.0', sha256='59c9b274bc451cf91a9ba1dd2c7fdcaf5d60b1b3aa83f2c9fa143417cc660722')
     version('1.71.0', sha256='d73a8da01e8bf8c7eda40b4c84915071a8c8a0df4a6734537ddde4a8580524ee')
     version('1.70.0', sha256='430ae8354789de4fd19ee52f3b1f739e1fba576f0aded0897c3c2bc00fb38778')
@@ -125,7 +126,7 @@ def libs(self):
 
     variant('cxxstd',
             default='98',
-            values=('98', '11', '14', '17'),
+            values=('98', '11', '14', '17', '2a'),
             multi=False,
             description='Use the specified C++ standard when building.')
     variant('debug', default=False,
@@ -172,6 +173,9 @@ def libs(self):
     conflicts('cxxstd=98', when='+fiber')  # Fiber requires >=C++11.
     conflicts('~context', when='+fiber')  # Fiber requires Context.
 
+    # C++20/2a is not support by Boost < 1.73.0
+    conflicts('cxxstd=2a', when='@:1.72.99')
+
     # C++17 is not supported by Boost<1.63.0.
     conflicts('cxxstd=17', when='@:1.62.99')
 
@@ -231,6 +235,18 @@ def libs(self):
     patch('clang-linux_add_option.patch', when='@1.56.0:1.63.0')
     patch('clang-linux_add_option2.patch', when='@1.47.0:1.55.0')
 
+    # C++20 concepts fix for Beast
+    # See https://github.com/boostorg/beast/pull/1927 for details
+    patch('https://www.boost.org/patches/1_73_0/0002-beast-coroutines.patch',
+          sha256='4dd507e1f5a29e3b87b15321a4d8c74afdc8331433edabf7aeab89b3c405d556',
+          when='@1.73.0')
+
+    # Cloning a status_code with indirecting_domain leads to segmentation fault
+    # See https://github.com/ned14/outcome/issues/223 for details
+    patch('https://www.boost.org/patches/1_73_0/0001-outcome-assert.patch',
+          sha256='246508e052c44b6f4e8c2542a71c06cacaa72cd1447ab8d2a542b987bc35ace9',
+          when='@1.73.0')
+
     def url_for_version(self, version):
         if version >= Version('1.63.0'):
             url = "https://dl.bintray.com/boostorg/release/{0}/source/boost_{1}.tar.bz2"

From 6013060c609582c55d5408c3f0febc651040ea31 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Tue, 5 May 2020 08:48:23 -0700
Subject: [PATCH 253/802] WarpX: RZ + PSATD (#16464)

Add additionally required dependencies to WarpX that are needed
for transformations in RZ geometry with spectral (PSATD) solvers.
---
 var/spack/repos/builtin/packages/warpx/package.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/warpx/package.py b/var/spack/repos/builtin/packages/warpx/package.py
index 55cdf3cb13b..dc19f916fec 100644
--- a/var/spack/repos/builtin/packages/warpx/package.py
+++ b/var/spack/repos/builtin/packages/warpx/package.py
@@ -39,10 +39,12 @@ class Warpx(MakefilePackage):
     variant('openpmd', default=True, description='Enable openPMD I/O')
     variant('ascent', default=False, description='Enable Ascent in situ vis')
 
-    depends_on('cuda', when='backend=cuda')
+    depends_on('cuda@9.2.88:', when='backend=cuda')
     depends_on('mpi', when='+mpi')
     depends_on('fftw@3:', when='+psatd')
     depends_on('fftw +mpi', when='+psatd +mpi')
+    depends_on('blaspp', when='+psatd dims=rz')
+    depends_on('lapackpp', when='+psatd dims=rz')
     depends_on('pkgconfig', type='build', when='+openpmd')
     depends_on('python', type='build')  # AMReX' build system info
     depends_on('openpmd-api@0.11.0:,dev', when='+openpmd')

From 0e60ec7f1c0c295f6535de03485b63e0c7c91547 Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Tue, 5 May 2020 10:50:06 -0500
Subject: [PATCH 254/802] perl-bio-searchio-hmmer: new package at 1.7.3
 (#16281)

* perl-bio-searchio-hmmer: new package at 1.7.3

* perl-bio-searchio-hmmer: add dependencies
---
 .../perl-bio-searchio-hmmer/package.py         | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/perl-bio-searchio-hmmer/package.py

diff --git a/var/spack/repos/builtin/packages/perl-bio-searchio-hmmer/package.py b/var/spack/repos/builtin/packages/perl-bio-searchio-hmmer/package.py
new file mode 100644
index 00000000000..ae1c8c0c785
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-bio-searchio-hmmer/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlBioSearchioHmmer(PerlPackage):
+    """BioPerl parser to HMMER output."""
+
+    homepage = "https://github.com/bioperl/bio-searchio-hmmer"
+    url      = "https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/Bio-SearchIO-hmmer-1.7.3.tar.gz"
+
+    version('1.7.3', sha256='686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246')
+
+    depends_on('perl-bioperl', type=('build', 'run'))
+    depends_on('perl-io-string', type=('build', 'run'))

From 70c9dd37a7d63a5846ed373f6ff0c6df1ae7b2d5 Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Tue, 5 May 2020 10:51:59 -0500
Subject: [PATCH 255/802] exonerate-gff3: new package at 2.3.0 (#11830)

---
 .../packages/exonerate-gff3/package.py        | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/exonerate-gff3/package.py

diff --git a/var/spack/repos/builtin/packages/exonerate-gff3/package.py b/var/spack/repos/builtin/packages/exonerate-gff3/package.py
new file mode 100644
index 00000000000..87bc23e071f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/exonerate-gff3/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class ExonerateGff3(AutotoolsPackage):
+    """This is an exonerate fork with added gff3 support.
+       Original website with user guides:
+       http://www.ebi.ac.uk/~guy/exonerate/"""
+
+    homepage = "https://github.com/hotdogee/exonerate-gff3/"
+    url      = "https://github.com/hotdogee/exonerate-gff3/archive/2.3.0.tar.gz"
+
+    version('2.3.0', sha256='eeab7ea8bc815fc4a37d4c3b89c625167a9a60a4a833b5cc96e32dc313eafd1f')
+
+    depends_on('glib')
+
+    # parallel builds fail occasionally
+    parallel = False

From 2cb4ae747d6dba8817f67ae98d78c39883cb2cff Mon Sep 17 00:00:00 2001
From: Chris White <white238@llnl.gov>
Date: Tue, 5 May 2020 08:52:32 -0700
Subject: [PATCH 256/802] Add Axom spack package (#15432)

* Add OpenMP variant to Umpire

* Initial implementation of Axom package

* Add Axom spack package and fix required dependencies

* Fix overzealous tag replacement

* Attempt to fix version error

* Fix python version attempt #2

* Update raja and umpire

* remove sys_type check

* Address comments in axom package

* Address Greg's comments

* Fix flake8

* more flake8

* Simplify MPIEXEC and MPIEXEC_NUMPROC_FLAG

* Fix typo

* Revert back to slurm check, fix cuda_arch checks

* Fix cuda_arch variant forwarding

* Add cub variant

* Add py-shroud

* Address comments

* Fix shroud path in axom

* Fix merge conflict

* Fix backwards if

* Fix flake8 and add copyright

* format for consistency
---
 .../repos/builtin/packages/axom/package.py    | 515 ++++++++++++++++++
 .../repos/builtin/packages/conduit/package.py |  58 +-
 .../builtin/packages/py-shroud/package.py     |  23 +
 .../repos/builtin/packages/raja/package.py    |  19 +-
 .../repos/builtin/packages/umpire/package.py  |  35 +-
 5 files changed, 613 insertions(+), 37 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/axom/package.py
 create mode 100644 var/spack/repos/builtin/packages/py-shroud/package.py

diff --git a/var/spack/repos/builtin/packages/axom/package.py b/var/spack/repos/builtin/packages/axom/package.py
new file mode 100644
index 00000000000..84eeac28b93
--- /dev/null
+++ b/var/spack/repos/builtin/packages/axom/package.py
@@ -0,0 +1,515 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+import os
+import socket
+from os.path import join as pjoin
+
+import llnl.util.tty as tty
+
+
+def cmake_cache_entry(name, value, comment=""):
+    """Generate a string for a cmake cache variable"""
+    return 'set({0} "{1}" CACHE PATH "{2}")\n\n'.format(name, value, comment)
+
+
+def cmake_cache_option(name, boolean_value, comment=""):
+    """Generate a string for a cmake configuration option"""
+
+    value = "ON" if boolean_value else "OFF"
+    return 'set({0} {1} CACHE BOOL "{2}")\n\n'.format(name, value, comment)
+
+
+def get_spec_path(spec, package_name, path_replacements={}, use_bin=False):
+    """Extracts the prefix path for the given spack package
+       path_replacements is a dictionary with string replacements for the path.
+    """
+
+    if not use_bin:
+        path = spec[package_name].prefix
+    else:
+        path = spec[package_name].prefix.bin
+
+    path = os.path.realpath(path)
+
+    for key in path_replacements:
+        path = path.replace(key, path_replacements[key])
+
+    return path
+
+
+class Axom(CMakePackage, CudaPackage):
+    """Axom provides a robust, flexible software infrastructure for the development
+       of multi-physics applications and computational tools."""
+
+    maintainers = ['white238']
+
+    homepage = "https://github.com/LLNL/axom"
+    git      = "https://github.com/LLNL/axom.git"
+
+    version('master', branch='master', submodules=True)
+    version('develop', branch='develop', submodules=True)
+    version('0.3.3', tag='v0.3.3', submodules="True")
+    version('0.3.2', tag='v0.3.2', submodules="True")
+    version('0.3.1', tag='v0.3.1', submodules="True")
+    version('0.3.0', tag='v0.3.0', submodules="True")
+    version('0.2.9', tag='v0.2.9', submodules="True")
+
+    phases = ["hostconfig", "cmake", "build", "install"]
+    root_cmakelists_dir = 'src'
+
+    # -----------------------------------------------------------------------
+    # Variants
+    # -----------------------------------------------------------------------
+    variant('debug', default=False,
+            description='Build debug instead of optimized version')
+
+    variant('fortran', default=True, description="Build with Fortran support")
+
+    variant("python",   default=False, description="Build python support")
+
+    variant("mpi",      default=True, description="Build MPI support")
+    variant('openmp',   default=True, description='Turn on OpenMP support.')
+
+    variant("mfem",     default=False, description="Build with mfem")
+    variant("hdf5",     default=True, description="Build with hdf5")
+    variant("lua",      default=False, description="Build with Lua")
+    variant("scr",      default=False, description="Build with SCR")
+    variant("umpire",   default=True, description="Build with umpire")
+
+    variant("raja",     default=True, description="Build with raja")
+    variant("cub",     default=True,
+            description="Build with RAJA's internal CUB support")
+
+    varmsg = "Build development tools (such as Sphinx, Uncrustify, etc...)"
+    variant("devtools",  default=False, description=varmsg)
+
+    # -----------------------------------------------------------------------
+    # Dependencies
+    # -----------------------------------------------------------------------
+    # Basics
+    depends_on("cmake@3.8.2:", type='build')
+    depends_on("mpi", when="+mpi")
+
+    # Libraries
+    depends_on("conduit~shared+python", when="+python")
+    depends_on("conduit~shared~python", when="~python")
+    depends_on("conduit~shared+python+hdf5", when="+hdf5+python")
+    depends_on("conduit~shared+python~hdf5", when="~hdf5+python")
+    depends_on("conduit~shared~python+hdf5", when="+hdf5~python")
+    depends_on("conduit~shared~python~hdf5", when="~hdf5~python")
+
+    # HDF5 needs to be the same as Conduit's
+    depends_on("hdf5@1.8.19:1.8.999~mpi~cxx~shared~fortran", when="+hdf5")
+
+    depends_on("lua", when="+lua")
+
+    depends_on("scr", when="+scr")
+
+    depends_on("raja~openmp", when="+raja~openmp")
+    depends_on("raja+openmp", when="+raja+openmp")
+    depends_on("raja+cuda", when="+raja+cuda")
+
+    depends_on("umpire~openmp", when="+umpire~openmp")
+    depends_on("umpire+openmp", when="+umpire+openmp")
+    depends_on("umpire+cuda+deviceconst", when="+umpire+cuda")
+
+    for sm_ in CudaPackage.cuda_arch_values:
+        depends_on('raja cuda_arch={0}'.format(sm_),
+                   when='+raja cuda_arch={0}'.format(sm_))
+        depends_on('umpire cuda_arch={0}'.format(sm_),
+                   when='+umpire cuda_arch={0}'.format(sm_))
+
+    depends_on("mfem~mpi~hypre~metis~gzstream", when="+mfem")
+
+    depends_on("python", when="+python")
+
+    # Devtools
+    depends_on("cppcheck", when="+devtools")
+    depends_on("doxygen", when="+devtools")
+    depends_on("graphviz", when="+devtools")
+    depends_on("python", when="+devtools")
+    depends_on("py-sphinx", when="+devtools")
+    depends_on("py-shroud", when="+devtools")
+    depends_on("uncrustify@0.61", when="+devtools")
+
+    def _get_sys_type(self, spec):
+        sys_type = spec.architecture
+        # if on llnl systems, we can use the SYS_TYPE
+        if "SYS_TYPE" in env:
+            sys_type = env["SYS_TYPE"]
+        return sys_type
+
+    def _get_host_config_path(self, spec):
+        hostname = socket.gethostname()
+        if "SYS_TYPE" in env:
+            # Are we on a LLNL system then strip node number
+            hostname = hostname.rstrip('1234567890')
+        filename = "{0}-{1}-{2}.cmake".format(hostname,
+                                              self._get_sys_type(spec),
+                                              spec.compiler)
+        dest_dir = self.stage.source_path
+        fullpath = os.path.abspath(pjoin(dest_dir, filename))
+        return fullpath
+
+    def hostconfig(self, spec, prefix):
+        """
+        This method creates a 'host-config' file that specifies
+        all of the options used to configure and build Axom.
+        """
+
+        c_compiler   = env["SPACK_CC"]
+        cpp_compiler = env["SPACK_CXX"]
+        f_compiler   = None
+
+        # see if we should enable fortran support
+        if "SPACK_FC" in env.keys():
+            # even if this is set, it may not exist
+            # do one more sanity check
+            if os.path.isfile(env["SPACK_FC"]):
+                f_compiler  = env["SPACK_FC"]
+
+        # cmake
+        if "+cmake" in spec:
+            cmake_exe = pjoin(spec['cmake'].prefix.bin, "cmake")
+        else:
+            cmake_exe = which("cmake")
+            if cmake_exe is None:
+                # error could not find cmake!
+                crash()
+            cmake_exe = cmake_exe.command
+        cmake_exe = os.path.realpath(cmake_exe)
+
+        host_config_path = self._get_host_config_path(spec)
+        cfg = open(host_config_path, "w")
+        cfg.write("#------------------{0}\n".format("-" * 60))
+        cfg.write("# !!!! This is a generated file, edit at own risk !!!!\n")
+        cfg.write("#------------------{0}\n".format("-" * 60))
+        cfg.write("# SYS_TYPE: {0}\n".format(self._get_sys_type(spec)))
+        cfg.write("# Compiler Spec: {0}\n".format(spec.compiler))
+        cfg.write("#------------------{0}\n".format("-" * 60))
+        # show path to cmake for reference and to be used by config-build.py
+        cfg.write("# CMake executable path: {0}\n".format(cmake_exe))
+        cfg.write("#------------------{0}\n\n".format("-" * 60))
+
+        # compiler settings
+        cfg.write("#------------------{0}\n".format("-" * 60))
+        cfg.write("# Compilers\n")
+        cfg.write("#------------------{0}\n\n".format("-" * 60))
+
+        cfg.write(cmake_cache_entry("CMAKE_C_COMPILER", c_compiler))
+        cfg.write(cmake_cache_entry("CMAKE_CXX_COMPILER", cpp_compiler))
+
+        if "+fortran" in spec or f_compiler is not None:
+            cfg.write(cmake_cache_option("ENABLE_FORTRAN", True))
+            cfg.write(cmake_cache_entry("CMAKE_Fortran_COMPILER", f_compiler))
+        else:
+            cfg.write(cmake_cache_option("ENABLE_FORTRAN", False))
+
+        # TPL locations
+        cfg.write("#------------------{0}\n".format("-" * 60))
+        cfg.write("# TPLs\n")
+        cfg.write("#------------------{0}\n\n".format("-" * 60))
+
+        # Try to find the common prefix of the TPL directory, including the
+        # compiler. If found, we will use this in the TPL paths
+        compiler_str = str(spec.compiler).replace('@', '-')
+        prefix_paths = prefix.split(compiler_str)
+        path_replacements = {}
+
+        if len(prefix_paths) == 2:
+            tpl_root = os.path.realpath(pjoin(prefix_paths[0], compiler_str))
+            path_replacements[tpl_root] = "${TPL_ROOT}"
+            cfg.write("# Root directory for generated TPLs\n")
+            cfg.write(cmake_cache_entry("TPL_ROOT", tpl_root))
+
+        conduit_dir = get_spec_path(spec, "conduit", path_replacements)
+        cfg.write(cmake_cache_entry("CONDUIT_DIR", conduit_dir))
+
+        # optional tpls
+
+        if "+mfem" in spec:
+            mfem_dir = get_spec_path(spec, "mfem", path_replacements)
+            cfg.write(cmake_cache_entry("MFEM_DIR", mfem_dir))
+        else:
+            cfg.write("# MFEM not built\n\n")
+
+        if "+hdf5" in spec:
+            hdf5_dir = get_spec_path(spec, "hdf5", path_replacements)
+            cfg.write(cmake_cache_entry("HDF5_DIR", hdf5_dir))
+        else:
+            cfg.write("# HDF5 not built\n\n")
+
+        if "+lua" in spec:
+            lua_dir = get_spec_path(spec, "lua", path_replacements)
+            cfg.write(cmake_cache_entry("LUA_DIR", lua_dir))
+        else:
+            cfg.write("# Lua not built\n\n")
+
+        if "+scr" in spec:
+            scr_dir = get_spec_path(spec, "scr", path_replacements)
+            cfg.write(cmake_cache_entry("SCR_DIR", scr_dir))
+        else:
+            cfg.write("# SCR not built\n\n")
+
+        if "+raja" in spec:
+            raja_dir = get_spec_path(spec, "raja", path_replacements)
+            cfg.write(cmake_cache_entry("RAJA_DIR", raja_dir))
+        else:
+            cfg.write("# RAJA not built\n\n")
+
+        if "+umpire" in spec:
+            umpire_dir = get_spec_path(spec, "umpire", path_replacements)
+            cfg.write(cmake_cache_entry("UMPIRE_DIR", umpire_dir))
+        else:
+            cfg.write("# Umpire not built\n\n")
+
+        cfg.write("#------------------{0}\n".format("-" * 60))
+        cfg.write("# MPI\n")
+        cfg.write("#------------------{0}\n\n".format("-" * 60))
+
+        if "+mpi" in spec:
+            cfg.write(cmake_cache_option("ENABLE_MPI", True))
+            cfg.write(cmake_cache_entry("MPI_C_COMPILER", spec['mpi'].mpicc))
+            cfg.write(cmake_cache_entry("MPI_CXX_COMPILER",
+                                        spec['mpi'].mpicxx))
+            if "+fortran" in spec or f_compiler is not None:
+                cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER",
+                                            spec['mpi'].mpifc))
+
+            # Check for slurm
+            using_slurm = False
+            slurm_checks = ['+slurm',
+                            'schedulers=slurm',
+                            'process_managers=slurm']
+            if any(spec['mpi'].satisfies(variant) for variant in slurm_checks):
+                using_slurm = True
+
+            # Determine MPIEXEC
+            if using_slurm:
+                if spec['mpi'].external:
+                    mpiexec = '/usr/bin/srun'
+                else:
+                    mpiexec = os.path.join(spec['slurm'].prefix.bin, 'srun')
+            else:
+                mpiexec = os.path.join(spec['mpi'].prefix.bin, 'mpirun')
+                if not os.path.exists(mpiexec):
+                    mpiexec = os.path.join(spec['mpi'].prefix.bin, 'mpiexec')
+
+            if not os.path.exists(mpiexec):
+                msg = "Unable to determine MPIEXEC, Axom tests may fail"
+                cfg.write("# {0}\n\n".format(msg))
+                tty.msg(msg)
+            else:
+                # starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE
+                # vs the older versions which expect MPIEXEC
+                if self.spec["cmake"].satisfies('@3.10:'):
+                    cfg.write(cmake_cache_entry("MPIEXEC_EXECUTABLE", mpiexec))
+                else:
+                    cfg.write(cmake_cache_entry("MPIEXEC", mpiexec))
+
+            # Determine MPIEXEC_NUMPROC_FLAG
+            if using_slurm:
+                cfg.write(cmake_cache_entry("MPIEXEC_NUMPROC_FLAG", "-n"))
+            else:
+                cfg.write(cmake_cache_entry("MPIEXEC_NUMPROC_FLAG", "-np"))
+
+            if spec['mpi'].name == 'spectrum-mpi':
+                cfg.write(cmake_cache_entry("BLT_MPI_COMMAND_APPEND",
+                                            "mpibind"))
+        else:
+            cfg.write(cmake_cache_option("ENABLE_MPI", False))
+
+        ##################################
+        # Devtools
+        ##################################
+
+        cfg.write("#------------------{0}\n".format("-" * 60))
+        cfg.write("# Devtools\n")
+        cfg.write("#------------------{0}\n\n".format("-" * 60))
+
+        # Add common prefix to path replacement list
+        if "+devtools" in spec:
+            # Grab common devtools root and strip the trailing slash
+            path1 = os.path.realpath(spec["uncrustify"].prefix)
+            path2 = os.path.realpath(spec["doxygen"].prefix)
+            devtools_root = os.path.commonprefix([path1, path2])[:-1]
+            path_replacements[devtools_root] = "${DEVTOOLS_ROOT}"
+            cfg.write("# Root directory for generated developer tools\n")
+            cfg.write(cmake_cache_entry("DEVTOOLS_ROOT", devtools_root))
+
+        if "+python" in spec or "+devtools" in spec:
+            python_path = os.path.realpath(spec['python'].command.path)
+            for key in path_replacements:
+                python_path = python_path.replace(key, path_replacements[key])
+            cfg.write(cmake_cache_entry("PYTHON_EXECUTABLE", python_path))
+
+        if "doxygen" in spec or "py-sphinx" in spec:
+            cfg.write(cmake_cache_option("ENABLE_DOCS", True))
+
+            if "doxygen" in spec:
+                doxygen_bin_dir = get_spec_path(spec, "doxygen",
+                                                path_replacements,
+                                                use_bin=True)
+                cfg.write(cmake_cache_entry("DOXYGEN_EXECUTABLE",
+                                            pjoin(doxygen_bin_dir,
+                                                  "doxygen")))
+
+            if "py-sphinx" in spec:
+                python_bin_dir = get_spec_path(spec, "python",
+                                               path_replacements,
+                                               use_bin=True)
+                cfg.write(cmake_cache_entry("SPHINX_EXECUTABLE",
+                                            pjoin(python_bin_dir,
+                                                  "sphinx-build")))
+        else:
+            cfg.write(cmake_cache_option("ENABLE_DOCS", False))
+
+        if "py-shroud" in spec:
+            shroud_bin_dir = get_spec_path(spec, "py-shroud",
+                                           path_replacements, use_bin=True)
+            cfg.write(cmake_cache_entry("SHROUD_EXECUTABLE",
+                                        pjoin(shroud_bin_dir, "shroud")))
+
+        if "uncrustify" in spec:
+            uncrustify_bin_dir = get_spec_path(spec, "uncrustify",
+                                               path_replacements,
+                                               use_bin=True)
+            cfg.write(cmake_cache_entry("UNCRUSTIFY_EXECUTABLE",
+                                        pjoin(uncrustify_bin_dir,
+                                              "uncrustify")))
+
+        if "cppcheck" in spec:
+            cppcheck_bin_dir = get_spec_path(spec, "cppcheck",
+                                             path_replacements, use_bin=True)
+            cfg.write(cmake_cache_entry("CPPCHECK_EXECUTABLE",
+                                        pjoin(cppcheck_bin_dir, "cppcheck")))
+
+        ##################################
+        # Other machine specifics
+        ##################################
+
+        cfg.write("#------------------{0}\n".format("-" * 60))
+        cfg.write("# Other machine specifics\n")
+        cfg.write("#------------------{0}\n\n".format("-" * 60))
+
+        # OpenMP
+        if "+openmp" in spec:
+            cfg.write(cmake_cache_option("ENABLE_OPENMP", True))
+        else:
+            cfg.write(cmake_cache_option("ENABLE_OPENMP", False))
+
+        # Enable death tests
+        if spec.satisfies('target=ppc64le:') and "+cuda" in spec:
+            cfg.write(cmake_cache_option("ENABLE_GTEST_DEATH_TESTS", False))
+        else:
+            cfg.write(cmake_cache_option("ENABLE_GTEST_DEATH_TESTS", True))
+
+        # Override XL compiler family
+        familymsg = ("Override to proper compiler family for XL")
+        if "xlf" in f_compiler:
+            cfg.write(cmake_cache_entry("CMAKE_Fortran_COMPILER_ID", "XL",
+                                        familymsg))
+        if "xlc" in c_compiler:
+            cfg.write(cmake_cache_entry("CMAKE_C_COMPILER_ID", "XL",
+                                        familymsg))
+        if "xlC" in cpp_compiler:
+            cfg.write(cmake_cache_entry("CMAKE_CXX_COMPILER_ID", "XL",
+                                        familymsg))
+
+        if spec.satisfies('target=ppc64le:'):
+            if "xlf" in f_compiler:
+                description = ("Converts C-style comments to Fortran style "
+                               "in preprocessed files")
+                cfg.write(cmake_cache_entry("BLT_FORTRAN_FLAGS",
+                                            "-WF,-C!  -qxlf2003=polymorphic",
+                                            description))
+                # Grab lib directory for the current fortran compiler
+                libdir = os.path.join(os.path.dirname(
+                                      os.path.dirname(f_compiler)), "lib")
+                description = ("Adds a missing rpath for libraries "
+                               "associated with the fortran compiler")
+                cfg.write(cmake_cache_entry("BLT_EXE_LINKER_FLAGS",
+                                            "-Wl,-rpath," + libdir,
+                                            description))
+
+            if "+cuda" in spec:
+                cfg.write("#------------------{0}\n".format("-" * 60))
+                cfg.write("# Cuda\n")
+                cfg.write("#------------------{0}\n\n".format("-" * 60))
+
+                cfg.write(cmake_cache_option("ENABLE_CUDA", True))
+
+                cudatoolkitdir = spec['cuda'].prefix
+                cfg.write(cmake_cache_entry("CUDA_TOOLKIT_ROOT_DIR",
+                                            cudatoolkitdir))
+                cudacompiler = "${CUDA_TOOLKIT_ROOT_DIR}/bin/nvcc"
+                cfg.write(cmake_cache_entry("CMAKE_CUDA_COMPILER",
+                                            cudacompiler))
+
+                cfg.write(cmake_cache_option("CUDA_SEPARABLE_COMPILATION",
+                                             True))
+
+                cfg.write(cmake_cache_option("AXOM_ENABLE_ANNOTATIONS", True))
+
+                if "+cub" in spec:
+                    cfg.write(cmake_cache_option("AXOM_ENABLE_CUB", True))
+                else:
+                    cfg.write(cmake_cache_option("AXOM_ENABLE_CUB", False))
+
+                # CUDA_FLAGS
+                cudaflags  = "-restrict "
+
+                if not spec.satisfies('cuda_arch=none'):
+                    cuda_arch = spec.variants['cuda_arch'].value
+                    axom_arch = 'sm_{0}'.format(cuda_arch[0])
+                    cfg.write(cmake_cache_entry("AXOM_CUDA_ARCH", axom_arch))
+                    cudaflags += "-arch ${AXOM_CUDA_ARCH} "
+                else:
+                    cfg.write("# cuda_arch could not be determined\n\n")
+
+                cudaflags += "-std=c++11 --expt-extended-lambda -G "
+                cfg.write(cmake_cache_entry("CMAKE_CUDA_FLAGS", cudaflags))
+
+                if "+mpi" in spec:
+                    cfg.write(cmake_cache_entry("CMAKE_CUDA_HOST_COMPILER",
+                                                "${MPI_CXX_COMPILER}"))
+                else:
+                    cfg.write(cmake_cache_entry("CMAKE_CUDA_HOST_COMPILER",
+                                                "${CMAKE_CXX_COMPILER}"))
+
+                cfg.write("# nvcc does not like gtest's 'pthreads' flag\n")
+                cfg.write(cmake_cache_option("gtest_disable_pthreads", True))
+
+        if ("gfortran" in f_compiler) and ("clang" in cpp_compiler):
+            clanglibdir = pjoin(os.path.dirname(
+                                os.path.dirname(cpp_compiler)), "lib")
+            flags = "-Wl,-rpath,{0}".format(clanglibdir)
+            description = ("Adds a missing rpath for libraries "
+                           "associated with the fortran compiler")
+            cfg.write(cmake_cache_entry("BLT_EXE_LINKER_FLAGS", flags,
+                                        description))
+
+        cfg.write("\n")
+        cfg.close()
+        tty.info("Spack generated Axom host-config file: " + host_config_path)
+
+    def cmake_args(self):
+        spec = self.spec
+        host_config_path = self._get_host_config_path(spec)
+
+        options = []
+        options.extend(['-C', host_config_path])
+        if self.run_tests is False:
+            options.append('-DENABLE_TESTS=OFF')
+        else:
+            options.append('-DENABLE_TESTS=ON')
+        return options
+
+    @run_after('install')
+    def install_cmake_cache(self):
+        install(self._get_host_config_path(spec), prefix)
diff --git a/var/spack/repos/builtin/packages/conduit/package.py b/var/spack/repos/builtin/packages/conduit/package.py
index ed1bd4f3d31..2e6ec094091 100644
--- a/var/spack/repos/builtin/packages/conduit/package.py
+++ b/var/spack/repos/builtin/packages/conduit/package.py
@@ -285,8 +285,10 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
         f_compiler = None
 
         if self.compiler.fc:
-            # even if this is set, it may not exist so do one more sanity check
-            f_compiler = which(env["SPACK_FC"])
+            # even if this is set, it may not exist
+            # do one more sanity check
+            if os.path.isfile(env["SPACK_FC"]):
+                f_compiler  = env["SPACK_FC"]
 
         #######################################################################
         # By directly fetching the names of the actual compilers we appear
@@ -299,6 +301,9 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
         if "SYS_TYPE" in env:
             sys_type = env["SYS_TYPE"]
 
+        # are we on a specific machine
+        on_blueos = 'blueos' in sys_type
+
         ##############################################
         # Find and record what CMake is used
         ##############################################
@@ -335,7 +340,7 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
         if "+fortran" in spec and f_compiler is not None:
             cfg.write(cmake_cache_entry("ENABLE_FORTRAN", "ON"))
             cfg.write(cmake_cache_entry("CMAKE_Fortran_COMPILER",
-                                        f_compiler.path))
+                                        f_compiler))
         else:
             cfg.write("# no fortran compiler found\n\n")
             cfg.write(cmake_cache_entry("ENABLE_FORTRAN", "OFF"))
@@ -345,16 +350,6 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
         else:
             cfg.write(cmake_cache_entry("BUILD_SHARED_LIBS", "OFF"))
 
-        # extra fun for blueos
-        if 'blueos_3' in sys_type and "+fortran" in spec:
-            if 'xl@coral' in os.getenv('SPACK_COMPILER_SPEC', ""):
-                # Fix missing std linker flag in xlc compiler
-                cfg.write(cmake_cache_entry("BLT_FORTRAN_FLAGS",
-                                            "-WF,-C! -qxlf2003=polymorphic"))
-                # Conduit can't link C++ into fortran for this spec, but works
-                # fine in host code
-                cfg.write(cmake_cache_entry("ENABLE_TESTS", "OFF"))
-
         #######################
         # Unit Tests
         #######################
@@ -363,6 +358,32 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
         else:
             cfg.write(cmake_cache_entry("ENABLE_TESTS", "OFF"))
 
+        # extra fun for blueos
+        if on_blueos:
+            # All of BlueOS compilers report clang due to nvcc,
+            # override to proper compiler family
+            if "xlc" in c_compiler:
+                cfg.write(cmake_cache_entry("CMAKE_C_COMPILER_ID", "XL"))
+            if "xlC" in cpp_compiler:
+                cfg.write(cmake_cache_entry("CMAKE_CXX_COMPILER_ID", "XL"))
+
+            if "+fortran" in spec:
+                if "xlf" in f_compiler:
+                    cfg.write(cmake_cache_entry("CMAKE_Fortran_COMPILER_ID",
+                                                "XL"))
+
+                if 'xl@coral' in os.getenv('SPACK_COMPILER_SPEC', ""):
+                    # Fix missing std linker flag in xlc compiler
+                    flags = "-WF,-C! -qxlf2003=polymorphic"
+                    cfg.write(cmake_cache_entry("BLT_FORTRAN_FLAGS",
+                                                flags))
+                    # Grab lib directory for the current fortran compiler
+                    libdir = os.path.join(os.path.dirname(
+                                          os.path.dirname(f_compiler)), "lib")
+                    flags = "-lstdc++ -Wl,-rpath," + libdir
+                    cfg.write(cmake_cache_entry("BLT_EXE_LINKER_FLAGS",
+                                                flags))
+
         #######################
         # Python
         #######################
@@ -419,7 +440,10 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
             cfg.write(cmake_cache_entry("ENABLE_MPI", "ON"))
             cfg.write(cmake_cache_entry("MPI_C_COMPILER", mpicc_path))
             cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", mpicxx_path))
-            cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", mpifc_path))
+            if "+fortran" in spec:
+                cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER",
+                                            mpifc_path))
+
             mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec')
             if os.path.isfile(mpiexe_bin):
                 # starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE
@@ -456,12 +480,6 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
 
         if "+hdf5" in spec:
             cfg.write(cmake_cache_entry("HDF5_DIR", spec['hdf5'].prefix))
-            # extra fun for BG/Q
-            if 'bgqos_0' in sys_type:
-                cfg.write(cmake_cache_entry('HDF5_C_LIBRARY_m',
-                                            '-lm', 'STRING'))
-                cfg.write(cmake_cache_entry('HDF5_C_LIBRARY_dl',
-                                            '-ldl', 'STRING'))
         else:
             cfg.write("# hdf5 not built by spack \n")
 
diff --git a/var/spack/repos/builtin/packages/py-shroud/package.py b/var/spack/repos/builtin/packages/py-shroud/package.py
new file mode 100644
index 00000000000..504c992f156
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-shroud/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyShroud(PythonPackage):
+    """Create Fortran wrappers for a C++ library."""
+
+    homepage = "https://github.com/LLNL/shroud"
+    git      = "https://github.com/LLNL/shroud.git"
+
+    version('develop', branch='develop')
+    version('master',  branch='master')
+    version('0.11.0', tag='v0.11.0')
+    version('0.10.1', tag='v0.10.1')
+    version('0.9.0', tag='v0.9.0')
+    version('0.8.0', tag='v0.8.0')
+
+    depends_on("py-setuptools", type='build')
+    depends_on("py-pyyaml@4.2b1:", type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/raja/package.py b/var/spack/repos/builtin/packages/raja/package.py
index 10a9265257b..de9652dbc1e 100644
--- a/var/spack/repos/builtin/packages/raja/package.py
+++ b/var/spack/repos/builtin/packages/raja/package.py
@@ -15,6 +15,7 @@ class Raja(CMakePackage, CudaPackage):
     version('develop', branch='develop', submodules='True')
     version('master',  branch='master',  submodules='True')
     version('0.11.0', tag='v0.11.0', submodules="True")
+    version('0.10.1', tag='v0.10.1', submodules="True")
     version('0.10.0', tag='v0.10.0', submodules="True")
     version('0.9.0', tag='v0.9.0', submodules="True")
     version('0.8.0', tag='v0.8.0', submodules="True")
@@ -27,11 +28,8 @@ class Raja(CMakePackage, CudaPackage):
     version('0.4.1', tag='v0.4.1', submodules="True")
     version('0.4.0', tag='v0.4.0', submodules="True")
 
-    variant('cuda', default=False, description='Build with CUDA backend')
     variant('openmp', default=True, description='Build OpenMP backend')
 
-    depends_on('cuda', when='+cuda')
-
     depends_on('cmake@3.8:', type='build')
     depends_on('cmake@3.9:', when='+cuda', type='build')
 
@@ -47,9 +45,16 @@ def cmake_args(self):
                 '-DENABLE_CUDA=On',
                 '-DCUDA_TOOLKIT_ROOT_DIR=%s' % (spec['cuda'].prefix)])
 
-            cuda_value = spec.variants['cuda_arch'].value
-            cuda_arch = cuda_value[0]
-            if cuda_arch is not None:
-                options.append('-DCUDA_ARCH=sm_{0}'.format(cuda_arch))
+            if not spec.satisfies('cuda_arch=none'):
+                cuda_arch = spec.variants['cuda_arch'].value
+                options.append('-DCUDA_ARCH=sm_{0}'.format(cuda_arch[0]))
+
+        # Work around spack adding -march=ppc64le to SPACK_TARGET_ARGS which
+        # is used by the spack compiler wrapper.  This can go away when BLT
+        # removes -Werror from GTest flags
+        if self.spec.satisfies('%clang target=ppc64le:') or not self.run_tests:
+            options.append('-DENABLE_TESTS=OFF')
+        else:
+            options.append('-DENABLE_TESTS=ON')
 
         return options
diff --git a/var/spack/repos/builtin/packages/umpire/package.py b/var/spack/repos/builtin/packages/umpire/package.py
index 90ea23dde31..fb6b779d1b3 100644
--- a/var/spack/repos/builtin/packages/umpire/package.py
+++ b/var/spack/repos/builtin/packages/umpire/package.py
@@ -7,7 +7,7 @@
 from spack import *
 
 
-class Umpire(CMakePackage):
+class Umpire(CMakePackage, CudaPackage):
     """An application-focused API for memory management on NUMA & GPU
     architectures"""
 
@@ -35,12 +35,13 @@ class Umpire(CMakePackage):
     version('0.1.4', tag='v0.1.4', submodules='True')
     version('0.1.3', tag='v0.1.3', submodules='True')
 
-    variant('cuda', default=False, description='Build with CUDA support')
-    variant('fortran', default=False, description='Build Fortran API')
+    variant('fortran', default=False, description='Build C/Fortran API')
     variant('c', default=True, description='Build C API')
     variant('numa', default=False, description='Enable NUMA support')
+    variant('openmp', default=False, description='Build with OpenMP support')
+    variant('deviceconst', default=False,
+            description='Enables support for constant device memory')
 
-    depends_on('cuda', when='+cuda')
     depends_on('cmake@3.8:', type='build')
     depends_on('cmake@3.9:', when='+cuda', type='build')
 
@@ -56,16 +57,30 @@ def cmake_args(self):
             options.extend([
                 '-DENABLE_CUDA=On',
                 '-DCUDA_TOOLKIT_ROOT_DIR=%s' % (spec['cuda'].prefix)])
+
+            if not spec.satisfies('cuda_arch=none'):
+                cuda_arch = spec.variants['cuda_arch'].value
+                flag = '-arch sm_{0}'.format(cuda_arch[0])
+                options.append('-DCMAKE_CUDA_FLAGS:STRING={0}'.format(flag))
+
+            if '+deviceconst' in spec:
+                options.append('-DENABLE_DEVICE_CONST=On')
         else:
             options.append('-DENABLE_CUDA=Off')
 
-        if '+c' in spec:
-            options.append('-DENABLE_C=On')
+        options.append('-DENABLE_C={0}'.format(
+            'On' if '+c' in spec else 'Off'))
 
-        if '+fortran' in spec:
-            options.append('-DENABLE_FORTRAN=On')
+        options.append('-DENABLE_FORTRAN={0}'.format(
+            'On' if '+fortran' in spec else 'Off'))
 
-        if '+numa' in spec:
-            options.append('-DENABLE_NUMA=On')
+        options.append('-DENABLE_NUMA={0}'.format(
+            'On' if '+numa' in spec else 'Off'))
+
+        options.append('-DENABLE_OPENMP={0}'.format(
+            'On' if '+openmp' in spec else 'Off'))
+
+        options.append('-DENABLE_TESTS={0}'.format(
+            'On' if self.run_tests else 'Off'))
 
         return options

From ff3769e2e2db7d0b6e2620ff78fdefa9f0386ed9 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Tue, 5 May 2020 10:59:28 -0600
Subject: [PATCH 257/802] cabana: add v0.3.0 & shared variant (#16466)

---
 var/spack/repos/builtin/packages/cabana/package.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/cabana/package.py b/var/spack/repos/builtin/packages/cabana/package.py
index b3bc87c061d..53ae6086445 100644
--- a/var/spack/repos/builtin/packages/cabana/package.py
+++ b/var/spack/repos/builtin/packages/cabana/package.py
@@ -14,6 +14,7 @@ class Cabana(CMakePackage):
     url      = "https://github.com/ECP-copa/Cabana/archive/0.1.0.tar.gz"
 
     version('master', branch='master')
+    version('0.3.0', sha256='fb67ab9aaf254b103ae0eb5cc913ddae3bf3cd0cf6010e9686e577a2981ca84f')
     version('0.2.0', sha256='3e0c0e224e90f4997f6c7e2b92f00ffa18f8bcff72f789e0908cea0828afc2cb')
     version('0.1.0', sha256='3280712facf6932b9d1aff375b24c932abb9f60a8addb0c0a1950afd0cb9b9cf')
     version('0.1.0-rc0', sha256='73754d38aaa0c2a1e012be6959787108fec142294774c23f70292f59c1bdc6c5')
@@ -21,6 +22,7 @@ class Cabana(CMakePackage):
     variant('serial', default=True, description="enable Serial backend (default)")
     variant('openmp', default=False, description="enable OpenMP backend")
     variant('cuda', default=False, description="enable Cuda backend")
+    variant('shared', default=True, description='Build shared libraries')
 
     depends_on("cmake@3.9:", type='build')
     depends_on("kokkos-legacy+serial", when="@:0.2.0+serial")
@@ -38,7 +40,9 @@ def cmake_args(self):
             '-DCabana_ENABLE_OpenMP=%s'  % (
                 'On' if '+openmp'  in self.spec else 'Off'),
             '-DCabana_ENABLE_Cuda=%s'  % (
-                'On' if '+cuda'  in self.spec else 'Off')
+                'On' if '+cuda'  in self.spec else 'Off'),
+            '-DBUILD_SHARED_LIBS=%s' % (
+                'On' if '+shared'  in self.spec else 'Off')
         ]
 
         return options

From de71b2828f1813e7cb4b1ae556aee0a78850a3e1 Mon Sep 17 00:00:00 2001
From: Jennifer Green <jgreen@lanl.gov>
Date: Tue, 5 May 2020 12:02:49 -0600
Subject: [PATCH 258/802] CMake: Cray XC40 system errors bootstrapping CMake
 (#16459)

* CMake: fix https://github.com/spack/spack/issues/16453 with a patch addressing both libhugetlbfs and icpc warnings on Cray XC40 systems

* Including CMake v3.17.2 in the patched versions
---
 .../packages/cmake/ignore_crayxc_warnings.patch       | 11 +++++++++++
 var/spack/repos/builtin/packages/cmake/package.py     |  5 +++++
 2 files changed, 16 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/cmake/ignore_crayxc_warnings.patch

diff --git a/var/spack/repos/builtin/packages/cmake/ignore_crayxc_warnings.patch b/var/spack/repos/builtin/packages/cmake/ignore_crayxc_warnings.patch
new file mode 100644
index 00000000000..85928f0e84e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cmake/ignore_crayxc_warnings.patch
@@ -0,0 +1,11 @@
+diff --git a/Source/Checks/cm_cxx_features.cmake b/Source/Checks/cm_cxx_features.cmake
+index fb68ed78c9..c6c1ba667f 100644
+--- a/Source/Checks/cm_cxx_features.cmake
++++ b/Source/Checks/cm_cxx_features.cmake
+@@ -17,2 +17,6 @@ function(cm_check_cxx_feature name)
+     set(check_output "${OUTPUT}")
++    # Filter out libhugetlbfs warnings
++    string(REGEX REPLACE "[^\n]*libhugetlbfs [^\n]*: WARNING[^\n]*" "" check_output "${check_output}")
++    # Filter out icpc warnings
++    string(REGEX REPLACE "[^\n]*icpc: command line warning #10121: overriding [^\n]*" "" check_output "${check_output}")
+     # Filter out MSBuild output that looks like a warning.
diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index 833573bf80e..acf5b1fcdc3 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -132,6 +132,11 @@ class Cmake(Package):
     # https://gitlab.kitware.com/cmake/cmake/issues/18232
     patch('nag-response-files.patch', when='@3.7:3.12')
 
+    # Cray libhugetlbfs and icpc warnings failing CXX tests
+    # https://gitlab.kitware.com/cmake/cmake/-/merge_requests/4698
+    # https://gitlab.kitware.com/cmake/cmake/-/merge_requests/4681
+    patch('ignore_crayxc_warnings.patch', when='@3.7:3.17.2')
+
     conflicts('+qt', when='^qt@5.4.0')  # qt-5.4.0 has broken CMake modules
 
     # https://gitlab.kitware.com/cmake/cmake/issues/18166

From aa9c98b6a2db58c8097a81e8074496d2c1c790d1 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Tue, 5 May 2020 20:22:32 +0200
Subject: [PATCH 259/802] Make usage example consistent with current MV
 variants (#16468)

Since #9481 Python's None is not permitted as a value for
MV variants. The string 'none' is used instead.

Add the same fix for the amgx and lammps packages
---
 lib/spack/docs/build_systems/cudapackage.rst       | 2 +-
 var/spack/repos/builtin/packages/amgx/package.py   | 2 +-
 var/spack/repos/builtin/packages/lammps/package.py | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/spack/docs/build_systems/cudapackage.rst b/lib/spack/docs/build_systems/cudapackage.rst
index b4561c69ed8..15150599d37 100644
--- a/lib/spack/docs/build_systems/cudapackage.rst
+++ b/lib/spack/docs/build_systems/cudapackage.rst
@@ -37,7 +37,7 @@ In order to use it, just add another base class to your package, for example:
             if '+cuda' in spec:
                 options.append('-DWITH_CUDA=ON')
                 cuda_arch = spec.variants['cuda_arch'].value
-                if cuda_arch is not None:
+                if cuda_arch != 'none':
                     options.append('-DCUDA_FLAGS=-arch=sm_{0}'.format(cuda_arch[0]))
             else:
                 options.append('-DWITH_CUDA=OFF')
diff --git a/var/spack/repos/builtin/packages/amgx/package.py b/var/spack/repos/builtin/packages/amgx/package.py
index ece1d67ee20..c03f3599df8 100644
--- a/var/spack/repos/builtin/packages/amgx/package.py
+++ b/var/spack/repos/builtin/packages/amgx/package.py
@@ -42,7 +42,7 @@ def cmake_args(self):
         if '+cuda' in self.spec:
             args.append('-DWITH_CUDA=ON')
             cuda_arch = self.spec.variants['cuda_arch'].value
-            if cuda_arch is not None:
+            if cuda_arch != 'none':
                 args.append('-DCUDA_ARCH={0}'.format(cuda_arch[0]))
         else:
             args.append('-DWITH_CUDA=OFF')
diff --git a/var/spack/repos/builtin/packages/lammps/package.py b/var/spack/repos/builtin/packages/lammps/package.py
index 2320cf00504..5bf2986858c 100644
--- a/var/spack/repos/builtin/packages/lammps/package.py
+++ b/var/spack/repos/builtin/packages/lammps/package.py
@@ -150,7 +150,7 @@ def cmake_args(self):
             args.append('-DPKG_GPU=ON')
             args.append('-DGPU_API=cuda')
             cuda_arch = spec.variants['cuda_arch'].value
-            if cuda_arch is not None:
+            if cuda_arch != 'none':
                 args.append('-DGPU_ARCH=sm_{0}'.format(cuda_arch[0]))
             args.append('-DCUDA_MPS_SUPPORT={0}'.format(
                 'ON' if '+cuda_mps' in spec else 'OFF'))

From eff8e1d20bf1c957546f696cf2fcb0b385e51807 Mon Sep 17 00:00:00 2001
From: Sajid Ali <30510036+s-sajid-ali@users.noreply.github.com>
Date: Tue, 5 May 2020 13:43:00 -0500
Subject: [PATCH 260/802] minor (#16467)

---
 var/spack/repos/builtin/packages/petsc/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index a4c151b5e27..d8da096f20e 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -16,13 +16,14 @@ class Petsc(Package):
     """
 
     homepage = "http://www.mcs.anl.gov/petsc/index.html"
-    url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.13.0.tar.gz"
+    url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.13.1.tar.gz"
     git = "https://gitlab.com/petsc/petsc.git"
     maintainers = ['balay', 'barrysmith', 'jedbrown']
 
     version('develop', branch='master')
     version('xsdk-0.2.0', tag='xsdk-0.2.0')
 
+    version('3.13.1', sha256='74a895e44e2ff1146838aaccb7613e7626d99e0eed64ca032c87c72d084efac3')
     version('3.13.0', sha256='f0ea543a54145c5d1387e25b121c3fd1b1ca834032c5a33f6f1d929e95bdf0e5')
     version('3.12.5', sha256='d676eb67e79314d6cca6422d7c477d2b192c830b89d5edc6b46934f7453bcfc0')
     version('3.12.4', sha256='56a941130da93bbacb3cfa74dcacea1e3cd8e36a0341f9ced09977b1457084c3')

From 7be7d672b788f807ec9ca8fdead07538806236a3 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Tue, 5 May 2020 11:45:01 -0700
Subject: [PATCH 261/802] OpenBLAS: Fix LLVM 9.0.0 ICE on macOS (#16471)

Recently added patch to port the LLVM 9.0.0 ICE with OpenBLAS and
AVX-512 instructions as well to AppleClang (11.0.3).
---
 .../openblas/openblas_appleclang11.patch      | 37 +++++++++++++++++++
 .../builtin/packages/openblas/package.py      |  3 ++
 2 files changed, 40 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/openblas/openblas_appleclang11.patch

diff --git a/var/spack/repos/builtin/packages/openblas/openblas_appleclang11.patch b/var/spack/repos/builtin/packages/openblas/openblas_appleclang11.patch
new file mode 100644
index 00000000000..88fc14aeb08
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openblas/openblas_appleclang11.patch
@@ -0,0 +1,37 @@
+From 90dba9f71668c0de77b77f32462c78fbbd424db1 Mon Sep 17 00:00:00 2001
+From: Martin Kroeker <martin@ruby.chemie.uni-freiburg.de>
+Date: Tue, 5 May 2020 10:44:50 +0200
+Subject: [PATCH] Duplicate earlier Clang 9.0.0 workaround for corresponding
+ Apple Clang version
+
+As discussed on the original PR #2329, the "Apple Clang 11.0.3" that appears to be based the same LLVM release produces the same miscompilation of this file.
+---
+ kernel/x86_64/dsymv_L_microk_skylakex-2.c | 7 ++++++-
+ 1 file changed, 6 insertions(+), 1 deletion(-)
+
+diff --git a/kernel/x86_64/dsymv_L_microk_skylakex-2.c b/kernel/x86_64/dsymv_L_microk_skylakex-2.c
+index bdcd914fb..f0df5aaa8 100644
+--- a/kernel/x86_64/dsymv_L_microk_skylakex-2.c
++++ b/kernel/x86_64/dsymv_L_microk_skylakex-2.c
+@@ -36,7 +36,9 @@ USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ #if defined(__clang_patchlevel__) && __clang_major__ == 9 && __clang_minor__ == 0 && __clang_patchlevel__ == 0
+ #pragma clang optimize off
+ #endif
+-
++#if defined(__apple_build_version__) && __clang_major__ == 11 && __clang_minor__ == 0 && __clang_patchlevel__ == 3
++#pragma clang optimize off
++#endif
+ static void dsymv_kernel_4x4(BLASLONG from, BLASLONG to, FLOAT **a, FLOAT *x, FLOAT *y, FLOAT *temp1, FLOAT *temp2)
+ {
+
+@@ -164,6 +166,9 @@ static void dsymv_kernel_4x4(BLASLONG from, BLASLONG to, FLOAT **a, FLOAT *x, FL
+ #if defined(__clang_patchlevel__) && __clang_major__ == 9 && __clang_minor__ == 0 && __clang_patchlevel__ == 0
+ #pragma clang optimize on
+ #endif
++#if defined(__apple_build_version__) && __clang_major__ == 11 && __clang_minor__ == 0 && __clang_patchlevel__ == 3
++#pragma clang optimize on
++#endif
+
+ #else
+ #include "dsymv_L_microk_haswell-2.c"
+
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 7d71702de0f..da2b461d396 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -92,6 +92,9 @@ class Openblas(MakefilePackage):
     # Fix https://github.com/xianyi/OpenBLAS/issues/2431
     # Patch derived from https://github.com/xianyi/OpenBLAS/pull/2424
     patch('openblas-0.3.8-darwin.patch', when='@0.3.8 platform=darwin')
+    # Fix ICE in LLVM 9.0.0 https://github.com/xianyi/OpenBLAS/pull/2329
+    # Patch as in https://github.com/xianyi/OpenBLAS/pull/2597
+    patch('openblas_appleclang11.patch', when='@0.3.8:0.3.9 %clang@11.0.3-apple')
 
     # Add conditions to f_check to determine the Fujitsu compiler
     patch('openblas_fujitsu.patch', when='%fj')

From dd3762d0f936aca41d11deb033e56d68d2036f2f Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Tue, 5 May 2020 13:58:46 -0700
Subject: [PATCH 262/802] cray platform: support cray Cluster and XC type
 machines (#12989)

Cray has two machine types. "XC" machines are the larger
machines more common in HPC, but "Cluster" machines are
also cropping up at some HPC sites. Cluster machines run
a slightly different form of the CrayPE programming environment,
and often come without default modules loaded. Cluster
machines also run different versions of some software, and run
a linux distro on the backend nodes instead of running Compute
Node Linux (CNL).

Below are the changes made to support "Cluster" machines in
Spack. Some of these changes are semi-related general upkeep
of the cray platform.

* cray platform: detect properly after module purge

* cray platform: support machines running OSs other than CNL

Make Cray backend OS delegate to LinuxDistro when no cle_release file
favor backend over frontend OS when name clashes

* cray platform: target detection uses multiple strategies

This commit improves the robustness of target
detection on Cray by trying multiple strategies.

The first one that produces results wins. If
nothing is found only the generic family of the
frontend host is used as a target.

* cray-libsci: add package from NERSC

* build_env: unload cray-libsci module when not explicitly needed

cray-libsci is a package in Spack. The cray PrgEnv
modules load it implicitly when we set up the compiler.
We now unload it after setting up the compiler and
only reload it when requested via external package.

* util/module_cmd: more robust module parsing

Cray modules have documentation inside the module
that is visible to the `module show` command.
Spack module parsing is now robust to documentation
inside modules.

* cce compiler: uses clang flags for versions >= 9.0

* build_env: push CRAY_LD_LIBRARY_PATH into everything

Some Cray modules add paths to CRAY_LD_LIBRARY_PATH
instead of LD_LIBRARY_PATH. This has performance benefits
at load time, but leads to Spack builds not finding their
dependencies from external modules.
Spack now prepends CRAY_LD_LIBRARY_PATH to
LD_LIBRARY_PATH before beginning the build.

* mvapich2: setup cray compilers when on cray

previously, mpich was the only mpi implementation to support
cray systems (because it is the MPI on Cray XC systems).
Cray cluster systems use mvapich2, which now supports cray
compiler wrappers.

* build_env: clean pkgconf from environment

Cray modules silently add pkgconf to the user environment
This can break builds that do not user pkgconf.
Now we remove it frmo the environment and add it again if it
is in the spec.

* cray platform: cheat modules for rome/zen2 module on naples/zen node

Cray modules for naples/zen architecture currently specify
rome/zen2. For now, we detect this and return zen for modules
named `craype-x86-rome`.

* compiler: compiler default versions

When detecting compiler default versions for target/compiler
compatibility checks, Spack previously ran the compiler without
setting up its environment. Now we setup a temporary environment
to run the compiler with its modules to detect its version.

* compilers/cce: improve logic to determine C/C++ std flags

* tests: fix existing tests to play nicely with new cray support

* tests: test new functionality

Some new functionality can only be tested on a cray system.
Add tests for what can be tested on a linux system.

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
---
 lib/spack/spack/architecture.py               |   9 +-
 lib/spack/spack/build_environment.py          |  13 +-
 lib/spack/spack/compiler.py                   |  40 +++++
 lib/spack/spack/compilers/cce.py              |  23 ++-
 .../{cnl.py => cray_backend.py}               |  25 ++-
 lib/spack/spack/platforms/cray.py             | 154 ++++++++++++------
 lib/spack/spack/spec.py                       |   6 +-
 lib/spack/spack/test/architecture.py          |   7 +-
 lib/spack/spack/test/cmd/dev_build.py         |  11 +-
 lib/spack/spack/test/compilers.py             |  55 ++++++-
 lib/spack/spack/test/operating_system.py      |  22 +--
 lib/spack/spack/util/module_cmd.py            |   8 +-
 .../builtin/packages/cray-libsci/package.py   |  50 +++++-
 .../builtin/packages/mvapich2/package.py      |  30 +++-
 14 files changed, 357 insertions(+), 96 deletions(-)
 rename lib/spack/spack/operating_systems/{cnl.py => cray_backend.py} (81%)

diff --git a/lib/spack/spack/architecture.py b/lib/spack/spack/architecture.py
index 38ed5baa7be..963fecd3751 100644
--- a/lib/spack/spack/architecture.py
+++ b/lib/spack/spack/architecture.py
@@ -209,14 +209,15 @@ def optimization_flags(self, compiler):
         compiler_version = compiler.version
         version_number, suffix = cpu.version_components(compiler.version)
         if not version_number or suffix not in ('', 'apple'):
-            # Try to deduce the correct version. Depending on where this
-            # function is called we might get either a CompilerSpec or a
-            # fully fledged compiler object
+            # Try to deduce the underlying version of the compiler, regardless
+            # of its name in compilers.yaml. Depending on where this function
+            # is called we might get either a CompilerSpec or a fully fledged
+            # compiler object.
             import spack.spec
             if isinstance(compiler, spack.spec.CompilerSpec):
                 compiler = spack.compilers.compilers_for_spec(compiler).pop()
             try:
-                compiler_version = compiler.cc_version(compiler.cc)
+                compiler_version = compiler.get_real_version()
             except spack.util.executable.ProcessError as e:
                 # log this and just return compiler.version instead
                 tty.debug(str(e))
diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 5e6ea00ce62..8d84cdaf65f 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -60,7 +60,7 @@
 from spack.util.environment import system_dirs
 from spack.error import NoLibrariesError, NoHeadersError
 from spack.util.executable import Executable
-from spack.util.module_cmd import load_module, get_path_from_module
+from spack.util.module_cmd import load_module, get_path_from_module, module
 from spack.util.log_parse import parse_log_events, make_log_context
 
 
@@ -141,12 +141,18 @@ def clean_environment():
     # can affect how some packages find libraries.  We want to make
     # sure that builds never pull in unintended external dependencies.
     env.unset('LD_LIBRARY_PATH')
+    env.unset('CRAY_LD_LIBRARY_PATH')
     env.unset('LIBRARY_PATH')
     env.unset('CPATH')
     env.unset('LD_RUN_PATH')
     env.unset('DYLD_LIBRARY_PATH')
     env.unset('DYLD_FALLBACK_LIBRARY_PATH')
 
+    # Remove all pkgconfig stuff from craype
+    for varname in os.environ.keys():
+        if 'PKGCONF' in varname:
+            env.unset(varname)
+
     build_lang = spack.config.get('config:build_language')
     if build_lang:
         # Override language-related variables. This can be used to force
@@ -717,6 +723,11 @@ def setup_package(pkg, dirty):
                 load_module("cce")
             load_module(mod)
 
+        # kludge to handle cray libsci being automatically loaded by PrgEnv
+        # modules on cray platform. Module unload does no damage when
+        # unnecessary
+        module('unload', 'cray-libsci')
+
         if pkg.architecture.target.module_name:
             load_module(pkg.architecture.target.module_name)
 
diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py
index 8afbe48c0c6..94dbb190d24 100644
--- a/lib/spack/spack/compiler.py
+++ b/lib/spack/spack/compiler.py
@@ -19,6 +19,7 @@
 import spack.spec
 import spack.architecture
 import spack.util.executable
+import spack.util.module_cmd
 import spack.compilers
 from spack.util.environment import filter_system_paths
 
@@ -434,6 +435,45 @@ def fc_pic_flag(self):
         Position Independent Code (PIC)."""
         return '-fPIC'
 
+    # Note: This is not a class method. The class methods are used to detect
+    # compilers on PATH based systems, and do not set up the run environment of
+    # the compiler. This method can be called on `module` based systems as well
+    def get_real_version(self):
+        """Query the compiler for its version.
+
+        This is the "real" compiler version, regardless of what is in the
+        compilers.yaml file, which the user can change to name their compiler.
+
+        Use the runtime environment of the compiler (modules and environment
+        modifications) to enable the compiler to run properly on any platform.
+        """
+        # store environment to replace later
+        backup_env = os.environ.copy()
+
+        # load modules and set env variables
+        for module in self.modules:
+            # On cray, mic-knl module cannot be loaded without cce module
+            # See: https://github.com/spack/spack/issues/3153
+            if os.environ.get("CRAY_CPU_TARGET") == 'mic-knl':
+                spack.util.module_cmd.load_module('cce')
+            spack.util.module_cmd.load_module(module)
+
+        # apply other compiler environment changes
+        env = spack.util.environment.EnvironmentModifications()
+        env.extend(spack.schema.environment.parse(self.environment))
+        env.apply_modifications()
+
+        cc = spack.util.executable.Executable(self.cc)
+        output = cc(self.version_argument,
+                    output=str, error=str,
+                    ignore_errors=tuple(self.ignore_version_errors))
+
+        # Restore environment
+        os.environ.clear()
+        os.environ.update(backup_env)
+
+        return self.extract_version_from_output(output)
+
     #
     # Compiler classes have methods for querying the version of
     # specific compiler executables.  This is used when discovering compilers.
diff --git a/lib/spack/spack/compilers/cce.py b/lib/spack/spack/compilers/cce.py
index 7aedb55a5d0..0d30a69d3e6 100644
--- a/lib/spack/spack/compilers/cce.py
+++ b/lib/spack/spack/compilers/cce.py
@@ -32,7 +32,12 @@ class Cce(Compiler):
                   'f77': 'cce/ftn',
                   'fc': 'cce/ftn'}
 
-    version_argument = '-V'
+    @property
+    def version_argument(self):
+        if self.version >= ver('9.0'):
+            return '--version'
+        return '-V'
+
     version_regex = r'[Vv]ersion.*?(\d+(\.\d+)+)'
 
     @classmethod
@@ -41,17 +46,23 @@ def verbose_flag(cls):
 
     @property
     def openmp_flag(self):
+        if self.version >= ver('9.0'):
+            return '-fopenmp'
         return "-h omp"
 
     @property
     def cxx11_flag(self):
+        if self.version >= ver('9.0'):
+            return '-std=c++11'
         return "-h std=c++11"
 
     @property
     def c99_flag(self):
-        if self.version >= ver('8.4'):
-            return '-h stc=c99,noconform,gnu'
-        if self.version >= ver('8.1'):
+        if self.version >= ver('9.0'):
+            return '-std=c99'
+        elif self.version >= ver('8.4'):
+            return '-h std=c99,noconform,gnu'
+        elif self.version >= ver('8.1'):
             return '-h c99,noconform,gnu'
         raise UnsupportedCompilerFlag(self,
                                       'the C99 standard',
@@ -60,7 +71,9 @@ def c99_flag(self):
 
     @property
     def c11_flag(self):
-        if self.version >= ver('8.5'):
+        if self.version >= ver('9.0'):
+            return '-std=c11'
+        elif self.version >= ver('8.5'):
             return '-h std=c11,noconform,gnu'
         raise UnsupportedCompilerFlag(self,
                                       'the C11 standard',
diff --git a/lib/spack/spack/operating_systems/cnl.py b/lib/spack/spack/operating_systems/cray_backend.py
similarity index 81%
rename from lib/spack/spack/operating_systems/cnl.py
rename to lib/spack/spack/operating_systems/cray_backend.py
index 3d4036cb470..91c0e6ae985 100644
--- a/lib/spack/spack/operating_systems/cnl.py
+++ b/lib/spack/spack/operating_systems/cray_backend.py
@@ -10,7 +10,7 @@
 
 import spack.error
 import spack.version
-from spack.architecture import OperatingSystem
+from spack.operating_systems.linux_distro import LinuxDistro
 from spack.util.module_cmd import module
 
 #: Possible locations of the Cray CLE release file,
@@ -68,7 +68,7 @@ def read_clerelease_file():
             return line.strip()
 
 
-class Cnl(OperatingSystem):
+class CrayBackend(LinuxDistro):
     """Compute Node Linux (CNL) is the operating system used for the Cray XC
     series super computers. It is a very stripped down version of GNU/Linux.
     Any compilers found through this operating system will be used with
@@ -79,7 +79,15 @@ class Cnl(OperatingSystem):
     def __init__(self):
         name = 'cnl'
         version = self._detect_crayos_version()
-        super(Cnl, self).__init__(name, version)
+        if version:
+            # If we found a CrayOS version, we do not want the information
+            # from LinuxDistro. In order to skip the logic from
+            # external.distro.linux_distribution, while still calling __init__
+            # methods further up the MRO, we skip LinuxDistro in the MRO and
+            # call the OperatingSystem superclass __init__ method
+            super(LinuxDistro, self).__init__(name, version)
+        else:
+            super(CrayBackend, self).__init__()
         self.modulecmd = module
 
     def __str__(self):
@@ -95,8 +103,15 @@ def _detect_crayos_version(cls):
             v = read_clerelease_file()
             return spack.version.Version(v)[0]
         else:
-            raise spack.error.UnsupportedPlatformError(
-                'Unable to detect Cray OS version')
+            # Not all Cray systems run CNL on the backend.
+            # Systems running in what Cray calls "cluster" mode run other
+            # linux OSs under the Cray PE.
+            # So if we don't detect any Cray OS version on the system,
+            # we return None. We can't ever be sure we will get a Cray OS
+            # version.
+            # Returning None allows the calling code to test for the value
+            # being "True-ish" rather than requiring a try/except block.
+            return None
 
     def arguments_to_detect_version_fn(self, paths):
         import spack.compilers
diff --git a/lib/spack/spack/platforms/cray.py b/lib/spack/spack/platforms/cray.py
index 6e8c79ef0cd..8c5fe525e63 100644
--- a/lib/spack/spack/platforms/cray.py
+++ b/lib/spack/spack/platforms/cray.py
@@ -4,30 +4,29 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import os
+import os.path
 import re
+import platform
+import llnl.util.cpu as cpu
 import llnl.util.tty as tty
 from spack.paths import build_env_path
 from spack.util.executable import Executable
 from spack.architecture import Platform, Target, NoPlatformError
 from spack.operating_systems.cray_frontend import CrayFrontend
-from spack.operating_systems.cnl import Cnl
+from spack.operating_systems.cray_backend import CrayBackend
 from spack.util.module_cmd import module
 
 
-def _get_modules_in_modulecmd_output(output):
-    '''Return list of valid modules parsed from modulecmd output string.'''
-    return [i for i in output.splitlines()
-            if len(i.split()) == 1]
+_craype_name_to_target_name = {
+    'x86-cascadelake': 'cascadelake',
+    'x86-naples': 'zen',
+    'x86-rome': 'zen',  # Cheating because we have the wrong modules on rzcrayz
+    'x86-skylake': 'skylake-avx512'
+}
 
 
-def _fill_craype_targets_from_modules(targets, modules):
-    '''Extend CrayPE CPU targets list with those found in list of modules.'''
-    # Craype- module prefixes that are not valid CPU targets.
-    non_targets = ('hugepages', 'network', 'target', 'accel', 'xtpe')
-    pattern = r'craype-(?!{0})(\S*)'.format('|'.join(non_targets))
-    for mod in modules:
-        if 'craype-' in mod:
-            targets.extend(re.findall(pattern, mod))
+def _target_name_from_craype_target_name(name):
+    return _craype_name_to_target_name.get(name, name)
 
 
 class Cray(Platform):
@@ -47,40 +46,34 @@ def __init__(self):
 
         # Make all craype targets available.
         for target in self._avail_targets():
-            name = target.replace('-', '_')
+            name = _target_name_from_craype_target_name(target)
             self.add_target(name, Target(name, 'craype-%s' % target))
 
-        self.add_target("x86_64", Target("x86_64"))
-        self.add_target("front_end", Target("x86_64"))
-        self.front_end = "x86_64"
-
-        # Get aliased targets from config or best guess from environment:
-        for name in ('front_end', 'back_end'):
-            _target = getattr(self, name, None)
-            if _target is None:
-                _target = os.environ.get('SPACK_' + name.upper())
-            if _target is None and name == 'back_end':
-                _target = self._default_target_from_env()
-            if _target is not None:
-                safe_name = _target.replace('-', '_')
-                setattr(self, name, safe_name)
-                self.add_target(name, self.targets[safe_name])
-
-        if self.back_end is not None:
-            self.default = self.back_end
-            self.add_target('default', self.targets[self.back_end])
-        else:
+        self.back_end = os.environ.get('SPACK_BACK_END',
+                                       self._default_target_from_env())
+        self.default = self.back_end
+        if self.back_end not in self.targets:
+            # We didn't find a target module for the backend
             raise NoPlatformError()
 
+        # Setup frontend targets
+        for name in cpu.targets:
+            if name not in self.targets:
+                self.add_target(name, Target(name))
+        self.front_end = os.environ.get('SPACK_FRONT_END', cpu.host().name)
+        if self.front_end not in self.targets:
+            self.add_target(self.front_end, Target(self.front_end))
+
         front_distro = CrayFrontend()
-        back_distro = Cnl()
+        back_distro = CrayBackend()
 
         self.default_os = str(back_distro)
         self.back_os = self.default_os
         self.front_os = str(front_distro)
 
         self.add_operating_system(self.back_os, back_distro)
-        self.add_operating_system(self.front_os, front_distro)
+        if self.front_os != self.back_os:
+            self.add_operating_system(self.front_os, front_distro)
 
     @classmethod
     def setup_platform_environment(cls, pkg, env):
@@ -104,9 +97,28 @@ def setup_platform_environment(cls, pkg, env):
         env.append_path("PKG_CONFIG_PATH", "/usr/lib64/pkgconfig")
         env.append_path("PKG_CONFIG_PATH", "/usr/local/lib64/pkgconfig")
 
+        # CRAY_LD_LIBRARY_PATH is used at build time by the cray compiler
+        # wrappers to augment LD_LIBRARY_PATH. This is to avoid long load
+        # times at runtime. This behavior is not always respected on cray
+        # "cluster" systems, so we reproduce it here.
+        if os.environ.get('CRAY_LD_LIBRARY_PATH'):
+            env.prepend_path('LD_LIBRARY_PATH',
+                             os.environ['CRAY_LD_LIBRARY_PATH'])
+
     @classmethod
     def detect(cls):
-        return os.environ.get('CRAYPE_VERSION') is not None
+        """
+        Detect whether this system is a cray machine.
+
+        We detect the cray platform based on the availability through `module`
+        of the cray programming environment. If this environment is available,
+        we can use it to find compilers, target modules, etc. If the cray
+        programming environment is not available via modules, then we will
+        treat it as a standard linux system, as the cray compiler wrappers
+        and other componenets of the cray programming environment are
+        irrelevant without module support.
+        """
+        return 'opt/cray' in os.environ.get('MODULEPATH', '')
 
     def _default_target_from_env(self):
         '''Set and return the default CrayPE target loaded in a clean login
@@ -119,22 +131,66 @@ def _default_target_from_env(self):
         if getattr(self, 'default', None) is None:
             bash = Executable('/bin/bash')
             output = bash(
-                '-lc', 'echo $CRAY_CPU_TARGET',
+                '--norc', '--noprofile', '-lc', 'echo $CRAY_CPU_TARGET',
                 env={'TERM': os.environ.get('TERM', '')},
-                output=str,
-                error=os.devnull
+                output=str, error=os.devnull
             )
-            output = ''.join(output.split())  # remove all whitespace
-            if output:
-                self.default = output
-                tty.debug("Found default module:%s" % self.default)
-        return self.default
+            default_from_module = ''.join(output.split())  # rm all whitespace
+            if default_from_module:
+                tty.debug("Found default module:%s" % default_from_module)
+                return default_from_module
+            else:
+                front_end = cpu.host().name
+                if front_end in list(
+                        map(lambda x: _target_name_from_craype_target_name(x),
+                            self._avail_targets())
+                ):
+                    tty.debug("default to front-end architecture")
+                    return cpu.host().name
+                else:
+                    return platform.machine()
 
     def _avail_targets(self):
         '''Return a list of available CrayPE CPU targets.'''
+
+        def modules_in_output(output):
+            """Returns a list of valid modules parsed from modulecmd output"""
+            return [i for i in re.split(r'\s\s+|\n', output)]
+
+        def target_names_from_modules(modules):
+            # Craype- module prefixes that are not valid CPU targets.
+            targets = []
+            for mod in modules:
+                if 'craype-' in mod:
+                    name = mod[7:]
+                    _n = name.replace('-', '_')  # test for mic-knl/mic_knl
+                    is_target_name = name in cpu.targets or _n in cpu.targets
+                    is_cray_target_name = name in _craype_name_to_target_name
+                    if is_target_name or is_cray_target_name:
+                        targets.append(name)
+
+            return targets
+
+        def modules_from_listdir():
+            craype_default_path = '/opt/cray/pe/craype/default/modulefiles'
+            if os.path.isdir(craype_default_path):
+                return os.listdir(craype_default_path)
+            return None
+
         if getattr(self, '_craype_targets', None) is None:
-            output = module('avail', '-t', 'craype-')
-            craype_modules = _get_modules_in_modulecmd_output(output)
-            self._craype_targets = targets = []
-            _fill_craype_targets_from_modules(targets, craype_modules)
+            strategies = [
+                lambda: modules_in_output(module('avail', '-t', 'craype-')),
+                modules_from_listdir
+            ]
+            for available_craype_modules in strategies:
+                craype_modules = available_craype_modules()
+                craype_targets = target_names_from_modules(craype_modules)
+                if craype_targets:
+                    self._craype_targets = craype_targets
+                    break
+            else:
+                # If nothing is found add platform.machine()
+                # to avoid Spack erroring out
+                self._craype_targets = [platform.machine()]
+
         return self._craype_targets
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index c6fe2da7627..0b9500246af 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -2239,7 +2239,11 @@ def concretize(self, tests=False):
                 for mod in compiler.modules:
                     md.load_module(mod)
 
-                s.external_path = md.get_path_from_module(s.external_module)
+                # get the path from the module
+                # the package can override the default
+                s.external_path = getattr(s.package, 'external_prefix',
+                                          md.get_path_from_module(
+                                              s.external_module))
 
         # Mark everything in the spec as concrete, as well.
         self._mark_concrete()
diff --git a/lib/spack/spack/test/architecture.py b/lib/spack/spack/test/architecture.py
index 552bc324bf9..48cec134d27 100644
--- a/lib/spack/spack/test/architecture.py
+++ b/lib/spack/spack/test/architecture.py
@@ -1,4 +1,3 @@
-
 # Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
@@ -41,7 +40,7 @@ def test_dict_functions_for_architecture():
 
 def test_platform():
     output_platform_class = spack.architecture.real_platform()
-    if os.environ.get('CRAYPE_VERSION') is not None:
+    if os.path.exists('/opt/cray/pe'):
         my_platform_class = Cray()
     elif os.path.exists('/bgsys'):
         my_platform_class = Bgq()
@@ -210,8 +209,8 @@ def test_optimization_flags_with_custom_versions(
     target = spack.architecture.Target(target_str)
     if real_version:
         monkeypatch.setattr(
-            spack.compiler.Compiler, 'cc_version', lambda x, y: real_version
-        )
+            spack.compiler.Compiler, 'get_real_version',
+            lambda x: real_version)
     opt_flags = target.optimization_flags(compiler)
     assert opt_flags == expected_flags
 
diff --git a/lib/spack/spack/test/cmd/dev_build.py b/lib/spack/spack/test/cmd/dev_build.py
index 5a7dfc273c2..37c40e787d4 100644
--- a/lib/spack/spack/test/cmd/dev_build.py
+++ b/lib/spack/spack/test/cmd/dev_build.py
@@ -80,8 +80,17 @@ def test_dev_build_drop_in(tmpdir, mock_packages, monkeypatch,
                            install_mockery):
     def print_spack_cc(*args):
         # Eat arguments and print environment variable to test
-        print(os.environ['CC'])
+        print(os.environ.get('CC', ''))
     monkeypatch.setattr(os, 'execvp', print_spack_cc)
+
+    # `module unload cray-libsci` in test environment causes failure
+    # It does not fail for actual installs
+    # build_environment.py imports module directly, so we monkeypatch it there
+    # rather than in module_cmd
+    def module(*args):
+        pass
+    monkeypatch.setattr(spack.build_environment, 'module', module)
+
     output = dev_build('-b', 'edit', '--drop-in', 'sh',
                        'dev-build-test-install@0.0.0')
     assert "lib/spack/env" in output
diff --git a/lib/spack/spack/test/compilers.py b/lib/spack/spack/test/compilers.py
index 24115ba562e..586bb215cfe 100644
--- a/lib/spack/spack/test/compilers.py
+++ b/lib/spack/spack/test/compilers.py
@@ -6,10 +6,13 @@
 import pytest
 
 import sys
+import os
 
 from copy import copy
 from six import iteritems
 
+import llnl.util.filesystem as fs
+
 import spack.spec
 import spack.compiler
 import spack.compilers as compilers
@@ -259,7 +262,7 @@ def test_cce_flags():
     supported_flag_test("cxx11_flag", "-h std=c++11", "cce@1.0")
     unsupported_flag_test("c99_flag", "cce@8.0")
     supported_flag_test("c99_flag", "-h c99,noconform,gnu", "cce@8.1")
-    supported_flag_test("c99_flag", "-h stc=c99,noconform,gnu", "cce@8.4")
+    supported_flag_test("c99_flag", "-h std=c99,noconform,gnu", "cce@8.4")
     unsupported_flag_test("c11_flag", "cce@8.4")
     supported_flag_test("c11_flag", "-h std=c11,noconform,gnu", "cce@8.5")
     supported_flag_test("cc_pic_flag",  "-h PIC", "cce@1.0")
@@ -615,3 +618,53 @@ def test_raising_if_compiler_target_is_over_specific(config):
         cfg = spack.compilers.get_compiler_config()
         with pytest.raises(ValueError):
             spack.compilers.get_compilers(cfg, 'gcc@9.0.1', arch_spec)
+
+
+def test_compiler_get_real_version(working_env, monkeypatch, tmpdir):
+    # Test variables
+    test_version = '2.2.2'
+
+    # Create compiler
+    gcc = str(tmpdir.join('gcc'))
+    with open(gcc, 'w') as f:
+        f.write("""#!/bin/bash
+if [[ $CMP_ON == "1" ]]; then
+    echo "$CMP_VER"
+fi
+""")
+    fs.set_executable(gcc)
+
+    # Add compiler to config
+    compiler_info = {
+        'spec': 'gcc@foo',
+        'paths': {
+            'cc': gcc,
+            'cxx': None,
+            'f77': None,
+            'fc': None,
+        },
+        'flags': {},
+        'operating_system': 'fake',
+        'target': 'fake',
+        'modules': ['turn_on'],
+        'environment': {
+            'set': {'CMP_VER': test_version},
+        },
+        'extra_rpaths': [],
+    }
+    compiler_dict = {'compiler': compiler_info}
+
+    # Set module load to turn compiler on
+    def module(*args):
+        if args[0] == 'show':
+            return ''
+        elif args[0] == 'load':
+            os.environ['CMP_ON'] = "1"
+    monkeypatch.setattr(spack.util.module_cmd, 'module', module)
+
+    # Run and confirm output
+    compilers = spack.compilers.get_compilers([compiler_dict])
+    assert len(compilers) == 1
+    compiler = compilers[0]
+    version = compiler.get_real_version()
+    assert version == test_version
diff --git a/lib/spack/spack/test/operating_system.py b/lib/spack/spack/test/operating_system.py
index 221712e5ef2..97def3feda2 100644
--- a/lib/spack/spack/test/operating_system.py
+++ b/lib/spack/spack/test/operating_system.py
@@ -3,7 +3,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import spack.operating_systems.cnl as cnl
+import spack.operating_systems.cray_backend as cray_backend
 
 
 def test_read_cle_release_file(tmpdir, monkeypatch):
@@ -20,8 +20,9 @@ def test_read_cle_release_file(tmpdir, monkeypatch):
 DUMMY=foo=bar
 """)
 
-    monkeypatch.setattr(cnl, '_cle_release_file', str(cle_release_path))
-    attrs = cnl.read_cle_release_file()
+    monkeypatch.setattr(cray_backend, '_cle_release_file',
+                        str(cle_release_path))
+    attrs = cray_backend.read_cle_release_file()
 
     assert attrs['RELEASE'] == '6.0.UP07'
     assert attrs['BUILD'] == '6.0.7424'
@@ -31,7 +32,7 @@ def test_read_cle_release_file(tmpdir, monkeypatch):
     assert attrs['PATCHSET'] == '35-201906112304'
     assert attrs['DUMMY'] == 'foo=bar'
 
-    assert cnl.Cnl._detect_crayos_version() == 6
+    assert cray_backend.CrayBackend._detect_crayos_version() == 6
 
 
 def test_read_clerelease_file(tmpdir, monkeypatch):
@@ -40,12 +41,12 @@ def test_read_clerelease_file(tmpdir, monkeypatch):
     with clerelease_path.open('w') as f:
         f.write('5.2.UP04\n')
 
-    monkeypatch.setattr(cnl, '_clerelease_file', str(clerelease_path))
-    v = cnl.read_clerelease_file()
+    monkeypatch.setattr(cray_backend, '_clerelease_file', str(clerelease_path))
+    v = cray_backend.read_clerelease_file()
 
     assert v == '5.2.UP04'
 
-    assert cnl.Cnl._detect_crayos_version() == 5
+    assert cray_backend.CrayBackend._detect_crayos_version() == 5
 
 
 def test_cle_release_precedence(tmpdir, monkeypatch):
@@ -67,7 +68,8 @@ def test_cle_release_precedence(tmpdir, monkeypatch):
     with clerelease_path.open('w') as f:
         f.write('5.2.UP04\n')
 
-    monkeypatch.setattr(cnl, '_clerelease_file', str(clerelease_path))
-    monkeypatch.setattr(cnl, '_cle_release_file', str(cle_release_path))
+    monkeypatch.setattr(cray_backend, '_clerelease_file', str(clerelease_path))
+    monkeypatch.setattr(cray_backend, '_cle_release_file',
+                        str(cle_release_path))
 
-    assert cnl.Cnl._detect_crayos_version() == 6
+    assert cray_backend.CrayBackend._detect_crayos_version() == 6
diff --git a/lib/spack/spack/util/module_cmd.py b/lib/spack/spack/util/module_cmd.py
index 74790156ae0..143ad3d43e7 100644
--- a/lib/spack/spack/util/module_cmd.py
+++ b/lib/spack/spack/util/module_cmd.py
@@ -87,7 +87,13 @@ def get_path_args_from_module_line(line):
         words_and_symbols = line.split(lua_quote)
         path_arg = words_and_symbols[-2]
     else:
-        path_arg = line.split()[2]
+        # The path arg is the 3rd "word" of the line in a TCL module
+        # OPERATION VAR_NAME PATH_ARG
+        words = line.split()
+        if len(words) > 2:
+            path_arg = line.split()[2]
+        else:
+            return []
 
     paths = path_arg.split(':')
     return paths
diff --git a/var/spack/repos/builtin/packages/cray-libsci/package.py b/var/spack/repos/builtin/packages/cray-libsci/package.py
index c0313a1e39e..d391f471c3d 100755
--- a/var/spack/repos/builtin/packages/cray-libsci/package.py
+++ b/var/spack/repos/builtin/packages/cray-libsci/package.py
@@ -2,10 +2,9 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from llnl.util.filesystem import LibraryList
-from spack import *
-import os
+from spack.concretize import NoBuildError
+from spack.util.module_cmd import module
+from spack.util.module_cmd import get_path_args_from_module_line
 
 
 class CrayLibsci(Package):
@@ -22,14 +21,53 @@ class CrayLibsci(Package):
     version("16.06.1")
     version("16.03.1")
 
+    variant("shared", default=True, description="enable shared libs")
+    variant("openmp", default=False, description="link with openmp")
+    variant("mpi", default=False, description="link with mpi libs")
+
     provides("blas")
     provides("lapack")
     provides("scalapack")
 
-    # NOTE: Cray compiler wrappers already include linking for the following
+    canonical_names = {
+        'gcc': 'GNU',
+        'cce': 'CRAY',
+        'intel': 'INTEL',
+    }
+
+    @property
+    def modname(self):
+        return "cray-libsci/{0}".format(self.version)
+
+    @property
+    def external_prefix(self):
+        libsci_module = module("show", self.modname).splitlines()
+
+        for line in libsci_module:
+            if "CRAY_LIBSCI_PREFIX_DIR" in line:
+                return get_path_args_from_module_line(line)[0]
+
     @property
     def blas_libs(self):
-        return LibraryList(os.path.join(self.prefix.lib, 'libsci.so'))
+        shared = True if "+shared" in self.spec else False
+        compiler = self.spec.compiler.name
+
+        if "+openmp" in self.spec and "+mpi" in self.spec:
+            lib = "libsci_{0}_mpi_mp"
+        elif "+openmp" in self.spec:
+            lib = "libsci_{0}_mp"
+        elif "+mpi" in self.spec:
+            lib = "libsci_{0}_mpi"
+        else:
+            lib = "libsci_{0}"
+
+        libname = lib.format(self.canonical_names[compiler].lower())
+
+        return find_libraries(
+            libname,
+            root=self.prefix.lib,
+            shared=shared,
+            recursive=False)
 
     @property
     def lapack_libs(self):
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index f6301a564a8..d8398b336da 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -208,10 +208,17 @@ def setup_run_environment(self, env):
             env.set('SLURM_MPI_TYPE', 'pmi2')
 
     def setup_dependent_build_environment(self, env, dependent_spec):
-        env.set('MPICC', os.path.join(self.prefix.bin, 'mpicc'))
-        env.set('MPICXX', os.path.join(self.prefix.bin, 'mpicxx'))
-        env.set('MPIF77', os.path.join(self.prefix.bin, 'mpif77'))
-        env.set('MPIF90', os.path.join(self.prefix.bin, 'mpif90'))
+        # On Cray, the regular compiler wrappers *are* the MPI wrappers.
+        if 'platform=cray' in self.spec:
+            env.set('MPICC',  spack_cc)
+            env.set('MPICXX', spack_cxx)
+            env.set('MPIF77', spack_fc)
+            env.set('MPIF90', spack_fc)
+        else:
+            env.set('MPICC',  join_path(self.prefix.bin, 'mpicc'))
+            env.set('MPICXX', join_path(self.prefix.bin, 'mpicxx'))
+            env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
+            env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
 
         env.set('MPICH_CC', spack_cc)
         env.set('MPICH_CXX', spack_cxx)
@@ -220,10 +227,17 @@ def setup_dependent_build_environment(self, env, dependent_spec):
         env.set('MPICH_FC', spack_fc)
 
     def setup_dependent_package(self, module, dependent_spec):
-        self.spec.mpicc  = os.path.join(self.prefix.bin, 'mpicc')
-        self.spec.mpicxx = os.path.join(self.prefix.bin, 'mpicxx')
-        self.spec.mpifc  = os.path.join(self.prefix.bin, 'mpif90')
-        self.spec.mpif77 = os.path.join(self.prefix.bin, 'mpif77')
+        if 'platform=cray' in self.spec:
+            self.spec.mpicc = spack_cc
+            self.spec.mpicxx = spack_cxx
+            self.spec.mpifc = spack_fc
+            self.spec.mpif77 = spack_f77
+        else:
+            self.spec.mpicc  = join_path(self.prefix.bin, 'mpicc')
+            self.spec.mpicxx = join_path(self.prefix.bin, 'mpicxx')
+            self.spec.mpifc  = join_path(self.prefix.bin, 'mpif90')
+            self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77')
+
         self.spec.mpicxx_shared_libs = [
             os.path.join(self.prefix.lib, 'libmpicxx.{0}'.format(dso_suffix)),
             os.path.join(self.prefix.lib, 'libmpi.{0}'.format(dso_suffix))

From fbdd2908774c7fc221c85fbeaa7b4d79709b9039 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Tue, 5 May 2020 15:31:13 -0600
Subject: [PATCH 263/802] kokkos: add v3.1.01 (#16470)

* kokkos: add v3.1.01

* kokkos: fix up versions

* kokkos-kernels: follow upstream versioning
---
 .../repos/builtin/packages/kokkos-kernels/package.py     | 8 +++-----
 var/spack/repos/builtin/packages/kokkos/package.py       | 9 ++++-----
 2 files changed, 7 insertions(+), 10 deletions(-)

diff --git a/var/spack/repos/builtin/packages/kokkos-kernels/package.py b/var/spack/repos/builtin/packages/kokkos-kernels/package.py
index d4ae6a33639..1613c204b80 100644
--- a/var/spack/repos/builtin/packages/kokkos-kernels/package.py
+++ b/var/spack/repos/builtin/packages/kokkos-kernels/package.py
@@ -11,14 +11,12 @@ class KokkosKernels(CMakePackage, CudaPackage):
 
     homepage = "https://github.com/kokkos/kokkos-kernels"
     git = "https://github.com/kokkos/kokkos-kernels.git"
+    url = "https://github.com/kokkos/kokkos-kernels/archive/3.1.00.tar.gz"
 
-    version('3.1',     url='https://github.com/kokkos/kokkos-kernels/archive/3.1.00.tar.gz',
-            sha256="27fea241ae92f41bd5b070b1a590ba3a56a06aca750207a98bea2f64a4a40c89",
-            default=True)
-    version('3.0',     url='https://github.com/kokkos/kokkos-kernels/archive/3.0.00.tar.gz',
-            sha256="e4b832aed3f8e785de24298f312af71217a26067aea2de51531e8c1e597ef0e6")
     version('develop', branch='develop')
     version('master',  branch='master')
+    version('3.1.00', sha256="27fea241ae92f41bd5b070b1a590ba3a56a06aca750207a98bea2f64a4a40c89")
+    version('3.0.00', sha256="e4b832aed3f8e785de24298f312af71217a26067aea2de51531e8c1e597ef0e6")
 
     depends_on("kokkos")
     depends_on("kokkos@develop", when="@develop")
diff --git a/var/spack/repos/builtin/packages/kokkos/package.py b/var/spack/repos/builtin/packages/kokkos/package.py
index 86cf01e7849..fef37d2ac7b 100644
--- a/var/spack/repos/builtin/packages/kokkos/package.py
+++ b/var/spack/repos/builtin/packages/kokkos/package.py
@@ -11,14 +11,13 @@ class Kokkos(CMakePackage, CudaPackage):
 
     homepage = "https://github.com/kokkos/kokkos"
     git = "https://github.com/kokkos/kokkos.git"
+    url = "https://github.com/kokkos/kokkos/archive/3.1.01.tar.gz"
 
     version('develop', branch='develop')
     version('master',  branch='master')
-    version('3.0', url="https://github.com/kokkos/kokkos/archive/3.0.00.tar.gz",
-            sha256="c00613d0194a4fbd0726719bbed8b0404ed06275f310189b3493f5739042a92b")
-    version('3.1', url="https://github.com/kokkos/kokkos/archive/3.1.00.tar.gz",
-            sha256="b935c9b780e7330bcb80809992caa2b66fd387e3a1c261c955d622dae857d878",
-            default=True)
+    version('3.1.01', sha256='ff5024ebe8570887d00246e2793667e0d796b08c77a8227fe271127d36eec9dd')
+    version('3.1.00', sha256="b935c9b780e7330bcb80809992caa2b66fd387e3a1c261c955d622dae857d878")
+    version('3.0.00', sha256="c00613d0194a4fbd0726719bbed8b0404ed06275f310189b3493f5739042a92b")
 
     depends_on("cmake@3.10:", type='build')
 

From 7e5874c25029c2649d5ded2621533b17bd7c5196 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 5 May 2020 16:56:03 -0500
Subject: [PATCH 264/802] PyTorch: add patches to fix build (#16477)

---
 .../builtin/packages/py-torch/package.py      | 14 ++++--
 .../builtin/packages/py-torch/xnnpack.patch   | 47 +++++++++++++++++++
 2 files changed, 58 insertions(+), 3 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/py-torch/xnnpack.patch

diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py
index 7329ba91741..b2b15c7dfc2 100644
--- a/var/spack/repos/builtin/packages/py-torch/package.py
+++ b/var/spack/repos/builtin/packages/py-torch/package.py
@@ -107,9 +107,6 @@ class PyTorch(PythonPackage, CudaPackage):
     conflicts('+tbb', when='@:1.1')
     # https://github.com/pytorch/pytorch/issues/35149
     conflicts('+fbgemm', when='@1.4.0')
-    # https://github.com/pytorch/pytorch/issues/35478
-    conflicts('%clang@11.0.3-apple',
-              msg='Apple Clang 11.0.3 segfaults at build-time')
 
     conflicts('cuda_arch=none', when='+cuda',
               msg='Must specify CUDA compute capabilities of your GPU, see '
@@ -170,6 +167,17 @@ class PyTorch(PythonPackage, CudaPackage):
     depends_on('py-six', type='test')
     depends_on('py-psutil', type='test')
 
+    # https://github.com/pytorch/pytorch/pull/35607
+    # https://github.com/pytorch/pytorch/pull/37865
+    # Fixes CMake configuration error when XNNPACK is disabled
+    patch('xnnpack.patch', when='@1.5.0')
+
+    # https://github.com/pytorch/pytorch/pull/37086
+    # Fixes compilation with Clang 9.0.0 and Apple Clang 11.0.3
+    patch('https://github.com/pytorch/pytorch/commit/e921cd222a8fbeabf5a3e74e83e0d8dfb01aa8b5.patch',
+          sha256='7781c7ec0a661bf5a946a659f80e90df9dba116ad168762f15b10547113ae600',
+          when='@1.1:1.5')
+
     # Both build and install run cmake/make/make install
     # Only run once to speed up build times
     phases = ['install']
diff --git a/var/spack/repos/builtin/packages/py-torch/xnnpack.patch b/var/spack/repos/builtin/packages/py-torch/xnnpack.patch
new file mode 100644
index 00000000000..154033081e7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-torch/xnnpack.patch
@@ -0,0 +1,47 @@
+diff --git a/caffe2/CMakeLists.txt b/caffe2/CMakeLists.txt
+index 8025a7de3c..0da37079d6 100644
+--- a/caffe2/CMakeLists.txt
++++ b/caffe2/CMakeLists.txt
+@@ -46,12 +46,19 @@ if (INTERN_BUILD_ATEN_OPS)
+   list(APPEND Caffe2_DEPENDENCY_INCLUDE ${ATen_THIRD_PARTY_INCLUDE})
+ endif()
+ 
++# {Q/X,etc} NPACK support is enabled by default, if none of these options
++# are selected, turn this flag ON to incidate the support is disabled
++set(NNPACK_AND_FAMILY_DISABLED OFF)
++if(NOT (USE_NNPACK OR USE_QNNPACK OR USE_PYTORCH_QNNPACK OR USE_XNNPACK))
++  set(NNPACK_AND_FAMILY_DISABLED ON)
++endif()
++
+ # ---[ Caffe2 build
+ # Note: the folders that are being commented out have not been properly
+ # addressed yet.
+ 
+ # For pthreadpool_new_if_impl. TODO: Remove when threadpools are unitied.
+-if (NOT MSVC)
++if (NOT MSVC AND NOT NNPACK_AND_FAMILY_DISABLED)
+   IF(NOT TARGET fxdiv)
+     SET(FXDIV_BUILD_TESTS OFF CACHE BOOL "")
+     SET(FXDIV_BUILD_BENCHMARKS OFF CACHE BOOL "")
+@@ -710,7 +717,7 @@ ELSEIF(USE_CUDA)
+ ENDIF()
+ 
+ 
+-if (NOT MSVC)
++if (NOT MSVC AND NOT NNPACK_AND_FAMILY_DISABLED)
+   TARGET_LINK_LIBRARIES(torch_cpu PRIVATE fxdiv)
+ endif()
+ 
+diff --git a/caffe2/utils/CMakeLists.txt b/caffe2/utils/CMakeLists.txt
+index 27aabb1315..3c7845c67d 100644
+--- a/caffe2/utils/CMakeLists.txt
++++ b/caffe2/utils/CMakeLists.txt
+@@ -36,7 +36,7 @@ list(APPEND Caffe2_CPU_SRCS
+ # ---[ threadpool/pthreadpool* is a local modification of the NNPACK
+ # pthreadpool with a very similar interface. Neither NNPACK, nor this
+ # thread pool supports Windows.
+-if (NOT MSVC)
++if (NOT MSVC AND NOT NNPACK_AND_FAMILY_DISABLED)
+   add_definitions(-DUSE_INTERNAL_THREADPOOL_IMPL)
+   set(Caffe2_CPU_SRCS ${Caffe2_CPU_SRCS}
+           utils/threadpool/pthreadpool.cc

From b030a81a5f1d4a02cf611fc771bbeaf0bfc7963e Mon Sep 17 00:00:00 2001
From: Peter Scheibel <scheibel1@llnl.gov>
Date: Tue, 5 May 2020 17:37:34 -0700
Subject: [PATCH 265/802] Automatically find externals (#15158)

Add a `spack external find` command that tries to populate
`packages.yaml` with external packages from the user's `$PATH`. This
focuses on finding build dependencies. Currently, support has only been
added for `cmake`.

For a package to be discoverable with `spack external find`, it must define:
  * an `executables` class attribute containing a list of
    regular expressions that match executable names.
  * a `determine_spec_details(prefix, specs_in_prefix)` method

Spack will call `determine_spec_details()` once for each prefix where
executables are found, passing in the path to the prefix and the path to
all found executables. The package is responsible for invoking the
executables and figuring out what type of installation(s) are in the
prefix, and returning one or more specs (each with version, variants or
whatever else the user decides to include in the spec).

The found specs and prefixes will be added to the user's `packages.yaml`
file. Providing the `--not-buildable` option will mark all generated
entries in `packages.yaml` as `buildable: False`
---
 lib/spack/docs/build_settings.rst             |  31 ++
 lib/spack/spack/cmd/external.py               | 271 ++++++++++++++++++
 lib/spack/spack/test/cmd/external.py          | 177 ++++++++++++
 share/spack/spack-completion.bash             |  20 +-
 .../packages/find-externals1/package.py       |  34 +++
 .../builtin/packages/automake/package.py      |  21 ++
 .../repos/builtin/packages/cmake/package.py   |  21 ++
 7 files changed, 574 insertions(+), 1 deletion(-)
 create mode 100644 lib/spack/spack/cmd/external.py
 create mode 100644 lib/spack/spack/test/cmd/external.py
 create mode 100644 var/spack/repos/builtin.mock/packages/find-externals1/package.py

diff --git a/lib/spack/docs/build_settings.rst b/lib/spack/docs/build_settings.rst
index cfd850af28a..dee892f272f 100644
--- a/lib/spack/docs/build_settings.rst
+++ b/lib/spack/docs/build_settings.rst
@@ -158,6 +158,37 @@ Spack can then use any of the listed external implementations of MPI
 to satisfy a dependency, and will choose depending on the compiler and
 architecture.
 
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Automatically Find External Packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+A user can run the :ref:`spack external find <spack-external-find>` command
+to search for system-provided packages and add them to ``packages.yaml``.
+After running this command your ``packages.yaml`` may include new entries:
+
+.. code-block:: yaml
+
+   packages:
+     cmake:
+       paths:
+         cmake@3.17.2: /usr
+
+Generally this is useful for detecting a small set of commonly-used packages;
+for now this is generally limited to finding build-only dependencies.
+Specific limitations include:
+
+* A package must define ``executables`` and ``determine_spec_details``
+  for Spack to locate instances of that package.
+* This is currently intended to find build dependencies rather than
+  library packages.
+* Spack does not overwrite existing entries in the package configuration:
+  If there is an external defined for a spec at any configuration scope,
+  then Spack will not add a new external entry (``spack config blame packages``
+  can help locate all external entries).
+* Currently this logic is focused on examining ``PATH`` and does not
+  search through modules (although it should find the package if a
+  module is loaded for it).
+
 .. _concretization-preferences:
 
 --------------------------
diff --git a/lib/spack/spack/cmd/external.py b/lib/spack/spack/cmd/external.py
new file mode 100644
index 00000000000..f93deaba037
--- /dev/null
+++ b/lib/spack/spack/cmd/external.py
@@ -0,0 +1,271 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from __future__ import print_function
+from collections import defaultdict, namedtuple
+import argparse
+import os
+import re
+import six
+
+import spack
+import spack.error
+import llnl.util.tty as tty
+import spack.util.spack_yaml as syaml
+import spack.util.environment
+import llnl.util.filesystem
+
+description = "add external packages to Spack configuration"
+section = "config"
+level = "short"
+
+
+def setup_parser(subparser):
+    sp = subparser.add_subparsers(
+        metavar='SUBCOMMAND', dest='external_command')
+
+    find_parser = sp.add_parser('find', help=external_find.__doc__)
+    find_parser.add_argument(
+        '--not-buildable', action='store_true', default=False,
+        help="packages with detected externals won't be built with Spack")
+    find_parser.add_argument('packages', nargs=argparse.REMAINDER)
+
+
+def is_executable(path):
+    return os.path.isfile(path) and os.access(path, os.X_OK)
+
+
+def _get_system_executables():
+    """Get the paths of all executables available from the current PATH.
+
+    For convenience, this is constructed as a dictionary where the keys are
+    the executable paths and the values are the names of the executables
+    (i.e. the basename of the executable path).
+
+    There may be multiple paths with the same basename. In this case it is
+    assumed there are two different instances of the executable.
+    """
+    path_hints = spack.util.environment.get_path('PATH')
+    search_paths = llnl.util.filesystem.search_paths_for_executables(
+        *path_hints)
+
+    path_to_exe = {}
+    # Reverse order of search directories so that an exe in the first PATH
+    # entry overrides later entries
+    for search_path in reversed(search_paths):
+        for exe in os.listdir(search_path):
+            exe_path = os.path.join(search_path, exe)
+            if is_executable(exe_path):
+                path_to_exe[exe_path] = exe
+    return path_to_exe
+
+
+ExternalPackageEntry = namedtuple(
+    'ExternalPackageEntry',
+    ['spec', 'base_dir'])
+
+
+def _generate_pkg_config(external_pkg_entries):
+    """Generate config according to the packages.yaml schema for a single
+    package.
+
+    This does not generate the entire packages.yaml. For example, given some
+    external entries for the CMake package, this could return::
+
+       { 'paths': {
+             'cmake@3.17.1': '/opt/cmake-3.17.1/',
+             'cmake@3.16.5': '/opt/cmake-3.16.5/'
+         }
+       }
+    """
+    paths_dict = syaml.syaml_dict()
+    for e in external_pkg_entries:
+        if not _spec_is_valid(e.spec):
+            continue
+        paths_dict[str(e.spec)] = e.base_dir
+    pkg_dict = syaml.syaml_dict()
+    pkg_dict['paths'] = paths_dict
+
+    return pkg_dict
+
+
+def _spec_is_valid(spec):
+    try:
+        str(spec)
+    except spack.error.SpackError:
+        # It is assumed here that we can at least extract the package name from
+        # the spec so we can look up the implementation of
+        # determine_spec_details
+        tty.warn('Constructed spec for {0} does not have a string'
+                 ' representation'.format(spec.name))
+        return False
+
+    try:
+        spack.spec.Spec(str(spec))
+    except spack.error.SpackError:
+        tty.warn('Constructed spec has a string representation but the string'
+                 ' representation does not evaluate to a valid spec: {0}'
+                 .format(str(spec)))
+        return False
+
+    return True
+
+
+def external_find(args):
+    if args.packages:
+        packages_to_check = list(spack.repo.get(pkg) for pkg in args.packages)
+    else:
+        packages_to_check = spack.repo.path.all_packages()
+
+    pkg_to_entries = _get_external_packages(packages_to_check)
+    _update_pkg_config(pkg_to_entries, args.not_buildable)
+
+
+def _group_by_prefix(paths):
+    groups = defaultdict(set)
+    for p in paths:
+        groups[os.path.dirname(p)].add(p)
+    return groups.items()
+
+
+def _convert_to_iterable(single_val_or_multiple):
+    x = single_val_or_multiple
+    if x is None:
+        return []
+    elif isinstance(x, six.string_types):
+        return [x]
+    elif isinstance(x, spack.spec.Spec):
+        # Specs are iterable, but a single spec should be converted to a list
+        return [x]
+
+    try:
+        iter(x)
+        return x
+    except TypeError:
+        return [x]
+
+
+def _determine_base_dir(prefix):
+    # Given a prefix where an executable is found, assuming that prefix ends
+    # with /bin/, strip off the 'bin' directory to get a Spack-compatible
+    # prefix
+    assert os.path.isdir(prefix)
+    if os.path.basename(prefix) == 'bin':
+        return os.path.dirname(prefix)
+
+
+def _get_predefined_externals():
+    # Pull from all scopes when looking for preexisting external package
+    # entries
+    pkg_config = spack.config.get('packages')
+    already_defined_specs = set()
+    for pkg_name, per_pkg_cfg in pkg_config.items():
+        paths = per_pkg_cfg.get('paths', {})
+        already_defined_specs.update(spack.spec.Spec(k) for k in paths)
+        modules = per_pkg_cfg.get('modules', {})
+        already_defined_specs.update(spack.spec.Spec(k) for k in modules)
+    return already_defined_specs
+
+
+def _update_pkg_config(pkg_to_entries, not_buildable):
+    predefined_external_specs = _get_predefined_externals()
+
+    pkg_to_cfg = {}
+    for pkg_name, ext_pkg_entries in pkg_to_entries.items():
+        new_entries = list(
+            e for e in ext_pkg_entries
+            if (e.spec not in predefined_external_specs))
+
+        pkg_config = _generate_pkg_config(new_entries)
+        if not_buildable:
+            pkg_config['buildable'] = False
+        pkg_to_cfg[pkg_name] = pkg_config
+
+    cfg_scope = spack.config.default_modify_scope()
+    pkgs_cfg = spack.config.get('packages', scope=cfg_scope)
+
+    spack.config._merge_yaml(pkgs_cfg, pkg_to_cfg)
+    spack.config.set('packages', pkgs_cfg, scope=cfg_scope)
+
+
+def _get_external_packages(packages_to_check, system_path_to_exe=None):
+    if not system_path_to_exe:
+        system_path_to_exe = _get_system_executables()
+
+    exe_pattern_to_pkgs = defaultdict(list)
+    for pkg in packages_to_check:
+        if hasattr(pkg, 'executables'):
+            for exe in pkg.executables:
+                exe_pattern_to_pkgs[exe].append(pkg)
+
+    pkg_to_found_exes = defaultdict(set)
+    for exe_pattern, pkgs in exe_pattern_to_pkgs.items():
+        compiled_re = re.compile(exe_pattern)
+        for path, exe in system_path_to_exe.items():
+            if compiled_re.search(exe):
+                for pkg in pkgs:
+                    pkg_to_found_exes[pkg].add(path)
+
+    pkg_to_entries = defaultdict(list)
+    resolved_specs = {}  # spec -> exe found for the spec
+
+    for pkg, exes in pkg_to_found_exes.items():
+        if not hasattr(pkg, 'determine_spec_details'):
+            tty.warn("{0} must define 'determine_spec_details' in order"
+                     " for Spack to detect externally-provided instances"
+                     " of the package.".format(pkg.name))
+            continue
+
+        # TODO: iterate through this in a predetermined order (e.g. by package
+        # name) to get repeatable results when there are conflicts. Note that
+        # if we take the prefixes returned by _group_by_prefix, then consider
+        # them in the order that they appear in PATH, this should be sufficient
+        # to get repeatable results.
+        for prefix, exes_in_prefix in _group_by_prefix(exes):
+            # TODO: multiple instances of a package can live in the same
+            # prefix, and a package implementation can return multiple specs
+            # for one prefix, but without additional details (e.g. about the
+            # naming scheme which differentiates them), the spec won't be
+            # usable.
+            specs = _convert_to_iterable(
+                pkg.determine_spec_details(prefix, exes_in_prefix))
+
+            if not specs:
+                tty.debug(
+                    'The following executables in {0} were decidedly not'
+                    'part of the package {1}: {2}'
+                    .format(prefix, pkg.name, ', '.join(exes_in_prefix))
+                )
+
+            for spec in specs:
+                pkg_prefix = _determine_base_dir(prefix)
+
+                if not pkg_prefix:
+                    tty.debug("{0} does not end with a 'bin/' directory: it"
+                              " cannot be added as a Spack package"
+                              .format(prefix))
+                    continue
+
+                if spec in resolved_specs:
+                    prior_prefix = ', '.join(resolved_specs[spec])
+
+                    tty.debug(
+                        "Executables in {0} and {1} are both associated"
+                        " with the same spec {2}"
+                        .format(prefix, prior_prefix, str(spec)))
+                    continue
+                else:
+                    resolved_specs[spec] = prefix
+
+                pkg_to_entries[pkg.name].append(
+                    ExternalPackageEntry(spec=spec, base_dir=pkg_prefix))
+
+    return pkg_to_entries
+
+
+def external(parser, args):
+    action = {'find': external_find}
+
+    action[args.external_command](args)
diff --git a/lib/spack/spack/test/cmd/external.py b/lib/spack/spack/test/cmd/external.py
new file mode 100644
index 00000000000..0bdf67fe3ee
--- /dev/null
+++ b/lib/spack/spack/test/cmd/external.py
@@ -0,0 +1,177 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import pytest
+import os
+import stat
+
+import spack
+from spack.spec import Spec
+from spack.cmd.external import ExternalPackageEntry
+from spack.main import SpackCommand
+
+
+@pytest.fixture()
+def create_exe(tmpdir_factory):
+    def _create_exe(exe_name, content):
+        base_prefix = tmpdir_factory.mktemp('base-prefix')
+        base_prefix.ensure('bin', dir=True)
+        exe_path = str(base_prefix.join('bin', exe_name))
+        with open(exe_path, 'w') as f:
+            f.write("""\
+#!/bin/bash
+
+echo "{0}"
+""".format(content))
+
+        st = os.stat(exe_path)
+        os.chmod(exe_path, st.st_mode | stat.S_IEXEC)
+        return exe_path
+
+    yield _create_exe
+
+
+def test_find_external_single_package(create_exe):
+    pkgs_to_check = [spack.repo.get('cmake')]
+
+    cmake_path = create_exe("cmake", "cmake version 1.foo")
+    system_path_to_exe = {cmake_path: 'cmake'}
+
+    pkg_to_entries = spack.cmd.external._get_external_packages(
+        pkgs_to_check, system_path_to_exe)
+
+    pkg, entries = next(iter(pkg_to_entries.items()))
+    single_entry = next(iter(entries))
+
+    assert single_entry.spec == Spec('cmake@1.foo')
+
+
+def test_find_external_two_instances_same_package(create_exe):
+    pkgs_to_check = [spack.repo.get('cmake')]
+
+    # Each of these cmake instances is created in a different prefix
+    cmake_path1 = create_exe("cmake", "cmake version 1.foo")
+    cmake_path2 = create_exe("cmake", "cmake version 3.17.2")
+    system_path_to_exe = {
+        cmake_path1: 'cmake',
+        cmake_path2: 'cmake'}
+
+    pkg_to_entries = spack.cmd.external._get_external_packages(
+        pkgs_to_check, system_path_to_exe)
+
+    pkg, entries = next(iter(pkg_to_entries.items()))
+    spec_to_path = dict((e.spec, e.base_dir) for e in entries)
+    assert spec_to_path[Spec('cmake@1.foo')] == (
+        spack.cmd.external._determine_base_dir(os.path.dirname(cmake_path1)))
+    assert spec_to_path[Spec('cmake@3.17.2')] == (
+        spack.cmd.external._determine_base_dir(os.path.dirname(cmake_path2)))
+
+
+def test_find_external_update_config(mutable_config):
+    pkg_to_entries = {
+        'cmake': [
+            ExternalPackageEntry(Spec('cmake@1.foo'), '/x/y1/'),
+            ExternalPackageEntry(Spec('cmake@3.17.2'), '/x/y2/'),
+        ]
+    }
+
+    spack.cmd.external._update_pkg_config(pkg_to_entries, False)
+
+    pkgs_cfg = spack.config.get('packages')
+    cmake_cfg = pkgs_cfg['cmake']
+    cmake_paths_cfg = cmake_cfg['paths']
+
+    assert cmake_paths_cfg['cmake@1.foo'] == '/x/y1/'
+    assert cmake_paths_cfg['cmake@3.17.2'] == '/x/y2/'
+
+
+def test_get_executables(working_env, create_exe):
+    cmake_path1 = create_exe("cmake", "cmake version 1.foo")
+
+    os.environ['PATH'] = ':'.join([os.path.dirname(cmake_path1)])
+    path_to_exe = spack.cmd.external._get_system_executables()
+    assert path_to_exe[cmake_path1] == 'cmake'
+
+
+external = SpackCommand('external')
+
+
+def test_find_external_cmd(mutable_config, working_env, create_exe):
+    """Test invoking 'spack external find' with additional package arguments,
+    which restricts the set of packages that Spack looks for.
+    """
+    cmake_path1 = create_exe("cmake", "cmake version 1.foo")
+
+    os.environ['PATH'] = ':'.join([os.path.dirname(cmake_path1)])
+    external('find', 'cmake')
+
+    pkgs_cfg = spack.config.get('packages')
+    cmake_cfg = pkgs_cfg['cmake']
+    cmake_paths_cfg = cmake_cfg['paths']
+
+    assert 'cmake@1.foo' in cmake_paths_cfg
+
+
+def test_find_external_cmd_not_buildable(
+        mutable_config, working_env, create_exe):
+    """When the user invokes 'spack external find --not-buildable', the config
+    for any package where Spack finds an external version should be marked as
+    not buildable.
+    """
+    cmake_path1 = create_exe("cmake", "cmake version 1.foo")
+    os.environ['PATH'] = ':'.join([os.path.dirname(cmake_path1)])
+    external('find', '--not-buildable', 'cmake')
+    pkgs_cfg = spack.config.get('packages')
+    assert not pkgs_cfg['cmake']['buildable']
+
+
+def test_find_external_cmd_full_repo(
+        mutable_config, working_env, create_exe, mutable_mock_repo):
+    """Test invoking 'spack external find' with no additional arguments, which
+    iterates through each package in the repository.
+    """
+
+    exe_path1 = create_exe(
+        "find-externals1-exe", "find-externals1 version 1.foo")
+
+    os.environ['PATH'] = ':'.join([os.path.dirname(exe_path1)])
+    external('find')
+
+    pkgs_cfg = spack.config.get('packages')
+    pkg_cfg = pkgs_cfg['find-externals1']
+    pkg_paths_cfg = pkg_cfg['paths']
+
+    assert 'find-externals1@1.foo' in pkg_paths_cfg
+
+
+def test_find_external_merge(mutable_config, mutable_mock_repo):
+    """Check that 'spack find external' doesn't overwrite an existing spec
+    entry in packages.yaml.
+    """
+    pkgs_cfg_init = {
+        'find-externals1': {
+            'paths': {
+                'find-externals1@1.1': '/preexisting-prefix/'
+            },
+            'buildable': False
+        }
+    }
+
+    mutable_config.update_config('packages', pkgs_cfg_init)
+
+    pkg_to_entries = {
+        'find-externals1': [
+            ExternalPackageEntry(Spec('find-externals1@1.1'), '/x/y1/'),
+            ExternalPackageEntry(Spec('find-externals1@1.2'), '/x/y2/'),
+        ]
+    }
+    spack.cmd.external._update_pkg_config(pkg_to_entries, False)
+
+    pkgs_cfg = spack.config.get('packages')
+    pkg_cfg = pkgs_cfg['find-externals1']
+    pkg_paths_cfg = pkg_cfg['paths']
+
+    assert pkg_paths_cfg['find-externals1@1.1'] == '/preexisting-prefix/'
+    assert pkg_paths_cfg['find-externals1@1.2'] == '/x/y2/'
diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash
index fce5360ff59..12d4c599b89 100755
--- a/share/spack/spack-completion.bash
+++ b/share/spack/spack-completion.bash
@@ -313,7 +313,7 @@ _spack() {
     then
         SPACK_COMPREPLY="-h --help -H --all-help --color -C --config-scope -d --debug --timestamp --pdb -e --env -D --env-dir -E --no-env --use-env-repo -k --insecure -l --enable-locks -L --disable-locks -m --mock -p --profile --sorted-profile --lines -v --verbose --stacktrace -V --version --print-shell-vars"
     else
-        SPACK_COMPREPLY="activate add arch blame bootstrap build build-env buildcache cd checksum ci clean clone commands compiler compilers concretize config configure containerize create deactivate debug dependencies dependents deprecate dev-build diy docs edit env extensions fetch find flake8 gc gpg graph help info install license list load location log-parse maintainers mirror module patch pkg providers pydoc python reindex remove rm repo resource restage setup spec stage test uninstall unload upload-s3 url verify versions view"
+        SPACK_COMPREPLY="activate add arch blame bootstrap build build-env buildcache cd checksum ci clean clone commands compiler compilers concretize config configure containerize create deactivate debug dependencies dependents deprecate dev-build diy docs edit env extensions external fetch find flake8 gc gpg graph help info install license list load location log-parse maintainers mirror module patch pkg providers pydoc python reindex remove rm repo resource restage setup spec stage test uninstall unload upload-s3 url verify versions view"
     fi
 }
 
@@ -817,6 +817,24 @@ _spack_extensions() {
     fi
 }
 
+_spack_external() {
+    if $list_options
+    then
+        SPACK_COMPREPLY="-h --help"
+    else
+        SPACK_COMPREPLY="find"
+    fi
+}
+
+_spack_external_find() {
+    if $list_options
+    then
+        SPACK_COMPREPLY="-h --help --not-buildable"
+    else
+        _all_packages
+    fi
+}
+
 _spack_fetch() {
     if $list_options
     then
diff --git a/var/spack/repos/builtin.mock/packages/find-externals1/package.py b/var/spack/repos/builtin.mock/packages/find-externals1/package.py
new file mode 100644
index 00000000000..25e26dcced4
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/find-externals1/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+import os
+import re
+
+
+class FindExternals1(AutotoolsPackage):
+    executables = ['find-externals1-exe']
+
+    url = "http://www.example.com/find-externals-1.0.tar.gz"
+
+    version('1.0', 'hash-1.0')
+
+    @classmethod
+    def determine_spec_details(cls, prefix, exes_in_prefix):
+        exe_to_path = dict(
+            (os.path.basename(p), p) for p in exes_in_prefix
+        )
+        if 'find-externals1-exe' not in exe_to_path:
+            return None
+
+        exe = spack.util.executable.Executable(
+            exe_to_path['find-externals1-exe'])
+        output = exe('--version', output=str)
+        if output:
+            match = re.search(r'find-externals1.*version\s+(\S+)', output)
+            if match:
+                version_str = match.group(1)
+                return Spec('find-externals1@{0}'.format(version_str))
diff --git a/var/spack/repos/builtin/packages/automake/package.py b/var/spack/repos/builtin/packages/automake/package.py
index 5327c90daf5..0e9d22cb375 100644
--- a/var/spack/repos/builtin/packages/automake/package.py
+++ b/var/spack/repos/builtin/packages/automake/package.py
@@ -5,6 +5,9 @@
 
 from spack import *
 
+import os
+import re
+
 
 class Automake(AutotoolsPackage, GNUMirrorPackage):
     """Automake -- make file builder part of autotools"""
@@ -25,6 +28,24 @@ class Automake(AutotoolsPackage, GNUMirrorPackage):
 
     build_directory = 'spack-build'
 
+    executables = ['automake']
+
+    @classmethod
+    def determine_spec_details(cls, prefix, exes_in_prefix):
+        exe_to_path = dict(
+            (os.path.basename(p), p) for p in exes_in_prefix
+        )
+        if 'automake' not in exe_to_path:
+            return None
+
+        exe = spack.util.executable.Executable(exe_to_path['automake'])
+        output = exe('--version', output=str)
+        if output:
+            match = re.search(r'GNU automake\)\s+(\S+)', output)
+            if match:
+                version_str = match.group(1)
+                return Spec('automake@{0}'.format(version_str))
+
     def patch(self):
         # The full perl shebang might be too long
         files_to_be_patched_fmt = 'bin/{0}.in'
diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index acf5b1fcdc3..cfc13c436db 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -5,6 +5,9 @@
 
 from spack import *
 
+import re
+import os
+
 
 class Cmake(Package):
     """A cross-platform, open-source build system. CMake is a family of
@@ -13,6 +16,8 @@ class Cmake(Package):
     url      = 'https://github.com/Kitware/CMake/releases/download/v3.15.5/cmake-3.15.5.tar.gz'
     maintainers = ['chuckatkins']
 
+    executables = ['cmake']
+
     version('3.17.1',   sha256='3aa9114485da39cbd9665a0bfe986894a282d5f0882b1dea960a739496620727')
     version('3.17.0',   sha256='b74c05b55115eacc4fa2b77a814981dbda05cdc95a53e279fe16b7b272f00847')
     version('3.16.5',   sha256='5f760b50b8ecc9c0c37135fae5fbf00a2fef617059aa9d61c1bb91653e5a8bfc')
@@ -146,6 +151,22 @@ class Cmake(Package):
 
     phases = ['bootstrap', 'build', 'install']
 
+    @classmethod
+    def determine_spec_details(cls, prefix, exes_in_prefix):
+        exe_to_path = dict(
+            (os.path.basename(p), p) for p in exes_in_prefix
+        )
+        if 'cmake' not in exe_to_path:
+            return None
+
+        cmake = spack.util.executable.Executable(exe_to_path['cmake'])
+        output = cmake('--version', output=str)
+        if output:
+            match = re.search(r'cmake.*version\s+(\S+)', output)
+            if match:
+                version_str = match.group(1)
+                return Spec('cmake@{0}'.format(version_str))
+
     def flag_handler(self, name, flags):
         if name == 'cxxflags' and self.compiler.name == 'fj':
             cxx11plus_flags = (self.compiler.cxx11_flag,

From bf203383bd2c9ebd07babf733e90eee31908dc75 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Wed, 6 May 2020 11:51:29 -0700
Subject: [PATCH 266/802] macOS Package Builds (nightly) (#16345)

Add nightly builds for popular and commonly used packages on
macOS that should improve the onramp user experience if
working well.
---
 .github/workflows/install_spack.sh |  4 +++
 .github/workflows/macos_python.yml | 58 ++++++++++++++++++++++++++++++
 README.md                          |  1 +
 3 files changed, 63 insertions(+)
 create mode 100755 .github/workflows/install_spack.sh
 create mode 100644 .github/workflows/macos_python.yml

diff --git a/.github/workflows/install_spack.sh b/.github/workflows/install_spack.sh
new file mode 100755
index 00000000000..aa8a68adc1d
--- /dev/null
+++ b/.github/workflows/install_spack.sh
@@ -0,0 +1,4 @@
+#!/usr/bin/env sh
+git clone https://github.com/spack/spack.git
+. spack/share/spack/setup-env.sh
+spack compilers
diff --git a/.github/workflows/macos_python.yml b/.github/workflows/macos_python.yml
new file mode 100644
index 00000000000..f67df2a6b51
--- /dev/null
+++ b/.github/workflows/macos_python.yml
@@ -0,0 +1,58 @@
+# These are nightly package tests for macOS
+# focus areas:
+# - initial user experience
+# - scientific python stack
+name: macOS builds nightly
+
+on:
+  schedule:
+    # nightly at 1 AM
+    - cron: '0 1 * * *'
+
+# GitHub Action Limits
+# https://help.github.com/en/actions/reference/workflow-syntax-for-github-actions
+
+jobs:
+  install_gcc:
+    name: gcc with clang
+    runs-on: macos-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: spack install
+      run: |
+        . .github/workflows/install_spack.sh
+        spack install -v gcc
+
+  install_jupyter_clang:
+    name: jupyter
+    runs-on: macos-latest
+    timeout-minutes: 600
+    steps:
+    - uses: actions/checkout@v2
+    - name: spack install
+      run: |
+        . .github/workflows/install_spack.sh
+        spack install -v py-jupyter %clang
+
+  install_scipy_clang:
+    name: scipy, mpl, pd
+    runs-on: macos-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: spack install
+      run: |
+        . .github/workflows/install_spack.sh
+        spack install -v py-scipy %clang
+        spack install -v py-matplotlib %clang
+        spack install -v py-pandas %clang
+
+  install_mpi4py_clang:
+    name: mpi4py, petsc4py
+    runs-on: macos-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: spack install
+      run: |
+        . .github/workflows/install_spack.sh
+        spack install -v py-mpi4py %clang
+        spack install -v py-petsc4py %clang
diff --git a/README.md b/README.md
index a97d8fef57f..12414ba179d 100644
--- a/README.md
+++ b/README.md
@@ -2,6 +2,7 @@
 
 [![Build Status](https://travis-ci.org/spack/spack.svg?branch=develop)](https://travis-ci.org/spack/spack)
 [![Linux Builds](https://github.com/spack/spack/workflows/linux%20builds/badge.svg)](https://github.com/spack/spack/actions)
+[![macOS Builds (nightly)](https://github.com/spack/spack/workflows/macOS%20builds%20nightly/badge.svg?branch=develop)](https://github.com/spack/spack/actions?query=workflow%3A%22macOS+builds+nightly%22)
 [![codecov](https://codecov.io/gh/spack/spack/branch/develop/graph/badge.svg)](https://codecov.io/gh/spack/spack)
 [![Read the Docs](https://readthedocs.org/projects/spack/badge/?version=latest)](https://spack.readthedocs.io)
 [![Slack](https://spackpm.herokuapp.com/badge.svg)](https://spackpm.herokuapp.com)

From d0220a990c488fdee227c5f9fa40a3cfd5206376 Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Wed, 6 May 2020 12:10:08 -0700
Subject: [PATCH 267/802] fix underscore/dash problems for mic_knl and
 skylake_avx512 (#16491)

---
 lib/spack/spack/platforms/cray.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/spack/spack/platforms/cray.py b/lib/spack/spack/platforms/cray.py
index 8c5fe525e63..2fccf2fe55e 100644
--- a/lib/spack/spack/platforms/cray.py
+++ b/lib/spack/spack/platforms/cray.py
@@ -21,7 +21,8 @@
     'x86-cascadelake': 'cascadelake',
     'x86-naples': 'zen',
     'x86-rome': 'zen',  # Cheating because we have the wrong modules on rzcrayz
-    'x86-skylake': 'skylake-avx512'
+    'x86-skylake': 'skylake_avx512',
+    'mic-knl': 'mic_knl'
 }
 
 

From 6d1e9c3ff4f2758e64e6244cba144eb5b23cb765 Mon Sep 17 00:00:00 2001
From: Scott Wittenburg <scott.wittenburg@kitware.com>
Date: Wed, 6 May 2020 13:17:28 -0600
Subject: [PATCH 268/802] margo: update dependency on argobots (#16489)

---
 var/spack/repos/builtin/packages/margo/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/margo/package.py b/var/spack/repos/builtin/packages/margo/package.py
index 30e124cac64..d43d29841f2 100644
--- a/var/spack/repos/builtin/packages/margo/package.py
+++ b/var/spack/repos/builtin/packages/margo/package.py
@@ -28,7 +28,7 @@ class Margo(AutotoolsPackage):
     depends_on('pkgconfig', type='build')
 
     depends_on('mercury')
-    depends_on('argobots@1.0rc1:')
+    depends_on('argobots@1.0:')
 
     build_directory = 'spack-build'
 

From 1aacdc4e18a44eec840fdf1c3f48e2c3a8b81ab3 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <eafischer2@alaska.edu>
Date: Wed, 6 May 2020 16:35:36 -0400
Subject: [PATCH 269/802] qscintilla (#16182)

* qscintilla

* Revert "qscintilla"

This reverts commit 00bd00ea3c5af4f29de5dd6961acf03fb51e2ea0.

* Move logic to qt package.

* flake8

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
---
 var/spack/repos/builtin/packages/qt/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 08721e85c24..ce689892f8e 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -222,6 +222,9 @@ def setup_run_environment(self, env):
 
     def setup_dependent_build_environment(self, env, dependent_spec):
         env.set('QTDIR', self.prefix)
+        # https://riverbankcomputing.com/pipermail/qscintilla/2015-January/001012.html
+        env.set('QMAKEFEATURES', join_path(
+            dependent_spec.stage.source_path, 'Qt4Qt5', 'features'))
 
     def setup_dependent_package(self, module, dependent_spec):
         module.qmake = Executable(join_path(self.spec.prefix.bin, 'qmake'))

From d1983d7395ca51e7ef87bd9a79614b2f760cd994 Mon Sep 17 00:00:00 2001
From: yellowhat <yellowhat46@gmail.com>
Date: Wed, 6 May 2020 21:36:29 +0100
Subject: [PATCH 270/802] blis: FIX threads option, HPL: enable opemp variant
 for 2.3 (#16476)

* blis: FIX threads option

* HPL: openmp variant is ignored for 2.3

* blis: FIX flake8

* blis: FIX spacing

* Update var/spack/repos/builtin/packages/hpl/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* hpl: FIX spec --> self.spec, FIX blas with amdblis

* HPL: fix flake8

* HPL: FIX flake8

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 var/spack/repos/builtin/packages/blis/package.py |  4 +++-
 var/spack/repos/builtin/packages/hpl/package.py  | 12 +++++++++---
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/blis/package.py b/var/spack/repos/builtin/packages/blis/package.py
index c2fc1545a3e..fd06bc455e9 100644
--- a/var/spack/repos/builtin/packages/blis/package.py
+++ b/var/spack/repos/builtin/packages/blis/package.py
@@ -104,7 +104,9 @@ def darwin_fix(self):
 
     @property
     def libs(self):
-        return find_libraries(['libblis'], root=self.prefix, recursive=True)
+        return find_libraries(
+            ["libblis", "libblis-mt"], root=self.prefix, recursive=True
+        )
 
 
 class Blis(BlisBase):
diff --git a/var/spack/repos/builtin/packages/hpl/package.py b/var/spack/repos/builtin/packages/hpl/package.py
index 05909653c09..579abe76188 100644
--- a/var/spack/repos/builtin/packages/hpl/package.py
+++ b/var/spack/repos/builtin/packages/hpl/package.py
@@ -101,9 +101,15 @@ def configure(self, spec, prefix):
 
     @when('@2.3:')
     def configure_args(self):
-        config = [
-            'CFLAGS=-O3'
-        ]
+        filter_file(
+            r"^libs10=.*", "libs10=%s" % self.spec["blas"].libs.ld_flags,
+            "configure"
+        )
+
+        if '+openmp' in self.spec:
+            config = ['CFLAGS=-O3 ' + self.compiler.openmp_flag]
+        else:
+            config = ['CFLAGS=-O3']
 
         if (self.spec.satisfies('^intel-mkl') or
             self.spec.satisfies('^intel-parallel-studio+mkl')):

From 74b3ae4803eb899fe0da7f762b601dd00dd9c376 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 6 May 2020 18:05:26 -0500
Subject: [PATCH 271/802] PyTorch/Torchvision: fix deptype (#16495)

---
 var/spack/repos/builtin/packages/py-torch/package.py       | 2 +-
 var/spack/repos/builtin/packages/py-torchvision/package.py | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py
index b2b15c7dfc2..024e0d95b23 100644
--- a/var/spack/repos/builtin/packages/py-torch/package.py
+++ b/var/spack/repos/builtin/packages/py-torch/package.py
@@ -124,7 +124,7 @@ class PyTorch(PythonPackage, CudaPackage):
     depends_on('py-future', when='@1.1: ^python@:2', type='build')
     depends_on('py-pyyaml', type=('build', 'run'))
     depends_on('py-typing', when='@0.4: ^python@:3.4', type=('build', 'run'))
-    depends_on('py-pybind11', when='@0.4:', type=('build', 'run'))
+    depends_on('py-pybind11', when='@0.4:', type=('build', 'link', 'run'))
     depends_on('blas')
     depends_on('lapack')
     depends_on('protobuf', when='@0.4:')
diff --git a/var/spack/repos/builtin/packages/py-torchvision/package.py b/var/spack/repos/builtin/packages/py-torchvision/package.py
index faee2f087a0..9d4c3a0efaf 100644
--- a/var/spack/repos/builtin/packages/py-torchvision/package.py
+++ b/var/spack/repos/builtin/packages/py-torchvision/package.py
@@ -32,9 +32,9 @@ class PyTorchvision(PythonPackage):
     depends_on('py-setuptools', type='build')
     depends_on('py-numpy', type=('build', 'run'))
     depends_on('py-six', when='@:0.5', type=('build', 'run'))
-    depends_on('py-torch@1.4:', when='@0.6:', type=('build', 'run'))
-    depends_on('py-torch@1.2:', when='@0.4:', type=('build', 'run'))
-    depends_on('py-torch@1.1:', type=('build', 'run'))
+    depends_on('py-torch@1.4:', when='@0.6:', type=('build', 'link', 'run'))
+    depends_on('py-torch@1.2:', when='@0.4:', type=('build', 'link', 'run'))
+    depends_on('py-torch@1.1:', type=('build', 'link', 'run'))
     # https://github.com/pytorch/vision/issues/1712
     depends_on('py-pillow@4.1.1:6', when='@:0.4', type=('build', 'run'))  # or py-pillow-simd
     depends_on('py-pillow@4.1.1:',  when='@0.5:', type=('build', 'run'))  # or py-pillow-simd

From 638784e4c38420df5bf0ac74dc7ce2469bca4549 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Thu, 7 May 2020 01:11:40 +0200
Subject: [PATCH 272/802] Add new version of Geant4 (#16497)

---
 var/spack/repos/builtin/packages/geant4/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/geant4/package.py b/var/spack/repos/builtin/packages/geant4/package.py
index 4bf35792aac..3cd041d1e97 100644
--- a/var/spack/repos/builtin/packages/geant4/package.py
+++ b/var/spack/repos/builtin/packages/geant4/package.py
@@ -17,6 +17,7 @@ class Geant4(CMakePackage):
 
     maintainers = ['drbenmorgan']
 
+    version('10.6.1', sha256='4fd64149ae26952672a81ce5579d3806fda4bd251d486897093ac57633a42b7e')
     version('10.6.0', sha256='eebe6a170546064ff81ab3b00f513ccd1d4122a026514982368d503ac55a4ee4')
     version('10.5.1', sha256='2397eb859dc4de095ff66059d8bda9f060fdc42e10469dd7890946293eeb0e39')
     version('10.4.3', sha256='67f3bb6405a2c77e573936c2b933f5a4a33915aa379626a2eb3012009b91e1da')

From e8753fe972f2527ea70619fdbcdd377ec6f32509 Mon Sep 17 00:00:00 2001
From: Kevin Manalo <kmanalo@users.noreply.github.com>
Date: Wed, 6 May 2020 19:12:14 -0400
Subject: [PATCH 273/802] OpenMPI - Update to 3.1.6 (#16496)

---
 var/spack/repos/builtin/packages/openmpi/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index d0da29d774f..700711c55e0 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -86,7 +86,8 @@ class Openmpi(AutotoolsPackage):
     version('4.0.2', sha256='900bf751be72eccf06de9d186f7b1c4b5c2fa9fa66458e53b77778dffdfe4057')  # libmpi.so.40.20.2
     version('4.0.1', sha256='cce7b6d20522849301727f81282201d609553103ac0b09162cf28d102efb9709')  # libmpi.so.40.20.1
     version('4.0.0', sha256='2f0b8a36cfeb7354b45dda3c5425ef8393c9b04115570b615213faaa3f97366b')  # libmpi.so.40.20.0
-    version('3.1.5', preferred=True, sha256='fbf0075b4579685eec8d56d34d4d9c963e6667825548554f5bf308610af72133')  # libmpi.so.40.10.4
+    version('3.1.6', preferred=True, sha256='50131d982ec2a516564d74d5616383178361c2f08fdd7d1202b80bdf66a0d279')  # libmpi.so.40.10.4
+    version('3.1.5', sha256='fbf0075b4579685eec8d56d34d4d9c963e6667825548554f5bf308610af72133')  # libmpi.so.40.10.4
     version('3.1.4', sha256='17a69e0054db530c7dc119f75bd07d079efa147cf94bf27e590905864fe379d6')  # libmpi.so.40.10.4
     version('3.1.3', sha256='8be04307c00f51401d3fb9d837321781ea7c79f2a5a4a2e5d4eaedc874087ab6')  # libmpi.so.40.10.3
     version('3.1.2', sha256='c654ed847f34a278c52a15c98add40402b4a90f0c540779f1ae6c489af8a76c5')  # libmpi.so.40.10.2

From d2709fd3766678961bc4d3a6728cc52448309b72 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 6 May 2020 18:12:28 -0500
Subject: [PATCH 274/802] TensorFlow: add new version (#16494)

---
 .../builtin/packages/py-tensorflow/package.py | 23 ++++++++++++-------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-tensorflow/package.py b/var/spack/repos/builtin/packages/py-tensorflow/package.py
index b46cfbb4cea..78138b1e8b1 100644
--- a/var/spack/repos/builtin/packages/py-tensorflow/package.py
+++ b/var/spack/repos/builtin/packages/py-tensorflow/package.py
@@ -11,11 +11,12 @@ class PyTensorflow(Package, CudaPackage):
     """
 
     homepage = "https://www.tensorflow.org"
-    url      = "https://github.com/tensorflow/tensorflow/archive/v2.1.0.tar.gz"
+    url      = "https://github.com/tensorflow/tensorflow/archive/v2.2.0.tar.gz"
 
     maintainers = ['adamjstewart']
     import_modules = ['tensorflow']
 
+    version('2.2.0',  sha256='69cd836f87b8c53506c4f706f655d423270f5a563b76dc1cfa60fbc3184185a3')
     version('2.1.0',  sha256='638e541a4981f52c69da4a311815f1e7989bf1d67a41d204511966e1daed14f7')
     version('2.0.1',  sha256='29197d30923b9670992ee4b9c6161f50c7452e9a4158c720746e846080ac245a')
     version('2.0.0',  sha256='49b5f0495cd681cbcb5296a4476853d4aea19a43bdd9f179c928a977308a0617')
@@ -82,6 +83,7 @@ class PyTensorflow(Package, CudaPackage):
     variant('dynamic_kernels', default=False, description='Build kernels into separate shared objects')
 
     extends('python')
+    depends_on('python@3:', type=('build', 'run'), when='@2.1:')
 
     # TODO: Older versions of TensorFlow don't list the viable version range,
     # just the minimum version of bazel that will work. The latest version of
@@ -89,7 +91,8 @@ class PyTensorflow(Package, CudaPackage):
     # Need to investigate further.
 
     # See _TF_MIN_BAZEL_VERSION and _TF_MAX_BAZEL_VERSION in configure.py
-    depends_on('bazel@0.27.1:0.29.1', type='build', when='@2.1:')
+    depends_on('bazel@2.0.0',         type='build', when='@2.2:')
+    depends_on('bazel@0.27.1:0.29.1', type='build', when='@2.1.0:2.1.999')
     depends_on('bazel@0.24.1:0.26.1', type='build', when='@1.15:2.0')
     # See call to check_bazel_version in configure.py
     depends_on('bazel@0.24.1:0.25.2', type='build', when='@1.14.0')
@@ -116,18 +119,22 @@ class PyTensorflow(Package, CudaPackage):
     # Listed under REQUIRED_PACKAGES in tensorflow/tools/pip_package/setup.py
     depends_on('py-absl-py@0.7.0:', type=('build', 'run'), when='@1.12.1,1.14:')
     depends_on('py-absl-py@0.1.6:', type=('build', 'run'), when='@1.5:')
-    depends_on('py-astor@0.6.0:', type=('build', 'run'), when='@1.6:')
+    depends_on('py-astunparse@1.6.3', type=('build', 'run'), when='@2.2:')
+    depends_on('py-astor@0.6.0:', type=('build', 'run'), when='@1.6:2.1')
     depends_on('py-backports-weakref@1.0:', type=('build', 'run'), when='@1.3: ^python@:3.3')
     depends_on('py-backports-weakref@1.0rc1', type=('build', 'run'), when='@1.2.0:1.2.1')
     depends_on('py-enum34@1.1.6:', type=('build', 'run'), when='@1.5: ^python@:3.3')
     depends_on('py-enum34@1.1.6:', type=('build', 'run'), when='@1.4.0:1.4.1')
-    depends_on('py-gast@0.2.2', type=('build', 'run'), when='@1.15:')
-    depends_on('py-gast@0.2.0:', type=('build', 'run'), when='@1.6:')
+    depends_on('py-gast@0.3.3', type=('build', 'run'), when='@2.2:')
+    depends_on('py-gast@0.2.2', type=('build', 'run'), when='@1.15:2.1')
+    depends_on('py-gast@0.2.0:', type=('build', 'run'), when='@1.6:1.14')
+    depends_on('py-google-pasta@0.1.8:', type=('build', 'run'), when='@2.1:')
     depends_on('py-google-pasta@0.1.6:', type=('build', 'run'), when='@1.14:')
     depends_on('py-google-pasta@0.1.2:', type=('build', 'run'), when='@1.12.1')
-    depends_on('py-keras-applications@1.0.8:', type=('build', 'run'), when='@1.15:')
-    depends_on('py-keras-applications@1.0.6:', type=('build', 'run'), when='@1.12:')
-    depends_on('py-keras-applications@1.0.5:', type=('build', 'run'), when='@1.11:')
+    depends_on('py-h5py@2.10.0:2.10.999', type=('build', 'run'), when='@2.2:')
+    depends_on('py-keras-applications@1.0.8:', type=('build', 'run'), when='@1.15:2.1')
+    depends_on('py-keras-applications@1.0.6:', type=('build', 'run'), when='@1.12:1.14')
+    depends_on('py-keras-applications@1.0.5:', type=('build', 'run'), when='@1.11.0:1.11.999')
     depends_on('py-keras-preprocessing@1.1.0:', type=('build', 'run'), when='@2.1:')
     depends_on('py-keras-preprocessing@1.0.5:', type=('build', 'run'), when='@1.12:')
     depends_on('py-keras-preprocessing@1.0.3:', type=('build', 'run'), when='@1.11:')

From b14befe61a848c20811aed24e9015277e64ebb30 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 6 May 2020 18:12:40 -0500
Subject: [PATCH 275/802] Bazel: add new versions (#16493)

---
 .../repos/builtin/packages/bazel/package.py   | 12 ++++++++++--
 .../bazel/unix_cc_configure-3.0.patch         | 19 +++++++++++++++++++
 2 files changed, 29 insertions(+), 2 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/bazel/unix_cc_configure-3.0.patch

diff --git a/var/spack/repos/builtin/packages/bazel/package.py b/var/spack/repos/builtin/packages/bazel/package.py
index e9509e990b9..abe427c9603 100644
--- a/var/spack/repos/builtin/packages/bazel/package.py
+++ b/var/spack/repos/builtin/packages/bazel/package.py
@@ -15,10 +15,17 @@ class Bazel(Package):
     numbers of users."""
 
     homepage = "https://bazel.build/"
-    url      = "https://github.com/bazelbuild/bazel/releases/download/1.2.0/bazel-1.2.0-dist.zip"
+    url      = "https://github.com/bazelbuild/bazel/releases/download/3.1.0/bazel-3.1.0-dist.zip"
 
     maintainers = ['adamjstewart']
 
+    version('3.1.0',  sha256='d7f40d0cac95a06cea6cb5b7f7769085257caebc3ee84269dd9298da760d5615')
+    version('3.0.0',  sha256='530f5132e0a50da7ebb0ed08d9b6f1ddfd0d7d9b5d0beb2df5d687a4c8daf6b3')
+    version('2.2.0',  sha256='9379878a834d105a47a87d3d7b981852dd9f64bc16620eacd564b48533e169a7')
+    version('2.1.1',  sha256='83f67f28f4e47ff69043307d1791c9bffe83949e84165d49058b84eded932647')
+    version('2.1.0',  sha256='3371cd9050989173a3b27364668328653a65653a50a85c320adc53953b4d5f46')
+    version('2.0.1',  sha256='a863ed9e6fc420fbd92e63a12fe1a5b9be1a7a36f11f61f1fdc582c813bbe543')
+    version('2.0.0',  sha256='724da3c656f68e787a86ebb9844773aa1c2e3a873cc39462a8f1b336153d6cbb')
     version('1.2.1',  sha256='255da49d0f012bc4f2c1d6d3ccdbe578e22fe97b8d124e1629a486fe2a09d3e1')
     version('1.2.0',  sha256='9cb46b0a18b9166730307a0e82bf4c02281a1cc6da0fb11239e6fe4147bdee6e')
     version('1.1.0',  sha256='4b66a8c93af7832ed32e7236cf454a05f3aa06d25a8576fc3f83114f142f95ab')
@@ -104,7 +111,8 @@ class Bazel(Package):
     patch('bazelconfiguration-0.3.patch', when='@:0.13')
 
     # Inject include paths
-    patch('unix_cc_configure-0.15.patch',  when='@0.15:')
+    patch('unix_cc_configure-3.0.patch',   when='@3:')
+    patch('unix_cc_configure-0.15.patch',  when='@0.15:2')
     patch('unix_cc_configure-0.10.patch',  when='@0.10:0.14')
     patch('unix_cc_configure-0.5.3.patch', when='@0.5.3:0.9')
     patch('cc_configure-0.5.0.patch', when='@0.5.0:0.5.2')
diff --git a/var/spack/repos/builtin/packages/bazel/unix_cc_configure-3.0.patch b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-3.0.patch
new file mode 100644
index 00000000000..1140b0c306c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-3.0.patch
@@ -0,0 +1,19 @@
+diff --git a/tools/cpp/unix_cc_configure.bzl b/tools/cpp/unix_cc_configure.bzl
+index 5feb10b76a..cde0b8f8f1 100644
+--- a/tools/cpp/unix_cc_configure.bzl
++++ b/tools/cpp/unix_cc_configure.bzl
+@@ -151,8 +151,14 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc, lang_flag, additional_fl
+         ).stdout.strip() + "/share"
+         inc_directories.append(_prepare_include_path(repository_ctx, resource_dir))
+ 
++    env = repository_ctx.os.environ
++    if "SPACK_INCLUDE_DIRS" in env:
++        for path in env["SPACK_INCLUDE_DIRS"].split(":"):
++            inc_directories.append(path)
++
+     return inc_directories
+ 
++
+ def _is_compiler_option_supported(repository_ctx, cc, option):
+     """Checks that `option` is supported by the C compiler. Doesn't %-escape the option."""
+     result = repository_ctx.execute([

From 2139c8e53ebde69095b643302291a35c4474515c Mon Sep 17 00:00:00 2001
From: Sergey Kosukhin <sergey.kosukhin@mpimet.mpg.de>
Date: Thu, 7 May 2020 01:14:10 +0200
Subject: [PATCH 276/802] py-netcdf4: make sure we don't use system hdf5.
 (#16492)

---
 .../builtin/packages/py-netcdf4/disable_pkgconf.patch      | 6 ++++++
 var/spack/repos/builtin/packages/py-netcdf4/package.py     | 7 +++++++
 2 files changed, 13 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-netcdf4/disable_pkgconf.patch

diff --git a/var/spack/repos/builtin/packages/py-netcdf4/disable_pkgconf.patch b/var/spack/repos/builtin/packages/py-netcdf4/disable_pkgconf.patch
new file mode 100644
index 00000000000..b2b690c7c3e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-netcdf4/disable_pkgconf.patch
@@ -0,0 +1,6 @@
+--- a/setup.py
++++ b/setup.py
+@@ -309,2 +309,3 @@ except OSError:
+     HAS_PKG_CONFIG = False
++HAS_PKG_CONFIG = False
+ 
diff --git a/var/spack/repos/builtin/packages/py-netcdf4/package.py b/var/spack/repos/builtin/packages/py-netcdf4/package.py
index a9dd01db2c2..5516bc751e3 100644
--- a/var/spack/repos/builtin/packages/py-netcdf4/package.py
+++ b/var/spack/repos/builtin/packages/py-netcdf4/package.py
@@ -25,6 +25,13 @@ class PyNetcdf4(PythonPackage):
     depends_on('netcdf-c')
     depends_on('hdf5@1.8.0:+hl')
 
+    # The installation script tries to find hdf5 using pkg-config. However, the
+    # version of hdf5 installed with Spack does not have pkg-config files.
+    # Therefore, if pkg-config finds hdf5.pc at all (e.g. provided by
+    # Ubuntu/Debian package manager), it is definitely not what we need. The
+    # following patch disables the usage of pkg-config at all.
+    patch('disable_pkgconf.patch')
+
     def setup_build_environment(self, env):
         """Ensure installed netcdf and hdf5 libraries are used"""
         # Explicitly set these variables so setup.py won't erroneously pick up

From 18e1e2424fb10cb13bcbd2b2d1d986700912e35c Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 6 May 2020 20:44:55 -0500
Subject: [PATCH 277/802] py-shapely: fix unit tests (#16500)

---
 .../builtin/packages/py-shapely/package.py      | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-shapely/package.py b/var/spack/repos/builtin/packages/py-shapely/package.py
index a6b2e8ceee1..a25e4d214fe 100644
--- a/var/spack/repos/builtin/packages/py-shapely/package.py
+++ b/var/spack/repos/builtin/packages/py-shapely/package.py
@@ -4,6 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import os
+import sys
 
 
 class PyShapely(PythonPackage):
@@ -38,7 +39,8 @@ class PyShapely(PythonPackage):
 
     # https://github.com/Toblerity/Shapely/pull/891
     patch('https://github.com/Toblerity/Shapely/commit/98f6b36710bbe05b4ab59231cb0e08b06fe8b69c.patch',
-          sha256='4984cd0590beb5091f213948a953f70cea08ea11c5db1de07ba98c19e3d13f06')
+          sha256='4984cd0590beb5091f213948a953f70cea08ea11c5db1de07ba98c19e3d13f06',
+          when='@:1.7')
 
     @when('^python@3.7:')
     def patch(self):
@@ -53,7 +55,14 @@ def setup_build_environment(self, env):
         env.set('GEOS_CONFIG',
                 join_path(self.spec['geos'].prefix.bin, 'geos-config'))
 
+        # Shapely uses ctypes.util.find_library, which searches LD_LIBRARY_PATH
+        # Our RPATH logic works fine, but the unit tests fail without this
+        # https://github.com/Toblerity/Shapely/issues/909
+        libs = ':'.join(self.spec['geos'].libs.directories)
+        if sys.platform == 'darwin':
+            env.prepend_path('DYLD_FALLBACK_LIBRARY_PATH', libs)
+        else:
+            env.prepend_path('LD_LIBRARY_PATH', libs)
+
     def test(self):
-        # Tests fail when 'geos' library not found in usual search directories
-        # python('-m', 'pytest')
-        pass
+        python('-m', 'pytest')

From 9c218079f00e9b3c7285cd94dcc7836531f722a5 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 6 May 2020 21:49:46 -0500
Subject: [PATCH 278/802] Install RMPISNOW wrapper in prefix.bin for r-snow
 (#16479)

If using mpirun, the R sessions can be started with a wrapper script
that helps set up the R session cluster. Put this wrapper in the PATH so
it is easily accessible.
---
 var/spack/repos/builtin/packages/r-snow/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/repos/builtin/packages/r-snow/package.py b/var/spack/repos/builtin/packages/r-snow/package.py
index 393ca504446..9d07e4943b7 100644
--- a/var/spack/repos/builtin/packages/r-snow/package.py
+++ b/var/spack/repos/builtin/packages/r-snow/package.py
@@ -17,3 +17,8 @@ class RSnow(RPackage):
     version('0.4-2', sha256='ee070187aea3607c9ca6235399b3db3e181348692405d038e962e06aefccabd7')
 
     depends_on('r@2.13.1:', type=('build', 'run'))
+
+    @run_after('install')
+    def install_wrapper(self):
+        mkdir(self.prefix.bin)
+        install('inst/RMPISNOW', self.prefix.bin)

From 8845358f10c5007137bd18c3dbc8e8d423f7db94 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Thu, 7 May 2020 04:51:04 +0200
Subject: [PATCH 279/802] New version of pylint + fix dependencies (#16443)

* New version of pylint + fix dependencies

* Update package.py

* Update package.py
---
 .../repos/builtin/packages/py-pylint/package.py     | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-pylint/package.py b/var/spack/repos/builtin/packages/py-pylint/package.py
index 02d8b8223fd..23cbfcf93a5 100644
--- a/var/spack/repos/builtin/packages/py-pylint/package.py
+++ b/var/spack/repos/builtin/packages/py-pylint/package.py
@@ -7,11 +7,12 @@
 
 
 class PyPylint(PythonPackage):
-    """array processing for numbers, strings, records, and objects."""
+    """python code static checker"""
 
     homepage = "https://pypi.python.org/pypi/pylint"
     url      = "https://pypi.io/packages/source/p/pylint/pylint-1.6.5.tar.gz"
 
+    version('2.3.1', sha256='723e3db49555abaf9bf79dc474c6b9e2935ad82230b10c1138a71ea41ac0fff1')
     version('2.3.0', sha256='ee80c7af4f127b2a480d83010c9f0e97beb8eaa652b78c2837d3ed30b12e1182')
     version('1.9.4', sha256='ee1e85575587c5b58ddafa25e1c1b01691ef172e139fc25585e5d3f02451da93')
     # version('1.7.2', sha256='ea6afb93a9ed810cf52ff3838eb3a15e2bf6a81b80de0eaede1ce442caa5ca69') # see dependencies
@@ -20,13 +21,19 @@ class PyPylint(PythonPackage):
     version('1.4.1', sha256='3e383060edd432cbbd0e8bd686f5facfe918047ffe1bb401ab5897cb6ee0f030')
 
     extends('python', ignore=r'bin/pytest')
+    depends_on('python@2.7:2.8,3.4:3.6', when='@:1', type=('build', 'run'))
+    depends_on('python@3.4:', when='@2:', type=('build', 'run'))
     depends_on('py-astroid', type=('build', 'run'))
     # note there is no working version of astroid for this
     depends_on('py-astroid@1.5.1:', type=('build', 'run'), when='@1.7:')
-    depends_on('py-astroid@1.6:1.9', type=('build', 'run'), when='@1.9.4:')
-    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-astroid@1.6:1.9', type=('build', 'run'), when='@1.9.4')
+    depends_on('py-astroid@2.0:', type=('build', 'run'), when='@2.2.0:')
+    depends_on('py-astroid@2.2.0:2.999.999', type=('build', 'run'), when='@2.3.0:')
+    depends_on('py-six', type=('build', 'run'), when='@1:')
     depends_on('py-isort@4.2.5:', type=('build', 'run'))
+    depends_on('py-isort@4.2.5:4.999', when='@2.3.1:', type=('build', 'run'))
     depends_on('py-mccabe', type=('build', 'run'))
+    depends_on('py-mccabe@0.6.0:0.6.999', when='@2.3.1:', type=('build', 'run'))
     depends_on('py-editdistance', type=('build', 'run'), when='@:1.7')
     depends_on('py-setuptools@17.1:', type='build')
     # depends_on('py-setuptools-scm@1.15.0:', type='build')

From 50a2690ce13388f3e5b13192cf09f757ed6389a1 Mon Sep 17 00:00:00 2001
From: takanori-ihara <62980219+takanori-ihara@users.noreply.github.com>
Date: Thu, 7 May 2020 11:53:16 +0900
Subject: [PATCH 280/802] Add new package:py-json5 (#16273)

* Add new package:py-json5

* Remove unnecessary line
---
 .../builtin/packages/py-json5/package.py      | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-json5/package.py

diff --git a/var/spack/repos/builtin/packages/py-json5/package.py b/var/spack/repos/builtin/packages/py-json5/package.py
new file mode 100644
index 00000000000..71b0b50156e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-json5/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyJson5(PythonPackage):
+    """The JSON5 Data Interchange Format (JSON5) is a superset of JSON that aims
+       to alleviate some of the limitations of JSON by expanding its syntax to
+       include some productions from ECMAScript 5.1."""
+
+    homepage = "https://github.com/dpranke/pyjson5"
+    url      = "https://pypi.io/packages/source/j/json5/json5-0.9.4.tar.gz"
+
+    version('0.9.4', sha256='2ebfad1cd502dca6aecab5b5c36a21c732c3461ddbc412fb0e9a52b07ddfe586')
+
+    depends_on('py-setuptools', type='build')

From 830f3f79d9f7d2d15907947a49914ac16a26f5c3 Mon Sep 17 00:00:00 2001
From: "Tomoki, Karatsu" <49965247+t-karatsu@users.noreply.github.com>
Date: Thu, 7 May 2020 11:55:09 +0900
Subject: [PATCH 281/802] openfoam: correspond to build with Fujitsu compiler.
 (#15941)

* openfoam: correspond to build with Fujitsu compiler.

* openfoam: add rules for Fujitsu compiler (on linuxARM64)

- the Fujitsu compiler is a clang derivative, so use a modified
  version of the clang rules if upstream does not supply anything
---
 .../builtin/packages/openfoam/package.py      | 36 ++++++++++++++++---
 1 file changed, 32 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/openfoam/package.py b/var/spack/repos/builtin/packages/openfoam/package.py
index fd915abae24..ce812f8effa 100644
--- a/var/spack/repos/builtin/packages/openfoam/package.py
+++ b/var/spack/repos/builtin/packages/openfoam/package.py
@@ -540,6 +540,35 @@ def patch(self):
                     rcfile,
                     backup=False)
 
+    @when('@1906: %fj')
+    @run_before('configure')
+    def make_fujitsu_rules(self):
+        """Create Fujitsu rules (clang variant) unless supplied upstream.
+        Implemented for 1906 and newer - older rules are messier to edit
+        """
+        general_rules = 'wmake/rules/General'
+        arch_rules = join_path('wmake/rules/linuxARM64')  # self.arch
+        src = arch_rules + 'Clang'
+        dst = arch_rules + 'Fujitsu'  # self.compiler
+
+        if os.path.exists(dst):
+            return
+
+        tty.info('Add Fujitsu wmake rules')
+        copy_tree(src, dst)
+
+        for cfg in ['c', 'c++', 'general']:
+            rule = join_path(dst, cfg)
+            filter_file('Clang', 'Fujitsu', rule, backup=False)
+
+        src = join_path(general_rules, 'Clang')
+        dst = join_path(general_rules, 'Fujitsu')  # self.compiler
+        copy_tree(src, dst)
+        filter_file('clang', spack_cc, join_path(dst, 'c'),
+                    backup=False, string=True)
+        filter_file('clang++', spack_cxx, join_path(dst, 'c++'),
+                    backup=False, string=True)
+
     def configure(self, spec, prefix):
         """Make adjustments to the OpenFOAM configuration files in their various
         locations: etc/bashrc, etc/config.sh/FEATURE and customizations that
@@ -800,7 +829,7 @@ class OpenfoamArch(object):
 
     #: Map spack compiler names to OpenFOAM compiler names
     #  By default, simply capitalize the first letter
-    compiler_mapping = {'intel': 'icc'}
+    compiler_mapping = {'intel': 'Icc', 'fj': 'Fujitsu'}
 
     def __init__(self, spec, **kwargs):
         # Some user settings, to be adjusted manually or via variants
@@ -855,10 +884,9 @@ def __init__(self, spec, **kwargs):
 
         self.arch = platform
 
-        # Capitalized version of the compiler name, which usually corresponds
-        # to how OpenFOAM will camel-case things.
+        # Capitalized version of the compiler name, which corresponds
+        # to how OpenFOAM handles things (eg, gcc -> Gcc).
         # Use compiler_mapping to handing special cases.
-        # Also handle special compiler options (eg, KNL)
         comp = spec.compiler.name
 
         if comp in self.compiler_mapping:

From 05dcfe829ed5d71764ee7bd2465edb620e4938d5 Mon Sep 17 00:00:00 2001
From: Eisuke Kawashima <e-kwsm@users.noreply.github.com>
Date: Thu, 7 May 2020 17:29:27 +0900
Subject: [PATCH 282/802] neovim: added v0.4.3 (#16410)

Use neovim's vendored dependencies for 0.4 and later
---
 .../repos/builtin/packages/neovim/package.py  | 53 +++++++++++++------
 1 file changed, 37 insertions(+), 16 deletions(-)

diff --git a/var/spack/repos/builtin/packages/neovim/package.py b/var/spack/repos/builtin/packages/neovim/package.py
index 8a574f58e99..a74d4816a86 100644
--- a/var/spack/repos/builtin/packages/neovim/package.py
+++ b/var/spack/repos/builtin/packages/neovim/package.py
@@ -4,15 +4,20 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 
+import os
 from spack import *
 
 
 class Neovim(CMakePackage):
-    """NeoVim: the future of vim"""
+    """Neovim: Vim-fork focused on extensibility and usability"""
 
-    homepage = "http://neovim.io"
-    url      = "https://github.com/neovim/neovim/archive/v0.3.4.tar.gz"
+    homepage = "https://neovim.io"
+    git = "https://github.com/neovim/neovim.git"
+    url = "https://github.com/neovim/neovim/archive/v0.4.3.tar.gz"
 
+    version('master', branch='master')
+    version('stable', tag='stable')
+    version('0.4.3', sha256='91a0b5d32204a821bf414690e6b48cf69224d1961d37158c2b383f6a6cf854d2')
     version('0.3.4', sha256='a641108bdebfaf319844ed46b1bf35d6f7c30ef5aeadeb29ba06e19c3274bc0e')
     version('0.3.1', sha256='bc5e392d4c076407906ccecbc283e1a44b7832c2f486cad81aa04cc29973ad22')
     version('0.3.0', sha256='f7acb61b16d3f521907d99c486b7a9f1e505e8b2a18c9ef69a6d7f18f29f74b8')
@@ -20,21 +25,37 @@ class Neovim(CMakePackage):
     version('0.2.1', sha256='9e2c068a8994c9023a5f84cde9eb7188d3c85996a7e42e611e3cd0996e345dd3')
     version('0.2.0', sha256='72e263f9d23fe60403d53a52d4c95026b0be428c1b9c02b80ab55166ea3f62b5')
 
-    depends_on('lua@5.1:5.2')
-    depends_on('lua-lpeg')
-    depends_on('lua-mpack')
-    depends_on('lua-bitlib')
-    depends_on('libuv')
-    depends_on('jemalloc')
-    depends_on('libtermkey')
-    depends_on('libvterm')
-    depends_on('unibilium')
-    depends_on('msgpack-c')
-    depends_on('gperf')
+    depends_on('cmake@3.0:', type='build')
+
+    depends_on('lua@5.1:5.2', when='@:0.4.0')
+    depends_on('lua-lpeg', when='@:0.4.0')
+    depends_on('lua-mpack', when='@:0.4.0')
+    depends_on('lua-bitlib', when='@:0.4.0')
+    depends_on('libuv', when='@:0.4.0')
+    depends_on('jemalloc', when='@:0.4.0')
+    depends_on('libtermkey', when='@:0.4.0')
+    depends_on('libvterm', when='@:0.4.0')
+    depends_on('unibilium', when='@:0.4.0')
+    depends_on('msgpack-c', when='@:0.4.0')
+    depends_on('gperf', when='@:0.4.0')
+
+    @run_before('cmake')
+    def build_dependencies(self):
+        if self.version < Version('0.4.0'):
+            return
+
+        deps_build_dir = '.deps'
+        options = [
+            '-G', self.generator,
+            os.path.join(os.path.abspath(self.root_cmakelists_dir),
+                         'third-party'),
+        ]
+        with working_dir(deps_build_dir, create=True):
+            cmake(*options)
+            make()
 
     def cmake_args(self):
         args = []
-        if self.version >= Version('0.2.1'):
+        if Version('0.2.1') <= self.version < Version('0.4.0'):
             args = ['-DPREFER_LUA=ON']
-
         return args

From b196e4396a8d2bb21cc50d26114d34cdacb3b727 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 7 May 2020 02:30:09 -0700
Subject: [PATCH 283/802]  bugfix: spack shouldn't fail in an incomplete
 environment (#16473)

Fixed #15884.

Spack asks every package linked into an environment to tell us how
environment variables should be modified when a spack environment is
activated. As part of this, specs in an environment are symlinked into
the environment's view (see #13249), and the package calculates
environment modifications with *the default view as the prefix*.

All of this works nicely for pointing the user's environment at the view
*if* every package is successfully linked. Unfortunately, right now we
only track what specs "should" be in a view, not which specs actually
are. So we end up calculating environment modifications on things that
aren't linked into thee view, and the exception isn't caught, so lots of
spack commands end up failing.

This fixes the issue by ignoring and warning about specs where
calculating environment modifications fails. So we can still keep using
Spack even if the current environment is incomplete.

We should probably also just avoid computing env modifications *entirely*
for unlinked packages, but right now that is a slow operation (requires a
lot of YAML parsing). We should revisit that when we have some better
state management for views, but the fix adopted here will still be
necessary, as we want spack commands to be resilient to other types of
bugs in `setup_run_environment()` and friends. That code is in packages
and we have to assume it could be buggy when we call it outside of builds
(as it might fail more than just the build).
---
 lib/spack/spack/environment.py  | 36 ++++++++++++++++++++++++---------
 lib/spack/spack/test/cmd/env.py | 22 ++++++++++++++++++++
 2 files changed, 49 insertions(+), 9 deletions(-)

diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index fff1485e3c3..43e91073e3c 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -1091,6 +1091,25 @@ def regenerate_views(self):
         for view in self.views.values():
             view.regenerate(specs, self.roots())
 
+    def _env_modifications_for_default_view(self, reverse=False):
+        all_mods = spack.util.environment.EnvironmentModifications()
+
+        errors = []
+        for _, spec in self.concretized_specs():
+            if spec in self.default_view and spec.package.installed:
+                try:
+                    mods = uenv.environment_modifications_for_spec(
+                        spec, self.default_view)
+                except Exception as e:
+                    msg = ("couldn't get environment settings for %s"
+                           % spec.format("{name}@{version} /{hash:7}"))
+                    errors.append((msg, str(e)))
+                    continue
+
+                all_mods.extend(mods.reversed() if reverse else mods)
+
+        return all_mods, errors
+
     def add_default_view_to_shell(self, shell):
         env_mod = spack.util.environment.EnvironmentModifications()
 
@@ -1101,10 +1120,11 @@ def add_default_view_to_shell(self, shell):
         env_mod.extend(uenv.unconditional_environment_modifications(
             self.default_view))
 
-        for _, spec in self.concretized_specs():
-            if spec in self.default_view and spec.package.installed:
-                env_mod.extend(uenv.environment_modifications_for_spec(
-                    spec, self.default_view))
+        mods, errors = self._env_modifications_for_default_view()
+        env_mod.extend(mods)
+        if errors:
+            for err in errors:
+                tty.warn(*err)
 
         # deduplicate paths from specs mapped to the same location
         for env_var in env_mod.group_by_name():
@@ -1122,11 +1142,9 @@ def rm_default_view_from_shell(self, shell):
         env_mod.extend(uenv.unconditional_environment_modifications(
             self.default_view).reversed())
 
-        for _, spec in self.concretized_specs():
-            if spec in self.default_view and spec.package.installed:
-                env_mod.extend(
-                    uenv.environment_modifications_for_spec(
-                        spec, self.default_view).reversed())
+        mods, _ = self._env_modifications_for_default_view(reverse=True)
+        env_mod.extend(mods)
+
         return env_mod.shell_modifications(shell)
 
     def _add_concrete_spec(self, spec, concrete, new=True):
diff --git a/lib/spack/spack/test/cmd/env.py b/lib/spack/spack/test/cmd/env.py
index 671d9869ed9..f8ed37e17c7 100644
--- a/lib/spack/spack/test/cmd/env.py
+++ b/lib/spack/spack/test/cmd/env.py
@@ -163,6 +163,28 @@ def test_env_install_single_spec(install_mockery, mock_fetch):
     assert e.specs_by_hash[e.concretized_order[0]].name == 'cmake-client'
 
 
+def test_env_modifications_error_on_activate(
+        install_mockery, mock_fetch, monkeypatch, capfd):
+    env('create', 'test')
+    install = SpackCommand('install')
+
+    e = ev.read('test')
+    with e:
+        install('cmake-client')
+
+    def setup_error(pkg, env):
+        raise RuntimeError("cmake-client had issues!")
+
+    pkg = spack.repo.path.get_pkg_class("cmake-client")
+    monkeypatch.setattr(pkg, "setup_run_environment", setup_error)
+    with e:
+        pass
+
+    _, err = capfd.readouterr()
+    assert "cmake-client had issues!" in err
+    assert "Warning: couldn't get environment settings" in err
+
+
 def test_env_install_same_spec_twice(install_mockery, mock_fetch, capfd):
     env('create', 'test')
 

From edd60f95c33b29c12d88fdfe380e0fbba68b0fdf Mon Sep 17 00:00:00 2001
From: asmaahassan90 <31959389+asmaahassan90@users.noreply.github.com>
Date: Thu, 7 May 2020 15:38:05 +0200
Subject: [PATCH 284/802] Add PGI version 19.7 and export OMPI variables
 (#16484)

* add PGI version 19.7

* use openmpi in pgi

exporting openmpi enviroment variables when installed with pgi

* fix lint
---
 var/spack/repos/builtin/packages/pgi/package.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/var/spack/repos/builtin/packages/pgi/package.py b/var/spack/repos/builtin/packages/pgi/package.py
index aa6e60ddcc4..bc5f8091094 100644
--- a/var/spack/repos/builtin/packages/pgi/package.py
+++ b/var/spack/repos/builtin/packages/pgi/package.py
@@ -21,6 +21,7 @@ class Pgi(Package):
     homepage = "http://www.pgroup.com/"
 
     version('19.10', sha256='ac9db73ba80a66fe3bc875f63aaa9e16f54674a4e88b25416432430ba8cf203d')
+    version('19.7',  sha256='439692aeb51eff464b968c3bfed4536ed7bd3ba6f8174bc0ebe2219a78fe62ae')
     version('19.4',  sha256='23eee0d4da751dd6f247d624b68b03538ebd172e63a053c41bb67013f07cf68e')
     version('19.1',  sha256='3e05a6db2bf80b5d15f6ff83188f20cb89dc23e233417921e5c0822e7e57d34f')
     version('18.10', sha256='4b3ff83d2a13de6001bed599246eff8e63ef711b8952d4a9ee12efd666b3e326')
@@ -98,3 +99,13 @@ def setup_run_environment(self, env):
         env.set('CXX', join_path(prefix.bin, 'pgc++'))
         env.set('F77', join_path(prefix.bin, 'pgfortran'))
         env.set('FC',  join_path(prefix.bin, 'pgfortran'))
+
+        if '+mpi' in self.spec:
+            ompi_dir = os.listdir(prefix.mpi)[0]
+            env.prepend_path('PATH', join_path(prefix.mpi, ompi_dir, 'bin'))
+            env.prepend_path('LD_LIBRARY_PATH', join_path(prefix.mpi, ompi_dir,
+                                                          'lib'))
+            env.prepend_path('C_INCLUDE_PATH', join_path(prefix.mpi, ompi_dir,
+                                                         'include'))
+            env.prepend_path('MANPATH', join_path(prefix.mpi, ompi_dir,
+                                                  'share/man'))

From 14685ae552cba53173383941fb3af08c13657057 Mon Sep 17 00:00:00 2001
From: Hadrien G <knights_of_ni@gmx.com>
Date: Thu, 7 May 2020 15:40:31 +0200
Subject: [PATCH 285/802] Adapt to the latest Acts developments (#16385)

* Adapt to the latest Acts developments

A long time ago, the Acts project (whose name was then capitalized ACTS) used
to maintain multiple software repositories:

- The heart of the tracking toolkit was located in the `acts-core` repository
- Fast simulation extensions were located in the `acts-fatras` repository
- Advanced usage examples were located in the `acts-framework` repository

This multi-repository organization, however, has been a source of constant
pain, which is why the various projects were gradually merged into a single
mono-repo, called `acts`. Today, with the integration of `acts-framework`,
this merging process is reaching completion.

The present pull request adapts the Acts package to this evolution by...

- Renaming the package to `acts`, reflecting the new repository name
- Renaming the `test` variant to `unit_tests`, reflecting current CMake naming
- Adding the new build variants that were inherited from `acts-framework`
- Acknowledging the change of semantics of the `examples` variant, and only
  supporting the new ones (as the former variant was almost unused)
- Liberally using alphabetical order to make the package code more readable
- Recording a large number of conflicts, some of which are introduced by the
  merging of `acts-framework` and some of which already existed before
- Using the new capitalization of "Acts"

* Add acts v0.23

* Update dd4hep version requirement

* Add acts v0.22.1 bugfix
---
 .../packages/{acts-core => acts}/package.py   | 72 ++++++++++++++-----
 1 file changed, 56 insertions(+), 16 deletions(-)
 rename var/spack/repos/builtin/packages/{acts-core => acts}/package.py (70%)

diff --git a/var/spack/repos/builtin/packages/acts-core/package.py b/var/spack/repos/builtin/packages/acts/package.py
similarity index 70%
rename from var/spack/repos/builtin/packages/acts-core/package.py
rename to var/spack/repos/builtin/packages/acts/package.py
index fc5b6cd4784..5df5f270cc9 100644
--- a/var/spack/repos/builtin/packages/acts-core/package.py
+++ b/var/spack/repos/builtin/packages/acts/package.py
@@ -6,9 +6,9 @@
 from spack import *
 
 
-class ActsCore(CMakePackage):
+class Acts(CMakePackage):
     """
-    A Common Tracking Software (ACTS)
+    A Common Tracking Software (Acts)
 
     This project contains an experiment-independent set of track reconstruction
     tools. The main philosophy is to provide high-level track reconstruction
@@ -33,7 +33,10 @@ class ActsCore(CMakePackage):
     git      = "https://github.com/acts-project/acts.git"
     maintainers = ['HadrienG2']
 
+    # Supported Acts versions
     version('master', branch='master')
+    version('0.23.0', commit='dc443dd7e663bc4d7fb3c1e3f1f75aaf57ffd4e4')
+    version('0.22.1', commit='ca1b8b1645db6b552f44c48d2ff34c8c29618f3a')
     version('0.22.0', commit='2c8228f5843685fc0ae69a8b95dd8fc001139efb')
     version('0.21.0', commit='10b719e68ddaca15b28ac25b3daddce8c0d3368d')
     version('0.20.0', commit='1d37a849a9c318e8ca4fa541ef8433c1f004637b')
@@ -64,13 +67,13 @@ class ActsCore(CMakePackage):
     version('0.08.1', commit='289bdcc320f0b3ff1d792e29e462ec2d3ea15df6')
     version('0.08.0', commit='99eedb38f305e3a1cd99d9b4473241b7cd641fa9')
 
-    # Variants that affect the core ACTS library
+    # Variants that affect the core Acts library
     variant('benchmarks', default=False, description='Build the performance benchmarks')
     variant('examples', default=False, description='Build the examples')
-    variant('tests', default=False, description='Build the unit tests')
     variant('integration_tests', default=False, description='Build the integration tests')
+    variant('unit_tests', default=False, description='Build the unit tests')
 
-    # Variants the enable / disable ACTS plugins
+    # Variants that enable / disable Acts plugins
     variant('dd4hep', default=False, description='Build the DD4hep plugin')
     variant('digitization', default=False, description='Build the geometric digitization plugin')
     variant('fatras', default=False, description='Build the FAst TRAcking Simulation package')
@@ -79,15 +82,44 @@ class ActsCore(CMakePackage):
     variant('legacy', default=False, description='Build the Legacy package')
     variant('tgeo', default=False, description='Build the TGeo plugin')
 
-    depends_on('cmake @3.11:', type='build')
+    # Variants that only affect Acts examples for now
+    variant('geant4', default=False, description='Build the Geant4-based examples')
+    variant('hepmc3', default=False, description='Build the HepMC3-based examples')
+    variant('pythia8', default=False, description='Build the Pythia8-based examples')
+
+    # Build dependencies
     depends_on('boost @1.62:1.69.99 +program_options +test', when='@:0.10.3')
-    depends_on('boost @1.62: +program_options +test', when='@0.10.4:0.18.0')
-    depends_on('boost @1.69: +program_options +test', when='@0.19.0:')
+    depends_on('boost @1.69: +filesystem +program_options +test', when='@0.10.4:')
+    depends_on('cmake @3.11:', type='build')
+    depends_on('dd4hep @1.10: +xercesc', when='+dd4hep')
+    depends_on('dd4hep @1.10: +geant4 +xercesc', when='+dd4hep +geant4')
     depends_on('eigen @3.2.9:', type='build')
-    depends_on('nlohmann-json @3.2.0:', when='@0.14.0: +json')
+    depends_on('geant4', when='+geant4')
+    depends_on('hepmc@3.1:', when='+hepmc3')
+    depends_on('heppdt', when='+hepmc3')
+    depends_on('intel-tbb', when='+examples')
+    depends_on('nlohmann-json @3.2.0:', when='@0.14: +json')
+    depends_on('pythia8', when='+pythia8')
     depends_on('root @6.10: cxxstd=14', when='+tgeo @:0.8.0')
     depends_on('root @6.10: cxxstd=17', when='+tgeo @0.8.1:')
-    depends_on('dd4hep @1.2: +xercesc', when='+dd4hep')
+
+    # Some variant combinations do not make sense
+    conflicts('+benchmarks', when='@:0.15')
+    conflicts('+dd4hep', when='-tgeo')
+    conflicts('+examples', when='@:0.22')
+    conflicts('+examples', when='-digitization')
+    conflicts('+examples', when='-fatras')
+    conflicts('+examples', when='-identification')
+    conflicts('+examples', when='-json')
+    conflicts('+examples', when='-tgeo')
+    conflicts('+fatras', when='@:0.15')
+    conflicts('+geant4', when='@:0.22')
+    conflicts('+geant4', when='-examples')
+    conflicts('+hepmc3', when='@:0.22')
+    conflicts('+hepmc3', when='-examples')
+    conflicts('+pythia8', when='@:0.22')
+    conflicts('+pythia8', when='-examples')
+    conflicts('+tgeo', when='-identification')
 
     def cmake_args(self):
         spec = self.spec
@@ -96,22 +128,30 @@ def cmake_variant(cmake_label, spack_variant):
             enabled = spec.satisfies('+' + spack_variant)
             return "-DACTS_BUILD_{0}={1}".format(cmake_label, enabled)
 
+        def example_cmake_variant(cmake_label, spack_variant):
+            enabled = spec.satisfies('+examples +' + spack_variant)
+            return "-DACTS_BUILD_EXAMPLES_{0}={1}".format(cmake_label, enabled)
+
         integration_tests_label = "INTEGRATIONTESTS"
-        tests_label = "UNITTESTS"
+        unit_tests_label = "UNITTESTS"
         if spec.satisfies('@:0.15.99'):
             integration_tests_label = "INTEGRATION_TESTS"
-            tests_label = "TESTS"
+            unit_tests_label = "TESTS"
 
         args = [
             cmake_variant("BENCHMARKS", "benchmarks"),
-            cmake_variant("EXAMPLES", "examples"),
-            cmake_variant(tests_label, "tests"),
-            cmake_variant(integration_tests_label, "integration_tests"),
-            cmake_variant("DIGITIZATION_PLUGIN", "digitization"),
             cmake_variant("DD4HEP_PLUGIN", "dd4hep"),
+            cmake_variant("DIGITIZATION_PLUGIN", "digitization"),
+            cmake_variant("EXAMPLES", "examples"),
+            example_cmake_variant("DD4HEP", "dd4hep"),
+            example_cmake_variant("GEANT4", "geant4"),
+            example_cmake_variant("HEPMC3", "hepmc3"),
+            example_cmake_variant("PYTHIA8", "pythia8"),
             cmake_variant("FATRAS", "fatras"),
             cmake_variant("IDENTIFICATION_PLUGIN", "identification"),
+            cmake_variant(integration_tests_label, "integration_tests"),
             cmake_variant("JSON_PLUGIN", "json"),
+            cmake_variant(unit_tests_label, "unit_tests"),
             cmake_variant("LEGACY", "legacy"),
             cmake_variant("TGEO_PLUGIN", "tgeo")
         ]

From 762e74e1e3d68b1f4d62b3c13ef3341be236e18e Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Thu, 7 May 2020 21:41:28 +0800
Subject: [PATCH 286/802] Add new package: ganglia (#16382)

* Add new package: ganglia

* ganglia: fix the libexpat depends
---
 .../repos/builtin/packages/ganglia/package.py | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/ganglia/package.py

diff --git a/var/spack/repos/builtin/packages/ganglia/package.py b/var/spack/repos/builtin/packages/ganglia/package.py
new file mode 100644
index 00000000000..ffccc3c14c5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ganglia/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ganglia(AutotoolsPackage):
+    """Ganglia is a scalable distributed monitoring system for high-performance
+    computing systems such as clusters and Grids. It is based on a hierarchical
+    design targeted at federations of clusters. Supports clusters up to 2000
+    nodes in size."""
+
+    homepage = "http://ganglia.sourceforge.net/"
+    url      = "http://jaist.dl.sourceforge.net/project/ganglia/ganglia%20monitoring%20core/3.7.2/ganglia-3.7.2.tar.gz"
+    list_url = "http://jaist.dl.sourceforge.net/project/ganglia/ganglia%20monitoring%20core"
+    list_depth = 1
+
+    version('3.7.2', sha256='042dbcaf580a661b55ae4d9f9b3566230b2232169a0898e91a797a4c61888409')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('apr')
+    depends_on('libconfuse')
+    depends_on('python@:2.7.999')
+    depends_on('pcre')
+    depends_on('libtirpc')
+    depends_on('expat')
+
+    def setup_build_environment(self, env):
+        env.prepend_path('CPATH', self.spec['libtirpc'].prefix.include.tirpc)
+        env.append_flags('LDFLAGS', '-ltirpc')

From 4b65efa8aef4149689a48e9df11c54a367f9af89 Mon Sep 17 00:00:00 2001
From: h-denpo <57649496+h-denpo@users.noreply.github.com>
Date: Thu, 7 May 2020 22:44:23 +0900
Subject: [PATCH 287/802] ADD New package revocap-refiner (#16499)

* ADD New package revocap-refiner
    """The University of Tokyo, CISS Project:
        Geometric processing, mesh processing, mesh generation"""

* Modify     homepage = "https://github.com/FrontISTR/REVOCAP_Refiner"
Modify    version('master', branch='master')
Modify    depends_on('swig', type='build')
Modify        install_tree('Refiner', prefix.include.refine)
Delete         mkdirp(prefix.include)
---
 .../packages/revocap-refiner/package.py       | 57 +++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/revocap-refiner/package.py

diff --git a/var/spack/repos/builtin/packages/revocap-refiner/package.py b/var/spack/repos/builtin/packages/revocap-refiner/package.py
new file mode 100644
index 00000000000..ca130ef7379
--- /dev/null
+++ b/var/spack/repos/builtin/packages/revocap-refiner/package.py
@@ -0,0 +1,57 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RevocapRefiner(MakefilePackage):
+    """The University of Tokyo, CISS Project:
+        Geometric processing, mesh processing, mesh generation"""
+
+    homepage = "https://github.com/FrontISTR/REVOCAP_Refiner"
+    git      = "https://github.com/FrontISTR/REVOCAP_Refiner.git"
+
+    version('master', branch='master')
+
+    depends_on('ruby', type='build')
+    depends_on('mpi')
+    depends_on('doxygen', type='build')
+    depends_on('swig', type='build')
+
+    parallel = False
+
+    def edit(self, spec, prefix):
+        cflags = ['-O']
+        cxxflags = ['-O',  self.compiler.pic_flag]
+        fflags = ['']
+        ldshare = ['']
+        libs = ['-lstdc++']
+        if spec.satisfies('%gcc'):
+            ldshare.append('g++ -shared -s')
+
+        m = FileFilter('MakefileConfig.in')
+        m.filter(r'CC\s=.*$', 'CC={0}'.format(spec['mpi'].mpicc))
+        m.filter(r'CFLAGS\s=.*$', 'CFLAGS={0}'.format(' '.join(cflags)))
+        m.filter(r'CXX\s*=.*$',  'CXX={0}'.format(spec['mpi'].mpicxx))
+        m.filter(r'CXXFLAGS\s*=.*$',
+                 'CXXFLAGS={0}'.format(' '.join(cxxflags)))
+        m.filter(r'AR\s*=.*$', 'AR=ar')
+        m.filter(r'ARFLAGS\s*=.*$', 'ARFLAGS=rsv')
+        m.filter(r'LD\s*=.*$', 'LD={0}'.format(spack_fc))
+        m.filter(r'LDFLAGS\s*=.*$',
+                 'LDFLAGS={0}'.format(' '.join(fflags)))
+        m.filter(r'LDSHARE\s*=.*$',
+                 'LDSHARE={0}'.format(' '.join(ldshare)))
+        m.filter(r'LIBS\s*=.*$', 'LIBS={0}'.format(' '.join(libs)))
+        m.filter(r'LIBPATH\s*=.*$', 'LIBPATH= ')
+        m.filter(r'RM\s*=.*$', 'RM=rm -f')
+        m.filter(r'DOXYGEN\s*=.*$', 'DOXYGEN=doxygen')
+        m.filter(r'TAR\s*=.*$', 'TAR=tar')
+        m.filter(r'SWIG\s*=.*$', 'SWIG=swig')
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('lib', prefix.lib)
+        install_tree('Refiner',  prefix.include.refine)

From 0103084558a9759a0ee8330f21163d64224b06fc Mon Sep 17 00:00:00 2001
From: Andrew Gaspar <agaspar@lanl.gov>
Date: Thu, 7 May 2020 13:38:21 -0600
Subject: [PATCH 288/802] Add Rust 1.43.1 (#16512)

---
 var/spack/repos/builtin/packages/rust/package.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/var/spack/repos/builtin/packages/rust/package.py b/var/spack/repos/builtin/packages/rust/package.py
index 8c0e6430e48..3e89f9b974d 100644
--- a/var/spack/repos/builtin/packages/rust/package.py
+++ b/var/spack/repos/builtin/packages/rust/package.py
@@ -85,6 +85,7 @@ class Rust(Package):
     # The `x.py` bootstrapping script did not exist prior to Rust 1.17. It
     # would be possible to support both, but for simplicitly, we only support
     # Rust 1.17 and newer
+    version('1.43.1', sha256='cde177b4a8c687da96f20de27630a1eb55c9d146a15e4c900d5c31cd3c3ac41d')
     version('1.43.0', sha256='75f6ac6c9da9f897f4634d5a07be4084692f7ccc2d2bb89337be86cfc18453a1')
     version('1.42.0', sha256='d2e8f931d16a0539faaaacd801e0d92c58df190269014b2360c6ab2a90ee3475')
     version('1.41.1', sha256='38c93d016e6d3e083aa15e8f65511d3b4983072c0218a529f5ee94dd1de84573')
@@ -125,6 +126,12 @@ class Rust(Package):
     # This dictionary contains a version: hash dictionary for each supported
     # Rust target.
     rust_releases = {
+        '1.43.1': {
+            'x86_64-unknown-linux-gnu':      '25cd71b95bba0daef56bad8c943a87368c4185b90983f4412f46e3e2418c0505',
+            'powerpc64le-unknown-linux-gnu': '1670f00b00cc1bed38d523a25dba7420de3c06986c15a0248e06299f80ce6124',
+            'aarch64-unknown-linux-gnu':     'fbb612387a64c9da2869725afffc1f66a72d6e7ba6667ba717cd52c33080b7fb',
+            'x86_64-apple-darwin':           'e1c3e1426a9e615079159d6b619319235e3ca7b395e7603330375bfffcbb7003'
+        },
         '1.43.0': {
             'x86_64-unknown-linux-gnu':      '069f34fa5cef92551724c83c36360df1ac66fe3942bc1d0e4d341ce79611a029',
             'powerpc64le-unknown-linux-gnu': 'c75c7ae4c94715fd6cc43d1d6fdd0952bc151f7cbe3054f66d99a529d5bb996f',

From 3c3d431492e4d50e6790bf71dd3a74e9e2459aec Mon Sep 17 00:00:00 2001
From: Themos Tsikas <ThemosTsikas@users.noreply.github.com>
Date: Thu, 7 May 2020 20:41:21 +0100
Subject: [PATCH 289/802] NAG Compiler 7.0 (Build 7017) download checksum
 (#16510)

---
 var/spack/repos/builtin/packages/nag/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/nag/package.py b/var/spack/repos/builtin/packages/nag/package.py
index 1c777f39880..ae191f9c085 100644
--- a/var/spack/repos/builtin/packages/nag/package.py
+++ b/var/spack/repos/builtin/packages/nag/package.py
@@ -12,7 +12,7 @@ class Nag(Package):
     homepage = "http://www.nag.com/nagware/np.asp"
     maintainers = ['ThemosTsikas']
 
-    version('7.0', sha256='328f35fc419415dad66ed3bf5c7bc7f3260d3f9977c7cf37b3e56c29abdf41f0')
+    version('7.0', sha256='bd53c988efe4bfd476a5f556ebd2b8924dc2a039f485e8e017581bca4e12ba01')
     version('6.2', sha256='9b60f6ffa4f4be631079676963e74eea25e8824512e5c864eb06758b2a3cdd2d')
     version('6.1', sha256='32580e0004e6798abf1fa52f0070281b28abeb0da2387530a4cc41218e813c7c')
 

From d7bd070ae9ab6b2094867f39fa7b7fab5520bdb9 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 7 May 2020 14:41:38 -0500
Subject: [PATCH 290/802] GDAL: add 3.1.0 (#16509)

---
 var/spack/repos/builtin/packages/gdal/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py
index af3165db1f7..88075f8a4e1 100644
--- a/var/spack/repos/builtin/packages/gdal/package.py
+++ b/var/spack/repos/builtin/packages/gdal/package.py
@@ -29,6 +29,7 @@ class Gdal(AutotoolsPackage):
         'osgeo.gdal_array', 'osgeo.gdalconst'
     ]
 
+    version('3.1.0',  sha256='e754a22242ccbec731aacdb2333b567d4c95b9b02d3ba1ea12f70508d244fcda')
     version('3.0.4',  sha256='5569a4daa1abcbba47a9d535172fc335194d9214fdb96cd0f139bb57329ae277')
     version('3.0.3',  sha256='e20add5802265159366f197a8bb354899e1693eab8dbba2208de14a457566109')
     version('3.0.2',  sha256='c3765371ce391715c8f28bd6defbc70b57aa43341f6e94605f04fe3c92468983')

From 1ed564a1e623812c3902d8c592e00e5a3367bcb3 Mon Sep 17 00:00:00 2001
From: Peter Scheibel <scheibel1@llnl.gov>
Date: Thu, 7 May 2020 14:01:58 -0700
Subject: [PATCH 291/802] Testing: fix unintended interactions between tests,
 part 2 (#16429)

This fixes some errors with setting up test configuration. These
errors do not cause current Spack tests to fail but do create
red herring issues elsewhere (see #15666). Fixing these errors
leads to more errors in tests that depended on the original
misconfigured state, so those are also addressed here.

This is an update to #16003 which accounts for some unit tests with
conflicting config/mutable_config fixtures. These conflicts were
not exposed until the mutable_config fixture was fixed. Details are
included below. The change which builds on #16003 is prefixed with
"(new)".

* For tests that use the real Spack package repository, the config
  needs to avoid using MPI providers that are not intended to be
  installed by Spack. Without this, it is possible that Spack tests
  which concretize the MPI virtual will end up trying to use an
  implementation that it shouldn't (e.g. one that is always
  provided externally). See #15666 for an example.
* The mutable_config test fixture was not initializing the scope
  roots to the right directories (so the resulting config was empty).
* The current_host fixture in the concretize.py tests was using the
  config fixture rather than mutable_config, and was polluting the
  config cache for other tests.
* One test in concretize.py was clearing a nonexistent cache
  (PackagePrefs._packages_config_cache). This reference has been
  removed.
* The test 'test_preferred_compilers' was was depending on cross
  test config pollution to succeed. The initial spec before
  concretization has been updated to updated to be explicit about
  the desired result.
* (new) For tests that use install_mockery and mutable_config,
  replace install_mockery with a separate install_mockery_mutable_config
  fixture that is exactly the same as install_mockery but uses the
  mutable_config fixture to avoid conflicts.
---
 lib/spack/spack/cmd/compiler.py               | 14 ++++++++++-
 lib/spack/spack/test/cmd/install.py           |  8 +++----
 lib/spack/spack/test/concretize.py            |  8 +++----
 .../spack/test/concretize_preferences.py      |  2 +-
 lib/spack/spack/test/conftest.py              | 24 +++++++++++++++++--
 .../spack/test/data/config/packages.yaml      |  3 +++
 6 files changed, 47 insertions(+), 12 deletions(-)

diff --git a/lib/spack/spack/cmd/compiler.py b/lib/spack/spack/cmd/compiler.py
index 625466f8c7f..c8f52af04d5 100644
--- a/lib/spack/spack/cmd/compiler.py
+++ b/lib/spack/spack/cmd/compiler.py
@@ -159,7 +159,19 @@ def compiler_list(args):
     tty.msg("Available compilers")
     index = index_by(spack.compilers.all_compilers(scope=args.scope),
                      lambda c: (c.spec.name, c.operating_system, c.target))
-    ordered_sections = sorted(index.items(), key=lambda item: item[0])
+
+    # For a container, take each element which does not evaluate to false and
+    # convert it to a string. For elements which evaluate to False (e.g. None)
+    # convert them to '' (in which case it still evaluates to False but is a
+    # string type). Tuples produced by this are guaranteed to be comparable in
+    # Python 3
+    convert_str = (
+        lambda tuple_container:
+        tuple(str(x) if x else '' for x in tuple_container))
+
+    index_str_keys = list(
+        (convert_str(x), y) for x, y in index.items())
+    ordered_sections = sorted(index_str_keys, key=lambda item: item[0])
     for i, (key, compilers) in enumerate(ordered_sections):
         if i >= 1:
             print()
diff --git a/lib/spack/spack/test/cmd/install.py b/lib/spack/spack/test/cmd/install.py
index dd52cea406f..4a5db55c015 100644
--- a/lib/spack/spack/test/cmd/install.py
+++ b/lib/spack/spack/test/cmd/install.py
@@ -722,8 +722,8 @@ def test_cdash_auth_token(tmpdir, install_mockery, capfd):
 
 
 def test_compiler_bootstrap(
-        install_mockery, mock_packages, mock_fetch, mock_archive,
-        mutable_config, monkeypatch):
+        install_mockery_mutable_config, mock_packages, mock_fetch,
+        mock_archive, mutable_config, monkeypatch):
     monkeypatch.setattr(spack.concretize.Concretizer,
                         'check_for_compiler_existence', False)
     spack.config.set('config:install_missing_compilers', True)
@@ -735,8 +735,8 @@ def test_compiler_bootstrap(
 
 @pytest.mark.regression('16221')
 def test_compiler_bootstrap_already_installed(
-        install_mockery, mock_packages, mock_fetch, mock_archive,
-        mutable_config, monkeypatch):
+        install_mockery_mutable_config, mock_packages, mock_fetch,
+        mock_archive, mutable_config, monkeypatch):
     monkeypatch.setattr(spack.concretize.Concretizer,
                         'check_for_compiler_existence', False)
     spack.config.set('config:install_missing_compilers', True)
diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index 232dfaeb4be..ec594e40885 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -12,7 +12,6 @@
 
 from spack.concretize import find_spec, NoValidVersionError
 from spack.error import SpecError
-from spack.package_prefs import PackagePrefs
 from spack.spec import Spec, CompilerSpec, ConflictsInSpecError
 from spack.version import ver
 from spack.util.mock_package import MockPackageMultiRepo
@@ -103,8 +102,6 @@ def current_host(request, monkeypatch):
         monkeypatch.setattr(spack.platforms.test.Test, 'default', cpu)
         yield target
     else:
-        # There's a cache that needs to be cleared for unit tests
-        PackagePrefs._packages_config_cache = None
         with spack.config.override('packages:all', {'target': [cpu]}):
             yield target
 
@@ -112,7 +109,10 @@ def current_host(request, monkeypatch):
     spack.architecture.get_platform.cache.clear()
 
 
-@pytest.mark.usefixtures('config', 'mock_packages')
+# This must use the mutable_config fixture because the test
+# adjusting_default_target_based_on_compiler uses the current_host fixture,
+# which changes the config.
+@pytest.mark.usefixtures('mutable_config', 'mock_packages')
 class TestConcretize(object):
     def test_concretize(self, spec):
         check_concretize(spec)
diff --git a/lib/spack/spack/test/concretize_preferences.py b/lib/spack/spack/test/concretize_preferences.py
index 922d5a11d87..ca4df6700ce 100644
--- a/lib/spack/spack/test/concretize_preferences.py
+++ b/lib/spack/spack/test/concretize_preferences.py
@@ -100,7 +100,7 @@ def test_preferred_compilers(self):
         # Try the last available compiler
         compiler = str(compiler_list[-1])
         update_packages('mpileaks', 'compiler', [compiler])
-        spec = concretize('mpileaks')
+        spec = concretize('mpileaks os=redhat6 target=x86')
         assert spec.compiler == spack.spec.CompilerSpec(compiler)
 
     def test_preferred_target(self, mutable_mock_repo):
diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py
index 736c5a55638..ae8fa80ab76 100644
--- a/lib/spack/spack/test/conftest.py
+++ b/lib/spack/spack/test/conftest.py
@@ -423,13 +423,13 @@ def config(mock_configuration):
 
 
 @pytest.fixture(scope='function')
-def mutable_config(tmpdir_factory, configuration_dir, monkeypatch):
+def mutable_config(tmpdir_factory, configuration_dir):
     """Like config, but tests can modify the configuration."""
     mutable_dir = tmpdir_factory.mktemp('mutable_config').join('tmp')
     configuration_dir.copy(mutable_dir)
 
     cfg = spack.config.Configuration(
-        *[spack.config.ConfigScope(name, str(mutable_dir))
+        *[spack.config.ConfigScope(name, str(mutable_dir.join(name)))
           for name in ['site', 'system', 'user']])
 
     with use_configuration(cfg):
@@ -602,6 +602,26 @@ def install_mockery(tmpdir, config, mock_packages, monkeypatch):
     spack.store.store = real_store
 
 
+@pytest.fixture(scope='function')
+def install_mockery_mutable_config(
+        tmpdir, mutable_config, mock_packages, monkeypatch):
+    """Hooks a fake install directory, DB, and stage directory into Spack.
+
+    This is specifically for tests which want to use 'install_mockery' but
+    also need to modify configuration (and hence would want to use
+    'mutable config'): 'install_mockery' does not support this.
+    """
+    real_store = spack.store.store
+    spack.store.store = spack.store.Store(str(tmpdir.join('opt')))
+
+    # We use a fake package, so temporarily disable checksumming
+    with spack.config.override('config:checksum', False):
+        yield
+
+    tmpdir.join('opt').remove()
+    spack.store.store = real_store
+
+
 @pytest.fixture()
 def mock_fetch(mock_archive):
     """Fake the URL for a package so it downloads from a file."""
diff --git a/lib/spack/spack/test/data/config/packages.yaml b/lib/spack/spack/test/data/config/packages.yaml
index c7256ddb334..63e63e525d6 100644
--- a/lib/spack/spack/test/data/config/packages.yaml
+++ b/lib/spack/spack/test/data/config/packages.yaml
@@ -1,4 +1,7 @@
 packages:
+  all:
+    providers:
+      mpi: [openmpi, mpich]
   externaltool:
     buildable: False
     paths:

From bff5708a4f9496487bb443acdbe0e387122c892e Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <eafischer2@alaska.edu>
Date: Thu, 7 May 2020 19:32:44 -0400
Subject: [PATCH 292/802] Revert changes to `qt` (#16516)

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
---
 var/spack/repos/builtin/packages/qt/package.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index ce689892f8e..08721e85c24 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -222,9 +222,6 @@ def setup_run_environment(self, env):
 
     def setup_dependent_build_environment(self, env, dependent_spec):
         env.set('QTDIR', self.prefix)
-        # https://riverbankcomputing.com/pipermail/qscintilla/2015-January/001012.html
-        env.set('QMAKEFEATURES', join_path(
-            dependent_spec.stage.source_path, 'Qt4Qt5', 'features'))
 
     def setup_dependent_package(self, module, dependent_spec):
         module.qmake = Executable(join_path(self.spec.prefix.bin, 'qmake'))

From 08f449ae9a4b18e5a8c1056278b6e925d1760678 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Fri, 8 May 2020 01:34:36 +0200
Subject: [PATCH 293/802] "spack checksum" QoL (#14311)

* Non-interactive mode for spack checksum; allow passing 'package@version' to spack checksum

* Flake8 fixes

* Update checksum.py

Fix typo

* Update spack-completion script

* Automatically set non-interactive mode if more than one version passed

* Update lib/spack/spack/cmd/checksum.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Add documentation and update spack-completion

* Flake8

* Rename option

* Update spack-completion

* Update lib/spack/spack/cmd/checksum.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update checksum.py

* Update stage.py

* Update create.py

Use batch mode when adding a new package

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 lib/spack/spack/cmd/checksum.py   |  9 +++++++++
 lib/spack/spack/cmd/create.py     |  2 +-
 lib/spack/spack/stage.py          | 11 ++++++++---
 share/spack/spack-completion.bash |  2 +-
 4 files changed, 19 insertions(+), 5 deletions(-)

diff --git a/lib/spack/spack/cmd/checksum.py b/lib/spack/spack/cmd/checksum.py
index eaeaf5337f9..97e7833af0d 100644
--- a/lib/spack/spack/cmd/checksum.py
+++ b/lib/spack/spack/cmd/checksum.py
@@ -26,6 +26,9 @@ def setup_parser(subparser):
     subparser.add_argument(
         '--keep-stage', action='store_true',
         help="don't clean up staging area when command completes")
+    subparser.add_argument(
+        '-b', '--batch', action='store_true',
+        help="don't ask which versions to checksum")
     arguments.add_common_arguments(subparser, ['package'])
     subparser.add_argument(
         'versions', nargs=argparse.REMAINDER,
@@ -33,6 +36,11 @@ def setup_parser(subparser):
 
 
 def checksum(parser, args):
+    # Did the user pass 'package@version' string?
+    if len(args.versions) == 0 and '@' in args.package:
+        args.versions = [args.package.split('@')[1]]
+        args.package = args.package.split('@')[0]
+
     # Make sure the user provided a package and not a URL
     if not valid_fully_qualified_module_name(args.package):
         tty.die("`spack checksum` accepts package names, not URLs.")
@@ -57,6 +65,7 @@ def checksum(parser, args):
 
     version_lines = spack.stage.get_checksums_for_versions(
         url_dict, pkg.name, keep_stage=args.keep_stage,
+        batch=(args.batch or len(args.versions) > 0),
         fetch_options=pkg.fetch_options)
 
     print()
diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py
index 304b531b492..7d12dc98a7d 100644
--- a/lib/spack/spack/cmd/create.py
+++ b/lib/spack/spack/cmd/create.py
@@ -629,7 +629,7 @@ def get_versions(args, name):
 
         versions = spack.stage.get_checksums_for_versions(
             url_dict, name, first_stage_function=guesser,
-            keep_stage=args.keep_stage)
+            keep_stage=args.keep_stage, batch=True)
     else:
         versions = unhashed_versions
 
diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py
index 54d370a50d9..5cac9e32a1c 100644
--- a/lib/spack/spack/stage.py
+++ b/lib/spack/spack/stage.py
@@ -753,7 +753,7 @@ def purge():
 
 def get_checksums_for_versions(
         url_dict, name, first_stage_function=None, keep_stage=False,
-        fetch_options=None):
+        fetch_options=None, batch=False):
     """Fetches and checksums archives from URLs.
 
     This function is called by both ``spack checksum`` and ``spack
@@ -767,6 +767,8 @@ def get_checksums_for_versions(
         first_stage_function (callable): function that takes a Stage and a URL;
             this is run on the stage of the first URL downloaded
         keep_stage (bool): whether to keep staging area when command completes
+        batch (bool): whether to ask user how many versions to fetch (false)
+            or fetch all versions (true)
         fetch_options (dict): Options used for the fetcher (such as timeout
             or cookies)
 
@@ -788,8 +790,11 @@ def get_checksums_for_versions(
                  for v in sorted_versions]))
     print()
 
-    archives_to_fetch = tty.get_number(
-        "How many would you like to checksum?", default=1, abort='q')
+    if batch:
+        archives_to_fetch = len(sorted_versions)
+    else:
+        archives_to_fetch = tty.get_number(
+            "How many would you like to checksum?", default=1, abort='q')
 
     if not archives_to_fetch:
         tty.die("Aborted.")
diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash
index 12d4c599b89..4b730499d2d 100755
--- a/share/spack/spack-completion.bash
+++ b/share/spack/spack-completion.bash
@@ -455,7 +455,7 @@ _spack_cd() {
 _spack_checksum() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help --keep-stage"
+        SPACK_COMPREPLY="-h --help --keep-stage -b --batch"
     else
         _all_packages
     fi

From e2d42672b702ac6a1a3fe182b903e6122945c033 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Fri, 8 May 2020 02:21:53 +0200
Subject: [PATCH 294/802] Config option to disable setting S_ISGID bit when
 creating installation directory (#14479)

* Add config option to disable setting S_ISGID bit when creating installation directory.

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
---
 etc/spack/defaults/config.yaml   | 4 ++++
 lib/spack/spack/package_prefs.py | 2 +-
 lib/spack/spack/schema/config.py | 1 +
 3 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/etc/spack/defaults/config.yaml b/etc/spack/defaults/config.yaml
index cc51060eae3..4e4b48296c5 100644
--- a/etc/spack/defaults/config.yaml
+++ b/etc/spack/defaults/config.yaml
@@ -157,3 +157,7 @@ config:
   # Has no effect on macOS. DO NOT MIX these within the same install tree.
   # See the Spack documentation for details.
   shared_linking: 'rpath'
+
+  # Set to 'false' to allow installation on filesystems that doesn't allow setgid bit
+  # manipulation by unprivileged user (e.g. AFS)
+  config:allow_sgid: true
diff --git a/lib/spack/spack/package_prefs.py b/lib/spack/spack/package_prefs.py
index 0158c7063a6..aa904a0792b 100644
--- a/lib/spack/spack/package_prefs.py
+++ b/lib/spack/spack/package_prefs.py
@@ -204,7 +204,7 @@ def get_package_dir_permissions(spec):
     attribute sticky for the directory. Package-specific settings take
     precedent over settings for ``all``"""
     perms = get_package_permissions(spec)
-    if perms & stat.S_IRWXG:
+    if perms & stat.S_IRWXG and spack.config.get('config:allow_sgid', True):
         perms |= stat.S_ISGID
     return perms
 
diff --git a/lib/spack/spack/schema/config.py b/lib/spack/spack/schema/config.py
index a05af2f4384..d56321d09c3 100644
--- a/lib/spack/spack/schema/config.py
+++ b/lib/spack/spack/schema/config.py
@@ -73,6 +73,7 @@
                     {'type': 'null'}
                 ],
             },
+            'allow_sgid': {'type': 'boolean'},
         },
     },
 }

From 4ebff5cef9e00bc858f85ca121dd47c9cf580ae9 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Fri, 8 May 2020 01:23:16 -0400
Subject: [PATCH 295/802] Documentation: typo in option description (#16518)

---
 lib/spack/spack/cmd/view.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/cmd/view.py b/lib/spack/spack/cmd/view.py
index 18c836736e6..bad155a456b 100644
--- a/lib/spack/spack/cmd/view.py
+++ b/lib/spack/spack/cmd/view.py
@@ -111,7 +111,7 @@ def setup_parser(sp):
             help='add package files to a filesystem view via symbolic links'),
         "hardlink": ssp.add_parser(
             'hardlink', aliases=['hard'],
-            help='add packages files to a filesystem via via hard links'),
+            help='add packages files to a filesystem view via hard links'),
         "remove": ssp.add_parser(
             'remove', aliases=['rm'],
             help='remove packages from a filesystem view'),

From f5844d3d816d9b4e38a8259b68765a3c3b094a4c Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Fri, 8 May 2020 01:12:45 -0700
Subject: [PATCH 296/802] all_urls: add urls[0] for versions (#16435)

This adds the `url` alternative `urls` to `package.all_urls`. With
this addition, one can find again new versions with
`spack versions <package>` for packages that are populated with
from mixin mirror `urls`.

Example: `util-macros` from x.org mixin.
---
 lib/spack/spack/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 40384077eae..9b6f0efb48b 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -2011,6 +2011,10 @@ def all_urls(self):
         if hasattr(self, 'url') and self.url:
             urls.append(self.url)
 
+        # fetch from first entry in urls to save time
+        if hasattr(self, 'urls') and self.urls:
+            urls.append(self.urls[0])
+
         for args in self.versions.values():
             if 'url' in args:
                 urls.append(args['url'])

From 9eaf7e42c803dd7e6f3b487152c95a5c34646814 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Fri, 8 May 2020 19:05:30 +0200
Subject: [PATCH 297/802] new version r-git2r-0.27.1 (#16529)

---
 var/spack/repos/builtin/packages/r-git2r/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/r-git2r/package.py b/var/spack/repos/builtin/packages/r-git2r/package.py
index 4f7613a21a5..dff31b8318a 100644
--- a/var/spack/repos/builtin/packages/r-git2r/package.py
+++ b/var/spack/repos/builtin/packages/r-git2r/package.py
@@ -15,6 +15,7 @@ class RGit2r(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/git2r_0.18.0.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/git2r"
 
+    version('0.27.1', sha256='099207f180aa45ddcc443cbb22487eafd14e1cd8e5979b3476214253fd773bc0')
     version('0.26.1', sha256='13d609286a0af4ef75ba76f2c2f856593603b8014e311b88896243a50b417435')
     version('0.26.0', sha256='56671389c3a50591e1dae3be8c3b0112d06d291f897d7fe14db17aea175616cf')
     version('0.18.0', sha256='91b32e49afb859c0c4f6f77988343645e9499e5046ef08d945d4d8149b6eff2d')

From 33e88db2d67758c3a565f99626dee0aa4cc8859d Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Fri, 8 May 2020 19:05:54 +0200
Subject: [PATCH 298/802] new version xrootd-4.12.0 (#16528)

---
 var/spack/repos/builtin/packages/xrootd/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/xrootd/package.py b/var/spack/repos/builtin/packages/xrootd/package.py
index 50d1484a8e8..cadf24b44ea 100644
--- a/var/spack/repos/builtin/packages/xrootd/package.py
+++ b/var/spack/repos/builtin/packages/xrootd/package.py
@@ -13,6 +13,7 @@ class Xrootd(CMakePackage):
     homepage = "http://xrootd.org"
     url      = "http://xrootd.org/download/v4.6.0/xrootd-4.6.0.tar.gz"
 
+    version('4.12.0', sha256='69ef4732256d9a88127de4bfdf96bbf73348e0c70ce1d756264871a0ffadd2fc')
     version('4.11.3', sha256='8e7a64fd55dfb452b6d5f76a9a97c493593943227b377623a3032da9197c7f65')
     version('4.11.2', sha256='4620824db97fcc37dc3dd26110da8e5c3aab1d8302e4921d4f32e83207060603')
     version('4.10.0', sha256='f07f85e27d72e9e8ff124173c7b53619aed8fcd36f9d6234c33f8f7fd511995b')

From 652e179ae64ace2db7771754cc782eca799b2c30 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Fri, 8 May 2020 19:17:48 +0200
Subject: [PATCH 299/802] Gaudi: syntax fix (#16523)

---
 var/spack/repos/builtin/packages/gaudi/package.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/gaudi/package.py b/var/spack/repos/builtin/packages/gaudi/package.py
index beae99c3cd5..ba8b8bcf636 100644
--- a/var/spack/repos/builtin/packages/gaudi/package.py
+++ b/var/spack/repos/builtin/packages/gaudi/package.py
@@ -102,9 +102,9 @@ def cmake_args(self):
 
     def setup_run_environment(self, env):
         # environment as in Gaudi.xenv
-        env.prepend.path('PATH', self.prefix.scripts)
-        env.prepend.path('PYTHONPATH', self.prefix.python)
-        env.prepend.path('ROOT_INCLUDE_PATH', self.prefix.include)
+        env.prepend_path('PATH', self.prefix.scripts)
+        env.prepend_path('PYTHONPATH', self.prefix.python)
+        env.prepend_path('ROOT_INCLUDE_PATH', self.prefix.include)
 
     def url_for_version(self, version):
         major = str(version[0])

From fae55550f9a8a37617a657ebbf3b0c5ff73f7bc5 Mon Sep 17 00:00:00 2001
From: h-denpo <57649496+h-denpo@users.noreply.github.com>
Date: Sat, 9 May 2020 02:22:04 +0900
Subject: [PATCH 300/802] New package (#16519)

Large Scale Assembly, Structural Correspondence,
       Multi Dynamics Simulator.In this program,
       a part of functions of ADVENTURE_Solid ver.1.1 module
---
 .../packages/revocap-coupler/package.py       | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/revocap-coupler/package.py

diff --git a/var/spack/repos/builtin/packages/revocap-coupler/package.py b/var/spack/repos/builtin/packages/revocap-coupler/package.py
new file mode 100644
index 00000000000..6bc128152da
--- /dev/null
+++ b/var/spack/repos/builtin/packages/revocap-coupler/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+from spack import *
+
+
+class RevocapCoupler(AutotoolsPackage):
+    """Large Scale Assembly, Structural Correspondence,
+       Multi Dynamics Simulator.In this program,
+       a part of functions of ADVENTURE_Solid ver.1.1 module"""
+
+    homepage = "http://www.ciss.iis.u-tokyo.ac.jp/dl/index.php"
+    url      = "file://{0}/REVOCAP_Coupler-2.1.tar.gz".format(os.getcwd())
+    version('2.1', sha256='9e7612d5c508ccdce23bff9ccbf62aeb635877bc2276cdc05c109de40f609f49')
+
+    depends_on('mpi')
+
+    def configure_args(self):
+        spec = self.spec
+        args = ['--with-mpicc=%s' % spec['mpi'].mpicc,
+                '--with-fortran=%s' % spec['mpi'].mpif77,
+                '--with-mpif90=%s' % spec['mpi'].mpifc]
+        return args

From 08528a73793660831c25bd9a9d5bc84600a37a4a Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Fri, 8 May 2020 19:24:42 +0200
Subject: [PATCH 301/802] Gaudi: separate variant for building documentation
 (#16515)

* Gaudi: separate variant for building documentation

* Update package.py
---
 var/spack/repos/builtin/packages/gaudi/package.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/gaudi/package.py b/var/spack/repos/builtin/packages/gaudi/package.py
index ba8b8bcf636..ed37ee96f7d 100644
--- a/var/spack/repos/builtin/packages/gaudi/package.py
+++ b/var/spack/repos/builtin/packages/gaudi/package.py
@@ -26,6 +26,8 @@ class Gaudi(CMakePackage):
 
     variant('optional', default=False,
             description='Build most optional components and tests')
+    variant('docs', default=False,
+            description='Build documentation with Doxygen')
     variant('vtune', default=False,
             description='Build with Intel VTune profiler support')
 
@@ -62,7 +64,7 @@ class Gaudi(CMakePackage):
     depends_on('clhep', when='+optional')
     depends_on('cppgsl', when='+optional')
     depends_on('cppunit', when='+optional')
-    depends_on('doxygen +graphviz', when='+optional')
+    depends_on('doxygen +graphviz', when='+docs')
     depends_on('gperftools', when='+optional')
     depends_on('gdb', when='+optional')
     depends_on('gsl', when='+optional')
@@ -92,7 +94,7 @@ def cmake_args(self):
             self.define_from_variant("GAUDI_USE_CPPUNIT", "optional"),
             self.define_from_variant("GAUDI_USE_UNWIND", "optional"),
             self.define_from_variant("GAUDI_USE_GPERFTOOLS", "optional"),
-            self.define_from_variant("GAUDI_USE_DOXYGEN", "optional"),
+            self.define_from_variant("GAUDI_USE_DOXYGEN", "docs"),
             self.define_from_variant("GAUDI_USE_INTELAMPLIFIER", "optional"),
             self.define_from_variant("GAUDI_USE_JEMALLOC", "optional"),
             # this is not really used in spack builds, but needs to be set

From b9415c6b530ba1dbe0755cc21e2d47768c2b31e0 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Fri, 8 May 2020 11:25:38 -0600
Subject: [PATCH 302/802] graphviz: fix cairo backend (#16511)

---
 var/spack/repos/builtin/packages/graphviz/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py
index 17197f18389..4f8e772f19d 100644
--- a/var/spack/repos/builtin/packages/graphviz/package.py
+++ b/var/spack/repos/builtin/packages/graphviz/package.py
@@ -95,7 +95,7 @@ class Graphviz(AutotoolsPackage):
     depends_on('ghostscript', when='+ghostscript')
     depends_on('gtkplus', when='+gtkplus')
     depends_on('gts', when='+gts')
-    depends_on('cairo+pdf', when='+pangocairo')
+    depends_on('cairo+pdf+png+svg', when='+pangocairo')
     depends_on('fontconfig', when='+pangocairo')
     depends_on('freetype', when='+pangocairo')
     depends_on('glib', when='+pangocairo')

From 1e9313a1911bef7135583c794272b76e0fd7bf86 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Fri, 8 May 2020 19:26:37 +0200
Subject: [PATCH 303/802] precice: Fix conflict with boost 1.73.0 (#16507)

---
 var/spack/repos/builtin/packages/precice/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/precice/package.py b/var/spack/repos/builtin/packages/precice/package.py
index 986bfa7f146..11250f60bda 100644
--- a/var/spack/repos/builtin/packages/precice/package.py
+++ b/var/spack/repos/builtin/packages/precice/package.py
@@ -42,6 +42,7 @@ class Precice(CMakePackage):
     depends_on('cmake@3.10.2:', type='build', when='@1.4:')
     depends_on('boost@1.60.0:')
     depends_on('boost@1.65.1:', when='@1.4:')
+    depends_on('boost@:1.72.99', when='@:2.0.2')
     depends_on('eigen@3.2:')
     depends_on('eigen@:3.3.7', type='build', when='@:1.5')  # bug in prettyprint
     depends_on('libxml2')

From e1c49d11bf5501515afa4ee5d4203ed5c232b48e Mon Sep 17 00:00:00 2001
From: Sergey Kosukhin <sergey.kosukhin@mpimet.mpg.de>
Date: Fri, 8 May 2020 19:27:28 +0200
Subject: [PATCH 304/802] py-netcdf4: a couple of improvements (#16505)

* py-netcdf4: avoid recompilation and make the older versions to work with HDF5@1.10:

* py-netcdf4: add a new version and introduce a maintainer list.
---
 .../py-netcdf4/check_hdf5version.patch        | 20 +++++++++++++++++++
 .../builtin/packages/py-netcdf4/package.py    | 10 ++++++++++
 2 files changed, 30 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-netcdf4/check_hdf5version.patch

diff --git a/var/spack/repos/builtin/packages/py-netcdf4/check_hdf5version.patch b/var/spack/repos/builtin/packages/py-netcdf4/check_hdf5version.patch
new file mode 100644
index 00000000000..c2c3bd025cd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-netcdf4/check_hdf5version.patch
@@ -0,0 +1,20 @@
+--- a/setup.py
++++ b/setup.py
+@@ -275,7 +275,7 @@ HDF5_DIR environment variable not set, checking some standard locations ..\n""")
+         for direc in dirstosearch:
+             sys.stdout.write('checking %s ...\n' % direc)
+             hdf5_version = check_hdf5version(os.path.join(direc, 'include'))
+-            if hdf5_version is None or hdf5_version[1:6] < '1.8.0':
++            if hdf5_version is None or [int(c) for c in hdf5_version[1:-1].split('.')] < [1, 8, 0]:
+                 continue
+             else:
+                 HDF5_dir = direc
+@@ -290,7 +290,7 @@ HDF5_DIR environment variable not set, checking some standard locations ..\n""")
+         hdf5_version = check_hdf5version(HDF5_incdir)
+         if hdf5_version is None:
+             raise ValueError('did not find HDF5 headers in %s' % HDF5_incdir)
+-        elif hdf5_version[1:6] < '1.8.0':
++        elif [int(c) for c in hdf5_version[1:-1].split('.')] < [1, 8, 0]:
+             raise ValueError('HDF5 version >= 1.8.0 is required')
+ 
+     if netCDF4_incdir is None and netCDF4_dir is None:
diff --git a/var/spack/repos/builtin/packages/py-netcdf4/package.py b/var/spack/repos/builtin/packages/py-netcdf4/package.py
index 5516bc751e3..d1c992db9cf 100644
--- a/var/spack/repos/builtin/packages/py-netcdf4/package.py
+++ b/var/spack/repos/builtin/packages/py-netcdf4/package.py
@@ -12,6 +12,9 @@ class PyNetcdf4(PythonPackage):
     homepage = "https://github.com/Unidata/netcdf4-python"
     url      = "https://pypi.io/packages/source/n/netCDF4/netCDF4-1.2.7.tar.gz"
 
+    maintainers = ['skosukhin']
+
+    version('1.5.3',   sha256='2a3ca855848f4bbf07fac366da77a681fcead18c0a8813d91d46302f562dc3be')
     version('1.4.2',   sha256='b934af350459cf9041bcdf5472e2aa56ed7321c018d918e9f325ec9a1f9d1a30')
     version('1.2.7',   sha256='0c449b60183ee06238a8f9a75de7b0eed3acaa7a374952ff9f1ff06beb8f94ba')
     version('1.2.3.1', sha256='55edd74ef9aabb1f7d1ea3ffbab9c555da2a95632a97f91c0242281dc5eb919f')
@@ -32,6 +35,13 @@ class PyNetcdf4(PythonPackage):
     # following patch disables the usage of pkg-config at all.
     patch('disable_pkgconf.patch')
 
+    # Older versions of the package get a false negative result when checking
+    # the version of HDF5.
+    patch('check_hdf5version.patch', when='@:1.2.9 ^hdf5@1.10:')
+
+    # We can skip the 'build' phase to avoid recompilation of the library.
+    phases = ['install']
+
     def setup_build_environment(self, env):
         """Ensure installed netcdf and hdf5 libraries are used"""
         # Explicitly set these variables so setup.py won't erroneously pick up

From 89c92a02062cf91c4e3e66fe86846e57bc3388b8 Mon Sep 17 00:00:00 2001
From: takanori-ihara <62980219+takanori-ihara@users.noreply.github.com>
Date: Sat, 9 May 2020 02:30:47 +0900
Subject: [PATCH 305/802] Add new package:py-pytest-check-links (#16503)

---
 .../packages/py-pytest-check-links/package.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-pytest-check-links/package.py

diff --git a/var/spack/repos/builtin/packages/py-pytest-check-links/package.py b/var/spack/repos/builtin/packages/py-pytest-check-links/package.py
new file mode 100644
index 00000000000..49269ce1f27
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pytest-check-links/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class PyPytestCheckLinks(PythonPackage):
+    """pytest plugin that checks URLs for HTML-containing files."""
+
+    homepage = "https://github.com/jupyterlab/pytest-check-links"
+    url      = "https://pypi.io/packages/source/p/pytest-check-links/pytest_check_links-0.3.4.tar.gz"
+
+    version('0.3.4', sha256='4b3216548431bf9796557e8ee8fd8e5e77a69a4690b3b2f9bcf6fb5af16a502b')
+
+    depends_on('py-setuptools@17.1:', type='build')
+    depends_on('py-pbr@1.9:', type='build')

From 4c42946201652832bb6dac3599e3242a2582350c Mon Sep 17 00:00:00 2001
From: Keita Iwabuchi <kiwabuchi@llnl.gov>
Date: Sat, 9 May 2020 02:31:20 +0900
Subject: [PATCH 306/802] Metall: add version 0.2 (#16502)

---
 var/spack/repos/builtin/packages/metall/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/metall/package.py b/var/spack/repos/builtin/packages/metall/package.py
index cec7669ad2f..ea1351fe50b 100644
--- a/var/spack/repos/builtin/packages/metall/package.py
+++ b/var/spack/repos/builtin/packages/metall/package.py
@@ -9,10 +9,12 @@ class Metall(CMakePackage):
 
     homepage = "https://github.com/LLNL/metall"
     git      = "https://github.com/LLNL/metall.git"
+    url      = "https://github.com/LLNL/metall/archive/v0.2.tar.gz"
 
     maintainers = ['KIwabuchi', 'rogerpearce', 'mayagokhale']
 
     version('develop', branch='develop')
+    version('0.2', sha256='35cdf3505d2f8d0282a0d5c60b69a0ec5ec6d77ac3facce7549eb874df27be1d')
 
     depends_on('boost@1.64:', type=('build', 'link'))
 

From 790e9ac6de65ff5e8701aec3d89fab5ad86f02de Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 8 May 2020 22:20:38 -0500
Subject: [PATCH 307/802] spaCy: add new package for en_core_web_sm model
 (#16539)

---
 .../py-spacy-models-en-core-web-sm/package.py   | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-spacy-models-en-core-web-sm/package.py

diff --git a/var/spack/repos/builtin/packages/py-spacy-models-en-core-web-sm/package.py b/var/spack/repos/builtin/packages/py-spacy-models-en-core-web-sm/package.py
new file mode 100644
index 00000000000..89119586638
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-spacy-models-en-core-web-sm/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class PySpacyModelsEnCoreWebSm(PythonPackage):
+    """English multi-task CNN trained on OntoNotes. Assigns context-specific
+    token vectors, POS tags, dependency parse and named entities."""
+
+    homepage = "https://spacy.io/models/en#en_core_web_sm"
+    url      = "https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-2.2.5/en_core_web_sm-2.2.5.tar.gz"
+
+    version('2.2.5', sha256='60b69065c97fd2e4972c33300205e1dead3501d2e0bfd6a182c3a033e337caee')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-spacy@2.2.2:', type=('build', 'run'))

From 5883e9df53258f7fe32cbf76f14abe9e42dfeebc Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Fri, 8 May 2020 20:24:03 -0700
Subject: [PATCH 308/802] ci: update Travis badge in README.md to point to
 travis-ci.com

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 12414ba179d..70913b33bcd 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 # <img src="https://cdn.rawgit.com/spack/spack/develop/share/spack/logo/spack-logo.svg" width="64" valign="middle" alt="Spack"/> Spack
 
-[![Build Status](https://travis-ci.org/spack/spack.svg?branch=develop)](https://travis-ci.org/spack/spack)
+[![Build Status](https://travis-ci.com/spack/spack.svg?branch=develop)](https://travis-ci.com/spack/spack)
 [![Linux Builds](https://github.com/spack/spack/workflows/linux%20builds/badge.svg)](https://github.com/spack/spack/actions)
 [![macOS Builds (nightly)](https://github.com/spack/spack/workflows/macOS%20builds%20nightly/badge.svg?branch=develop)](https://github.com/spack/spack/actions?query=workflow%3A%22macOS+builds+nightly%22)
 [![codecov](https://codecov.io/gh/spack/spack/branch/develop/graph/badge.svg)](https://codecov.io/gh/spack/spack)

From 7b8e5c89999621d3e036e52998a541c3a34e8fd0 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Fri, 8 May 2020 23:04:07 -0700
Subject: [PATCH 309/802] bugfix: don't use sys.stdout as a default arg value
 (#16541)

After migrating to `travis-ci.com`, we saw I/O issues in our tests --
tests that relied on `capfd` and `capsys` were failing. We've also seen
this in GitHub actions, and it's kept us from switching to them so far.

Turns out that the issue is that using streams like `sys.stdout` as
default arguments doesn't play well with `pytest` and output redirection,
as `pytest` changes the values of `sys.stdout` and `sys.stderr`. if these
values are evaluated before output redirection (as they are when used as
default arg values), output won't be captured properly later.

- [x] replace all stream default arg values with `None`, and only assign stream
      values inside functions.
- [x] fix tests we didn't notice were relying on this erroneous behavior
---
 lib/spack/llnl/util/argparsewriter.py   | 9 +++++----
 lib/spack/llnl/util/tty/color.py        | 6 ++++--
 lib/spack/spack/cmd/commands.py         | 3 ++-
 lib/spack/spack/cmd/dependencies.py     | 6 +++++-
 lib/spack/spack/cmd/dependents.py       | 5 ++++-
 lib/spack/spack/cmd/find.py             | 3 ++-
 lib/spack/spack/cmd/modules/__init__.py | 3 ++-
 lib/spack/spack/test/cmd/find.py        | 2 +-
 8 files changed, 25 insertions(+), 12 deletions(-)

diff --git a/lib/spack/llnl/util/argparsewriter.py b/lib/spack/llnl/util/argparsewriter.py
index f43595145e4..8ecf6acc88e 100644
--- a/lib/spack/llnl/util/argparsewriter.py
+++ b/lib/spack/llnl/util/argparsewriter.py
@@ -45,18 +45,18 @@ def __init__(self, prog, description, usage,
 class ArgparseWriter(argparse.HelpFormatter):
     """Analyzes an argparse ArgumentParser for easy generation of help."""
 
-    def __init__(self, prog, out=sys.stdout, aliases=False):
+    def __init__(self, prog, out=None, aliases=False):
         """Initializes a new ArgparseWriter instance.
 
         Parameters:
             prog (str): the program name
-            out (file object): the file to write to
+            out (file object): the file to write to (default sys.stdout)
             aliases (bool): whether or not to include subparsers for aliases
         """
         super(ArgparseWriter, self).__init__(prog)
         self.level = 0
         self.prog = prog
-        self.out = out
+        self.out = sys.stdout if out is None else out
         self.aliases = aliases
 
     def parse(self, parser, prog):
@@ -167,7 +167,7 @@ def write(self, parser):
 class ArgparseRstWriter(ArgparseWriter):
     """Write argparse output as rst sections."""
 
-    def __init__(self, prog, out=sys.stdout, aliases=False,
+    def __init__(self, prog, out=None, aliases=False,
                  rst_levels=_rst_levels):
         """Create a new ArgparseRstWriter.
 
@@ -178,6 +178,7 @@ def __init__(self, prog, out=sys.stdout, aliases=False,
             rst_levels (list of str): list of characters
                 for rst section headings
         """
+        out = sys.stdout if out is None else out
         super(ArgparseRstWriter, self).__init__(prog, out, aliases)
         self.rst_levels = rst_levels
 
diff --git a/lib/spack/llnl/util/tty/color.py b/lib/spack/llnl/util/tty/color.py
index 79f62c00403..b6f5ec782f9 100644
--- a/lib/spack/llnl/util/tty/color.py
+++ b/lib/spack/llnl/util/tty/color.py
@@ -215,20 +215,22 @@ def cextra(string):
     return len(''.join(re.findall(r'\033[^m]*m', string)))
 
 
-def cwrite(string, stream=sys.stdout, color=None):
+def cwrite(string, stream=None, color=None):
     """Replace all color expressions in string with ANSI control
        codes and write the result to the stream.  If color is
        False, this will write plain text with no color.  If True,
        then it will always write colored output.  If not supplied,
        then it will be set based on stream.isatty().
     """
+    stream = sys.stdout if stream is None else stream
     if color is None:
         color = get_color_when()
     stream.write(colorize(string, color=color))
 
 
-def cprint(string, stream=sys.stdout, color=None):
+def cprint(string, stream=None, color=None):
     """Same as cwrite, but writes a trailing newline to the stream."""
+    stream = sys.stdout if stream is None else stream
     cwrite(string + "\n", stream, color)
 
 
diff --git a/lib/spack/spack/cmd/commands.py b/lib/spack/spack/cmd/commands.py
index 3664fce477e..be934e0048b 100644
--- a/lib/spack/spack/cmd/commands.py
+++ b/lib/spack/spack/cmd/commands.py
@@ -78,9 +78,10 @@ def setup_parser(subparser):
 class SpackArgparseRstWriter(ArgparseRstWriter):
     """RST writer tailored for spack documentation."""
 
-    def __init__(self, prog, out=sys.stdout, aliases=False,
+    def __init__(self, prog, out=None, aliases=False,
                  documented_commands=[],
                  rst_levels=['-', '-', '^', '~', ':', '`']):
+        out = sys.stdout if out is None else out
         super(SpackArgparseRstWriter, self).__init__(
             prog, out, aliases, rst_levels)
         self.documented = documented_commands
diff --git a/lib/spack/spack/cmd/dependencies.py b/lib/spack/spack/cmd/dependencies.py
index 7f390341ef4..bbccbe23ee9 100644
--- a/lib/spack/spack/cmd/dependencies.py
+++ b/lib/spack/spack/cmd/dependencies.py
@@ -3,6 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import sys
+
 import llnl.util.tty as tty
 from llnl.util.tty.colify import colify
 
@@ -43,7 +45,9 @@ def dependencies(parser, args):
         spec = spack.cmd.disambiguate_spec(specs[0], env)
 
         format_string = '{name}{@version}{%compiler}{/hash:7}'
-        tty.msg("Dependencies of %s" % spec.format(format_string, color=True))
+        if sys.stdout.isatty():
+            tty.msg(
+                "Dependencies of %s" % spec.format(format_string, color=True))
         deps = spack.store.db.installed_relatives(
             spec, 'children', args.transitive, deptype=args.deptype)
         if deps:
diff --git a/lib/spack/spack/cmd/dependents.py b/lib/spack/spack/cmd/dependents.py
index 89fd15ffdab..5563701801a 100644
--- a/lib/spack/spack/cmd/dependents.py
+++ b/lib/spack/spack/cmd/dependents.py
@@ -3,6 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import sys
+
 import llnl.util.tty as tty
 from llnl.util.tty.colify import colify
 
@@ -84,7 +86,8 @@ def dependents(parser, args):
         spec = spack.cmd.disambiguate_spec(specs[0], env)
 
         format_string = '{name}{@version}{%compiler}{/hash:7}'
-        tty.msg("Dependents of %s" % spec.cformat(format_string))
+        if sys.stdout.isatty():
+            tty.msg("Dependents of %s" % spec.cformat(format_string))
         deps = spack.store.db.installed_relatives(
             spec, 'parents', args.transitive)
         if deps:
diff --git a/lib/spack/spack/cmd/find.py b/lib/spack/spack/cmd/find.py
index fa36e1cd267..db229aca7e3 100644
--- a/lib/spack/spack/cmd/find.py
+++ b/lib/spack/spack/cmd/find.py
@@ -7,6 +7,7 @@
 
 import copy
 import os
+import sys
 
 import llnl.util.tty as tty
 import llnl.util.tty.color as color
@@ -236,7 +237,7 @@ def find(parser, args):
     else:
         if env:
             display_env(env, args, decorator)
-        if args.groups:
+        if sys.stdout.isatty() and args.groups:
             tty.msg("%s" % plural(len(results), 'installed package'))
         cmd.display_specs(
             results, args, decorator=decorator, all_headers=True)
diff --git a/lib/spack/spack/cmd/modules/__init__.py b/lib/spack/spack/cmd/modules/__init__.py
index 6555b8c8a7e..7d51224e146 100644
--- a/lib/spack/spack/cmd/modules/__init__.py
+++ b/lib/spack/spack/cmd/modules/__init__.py
@@ -119,8 +119,9 @@ def one_spec_or_raise(specs):
     " this command with debug output enabled for more details.")
 
 
-def loads(module_type, specs, args, out=sys.stdout):
+def loads(module_type, specs, args, out=None):
     """Prompt the list of modules associated with a list of specs"""
+    out = sys.stdout if out is None else out
 
     # Get a comprehensive list of specs
     if args.recurse_dependencies:
diff --git a/lib/spack/spack/test/cmd/find.py b/lib/spack/spack/test/cmd/find.py
index 8516569592d..8d3c68d31aa 100644
--- a/lib/spack/spack/test/cmd/find.py
+++ b/lib/spack/spack/test/cmd/find.py
@@ -324,7 +324,7 @@ def test_find_prefix_in_env(mutable_mock_env_path, install_mockery, mock_fetch,
 
 def test_find_loaded(database, working_env):
     output = find('--loaded', '--group')
-    assert output == ''  # 0 packages installed printed separately
+    assert output == ''
 
     os.environ[uenv.spack_loaded_hashes_var] = ':'.join(
         [x.dag_hash() for x in spack.store.db.query()])

From 8671ac6a1aa4cb40e31b8b1e08f0986ab23df15c Mon Sep 17 00:00:00 2001
From: Cyrus Harrison <cyrush@llnl.gov>
Date: Sat, 9 May 2020 10:28:33 -0700
Subject: [PATCH 310/802] update visit package with 3.1.1 release and add
 comments (#16498)

---
 .../repos/builtin/packages/visit/package.py   | 150 +++++++++++++++++-
 ...hanges.patch => spack-changes-3.0.1.patch} |   0
 .../packages/visit/spack-changes-3.1.patch    |  11 ++
 3 files changed, 154 insertions(+), 7 deletions(-)
 rename var/spack/repos/builtin/packages/visit/{spack-changes.patch => spack-changes-3.0.1.patch} (100%)
 create mode 100644 var/spack/repos/builtin/packages/visit/spack-changes-3.1.patch

diff --git a/var/spack/repos/builtin/packages/visit/package.py b/var/spack/repos/builtin/packages/visit/package.py
index aa791284c0b..cd72bcda2c4 100644
--- a/var/spack/repos/builtin/packages/visit/package.py
+++ b/var/spack/repos/builtin/packages/visit/package.py
@@ -8,10 +8,44 @@
 
 class Visit(CMakePackage):
     """VisIt is an Open Source, interactive, scalable, visualization,
-       animation and analysis tool."""
+       animation and analysis tool. See comments in VisIt's package.py
+       for tips about building VisIt with spack.
+    """
+    ############################
+    # Suggestions for building:
+    ############################
+    # cyrush note:
+    #
+    # Out of the box, VisIt's python 2 requirement will cause
+    # spack spec constraint errors due Qt + Mesa build
+    # dependencies.
+    #
+    # You can avoid this using:
+    #
+    # linux:
+    #  spack install visit ^python+shared ^glib@2.56.3 ^py-setuptools@44.1.0
+    #
+    # macOS:
+    #  spack install visit ^python+shared ^glib@2.56.3 ^py-setuptools@44.1.0 \
+    #                      ^qt~framework
+    #
+    # Rpath issues undermine qwt (not qt) when a build as a framework
+    # VisIt's osxfixup resolves this for us in other cases,
+    # but we can't use osxfixup with spack b/c it will undermine other libs.
+    #
+    # Even with these changes, VisIt's Python CLI does not work on macOS,
+    # there is a linking issue related to OpenSSL.
+    # (dyld: Symbol not found: _GENERAL_NAME_free - which comes from OpenSSL)
+    #
+    ############################
     homepage = "https://wci.llnl.gov/simulation/computer-codes/visit/"
-    url = "https://portal.nersc.gov/project/visit/releases/3.0.1/visit3.0.1.tar.gz"
+    git      = "https://github.com/visit-dav/visit.git"
+    url = "https://github.com/visit-dav/visit/releases/download/v3.1.1/visit3.1.1.tar.gz"
 
+    maintainers = ['cyrush']
+
+    version('develop', branch='develop')
+    version('3.1.1', sha256='0b60ac52fd00aff3cf212a310e36e32e13ae3ca0ddd1ea3f54f75e4d9b6c6cf0')
     version('3.0.1', sha256='a506d4d83b8973829e68787d8d721199523ce7ec73e7594e93333c214c2c12bd')
     version('2.13.3', sha256='cf0b3d2e39e1cd102dd886d3ef6da892733445e362fc28f24d9682012cccf2e5')
     version('2.13.0', sha256='716644b8e78a00ff82691619d4d1e7a914965b6535884890b667b97ba08d6a0f')
@@ -28,19 +62,109 @@ class Visit(CMakePackage):
     variant('python', default=True, description='Enable Python support')
     variant('mpi',    default=True, description='Enable parallel engine')
 
-    patch('spack-changes.patch')
+    patch('spack-changes-3.1.patch', when="@3.1.0:,develop")
+    patch('spack-changes-3.0.1.patch', when="@3.0.1")
     patch('nonframework-qwt.patch', when='^qt~framework platform=darwin')
     patch('parallel-hdf5.patch', when='+hdf5+mpi')
 
+    #############################################
+    # Full List of dependencies from build_visit
+    #############################################
+    # cyrush note:
+    #  I added these here to give folks details
+    #  to help eventually build up to full
+    #  support for visit
+    #############################################
+    # =====================================
+    # core:
+    # =====================================
+    #  cmake (build)
+    #  vtk
+    #  qt
+    #  qwt
+    #  python
+    #  mpi
+    #
+    # =====================================
+    # rendering (optional):
+    # =====================================
+    # icet
+    # vtk-m
+    # vtk-h
+    # llvm
+    # mesagl
+    # osmesa
+    # tbb
+    # embree
+    # ispc
+    # ospray
+    #
+    # =====================================
+    # python modules:
+    # =====================================
+    # numpy
+    # pillow
+    # mpi4py
+    # seedme
+    # sphinx (build, docs)
+    # sphinx rtd theme (build, docs)
+    # pyqt (visit support deprecated)
+    # pyside (note: we want pyside 2)
+    #
+    # =====================================
+    # testing related:
+    # =====================================
+    # p7zip (build, test)
+    #
+    # =====================================
+    # io libs:
+    # =====================================
+    # adios
+    # adios2
+    # advio
+    # boost
+    # boxlib
+    # cfitsio
+    # cgns
+    # conduit
+    # damaris
+    # fastbit
+    # fastquery
+    # gdal
+    # h5part
+    # hdf4
+    # hdf5
+    # mdsplus
+    # mfem
+    # mili
+    # moab
+    # mxml
+    # nektarpp
+    # netcdf
+    # openexr
+    # pidx
+    # silo
+    # stripack
+    # szip
+    # tbb
+    # uintah
+    # xdmf
+    # xercesc
+    # xsd
+    # zlib
+    #
+    # =====================================
+
     depends_on('cmake@3.0:', type='build')
     # https://github.com/visit-dav/visit/issues/3498
-    depends_on('vtk@8.1.0:8.1.999+opengl2', when='@3.0:3.0.1')
+    depends_on('vtk@8.1.0:8.1.999+opengl2~python', when='~python @3.0:3.999,develop')
+    depends_on('vtk@8.1.0:8.1.999+opengl2+python', when='+python @3.0:3.999,develop')
     depends_on('vtk@6.1.0~opengl2', when='@:2.999')
-    depends_on('vtk+python', when='+python @3.0:')
+    depends_on('vtk+python', when='+python @3.0:,develop')
     depends_on('vtk~mpi', when='~mpi')
     depends_on('vtk+qt', when='+gui')
     depends_on('qt@4.8.6:4.999', when='+gui @:2.999')
-    depends_on('qt@5.10:', when='+gui @3.0:')
+    depends_on('qt@5.10:', when='+gui @3.0:,develop')
     depends_on('qwt', when='+gui')
     depends_on('python@2.6:2.8', when='+python')
     # VisIt uses Silo's 'ghost zone' data structures, which are only available
@@ -59,7 +183,7 @@ class Visit(CMakePackage):
 
     root_cmakelists_dir = 'src'
 
-    @when('@3.0.0:3.0.1')
+    @when('@3.0.0:3.999,develop')
     def patch(self):
         # Some of VTK's targets don't create explicit libraries, so there is no
         # 'vtktiff'. Instead, replace with the library variable defined from
@@ -90,8 +214,20 @@ def cmake_args(self):
             '-DCMAKE_C_FLAGS=' + ' '.join(cc_flags),
         ]
 
+        if spec.satisfies('@3.1:'):
+            args.append('-DFIXUP_OSX=OFF')
+
         if '+python' in spec:
+            args.append('-DVISIT_PYTHON_SCRIPTING=ON')
+            # keep this off, we have an openssl + python linking issue
+            # that appears in spack
+            args.append('-DVISIT_PYTHON_FILTERS=OFF')
             args.append('-DPYTHON_DIR:PATH={0}'.format(spec['python'].home))
+        else:
+            args.append('-DVISIT_PYTHON_SCRIPTING=OFF')
+            # keep this off, we have an openssl + python linking issue
+            # that appears in spack
+            args.append('-DVISIT_PYTHON_FILTERS=OFF')
 
         if '+gui' in spec:
             qt_bin = spec['qt'].prefix.bin
diff --git a/var/spack/repos/builtin/packages/visit/spack-changes.patch b/var/spack/repos/builtin/packages/visit/spack-changes-3.0.1.patch
similarity index 100%
rename from var/spack/repos/builtin/packages/visit/spack-changes.patch
rename to var/spack/repos/builtin/packages/visit/spack-changes-3.0.1.patch
diff --git a/var/spack/repos/builtin/packages/visit/spack-changes-3.1.patch b/var/spack/repos/builtin/packages/visit/spack-changes-3.1.patch
new file mode 100644
index 00000000000..def9ebcb4a3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/visit/spack-changes-3.1.patch
@@ -0,0 +1,11 @@
+--- a/src/CMakeLists.txt	2019-08-11 17:06:04.000000000 -0400
++++ b/src/CMakeLists.txt	2019-08-11 17:06:20.000000000 -0400
+@@ -459,6 +459,7 @@
+     cmake_policy(SET CMP0033 OLD)
+     cmake_policy(SET CMP0057 NEW)
+     cmake_policy(SET CMP0062 NEW)
++    cmake_policy(SET CMP0068 NEW)
+     IF(WIN32)
+         # don't automatically link with qtmain
+         cmake_policy(SET CMP0020 OLD)
+

From b06bc31029e13c508814857812415df7b5ea6ff4 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Sat, 9 May 2020 19:41:50 +0200
Subject: [PATCH 311/802] Increase coverage of spack.relocate (#16475)

- add docstrings and make parameter names consistent in `relocate.py`
- Make `replace_prefix_*` and other functions private (as they are implementation details)
- remove unused function _replace_prefix_nullterm()

- Add unit tests for `relocate.py` functions
  - add patchelf to Travis and use it during tests
  - add hello_world fixture with a compiled binary, so we can test relocation
---
 .travis.yml                      |  20 +++
 lib/spack/spack/relocate.py      | 268 +++++++++++++++++--------------
 lib/spack/spack/test/relocate.py | 120 +++++++++++++-
 3 files changed, 287 insertions(+), 121 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 227f6fc955f..bc914ef5126 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -32,6 +32,25 @@ jobs:
       dist: trusty
       os: linux
       language: python
+      addons:
+        apt:
+          # Everything but patchelf, that is not available for trusty
+          packages:
+            - ccache
+            - cmake
+            - gfortran
+            - graphviz
+            - gnupg2
+            - kcov
+            - mercurial
+            - ninja-build
+            - perl
+            - perl-base
+            - realpath
+            - r-base
+            - r-base-core
+            - r-base-dev
+            - zsh
       env: [ TEST_SUITE=unit, COVERAGE=true ]
     - python: '2.7'
       os: linux
@@ -84,6 +103,7 @@ addons:
       - kcov
       - mercurial
       - ninja-build
+      - patchelf
       - perl
       - perl-base
       - realpath
diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py
index 41faf273cd5..94fd2b58bfe 100644
--- a/lib/spack/spack/relocate.py
+++ b/lib/spack/spack/relocate.py
@@ -11,6 +11,7 @@
 import llnl.util.tty as tty
 import macholib.MachO
 import macholib.mach_o
+import spack.architecture
 import spack.cmd
 import spack.repo
 import spack.spec
@@ -385,57 +386,79 @@ def macholib_get_paths(cur_path):
     return (rpaths, deps, ident)
 
 
-def modify_elf_object(path_name, new_rpaths):
-    """
-    Replace orig_rpath with new_rpath in RPATH of elf object path_name
+def _set_elf_rpaths(target, rpaths):
+    """Replace the original RPATH of the target with the paths passed
+    as arguments.
+
+    This function uses ``patchelf`` to set RPATHs.
+
+    Args:
+        target: target executable. Must be an ELF object.
+        rpaths: paths to be set in the RPATH
+
+    Returns:
+        A string concatenating the stdout and stderr of the call
+        to ``patchelf``
     """
+    # Join the paths using ':' as a separator
+    rpaths_str = ':'.join(rpaths)
 
-    new_joined = ':'.join(new_rpaths)
-
-    # if we're relocating patchelf itself, use it
-    bak_path = path_name + ".bak"
-
-    if path_name[-13:] == "/bin/patchelf":
-        shutil.copy(path_name, bak_path)
-        patchelf = executable.Executable(bak_path)
-    else:
-        patchelf = executable.Executable(_patchelf())
+    # If we're relocating patchelf itself, make a copy and use it
+    bak_path = None
+    if target.endswith("/bin/patchelf"):
+        bak_path = target + ".bak"
+        shutil.copy(target, bak_path)
 
+    patchelf, output = executable.Executable(bak_path or _patchelf()), None
     try:
-        patchelf('--force-rpath', '--set-rpath', '%s' % new_joined,
-                 '%s' % path_name, output=str, error=str)
+        # TODO: revisit the use of --force-rpath as it might be conditional
+        # TODO: if we want to support setting RUNPATH from binary packages
+        patchelf_args = ['--force-rpath', '--set-rpath', rpaths_str, target]
+        output = patchelf(*patchelf_args, output=str, error=str)
     except executable.ProcessError as e:
-        msg = 'patchelf --force-rpath --set-rpath %s failed with error %s' % (
-            path_name, e)
-        tty.warn(msg)
-    if os.path.exists(bak_path):
-        os.remove(bak_path)
+        msg = 'patchelf --force-rpath --set-rpath {0} failed with error {1}'
+        tty.warn(msg.format(target, e))
+    finally:
+        if bak_path and os.path.exists(bak_path):
+            os.remove(bak_path)
+    return output
 
 
 def needs_binary_relocation(m_type, m_subtype):
-    """
-    Check whether the given filetype is a binary that may need relocation.
+    """Returns True if the file with MIME type/subtype passed as arguments
+    needs binary relocation, False otherwise.
+
+    Args:
+        m_type (str): MIME type of the file
+        m_subtype (str): MIME subtype of the file
     """
     if m_type == 'application':
-        if (m_subtype == 'x-executable' or m_subtype == 'x-sharedlib' or
-                m_subtype == 'x-mach-binary'):
+        if m_subtype in ('x-executable', 'x-sharedlib', 'x-mach-binary'):
             return True
     return False
 
 
 def needs_text_relocation(m_type, m_subtype):
+    """Returns True if the file with MIME type/subtype passed as arguments
+    needs text relocation, False otherwise.
+
+    Args:
+        m_type (str): MIME type of the file
+        m_subtype (str): MIME subtype of the file
     """
-    Check whether the given filetype is text that may need relocation.
-    """
-    return (m_type == "text")
+    return m_type == 'text'
 
 
-def replace_prefix_text(path_name, old_dir, new_dir):
+def _replace_prefix_text(filename, old_dir, new_dir):
+    """Replace all the occurrences of the old install prefix with a
+    new install prefix in text files that are utf-8 encoded.
+
+    Args:
+        filename (str): target text file (utf-8 encoded)
+        old_dir (str): directory to be searched in the file
+        new_dir (str): substitute for the old directory
     """
-    Replace old install prefix with new install prefix
-    in text files using utf-8 encoded strings.
-    """
-    with open(path_name, 'rb+') as f:
+    with open(filename, 'rb+') as f:
         data = f.read()
         f.seek(0)
         # Replace old_dir with new_dir if it appears at the beginning of a path
@@ -454,13 +477,18 @@ def replace_prefix_text(path_name, old_dir, new_dir):
         f.truncate()
 
 
-def replace_prefix_bin(path_name, old_dir, new_dir):
-    """
-    Attempt to replace old install prefix with new install prefix
-    in binary files by prefixing new install prefix with os.sep
-    until the lengths of the prefixes are the same.
-    """
+def _replace_prefix_bin(filename, old_dir, new_dir):
+    """Replace all the occurrences of the old install prefix with a
+    new install prefix in binary files.
 
+    The new install prefix is prefixed with ``os.sep`` until the
+    lengths of the prefixes are the same.
+
+    Args:
+        filename (str): target binary file
+        old_dir (str): directory to be searched in the file
+        new_dir (str): substitute for the old directory
+    """
     def replace(match):
         occurances = match.group().count(old_dir.encode('utf-8'))
         olen = len(old_dir.encode('utf-8'))
@@ -468,11 +496,12 @@ def replace(match):
         padding = (olen - nlen) * occurances
         if padding < 0:
             return data
-        return match.group().replace(old_dir.encode('utf-8'),
-                                     os.sep.encode('utf-8') * padding +
-                                     new_dir.encode('utf-8'))
+        return match.group().replace(
+            old_dir.encode('utf-8'),
+            os.sep.encode('utf-8') * padding + new_dir.encode('utf-8')
+        )
 
-    with open(path_name, 'rb+') as f:
+    with open(filename, 'rb+') as f:
         data = f.read()
         f.seek(0)
         original_data_len = len(data)
@@ -482,43 +511,7 @@ def replace(match):
         ndata = pat.sub(replace, data)
         if not len(ndata) == original_data_len:
             raise BinaryStringReplacementError(
-                path_name, original_data_len, len(ndata))
-        f.write(ndata)
-        f.truncate()
-
-
-def replace_prefix_nullterm(path_name, old_dir, new_dir):
-    """
-    Attempt to replace old install prefix with new install prefix
-    in binary files by replacing with null terminated string
-    that is the same length unless the old path is shorter
-    Used on linux to replace mach-o rpaths
-    """
-
-    def replace(match):
-        occurances = match.group().count(old_dir.encode('utf-8'))
-        olen = len(old_dir.encode('utf-8'))
-        nlen = len(new_dir.encode('utf-8'))
-        padding = (olen - nlen) * occurances
-        if padding < 0:
-            return data
-        return match.group().replace(old_dir.encode('utf-8'),
-                                     new_dir.encode('utf-8')) + b'\0' * padding
-
-    if len(new_dir) > len(old_dir):
-        raise BinaryTextReplaceError(old_dir, new_dir)
-
-    with open(path_name, 'rb+') as f:
-        data = f.read()
-        f.seek(0)
-        original_data_len = len(data)
-        pat = re.compile(re.escape(old_dir).encode('utf-8') + b'([^\0]*?)\0')
-        if not pat.search(data):
-            return
-        ndata = pat.sub(replace, data)
-        if not len(ndata) == original_data_len:
-            raise BinaryStringReplacementError(
-                path_name, original_data_len, len(ndata))
+                filename, original_data_len, len(ndata))
         f.write(ndata)
         f.truncate()
 
@@ -597,50 +590,89 @@ def relocate_macho_binaries(path_names, old_layout_root, new_layout_root,
                                        paths_to_paths)
 
 
-def elf_find_paths(orig_rpaths, old_layout_root, prefix_to_prefix):
-    new_rpaths = list()
+def _transform_rpaths(orig_rpaths, orig_root, new_prefixes):
+    """Return an updated list of RPATHs where each entry in the original list
+    starting with the old root is relocated to another place according to the
+    mapping passed as argument.
+
+    Args:
+        orig_rpaths (list): list of the original RPATHs
+        orig_root (str): original root to be substituted
+        new_prefixes (dict): dictionary that maps the original prefixes to
+            where they should be relocated
+
+    Returns:
+        List of paths
+    """
+    new_rpaths = []
     for orig_rpath in orig_rpaths:
-        if orig_rpath.startswith(old_layout_root):
-            for old_prefix, new_prefix in prefix_to_prefix.items():
-                if orig_rpath.startswith(old_prefix):
-                    new_rpaths.append(re.sub(re.escape(old_prefix),
-                                             new_prefix, orig_rpath))
-        else:
+        # If the original RPATH doesn't start with the target root
+        # append it verbatim and proceed
+        if not orig_rpath.startswith(orig_root):
             new_rpaths.append(orig_rpath)
+            continue
+
+        # Otherwise inspect the mapping and transform + append any prefix
+        # that starts with a registered key
+        for old_prefix, new_prefix in new_prefixes.items():
+            if orig_rpath.startswith(old_prefix):
+                new_rpaths.append(
+                    re.sub(re.escape(old_prefix), new_prefix, orig_rpath)
+                )
+
     return new_rpaths
 
 
-def relocate_elf_binaries(path_names, old_layout_root, new_layout_root,
-                          prefix_to_prefix, rel, old_prefix, new_prefix):
-    """
-    Use patchelf to get the original rpaths and then replace them with
+def relocate_elf_binaries(binaries, orig_root, new_root,
+                          new_prefixes, rel, orig_prefix, new_prefix):
+    """Relocate the binaries passed as arguments by changing their RPATHs.
+
+    Use patchelf to get the original RPATHs and then replace them with
     rpaths in the new directory layout.
-    New rpaths are determined from a dictionary mapping the prefixes in the
+
+    New RPATHs are determined from a dictionary mapping the prefixes in the
     old directory layout to the prefixes in the new directory layout if the
     rpath was in the old layout root, i.e. system paths are not replaced.
+
+    Args:
+        binaries (list): list of binaries that might need relocation, located
+            in the new prefix
+        orig_root (str): original root to be substituted
+        new_root (str): new root to be used, only relevant for relative RPATHs
+        new_prefixes (dict): dictionary that maps the original prefixes to
+            where they should be relocated
+        rel (bool): True if the RPATHs are relative, False if they are absolute
+        orig_prefix (str): prefix where the executable was originally located
+        new_prefix (str): prefix where we want to relocate the executable
     """
-    for path_name in path_names:
-        orig_rpaths = _elf_rpaths_for(path_name)
-        new_rpaths = list()
+    for new_binary in binaries:
+        orig_rpaths = _elf_rpaths_for(new_binary)
+        # TODO: Can we deduce `rel` from the original RPATHs?
         if rel:
-            # get the file path in the old_prefix
-            orig_path_name = re.sub(re.escape(new_prefix), old_prefix,
-                                    path_name)
-            # get the normalized rpaths in the old prefix using the file path
+            # Get the file path in the original prefix
+            orig_binary = re.sub(
+                re.escape(new_prefix), orig_prefix, new_binary
+            )
+
+            # Get the normalized RPATHs in the old prefix using the file path
             # in the orig prefix
-            orig_norm_rpaths = _normalize_relative_paths(orig_path_name,
-                                                         orig_rpaths)
-            # get the normalize rpaths in the new prefix
-            norm_rpaths = elf_find_paths(orig_norm_rpaths, old_layout_root,
-                                         prefix_to_prefix)
-            # get the relativized rpaths in the new prefix
-            new_rpaths = _make_relative(path_name, new_layout_root,
-                                        norm_rpaths)
-            modify_elf_object(path_name, new_rpaths)
+            orig_norm_rpaths = _normalize_relative_paths(
+                orig_binary, orig_rpaths
+            )
+            # Get the normalize RPATHs in the new prefix
+            new_norm_rpaths = _transform_rpaths(
+                orig_norm_rpaths, orig_root, new_prefixes
+            )
+            # Get the relative RPATHs in the new prefix
+            new_rpaths = _make_relative(
+                new_binary, new_root, new_norm_rpaths
+            )
+            _set_elf_rpaths(new_binary, new_rpaths)
         else:
-            new_rpaths = elf_find_paths(orig_rpaths, old_layout_root,
-                                        prefix_to_prefix)
-            modify_elf_object(path_name, new_rpaths)
+            new_rpaths = _transform_rpaths(
+                orig_rpaths, orig_root, new_prefixes
+            )
+            _set_elf_rpaths(new_binary, new_rpaths)
 
 
 def make_link_relative(cur_path_names, orig_path_names):
@@ -684,7 +716,7 @@ def make_elf_binaries_relative(cur_path_names, orig_path_names,
         if orig_rpaths:
             new_rpaths = _make_relative(orig_path, old_layout_root,
                                         orig_rpaths)
-            modify_elf_object(cur_path, new_rpaths)
+            _set_elf_rpaths(cur_path, new_rpaths)
 
 
 def check_files_relocatable(cur_path_names, allow_root):
@@ -738,11 +770,11 @@ def relocate_text(path_names, old_layout_root, new_layout_root,
     sbangnew = '#!/bin/bash %s/bin/sbang' % new_spack_prefix
 
     for path_name in path_names:
-        replace_prefix_text(path_name, old_install_prefix, new_install_prefix)
+        _replace_prefix_text(path_name, old_install_prefix, new_install_prefix)
         for orig_dep_prefix, new_dep_prefix in prefix_to_prefix.items():
-            replace_prefix_text(path_name, orig_dep_prefix, new_dep_prefix)
-        replace_prefix_text(path_name, old_layout_root, new_layout_root)
-        replace_prefix_text(path_name, sbangre, sbangnew)
+            _replace_prefix_text(path_name, orig_dep_prefix, new_dep_prefix)
+        _replace_prefix_text(path_name, old_layout_root, new_layout_root)
+        _replace_prefix_text(path_name, sbangre, sbangnew)
 
 
 def relocate_text_bin(path_names, old_layout_root, new_layout_root,
@@ -758,9 +790,9 @@ def relocate_text_bin(path_names, old_layout_root, new_layout_root,
         for path_name in path_names:
             for old_dep_prefix, new_dep_prefix in prefix_to_prefix.items():
                 if len(new_dep_prefix) <= len(old_dep_prefix):
-                    replace_prefix_bin(
+                    _replace_prefix_bin(
                         path_name, old_dep_prefix, new_dep_prefix)
-            replace_prefix_bin(path_name, old_spack_prefix, new_spack_prefix)
+            _replace_prefix_bin(path_name, old_spack_prefix, new_spack_prefix)
     else:
         if len(path_names) > 0:
             raise BinaryTextReplaceError(
diff --git a/lib/spack/spack/test/relocate.py b/lib/spack/spack/test/relocate.py
index a2bba52f401..a594f1a9ba6 100644
--- a/lib/spack/spack/test/relocate.py
+++ b/lib/spack/spack/test/relocate.py
@@ -103,6 +103,31 @@ def _factory(output):
     return _factory
 
 
+@pytest.fixture()
+def hello_world(tmpdir):
+    source = tmpdir.join('main.c')
+    source.write("""
+#include <stdio.h>
+int main(){
+    printf("Hello world!");
+}
+""")
+
+    def _factory(rpaths):
+        gcc = spack.util.executable.which('gcc')
+        executable = source.dirpath('main.x')
+        rpath_str = ':'.join(rpaths)
+        opts = [
+            '-Wl,--disable-new-dtags',
+            '-Wl,-rpath={0}'.format(rpath_str),
+            str(source), '-o', str(executable)
+        ]
+        gcc(*opts)
+        return executable
+
+    return _factory
+
+
 @pytest.mark.requires_executables(
     '/usr/bin/gcc', 'patchelf', 'strings', 'file'
 )
@@ -118,9 +143,7 @@ def test_file_is_relocatable(source_file, is_relocatable):
     assert spack.relocate.file_is_relocatable(executable) is is_relocatable
 
 
-@pytest.mark.requires_executables(
-    'patchelf', 'strings', 'file'
-)
+@pytest.mark.requires_executables('patchelf', 'strings', 'file')
 def test_patchelf_is_relocatable():
     patchelf = spack.relocate._patchelf()
     assert llnl.util.filesystem.is_exe(patchelf)
@@ -194,3 +217,94 @@ def test_normalize_relative_paths(start_path, relative_paths, expected):
         start_path, relative_paths
     )
     assert normalized == expected
+
+
+def test_set_elf_rpaths(mock_patchelf):
+    # Try to relocate a mock version of patchelf and check
+    # the call made to patchelf itself
+    patchelf = mock_patchelf('echo $@')
+    rpaths = ['/usr/lib', '/usr/lib64', '/opt/local/lib']
+    output = spack.relocate._set_elf_rpaths(patchelf, rpaths)
+
+    # Assert that the arguments of the call to patchelf are as expected
+    assert '--force-rpath' in output
+    assert '--set-rpath ' + ':'.join(rpaths) in output
+    assert patchelf in output
+
+
+def test_set_elf_rpaths_warning(mock_patchelf):
+    # Mock a failing patchelf command and ensure it warns users
+    patchelf = mock_patchelf('exit 1')
+    rpaths = ['/usr/lib', '/usr/lib64', '/opt/local/lib']
+    # To avoid using capfd in order to check if the warning was triggered
+    # here we just check that output is not set
+    output = spack.relocate._set_elf_rpaths(patchelf, rpaths)
+    assert output is None
+
+
+@pytest.mark.requires_executables('patchelf', 'strings', 'file', 'gcc')
+def test_replace_prefix_bin(hello_world):
+    # Compile an "Hello world!" executable and set RPATHs
+    executable = hello_world(rpaths=['/usr/lib', '/usr/lib64'])
+
+    # Relocate the RPATHs
+    spack.relocate._replace_prefix_bin(str(executable), '/usr', '/foo')
+
+    # Check that the RPATHs changed
+    patchelf = spack.util.executable.which('patchelf')
+    output = patchelf('--print-rpath', str(executable), output=str)
+    assert output.strip() == '/foo/lib:/foo/lib64'
+
+
+@pytest.mark.requires_executables('patchelf', 'strings', 'file', 'gcc')
+def test_relocate_elf_binaries_absolute_paths(hello_world, tmpdir):
+    # Create an executable, set some RPATHs, copy it to another location
+    orig_binary = hello_world(rpaths=[str(tmpdir.mkdir('lib')), '/usr/lib64'])
+    new_root = tmpdir.mkdir('another_dir')
+    shutil.copy(str(orig_binary), str(new_root))
+
+    # Relocate the binary
+    new_binary = new_root.join('main.x')
+    spack.relocate.relocate_elf_binaries(
+        binaries=[str(new_binary)],
+        orig_root=str(orig_binary.dirpath()),
+        new_root=None,  # Not needed when relocating absolute paths
+        new_prefixes={
+            str(tmpdir): '/foo'
+        },
+        rel=False,
+        # Not needed when relocating absolute paths
+        orig_prefix=None, new_prefix=None
+    )
+
+    # Check that the RPATHs changed
+    patchelf = spack.util.executable.which('patchelf')
+    output = patchelf('--print-rpath', str(new_binary), output=str)
+    assert output.strip() == '/foo/lib:/usr/lib64'
+
+
+@pytest.mark.requires_executables('patchelf', 'strings', 'file', 'gcc')
+def test_relocate_elf_binaries_relative_paths(hello_world, tmpdir):
+    # Create an executable, set some RPATHs, copy it to another location
+    orig_binary = hello_world(
+        rpaths=['$ORIGIN/lib', '$ORIGIN/lib64', '/opt/local/lib']
+    )
+    new_root = tmpdir.mkdir('another_dir')
+    shutil.copy(str(orig_binary), str(new_root))
+
+    # Relocate the binary
+    new_binary = new_root.join('main.x')
+    spack.relocate.relocate_elf_binaries(
+        binaries=[str(new_binary)],
+        orig_root=str(orig_binary.dirpath()),
+        new_root=str(new_root),
+        new_prefixes={str(tmpdir): '/foo'},
+        rel=True,
+        orig_prefix=str(orig_binary.dirpath()),
+        new_prefix=str(new_root)
+    )
+
+    # Check that the RPATHs changed
+    patchelf = spack.util.executable.which('patchelf')
+    output = patchelf('--print-rpath', str(new_binary), output=str)
+    assert output.strip() == '/foo/lib:/foo/lib64:/opt/local/lib'

From b668bde7ec6e6d3156149573c52ad7f93e292af2 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Sat, 9 May 2020 20:04:20 +0200
Subject: [PATCH 312/802] Fix dependency of geant4 (amends #16497) (#16504)

* Fix dependency of geant4 (amends #16497)

* Update geant4-data dependencies

* Reviewer comments (part 1/2)

* Reviewer comments (part 2/2)

* Update var/spack/repos/builtin/packages/geant4-data/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../repos/builtin/packages/g4emlow/package.py |  1 +
 .../builtin/packages/geant4-data/package.py   | 22 ++++++++++---------
 .../repos/builtin/packages/geant4/package.py  |  1 +
 3 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/var/spack/repos/builtin/packages/g4emlow/package.py b/var/spack/repos/builtin/packages/g4emlow/package.py
index 713b9da6311..e7b34000cdd 100644
--- a/var/spack/repos/builtin/packages/g4emlow/package.py
+++ b/var/spack/repos/builtin/packages/g4emlow/package.py
@@ -15,6 +15,7 @@ class G4emlow(Package):
     maintainers = ['drbenmorgan']
 
     # Only versions relevant to Geant4 releases built by spack are added
+    version('7.9.1', sha256='820c106e501c64c617df6c9e33a0f0a3822ffad059871930f74b8cc37f043ccb')
     version('7.9', sha256='4abf9aa6cda91e4612676ce4d2d8a73b91184533aa66f9aad19a53a8c4dc3aff')
     version('7.7', sha256='16dec6adda6477a97424d749688d73e9bd7d0b84d0137a67cf341f1960984663')
     version('7.3', sha256='583aa7f34f67b09db7d566f904c54b21e95a9ac05b60e2bfb794efb569dba14e')
diff --git a/var/spack/repos/builtin/packages/geant4-data/package.py b/var/spack/repos/builtin/packages/geant4-data/package.py
index 4157fb76c6e..01c46c218dc 100644
--- a/var/spack/repos/builtin/packages/geant4-data/package.py
+++ b/var/spack/repos/builtin/packages/geant4-data/package.py
@@ -15,6 +15,7 @@ class Geant4Data(BundlePackage):
 
     maintainers = ['drbenmorgan']
 
+    version('10.6.1')
     version('10.6.0')
     version('10.5.1')
     version('10.4.3')
@@ -28,17 +29,18 @@ class Geant4Data(BundlePackage):
     # they generally don't change on the patch level
     # Can move to declaring on a dataset basis if needed
     # geant4@10.6.X
-    depends_on("g4ndl@4.6", when='@10.6.0')
+    depends_on("g4ndl@4.6", when='@10.6.0:10.6.9999')
     depends_on("g4emlow@7.9", when='@10.6.0')
-    depends_on("g4photonevaporation@5.5", when='@10.6.0')
-    depends_on("g4radioactivedecay@5.4", when='@10.6.0')
-    depends_on("g4particlexs@2.1", when='@10.6.0')
-    depends_on("g4pii@1.3", when='@10.6.0')
-    depends_on("g4realsurface@2.1.1", when='@10.6.0')
-    depends_on("g4saiddata@2.0", when='@10.6.0')
-    depends_on("g4abla@3.1", when='@10.6.0')
-    depends_on("g4incl@1.0", when='@10.6.0')
-    depends_on("g4ensdfstate@2.2", when='@10.6.0')
+    depends_on("g4emlow@7.9.1", when='@10.6.1:10.6.9999')
+    depends_on("g4photonevaporation@5.5", when='@10.6.0:10.6.9999')
+    depends_on("g4radioactivedecay@5.4", when='@10.6.0:10.6.9999')
+    depends_on("g4particlexs@2.1", when='@10.6.0:10.6.9999')
+    depends_on("g4pii@1.3", when='@10.6.0:10.6.9999')
+    depends_on("g4realsurface@2.1.1", when='@10.6.0:10.6.9999')
+    depends_on("g4saiddata@2.0", when='@10.6.0:10.6.9999')
+    depends_on("g4abla@3.1", when='@10.6.0:10.6.9999')
+    depends_on("g4incl@1.0", when='@10.6.0:10.6.9999')
+    depends_on("g4ensdfstate@2.2", when='@10.6.0:10.6.9999')
 
     # geant4@10.5.X
     depends_on("g4ndl@4.5", when='@10.5.0:10.5.9999')
diff --git a/var/spack/repos/builtin/packages/geant4/package.py b/var/spack/repos/builtin/packages/geant4/package.py
index 3cd041d1e97..364acbce36e 100644
--- a/var/spack/repos/builtin/packages/geant4/package.py
+++ b/var/spack/repos/builtin/packages/geant4/package.py
@@ -41,6 +41,7 @@ class Geant4(CMakePackage):
     depends_on('cmake@3.5:', type='build')
     depends_on('cmake@3.8:', type='build', when='@10.6.0:')
 
+    depends_on('geant4-data@10.6.1', when='@10.6.1')
     depends_on('geant4-data@10.6.0', when='@10.6.0')
     depends_on('geant4-data@10.5.1', when='@10.5.1')
     depends_on('geant4-data@10.4.3', when='@10.4.3')

From a868b1c756fa6ec6593a0a2ffa96203a111873e4 Mon Sep 17 00:00:00 2001
From: "Nichols A. Romero" <naromero77@users.noreply.github.com>
Date: Sat, 9 May 2020 13:05:11 -0500
Subject: [PATCH 313/802] QMCPACK Update May 2020 (#16542)

* Add naromero77 as a maintainer for QMCPACK Spack package.

* Add QMCPACK 3.9.2

* Remove QE-to-QMCPACK wave function converter from QMCPACK Spack package. Already been moved to QE Spack package.
---
 .../repos/builtin/packages/qmcpack/package.py | 25 ++-----------------
 1 file changed, 2 insertions(+), 23 deletions(-)

diff --git a/var/spack/repos/builtin/packages/qmcpack/package.py b/var/spack/repos/builtin/packages/qmcpack/package.py
index 9484e8a1693..5307b3d2d5c 100644
--- a/var/spack/repos/builtin/packages/qmcpack/package.py
+++ b/var/spack/repos/builtin/packages/qmcpack/package.py
@@ -14,7 +14,7 @@ class Qmcpack(CMakePackage, CudaPackage):
     # Package information
     homepage = "http://www.qmcpack.org/"
     git      = "https://github.com/QMCPACK/qmcpack.git"
-
+    maintainers = ['naromero77']
     tags = ['ecp', 'ecp-apps']
 
     # This download method is untrusted, and is not recommended by the
@@ -22,6 +22,7 @@ class Qmcpack(CMakePackage, CudaPackage):
     # can occasionally change.
     # NOTE: 12/19/2017 QMCPACK 3.0.0 does not build properly with Spack.
     version('develop')
+    version('3.9.2', tag='v3.9.2')
     version('3.9.1', tag='v3.9.1')
     version('3.9.0', tag='v3.9.0')
     version('3.8.0', tag='v3.8.0')
@@ -54,8 +55,6 @@ class Qmcpack(CMakePackage, CudaPackage):
             description='Install with support for basic data analysis tools')
     variant('gui', default=False,
             description='Install with Matplotlib (long installation time)')
-    variant('qe', default=False,
-            description='Install with patched Quantum Espresso 6.4.1')
     variant('afqmc', default=False,
             description='Install with AFQMC support. NOTE that if used in '
                         'combination with CUDA, only AFQMC will have CUDA.')
@@ -85,12 +84,6 @@ class Qmcpack(CMakePackage, CudaPackage):
         when='+cuda@:3.4.0',
         msg='QMCPACK CUDA+SOA variant does not exist prior to v. 3.5.0.')
 
-    conflicts(
-        '+qe',
-        when='~mpi',
-        msg='Serial QMCPACK with serial QE converter not supported. '
-        'Configure in serial QE + serial HDF5 will not run correctly.')
-
     conflicts('^openblas+ilp64',
               msg='QMCPACK does not support OpenBLAS 64-bit integer variant')
 
@@ -140,8 +133,6 @@ class Qmcpack(CMakePackage, CudaPackage):
     # HDF5
     depends_on('hdf5~mpi', when='~phdf5')
     depends_on('hdf5+mpi', when='+phdf5')
-    depends_on('hdf5+hl+fortran~mpi', when='+qe~phdf5')
-    depends_on('hdf5+hl+fortran+mpi', when='+qe+phdf5')
 
     # Math libraries
     depends_on('blas')
@@ -159,18 +150,6 @@ class Qmcpack(CMakePackage, CudaPackage):
     # py-matplotlib leads to a long complex DAG for dependencies
     depends_on('py-matplotlib', when='+gui', type='run')
 
-    # B-spline basis calculation require a patched version of
-    # Quantum Espresso 6.4.1 (see QMCPACK manual)
-    patch_url = 'https://raw.githubusercontent.com/QMCPACK/qmcpack/develop/external_codes/quantum_espresso/add_pw2qmcpack_to_qe-6.4.1.diff'
-    patch_checksum = '57cb1b06ee2653a87c3acc0dd4f09032fcf6ce6b8cbb9677ae9ceeb6a78f85e2'
-    depends_on('quantum-espresso~patch@6.4.1+mpi hdf5=parallel',
-               patches=patch(patch_url, sha256=patch_checksum),
-               when='+qe+phdf5', type='run')
-
-    depends_on('quantum-espresso~patch@6.4.1+mpi hdf5=serial',
-               patches=patch(patch_url, sha256=patch_checksum),
-               when='+qe~phdf5', type='run')
-
     # Backport several patches from recent versions of QMCPACK
     # The test_numerics unit test is broken prior to QMCPACK 3.3.0
     patch_url = 'https://patch-diff.githubusercontent.com/raw/QMCPACK/qmcpack/pull/621.patch'

From 54fee4b400a5d37f3208ec53e1b45965b9942886 Mon Sep 17 00:00:00 2001
From: Jen Herting <jen@herting.cc>
Date: Sat, 9 May 2020 14:05:33 -0400
Subject: [PATCH 314/802] New package: py-addict (#16535)

* [py-addict] created template

* [py-addict] added homepage and description

* [py-addict] cleaned up fixmes

* [py-addict] depends on py-setuptools
---
 .../builtin/packages/py-addict/package.py     | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-addict/package.py

diff --git a/var/spack/repos/builtin/packages/py-addict/package.py b/var/spack/repos/builtin/packages/py-addict/package.py
new file mode 100644
index 00000000000..b4b27f9975b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-addict/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyAddict(PythonPackage):
+    """addict is a Python module that gives you dictionaries
+    whose values are both gettable and settable using
+    attributes, in addition to standard item-syntax."""
+
+    homepage = "https://github.com/mewwts/addict"
+    url      = "https://github.com/mewwts/addict/archive/v2.2.1.tar.gz"
+
+    version('2.2.1', sha256='398bba9e7fa25e2ce144c5c4b8ec6208e89b9445869403dfa88ab66ec110fa12')
+
+    depends_on('py-setuptools', type='build')

From 6e46603470ec9abc4ac64499d4d7d71a399228e1 Mon Sep 17 00:00:00 2001
From: Larry Knox <lrknox@hdfgroup.org>
Date: Sat, 9 May 2020 13:05:55 -0500
Subject: [PATCH 315/802] Add maintainers and variants for building with
 default earlier api versions. (#16534)

* Add maintainers.
Add variants for building with default earlier api versions.

* Update var/spack/repos/builtin/packages/hdf5/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 var/spack/repos/builtin/packages/hdf5/package.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index b4f427ff7b5..57032141498 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -20,6 +20,7 @@ class Hdf5(AutotoolsPackage):
     list_url = "https://support.hdfgroup.org/ftp/HDF5/releases"
     list_depth = 3
     git      = "https://bitbucket.hdfgroup.org/scm/hdffv/hdf5.git"
+    maintainers = ['lrknox']
 
     version('develop', branch='develop')
 
@@ -63,6 +64,13 @@ class Hdf5(AutotoolsPackage):
     variant('szip', default=False, description='Enable szip support')
     variant('pic', default=True,
             description='Produce position-independent code (for shared libs)')
+    # Build HDF5 with API compaitibility.
+    variant('api', default='none', description='choose api compatibility', values=('v114', 'v112', 'v110', 'v18', 'v16'), multi=False)
+
+    conflicts('api=v114', when='@1.6:1.12.99', msg='v114 is not compatible with this release')
+    conflicts('api=v112', when='@1.6:1.10.99', msg='v112 is not compatible with this release')
+    conflicts('api=v110', when='@1.6:1.8.99', msg='v110 is not compatible with this release')
+    conflicts('api=v18', when='@1.6:1.6.99', msg='v18 is not compatible with this release')
 
     depends_on('autoconf', type='build', when='@develop')
     depends_on('automake', type='build', when='@develop')
@@ -230,6 +238,10 @@ def configure_args(self):
         extra_args += self.enable_or_disable('hl')
         extra_args += self.enable_or_disable('fortran')
 
+        api = self.spec.variants['api'].value
+        if api != 'none':
+            extra_args.append('--with-default-api-version=' + api)
+
         if '+szip' in self.spec:
             extra_args.append('--with-szlib=%s' % self.spec['szip'].prefix)
         else:

From 69ea6de06934fd8f7dc8fb89e15f9cea3499814e Mon Sep 17 00:00:00 2001
From: vvolkl <valentin.volkl@cern.ch>
Date: Sat, 9 May 2020 21:54:07 +0200
Subject: [PATCH 316/802] [dd4hep] variant and run env updates (#16524)

* [dd4hep] variant and run env updates

* address comments from #16524
---
 var/spack/repos/builtin/packages/dd4hep/package.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/dd4hep/package.py b/var/spack/repos/builtin/packages/dd4hep/package.py
index abfdb5d19c0..76de6090c5c 100644
--- a/var/spack/repos/builtin/packages/dd4hep/package.py
+++ b/var/spack/repos/builtin/packages/dd4hep/package.py
@@ -36,7 +36,7 @@ class Dd4hep(CMakePackage):
 
     variant('xercesc', default=False, description="Enable 'Detector Builders' based on XercesC")
     variant('geant4', default=False, description="Enable the simulation part based on Geant4")
-    variant('testing', default=False, description="Enable and build tests")
+    variant('assimp', default=False, description="Enable CAD interface based on Assimp")
 
     depends_on('cmake @3.12:', type='build')
     depends_on('boost @1.49:')
@@ -44,6 +44,7 @@ class Dd4hep(CMakePackage):
     extends('python')
     depends_on('xerces-c', when='+xercesc')
     depends_on('geant4@10.2.2:', when='+geant4')
+    depends_on('assimp', when='+assimp')
 
     def cmake_args(self):
         spec = self.spec
@@ -55,13 +56,18 @@ def cmake_args(self):
             "-DCMAKE_CXX_STANDARD={0}".format(cxxstd),
             "-DDD4HEP_USE_XERCESC={0}".format(spec.satisfies('+xercesc')),
             "-DDD4HEP_USE_GEANT4={0}".format(spec.satisfies('+geant4')),
-            "-DBUILD_TESTING={0}".format(spec.satisfies('+testing')),
+            "-DDD4HEP_LOAD_ASSIMP={0}".format(spec.satisfies('+assimp')),
+            "-DBUILD_TESTING={0}".format(self.run_tests),
             "-DBOOST_ROOT={0}".format(spec['boost'].prefix),
             "-DBoost_NO_BOOST_CMAKE=ON",
             "-DPYTHON_EXECUTABLE={0}".format(spec['python'].command.path),
         ]
         return args
 
+    def setup_run_environment(self, env):
+        # used p.ex. in ddsim to find DDDetectors dir
+        env.set("DD4hepINSTALL", self.prefix)
+
     def url_for_version(self, version):
         # dd4hep releases are dashes and padded with a leading zero
         # the patch version is omitted when 0

From 05203ec3fb027f7e5e167bb362bda3a21db4afa9 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Sat, 9 May 2020 22:35:14 +0200
Subject: [PATCH 317/802] Add unit test on MacOS using Github Actions (#14220)

- Remove macos tests from travis
- Add macos tests in github actions.
---
 .codecov.yml                            |  3 +-
 .github/workflows/macos_unit_tests.yaml | 48 +++++++++++++++++++++++++
 .travis.yml                             | 20 -----------
 README.md                               |  1 +
 4 files changed, 50 insertions(+), 22 deletions(-)
 create mode 100644 .github/workflows/macos_unit_tests.yaml

diff --git a/.codecov.yml b/.codecov.yml
index a70b19c39c1..cc4954132f5 100644
--- a/.codecov.yml
+++ b/.codecov.yml
@@ -4,8 +4,7 @@ coverage:
   range: 60...90
   status:
     project:
-      default:
-        threshold: 0.3%
+      default: yes
 
 ignore:
   - lib/spack/spack/test/.*
diff --git a/.github/workflows/macos_unit_tests.yaml b/.github/workflows/macos_unit_tests.yaml
new file mode 100644
index 00000000000..f903daa034a
--- /dev/null
+++ b/.github/workflows/macos_unit_tests.yaml
@@ -0,0 +1,48 @@
+name: macos tests
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+  pull_request:
+    branches:
+      - master
+      - develop
+jobs:
+  build:
+
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        python-version: [3.7]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install Python packages
+      run: |
+          pip install --upgrade pip six setuptools
+          pip install --upgrade codecov coverage==4.5.4
+          pip install --upgrade flake8 pep8-naming
+    - name: Setup Homebrew packages
+      run: |
+        brew update
+        brew upgrade
+        brew install gcc gnupg2 dash kcov
+    - name: Run unit tests
+      run: |
+        git --version
+        git fetch origin develop:develop
+        . share/spack/setup-env.sh
+        coverage run $(which spack) test
+        coverage combine
+        coverage xml
+    - name: Upload to codecov.io
+      uses: codecov/codecov-action@v1
+      with:
+        file: ./coverage.xml
+        flags: unittests,macos
diff --git a/.travis.yml b/.travis.yml
index bc914ef5126..a11b00f34ef 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -76,10 +76,6 @@ jobs:
       os: linux
       language: python
       env: TEST_SUITE=doc
-    - os: osx
-      language: generic
-      env: [ TEST_SUITE=unit, PYTHON_VERSION=2.7, COVERAGE=true ]
-      if: type != pull_request
 
 stages:
   - 'style checks'
@@ -111,15 +107,6 @@ addons:
       - r-base-core
       - r-base-dev
       - zsh
-  # for Mac builds, we use Homebrew
-  homebrew:
-    packages:
-      - python@2
-      - gcc
-      - gnupg2
-      - ccache
-      - dash
-      - kcov
     update: true
 
 # ~/.ccache needs to be cached directly as Travis is not taking care of it
@@ -130,14 +117,7 @@ cache:
   directories:
     - ~/.ccache
 
-# Work around Travis's lack of support for Python on OSX
 before_install:
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
-        pip2 install --upgrade pip;
-        pip2 install virtualenv;
-        virtualenv venv;
-        source venv/bin/activate;
-    fi
   - ccache -M 2G && ccache -z
 
 # Install various dependencies
diff --git a/README.md b/README.md
index 70913b33bcd..a55828808d5 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,6 @@
 # <img src="https://cdn.rawgit.com/spack/spack/develop/share/spack/logo/spack-logo.svg" width="64" valign="middle" alt="Spack"/> Spack
 
+[![](https://github.com/spack/spack/workflows/macos%20tests/badge.svg)](https://github.com/spack/spack/actions)
 [![Build Status](https://travis-ci.com/spack/spack.svg?branch=develop)](https://travis-ci.com/spack/spack)
 [![Linux Builds](https://github.com/spack/spack/workflows/linux%20builds/badge.svg)](https://github.com/spack/spack/actions)
 [![macOS Builds (nightly)](https://github.com/spack/spack/workflows/macOS%20builds%20nightly/badge.svg?branch=develop)](https://github.com/spack/spack/actions?query=workflow%3A%22macOS+builds+nightly%22)

From 2b234b7a66fe57583ba7fd4d586352d1f1b8ab4f Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Sat, 9 May 2020 14:48:26 -0700
Subject: [PATCH 318/802] macOS nightly: two cores

All GitHub actions provide two cores. Just make sure this does not
get oversubscribed with potentially visible additional physical
cores.
---
 .github/workflows/install_spack.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/install_spack.sh b/.github/workflows/install_spack.sh
index aa8a68adc1d..5efae461a53 100755
--- a/.github/workflows/install_spack.sh
+++ b/.github/workflows/install_spack.sh
@@ -1,4 +1,5 @@
 #!/usr/bin/env sh
 git clone https://github.com/spack/spack.git
+echo -e "config:\n  build_jobs: 2" > spack/etc/spack/config.yaml
 . spack/share/spack/setup-env.sh
 spack compilers

From 29105da445387d7c46952dfc0f06f4d308cc1fb3 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Sat, 9 May 2020 14:49:56 -0700
Subject: [PATCH 319/802] macOS nightly: +1hr py-jupyter

check if failures ares actually a real timeout or an error that
just causes a hang.
---
 .github/workflows/macos_python.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/macos_python.yml b/.github/workflows/macos_python.yml
index f67df2a6b51..e136102a466 100644
--- a/.github/workflows/macos_python.yml
+++ b/.github/workflows/macos_python.yml
@@ -26,7 +26,7 @@ jobs:
   install_jupyter_clang:
     name: jupyter
     runs-on: macos-latest
-    timeout-minutes: 600
+    timeout-minutes: 700
     steps:
     - uses: actions/checkout@v2
     - name: spack install

From 8c120304987af404e2493d18b6313af28596d4d7 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Sat, 9 May 2020 23:18:55 +0200
Subject: [PATCH 320/802] Fix MacOS tests on develop

The -u option allows to update the current head,
so tests won't fail if we are on develop
---
 .github/workflows/macos_unit_tests.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/macos_unit_tests.yaml b/.github/workflows/macos_unit_tests.yaml
index f903daa034a..da970edc7ac 100644
--- a/.github/workflows/macos_unit_tests.yaml
+++ b/.github/workflows/macos_unit_tests.yaml
@@ -36,7 +36,7 @@ jobs:
     - name: Run unit tests
       run: |
         git --version
-        git fetch origin develop:develop
+        git fetch -u origin develop:develop
         . share/spack/setup-env.sh
         coverage run $(which spack) test
         coverage combine

From 358242d2a808e6f1e183334e6b26667258c77d6b Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sun, 10 May 2020 10:04:28 -0500
Subject: [PATCH 321/802] DGL: add new version (#16547)

---
 var/spack/repos/builtin/packages/py-dgl/package.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-dgl/package.py b/var/spack/repos/builtin/packages/py-dgl/package.py
index b1b1c37586f..544b527f69b 100644
--- a/var/spack/repos/builtin/packages/py-dgl/package.py
+++ b/var/spack/repos/builtin/packages/py-dgl/package.py
@@ -19,6 +19,7 @@ class PyDgl(CMakePackage):
     maintainers = ['adamjstewart']
 
     version('master', branch='master', submodules=True)
+    version('0.4.3', tag='0.4.3', submodules=True)
     version('0.4.2', tag='0.4.2', submodules=True)
 
     variant('cuda',   default=True, description='Build with CUDA')
@@ -31,6 +32,7 @@ class PyDgl(CMakePackage):
     depends_on('llvm-openmp', when='%clang platform=darwin +openmp')
 
     # Python dependencies
+    # See python/setup.py
     extends('python')
     depends_on('python@3.5:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
@@ -38,12 +40,17 @@ class PyDgl(CMakePackage):
     depends_on('py-numpy@1.14.0:', type=('build', 'run'))
     depends_on('py-scipy@1.1.0:', type=('build', 'run'))
     depends_on('py-networkx@2.1:', type=('build', 'run'))
+    depends_on('py-requests@2.19.0:', when='@0.4.3:', type=('build', 'run'))
 
     # Backends
-    depends_on('py-torch@0.4.1:',    when='backend=pytorch',    type='run')
-    depends_on('mxnet@1.5:',         when='backend=mxnet',      type='run')
+    # See https://github.com/dmlc/dgl#installation
+    depends_on('py-torch@1.2.0:', when='@0.4.3: backend=pytorch', type='run')
+    depends_on('py-torch@0.4.1:', when='backend=pytorch', type='run')
+    depends_on('mxnet@1.5.1:', when='@0.4.3: backend=pytorch', type='run')
+    depends_on('mxnet@1.5.0:', when='backend=mxnet', type='run')
+    depends_on('py-tensorflow@2.1:', when='@0.4.3: backend=tensorflow', type='run')
     depends_on('py-tensorflow@2.0:', when='backend=tensorflow', type='run')
-    depends_on('py-tfdlpack',        when='backend=tensorflow', type='run')
+    depends_on('py-tfdlpack', when='backend=tensorflow', type='run')
 
     build_directory = 'build'
 

From ff869a7d68685ee80b874fcccfab12b4eceba74c Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Sun, 10 May 2020 22:29:18 +0200
Subject: [PATCH 322/802] new version r-callr (#16552)

---
 var/spack/repos/builtin/packages/r-callr/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/r-callr/package.py b/var/spack/repos/builtin/packages/r-callr/package.py
index 3c964e0400e..22122f8030c 100644
--- a/var/spack/repos/builtin/packages/r-callr/package.py
+++ b/var/spack/repos/builtin/packages/r-callr/package.py
@@ -15,6 +15,7 @@ class RCallr(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/callr_1.0.0.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/callr/"
 
+    version('3.4.3', sha256='01b7277f20c1d662c6bebbfa2798d179922b36d4148b4298853579aeda0382b5')
     version('3.3.1', sha256='bf60da47357d3336aa395b0c9643235a621763c80d28bc9bb2257767d0a37967')
     version('3.2.0', sha256='4bb47b1018e8eb5c683a86c05d0d9b8b25848db1f1b30e92cfebedc0ce14b0e8')
     version('3.0.0', sha256='e36361086c65660a6ecbbc09b5ecfcddee6b59caf75e983e48b21d3b8defabe7')

From 3210e5999e1207ed7ef9aa187996c1ca39b091db Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Sun, 10 May 2020 22:31:08 +0200
Subject: [PATCH 323/802] new version r-covr (#16554)

---
 var/spack/repos/builtin/packages/r-covr/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/r-covr/package.py b/var/spack/repos/builtin/packages/r-covr/package.py
index b3daeac584a..e2c60194dbd 100644
--- a/var/spack/repos/builtin/packages/r-covr/package.py
+++ b/var/spack/repos/builtin/packages/r-covr/package.py
@@ -20,6 +20,7 @@ class RCovr(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/covr_3.0.1.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/covr"
 
+    version('3.5.0', sha256='cb919912018130164a40803ac573a37dde2186678c058c03c6303d79604979df')
     version('3.3.0', sha256='c0aa0bd7b2dc05effdc2367c59d45294f46858930d1b14efb393b205021fc65a')
     version('3.2.1', sha256='ea90daa48011e4ac4431ae47ee02fad98f54b529fc3900281cbeef7a2edef0a0')
     version('3.2.0', sha256='b26135306b1d6b14dd4deb481359dd919a7ca1e802ca5479fed394dcf35f0ef9')

From f32d561e9b82328938c39d834a07e06a21acbf37 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Sun, 10 May 2020 22:31:58 +0200
Subject: [PATCH 324/802] new version r-dt (#16555)

---
 var/spack/repos/builtin/packages/r-dt/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/r-dt/package.py b/var/spack/repos/builtin/packages/r-dt/package.py
index a4d810b238e..b1e899093a9 100644
--- a/var/spack/repos/builtin/packages/r-dt/package.py
+++ b/var/spack/repos/builtin/packages/r-dt/package.py
@@ -16,6 +16,7 @@ class RDt(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/DT_0.1.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/DT"
 
+    version('0.13', sha256='79a073fe96980ce150d790ab76133c9e80bd463270c34d149c03934a622d63b5')
     version('0.8', sha256='90195054148806cf31c7db5c41f72d5389c75adc0b1183606a9babd2c6ae8e21')
     version('0.7', sha256='1de3f170deccd9e3aaefc057dd87c498e3b3f7f88eff645cf165ac34ffe3de2c')
     version('0.6', sha256='2ed68e9d161559171fa74b6105eee87b98acf755eae072b38ada60a83d427916')

From 5dc51c21bb1d22df755a1b254cdb7ff63a358ef1 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 11 May 2020 00:38:26 +0200
Subject: [PATCH 325/802] new version r-jsonlite (#16557)

---
 var/spack/repos/builtin/packages/r-jsonlite/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py
index 68b3811d5dc..590134065af 100644
--- a/var/spack/repos/builtin/packages/r-jsonlite/package.py
+++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py
@@ -22,6 +22,7 @@ class RJsonlite(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/jsonlite_1.5.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/jsonlite"
 
+    version('1.6.1', sha256='74921dd249857a23afabc1ad1485a63a48828e57f240f0619deb04c60f883377')
     version('1.6', sha256='88c5b425229966b7409145a6cabc72db9ed04f8c37ee95901af0146bb285db53')
     version('1.5', sha256='6490371082a387cb1834048ad8cdecacb8b6b6643751b50298c741490c798e02')
     version('1.2', sha256='cb6b4660468d2db84ed09c7b8fefd169fcfc13e1e6b4e7ce64dce2713f34264d')

From 36941e3d949e033986c85584afeb51b5eba6b6a9 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 11 May 2020 00:38:38 +0200
Subject: [PATCH 326/802] new version r-pkgbuild (#16559)

---
 var/spack/repos/builtin/packages/r-pkgbuild/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/r-pkgbuild/package.py b/var/spack/repos/builtin/packages/r-pkgbuild/package.py
index 33ca13d0953..5dd2a8c97e1 100644
--- a/var/spack/repos/builtin/packages/r-pkgbuild/package.py
+++ b/var/spack/repos/builtin/packages/r-pkgbuild/package.py
@@ -13,6 +13,7 @@ class RPkgbuild(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/pkgbuild_1.0.3.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgbuild/"
 
+    version('1.0.8', sha256='b149fcf3e98ef148945ff9f4272512cd03e21408c235ec6c0548167fd41219a1')
     version('1.0.4', sha256='2934efa5ff9ccfe1636d360aedec36713f3bb3128a493241dbb728d842ea3b5f')
     version('1.0.3', sha256='c93aceb499886e42bcd61eb7fb59e47a76c9ba5ab5349a426736d46c8ce21f4d')
 

From 6c820dd6b538177ac8c05a1382da3876ad8b5fb6 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 11 May 2020 00:38:51 +0200
Subject: [PATCH 327/802] new version r-glue (#16558)

---
 var/spack/repos/builtin/packages/r-glue/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/r-glue/package.py b/var/spack/repos/builtin/packages/r-glue/package.py
index b6489eedd7e..1472728e93d 100644
--- a/var/spack/repos/builtin/packages/r-glue/package.py
+++ b/var/spack/repos/builtin/packages/r-glue/package.py
@@ -17,6 +17,7 @@ class RGlue(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/glue_1.2.0.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/glue"
 
+    version('1.4.0', sha256='ea6c409f7141754baa090deba96cff270a11b185452cf9e6fb69cb148a9069c1')
     version('1.3.1', sha256='4fc1f2899d71a634e1f0adb7942772feb5ac73223891abe30ea9bd91d3633ea8')
     version('1.3.0', sha256='789e5a44c3635c3d3db26666e635e88adcf61cd02b75465125d95d7a12291cee')
     version('1.2.0', sha256='19275b34ee6a1bcad05360b7eb996cebaa1402f189a5dfb084e695d423f2296e')

From 7d3b40fba45df7c6075d2668ab87708f34e1cd17 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 11 May 2020 00:39:20 +0200
Subject: [PATCH 328/802] new version r-rcpp (#16549)

---
 var/spack/repos/builtin/packages/r-rcpp/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py
index 4d9b6dae2c0..d479880153e 100644
--- a/var/spack/repos/builtin/packages/r-rcpp/package.py
+++ b/var/spack/repos/builtin/packages/r-rcpp/package.py
@@ -21,6 +21,7 @@ class RRcpp(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/Rcpp_0.12.13.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/Rcpp"
 
+    version('1.0.4.6', sha256='45af675ddbbe155e671453b2e84fe32250bb98d4ccb4342b61c1e25cff10b302')
     version('1.0.2', sha256='ad9338d6fc89dd116a3e2c5ecef1956e4be63b6c6aa1b21b2e5f249d65a5129c')
     version('1.0.0',   sha256='b7378bf0dda17ef72aa3f2a318a9cb5667bef50b601dc1096431e17426e18bc2')
     version('0.12.19', sha256='63aeb6d4b58cd2899ded26f38a77d461397d5b0dc5936f187d3ca6cd958ab582')

From c03d4688e42b30bb7a9299d1a523bcf7ac55c080 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sun, 10 May 2020 19:40:00 -0500
Subject: [PATCH 329/802] PyTorch: fix master and mkldnn builds (#16560)

---
 var/spack/repos/builtin/packages/py-torch/package.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py
index 024e0d95b23..ce69a5581c6 100644
--- a/var/spack/repos/builtin/packages/py-torch/package.py
+++ b/var/spack/repos/builtin/packages/py-torch/package.py
@@ -247,7 +247,7 @@ def enable_or_disable(variant, keyword='USE', var=None, newer=False):
 
         enable_or_disable('mkldnn')
         if '@0.4:0.4.1+mkldnn' in self.spec:
-            env.set('MKLDNN_HOME', self.spec['intel-mkl-dnn'].prefix)
+            env.set('MKLDNN_HOME', self.spec['onednn'].prefix)
 
         enable_or_disable('nnpack')
         enable_or_disable('qnnpack')
@@ -270,8 +270,9 @@ def enable_or_disable(variant, keyword='USE', var=None, newer=False):
         enable_or_disable('lmdb', newer=True)
         enable_or_disable('binary', keyword='BUILD', newer=True)
 
-        env.set('PYTORCH_BUILD_VERSION', self.version)
-        env.set('PYTORCH_BUILD_NUMBER', 0)
+        if not self.spec.satisfies('@master'):
+            env.set('PYTORCH_BUILD_VERSION', self.version)
+            env.set('PYTORCH_BUILD_NUMBER', 0)
 
         # BLAS to be used by Caffe2
         if '^mkl' in self.spec:

From fa8dede6cd3dec2c7286d01f23f9bc34d6955949 Mon Sep 17 00:00:00 2001
From: takanori-ihara <62980219+takanori-ihara@users.noreply.github.com>
Date: Mon, 11 May 2020 11:32:53 +0900
Subject: [PATCH 330/802] Add new package:py-jupyterlab-server (#16561)

---
 .../packages/py-jupyterlab-server/package.py  | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-jupyterlab-server/package.py

diff --git a/var/spack/repos/builtin/packages/py-jupyterlab-server/package.py b/var/spack/repos/builtin/packages/py-jupyterlab-server/package.py
new file mode 100644
index 00000000000..20c6fc4a0ee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-jupyterlab-server/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyJupyterlabServer(PythonPackage):
+    """A set of server components for JupyterLab and JupyterLab
+       like applications"""
+
+    homepage = "https://pypi.org/project/jupyterlab-server/"
+    url      = "https://pypi.io/packages/source/j/jupyterlab_server/jupyterlab_server-1.1.0.tar.gz"
+
+    version('1.1.0', sha256='bac27e2ea40f686e592d6429877e7d46947ea76c08c878081b028c2c89f71733')
+
+    depends_on('python@3.5:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+
+    depends_on('py-requests', type=('build', 'run'))
+    depends_on('py-json5', type=('build', 'run'))
+    depends_on('py-jsonschema@3.0.1:', type=('build', 'run'))
+    depends_on('py-notebook@4.2.0:', type=('build', 'run'))
+    depends_on('py-jinja2@2.10:', type=('build', 'run'))

From e08792cbcbb9f1bb3b43abfb0984dd76679dbc50 Mon Sep 17 00:00:00 2001
From: takanori-ihara <62980219+takanori-ihara@users.noreply.github.com>
Date: Mon, 11 May 2020 17:35:44 +0900
Subject: [PATCH 331/802] py-jupyterlab: added package at v2.1.0 (#16562)

---
 .../builtin/packages/py-jupyterlab/package.py | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-jupyterlab/package.py

diff --git a/var/spack/repos/builtin/packages/py-jupyterlab/package.py b/var/spack/repos/builtin/packages/py-jupyterlab/package.py
new file mode 100644
index 00000000000..d1ae7844ea8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-jupyterlab/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyJupyterlab(PythonPackage):
+    """JupyterLab is the next-generation web-based user interface
+       for Project Jupyter."""
+
+    homepage = "https://jupyterlab.readthedocs.io/"
+    url      = "https://pypi.io/packages/source/j/jupyterlab/jupyterlab-2.1.0.tar.gz"
+
+    version('2.1.0', sha256='8c239aababf5baa0b3d36e375fddeb9fd96f3a9a24a8cda098d6a414f5bbdc81')
+
+    depends_on('python@3:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+
+    depends_on('py-notebook@4.3.1:', type=('build', 'run'))
+    depends_on('py-tornado@6.0.3:', type=('build', 'run'))
+    depends_on('py-jupyterlab-server@1.1.0:', type=('build', 'run'))
+    depends_on('py-jinja2@2.10:', type=('build', 'run'))
+
+    depends_on('py-pytest', type='test')
+    depends_on('py-pytest-check-links', type='test')
+    depends_on('py-requests', type='test')
+    depends_on('py-wheel', type='test')
+    depends_on('py-virtualenv', type='test')

From ff6a0fc7b038920f96ffa5dc4b9ef9b5b517081a Mon Sep 17 00:00:00 2001
From: Sinan <sbulutw@gmail.com>
Date: Mon, 11 May 2020 01:43:56 -0700
Subject: [PATCH 332/802] py-configobj: remove url function (#16522)

It seems the pypi version of the package somehow compiles just fine

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
---
 .../repos/builtin/packages/py-configobj/package.py     | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-configobj/package.py b/var/spack/repos/builtin/packages/py-configobj/package.py
index 6b8521405de..350695780de 100644
--- a/var/spack/repos/builtin/packages/py-configobj/package.py
+++ b/var/spack/repos/builtin/packages/py-configobj/package.py
@@ -16,15 +16,5 @@ class PyConfigobj(PythonPackage):
     version('5.0.6', sha256='a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902')
     version('4.7.2', sha256='515ff923462592e8321df8b48c47e3428f8d406ee22b8de77bef969d1af11171')
 
-    # The version on PyPi seems to be outdated (2014) although confusingly
-    # enough version number is the same as the latest release on github.
     depends_on('py-six', type=('build', 'run'))
     depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
-
-    def url_for_version(self, version):
-        if version <= Version('5.0.0'):
-            url = "https://pypi.io/packages/source/c/configobj/configobj-{0}.tar.gz"
-        else:
-            url = "https://github.com/DiffSK/configobj/archive/v{0}.tar.gz"
-
-        return url.format(version)

From 03d0a7ee1eada90cd6a9fd493bccf48eab0ea468 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 11 May 2020 16:22:19 +0200
Subject: [PATCH 333/802] gcc: added v10.1.0 (#16525)

---
 .../repos/builtin/packages/gcc/package.py     | 17 +++++++++++---
 .../repos/builtin/packages/gcc/zstd.patch     | 23 +++++++++++++++++++
 2 files changed, 37 insertions(+), 3 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/gcc/zstd.patch

diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index cf16f1bc8f7..54bebcdb782 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -25,6 +25,8 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
 
     version('develop', svn=svn + 'trunk')
 
+    version('10.1.0', sha256='b6898a23844b656f1b68691c5c012036c2e694ac4b53a8918d4712ad876e7ea2')
+
     version('9.3.0', sha256='71e197867611f6054aa1119b13a0c0abac12834765fe2d81f35ac57f84f742d1')
     version('9.2.0', sha256='ea6ef08f121239da5695f76c9b33637a118dcf63e24164422231917fa61fb206')
     version('9.1.0', sha256='79a66834e96a6050d8fe78db2c3b32fb285b230b855d0a66288235bc04b327a0')
@@ -92,8 +94,9 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
     depends_on('gmp@4.3.2:')
     # GCC 7.3 does not compile with newer releases on some platforms, see
     #   https://github.com/spack/spack/issues/6902#issuecomment-433030376
-    depends_on('mpfr@2.4.2:3.1.6')
-    depends_on('mpc@0.8.1:', when='@4.5:')
+    depends_on('mpfr@2.4.2:3.1.6', when='@:9.9')
+    depends_on('mpfr@3.1.0:', when='@10:')
+    depends_on('mpc@1.0.1:', when='@4.5:')
     # Already released GCC versions do not support any newer version of ISL
     #   GCC 5.4 https://github.com/spack/spack/issues/6902#issuecomment-433072097
     #   GCC 7.3 https://github.com/spack/spack/issues/6902#issuecomment-433030376
@@ -101,8 +104,10 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
     depends_on('isl@0.14', when='@5.0:5.2')
     depends_on('isl@0.15', when='@5.3:5.9')
     depends_on('isl@0.15:0.18', when='@6:8.9')
-    depends_on('isl@0.15:0.20', when='@9:')
+    depends_on('isl@0.15:0.20', when='@9:9.9')
+    depends_on('isl@0.15:', when='@10:')
     depends_on('zlib', when='@6:')
+    depends_on('zstd', when='@10:')
     depends_on('iconv', when='platform=darwin')
     depends_on('gnat', when='languages=ada')
     depends_on('binutils~libiberty', when='+binutils')
@@ -252,6 +257,9 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
     patch('sys_ustat.h.patch', when='@5.0:6.4,7.0:7.3,8.1')
     patch('sys_ustat-4.9.patch', when='@4.9')
 
+    # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=95005
+    patch('zstd.patch', when='@10:')
+
     build_directory = 'spack-build'
 
     def url_for_version(self, version):
@@ -312,6 +320,9 @@ def configure_args(self):
         if self.version >= Version('6'):
             options.append('--with-system-zlib')
 
+        if 'zstd' in spec:
+            options.append('--with-zstd={0}'.format(spec['zstd'].prefix))
+
         # Enabling language "jit" requires --enable-host-shared.
         if 'languages=jit' in spec:
             options.append('--enable-host-shared')
diff --git a/var/spack/repos/builtin/packages/gcc/zstd.patch b/var/spack/repos/builtin/packages/gcc/zstd.patch
new file mode 100644
index 00000000000..362da1606fc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/zstd.patch
@@ -0,0 +1,23 @@
+--- a/gcc/Makefile.in	2020-05-08 11:50:17.962838228 +0200
++++ b/gcc/Makefile.in	2020-05-08 11:50:58.220960817 +0200
+@@ -1075,6 +1075,11 @@
+ # Libs needed (at present) just for jcf-dump.
+ LDEXP_LIB = @LDEXP_LIB@
+ 
++ifneq (@ZSTD_INCLUDE@,)
++ZSTD_INCLUDE = -I@ZSTD_INCLUDE@
++else
++ZSTD_INCLUDE =
++endif
+ ZSTD_LIB = @ZSTD_LIB@
+ 
+ # Likewise, for use in the tools that must run on this machine
+@@ -2275,7 +2280,7 @@
+ version.o: $(REVISION) $(DATESTAMP) $(BASEVER) $(DEVPHASE)
+ 
+ # lto-compress.o needs $(ZLIBINC) added to the include flags.
+-CFLAGS-lto-compress.o += $(ZLIBINC)
++CFLAGS-lto-compress.o += $(ZLIBINC) $(ZSTD_INCLUDE)
+ 
+ CFLAGS-lto-streamer-in.o += -DTARGET_MACHINE=\"$(target_noncanonical)\"
+ 

From c220a22b691b264281b4e371a49ae97df94e18f7 Mon Sep 17 00:00:00 2001
From: Jen Herting <jen@herting.cc>
Date: Mon, 11 May 2020 13:14:22 -0400
Subject: [PATCH 334/802] New package: py-mmcv (#16536)

* [py-mmcv] Created template

* [py-mmcv] added description and homepage

* [py-mmcv] requires python 3.6+

* [py-mmcv] added dependencies

* [py-mmcv] depends on opencv

* [py-mmcv] cleaned up fixmes

* [py-mmcv] requires numpy >= 1.11.1
---
 .../repos/builtin/packages/py-mmcv/package.py | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-mmcv/package.py

diff --git a/var/spack/repos/builtin/packages/py-mmcv/package.py b/var/spack/repos/builtin/packages/py-mmcv/package.py
new file mode 100644
index 00000000000..fbe0fdfe0a4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-mmcv/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyMmcv(PythonPackage):
+    """MMCV is a foundational python library for computer
+    vision research and supports many research projects in
+    MMLAB, such as MMDetection and MMAction."""
+
+    homepage = "https://mmcv.readthedocs.io/en/latest/"
+    url      = "https://github.com/open-mmlab/mmcv/archive/v0.5.1.tar.gz"
+
+    version('0.5.1', sha256='7c5ad30d9b61e44019e81ef46c406aa85dd08b5d0ba12ddd5cdc9c445835a55e')
+
+    depends_on('python@3.6:', type=('build', 'run'))
+    depends_on('py-addict', type=('build', 'run'))
+    depends_on('py-numpy@1.11.1:', type=('build', 'run'))
+    depends_on('py-pyyaml', type=('build', 'run'))
+    depends_on('opencv+python', type=('build', 'run'))
+    depends_on('py-cython', type='build')

From cd2e906702dad47bcc76fbfa3f46c5010bb17d0b Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 11 May 2020 19:31:40 +0200
Subject: [PATCH 335/802] netcdf-fortran: Fix build with gcc@10: (#16573)

---
 var/spack/repos/builtin/packages/netcdf-fortran/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
index e4dd1ea8840..f4bfe9a9795 100644
--- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
@@ -84,6 +84,11 @@ def flag_handler(self, name, flags):
             # building takes place outside of Spack environment, i.e.
             # without Spack's compiler wrappers.
             config_flags = [self.spec['netcdf-c'].libs.search_flags]
+        elif name == 'fflags' and self.spec.satisfies('%gcc@10:'):
+            # https://github.com/Unidata/netcdf-fortran/issues/212
+            if config_flags is None:
+                config_flags = []
+            config_flags.append('-fallow-argument-mismatch')
 
         return flags, None, config_flags
 

From 20a4e5efe87218fc5a6c46bad3399387bc9d3964 Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Mon, 11 May 2020 12:32:36 -0500
Subject: [PATCH 336/802] stata: add new libpng dependency (#16582)

---
 var/spack/repos/builtin/packages/stata/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/stata/package.py b/var/spack/repos/builtin/packages/stata/package.py
index 6a34f8b593d..263fc60cd06 100644
--- a/var/spack/repos/builtin/packages/stata/package.py
+++ b/var/spack/repos/builtin/packages/stata/package.py
@@ -30,8 +30,8 @@ class Stata(Package):
     version('16', 'a13a6a92558eeb3c6cb3013c458a6777e54c21af43599df6b0a924f5f5c2d5d2')
     version('15', '2486f4c7db1e7b453004c7bd3f8da40ba1e30be150613065c7b82b1915259016')
 
-    # V15 depends on libpng v12 and fails with other versions of libpng
-    depends_on('libpng@1.2.57')
+    depends_on('libpng@1.2.57', when='@15', type='run')
+    depends_on('libpng@1.6:1.6.99', when='@16', type='run')
 
     # STATA is downloaded from user/pass protected ftp as Stata15Linux64.tar.gz
     def url_for_version(self, version):

From 2c009a3226a6afc0dfa031722d30fff0dd0bd487 Mon Sep 17 00:00:00 2001
From: Andrew Gaspar <agaspar@lanl.gov>
Date: Mon, 11 May 2020 11:33:34 -0600
Subject: [PATCH 337/802] Map the spack skylake arch to Kokkos BDW, rather than
 SKX (#16583)

SKX includes AVX-512 extensions that consumer Skylake processors do
not have. Therefore, map Skylake to the prior arch to work on
these systems. Skylake-X processors will still map as the
skylake_avx512 spack arch and get the correct optimzations.
---
 var/spack/repos/builtin/packages/kokkos/package.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/kokkos/package.py b/var/spack/repos/builtin/packages/kokkos/package.py
index fef37d2ac7b..b5277e40a8e 100644
--- a/var/spack/repos/builtin/packages/kokkos/package.py
+++ b/var/spack/repos/builtin/packages/kokkos/package.py
@@ -120,7 +120,12 @@ class Kokkos(CMakePackage, CudaPackage):
         "core2": None,
         "ivybridge": "SNB",
         "broadwell": "BDW",
-        "skylake": "SKX",
+        # @AndrewGaspar: Kokkos does not have an arch for plain-skylake - only
+        # for Skylake-X (i.e. Xeon). For now, I'm mapping this to Broadwell
+        # until Kokkos learns to optimize for SkyLake without the AVX-512
+        # extensions. SkyLake with AVX-512 will still be optimized using the
+        # separate `skylake_avx512` arch.
+        "skylake": "BDW",
         "icelake": "SKX",
         "skylake_avx512": "SKX",
     }

From 5e348f71335ed917bd858c7682c30f2b23784532 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 11 May 2020 19:43:38 +0200
Subject: [PATCH 338/802] r-digest : version updated (#16578)

---
 var/spack/repos/builtin/packages/r-digest/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/r-digest/package.py b/var/spack/repos/builtin/packages/r-digest/package.py
index bb32198c858..6d02efcbdf8 100644
--- a/var/spack/repos/builtin/packages/r-digest/package.py
+++ b/var/spack/repos/builtin/packages/r-digest/package.py
@@ -28,6 +28,7 @@ class RDigest(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/digest_0.6.12.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/digest"
 
+    version('0.6.25', sha256='15ccadb7b8bccaa221b6700bb549011719d0f4b38dbd3a1f29face3e019e2de5')
     version('0.6.20', sha256='05674b0b5d888461ff770176c67b10a11be062b0fee5dbd9298f25a9a49830c7')
     version('0.6.19', sha256='28d159bd589ecbd01b8da0826eaed417f5c1bf5a11b79e76bf67ce8d935cccf4')
     version('0.6.12', sha256='a479463f120037ad8e88bb1387170842e635a1f07ce7e3575316efd6e14d9eab')

From 3ddf6c0845a59487ed3645c86861af567f6fdfd7 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 11 May 2020 19:48:51 +0200
Subject: [PATCH 339/802] r-rlang : new version (#16575)

---
 var/spack/repos/builtin/packages/r-rlang/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/r-rlang/package.py b/var/spack/repos/builtin/packages/r-rlang/package.py
index ae099f7b9a4..9b258b65656 100644
--- a/var/spack/repos/builtin/packages/r-rlang/package.py
+++ b/var/spack/repos/builtin/packages/r-rlang/package.py
@@ -14,6 +14,7 @@ class RRlang(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/rlang_0.2.2.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/rlang"
 
+    version('0.4.6', sha256='3a81b107765fd6ac0ad716c428d01878775ded9208ba125d43c890c73d2533ca')
     version('0.4.0', sha256='9748a4a217548bbe5631c18fd88c94811950446f798ff21fb327703aebaa150d')
     version('0.3.4', sha256='4e467f7b0dcbde91b60c292137d2c69cecaa713a6e4c9b7157ef6fd5453b7ade')
     version('0.3.1', sha256='30427b2be2288e88acd30c4ea348ee06043a649fd73623a63148b1ad96317151')

From 4c666034dcf9a8e9252703c642a48d5f2949738c Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 11 May 2020 19:49:27 +0200
Subject: [PATCH 340/802] r-rstudioapi : new version (#16574)

---
 var/spack/repos/builtin/packages/r-rstudioapi/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py
index e9c73695aa0..07f3919c58f 100644
--- a/var/spack/repos/builtin/packages/r-rstudioapi/package.py
+++ b/var/spack/repos/builtin/packages/r-rstudioapi/package.py
@@ -14,6 +14,7 @@ class RRstudioapi(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/rstudioapi_0.7.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/rstudioapi"
 
+    version('0.11', sha256='13e07fb7e2eba8cf1d885db2721901d676d219a1042d7ef5d166125e4905306b')
     version('0.10', sha256='80c5aa3063bcab649904cb92f0b164edffa2f6b0e6a8f7ea28ae317b80e1ab96')
     version('0.9.0', sha256='5149a2830ae7134c396ce64764b263cf9f348d4399f53da3804f40d7d5bec13e')
     version('0.7', sha256='a541bc76ef082d2c27e42fd683f8262cb195b1497af3509178d2642870397a8c')

From 43c9ad34216a282a50cc1bbd107949c24db38835 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Mon, 11 May 2020 19:55:18 +0200
Subject: [PATCH 341/802] Remove 'spack bootstrap' and associated docs (#15179)

fixes #15145

This commit removes the outdated `spack bootstrap`
command and any reference to it in the documentation
and unit tests.
---
 .travis.yml                            |  5 --
 lib/spack/docs/getting_started.rst     | 52 +----------------
 lib/spack/docs/module_file_support.rst | 18 ++----
 lib/spack/docs/workflows.rst           |  3 +-
 lib/spack/spack/cmd/bootstrap.py       | 80 --------------------------
 share/spack/qa/run-bootstrap-tests     | 37 ------------
 share/spack/spack-completion.bash      |  6 +-
 7 files changed, 9 insertions(+), 192 deletions(-)
 delete mode 100644 lib/spack/spack/cmd/bootstrap.py
 delete mode 100755 share/spack/qa/run-bootstrap-tests

diff --git a/.travis.yml b/.travis.yml
index a11b00f34ef..9e2a7973935 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -22,11 +22,6 @@ jobs:
       os: linux
       language: python
       env: TEST_SUITE=flake8
-# Shell integration with module files
-    - python: '3.8'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=bootstrap ]
     - stage: 'unit tests + documentation'
       python: '2.6'
       dist: trusty
diff --git a/lib/spack/docs/getting_started.rst b/lib/spack/docs/getting_started.rst
index 8de9d276623..1fbddbd4a98 100644
--- a/lib/spack/docs/getting_started.rst
+++ b/lib/spack/docs/getting_started.rst
@@ -71,10 +71,6 @@ This automatically adds Spack to your ``PATH`` and allows the ``spack``
 command to be used to execute spack :ref:`commands <shell-support>` and
 :ref:`useful packaging commands <packaging-shell-support>`.
 
-If :ref:`environment-modules <InstallEnvironmentModules>` is
-installed and available, the ``spack`` command can also load and unload
-:ref:`modules <modules>`.
-
 ^^^^^^^^^^^^^^^^^
 Clean Environment
 ^^^^^^^^^^^^^^^^^
@@ -900,9 +896,8 @@ Core Spack Utilities
 ^^^^^^^^^^^^^^^^^^^^
 
 Core Spack uses the following packages, mainly to download and unpack
-source code, and to load generated environment modules: ``curl``,
-``env``, ``git``, ``go``, ``hg``, ``svn``, ``tar``, ``unzip``,
-``patch``, ``environment-modules``.
+source code: ``curl``, ``env``, ``git``, ``go``, ``hg``, ``svn``,
+``tar``, ``unzip``, ``patch``
 
 As long as the user's environment is set up to successfully run these
 programs from outside of Spack, they should work inside of Spack as
@@ -910,10 +905,6 @@ well.  They can generally be activated as in the ``curl`` example above;
 or some systems might already have an appropriate hand-built
 environment module that may be loaded.  Either way works.
 
-If you find that you are missing some of these programs, ``spack`` can
-build some of them for you with ``spack bootstrap``. Currently supported
-programs are ``environment-modules``.
-
 A few notes on specific programs in this list:
 
 """"""""""""""""""""""""""
@@ -941,45 +932,6 @@ other programs will also not work, because they also rely on OpenSSL.
 Once ``curl`` has been installed, you can similarly install the others.
 
 
-.. _InstallEnvironmentModules:
-
-"""""""""""""""""""
-Environment Modules
-"""""""""""""""""""
-
-In order to use Spack's generated module files, you must have
-installed ``environment-modules`` or ``lmod``. The simplest way
-to get the latest version of either of these tools is installing
-it as part of Spack's bootstrap procedure:
-
-.. code-block:: console
-
-   $ spack bootstrap
-
-.. warning::
-   At the moment ``spack bootstrap`` is only able to install ``environment-modules``.
-   Extending its capabilities to prefer ``lmod`` where possible is in the roadmap,
-   and likely to happen before the next release.
-
-Alternatively, on many Linux distributions, you can install a pre-built binary
-from the vendor's repository. On Fedora/RHEL/CentOS, for example, this can be
-done with the command:
-
-.. code-block:: console
-
-   $ yum install environment-modules
-
-Once you have the tool installed and available in your path, you can source
-Spack's setup file:
-
-.. code-block:: console
-
-   $ source share/spack/setup-env.sh
-
-This activates :ref:`shell support <shell-support>` and makes commands like
-``spack load`` available for use.
-
-
 ^^^^^^^^^^^^^^^^^
 Package Utilities
 ^^^^^^^^^^^^^^^^^
diff --git a/lib/spack/docs/module_file_support.rst b/lib/spack/docs/module_file_support.rst
index 01a13cdf3e4..4ddd42139c6 100644
--- a/lib/spack/docs/module_file_support.rst
+++ b/lib/spack/docs/module_file_support.rst
@@ -17,22 +17,16 @@ Spack integrates with `Environment Modules
 <http://lmod.readthedocs.io/en/latest/>`_ by
 providing post-install hooks that generate module files and commands to manipulate them.
 
-.. note::
-
-   If your machine does not already have a module system installed,
-   we advise you to use either Environment Modules or LMod. See :ref:`InstallEnvironmentModules`
-   for more details.
-
 .. _shell-support:
 
 ----------------------------
 Using module files via Spack
 ----------------------------
 
-If you have installed a supported module system either manually or through
-``spack bootstrap``, you should be able to run either ``module avail`` or
-``use -l spack`` to see what module files have been installed.  Here is
-sample output of those programs, showing lots of installed packages:
+If you have installed a supported module system you should be able to
+run either ``module avail`` or ``use -l spack`` to see what module
+files have been installed.  Here is sample output of those programs,
+showing lots of installed packages:
 
 .. code-block:: console
 
@@ -93,9 +87,7 @@ Note that in the latter case it is necessary to explicitly set ``SPACK_ROOT``
 before sourcing the setup file (you will get a meaningful error message
 if you don't).
 
-When ``bash`` and ``ksh`` users update their environment with ``setup-env.sh``, it will check for spack-installed environment modules and add the ``module`` command to their environment; This only occurs if the module command is not already available. You can install ``environment-modules`` with ``spack bootstrap`` as described in :ref:`InstallEnvironmentModules`.
-
-Finally, if you want to have Spack's shell support available on the command line at
+If you want to have Spack's shell support available on the command line at
 any login you can put this source line in one of the files that are sourced
 at startup (like ``.profile``, ``.bashrc`` or ``.cshrc``). Be aware though
 that the startup time may be slightly increased because of that.
diff --git a/lib/spack/docs/workflows.rst b/lib/spack/docs/workflows.rst
index 690d02d0203..17ca6950823 100644
--- a/lib/spack/docs/workflows.rst
+++ b/lib/spack/docs/workflows.rst
@@ -1442,8 +1442,7 @@ The following functionality is prepared:
 
 #. Base image: the example starts from a minimal ubuntu.
 
-#. Pre-install the spack dependencies, including modules from the packages.
-   This avoids needing to build those from scratch via ``spack bootstrap``.
+#. Pre-install the spack dependencies.
    Package installs are followed by a clean-up of the system package index,
    to avoid outdated information and it saves space.
 
diff --git a/lib/spack/spack/cmd/bootstrap.py b/lib/spack/spack/cmd/bootstrap.py
deleted file mode 100644
index 53c284ab6d8..00000000000
--- a/lib/spack/spack/cmd/bootstrap.py
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-import llnl.util.cpu
-import llnl.util.tty as tty
-
-import spack.repo
-import spack.spec
-import spack.cmd.common.arguments as arguments
-
-description = "Bootstrap packages needed for spack to run smoothly"
-section = "admin"
-level = "long"
-
-
-def setup_parser(subparser):
-    arguments.add_common_arguments(subparser, ['jobs'])
-    subparser.add_argument(
-        '--keep-prefix', action='store_true', dest='keep_prefix',
-        help="don't remove the install prefix if installation fails")
-    subparser.add_argument(
-        '--keep-stage', action='store_true', dest='keep_stage',
-        help="don't remove the build stage if installation succeeds")
-    arguments.add_common_arguments(subparser, ['no_checksum'])
-    subparser.add_argument(
-        '-v', '--verbose', action='store_true', dest='verbose',
-        help="display verbose build output while installing")
-
-    cache_group = subparser.add_mutually_exclusive_group()
-    cache_group.add_argument(
-        '--use-cache', action='store_true', dest='use_cache', default=True,
-        help="check for pre-built Spack packages in mirrors (default)")
-    cache_group.add_argument(
-        '--no-cache', action='store_false', dest='use_cache', default=True,
-        help="do not check for pre-built Spack packages in mirrors")
-    cache_group.add_argument(
-        '--cache-only', action='store_true', dest='cache_only', default=False,
-        help="only install package from binary mirrors")
-
-    cd_group = subparser.add_mutually_exclusive_group()
-    arguments.add_common_arguments(cd_group, ['clean', 'dirty'])
-
-
-def bootstrap(parser, args, **kwargs):
-    kwargs.update({
-        'keep_prefix': args.keep_prefix,
-        'keep_stage': args.keep_stage,
-        'install_deps': 'dependencies',
-        'verbose': args.verbose,
-        'dirty': args.dirty,
-        'use_cache': args.use_cache,
-        'cache_only': args.cache_only
-    })
-
-    # Define requirement dictionary defining general specs which need
-    # to be satisfied, and the specs to install when the general spec
-    # isn't satisfied.
-    requirement_dict = {
-        # Install environment-modules with generic optimizations
-        'environment-modules': 'environment-modules~X target={0}'.format(
-            llnl.util.cpu.host().family
-        )
-    }
-
-    for requirement in requirement_dict:
-        installed_specs = spack.store.db.query(requirement)
-        if(len(installed_specs) > 0):
-            tty.msg("Requirement %s is satisfied with installed "
-                    "package %s" % (requirement, installed_specs[0]))
-        else:
-            # Install requirement
-            spec_to_install = spack.spec.Spec(requirement_dict[requirement])
-            spec_to_install.concretize()
-            tty.msg("Installing %s to satisfy requirement for %s" %
-                    (spec_to_install, requirement))
-            kwargs['explicit'] = True
-            package = spack.repo.get(spec_to_install)
-            package.do_install(**kwargs)
diff --git a/share/spack/qa/run-bootstrap-tests b/share/spack/qa/run-bootstrap-tests
deleted file mode 100755
index 9532d2d801a..00000000000
--- a/share/spack/qa/run-bootstrap-tests
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/bin/bash -e
-#
-# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-#
-# Description:
-#     Checks that Spack shell integration with modules works correctly.
-#
-# Usage:
-#     run-bootstrap-tests
-#
-. "$(dirname $0)/setup.sh"
-check_dependencies ${coverage} git hg svn
-
-# Fetch the sources in a mirror, and add it to Spack
-mkdir -p ~/.mirror
-bin/spack mirror add travis ~/.mirror
-bin/spack mirror create -D -d ~/.mirror environment-modules~X
-
-
-# Move to root directory of Spack
-# Allows script to be run from anywhere
-cd "$SPACK_ROOT"
-
-# Print compiler information
-spack config get compilers
-
-# Run some build smoke tests, potentially with code coverage
-${coverage_run} bin/spack bootstrap
-
-# Check module integration
-. "share/spack/setup-env.sh"
-module av || exit 1
-spack load tcl || exit 1
diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash
index 4b730499d2d..9017f4fe570 100755
--- a/share/spack/spack-completion.bash
+++ b/share/spack/spack-completion.bash
@@ -313,7 +313,7 @@ _spack() {
     then
         SPACK_COMPREPLY="-h --help -H --all-help --color -C --config-scope -d --debug --timestamp --pdb -e --env -D --env-dir -E --no-env --use-env-repo -k --insecure -l --enable-locks -L --disable-locks -m --mock -p --profile --sorted-profile --lines -v --verbose --stacktrace -V --version --print-shell-vars"
     else
-        SPACK_COMPREPLY="activate add arch blame bootstrap build build-env buildcache cd checksum ci clean clone commands compiler compilers concretize config configure containerize create deactivate debug dependencies dependents deprecate dev-build diy docs edit env extensions external fetch find flake8 gc gpg graph help info install license list load location log-parse maintainers mirror module patch pkg providers pydoc python reindex remove rm repo resource restage setup spec stage test uninstall unload upload-s3 url verify versions view"
+        SPACK_COMPREPLY="activate add arch blame build build-env buildcache cd checksum ci clean clone commands compiler compilers concretize config configure containerize create deactivate debug dependencies dependents deprecate dev-build diy docs edit env extensions external fetch find flake8 gc gpg graph help info install license list load location log-parse maintainers mirror module patch pkg providers pydoc python reindex remove rm repo resource restage setup spec stage test uninstall unload upload-s3 url verify versions view"
     fi
 }
 
@@ -348,10 +348,6 @@ _spack_blame() {
     fi
 }
 
-_spack_bootstrap() {
-    SPACK_COMPREPLY="-h --help -j --jobs --keep-prefix --keep-stage -n --no-checksum -v --verbose --use-cache --no-cache --cache-only --clean --dirty"
-}
-
 _spack_build() {
     if $list_options
     then

From 5ed5c55ebdc5188d4578169475059b4482580e66 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 11 May 2020 19:55:36 +0200
Subject: [PATCH 342/802] mpich: Fix build with gcc@10: (#16568)

---
 var/spack/repos/builtin/packages/mpich/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index 878abc6b5cd..7b8c807cce3 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -156,6 +156,10 @@ def setup_build_environment(self, env):
         env.unset('F90')
         env.unset('F90FLAGS')
 
+        # https://bugzilla.redhat.com/show_bug.cgi?id=1795817
+        if self.spec.satisfies('%gcc@10:'):
+            env.set('FFLAGS', '-fallow-argument-mismatch')
+
     def setup_dependent_build_environment(self, env, dependent_spec):
         # On Cray, the regular compiler wrappers *are* the MPI wrappers.
         if 'platform=cray' in self.spec:

From 98fd62254f4de2c9583b91d03723e54233434272 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Mon, 11 May 2020 12:56:07 -0500
Subject: [PATCH 343/802] py-plac: remove erroneous argparse dependency
 (#16584)

---
 var/spack/repos/builtin/packages/py-plac/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-plac/package.py b/var/spack/repos/builtin/packages/py-plac/package.py
index 098dbb65c3d..18d18cf5ddf 100644
--- a/var/spack/repos/builtin/packages/py-plac/package.py
+++ b/var/spack/repos/builtin/packages/py-plac/package.py
@@ -13,4 +13,4 @@ class PyPlac(PythonPackage):
     version('1.1.3', sha256='398cb947c60c4c25e275e1f1dadf027e7096858fb260b8ece3b33bcff90d985f')
 
     depends_on('py-setuptools', type='build')
-    depends_on('py-argparse', type=('build', 'run'))
+    depends_on('py-argparse', when='^python@:2.6', type=('build', 'run'))

From 1367b63e99a01d6b91d80037d6b7da3fb7732a00 Mon Sep 17 00:00:00 2001
From: asmaahassan90 <31959389+asmaahassan90@users.noreply.github.com>
Date: Mon, 11 May 2020 19:56:50 +0200
Subject: [PATCH 344/802] Add avizo version 2020.1 (#16567)

---
 var/spack/repos/builtin/packages/avizo/package.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/avizo/package.py b/var/spack/repos/builtin/packages/avizo/package.py
index 352af737632..c8f769b9b23 100644
--- a/var/spack/repos/builtin/packages/avizo/package.py
+++ b/var/spack/repos/builtin/packages/avizo/package.py
@@ -18,6 +18,10 @@ class Avizo(Package):
 
     homepage = "https://www.thermofisher.com/sa/en/home/industrial/electron-microscopy/electron-microscopy-instruments-workflow-solutions/3d-visualization-analysis-software.html"
 
+    version('2020.1',
+            sha256='9321aaa276567eebf116e268353c33a4c930d768d22793f921338e1d8cefe991',
+            url="file://{0}/Avizo-20201-Linux64-gcc48.bin".format(os.getcwd()),
+            expand=False)
     version('2019.4',
             sha256='a637720535bcbe254ab56368004a9544c64ec36186373fa24f26cee279685248',
             url="file://{0}/Avizo-20194-Linux64-gcc48.bin".format(os.getcwd()),
@@ -34,13 +38,15 @@ class Avizo(Package):
     gcc_ver = {
         "9.7.0": "44",
         "2019.3": "48",
-        "2019.4": "48"
+        "2019.4": "48",
+        "2020.1": "48"
     }
 
     install_dir = {
         "9.7.0": 'Avizo-9.7.0',
         "2019.3": join_path('..', 'Avizo'),
-        "2019.4": join_path('..', 'Avizo')
+        "2019.4": join_path('..', 'Avizo'),
+        "2020.1": join_path('..', 'Avizo')
     }
 
     # Licensing

From 97779e3539b34d15fde1a1be296efe40790b10dd Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 11 May 2020 23:54:08 +0200
Subject: [PATCH 345/802] adios: Fix build with gcc@10: (#16569)

---
 var/spack/repos/builtin/packages/adios/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/repos/builtin/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py
index c850b3058b5..4bcd3f69d6f 100644
--- a/var/spack/repos/builtin/packages/adios/package.py
+++ b/var/spack/repos/builtin/packages/adios/package.py
@@ -127,6 +127,11 @@ def with_or_without_hdf5(self, activated):
 
         return '--without-phdf5'
 
+    def setup_build_environment(self, env):
+        # https://github.com/ornladios/ADIOS/issues/206
+        if self.spec.satisfies('%gcc@10: +fortran'):
+            env.set('FCFLAGS', '-fallow-argument-mismatch')
+
     def configure_args(self):
         spec = self.spec
         self.validate(spec)

From 35c3478fcd5063199f9d2a45402209c2149a3f51 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 11 May 2020 23:54:28 +0200
Subject: [PATCH 346/802] fio: Add 3.19 (#16571)

Earlier versions are not compatible with gcc@10:.
---
 var/spack/repos/builtin/packages/fio/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/fio/package.py b/var/spack/repos/builtin/packages/fio/package.py
index 90064be1d52..4fdc44fae2b 100644
--- a/var/spack/repos/builtin/packages/fio/package.py
+++ b/var/spack/repos/builtin/packages/fio/package.py
@@ -16,6 +16,7 @@ class Fio(AutotoolsPackage):
     homepage = "https://github.com/axboe/fio"
     url = "https://github.com/axboe/fio/archive/fio-2.19.tar.gz"
 
+    version('3.19', sha256='809963b1d023dbc9ac7065557af8129aee17b6895e0e8c5ca671b0b14285f404')
     version('3.16', sha256='c7731a9e831581bab7104da9ea60c9f44e594438dbe95dff26726ca0285e7b93')
     version('2.19', sha256='61fb03a18703269b781aaf195cb0d7931493bbb5bfcc8eb746d5d66d04ed77f7')
 
@@ -32,6 +33,9 @@ class Fio(AutotoolsPackage):
     conflicts('+libaio', when='platform=darwin',
               msg='libaio does not support Darwin')
 
+    conflicts('@:3.18', when='%gcc@10:',
+              msg='gcc@10: sets -fno-common by default')
+
     def configure_args(self):
         config_args = []
 

From fa702b8311faf7fa073d9ae852a82c1f50199172 Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Mon, 11 May 2020 16:02:56 -0700
Subject: [PATCH 347/802] python: add -fwrapv to cflags for python@3.8.0:
 %intel (#16592)

---
 var/spack/repos/builtin/packages/python/package.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index a9b04a2d5b5..aac98d11ade 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -258,6 +258,15 @@ def setup_build_environment(self, env):
         env.unset('PYTHONPATH')
         env.unset('PYTHONHOME')
 
+    def flag_handler(self, name, flags):
+        # python 3.8 requires -fwrapv when compiled with intel
+        if self.spec.satisfies('@3.8: %intel'):
+            if name == 'cflags':
+                flags.append('-fwrapv')
+
+        # allow flags to be passed through compiler wrapper
+        return (flags, None, None)
+
     def configure_args(self):
         spec = self.spec
         config_args = []

From b526a902207c9e089269f51b68621c18312db8d0 Mon Sep 17 00:00:00 2001
From: Sajid Ali <30510036+s-sajid-ali@users.noreply.github.com>
Date: Mon, 11 May 2020 18:27:38 -0500
Subject: [PATCH 348/802] Charm++: fix build prefix; add ucx/pmi support
 (#15666)

* Add pmi support (required by ucx, ofi, and gni backends)
* Add support for ucx backend
* Add dependency on MPI for pmi=simplepmi, slurmpmi, or slurmpmi2
* Remove charmpp as an MPI provider since the changes in this PR can
  add MPI as a dependency (mentioned previously)
* Install into transport_protocol-OS-arch subdirectory to match
  default charmpp installation behavior (which helps dependents find it)
---
 lib/spack/spack/test/cmd/providers.py         |   3 +-
 .../repos/builtin/packages/charmpp/package.py | 142 +++++++++++++-----
 .../repos/builtin/packages/namd/package.py    |  24 ++-
 3 files changed, 125 insertions(+), 44 deletions(-)

diff --git a/lib/spack/spack/test/cmd/providers.py b/lib/spack/spack/test/cmd/providers.py
index 3d537c553fb..dd0c8a9eb72 100644
--- a/lib/spack/spack/test/cmd/providers.py
+++ b/lib/spack/spack/test/cmd/providers.py
@@ -22,8 +22,7 @@ def test_it_just_runs(pkg):
 
 
 @pytest.mark.parametrize('vpkg,provider_list', [
-    (('mpi',), ['charmpp@6.7.1:',
-                'intel-mpi',
+    (('mpi',), ['intel-mpi',
                 'intel-parallel-studio',
                 'mpich',
                 'mpich@1:',
diff --git a/var/spack/repos/builtin/packages/charmpp/package.py b/var/spack/repos/builtin/packages/charmpp/package.py
index 158dd599378..e9a133604c9 100644
--- a/var/spack/repos/builtin/packages/charmpp/package.py
+++ b/var/spack/repos/builtin/packages/charmpp/package.py
@@ -58,10 +58,18 @@ class Charmpp(Package):
         "backend",
         default="netlrts",
         values=("mpi", "multicore", "netlrts", "verbs", "gni",
-                "ofi", "pami", "pamilrts"),
+                "ucx", "ofi", "pami", "pamilrts"),
         description="Set the backend to use"
     )
 
+    # Process management interface
+    variant(
+        "pmi",
+        default="none",
+        values=("none", "simplepmi", "slurmpmi", "slurmpmi2", "pmix"),
+        description="The ucx/ofi/gni backends need PMI to run!"
+    )
+
     # Other options
     variant("papi", default=False, description="Enable PAPI integration")
     variant("syncft", default=False, description="Compile with Charm++ fault tolerance support")
@@ -78,29 +86,23 @@ class Charmpp(Package):
     variant("production", default=True, description="Build charm++ with all optimizations")
     variant("tracing", default=False, description="Enable tracing modules")
 
-    # FIXME: backend=mpi also provides mpi, but spack does not support
-    # depends_on("mpi") and provides("mpi") in the same package currently.
-    for b in ['multicore', 'netlrts', 'verbs', 'gni', 'ofi', 'pami',
-              'pamilrts']:
-        provides('mpi@2', when='@6.7.1: build-target=AMPI backend={0}'.format(b))
-        provides('mpi@2', when='@6.7.1: build-target=LIBS backend={0}'.format(b))
-
-    def setup_dependent_build_environment(self, env, dependent_spec):
-        env.set('MPICC',  self.prefix.bin.ampicc)
-        env.set('MPICXX', self.prefix.bin.ampicxx)
-        env.set('MPIF77', self.prefix.bin.ampif77)
-        env.set('MPIF90', self.prefix.bin.ampif90)
-
-    def setup_dependent_package(self, module, dependent_spec):
-        self.spec.mpicc  = self.prefix.bin.ampicc
-        self.spec.mpicxx = self.prefix.bin.ampicxx
-        self.spec.mpifc  = self.prefix.bin.ampif90
-        self.spec.mpif77 = self.prefix.bin.ampif77
-
     depends_on("mpi", when="backend=mpi")
     depends_on("papi", when="+papi")
     depends_on("cuda", when="+cuda")
 
+    depends_on("ucx", when="backend=ucx")
+    depends_on("slurm@:17-11-9-2", when="pmi=slurmpmi")
+    depends_on("slurm@17-11-9-2:", when="pmi=slurmpmi2")
+
+    # FIXME : As of now spack's OpenMPI recipe does not have a PMIx variant
+    # But if users have external installs of OpenMPI with PMIx support, this
+    # will allow them to build charm++ with it.
+    depends_on("openmpi", when="pmi=pmix")
+
+    depends_on("mpi", when="pmi=simplepmi")
+    depends_on("mpi", when="pmi=slurmpmi")
+    depends_on("mpi", when="pmi=slurmpmi2")
+
     # Git versions of Charm++ require automake and autoconf
     depends_on("automake", when="@develop")
     depends_on("autoconf", when="@develop")
@@ -108,11 +110,12 @@ def setup_dependent_package(self, module, dependent_spec):
     conflicts("~tracing", "+papi")
 
     conflicts("backend=multicore", "+smp")
+    conflicts("backend=ucx", when="@:6.9.99")
 
-    def install(self, spec, prefix):
-        target = spec.variants["build-target"].value
-
+    @property
+    def charmarch(self):
         plat = sys.platform
+
         if plat.startswith("linux"):
             plat = "linux"
         elif plat.startswith("win"):
@@ -123,12 +126,13 @@ def install(self, spec, prefix):
             plat = "cnk"
 
         mach = platform.machine()
+
         if mach.startswith("ppc"):
             mach = "ppc"
         elif mach.startswith("arm"):
             mach = "arm"
 
-        comm = spec.variants['backend'].value
+        comm = self.spec.variants['backend'].value
 
         # Define Charm++ version names for various (plat, mach, comm)
         # combinations. Note that not all combinations are supported.
@@ -145,6 +149,7 @@ def install(self, spec, prefix):
             ("linux",   "x86_64",   "netlrts"):     "netlrts-linux-x86_64",
             ("linux",   "x86_64",   "verbs"):       "verbs-linux-x86_64",
             ("linux",   "x86_64",   "ofi"):         "ofi-linux-x86_64",
+            ("linux",   "x86_64",   "ucx"):         "ucx-linux-x86_64",
             ("linux",   "x86_64",   "uth"):         "uth-linux-x86_64",
             ("linux",   "ppc",      "mpi"):         "mpi-linux-ppc",
             ("linux",   "ppc",      "multicore"):   "multicore-linux-ppc",
@@ -167,7 +172,47 @@ def install(self, spec, prefix):
                 "The communication mechanism %s is not supported "
                 "on a %s platform with a %s CPU" %
                 (comm, plat, mach))
-        version = versions[(plat, mach, comm)]
+
+        return versions[(plat, mach, comm)]
+
+    # FIXME: backend=mpi also provides mpi, but spack does not support
+    # depends_on("mpi") and provides("mpi") in the same package currently.
+    # for b in ['multicore', 'netlrts', 'verbs', 'gni', 'ofi', 'pami',
+    #          'pamilrts']:
+    #    provides('mpi@2', when='@6.7.1:
+    #            build-target=AMPI backend={0}'.format(b))
+    #    provides('mpi@2', when='@6.7.1:
+    #            build-target=LIBS backend={0}'.format(b))
+
+    def install(self, spec, prefix):
+
+        if not("backend=mpi" in self.spec) or \
+           not("backend=netlrts" in self.spec):
+            if ("+pthreads" in self.spec):
+                raise InstallError("The pthreads option is only\
+                                    available on the Netlrts and MPI \
+                                    network layers.")
+
+        if ("backend=ucx" in self.spec) or \
+           ("backend=ofi" in self.spec) or \
+           ("backend=gni" in self.spec):
+            if ("pmi=none" in self.spec):
+                raise InstallError("The UCX/OFI/GNI backends need \
+                                    PMI to run. Please add pmi=... \
+                                    Note that PMIx is the preferred \
+                                    option.")
+
+        if ("pmi=simplepmi" in self.spec) or \
+           ("pmi=slurmpmi" in self.spec) or \
+           ("pmi=slurmpmi2" in self.spec):
+            if ("^openmpi" in self.spec):
+                raise InstallError("To use any process management \
+                                    interface other than PMIx, \
+                                    a non OpenMPI based MPI must be \
+                                    present on the system")
+
+        target = spec.variants["build-target"].value
+        builddir = prefix + "/" + str(self.charmarch)
 
         # We assume that Spack's compiler wrappers make this work. If
         # not, then we need to query the compiler vendor from Spack
@@ -176,9 +221,17 @@ def install(self, spec, prefix):
             os.path.basename(self.compiler.cc),
             os.path.basename(self.compiler.fc),
             "-j%d" % make_jobs,
-            "--destination=%s" % prefix,
+            "--destination=%s" % builddir,
         ]
 
+        if "pmi=slurmpmi" in spec:
+            options.append("slurmpmi")
+        if "pmi=slurmpmi2" in spec:
+            options.append("slurmpmi2")
+        if "pmi=pmix" in spec:
+            options.append("ompipmix")
+            options.extend(["--basedir=%s" % spec["openmpi"].prefix])
+
         if 'backend=mpi' in spec:
             # in intelmpi <prefix>/include and <prefix>/lib fails so --basedir
             # cannot be used
@@ -190,6 +243,9 @@ def install(self, spec, prefix):
                 '--libdir={0}'.format(libdir)
                 for libdir in spec["mpi"].libs.directories
             ])
+
+        if "backend=ucx" in spec:
+            options.extend(["--basedir=%s" % spec["ucx"].prefix])
         if "+papi" in spec:
             options.extend(["papi", "--basedir=%s" % spec["papi"].prefix])
         if "+smp" in spec:
@@ -223,11 +279,11 @@ def install(self, spec, prefix):
         # could dissect the build script; the build instructions say
         # this wouldn't be difficult.
         build = Executable(join_path(".", "build"))
-        build(target, version, *options)
+        build(target, self.charmarch, *options)
 
         # Charm++'s install script does not copy files, it only creates
         # symbolic links. Fix this.
-        for dirpath, dirnames, filenames in os.walk(prefix):
+        for dirpath, dirnames, filenames in os.walk(builddir):
             for filename in filenames:
                 filepath = join_path(dirpath, filename)
                 if os.path.islink(filepath):
@@ -239,18 +295,32 @@ def install(self, spec, prefix):
                         os.rename(tmppath, filepath)
                     except (IOError, OSError):
                         pass
-        shutil.rmtree(join_path(prefix, "tmp"))
+        shutil.rmtree(join_path(builddir, "tmp"))
 
-        # A broken 'doc' link in the prefix can break the build.
-        # Remove it and replace it if it is broken.
-        try:
-            os.stat(prefix.doc)
-        except OSError:
-            os.remove(prefix.doc)
-            mkdirp(prefix.doc)
+        if self.spec.satisfies('@6.9.99'):
+            # A broken 'doc' link in the prefix can break the build.
+            # Remove it and replace it if it is broken.
+            try:
+                os.stat(prefix.doc)
+            except OSError:
+                os.remove(prefix.doc)
+                mkdirp(prefix.doc)
 
     @run_after('install')
     @on_package_attributes(run_tests=True)
     def check_build(self):
         make('-C', join_path(self.stage.source_path, 'charm/tests'),
              'test', parallel=False)
+
+    def setup_dependent_build_environment(self, env, dependent_spec):
+        env.set('MPICC',  self.prefix.bin.ampicc)
+        env.set('MPICXX', self.prefix.bin.ampicxx)
+        env.set('MPIF77', self.prefix.bin.ampif77)
+        env.set('MPIF90', self.prefix.bin.ampif90)
+
+    def setup_dependent_package(self, module, dependent_spec):
+        self.spec.mpicc     = self.prefix.bin.ampicc
+        self.spec.mpicxx    = self.prefix.bin.ampicxx
+        self.spec.mpifc     = self.prefix.bin.ampif90
+        self.spec.mpif77    = self.prefix.bin.ampif77
+        self.spec.charmarch = self.charmarch
diff --git a/var/spack/repos/builtin/packages/namd/package.py b/var/spack/repos/builtin/packages/namd/package.py
index dcd80e94a85..d6f5b11b4a7 100644
--- a/var/spack/repos/builtin/packages/namd/package.py
+++ b/var/spack/repos/builtin/packages/namd/package.py
@@ -15,8 +15,11 @@ class Namd(MakefilePackage):
 
     homepage = "http://www.ks.uiuc.edu/Research/namd/"
     url      = "file://{0}/NAMD_2.12_Source.tar.gz".format(os.getcwd())
+    git      = "https://charm.cs.illinois.edu/gerrit/namd.git"
     manual_download = True
 
+    version("develop", branch="master")
+    version('2.14b1', sha256='9407e54f5271b3d3039a5a9d2eae63c7e108ce31b7481e2197c19e1125b43919')
     version('2.13', '9e3323ed856e36e34d5c17a7b0341e38')
     version('2.12', '2a1191909b1ab03bf0205971ad4d8ee9')
 
@@ -26,7 +29,9 @@ class Namd(MakefilePackage):
     variant('interface', default='none', values=('none', 'tcl', 'python'),
             description='Enables TCL and/or python interface')
 
-    depends_on('charmpp')
+    depends_on('charmpp@6.10.1:', when="@2.14b1:")
+    depends_on('charmpp@6.8.2', when="@2.13")
+    depends_on('charmpp@6.7.1', when="@2.12")
 
     depends_on('fftw@:2.99', when="fftw=2")
     depends_on('fftw@3:', when="fftw=3")
@@ -73,17 +78,24 @@ def edit(self, spec, prefix):
             with open('{0}.arch'.format(self.build_directory), 'w') as fh:
                 # this options are take from the default provided
                 # configuration files
-                optims_opts = {
-                    'gcc': '-m64 -O3 -fexpensive-optimizations -ffast-math',
-                    'intel': '-O2 -ip'
-                }
+                # https://github.com/UIUC-PPL/charm/pull/2778
+                if self.spec.satisfies('^charmpp@:6.10.1'):
+                    optims_opts = {
+                        'gcc': '-m64 -O3 -fexpensive-optimizations \
+                                -ffast-math -lpthread',
+                        'intel': '-O2 -ip'}
+                else:
+                    optims_opts = {
+                        'gcc': '-m64 -O3 -fexpensive-optimizations \
+                                -ffast-math',
+                        'intel': '-O2 -ip'}
 
                 optim_opts = optims_opts[self.compiler.name] \
                     if self.compiler.name in optims_opts else ''
 
                 fh.write('\n'.join([
                     'NAMD_ARCH = {0}'.format(self.arch),
-                    'CHARMARCH = ',
+                    'CHARMARCH = {0}'.format(self.spec['charmpp'].charmarch),
                     'CXX = {0.cxx} {0.cxx11_flag}'.format(
                         self.compiler),
                     'CXXOPTS = {0}'.format(optim_opts),

From a59b92d3035401f061f1740a9ea88b7d5a1978d6 Mon Sep 17 00:00:00 2001
From: "Tomoki, Karatsu" <49965247+t-karatsu@users.noreply.github.com>
Date: Tue, 12 May 2020 16:40:11 +0900
Subject: [PATCH 349/802] xabclib: added support for Fujitsu compiler. (#16596)

- Added Fujitsu compiler options that have the same functions as the options added for GCC
- Added option to link C objects
---
 var/spack/repos/builtin/packages/xabclib/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/xabclib/package.py b/var/spack/repos/builtin/packages/xabclib/package.py
index 3a851b21afd..80f691d31b5 100644
--- a/var/spack/repos/builtin/packages/xabclib/package.py
+++ b/var/spack/repos/builtin/packages/xabclib/package.py
@@ -21,6 +21,8 @@ def edit(self, spec, prefix):
         fc = [spack_fc, '-O3', self.compiler.openmp_flag]
         if spec.satisfies('%gcc'):
             fc.extend(['-ffixed-form', '-cpp'])
+        elif spec.satisfies('%fj'):
+            fc.extend(['-Fixed', '-Cpp'])
         filter_file(
             '^rm libOpenAT.a$',
             'rm -f libOpenAT.a',
@@ -44,6 +46,8 @@ def edit(self, spec, prefix):
                 'LD += .*$',
                 'LD = {0}'.format(' '.join(fc))
             )
+            if spec.satisfies('%fj') and 'samples_c' in makefile:
+                m.filter('$(LD)', '$(LD) -mlcmain=main', string=True)
 
     def build(self, spec, prefix):
         sh = which('sh')

From 269bcfe1c8fa404dc5cb0ab3c94459edc16fd72a Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 12 May 2020 00:41:31 -0700
Subject: [PATCH 350/802] clingo: update package (#16594)

`clingo` has some undocumented dependencies:
- `bison`, for which the default macos version is too old
- `re2c`, which isn't always available

Also, the python installation was not set up properly. Clingo by default
does an install in `~/.local`, so we need to disable that and add a few
other options to get things right.

- [x] add `bison` dependency
- [x] add `re2c` dependency
- [x] make `doxygen` dependency optional (and patch if needed)
- [x] add options to fix `python` build
- [x] make python build optional but on by default
---
 .../repos/builtin/packages/clingo/package.py  | 36 +++++++++++++++----
 1 file changed, 29 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/clingo/package.py b/var/spack/repos/builtin/packages/clingo/package.py
index 8f1b64af60b..d839ff3f332 100644
--- a/var/spack/repos/builtin/packages/clingo/package.py
+++ b/var/spack/repos/builtin/packages/clingo/package.py
@@ -18,13 +18,32 @@ class Clingo(CMakePackage):
 
     homepage = "https://potassco.org/clingo/"
     url      = "https://github.com/potassco/clingo/archive/v5.2.2.tar.gz"
+    git      = 'https://github.com/potassco/clingo.git'
 
+    maintainers = ["tgamblin"]
+
+    version('develop', branch='wip', submodules=True)
     version('5.4.0', sha256='e2de331ee0a6d254193aab5995338a621372517adcf91568092be8ac511c18f3')
     version('5.3.0', sha256='b0d406d2809352caef7fccf69e8864d55e81ee84f4888b0744894977f703f976')
     version('5.2.2', sha256='da1ef8142e75c5a6f23c9403b90d4f40b9f862969ba71e2aaee9a257d058bfcf')
 
-    depends_on('doxygen', type=('build'))
-    depends_on('python')
+    variant("docs", default=False, description="build documentation with Doxyegen")
+    variant("python", default=True, description="build with python bindings")
+
+    depends_on('doxygen', type="build", when="+docs")
+    depends_on('re2c@0.13:', type="build")
+    depends_on('bison@2.5:', type="build")
+
+    depends_on('python', type=("build", "link", "run"), when="+python")
+
+    def patch(self):
+        # Doxygen is optional but can't be disabled with a -D, so patch
+        # it out if it's really supposed to be disabled
+        if '+docs' not in self.spec:
+            filter_file(r'find_package\(Doxygen\)',
+                        'message("Doxygen disabled for Spack build.")',
+                        'clasp/CMakeLists.txt',
+                        'clasp/libpotassco/CMakeLists.txt')
 
     def cmake_args(self):
         try:
@@ -32,8 +51,11 @@ def cmake_args(self):
         except UnsupportedCompilerFlag:
             InstallError('clingo requires a C++14-compliant C++ compiler')
 
-        args = ['-DCLINGO_BUILD_WITH_PYTHON=ON',
-                '-DCLING_BUILD_PY_SHARED=ON',
-                '-DPYCLINGO_USE_INSTALL_PREFIX=ON',
-                '-DCLINGO_BUILD_WITH_LUA=OFF']
-        return args
+        return [
+            '-DCLINGO_REQUIRE_PYTHON=ON',
+            '-DCLINGO_BUILD_WITH_PYTHON=ON',
+            '-DCLINGO_BUILD_PY_SHARED=ON',
+            '-DPYCLINGO_USER_INSTALL=OFF',
+            '-DPYCLINGO_USE_INSTALL_PREFIX=ON',
+            '-DCLINGO_BUILD_WITH_LUA=OFF'
+        ]

From 80e7a615974a02a16ebe68f42c32e49af4e2a4be Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Tue, 12 May 2020 03:09:01 -0500
Subject: [PATCH 351/802] prokka: new package at v1.14.6 (#16282)

---
 .../repos/builtin/packages/prokka/package.py  | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/prokka/package.py

diff --git a/var/spack/repos/builtin/packages/prokka/package.py b/var/spack/repos/builtin/packages/prokka/package.py
new file mode 100644
index 00000000000..eedb5fde081
--- /dev/null
+++ b/var/spack/repos/builtin/packages/prokka/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Prokka(Package):
+    """Prokka is a software tool to annotate bacterial, archaeal and viral
+       genomes quickly and produce standards-compliant output files."""
+
+    homepage = "https://github.com/tseemann/prokka"
+    url      = "https://github.com/tseemann/prokka/archive/v1.14.5.tar.gz"
+
+    version('1.14.6', sha256='f730b5400ea9e507bfe6c5f3d22ce61960a897195c11571c2e1308ce2533faf8')
+
+    depends_on('perl', type='run')
+    depends_on('perl-bioperl', type='run')
+    depends_on('perl-xml-simple', type='run')
+    depends_on('perl-bio-searchio-hmmer', type='run')
+    depends_on('hmmer', type='run')
+    depends_on('blast-plus', type='run')
+    depends_on('prodigal', type='run')
+    depends_on('tbl2asn', type='run')
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('binaries', prefix.binaries)
+        install_tree('db', prefix.db)
+        install_tree('doc', prefix.doc)

From a44f487a1d5b2f88675d4053485c338c64340a76 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 12 May 2020 02:15:42 -0700
Subject: [PATCH 352/802] z3: update python dependency (#16597)

-[x] `z3` needs a dependency on `py-setuptools`
-[x] `z3` has a run dependency on `python`, so we might as well make
     building with the python bindings default
---
 var/spack/repos/builtin/packages/z3/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/z3/package.py b/var/spack/repos/builtin/packages/z3/package.py
index 71eafb0a3b8..462316cbdfd 100644
--- a/var/spack/repos/builtin/packages/z3/package.py
+++ b/var/spack/repos/builtin/packages/z3/package.py
@@ -21,8 +21,9 @@ class Z3(MakefilePackage):
 
     phases = ['bootstrap', 'build', 'install']
 
-    variant('python', default=False, description='Enable python binding')
+    variant('python', default=True, description='Enable python binding')
     depends_on('python', type=('build', 'run'))
+    depends_on('py-setuptools', type=('run'), when='+python')
     extends('python', when='+python')
 
     # Referenced: https://github.com/Z3Prover/z3/issues/1016

From 15112f9dbad98ae264351dd3dc28341f7f8125d1 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Tue, 12 May 2020 13:56:58 +0200
Subject: [PATCH 353/802] gcc: fix several issues (#16599)

- GCC has moved to Git
- The develop/master version requires flex
- Add myself as a maintainer
- Set the library path in the zstd patch
---
 .../repos/builtin/packages/gcc/package.py     | 16 +++----
 .../repos/builtin/packages/gcc/zstd.patch     | 42 ++++++++++++++-----
 2 files changed, 40 insertions(+), 18 deletions(-)

diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index 54bebcdb782..aae26bfae9b 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -19,11 +19,13 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
 
     homepage = 'https://gcc.gnu.org'
     gnu_mirror_path = 'gcc/gcc-9.2.0/gcc-9.2.0.tar.xz'
-    svn      = 'svn://gcc.gnu.org/svn/gcc/'
+    git      = 'git://gcc.gnu.org/git/gcc.git'
     list_url = 'http://ftp.gnu.org/gnu/gcc/'
     list_depth = 1
 
-    version('develop', svn=svn + 'trunk')
+    maintainers = ['michaelkuhn']
+
+    version('master', branch='master')
 
     version('10.1.0', sha256='b6898a23844b656f1b68691c5c012036c2e694ac4b53a8918d4712ad876e7ea2')
 
@@ -90,6 +92,8 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
             default=False,
             description='Target nvptx offloading to NVIDIA GPUs')
 
+    depends_on('flex', type='build', when='@master')
+
     # https://gcc.gnu.org/install/prerequisites.html
     depends_on('gmp@4.3.2:')
     # GCC 7.3 does not compile with newer releases on some platforms, see
@@ -117,14 +121,12 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
     # The server is sometimes a bit slow to respond
     timeout = {'timeout': 60}
 
-    resource(
-             name='newlib',
+    resource(name='newlib',
              url='ftp://sourceware.org/pub/newlib/newlib-3.0.0.20180831.tar.gz',
              sha256='3ad3664f227357df15ff34e954bfd9f501009a647667cd307bf0658aefd6eb5b',
              destination='newlibsource',
              when='+nvptx',
-             fetch_options=timeout
-            )
+             fetch_options=timeout)
 
     # nvptx-tools does not seem to work as a dependency,
     # but does fine when the source is inside the gcc build directory
@@ -267,7 +269,7 @@ def url_for_version(self, version):
         # mirrors are tried. It takes care of modifying the suffix of gnu
         # mirror path so that Spack will also look for the correct file in
         # the mirrors
-        if (version < Version('6.4.0')and version != Version('5.5.0')) \
+        if (version < Version('6.4.0') and version != Version('5.5.0')) \
                 or version == Version('7.1.0'):
             self.gnu_mirror_path = self.gnu_mirror_path.replace('xz', 'bz2')
         return super(Gcc, self).url_for_version(version)
diff --git a/var/spack/repos/builtin/packages/gcc/zstd.patch b/var/spack/repos/builtin/packages/gcc/zstd.patch
index 362da1606fc..8fb7583a0c2 100644
--- a/var/spack/repos/builtin/packages/gcc/zstd.patch
+++ b/var/spack/repos/builtin/packages/gcc/zstd.patch
@@ -1,23 +1,43 @@
---- a/gcc/Makefile.in	2020-05-08 11:50:17.962838228 +0200
-+++ b/gcc/Makefile.in	2020-05-08 11:50:58.220960817 +0200
-@@ -1075,6 +1075,11 @@
+--- a/gcc/Makefile.in
++++ b/gcc/Makefile.in
+@@ -1075,7 +1075,8 @@ GNATMAKE = @GNATMAKE@
  # Libs needed (at present) just for jcf-dump.
  LDEXP_LIB = @LDEXP_LIB@
  
-+ifneq (@ZSTD_INCLUDE@,)
-+ZSTD_INCLUDE = -I@ZSTD_INCLUDE@
-+else
-+ZSTD_INCLUDE =
-+endif
- ZSTD_LIB = @ZSTD_LIB@
+-ZSTD_LIB = @ZSTD_LIB@
++ZSTD_INC = @ZSTD_CPPFLAGS@
++ZSTD_LIB = @ZSTD_LDFLAGS@ @ZSTD_LIB@
  
  # Likewise, for use in the tools that must run on this machine
-@@ -2275,7 +2280,7 @@
+ # even if we are cross-building GCC.
+@@ -2275,7 +2276,7 @@ CFLAGS-version.o += -DBASEVER=$(BASEVER_s) -DDATESTAMP=$(DATESTAMP_s) \
  version.o: $(REVISION) $(DATESTAMP) $(BASEVER) $(DEVPHASE)
  
  # lto-compress.o needs $(ZLIBINC) added to the include flags.
 -CFLAGS-lto-compress.o += $(ZLIBINC)
-+CFLAGS-lto-compress.o += $(ZLIBINC) $(ZSTD_INCLUDE)
++CFLAGS-lto-compress.o += $(ZLIBINC) $(ZSTD_INC)
  
  CFLAGS-lto-streamer-in.o += -DTARGET_MACHINE=\"$(target_noncanonical)\"
  
+--- a/gcc/configure
++++ b/gcc/configure
+@@ -786,6 +786,8 @@ LTLIBICONV
+ LIBICONV
+ ZSTD_LIB
+ ZSTD_INCLUDE
++ZSTD_LDFLAGS
++ZSTD_CPPFLAGS
+ DL_LIB
+ LDEXP_LIB
+ EXTRA_GCC_LIBS
+--- a/gcc/configure.ac
++++ b/gcc/configure.ac
+@@ -1339,6 +1339,8 @@ AC_SUBST(ZSTD_INCLUDE)
+ AC_SUBST(ZSTD_LIB)
+ ZSTD_CPPFLAGS=
+ ZSTD_LDFLAGS=
++AC_SUBST(ZSTD_CPPFLAGS)
++AC_SUBST(ZSTD_LDFLAGS)
+ AC_ARG_WITH(zstd,
+ 	[AS_HELP_STRING([--with-zstd=PATH],
+ 		[specify prefix directory for installed zstd library.

From d1a5dc792ea9828433a207818ab5805a5bd0a2f0 Mon Sep 17 00:00:00 2001
From: Sergey Kosukhin <sergey.kosukhin@mpimet.mpg.de>
Date: Tue, 12 May 2020 16:35:11 +0200
Subject: [PATCH 354/802] py-dask: new version (#16531)

* py-dask: new version

* py-dask: update the constraints.

* py-dask: add a list of maintainers.
---
 .../repos/builtin/packages/py-dask/package.py | 139 +++++++++++++++---
 .../builtin/packages/py-fsspec/package.py     |   4 +
 .../builtin/packages/py-partd/package.py      |   3 +
 3 files changed, 122 insertions(+), 24 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-dask/package.py b/var/spack/repos/builtin/packages/py-dask/package.py
index 4967306f63d..b6f3a07f10a 100644
--- a/var/spack/repos/builtin/packages/py-dask/package.py
+++ b/var/spack/repos/builtin/packages/py-dask/package.py
@@ -12,6 +12,9 @@ class PyDask(PythonPackage):
     homepage = "https://github.com/dask/dask/"
     url      = "https://pypi.io/packages/source/d/dask/dask-1.1.0.tar.gz"
 
+    maintainers = ['skosukhin']
+
+    version('2.16.0', sha256='2af5b0dcd48ce679ce0321cf91de623f4fe376262789b951fefa3c334002f350')
     version('1.2.2', sha256='5e7876bae2a01b355d1969b73aeafa23310febd8c353163910b73e93dc7e492c')
     version('1.1.2', sha256='93b355b9a9c9a3ddbb39fab99d5759aad5cfd346f4520b87788970e80cf97256')
     version('1.1.0', sha256='e76088e8931b326c05a92d2658e07b94a6852b42c13a7560505a8b2354871454')
@@ -21,10 +24,18 @@ class PyDask(PythonPackage):
     variant('array',       default=True, description='Install requirements for dask.array')
     variant('bag',         default=True, description='Install requirements for dask.bag')
     variant('dataframe',   default=True, description='Install requirements for dask.dataframe')
-    variant('delayed',     default=True, description='Install requirements for dask.delayed')
     variant('distributed', default=True, description='Install requirements for dask.distributed')
+    variant('diagnostics', default=False, description='Install requirements for dask.diagnostics')
+    variant('delayed',     default=True, description='Install requirements for dask.delayed (dask.imperative)')
+    variant('yaml',        default=True, description='Ensure support for YAML configuration files')
 
-    conflicts('+distributed', when='@:1.2.1')  # Only present in 1.2.2+
+    conflicts('+distributed', when='@:0.4.0,0.7.6:0.8.1')
+    conflicts('+diagnostics', when='@:0.5.0')
+    conflicts('+yaml', when='@:0.17.5')
+
+    depends_on('python@2.7:2.8,3.5:',   type=('build', 'run'))
+    depends_on('python@3.5:',           type=('build', 'run'), when='@2.0.0:')
+    depends_on('python@3.6:',           type=('build', 'run'), when='@2.7.0:')
 
     depends_on('py-setuptools',         type='build')
     depends_on('py-pytest@3.1.0:',      type='test')
@@ -32,35 +43,107 @@ class PyDask(PythonPackage):
     depends_on('py-pytest-runner',      type='test')
 
     # Requirements for dask.array
-    depends_on('py-numpy@1.11.0:',      type=('build', 'run'), when='+array')
-    depends_on('py-numpy@1.13.0:',      type=('build', 'run'), when='@1.2.2: +array')
-    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='+array')
+    depends_on('py-numpy@1.10.4:',      type=('build', 'run'), when='+array')
+    depends_on('py-numpy@1.11.0:',      type=('build', 'run'), when='@0.17.3: +array')
+    depends_on('py-numpy@1.13.0:',      type=('build', 'run'), when='@1.2.1: +array')
+
+    depends_on('py-toolz',              type=('build', 'run'), when='+array')
+    depends_on('py-toolz@0.7.2:',       type=('build', 'run'), when='@0.7.0: +array')
+    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='@0.14.1: +array')
+    depends_on('py-toolz@0.8.2:',       type=('build', 'run'), when='@2.13.0: +array')
 
     # Requirements for dask.bag
-    depends_on('py-cloudpickle@0.2.1:', type=('build', 'run'), when='+bag')
-    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='+bag')
-    depends_on('py-partd@0.3.8:',       type=('build', 'run'), when='+bag')
+    depends_on('py-dill',               type=('build', 'run'), when='@:0.7.5 +bag')
+    depends_on('py-cloudpickle',        type=('build', 'run'), when='@0.7.6: +bag')
+    depends_on('py-cloudpickle@0.2.1:', type=('build', 'run'), when='@0.8.2: +bag')
+    depends_on('py-cloudpickle@0.2.2:', type=('build', 'run'), when='@2.13.0: +bag')
+
+    depends_on('py-fsspec@0.3.3:',      type=('build', 'run'), when='@2.2.0: +bag')
+    depends_on('py-fsspec@0.5.1:',      type=('build', 'run'), when='@2.5.0: +bag')
+    depends_on('py-fsspec@0.6.0:',      type=('build', 'run'), when='@2.8.0: +bag')
+
+    depends_on('py-toolz',              type=('build', 'run'), when='+bag')
+    depends_on('py-toolz@0.7.2:',       type=('build', 'run'), when='@0.7.0: +bag')
+    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='@0.14.1: +bag')
+    depends_on('py-toolz@0.8.2:',       type=('build', 'run'), when='@2.13.0: +bag')
+
+    depends_on('py-partd',              type=('build', 'run'), when='+bag')
+    depends_on('py-partd@0.3.2:',       type=('build', 'run'), when='@0.6.0: +bag')
+    depends_on('py-partd@0.3.3:',       type=('build', 'run'), when='@0.9.0: +bag')
+    depends_on('py-partd@0.3.5:',       type=('build', 'run'), when='@0.10.2: +bag')
+    depends_on('py-partd@0.3.6:',       type=('build', 'run'), when='@0.12.0: +bag')
+    depends_on('py-partd@0.3.7:',       type=('build', 'run'), when='@0.13.0: +bag')
+    depends_on('py-partd@0.3.8:',       type=('build', 'run'), when='@0.15.0: +bag')
+    depends_on('py-partd@0.3.10:',      type=('build', 'run'), when='@2.0.0: +bag')
 
     # Requirements for dask.dataframe
-    depends_on('py-numpy@1.11.0:',      type=('build', 'run'), when='+dataframe')
-    depends_on('py-numpy@1.13.0:',      type=('build', 'run'), when='@1.2.2: +dataframe')
-    depends_on('py-pandas@0.19.0:',     type=('build', 'run'), when='+dataframe')
-    depends_on('py-pandas@0.21.0:',     type=('build', 'run'), when='@1.2.2: +dataframe')
-    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='+dataframe')
-    depends_on('py-partd@0.3.8:',       type=('build', 'run'), when='+dataframe')
-    depends_on('py-cloudpickle@0.2.1:', type=('build', 'run'), when='+dataframe')
+    depends_on('py-numpy@1.10.4:',      type=('build', 'run'), when='+dataframe')
+    depends_on('py-numpy@1.11.0:',      type=('build', 'run'), when='@0.17.3: +dataframe')
+    depends_on('py-numpy@1.13.0:',      type=('build', 'run'), when='@1.2.1: +dataframe')
 
-    # Requirements for dask.delayed
-    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='+delayed')
+    depends_on('py-pandas@0.16.0:',     type=('build', 'run'), when='+dataframe')
+    depends_on('py-pandas@0.18.0:',     type=('build', 'run'), when='@0.9.0: +dataframe')
+    depends_on('py-pandas@0.19.0:',     type=('build', 'run'), when='@0.14.0: +dataframe')
+    depends_on('py-pandas@0.21.0:',     type=('build', 'run'), when='@1.2.1: +dataframe')
+    depends_on('py-pandas@0.23.0:',     type=('build', 'run'), when='@2.11.0: +dataframe')
+
+    depends_on('py-toolz',              type=('build', 'run'), when='+dataframe')
+    depends_on('py-toolz@0.7.2:',       type=('build', 'run'), when='@0.7.0: +dataframe')
+    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='@0.14.1: +dataframe')
+    depends_on('py-toolz@0.8.2:',       type=('build', 'run'), when='@2.13.0: +dataframe')
+
+    depends_on('py-partd',              type=('build', 'run'), when='+dataframe')
+    depends_on('py-partd@0.3.2:',       type=('build', 'run'), when='@0.6.0: +dataframe')
+    depends_on('py-partd@0.3.3:',       type=('build', 'run'), when='@0.9.0: +dataframe')
+    depends_on('py-partd@0.3.5:',       type=('build', 'run'), when='@0.10.2: +dataframe')
+    depends_on('py-partd@0.3.7:',       type=('build', 'run'), when='@0.13.0: +dataframe')
+    depends_on('py-partd@0.3.8:',       type=('build', 'run'), when='@0.15.0: +dataframe')
+    depends_on('py-partd@0.3.10:',      type=('build', 'run'), when='@2.0.0: +dataframe')
+
+    depends_on('py-cloudpickle@0.2.1:', type=('build', 'run'), when='@0.8.2:2.6.0 +dataframe')
+
+    depends_on('py-fsspec@0.3.3:',      type=('build', 'run'), when='@2.2.0: +dataframe')
+    depends_on('py-fsspec@0.5.1:',      type=('build', 'run'), when='@2.5.0: +dataframe')
+    depends_on('py-fsspec@0.6.0:',      type=('build', 'run'), when='@2.8.0: +dataframe')
 
     # Requirements for dask.distributed
-    depends_on('py-distributed@1.22:',  type=('build', 'run'), when='+distributed')
+    depends_on('py-dill',               type=('build', 'run'), when='@:0.7.5 +distributed')
+    depends_on('py-pyzmq',              type=('build', 'run'), when='@:0.7.5 +distributed')
+    depends_on('py-distributed',        type=('build', 'run'), when='@0.8.2: +distributed')
+    depends_on('py-distributed@1.9:',   type=('build', 'run'), when='@0.9.0: +distributed')
+    depends_on('py-distributed@1.10:',  type=('build', 'run'), when='@0.10.0: +distributed')
+    depends_on('py-distributed@1.14:',  type=('build', 'run'), when='@0.12.0: +distributed')
+    depends_on('py-distributed@1.15:',  type=('build', 'run'), when='@0.13.0: +distributed')
+    depends_on('py-distributed@1.16:',  type=('build', 'run'), when='@0.14.1: +distributed')
+    depends_on('py-distributed@1.20:',  type=('build', 'run'), when='@0.16.0: +distributed')
+    depends_on('py-distributed@1.21:',  type=('build', 'run'), when='@0.17.0: +distributed')
+    depends_on('py-distributed@1.22:',  type=('build', 'run'), when='@0.18.0: +distributed')
+    depends_on('py-distributed@2.0:',   type=('build', 'run'), when='@2.0.0: +distributed')
+
+    # Requirements for dask.diagnostics
+    depends_on('py-bokeh',              type=('build', 'run'), when='+diagnostics')
+    depends_on('py-bokeh@1.0.0:',       type=('build', 'run'), when='@2.0.0: +diagnostics')
+
+    # Requirements for dask.delayed
+    depends_on('py-cloudpickle@0.2.1:', type=('build', 'run'), when='@2,7.0: +delayed')
+    depends_on('py-cloudpickle@0.2.2:', type=('build', 'run'), when='@2.13.0: +delayed')
+
+    depends_on('py-toolz@0.7.2:',       type=('build', 'run'), when='@0.8.1: +delayed')
+    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='@0.14.1: +delayed')
+    depends_on('py-toolz@0.8.2:',       type=('build', 'run'), when='@2.13.0: +delayed')
+
+    # Support for YAML configuration files
+    depends_on('py-pyyaml',             type=('build', 'run'), when='+yaml')
 
     @property
     def import_modules(self):
-        modules = [
-            'dask', 'dask.bytes', 'dask.diagnostics', 'dask.store'
-        ]
+        modules = ['dask']
+
+        if self.spec.satisfies('@0.9.0:'):
+            modules.append('dask.bytes')
+
+        if self.spec.satisfies('@:0.20.2'):
+            modules.append('dask.store')
 
         if '+array' in self.spec:
             modules.append('dask.array')
@@ -68,9 +151,17 @@ def import_modules(self):
         if '+bag' in self.spec:
             modules.append('dask.bag')
 
+        if self.spec.satisfies('@:0.7.5 +distributed'):
+            modules.append('dask.distributed')
+
         if '+dataframe' in self.spec:
-            modules.extend([
-                'dask.dataframe', 'dask.dataframe.io', 'dask.dataframe.tseries'
-            ])
+            modules.append('dask.dataframe')
+            if self.spec.satisfies('@0.8.2:'):
+                modules.append('dask.dataframe.tseries')
+            if self.spec.satisfies('@0.12.0:'):
+                modules.append('dask.dataframe.io')
+
+        if '+diagnostics' in self.spec:
+            modules.append('dask.diagnostics')
 
         return modules
diff --git a/var/spack/repos/builtin/packages/py-fsspec/package.py b/var/spack/repos/builtin/packages/py-fsspec/package.py
index 6302fff6d7c..bf82fc803a0 100644
--- a/var/spack/repos/builtin/packages/py-fsspec/package.py
+++ b/var/spack/repos/builtin/packages/py-fsspec/package.py
@@ -12,7 +12,11 @@ class PyFsspec(PythonPackage):
     homepage = "https://github.com/intake/filesystem_spec"
     url      = "https://pypi.io/packages/source/f/fsspec/fsspec-0.4.4.tar.gz"
 
+    import_modules = ['fsspec', 'fsspec.implementations']
+
+    version('0.7.3', sha256='1b540552c93b47e83c568e87507d6e02993e6d1b30bc7285f2336c81c5014103')
     version('0.4.4', sha256='97697a46e8bf8be34461c2520d6fc4bfca0ed749b22bb2b7c21939fd450a7d63')
 
     depends_on('python@3.5:', type=('build', 'run'))
+    depends_on('python@3.6:', type=('build', 'run'), when='@0.6.3:')
     depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-partd/package.py b/var/spack/repos/builtin/packages/py-partd/package.py
index 616f960f231..8e99413822a 100644
--- a/var/spack/repos/builtin/packages/py-partd/package.py
+++ b/var/spack/repos/builtin/packages/py-partd/package.py
@@ -14,8 +14,11 @@ class PyPartd(PythonPackage):
 
     import_modules = ['partd']
 
+    version('1.1.0', sha256='6e258bf0810701407ad1410d63d1a15cfd7b773fd9efe555dac6bb82cc8832b0')
+    version('0.3.10', sha256='33722a228ebcd1fa6f44b1631bdd4cff056376f89eb826d7d880b35b637bcfba')
     version('0.3.8', sha256='67291f1c4827cde3e0148b3be5d69af64b6d6169feb9ba88f0a6cfe77089400f')
 
+    depends_on('python@3.5:', type=('build', 'run'), when='@1.1.0:')
     depends_on('py-setuptools', type='build')
     depends_on('py-locket', type=('build', 'run'))
     depends_on('py-toolz', type=('build', 'run'))

From 7813e4146459f9460f0e6c0d6809d055130e903b Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Tue, 12 May 2020 23:39:19 +0900
Subject: [PATCH 355/802] caffe: fixed build error (#16520)

* opencv 3.2 requires cmake 3.11 or older.
caffe dependency is changed.

* revert opencv variant to caffe.
backport to opencv errors.
---
 .../repos/builtin/packages/caffe/package.py   |   2 +-
 .../packages/opencv/opencv3.2_cmake.patch     |  84 +++++++++++++
 .../packages/opencv/opencv3.2_ffmpeg.patch    | 107 ++++++++++++++++
 .../packages/opencv/opencv3.2_python3.7.patch |  22 ++++
 .../packages/opencv/opencv3.2_regacyvtk.patch | 119 ++++++++++++++++++
 .../packages/opencv/opencv3.2_vtk.patch       |  20 +++
 .../repos/builtin/packages/opencv/package.py  |   9 ++
 7 files changed, 362 insertions(+), 1 deletion(-)
 create mode 100755 var/spack/repos/builtin/packages/opencv/opencv3.2_cmake.patch
 create mode 100755 var/spack/repos/builtin/packages/opencv/opencv3.2_ffmpeg.patch
 create mode 100755 var/spack/repos/builtin/packages/opencv/opencv3.2_python3.7.patch
 create mode 100755 var/spack/repos/builtin/packages/opencv/opencv3.2_regacyvtk.patch
 create mode 100755 var/spack/repos/builtin/packages/opencv/opencv3.2_vtk.patch

diff --git a/var/spack/repos/builtin/packages/caffe/package.py b/var/spack/repos/builtin/packages/caffe/package.py
index e07f545f739..7df83b1d537 100644
--- a/var/spack/repos/builtin/packages/caffe/package.py
+++ b/var/spack/repos/builtin/packages/caffe/package.py
@@ -40,7 +40,7 @@ class Caffe(CMakePackage):
     depends_on('protobuf')
     depends_on('glog')
     depends_on('gflags')
-    depends_on('hdf5')
+    depends_on('hdf5 +hl +cxx')
 
     # Optional dependencies
     depends_on('opencv@3.2.0+core+highgui+imgproc', when='+opencv')
diff --git a/var/spack/repos/builtin/packages/opencv/opencv3.2_cmake.patch b/var/spack/repos/builtin/packages/opencv/opencv3.2_cmake.patch
new file mode 100755
index 00000000000..c479fb450e4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opencv/opencv3.2_cmake.patch
@@ -0,0 +1,84 @@
+commit dd7f88bd68f95e56437035cc95d4af482482fcc2
+Author: Alexander Alekhin <alexander.alekhin@intel.com>
+Date:   Thu Jun 7 12:32:48 2018 +0300
+
+    python: support standalone Python bindings build
+    
+    - requires OpenCV source directory
+    - requires OpenCV binary directory with built modules and 'python_bindings_generator' target
+
+diff --git a/cmake/OpenCVDetectPython.cmake b/cmake/OpenCVDetectPython.cmake
+index 6dec76ff66..b6c7a2535c 100644
+--- a/cmake/OpenCVDetectPython.cmake
++++ b/cmake/OpenCVDetectPython.cmake
+@@ -27,6 +27,12 @@ function(find_python preferred_version min_version library_env include_dir_env
+          debug_library include_path include_dir include_dir2 packages_path
+          numpy_include_dirs numpy_version)
+ if(NOT ${found})
++  if(" ${executable}" STREQUAL " PYTHON_EXECUTABLE")
++    set(__update_python_vars 0)
++  else()
++    set(__update_python_vars 1)
++  endif()
++
+   ocv_check_environment_variables(${executable})
+   if(${executable})
+     set(PYTHON_EXECUTABLE "${${executable}}")
+@@ -47,7 +53,7 @@ if(NOT ${found})
+     endforeach()
+   endif()
+ 
+-  string(REGEX MATCH "^[0-9]+" _preferred_version_major ${preferred_version})
++  string(REGEX MATCH "^[0-9]+" _preferred_version_major "${preferred_version}")
+ 
+   find_host_package(PythonInterp "${preferred_version}")
+   if(NOT PYTHONINTERP_FOUND)
+@@ -56,7 +62,7 @@ if(NOT ${found})
+ 
+   if(PYTHONINTERP_FOUND)
+     # Check if python major version is correct
+-    if(${_preferred_version_major} EQUAL ${PYTHON_VERSION_MAJOR})
++    if("${_preferred_version_major}" STREQUAL "" OR "${_preferred_version_major}" STREQUAL "${PYTHON_VERSION_MAJOR}")
+       # Copy outputs
+       set(_found ${PYTHONINTERP_FOUND})
+       set(_executable ${PYTHON_EXECUTABLE})
+@@ -65,7 +71,9 @@ if(NOT ${found})
+       set(_version_minor ${PYTHON_VERSION_MINOR})
+       set(_version_patch ${PYTHON_VERSION_PATCH})
+     endif()
++  endif()
+ 
++  if(__update_python_vars)
+     # Clear find_host_package side effects
+     unset(PYTHONINTERP_FOUND)
+     unset(PYTHON_EXECUTABLE CACHE)
+@@ -109,7 +117,8 @@ if(NOT ${found})
+         set(_library_release ${PYTHON_LIBRARY_RELEASE})
+         set(_include_dir ${PYTHON_INCLUDE_DIR})
+         set(_include_dir2 ${PYTHON_INCLUDE_DIR2})
+-
++      endif()
++      if(__update_python_vars)
+         # Clear find_package side effects
+         unset(PYTHONLIBS_FOUND)
+         unset(PYTHON_LIBRARIES)
+@@ -160,7 +169,7 @@ if(NOT ${found})
+         unset(_path)
+       endif()
+ 
+-      set(_numpy_include_dirs ${${numpy_include_dirs}})
++      set(_numpy_include_dirs "${${numpy_include_dirs}}")
+ 
+       if(NOT _numpy_include_dirs)
+         if(CMAKE_CROSSCOMPILING)
+@@ -222,6 +231,10 @@ if(NOT ${found})
+ endif()
+ endfunction(find_python)
+ 
++if(OPENCV_PYTHON_SKIP_DETECTION)
++  return()
++endif()
++
+ find_python(2.7 "${MIN_VER_PYTHON2}" PYTHON2_LIBRARY PYTHON2_INCLUDE_DIR
+     PYTHON2INTERP_FOUND PYTHON2_EXECUTABLE PYTHON2_VERSION_STRING
+     PYTHON2_VERSION_MAJOR PYTHON2_VERSION_MINOR PYTHON2LIBS_FOUND
diff --git a/var/spack/repos/builtin/packages/opencv/opencv3.2_ffmpeg.patch b/var/spack/repos/builtin/packages/opencv/opencv3.2_ffmpeg.patch
new file mode 100755
index 00000000000..d7786308d8c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opencv/opencv3.2_ffmpeg.patch
@@ -0,0 +1,107 @@
+commit b1d208891b9f6ae3968730b120a5d0dcbba679d0
+Author: Jonathan Viney <jonathan.viney@gmail.com>
+Date:   Sun Nov 19 07:08:41 2017 +1300
+
+    Merge pull request #10011 from jviney:master
+    
+    Fix build with FFmpeg master. Some deprecated APIs have been removed. (#10011)
+    
+    * Fix build with FFmpeg master.
+    
+    * ffmpeg: update AVFMT_RAWPICTURE support removal
+
+diff --git a/modules/videoio/src/cap_ffmpeg_impl.hpp b/modules/videoio/src/cap_ffmpeg_impl.hpp
+index 5f51e65134..46461483a7 100644
+--- a/modules/videoio/src/cap_ffmpeg_impl.hpp
++++ b/modules/videoio/src/cap_ffmpeg_impl.hpp
+@@ -149,6 +149,10 @@ extern "C" {
+ #define AV_PIX_FMT_GRAY16BE PIX_FMT_GRAY16BE
+ #endif
+ 
++#ifndef PKT_FLAG_KEY
++#define PKT_FLAG_KEY AV_PKT_FLAG_KEY
++#endif
++
+ #if LIBAVUTIL_BUILD >= (LIBAVUTIL_VERSION_MICRO >= 100 \
+     ? CALC_FFMPEG_VERSION(52, 38, 100) : CALC_FFMPEG_VERSION(52, 13, 0))
+ #define USE_AV_FRAME_GET_BUFFER 1
+@@ -1570,7 +1574,11 @@ static AVStream *icv_add_video_stream_FFMPEG(AVFormatContext *oc,
+     // some formats want stream headers to be seperate
+     if(oc->oformat->flags & AVFMT_GLOBALHEADER)
+     {
++#if LIBAVCODEC_BUILD > CALC_FFMPEG_VERSION(56, 35, 0)
++        c->flags |= AV_CODEC_FLAG_GLOBAL_HEADER;
++#else
+         c->flags |= CODEC_FLAG_GLOBAL_HEADER;
++#endif
+     }
+ #endif
+ 
+@@ -1598,23 +1606,24 @@ static int icv_av_write_frame_FFMPEG( AVFormatContext * oc, AVStream * video_st,
+ #endif
+     int ret = OPENCV_NO_FRAMES_WRITTEN_CODE;
+ 
+-    if (oc->oformat->flags & AVFMT_RAWPICTURE) {
++#if LIBAVFORMAT_BUILD < CALC_FFMPEG_VERSION(57, 0, 0)
++    if (oc->oformat->flags & AVFMT_RAWPICTURE)
++    {
+         /* raw video case. The API will change slightly in the near
+            futur for that */
+         AVPacket pkt;
+         av_init_packet(&pkt);
+ 
+-#ifndef PKT_FLAG_KEY
+-#define PKT_FLAG_KEY AV_PKT_FLAG_KEY
+-#endif
+-
+         pkt.flags |= PKT_FLAG_KEY;
+         pkt.stream_index= video_st->index;
+         pkt.data= (uint8_t *)picture;
+         pkt.size= sizeof(AVPicture);
+ 
+         ret = av_write_frame(oc, &pkt);
+-    } else {
++    }
++    else
++#endif
++    {
+         /* encode the image */
+         AVPacket pkt;
+         av_init_packet(&pkt);
+@@ -1772,7 +1781,9 @@ void CvVideoWriter_FFMPEG::close()
+     /* write the trailer, if any */
+     if(ok && oc)
+     {
+-        if( (oc->oformat->flags & AVFMT_RAWPICTURE) == 0 )
++#if LIBAVFORMAT_BUILD < CALC_FFMPEG_VERSION(57, 0, 0)
++        if (!(oc->oformat->flags & AVFMT_RAWPICTURE))
++#endif
+         {
+             for(;;)
+             {
+@@ -2071,7 +2082,11 @@ bool CvVideoWriter_FFMPEG::open( const char * filename, int fourcc,
+ 
+     outbuf = NULL;
+ 
+-    if (!(oc->oformat->flags & AVFMT_RAWPICTURE)) {
++
++#if LIBAVFORMAT_BUILD < CALC_FFMPEG_VERSION(57, 0, 0)
++    if (!(oc->oformat->flags & AVFMT_RAWPICTURE))
++#endif
++    {
+         /* allocate output buffer */
+         /* assume we will never get codec output with more than 4 bytes per pixel... */
+         outbuf_size = width*height*4;
+@@ -2376,7 +2391,11 @@ AVStream* OutputMediaStream_FFMPEG::addVideoStream(AVFormatContext *oc, CV_CODEC
+         // some formats want stream headers to be seperate
+         if (oc->oformat->flags & AVFMT_GLOBALHEADER)
+         {
+-            c->flags |= CODEC_FLAG_GLOBAL_HEADER;
++            #if LIBAVCODEC_BUILD > CALC_FFMPEG_VERSION(56, 35, 0)
++                c->flags |= AV_CODEC_FLAG_GLOBAL_HEADER;
++            #else
++                c->flags |= CODEC_FLAG_GLOBAL_HEADER;
++            #endif
+         }
+     #endif
+ 
diff --git a/var/spack/repos/builtin/packages/opencv/opencv3.2_python3.7.patch b/var/spack/repos/builtin/packages/opencv/opencv3.2_python3.7.patch
new file mode 100755
index 00000000000..d96011330d6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opencv/opencv3.2_python3.7.patch
@@ -0,0 +1,22 @@
+commit 0c4328fbf3da0da57a91b2133578c5100370b867
+Author: ilovezfs <ilovezfs@icloud.com>
+Date:   Tue Jul 3 06:31:39 2018 +0000
+
+    Python 3.7 compatability
+    
+    The result of PyUnicode_AsUTF8() is now of type const char * rather of
+    char *.
+
+diff --git a/modules/python/src2/cv2.cpp b/modules/python/src2/cv2.cpp
+index e16fcbacf2..5a6bf7ef62 100644
+--- a/modules/python/src2/cv2.cpp
++++ b/modules/python/src2/cv2.cpp
+@@ -916,7 +916,7 @@ bool pyopencv_to(PyObject* obj, String& value, const char* name)
+     (void)name;
+     if(!obj || obj == Py_None)
+         return true;
+-    char* str = PyString_AsString(obj);
++    const char* str = PyString_AsString(obj);
+     if(!str)
+         return false;
+     value = String(str);
diff --git a/var/spack/repos/builtin/packages/opencv/opencv3.2_regacyvtk.patch b/var/spack/repos/builtin/packages/opencv/opencv3.2_regacyvtk.patch
new file mode 100755
index 00000000000..f5341c62fa9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opencv/opencv3.2_regacyvtk.patch
@@ -0,0 +1,119 @@
+commit 235889ddbb1aaa4f0dfaee730f42a8476c0e50f0
+Author: jasjuang <jasjuang@gmail.com>
+Date:   Thu Dec 21 01:33:25 2017 -0800
+
+    handle legacy VTK functions
+
+diff --git a/modules/viz/src/clouds.cpp b/modules/viz/src/clouds.cpp
+index 48d057d2a8..ab8fd43e40 100644
+--- a/modules/viz/src/clouds.cpp
++++ b/modules/viz/src/clouds.cpp
+@@ -77,7 +77,9 @@ cv::viz::WCloud::WCloud(cv::InputArray cloud, cv::InputArray colors, cv::InputAr
+     vtkSmartPointer<vtkPolyDataMapper> mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
+     VtkUtils::SetInputData(mapper, cloud_source->GetOutput());
+     mapper->SetScalarModeToUsePointData();
++#if VTK_MAJOR_VERSION < 8
+     mapper->ImmediateModeRenderingOff();
++#endif
+     mapper->SetScalarRange(0, 255);
+     mapper->ScalarVisibilityOn();
+ 
+@@ -117,7 +119,9 @@ cv::viz::WPaintedCloud::WPaintedCloud(InputArray cloud)
+ 
+     vtkSmartPointer<vtkPolyDataMapper> mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
+     VtkUtils::SetInputData(mapper, vtkPolyData::SafeDownCast(elevation->GetOutput()));
++#if VTK_MAJOR_VERSION < 8
+     mapper->ImmediateModeRenderingOff();
++#endif
+     mapper->ScalarVisibilityOn();
+     mapper->SetColorModeToMapScalars();
+ 
+@@ -143,7 +147,9 @@ cv::viz::WPaintedCloud::WPaintedCloud(InputArray cloud, const Point3d& p1, const
+ 
+     vtkSmartPointer<vtkPolyDataMapper> mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
+     VtkUtils::SetInputData(mapper, vtkPolyData::SafeDownCast(elevation->GetOutput()));
++#if VTK_MAJOR_VERSION < 8
+     mapper->ImmediateModeRenderingOff();
++#endif
+     mapper->ScalarVisibilityOn();
+     mapper->SetColorModeToMapScalars();
+ 
+@@ -182,7 +188,9 @@ cv::viz::WPaintedCloud::WPaintedCloud(InputArray cloud, const Point3d& p1, const
+ 
+     vtkSmartPointer<vtkPolyDataMapper> mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
+     VtkUtils::SetInputData(mapper, vtkPolyData::SafeDownCast(elevation->GetOutput()));
++#if VTK_MAJOR_VERSION < 8
+     mapper->ImmediateModeRenderingOff();
++#endif
+     mapper->ScalarVisibilityOn();
+     mapper->SetColorModeToMapScalars();
+     mapper->SetLookupTable(color_transfer);
+@@ -211,7 +219,9 @@ cv::viz::WCloudCollection::WCloudCollection()
+     vtkSmartPointer<vtkPolyDataMapper> mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
+     mapper->SetInputConnection(append_filter->GetOutputPort());
+     mapper->SetScalarModeToUsePointData();
++#if VTK_MAJOR_VERSION < 8
+     mapper->ImmediateModeRenderingOff();
++#endif
+     mapper->SetScalarRange(0, 255);
+     mapper->ScalarVisibilityOn();
+ 
+@@ -416,7 +426,9 @@ cv::viz::WMesh::WMesh(const Mesh &mesh)
+ 
+     vtkSmartPointer<vtkPolyDataMapper> mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
+     mapper->SetScalarModeToUsePointData();
++#if VTK_MAJOR_VERSION < 8
+     mapper->ImmediateModeRenderingOff();
++#endif
+     VtkUtils::SetInputData(mapper, polydata);
+ 
+     vtkSmartPointer<vtkActor> actor = vtkSmartPointer<vtkActor>::New();
+@@ -468,7 +480,9 @@ cv::viz::WWidgetMerger::WWidgetMerger()
+     vtkSmartPointer<vtkPolyDataMapper> mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
+     mapper->SetInputConnection(append_filter->GetOutputPort());
+     mapper->SetScalarModeToUsePointData();
++#if VTK_MAJOR_VERSION < 8
+     mapper->ImmediateModeRenderingOff();
++#endif
+     mapper->SetScalarRange(0, 255);
+     mapper->ScalarVisibilityOn();
+ 
+diff --git a/modules/viz/src/widget.cpp b/modules/viz/src/widget.cpp
+index 0473c274bc..b324a4e26c 100644
+--- a/modules/viz/src/widget.cpp
++++ b/modules/viz/src/widget.cpp
+@@ -91,7 +91,9 @@ cv::viz::Widget cv::viz::Widget::fromPlyFile(const String &file_name)
+ 
+     vtkSmartPointer<vtkDataSetMapper> mapper = vtkSmartPointer<vtkDataSetMapper>::New();
+     mapper->SetInputConnection( reader->GetOutputPort() );
++#if VTK_MAJOR_VERSION < 8
+     mapper->ImmediateModeRenderingOff();
++#endif
+ 
+     vtkSmartPointer<vtkActor> actor = vtkSmartPointer<vtkActor>::New();
+     actor->GetProperty()->SetInterpolationToFlat();
+@@ -113,7 +115,11 @@ void cv::viz::Widget::setRenderingProperty(int property, double value)
+         case POINT_SIZE:          actor->GetProperty()->SetPointSize(float(value)); break;
+         case OPACITY:             actor->GetProperty()->SetOpacity(value);          break;
+         case LINE_WIDTH:          actor->GetProperty()->SetLineWidth(float(value)); break;
++#if VTK_MAJOR_VERSION < 8
+         case IMMEDIATE_RENDERING: actor->GetMapper()->SetImmediateModeRendering(int(value)); break;
++#else
++        case IMMEDIATE_RENDERING: std::cerr << "this property has no effect" << std::endl; break;
++#endif
+         case AMBIENT:             actor->GetProperty()->SetAmbient(float(value)); break;
+         case LIGHTING:
+         {
+@@ -191,8 +197,11 @@ double cv::viz::Widget::getRenderingProperty(int property) const
+         case POINT_SIZE: value = actor->GetProperty()->GetPointSize(); break;
+         case OPACITY:    value = actor->GetProperty()->GetOpacity();   break;
+         case LINE_WIDTH: value = actor->GetProperty()->GetLineWidth(); break;
++#if VTK_MAJOR_VERSION < 8
+         case IMMEDIATE_RENDERING:  value = actor->GetMapper()->GetImmediateModeRendering();  break;
+-
++#else
++        case IMMEDIATE_RENDERING: std::cerr << "this property has no effect" << std::endl; break;
++#endif
+         case FONT_SIZE:
+         {
+             vtkTextActor* text_actor = vtkTextActor::SafeDownCast(actor);
diff --git a/var/spack/repos/builtin/packages/opencv/opencv3.2_vtk.patch b/var/spack/repos/builtin/packages/opencv/opencv3.2_vtk.patch
new file mode 100755
index 00000000000..e5eecd70928
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opencv/opencv3.2_vtk.patch
@@ -0,0 +1,20 @@
+commit d810c73396ec7931addf3e7f75b17daf4e184bf4
+Author: Adam Rankin <adam.rankin@gmail.com>
+Date:   Sun Mar 11 22:28:18 2018 -0400
+
+    Update precomp.hpp
+    
+    Enabling build of visualization module when using VTK 9 (current HEAD of d5bbb9e99bbc6d11d2196c48bfd8f33508554551)
+
+diff --git a/modules/viz/src/precomp.hpp b/modules/viz/src/precomp.hpp
+index 369db191d3..dc5a5db1ea 100644
+--- a/modules/viz/src/precomp.hpp
++++ b/modules/viz/src/precomp.hpp
+@@ -104,6 +104,7 @@
+ #include <vtkMath.h>
+ #include <vtkExtractEdges.h>
+ #include <vtkFrustumSource.h>
++#include <vtkTexture.h>
+ #include <vtkTextureMapToPlane.h>
+ #include <vtkPolyDataNormals.h>
+ #include <vtkAlgorithmOutput.h>
diff --git a/var/spack/repos/builtin/packages/opencv/package.py b/var/spack/repos/builtin/packages/opencv/package.py
index 0e5bca79075..c589e7fdd28 100644
--- a/var/spack/repos/builtin/packages/opencv/package.py
+++ b/var/spack/repos/builtin/packages/opencv/package.py
@@ -121,6 +121,12 @@ class Opencv(CMakePackage, CudaPackage):
     # the current development branch of OpenCV. See #8461 for more information.
     patch('dnn_cuda.patch', when='@3.3.0:3.4.1+cuda+dnn')
 
+    patch('opencv3.2_cmake.patch', when='@3.2')
+    patch('opencv3.2_vtk.patch', when='@3.2+vtk')
+    patch('opencv3.2_regacyvtk.patch', when='@3.2+vtk')
+    patch('opencv3.2_ffmpeg.patch', when='@3.2+videoio')
+    patch('opencv3.2_python3.7.patch', when='@3.2+python')
+
     depends_on('eigen', when='+eigen')
     depends_on('zlib', when='+zlib')
     depends_on('libpng', when='+png')
@@ -147,6 +153,9 @@ class Opencv(CMakePackage, CudaPackage):
     conflicts('cuda@10:', when='+cudacodec')
     conflicts('cuda', when='~contrib', msg='cuda support requires +contrib')
 
+    # IPP is provided x86_64 only
+    conflicts('+ipp', when="arch=aarch64:")
+
     extends('python', when='+python')
 
     def cmake_args(self):

From e36aa96392eb4c1488478a846410fd915cb75167 Mon Sep 17 00:00:00 2001
From: Andrew W Elble <aweits@rit.edu>
Date: Tue, 12 May 2020 12:24:30 -0400
Subject: [PATCH 356/802] py-horovod: link dependency for py-torch (#16600)

fix for same reasons as #16495.
---
 var/spack/repos/builtin/packages/py-horovod/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-horovod/package.py b/var/spack/repos/builtin/packages/py-horovod/package.py
index c740486853d..955e68ff1ab 100644
--- a/var/spack/repos/builtin/packages/py-horovod/package.py
+++ b/var/spack/repos/builtin/packages/py-horovod/package.py
@@ -46,7 +46,7 @@ class PyHorovod(PythonPackage):
 
     # Framework dependencies
     depends_on('py-tensorflow@1.1.0:',  type=('build', 'link', 'run'), when='frameworks=tensorflow')
-    depends_on('py-torch@0.4.0:',       type=('build', 'run'),         when='frameworks=pytorch')
+    depends_on('py-torch@0.4.0:',       type=('build', 'link', 'run'), when='frameworks=pytorch')
     depends_on('py-torchvision',        type=('build', 'run'),         when='frameworks=pytorch')
     depends_on('py-cffi@1.4.0:',        type=('build', 'run'),         when='frameworks=pytorch')
     depends_on('mxnet@1.4.1:+python',   type=('build', 'link', 'run'), when='frameworks=mxnet')

From 8b06bd719888539964a2061100224b4a07ed2baf Mon Sep 17 00:00:00 2001
From: "Jose E. Roman" <jroman@dsic.upv.es>
Date: Tue, 12 May 2020 18:33:46 +0200
Subject: [PATCH 357/802] New patch release SLEPc 3.13.2 (#16601)

---
 var/spack/repos/builtin/packages/slepc/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py
index 042a8ecd155..13b88188407 100644
--- a/var/spack/repos/builtin/packages/slepc/package.py
+++ b/var/spack/repos/builtin/packages/slepc/package.py
@@ -18,6 +18,7 @@ class Slepc(Package):
     maintainers = ['joseeroman', 'balay']
 
     version('master', branch='master')
+    version('3.13.2', sha256='04cb8306cb5d4d990509710d7f8ae949bdc2c7eb850930b8d0b0b5ca99f6c70d')
     version('3.13.1', sha256='f4a5ede4ebdee5e15153ce31c1421209c7b794bd94be1430018615fb0838b879')
     version('3.13.0', sha256='f1f3c2d13a1a6914e7bf4746d38761e107ea866f50927b639e4ad5918dd1e53b')
     version('3.12.2', sha256='a586ce572a928ed87f04961850992a9b8e741677397cbaa3fb028323eddf4598')

From 278f8eb7fe66487cc4ce02975be285e3555d627c Mon Sep 17 00:00:00 2001
From: "Tomoki, Karatsu" <49965247+t-karatsu@users.noreply.github.com>
Date: Wed, 13 May 2020 01:34:28 +0900
Subject: [PATCH 358/802] modylas: Add flag to use preprocessor when building
 with Fujitsu compiler. (#16598)

---
 var/spack/repos/builtin/packages/modylas/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/modylas/package.py b/var/spack/repos/builtin/packages/modylas/package.py
index 1241d3a8ed1..ada4bc7fed1 100644
--- a/var/spack/repos/builtin/packages/modylas/package.py
+++ b/var/spack/repos/builtin/packages/modylas/package.py
@@ -40,6 +40,8 @@ def setup_build_environment(self, env):
         fflags = ['-O3', self.compiler.openmp_flag]
         if self.spec.satisfies('%gcc'):
             fflags.append('-cpp')
+        elif self.spec.satisfies('%fj'):
+            fflags.append('-Cpp')
         env.set('FCFLAGS', ' '.join(fflags))
 
     def configure_args(self):

From 7c327ed44720adb48f2ab5f29846dcf41154bae7 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Tue, 12 May 2020 18:35:41 +0200
Subject: [PATCH 359/802] r-knitr : dependencies and version updated (#16579)

* r-knitr : dependencies and version updated

* Adding version conditions for dependencies
---
 var/spack/repos/builtin/packages/r-knitr/package.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/r-knitr/package.py b/var/spack/repos/builtin/packages/r-knitr/package.py
index bde3fe85bda..c3af15f155f 100644
--- a/var/spack/repos/builtin/packages/r-knitr/package.py
+++ b/var/spack/repos/builtin/packages/r-knitr/package.py
@@ -15,6 +15,7 @@ class RKnitr(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/knitr_1.14.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/knitr"
 
+    version('1.28', sha256='05ee01da31d715bf24793efb3e4ef3bb3101ef1e1ab2d760c645fc5b9d40232a')
     version('1.24', sha256='e80c2043b445a7e576b62ae8510cce89322660fe388881d799a706d35cd27b89')
     version('1.23', sha256='063bfb3300fc9f3e7d223c346e19b93beced0e6784470b9bef2524868a206a99')
     version('1.17', sha256='9484a2b2c7b0c2aae24ab7f4eec6db48affbceb0e42bd3d69e34d953fe92f401')
@@ -25,8 +26,8 @@ class RKnitr(RPackage):
     depends_on('r@3.1.0:', when='@1.15:1.22', type=('build', 'run'))
     depends_on('r@3.2.3:', when='@1.23:', type=('build', 'run'))
     depends_on('r-evaluate@0.10:', type=('build', 'run'))
-    depends_on('r-digest@:1.17', type=('build', 'run'))
-    depends_on('r-formatr@:1.14', type=('build', 'run'))
+    depends_on('r-digest@:1.17', when='@:1.24', type=('build', 'run'))
+    depends_on('r-formatr@:1.14', when='@:1.24', type=('build', 'run'))
     depends_on('r-highr', type=('build', 'run'))
     depends_on('r-stringr@0.6:', type=('build', 'run'))
     depends_on('r-markdown', type=('build', 'run'))

From 14b80ecaf2e9bad0ce7c9864e7296fc3b68d35c6 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Tue, 12 May 2020 18:36:25 +0200
Subject: [PATCH 360/802] r-withr : dependencies and version updated (#16577)

* r-withr : dependencies and version updated

* Adding version conditions for dependencies
---
 var/spack/repos/builtin/packages/r-withr/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/r-withr/package.py b/var/spack/repos/builtin/packages/r-withr/package.py
index a1fbce55b14..42e2e2427fd 100644
--- a/var/spack/repos/builtin/packages/r-withr/package.py
+++ b/var/spack/repos/builtin/packages/r-withr/package.py
@@ -16,8 +16,10 @@ class RWithr(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/withr_1.0.2.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/withr"
 
+    version('2.2.0', sha256='4c21e51cf48f8c281ddd5f5ec358ac446df3c982104fd00bfe62d9259d73b582')
     version('2.1.2', sha256='41366f777d8adb83d0bdbac1392a1ab118b36217ca648d3bb9db763aa7ff4686')
     version('1.0.2', sha256='2391545020adc4256ee7c2e31c30ff6f688f0b6032e355e1ce8f468cab455f10')
     version('1.0.1', sha256='7e245fdd17d290ff9e7c237159804dd06e1c6a3efe7855ed641eb0765a1e727d')
 
     depends_on('r@3.0.2:', type=('build', 'run'))
+    depends_on('r@3.2:', when='@2.2:', type=('build', 'run'))

From 173823e77d730797722eb51ad79d8da3afb6f6fd Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Tue, 12 May 2020 18:39:08 +0200
Subject: [PATCH 361/802] r-rversions : new package (#16572)

* r-rversions : new package

* URL updated r-rversions
---
 .../builtin/packages/r-rversions/package.py   | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-rversions/package.py

diff --git a/var/spack/repos/builtin/packages/r-rversions/package.py b/var/spack/repos/builtin/packages/r-rversions/package.py
new file mode 100644
index 00000000000..7d0224fd90b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rversions/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRversions(RPackage):
+    """Query the main 'R' 'SVN' repository to find the versions
+       'r-release' and 'r-oldrel' refer to, and also all previous 'R'
+       versions and their release dates.
+    """
+
+    homepage = "https://cloud.r-project.org/package=rversions"
+    url      = "https://cloud.r-project.org/src/contrib/rversions_2.0.1.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/rversions"
+
+    version('2.0.1', sha256='51ec1f64e7d628e88d716a020d5d521eba71d472e3c9ae7b694428ef6dd786c5')
+    version('2.0.0', sha256='b50c321d9e973284ae6b1d0c89bd46a40f5174de51fb28e3c77cd12ef34f6f56')
+    version('1.1.0', sha256='14a5a2f06b74e332fd9cbd4d715baa6165f5269c9ba2c0b9f1d0c6540dde9c3c')
+    version('1.0.3', sha256='21d0809f46505de89a2be7be9449e39c39cff5bc77e584dec976ee6c0b884f44')
+    version('1.0.2', sha256='c8ec8e24524cc42893e445e01e1a65d15889d28959877cd6b3c5e5f08221b176')
+    version('1.0.1', sha256='9099d37d2f6cc1cab0cd0fdddfb9657c7bd3651226810b496e2808f458c80ae3')
+    version('1.0.0', sha256='ce1e5368ff1d15665ca2db700521a96cf44f0e78daaab68aabbdaf7ed7393b4d')
+
+    depends_on('r-curl', type=('build', 'run'))
+    depends_on('r-xml2@1.0.0:', type=('build', 'run'))

From 7528e1eb455a43877ac71171ccdc118d4926121f Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Tue, 12 May 2020 18:39:39 +0200
Subject: [PATCH 362/802] r-purrr : dependencies and version update (#16566)

* r-purrr : dependencies and version update

* Dependencies updated for condition
---
 var/spack/repos/builtin/packages/r-purrr/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/r-purrr/package.py b/var/spack/repos/builtin/packages/r-purrr/package.py
index da5220dfefa..24e3145aac6 100644
--- a/var/spack/repos/builtin/packages/r-purrr/package.py
+++ b/var/spack/repos/builtin/packages/r-purrr/package.py
@@ -13,11 +13,13 @@ class RPurrr(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/purrr_0.2.4.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/purrr"
 
+    version('0.3.4', sha256='23ebc93bc9aed9e7575e8eb9683ff4acc0270ef7d6436cc2ef4236a9734840b2')
     version('0.3.2', sha256='27c74dd9e4f6f14bf442473df22bcafc068822f7f138f0870326532f143a9a31')
     version('0.3.1', sha256='c2a3c9901192efd8a04976676f84885a005db88deb1432e4750900c7b3b7883b')
     version('0.2.4', sha256='ed8d0f69d29b95c2289ae52be08a0e65f8171abb6d2587de7b57328bf3b2eb71')
 
     depends_on('r@3.1:', type=('build', 'run'))
+    depends_on('r@3.2:', when='@0.3.3:', type=('build', 'run'))
     depends_on('r-magrittr@1.5:', type=('build', 'run'))
     depends_on('r-rlang@0.3.1:', type=('build', 'run'))
     depends_on('r-tibble', when='@:0.2.9', type=('build', 'run'))

From b99a5369ce002a05ad6bc6c2884ab4d89b233b94 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Tue, 12 May 2020 18:40:55 +0200
Subject: [PATCH 363/802] r-roxygen : dependencies and version updated (#16565)

* r-roxygen : dependencies and version updated

* Dependencies updated for condition
---
 var/spack/repos/builtin/packages/r-roxygen2/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/repos/builtin/packages/r-roxygen2/package.py b/var/spack/repos/builtin/packages/r-roxygen2/package.py
index bd129a375e8..66c51eb4879 100644
--- a/var/spack/repos/builtin/packages/r-roxygen2/package.py
+++ b/var/spack/repos/builtin/packages/r-roxygen2/package.py
@@ -14,19 +14,24 @@ class RRoxygen2(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/roxygen2_5.0.1.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/roxygen2"
 
+    version('7.1.0', sha256='7e9b36f6e7c01a5c8c4747340b3d0c064ce2e48c93fcfbfe45139854fae74103')
     version('6.1.1', sha256='ed46b7e062e0dfd8de671c7a5f6d120fb2b720982e918dbeb01e6985694c0273')
     version('5.0.1', sha256='9f755ddd08358be436f08b02df398e50e7508b856131aeeed235099bb3a7eba5')
 
     depends_on('r@3.0.2:', when='@:6.0.1', type=('build', 'run'))
+    depends_on('r@3.2:', when='@7.1.0:', type=('build', 'run'))
     depends_on('r@3.1:', when='@6.1.0:', type=('build', 'run'))
     depends_on('r-brew', type=('build', 'run'))
     depends_on('r-commonmark', type=('build', 'run'))
     depends_on('r-desc@1.2.0:', type=('build', 'run'))
+    depends_on('r-knitr', when='@7.1.0:', type=('build', 'run'))
     depends_on('r-digest', type=('build', 'run'))
     depends_on('r-pkgload@1.0.2:', type=('build', 'run'))
     depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-purrr@0.3.3:', when='@7.1.0:', type=('build', 'run'))
     depends_on('r-r6@2.1.2:', type=('build', 'run'))
     depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
+    depends_on('r-rlang', when='@7.1.0:', type=('build', 'run'))
     depends_on('r-stringi', type=('build', 'run'))
     depends_on('r-stringr@1.0.0:', type=('build', 'run'))
     depends_on('r-xml2', type=('build', 'run'))

From d4c8c8b80d10828d9066fb1e2f58f9713de5c2ca Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Tue, 12 May 2020 18:41:20 +0200
Subject: [PATCH 364/802] r-rematch2 : new package (#16563)

* r-rematch2 : new package

* Updating URL
---
 .../builtin/packages/r-rematch2/package.py    | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-rematch2/package.py

diff --git a/var/spack/repos/builtin/packages/r-rematch2/package.py b/var/spack/repos/builtin/packages/r-rematch2/package.py
new file mode 100644
index 00000000000..2d07db3a234
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rematch2/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRematch2(RPackage):
+    """Wrappers on 'regexpr' and 'gregexpr' to return
+       the match results in tidy data frames.
+    """
+
+    homepage = "https://cloud.r-project.org/package=rematch2"
+    url      = "https://cloud.r-project.org/src/contrib/rematch2_2.1.2.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/rematch2"
+
+    version('2.1.2', sha256='fe9cbfe99dd7731a0a2a310900d999f80e7486775b67f3f8f388c30737faf7bb')
+    version('2.1.1', sha256='d0423a418e8b46ac3a4819af7a7d19c39ca7c8c862c1e9a1c1294aa19152518f')
+    version('2.1.0', sha256='78677071bd44b40e562df1da6f0c6bdeae44caf973f97ff8286b8c994db59f01')
+    version('2.0.1', sha256='0612bb904334bd022ba6d1e69925b1e85f8e86b15ec65476777828776e89609a')
+
+    depends_on('r-tibble')

From bfa707dfc4a6b78adada7218926b6a7d932d2fbb Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Tue, 12 May 2020 18:41:41 +0200
Subject: [PATCH 365/802] new version r-ellipsis (#16556)

* new version r-ellipsis

* r-ellipsis : R dependency updated

* Adding version conditions for dependencies
---
 var/spack/repos/builtin/packages/r-ellipsis/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/r-ellipsis/package.py b/var/spack/repos/builtin/packages/r-ellipsis/package.py
index 4f5349f3e58..3c583459f8c 100644
--- a/var/spack/repos/builtin/packages/r-ellipsis/package.py
+++ b/var/spack/repos/builtin/packages/r-ellipsis/package.py
@@ -16,7 +16,9 @@ class REllipsis(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/ellipsis_0.2.0.1.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/ellipsis"
 
+    version('0.3.0', sha256='0bf814cb7a1f0ee1f2949bdc98752a0d535f2a9489280dd4d8fcdb10067ee907')
     version('0.2.0.1', sha256='0e6528c5e8016c3617cc1cfcdb5a4bfeb073e0bd5ea76b43e56b0c3208a0a943')
 
     depends_on('r@3.1:', type=('build', 'run'))
+    depends_on('r@3.2:', when='@0.3:', type=('build', 'run'))
     depends_on('r-rlang@0.3.0:', type=('build', 'run'))

From 78d8dd08159543ef2bb049033fd9e6197807110b Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Tue, 12 May 2020 18:42:20 +0200
Subject: [PATCH 366/802] new version r-cli (#16553)

* new version r-cli

* r-cli : dependencies updated

* Adding version conditions for dependencies
---
 var/spack/repos/builtin/packages/r-cli/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/r-cli/package.py b/var/spack/repos/builtin/packages/r-cli/package.py
index 7f5cc52a0cc..d8a169c7791 100644
--- a/var/spack/repos/builtin/packages/r-cli/package.py
+++ b/var/spack/repos/builtin/packages/r-cli/package.py
@@ -15,6 +15,7 @@ class RCli(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/cli_1.0.0.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/cli"
 
+    version('2.0.2', sha256='490834e5b80eb036befa0e150996bcab1c4d5d168c3d45209926e52d0d5413b6')
     version('1.1.0', sha256='4fc00fcdf4fdbdf9b5792faee8c7cf1ed5c4f45b1221d961332cda82dbe60d0a')
     version('1.0.1', sha256='ef80fbcde15760fd55abbf9413b306e3971b2a7034ab8c415fb52dc0088c5ee4')
     version('1.0.0', sha256='8fa3dbfc954ca61b8510f767ede9e8a365dac2ef95fe87c715a0f37d721b5a1d')
@@ -22,3 +23,5 @@ class RCli(RPackage):
     depends_on('r@2.10:', type=('build', 'run'))
     depends_on('r-assertthat', type=('build', 'run'))
     depends_on('r-crayon@1.3.4:', type=('build', 'run'))
+    depends_on('r-glue', when='@2:', type=('build', 'run'))
+    depends_on('r-fansi', when='@2:', type=('build', 'run'))

From 154c0f57711dc6e7cd81e2e125bcfb437bdf8d62 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Tue, 12 May 2020 18:42:58 +0200
Subject: [PATCH 367/802] new version r-rcurl (#16550)

* new version r-rcurl

* RCurl dependency R version updated

* Adding version conditions
---
 var/spack/repos/builtin/packages/r-rcurl/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/r-rcurl/package.py b/var/spack/repos/builtin/packages/r-rcurl/package.py
index 4fe4b6454e5..51586cc6915 100644
--- a/var/spack/repos/builtin/packages/r-rcurl/package.py
+++ b/var/spack/repos/builtin/packages/r-rcurl/package.py
@@ -22,9 +22,11 @@ class RRcurl(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/RCurl_1.95-4.8.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/RCurl"
 
+    version('1.98-1.2', sha256='5d74a0cdc3c5684b0348b959f67039e3c2a5da2bbb6176f6800a94124895a7a8')
     version('1.95-4.12', sha256='393779efafdf40823dac942a1e028905d65c34f3d41cfd21bcd225e411385ff4')
     version('1.95-4.8', sha256='e72243251bbbec341bc5864305bb8cc23d311d19c5d0d9310afec7eb35aa2bfb')
 
+    depends_on('r@3.4.0:', when='@1.98:', type=('build', 'run'))
     depends_on('r@3.0.0:', type=('build', 'run'))
     depends_on('r-bitops', type=('build', 'run'))
     depends_on('curl')

From 0307111dd8d562de5de055f6a50c4352f0fb28a5 Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Tue, 12 May 2020 10:23:42 -0700
Subject: [PATCH 368/802] bugfix: reorder variants in Spec strings (#16462)

* change print order for variants to avoid zsh parsing bugs

* change tests for new variant parse order
---
 lib/spack/spack/test/spec_syntax.py |  4 ++--
 lib/spack/spack/test/variant.py     |  2 +-
 lib/spack/spack/variant.py          | 29 ++++++++++++++---------------
 3 files changed, 17 insertions(+), 18 deletions(-)

diff --git a/lib/spack/spack/test/spec_syntax.py b/lib/spack/spack/test/spec_syntax.py
index a5f7b6fdb01..688c89022cb 100644
--- a/lib/spack/spack/test/spec_syntax.py
+++ b/lib/spack/spack/test/spec_syntax.py
@@ -177,7 +177,7 @@ def test_full_specs(self):
             " ^stackwalker@8.1_1e")
         self.check_parse(
             "mvapich_foo"
-            " ^_openmpi@1.2:1.4,1.6%intel@12.1 debug=2 ~qt_4"
+            " ^_openmpi@1.2:1.4,1.6%intel@12.1~qt_4 debug=2"
             " ^stackwalker@8.1_1e")
         self.check_parse(
             'mvapich_foo'
@@ -185,7 +185,7 @@ def test_full_specs(self):
             ' ^stackwalker@8.1_1e')
         self.check_parse(
             "mvapich_foo"
-            " ^_openmpi@1.2:1.4,1.6%intel@12.1 debug=2 ~qt_4"
+            " ^_openmpi@1.2:1.4,1.6%intel@12.1~qt_4 debug=2"
             " ^stackwalker@8.1_1e arch=test-redhat6-x86")
 
     def test_canonicalize(self):
diff --git a/lib/spack/spack/test/variant.py b/lib/spack/spack/test/variant.py
index d1657b71b73..10e8ea7e7fa 100644
--- a/lib/spack/spack/test/variant.py
+++ b/lib/spack/spack/test/variant.py
@@ -694,7 +694,7 @@ def test_str(self):
         c['foobar'] = SingleValuedVariant('foobar', 'fee')
         c['feebar'] = SingleValuedVariant('feebar', 'foo')
         c['shared'] = BoolValuedVariant('shared', True)
-        assert str(c) == ' feebar=foo foo=bar,baz foobar=fee +shared'
+        assert str(c) == '+shared feebar=foo foo=bar,baz foobar=fee'
 
 
 def test_disjoint_set_initialization_errors():
diff --git a/lib/spack/spack/variant.py b/lib/spack/spack/variant.py
index 3915fe00fa5..0443b68ec30 100644
--- a/lib/spack/spack/variant.py
+++ b/lib/spack/spack/variant.py
@@ -567,25 +567,24 @@ def __str__(self):
         # print keys in order
         sorted_keys = sorted(self.keys())
 
+        # Separate boolean variants from key-value pairs as they print
+        # differently. All booleans go first to avoid ' ~foo' strings that
+        # break spec reuse in zsh.
+        bool_keys = []
+        kv_keys = []
+        for key in sorted_keys:
+            bool_keys.append(key) if isinstance(self[key].value, bool) \
+                else kv_keys.append(key)
+
         # add spaces before and after key/value variants.
         string = StringIO()
 
-        kv = False
-        for key in sorted_keys:
-            vspec = self[key]
+        for key in bool_keys:
+            string.write(str(self[key]))
 
-            if not isinstance(vspec.value, bool):
-                # add space before all kv pairs.
-                string.write(' ')
-                kv = True
-            else:
-                # not a kv pair this time
-                if kv:
-                    # if it was LAST time, then pad after.
-                    string.write(' ')
-                kv = False
-
-            string.write(str(vspec))
+        for key in kv_keys:
+            string.write(' ')
+            string.write(str(self[key]))
 
         return string.getvalue()
 

From 9bdf4564dbf1276881a1e25bb26f9ea42e606346 Mon Sep 17 00:00:00 2001
From: Nick Booher <njbooher@iastate.edu>
Date: Tue, 12 May 2020 14:26:44 -0500
Subject: [PATCH 369/802] revbayes: update for 1.1.0 (#16603)

* revbayes: update for 1.1.0

* revbayes: Fix flake8
---
 .../builtin/packages/revbayes/package.py      | 28 +++++++++++++------
 1 file changed, 20 insertions(+), 8 deletions(-)

diff --git a/var/spack/repos/builtin/packages/revbayes/package.py b/var/spack/repos/builtin/packages/revbayes/package.py
index 5e02dc974da..e419d17c55f 100644
--- a/var/spack/repos/builtin/packages/revbayes/package.py
+++ b/var/spack/repos/builtin/packages/revbayes/package.py
@@ -11,10 +11,11 @@ class Revbayes(CMakePackage):
        and an interpreted language."""
 
     homepage = "https://revbayes.github.io"
-    url      = "https://github.com/revbayes/revbayes/archive/v1.0.11.tar.gz"
+    url      = "https://github.com/revbayes/revbayes/archive/1.1.0.tar.gz"
     git      = "https://github.com/revbayes/revbayes.git"
 
     version('develop', branch='development')
+    version('1.1.0', sha256='6adede8148cb10e4e75dba8da28cf5c747ea8de71a5aa24990ab9ae17e43b0b1')
     version('1.0.13', sha256='e85e2e1fe182fe9f504900150d936a06d252a362c591b9d3d8272dd085aa85d9')
     version('1.0.12', sha256='80c926bb6b37288d02e36e07b44e4663841cd1fe541e2cc0b0e44c89ca929759')
     version('1.0.11', sha256='03052194baa220dde7e622a739f09f34393f67ea00a0b163b409d313d7fc7c02')
@@ -29,17 +30,27 @@ class Revbayes(CMakePackage):
 
     def url_for_version(self, version):
         if version > Version('1.0.13'):
-            return 'https://github.com/revbayes/revbayes/archive/v{0}.tar.gz'.format(version)
+            return 'https://github.com/revbayes/revbayes/archive/{0}.tar.gz'.format(version)
         else:
             return 'https://github.com/revbayes/revbayes.archive/archive/v{0}.tar.gz'.format(version)
 
     @property
     def root_cmakelists_dir(self):
-        if self.spec.version > Version('1.0.13') and '+mpi' in self.spec:
-            return 'projects/cmake/build-mpi'
+        if self.spec.version > Version('1.0.13'):
+            return 'src'
         else:
             return 'projects/cmake/build'
 
+    @when('@1.1.0:')
+    def cmake_args(self):
+        args = []
+        if '+mpi' in self.spec:
+            args.extend([
+                self.define('MPI', 'ON'),
+                self.define('RB_EXEC_NAME', 'rb-mpi'),
+            ])
+        return args
+
     @run_before('cmake')
     def regenerate(self):
         with working_dir(join_path('projects', 'cmake')):
@@ -49,10 +60,11 @@ def regenerate(self):
                 generate_version()
                 dest = join_path('..', '..', 'src', 'revlanguage', 'utils')
                 install('GitVersion.cpp', dest)
-            edit = FileFilter('regenerate.sh')
-            edit.filter('boost="true"', 'boost="false"')
-            if '+mpi' in self.spec:
-                edit.filter('mpi="false"', 'mpi="true"')
+            else:
+                edit = FileFilter('regenerate.sh')
+                edit.filter('boost="true"', 'boost="false"')
+                if '+mpi' in self.spec:
+                    edit.filter('mpi="false"', 'mpi="true"')
             regenerate = Executable('./regenerate.sh')
             regenerate()
 

From 6b41fb88a988cf35099ea5f5ecf7a3b42a5d7e1b Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 12 May 2020 14:33:10 -0500
Subject: [PATCH 370/802] py-threadpoolctl: add new package (#16606)

---
 .../packages/py-threadpoolctl/package.py      | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-threadpoolctl/package.py

diff --git a/var/spack/repos/builtin/packages/py-threadpoolctl/package.py b/var/spack/repos/builtin/packages/py-threadpoolctl/package.py
new file mode 100644
index 00000000000..f28c9a37b52
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-threadpoolctl/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class PyThreadpoolctl(PythonPackage):
+    """Python helpers to limit the number of threads used in the
+    threadpool-backed of common native libraries used for scientific
+    computing and data science (e.g. BLAS and OpenMP)."""
+
+    homepage = "https://github.com/joblib/threadpoolctl"
+    url      = "https://pypi.io/packages/source/t/threadpoolctl/threadpoolctl-2.0.0.tar.gz"
+
+    import_modules = ['threadpoolctl']
+
+    version('2.0.0', sha256='48b3e3e9ee079d6b5295c65cbe255b36a3026afc6dde3fb49c085cd0c004bbcf')
+
+    depends_on('python@3.5:', type=('build', 'run'))

From 11fa61665f2c921d6c9af82d9556e2985a2f3bd4 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Tue, 12 May 2020 22:56:01 +0200
Subject: [PATCH 371/802] travis: use bionic as default for Linux (#16521)

Modifications:

- [x] Travis now uses `bionic` as a default (`xenial` used for Python 3.5, `trusty` for Python 2.6)
- [x] Shell unit tests have been factored into their own run
- [x] `kcov` is built only for tests that upload coverage results

Overall with this we shave 3-4 mins. on each run and add an additional run of about 3 min. For some reason `kcov` 38 fails forwarding output when used with Python unit tests, so I used v34 for that and v38 (latest) for shell testing. Previously we were using v25.
---
 .travis.yml                    | 40 +++++++++++++++++--------------
 share/spack/qa/run-shell-tests | 43 ++++++++++++++++++++++++++++++++++
 share/spack/qa/run-unit-tests  | 25 --------------------
 3 files changed, 66 insertions(+), 42 deletions(-)
 create mode 100755 share/spack/qa/run-shell-tests

diff --git a/.travis.yml b/.travis.yml
index 9e2a7973935..8107ad876d8 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -12,7 +12,7 @@ branches:
 # Build matrix
 #=============================================================================
 
-dist: xenial
+dist: bionic
 
 jobs:
   fast_finish: true
@@ -32,27 +32,22 @@ jobs:
           # Everything but patchelf, that is not available for trusty
           packages:
             - ccache
-            - cmake
             - gfortran
             - graphviz
             - gnupg2
             - kcov
             - mercurial
             - ninja-build
-            - perl
-            - perl-base
             - realpath
-            - r-base
-            - r-base-core
-            - r-base-dev
             - zsh
       env: [ TEST_SUITE=unit, COVERAGE=true ]
     - python: '2.7'
       os: linux
       language: python
-      env: [ TEST_SUITE=unit, COVERAGE=true ]
+      env: [ TEST_SUITE=unit, COVERAGE=true, KCOV_VERSION=34 ]
     - python: '3.5'
       os: linux
+      dist: xenial
       language: python
       env: TEST_SUITE=unit
     - python: '3.6'
@@ -66,7 +61,11 @@ jobs:
     - python: '3.8'
       os: linux
       language: python
-      env: [ TEST_SUITE=unit, COVERAGE=true ]
+      env: [ TEST_SUITE=unit, COVERAGE=true, KCOV_VERSION=34 ]
+    - python: '3.8'
+      os: linux
+      language: python
+      env: [ TEST_SUITE=shell, COVERAGE=true, KCOV_VERSION=38 ]
     - python: '3.8'
       os: linux
       language: python
@@ -87,20 +86,13 @@ addons:
   apt:
     packages:
       - ccache
-      - cmake
+      - coreutils
       - gfortran
       - graphviz
       - gnupg2
-      - kcov
       - mercurial
       - ninja-build
       - patchelf
-      - perl
-      - perl-base
-      - realpath
-      - r-base
-      - r-base-core
-      - r-base-dev
       - zsh
     update: true
 
@@ -114,6 +106,16 @@ cache:
 
 before_install:
   - ccache -M 2G && ccache -z
+  # Install kcov manually, since it's not packaged for bionic beaver
+  - if [[ "$KCOV_VERSION" ]]; then
+        sudo apt-get -y install cmake binutils-dev libcurl4-openssl-dev zlib1g-dev libdw-dev libiberty-dev;
+        KCOV_ROOT=$(mktemp -d);
+        wget --output-document=${KCOV_ROOT}/${KCOV_VERSION}.tar.gz https://github.com/SimonKagstrom/kcov/archive/v${KCOV_VERSION}.tar.gz;
+        tar -C ${KCOV_ROOT} -xzvf ${KCOV_ROOT}/${KCOV_VERSION}.tar.gz;
+        mkdir -p ${KCOV_ROOT}/build;
+        cd ${KCOV_ROOT}/build && cmake -Wno-dev ${KCOV_ROOT}/kcov-${KCOV_VERSION} && cd - ;
+        make -C ${KCOV_ROOT}/build && sudo  make -C ${KCOV_ROOT}/build install;
+    fi
 
 # Install various dependencies
 install:
@@ -151,6 +153,10 @@ after_success:
                         --flags "${TEST_SUITE}${TRAVIS_OS_NAME}";
             fi
             ;;
+        shell)
+            codecov --env PYTHON_VERSION
+            --required
+            --flags "${TEST_SUITE}${TRAVIS_OS_NAME}";
     esac
 
 #=============================================================================
diff --git a/share/spack/qa/run-shell-tests b/share/spack/qa/run-shell-tests
new file mode 100755
index 00000000000..31c1c1548b1
--- /dev/null
+++ b/share/spack/qa/run-shell-tests
@@ -0,0 +1,43 @@
+#!/bin/bash -e
+#
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
+# Description:
+#     Runs Spack shell tests.
+#
+# Usage:
+#     run-shell-tests
+
+#-----------------------------------------------------------
+# Run a few initial commands and set up test environment
+#-----------------------------------------------------------
+ORIGINAL_PATH="$PATH"
+
+. "$(dirname $0)/setup.sh"
+check_dependencies $coverage git hg svn
+
+# Clean the environment by removing Spack from the path and getting rid of
+# the spack shell function
+export PATH="$ORIGINAL_PATH"
+unset spack
+
+# Start in the spack root directory
+cd "$SPACK_ROOT"
+
+# Run bash tests with coverage enabled, but pipe output to /dev/null
+# because it seems that kcov seems to undo the script's redirection
+if [ "$COVERAGE" = true ]; then
+    "$QA_DIR/bashcov" "$QA_DIR/setup-env-test.sh" &> /dev/null
+    "$QA_DIR/bashcov" "$QA_DIR/completion-test.sh" &> /dev/null
+else
+    bash "$QA_DIR/setup-env-test.sh"
+    bash "$QA_DIR/completion-test.sh"
+fi
+
+# Run the test scripts for their output (these will print nicely)
+zsh  "$QA_DIR/setup-env-test.sh"
+dash "$QA_DIR/setup-env-test.sh"
diff --git a/share/spack/qa/run-unit-tests b/share/spack/qa/run-unit-tests
index 4bd04bcbb98..7c4abb14130 100755
--- a/share/spack/qa/run-unit-tests
+++ b/share/spack/qa/run-unit-tests
@@ -47,28 +47,3 @@ fi
 # Run unit tests with code coverage
 #-----------------------------------------------------------
 $coverage_run $(which spack) test -x --verbose
-
-#-----------------------------------------------------------
-# Run tests for setup-env.sh
-#-----------------------------------------------------------
-# Clean the environment by removing Spack from the path and getting rid of
-# the spack shell function
-export PATH="$ORIGINAL_PATH"
-unset spack
-
-# start in the spack root directory
-cd "$SPACK_ROOT"
-
-# Run bash tests with coverage enabled, but pipe output to /dev/null
-# because it seems that kcov seems to undo the script's redirection
-if [ "$BASH_COVERAGE" = true ]; then
-    "$QA_DIR/bashcov" "$QA_DIR/setup-env-test.sh" &> /dev/null
-    "$QA_DIR/bashcov" "$QA_DIR/completion-test.sh" &> /dev/null
-fi
-
-# run the test scripts for their output (these will print nicely)
-bash "$QA_DIR/setup-env-test.sh"
-zsh  "$QA_DIR/setup-env-test.sh"
-dash "$QA_DIR/setup-env-test.sh"
-
-bash "$QA_DIR/completion-test.sh"

From 1d76067d7a38068f16822fe421c697084e5ce1c7 Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Tue, 12 May 2020 16:43:43 -0500
Subject: [PATCH 372/802] zstd: add 1.4.4 (#16608)

---
 var/spack/repos/builtin/packages/zstd/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/zstd/package.py b/var/spack/repos/builtin/packages/zstd/package.py
index 8cc37ab3d52..901b02b278c 100644
--- a/var/spack/repos/builtin/packages/zstd/package.py
+++ b/var/spack/repos/builtin/packages/zstd/package.py
@@ -14,6 +14,7 @@ class Zstd(MakefilePackage):
     homepage = "http://facebook.github.io/zstd/"
     url      = "https://github.com/facebook/zstd/archive/v1.4.3.tar.gz"
 
+    version('1.4.4', sha256='a364f5162c7d1a455cc915e8e3cf5f4bd8b75d09bc0f53965b0c9ca1383c52c8')
     version('1.4.3', sha256='5eda3502ecc285c3c92ee0cc8cd002234dee39d539b3f692997a0e80de1d33de')
     version('1.4.2', sha256='7a6e1dad34054b35e2e847eb3289be8820a5d378228802239852f913c6dcf6a7')
     version('1.4.0', sha256='63be339137d2b683c6d19a9e34f4fb684790e864fee13c7dd40e197a64c705c1')

From b4e587bd0b8f489eb367c83225c1a2fe67292444 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 12 May 2020 16:43:56 -0500
Subject: [PATCH 373/802] py-scikit-learn: add new version (#16607)

---
 .../repos/builtin/packages/py-scikit-learn/package.py    | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-scikit-learn/package.py b/var/spack/repos/builtin/packages/py-scikit-learn/package.py
index 4c717e20eef..9d3fa4ff2c2 100644
--- a/var/spack/repos/builtin/packages/py-scikit-learn/package.py
+++ b/var/spack/repos/builtin/packages/py-scikit-learn/package.py
@@ -3,14 +3,12 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-from spack import *
-
 
 class PyScikitLearn(PythonPackage):
     """A set of python modules for machine learning and data mining."""
 
     homepage = "https://pypi.python.org/pypi/scikit-learn"
-    url      = "https://pypi.io/packages/source/s/scikit-learn/scikit-learn-0.22.tar.gz"
+    url      = "https://pypi.io/packages/source/s/scikit-learn/scikit-learn-0.23.0.tar.gz"
     git      = "https://github.com/scikit-learn/scikit-learn.git"
 
     maintainers = ['adamjstewart']
@@ -33,6 +31,7 @@ class PyScikitLearn(PythonPackage):
     ]
 
     version('master', branch='master')
+    version('0.23.0', sha256='639a53df6273acc6a7510fb0c658b94e0c70bb13dafff9d14932c981ff9baff4')
     version('0.22.1', sha256='51ee25330fc244107588545c70e2f3570cfc4017cff09eed69d6e1d82a212b7d')
     version('0.22',   sha256='314abf60c073c48a1e95feaae9f3ca47a2139bd77cebb5b877c23a45c9e03012')
     version('0.21.3', sha256='eb9b8ebf59eddd8b96366428238ab27d05a19e89c5516ce294abc35cea75d003')
@@ -53,13 +52,17 @@ class PyScikitLearn(PythonPackage):
     depends_on('python@2.6:2.8,3.3:', when='@:0.19', type=('build', 'run'))
     depends_on('python@2.7:2.8,3.4:', when='@0.20.0:0.20.999', type=('build', 'run'))
     depends_on('python@3.5:', when='@0.21:', type=('build', 'run'))
+    depends_on('python@3.6:', when='@0.23:', type=('build', 'run'))
     depends_on('py-numpy@1.6.1:', when='@:0.19', type=('build', 'run'))
     depends_on('py-numpy@1.8.2:', when='@0.20.0:0.20.999', type=('build', 'run'))
     depends_on('py-numpy@1.11.0:', when='@0.21:', type=('build', 'run'))
+    depends_on('py-numpy@1.13.3:', when='@0.23:', type=('build', 'run'))
     depends_on('py-scipy@0.9:', when='@:0.19', type=('build', 'run'))
     depends_on('py-scipy@0.13.3:', when='@0.20.0:0.20.999', type=('build', 'run'))
     depends_on('py-scipy@0.17.0:', when='@0.21:', type=('build', 'run'))
+    depends_on('py-scipy@0.19.1:', when='@0.23:', type=('build', 'run'))
     depends_on('py-joblib@0.11:', type=('build', 'run'))
+    depends_on('py-threadpoolctl@2.0.0:', when='@0.23:', type=('build', 'run'))
     depends_on('py-cython@0.23:', type='build')
     depends_on('py-cython@0.28.5:', when='@0.21:', type='build')
     depends_on('py-pytest@3.3.0:', type='test')

From ab924079404a918a97c3d8d86dfe67f43466591b Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Wed, 13 May 2020 00:05:01 +0200
Subject: [PATCH 374/802] r-testthat : dependencies and version updated
 (#16576)

* r-testthat : dependencies and version updated

* Adding version conditions for dependencies

* r-testthat: Fix dependecies condition
---
 var/spack/repos/builtin/packages/r-testthat/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/r-testthat/package.py b/var/spack/repos/builtin/packages/r-testthat/package.py
index e0712387bde..413aa0d63b7 100644
--- a/var/spack/repos/builtin/packages/r-testthat/package.py
+++ b/var/spack/repos/builtin/packages/r-testthat/package.py
@@ -14,17 +14,21 @@ class RTestthat(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/testthat_1.0.2.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/testthat"
 
+    version('2.3.2', sha256='1a268d8df07f7cd8d282d03bb96ac2d96a24a95c9aa52f4cca5138a09dd8e06c')
     version('2.2.1', sha256='67ee0512bb312695c81fd74338bb8ce9e2e58763681ddbcdfdf35f52dfdb0b78')
     version('2.1.0', sha256='cf5fa7108111b32b86e70819352f86b57ab4e835221bb1e83642d52a1fdbcdd4')
     version('1.0.2', sha256='0ef7df0ace1fddf821d329f9d9a5d42296085350ae0d94af62c45bd203c8415e')
 
     depends_on('r@3.1:', type=('build', 'run'))
     depends_on('r-digest', type=('build', 'run'))
+    depends_on('r-ellipsis', when='@2.3.2:', type=('build', 'run'))
+    depends_on('r-pkgload', when='@2.3.2:', type=('build', 'run'))
     depends_on('r-crayon@1.3.4:', type=('build', 'run'))
     depends_on('r-praise', type=('build', 'run'))
     depends_on('r-magrittr', type=('build', 'run'))
     depends_on('r-r6@2.2.0:', type=('build', 'run'))
     depends_on('r-cli', when='@2.0.0:', type=('build', 'run'))
     depends_on('r-rlang@0.3.0:', when='@2.0.0:', type=('build', 'run'))
+    depends_on('r-rlang@0.4.1:', when='@2.3.2:', type=('build', 'run'))
     depends_on('r-withr@2.0.0:', when='@2.0.0:', type=('build', 'run'))
     depends_on('r-evaluate', when='@2.2.0:', type=('build', 'run'))

From 0f2a58127663ab58ee4416f1b57a2c380ef1ef71 Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Tue, 12 May 2020 17:05:19 -0500
Subject: [PATCH 375/802] velvetoptimiser: new package at 2.2.6 (#16611)

---
 .../packages/velvetoptimiser/package.py       | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/velvetoptimiser/package.py

diff --git a/var/spack/repos/builtin/packages/velvetoptimiser/package.py b/var/spack/repos/builtin/packages/velvetoptimiser/package.py
new file mode 100644
index 00000000000..8a71bb6ad06
--- /dev/null
+++ b/var/spack/repos/builtin/packages/velvetoptimiser/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Velvetoptimiser(Package):
+    """Automatically optimise three of Velvet's assembly parameters."""
+
+    homepage = "https://github.com/tseemann/VelvetOptimiser"
+    url      = "https://github.com/tseemann/VelvetOptimiser/archive/2.2.6.tar.gz"
+
+    version('2.2.6', sha256='b407db61b58ed983760b80a3a40c8f8a355851ecfab3e61a551bed29bf5b40b3')
+
+    depends_on('velvet@1.1:', type='run')
+    depends_on('perl@5.8.8:', type='run')
+    depends_on('perl-bioperl@1.4:', type='run')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)

From f43b7824caf2a699b20b94f10dca2d23be38c6b9 Mon Sep 17 00:00:00 2001
From: Pariksheet Nanda <pariksheet.nanda@uconn.edu>
Date: Tue, 12 May 2020 18:06:18 -0400
Subject: [PATCH 376/802] py-plotly: unfix dependency versions (fixes #16544)
 (#16546)

* py-plotly: unfix dependency versions (fixes #16544)

* py-plotly: add missing dependencies for #16546

* py-plotly: match setup.py instead of requirements.txt for #16546
---
 var/spack/repos/builtin/packages/py-plotly/package.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-plotly/package.py b/var/spack/repos/builtin/packages/py-plotly/package.py
index 72a0727be51..7a62596eeae 100644
--- a/var/spack/repos/builtin/packages/py-plotly/package.py
+++ b/var/spack/repos/builtin/packages/py-plotly/package.py
@@ -15,6 +15,8 @@ class PyPlotly(PythonPackage):
     version('2.2.0', sha256='ca668911ffb4d11fed6d7fbb12236f8ecc6a7209db192326bcb64bdb41451a58')
 
     depends_on('py-setuptools', type='build')
-    depends_on('py-requests@2.3.0', type=('build', 'run'))
-    depends_on('py-six@1.8.0', type=('build', 'run'))
-    depends_on('py-pytz@2014.9', type=('build', 'run'))
+    depends_on('py-decorator@4.0.6:', type=('build', 'run'))
+    depends_on('py-nbformat@4.2.0:', type=('build', 'run'))
+    depends_on('py-requests', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-pytz', type=('build', 'run'))

From fdf38ec991ceb4059590e7a769fc11db4458aa0f Mon Sep 17 00:00:00 2001
From: Chris White <white238@llnl.gov>
Date: Tue, 12 May 2020 16:57:25 -0700
Subject: [PATCH 377/802] Fix axom install target (#16613)

---
 var/spack/repos/builtin/packages/axom/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/axom/package.py b/var/spack/repos/builtin/packages/axom/package.py
index 84eeac28b93..46b411b4e7a 100644
--- a/var/spack/repos/builtin/packages/axom/package.py
+++ b/var/spack/repos/builtin/packages/axom/package.py
@@ -512,4 +512,4 @@ def cmake_args(self):
 
     @run_after('install')
     def install_cmake_cache(self):
-        install(self._get_host_config_path(spec), prefix)
+        install(self._get_host_config_path(self.spec), prefix)

From 701fc1fdb15253f771aeec330a66b992d8c55dce Mon Sep 17 00:00:00 2001
From: Peter Scheibel <scheibel1@llnl.gov>
Date: Tue, 12 May 2020 17:08:08 -0700
Subject: [PATCH 378/802] Update docs on "spack external find" (#16482)

This improves the documentation for `spack external find` in several ways:

* Provide a code example of implementing `determine_spec_details` for a package
* Explain how to define executables to look for (and also e.g. that they are treated as regular expressions and so can pull in unexpected files).
* Add the "why" for a couple of constraints (i.e. explain that this logic only works for build/run deps because it examines `PATH` for executables)
* Spread the docs between build customization and packaging sections
* Add cross-references
* Add a label so that `spack external find` is linked from the command reference.
---
 lib/spack/docs/build_settings.rst  | 24 +++++++----
 lib/spack/docs/packaging_guide.rst | 64 ++++++++++++++++++++++++++++++
 2 files changed, 80 insertions(+), 8 deletions(-)

diff --git a/lib/spack/docs/build_settings.rst b/lib/spack/docs/build_settings.rst
index dee892f272f..9f67d8c14f5 100644
--- a/lib/spack/docs/build_settings.rst
+++ b/lib/spack/docs/build_settings.rst
@@ -158,11 +158,13 @@ Spack can then use any of the listed external implementations of MPI
 to satisfy a dependency, and will choose depending on the compiler and
 architecture.
 
+.. _cmd-spack-external-find:
+
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Automatically Find External Packages
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-A user can run the :ref:`spack external find <spack-external-find>` command
+You can run the :ref:`spack external find <spack-external-find>` command
 to search for system-provided packages and add them to ``packages.yaml``.
 After running this command your ``packages.yaml`` may include new entries:
 
@@ -177,17 +179,23 @@ Generally this is useful for detecting a small set of commonly-used packages;
 for now this is generally limited to finding build-only dependencies.
 Specific limitations include:
 
-* A package must define ``executables`` and ``determine_spec_details``
-  for Spack to locate instances of that package.
-* This is currently intended to find build dependencies rather than
-  library packages.
+* Packages are not discoverable by default: For a package to be
+  discoverable with ``spack external find``, it needs to add special
+  logic. See :ref:`here <make-package-findable>` for more details.
+* The current implementation only collects and examines executable files,
+  so it is typically only useful for build/run dependencies (in some cases
+  if a library package also provides an executable, it may be possible to
+  extract a meaningful Spec by running the executable - for example the
+  compiler wrappers in MPI implementations).
+* The logic does not search through module files, it can only detect
+  packages with executables defined in ``PATH``; you can help Spack locate
+  externals which use module files by loading any associated modules for
+  packages that you want Spack to know about before running
+  ``spack external find``.
 * Spack does not overwrite existing entries in the package configuration:
   If there is an external defined for a spec at any configuration scope,
   then Spack will not add a new external entry (``spack config blame packages``
   can help locate all external entries).
-* Currently this logic is focused on examining ``PATH`` and does not
-  search through modules (although it should find the package if a
-  module is loaded for it).
 
 .. _concretization-preferences:
 
diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index 7abadaac820..840c29454b9 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -4048,6 +4048,70 @@ File functions
 :py:func:`touch(path) <spack.touch>`
   Create an empty file at ``path``.
 
+.. _make-package-findable:
+
+----------------------------------------------------------
+Making a package discoverable with ``spack external find``
+----------------------------------------------------------
+
+To make a package discoverable with
+:ref:`spack external find <cmd-spack-external-find>` you must
+define one or more executables associated with the package and must
+implement a method to generate a Spec when given an executable.
+
+The executables are specified as a package level ``executables``
+attribute which is a list of strings (see example below); each string
+is treated as a regular expression (e.g. 'gcc' would match 'gcc', 'gcc-8.3',
+'my-weird-gcc', etc.).
+
+The method ``determine_spec_details`` has the following signature:
+
+.. code-block:: python
+
+   def determine_spec_details(prefix, exes_in_prefix):
+       # exes_in_prefix = a set of paths, each path is an executable
+       # prefix = a prefix that is common to each path in exes_in_prefix
+
+       # return None or [] if none of the exes represent an instance of
+       # the package. Return one or more Specs for each instance of the
+       # package which is thought to be installed in the provided prefix
+
+``determine_spec_details`` takes as parameters a set of discovered
+executables (which match those specified by the user) as well as a
+common prefix shared by all of those executables. The function must
+return one or more Specs associated with the executables (it can also
+return ``None`` to indicate that no provided executables are associated
+with the package).
+
+Say for example we have a package called ``foo-package`` which
+builds an executable called ``foo``. ``FooPackage`` would appear as
+follows:
+
+.. code-block:: python
+
+   class FooPackage(Package):
+       homepage = "..."
+       url = "..."
+
+       version(...)
+
+       # Each string provided here is treated as a regular expression, and
+       # would match for example 'foo', 'foobar', and 'bazfoo'.
+       executables = ['foo']
+
+       @classmethod
+       def determine_spec_details(cls, prefix, exes_in_prefix):
+           candidates = list(x for x in exes_in_prefix
+                             if os.path.basename(x) == 'foo')
+           if not candidates:
+               return
+           # This implementation is lazy and only checks the first candidate
+           exe_path = candidates[0]
+           exe = spack.util.executable.Executable(exe_path)
+           output = exe('--version')
+           version_str = ...  # parse output for version string
+           return Spec('foo-package@{0}'.format(version_str))
+
 .. _package-lifecycle:
 
 -----------------------------

From aaf3388cfe8cf271aa925b72e4126ee2deade927 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Wed, 13 May 2020 14:53:49 +0200
Subject: [PATCH 379/802] esmf: fix build with gcc@10: (#16622)

---
 var/spack/repos/builtin/packages/esmf/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/esmf/package.py b/var/spack/repos/builtin/packages/esmf/package.py
index d63af514ff3..b533851228f 100644
--- a/var/spack/repos/builtin/packages/esmf/package.py
+++ b/var/spack/repos/builtin/packages/esmf/package.py
@@ -146,6 +146,9 @@ def edit(self, spec, prefix):
             # Build an optimized version of the library.
             os.environ['ESMF_BOPT'] = 'O'
 
+        if self.spec.satisfies('%gcc@10:'):
+            os.environ['ESMF_F90COMPILEOPTS'] = '-fallow-argument-mismatch'
+
         #######
         # MPI #
         #######

From b4052eb3b89d00942e1bfd3fae1d2c8b37205663 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Wed, 13 May 2020 14:57:12 +0200
Subject: [PATCH 380/802] tcsh: fix build with gcc@10: (#16621)

---
 .../repos/builtin/packages/tcsh/package.py    | 21 ++++++++++---------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/var/spack/repos/builtin/packages/tcsh/package.py b/var/spack/repos/builtin/packages/tcsh/package.py
index 90625e352d2..7cdd8bb4120 100644
--- a/var/spack/repos/builtin/packages/tcsh/package.py
+++ b/var/spack/repos/builtin/packages/tcsh/package.py
@@ -27,16 +27,17 @@ def fedora_patch(commit, file, **kwargs):  # noqa
         patch('{0}{1}'.format(prefix, file), **kwargs)
 
     # Upstream patches
-    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-000-add-all-flags-for-gethost-build.patch',       when='@6.20.00', sha256='f8266916189ebbdfbad5c2c28ac00ed25f07be70f054d9830eb84ba84b3d03ef')
-    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-001-delay-arginp-interpreting.patch',             when='@6.20.00', sha256='57c7a9b0d94dd41e4276b57b0a4a89d91303d36180c1068b9e3ab8f6149b18dd')
-    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-002-type-of-read-in-prompt-confirm.patch',        when='@6.20.00', sha256='837a6a82f815c0905cf7ea4c4ef0112f36396fc8b2138028204000178a1befa5')
-    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-003-fix-out-of-bounds-read.patch',                when='@6.20.00', sha256='f973bd33a7fd8af0002a9b8992216ffc04fdf2927917113e42e58f28b702dc14')
-    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-004-do-not-use-old-pointer-tricks.patch',         when='@6.20.00', sha256='333e111ed39f7452f904590b47b996812590b8818f1c51ad68407dc05a1b18b0')
-    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-005-reset-fixes-numbering.patch',                 when='@6.20.00', sha256='d1b54b5c5432faed9791ffde813560e226896a68fc5933d066172bcf3b2eb8bd')
-    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-006-cleanup-in-readme-files.patch',               when='@6.20.00', sha256='b4e7428ac6c2918beacc1b73f33e784ac520ef981d87e98285610b1bfa299d7b')
-    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-007-look-for-tgetent-in-libtinfo.patch',          when='@6.20.00', sha256='e6c88ffc291c9d4bda4d6bedf3c9be89cb96ce7dc245163e251345221fa77216')
-    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-008-guard-ascii-only-reversion.patch',            when='@6.20.00', sha256='7ee195e4ce4c9eac81920843b4d4d27254bec7b43e0b744f457858a9f156e621')
-    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-009-fix-regexp-for-backlash-quoting-tests.patch', when='@6.20.00', sha256='d2358c930d5ab89e5965204dded499591b42a22d0a865e2149b8c0f1446fac34')
+    fedora_patch('96b95844cc685b11ed0cc215137e394da4505d41', 'tcsh-6.22.02-avoid-gcc-to-fail.patch',                         when='@:6.22.02', sha256='392615011adb7afeb0010152409a37b150f03dbde5b534503e9cd7363b742a19')
+    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-000-add-all-flags-for-gethost-build.patch',       when='@6.20.00',  sha256='f8266916189ebbdfbad5c2c28ac00ed25f07be70f054d9830eb84ba84b3d03ef')
+    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-001-delay-arginp-interpreting.patch',             when='@6.20.00',  sha256='57c7a9b0d94dd41e4276b57b0a4a89d91303d36180c1068b9e3ab8f6149b18dd')
+    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-002-type-of-read-in-prompt-confirm.patch',        when='@6.20.00',  sha256='837a6a82f815c0905cf7ea4c4ef0112f36396fc8b2138028204000178a1befa5')
+    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-003-fix-out-of-bounds-read.patch',                when='@6.20.00',  sha256='f973bd33a7fd8af0002a9b8992216ffc04fdf2927917113e42e58f28b702dc14')
+    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-004-do-not-use-old-pointer-tricks.patch',         when='@6.20.00',  sha256='333e111ed39f7452f904590b47b996812590b8818f1c51ad68407dc05a1b18b0')
+    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-005-reset-fixes-numbering.patch',                 when='@6.20.00',  sha256='d1b54b5c5432faed9791ffde813560e226896a68fc5933d066172bcf3b2eb8bd')
+    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-006-cleanup-in-readme-files.patch',               when='@6.20.00',  sha256='b4e7428ac6c2918beacc1b73f33e784ac520ef981d87e98285610b1bfa299d7b')
+    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-007-look-for-tgetent-in-libtinfo.patch',          when='@6.20.00',  sha256='e6c88ffc291c9d4bda4d6bedf3c9be89cb96ce7dc245163e251345221fa77216')
+    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-008-guard-ascii-only-reversion.patch',            when='@6.20.00',  sha256='7ee195e4ce4c9eac81920843b4d4d27254bec7b43e0b744f457858a9f156e621')
+    fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-009-fix-regexp-for-backlash-quoting-tests.patch', when='@6.20.00',  sha256='d2358c930d5ab89e5965204dded499591b42a22d0a865e2149b8c0f1446fac34')
 
     # Downstream patches
     fedora_patch('8a6066c901fb4fc75013dd488ba958387f00c74d', 'tcsh-6.20.00-manpage-memoryuse.patch', sha256='3a4e60fe56a450632140c48acbf14d22850c1d72835bf441e3f8514d6c617a9f')  # noqa: E501

From 4777284f082e5e4d8bfa89b7486e22e3fffb02fe Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Wed, 13 May 2020 22:06:25 +0900
Subject: [PATCH 381/802] charmpp: support for aarch64. (#16619)

---
 var/spack/repos/builtin/packages/charmpp/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/charmpp/package.py b/var/spack/repos/builtin/packages/charmpp/package.py
index e9a133604c9..fc1680f9af3 100644
--- a/var/spack/repos/builtin/packages/charmpp/package.py
+++ b/var/spack/repos/builtin/packages/charmpp/package.py
@@ -158,6 +158,8 @@ def charmarch(self):
             ("linux",   "ppc",      "verbs"):       "verbs-linux-ppc64le",
             ("linux",   "arm",      "netlrts"):     "netlrts-linux-arm7",
             ("linux",   "arm",      "multicore"):   "multicore-arm7",
+            ("linux",   "aarch64",  "netlrts"):     "netlrts-linux-arm8",
+            ("linux",   "aarch64",  "multicore"):   "multicore-arm8",
             ("win",     "x86_64",   "mpi"):         "mpi-win-x86_64",
             ("win",     "x86_64",   "multicore"):   "multicore-win-x86_64",
             ("win",     "x86_64",   "netlrts"):     "netlrts-win-x86_64",

From a740c361cd44506caa3837f19fa1f70e4764ac94 Mon Sep 17 00:00:00 2001
From: "Tomoki, Karatsu" <49965247+t-karatsu@users.noreply.github.com>
Date: Wed, 13 May 2020 22:10:07 +0900
Subject: [PATCH 382/802] ppopen-appl-fdm: added support to Fujitsu compilers.
 (#16616)

---
 .../packages/ppopen-appl-fdm/iargc_definition.patch | 13 +++++++++++++
 .../builtin/packages/ppopen-appl-fdm/package.py     |  5 ++++-
 2 files changed, 17 insertions(+), 1 deletion(-)
 create mode 100644 var/spack/repos/builtin/packages/ppopen-appl-fdm/iargc_definition.patch

diff --git a/var/spack/repos/builtin/packages/ppopen-appl-fdm/iargc_definition.patch b/var/spack/repos/builtin/packages/ppopen-appl-fdm/iargc_definition.patch
new file mode 100644
index 00000000000..4f149873aef
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ppopen-appl-fdm/iargc_definition.patch
@@ -0,0 +1,13 @@
+--- spack-src/tools/seismic_2D-tools/m_getopt.f90.org	2020-05-13 10:14:41.822006522 +0900
++++ spack-src/tools/seismic_2D-tools/m_getopt.f90	2020-05-13 10:17:01.102690012 +0900
+@@ -80,7 +80,9 @@
+     character(256), allocatable :: argv(:)
+     integer :: i
+     character(256) :: optkey
+-    
++
++    integer, external :: iargc
++
+     narg = iargc()
+     allocate( argv(1:narg) )
+     
diff --git a/var/spack/repos/builtin/packages/ppopen-appl-fdm/package.py b/var/spack/repos/builtin/packages/ppopen-appl-fdm/package.py
index 450ae99efbf..1b3acfd6921 100755
--- a/var/spack/repos/builtin/packages/ppopen-appl-fdm/package.py
+++ b/var/spack/repos/builtin/packages/ppopen-appl-fdm/package.py
@@ -24,7 +24,10 @@ class PpopenApplFdm(MakefilePackage):
     patch('unused.patch')
     # remove iargc external definition
     # iargc is intrinsic in gfortran
-    patch('gfortran_iargc.patch')
+    patch('gfortran_iargc.patch', when='%gcc')
+
+    # Fixed a problem that 'iargc' was not declared in advance
+    patch('iargc_definition.patch', when='%fj')
 
     depends_on('ppopen-math-vis', type='link')
     depends_on('mpi')

From f6fbf8b8d33f32b5c293fd5f142a31d7582374b6 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Wed, 13 May 2020 16:22:53 +0200
Subject: [PATCH 383/802] r-xml2: new version & updated dependencies (#16604)

* r-xml2: new version & updated dependencies

* r-xml2: updated dependencies
---
 var/spack/repos/builtin/packages/r-xml2/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/r-xml2/package.py b/var/spack/repos/builtin/packages/r-xml2/package.py
index 55edf949ea0..7e12f208bf1 100644
--- a/var/spack/repos/builtin/packages/r-xml2/package.py
+++ b/var/spack/repos/builtin/packages/r-xml2/package.py
@@ -14,11 +14,12 @@ class RXml2(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/xml2_1.1.1.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/xml2"
 
+    version('1.3.2', sha256='df22f9e7e3189d8c9b8804eaf0105324fdac983cffe743552f6d76613600a4cf')
     version('1.2.2', sha256='3050f147c4335be2925a576557bbda36bd52a5bba3110d47b740a2dd811a78f4')
     version('1.2.1', sha256='5615bbc94607efc3bc192551992b349091df802ae34b855cfa817733f2690605')
     version('1.1.1', sha256='00f3e3b66b76760c19da5f6dddc98e6f30de36a96b211e59e1a3f4ff58763116')
 
     depends_on('r@3.1.0:', type=('build', 'run'))
-    depends_on('r-rcpp@0.12.12:', type=('build', 'run'))
+    depends_on('r-rcpp@0.12.12:', when='@:1.2', type=('build', 'run'))
     depends_on('r-bh', when='@:1.1.1', type=('build', 'run'))
     depends_on('libxml2')

From 308f016f31fda65c50534ef351cc4f7a6405c03d Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Wed, 13 May 2020 16:44:50 +0200
Subject: [PATCH 384/802] parallel-netcdf: fix build with gcc@10: (#16620)

---
 .../packages/parallel-netcdf/package.py       | 26 ++++++++++++++-----
 1 file changed, 20 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
index dc2f1b4ac37..722efab16e4 100644
--- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py
+++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
@@ -95,13 +95,27 @@ def configure_args(self):
         args += self.enable_or_disable('cxx')
         args += self.enable_or_disable('fortran')
 
+        flags = {
+            'CFLAGS': [],
+            'CXXFLAGS': [],
+            'FFLAGS': [],
+            'FCFLAGS': [],
+        }
+
         if '+pic' in self.spec:
-            args.extend([
-                'CFLAGS='   + self.compiler.cc_pic_flag,
-                'CXXFLAGS=' + self.compiler.cxx_pic_flag,
-                'FFLAGS='   + self.compiler.f77_pic_flag,
-                'FCFLAGS='  + self.compiler.fc_pic_flag,
-            ])
+            flags['CFLAGS'].append(self.compiler.cc_pic_flag)
+            flags['CXXFLAGS'].append(self.compiler.cxx_pic_flag)
+            flags['FFLAGS'].append(self.compiler.f77_pic_flag)
+            flags['FCFLAGS'].append(self.compiler.fc_pic_flag)
+
+        # https://github.com/Parallel-NetCDF/PnetCDF/issues/61
+        if self.spec.satisfies('%gcc@10:'):
+            flags['FFLAGS'].append('-fallow-argument-mismatch')
+            flags['FCFLAGS'].append('-fallow-argument-mismatch')
+
+        for key, value in sorted(flags.items()):
+            if value:
+                args.append('{0}={1}'.format(key, ' '.join(value)))
 
         if self.version >= Version('1.8'):
             args.append('--enable-relax-coord-bound')

From 043d50754052a7dca68ebd92160927859627563a Mon Sep 17 00:00:00 2001
From: lpritch-lanl <65038207+lpritch-lanl@users.noreply.github.com>
Date: Wed, 13 May 2020 08:47:01 -0600
Subject: [PATCH 385/802] py-pint: added versions up to v0.11 (#16537)

Co-authored-by: Lori Pritchett-Sheats <lpritch@pn2002926.lanl.gov>
---
 var/spack/repos/builtin/packages/py-pint/package.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-pint/package.py b/var/spack/repos/builtin/packages/py-pint/package.py
index 6287cc76bd2..fd2736f7c6b 100644
--- a/var/spack/repos/builtin/packages/py-pint/package.py
+++ b/var/spack/repos/builtin/packages/py-pint/package.py
@@ -12,9 +12,15 @@ class PyPint(PythonPackage):
     It allows arithmetic operations between them and conversions from and
     to different units."""
 
-    homepage = "https://pypi.python.org/pypi/pint"
-    url      = "https://pypi.io/packages/source/p/pint/Pint-0.8.1.tar.gz"
+    homepage = "https://pypi.org/project/Pint"
+    url = "https://pypi.io/packages/source/p/pint/Pint-0.11.tar.gz"
 
+    version('0.11', sha256='308f1070500e102f83b6adfca6db53debfce2ffc5d3cbe3f6c367da359b5cf4d')
+    version('0.10.1', sha256='d739c364b8326fe3d70773d5720fa8b005ea6158695cad042677a588480c86e6')
+    version('0.10', sha256='38a4d6e242b8bab693cd83a5f5ade3d816463b498658e7ab14ce64c4d458c88b')
+    version('0.9', sha256='32d8a9a9d63f4f81194c0014b3b742679dce81a26d45127d9810a68a561fe4e2')
     version('0.8.1', sha256='afcf31443a478c32bbac4b00337ee9026a13d0e2ac83d30c79151462513bb0d4')
 
-    depends_on('py-setuptools', type='build')
+    depends_on('python@3.6:', type=('build', 'run'), when='@0.10:')
+    depends_on('py-setuptools', type=('build', ))
+    depends_on('py-setuptools-scm', type=('build', ))

From fa57f1da2991e4205c4ece0ef7754a2c4ffe50dd Mon Sep 17 00:00:00 2001
From: "Nichols A. Romero" <naromero77@users.noreply.github.com>
Date: Wed, 13 May 2020 12:41:16 -0500
Subject: [PATCH 386/802] QE Update May 2020 (#16627)

* Clarify comments about QMCPACK-to-QE converter.

* Allow hdf5=serial with QE 6.4.1 + qmcpack, but apply filter_file.

* Ammend comments about the use of the filter_file.
---
 .../builtin/packages/quantum-espresso/package.py    | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/quantum-espresso/package.py b/var/spack/repos/builtin/packages/quantum-espresso/package.py
index 59f5c33f3d1..3c8b2c9d021 100644
--- a/var/spack/repos/builtin/packages/quantum-espresso/package.py
+++ b/var/spack/repos/builtin/packages/quantum-espresso/package.py
@@ -128,8 +128,8 @@ class QuantumEspresso(Package):
     # folder QE expects as a link, we issue a conflict here.
     conflicts('+elpa', when='@:5.4.0')
 
-    # Some QMCPACK converters only without internal patches. HDF5
-    # is a hard requirement. Need to do two HDF5 cases explicitly
+    # Some QMCPACK converters are incompatible with upstream patches.
+    # HDF5 is a hard requirement. Need to do two HDF5 cases explicitly
     # since Spack lacks support for expressing NOT operation.
     conflicts(
         '@6.4+patch',
@@ -138,7 +138,7 @@ class QuantumEspresso(Package):
         'deactivatation of upstream patches'
     )
     conflicts(
-        'hdf5=serial',
+        '@6.3:6.4.0 hdf5=serial',
         when='+qmcpack',
         msg='QE-to-QMCPACK wave function converter only '
         'supported with parallel HDF5'
@@ -330,9 +330,12 @@ def install(self, spec, prefix):
         configure(*options)
 
         # Filter file must be applied after configure executes
-        # QE 6.4.0 to QE 6.4 have `-L` missing in front of zlib library
+        # QE 6.1.0 to QE 6.4 have `-L` missing in front of zlib library
+        # This issue is backported through an internal patch in 6.4.1, but
+        # can't be applied to the '+qmcpack' variant
         if spec.variants['hdf5'].value != 'none':
-            if spec.satisfies('@6.1.0:6.4.0'):
+            if (spec.satisfies('@6.1.0:6.4.0') or
+                (spec.satisfies('@6.4.1') and '+qmcpack' in spec)):
                 make_inc = join_path(self.stage.source_path, 'make.inc')
                 zlib_libs = spec['zlib'].prefix.lib + ' -lz'
                 filter_file(

From 9b8082ecf3103d1393792f17565f10917457ac30 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Wed, 13 May 2020 19:42:16 +0200
Subject: [PATCH 387/802] r-exactextractr: new package (#16626)

---
 .../packages/r-exactextractr/package.py       | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-exactextractr/package.py

diff --git a/var/spack/repos/builtin/packages/r-exactextractr/package.py b/var/spack/repos/builtin/packages/r-exactextractr/package.py
new file mode 100644
index 00000000000..abe1b945e91
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-exactextractr/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RExactextractr(AutotoolsPackage):
+    """Provides a replacement for the 'extract' function from the 'raster'
+       package that is suitable for extracting raster values using 'sf'
+       polygons.
+    """
+
+    homepage = "https://cloud.r-project.org/package=exactextractr"
+    url      = "https://cran.r-project.org/src/contrib/exactextractr_0.3.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/exactextractr"
+
+    version('0.3.0', sha256='c7fb38b38b9dc8b3ca5b8f1f84f4ba3256efd331f2b4636b496d42689ffc3fb0')
+    version('0.2.1', sha256='d0b998c77c3fd9265a600a0e08e9bf32a2490a06c19df0d0c0dea4b5c9ab5773')
+
+    depends_on('r@3.4:', type=('build', 'run'))
+    depends_on('r-raster', type=('build', 'run'))
+    depends_on('r-sf', type=('build', 'run'))
+    depends_on('r-rcpp@0.12.12:', type=('build', 'run'))
+    depends_on('geos@3.5:', type=('build', 'run', 'link'))

From a9ee4da67012344d6ab31db901556dbeb00b2b52 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Wed, 13 May 2020 19:45:12 +0200
Subject: [PATCH 388/802] ncl: Fix build with gcc@10: (#16624)

---
 var/spack/repos/builtin/packages/ncl/package.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/var/spack/repos/builtin/packages/ncl/package.py b/var/spack/repos/builtin/packages/ncl/package.py
index e6e09faae1e..4d9980ecc55 100644
--- a/var/spack/repos/builtin/packages/ncl/package.py
+++ b/var/spack/repos/builtin/packages/ncl/package.py
@@ -30,6 +30,9 @@ class Ncl(Package):
     patch('ymake-filter.patch', when="@6.4.0")
     # ymake additional local library and includes will be filtered improperly
     patch('ymake.patch', when="@6.4.0:")
+    # ncl does not build with gcc@10:
+    # https://github.com/NCAR/ncl/issues/123
+    patch('https://src.fedoraproject.org/rpms/ncl/raw/12778c55142b5b1ccc26dfbd7857da37332940c2/f/ncl-boz.patch', when='%gcc@10:', sha256='64f3502c9deab48615a4cbc26073173081c0774faf75778b044d251e45d238f7')
 
     # This installation script is implemented according to this manual:
     # http://www.ncl.ucar.edu/Download/build_from_src.shtml
@@ -144,6 +147,10 @@ def prepare_site_config(self):
             cc_flags.append('-fp-model precise')
             c2f_flags.extend(['-lifcore', '-lifport'])
 
+        if self.spec.satisfies('%gcc@10:'):
+            fc_flags.append('-fallow-argument-mismatch')
+            cc_flags.append('-fcommon')
+
         with open('./config/Spack', 'w') as f:
             f.writelines([
                 '#define HdfDefines\n',

From 66b896d286b3b9edc269a60bdfffe44163a904b1 Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Thu, 14 May 2020 02:49:42 +0900
Subject: [PATCH 389/802] conda4aarch64:New Package. (#16617)

---
 .../builtin/packages/conda4aarch64/package.py | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/conda4aarch64/package.py

diff --git a/var/spack/repos/builtin/packages/conda4aarch64/package.py b/var/spack/repos/builtin/packages/conda4aarch64/package.py
new file mode 100644
index 00000000000..fe7ede5c147
--- /dev/null
+++ b/var/spack/repos/builtin/packages/conda4aarch64/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Conda4aarch64(Package):
+    """Conda for aarch64"""
+
+    homepage = "https://anaconda.org/c4aarch64/"
+    url      = "https://github.com/jjhelmus/conda4aarch64/releases/download/1.0.0/c4aarch64_installer-1.0.0-Linux-aarch64.sh"
+
+    conflicts('arch=x86_64:')
+    conflicts('arch=ppc64:')
+    conflicts('arch=ppc64le:')
+
+    version('1.0.0', sha256='165565dc7e7cc74c9ef8fd75d309fb7b81a6d1bc5e2eab48aafa7b836a7427af', expand=False)
+
+    def install(self, spec, prefix):
+        conda_script = self.stage.archive_file
+        bash = which('bash')
+        bash(conda_script, '-b', '-f', '-p', self.prefix)

From f294c264a10364caa33b2ec4d00aa196d5af6b67 Mon Sep 17 00:00:00 2001
From: Nick Booher <njbooher@iastate.edu>
Date: Wed, 13 May 2020 12:54:21 -0500
Subject: [PATCH 390/802] revbayes: Update checksum (#16628)

---
 var/spack/repos/builtin/packages/revbayes/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/revbayes/package.py b/var/spack/repos/builtin/packages/revbayes/package.py
index e419d17c55f..e3703b2e527 100644
--- a/var/spack/repos/builtin/packages/revbayes/package.py
+++ b/var/spack/repos/builtin/packages/revbayes/package.py
@@ -15,7 +15,7 @@ class Revbayes(CMakePackage):
     git      = "https://github.com/revbayes/revbayes.git"
 
     version('develop', branch='development')
-    version('1.1.0', sha256='6adede8148cb10e4e75dba8da28cf5c747ea8de71a5aa24990ab9ae17e43b0b1')
+    version('1.1.0', sha256='a9f35178d8289d0dd32c9d936f6384f260e8e81e7b80a5155169064a24666012')
     version('1.0.13', sha256='e85e2e1fe182fe9f504900150d936a06d252a362c591b9d3d8272dd085aa85d9')
     version('1.0.12', sha256='80c926bb6b37288d02e36e07b44e4663841cd1fe541e2cc0b0e44c89ca929759')
     version('1.0.11', sha256='03052194baa220dde7e622a739f09f34393f67ea00a0b163b409d313d7fc7c02')

From 37e307e8cde4009950b1feb8a53d33fb3b1fa571 Mon Sep 17 00:00:00 2001
From: Ben Bergen <bergen@lanl.gov>
Date: Wed, 13 May 2020 12:02:38 -0600
Subject: [PATCH 391/802] Added alias and bash completion for spacktivate
 (#16472)

---
 share/spack/bash/spack-completion.in | 7 +++++++
 share/spack/setup-env.csh            | 1 +
 share/spack/setup-env.sh             | 2 ++
 share/spack/spack-completion.bash    | 7 +++++++
 4 files changed, 17 insertions(+)

diff --git a/share/spack/bash/spack-completion.in b/share/spack/bash/spack-completion.in
index 164fc5c5b3d..80ba94ed876 100755
--- a/share/spack/bash/spack-completion.in
+++ b/share/spack/bash/spack-completion.in
@@ -304,6 +304,13 @@ _pretty_print() {
 
 complete -o bashdefault -o default -F _bash_completion_spack spack
 
+# Completion for spacktivate
+complete -o bashdefault -o default -F _bash_completion_spack spacktivate
+
+_spacktivate() {
+  _spack_env_activate
+}
+
 # Spack commands
 #
 # Everything below here is auto-generated.
diff --git a/share/spack/setup-env.csh b/share/spack/setup-env.csh
index 67357c94e49..edbf51e8e28 100755
--- a/share/spack/setup-env.csh
+++ b/share/spack/setup-env.csh
@@ -18,6 +18,7 @@ if ($?SPACK_ROOT) then
 
     # Command aliases point at separate source files
     alias spack          'set _sp_args = (\!*); source $_spack_share_dir/csh/spack.csh'
+    alias spacktivate    'spack env activate'
     alias _spack_pathadd 'set _pa_args = (\!*) && source $_spack_share_dir/csh/pathadd.csh'
 
     # Set variables needed by this script
diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh
index d3aed61d1a7..032247cd8f3 100755
--- a/share/spack/setup-env.sh
+++ b/share/spack/setup-env.sh
@@ -242,6 +242,8 @@ if [ "$_sp_shell" = bash ]; then
     export -f spack
 fi
 
+alias spacktivate="spack env activate"
+
 #
 # Figure out where this file is.
 #
diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash
index 9017f4fe570..b7b45fb0d77 100755
--- a/share/spack/spack-completion.bash
+++ b/share/spack/spack-completion.bash
@@ -304,6 +304,13 @@ _pretty_print() {
 
 complete -o bashdefault -o default -F _bash_completion_spack spack
 
+# Completion for spacktivate
+complete -o bashdefault -o default -F _bash_completion_spack spacktivate
+
+_spacktivate() {
+  _spack_env_activate
+}
+
 # Spack commands
 #
 # Everything below here is auto-generated.

From 7411fe2d4322bcd987b41842cafc5afd15b3a991 Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Wed, 13 May 2020 14:31:33 -0700
Subject: [PATCH 392/802] cmake build system: filter system paths from rpaths
 (#16612)

---
 lib/spack/spack/build_environment.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 8d84cdaf65f..3510ae8ac8d 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -615,7 +615,7 @@ def get_rpaths(pkg):
     # module show output.
     if pkg.compiler.modules and len(pkg.compiler.modules) > 1:
         rpaths.append(get_path_from_module(pkg.compiler.modules[1]))
-    return rpaths
+    return list(dedupe(filter_system_paths(rpaths)))
 
 
 def get_std_cmake_args(pkg):

From c50b586e06c1fa3ffd997adbd9d4e711a6c6ca46 Mon Sep 17 00:00:00 2001
From: Nathan <35582439+yee29@users.noreply.github.com>
Date: Wed, 13 May 2020 15:25:07 -0700
Subject: [PATCH 393/802] Helics: add python variant (#16625)

* Adding varient for python interface in HELICS

* Append python interface to pythonpath

* cleaning up blank lines

* Update var/spack/repos/builtin/packages/helics/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 var/spack/repos/builtin/packages/helics/package.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/var/spack/repos/builtin/packages/helics/package.py b/var/spack/repos/builtin/packages/helics/package.py
index ba804784369..9736cb6d66f 100644
--- a/var/spack/repos/builtin/packages/helics/package.py
+++ b/var/spack/repos/builtin/packages/helics/package.py
@@ -39,6 +39,7 @@ class Helics(CMakePackage):
     variant('asio', default=True, description="Compile with ASIO libraries")
     variant('swig', default=False, description="Build language bindings with SWIG")
     variant('webserver', default=True, description="Enable the integrated webserver in the HELICS broker server")
+    variant('python', default=False, description="Enable Python interface")
 
     # Build dependency
     depends_on('git', type='build', when='@master:')
@@ -48,6 +49,7 @@ class Helics(CMakePackage):
 
     depends_on('libzmq@4.3:', when='+zmq')
     depends_on('mpi@2', when='+mpi')
+    depends_on('python@3:', when='+python')
 
     # OpenMPI doesn't work with HELICS <=2.4.1
     conflicts('^openmpi', when='@:2.4.1 +mpi')
@@ -60,6 +62,8 @@ class Helics(CMakePackage):
     conflicts('+tcp', when='~asio')
     conflicts('+udp', when='~asio')
 
+    extends('python', when='+python')
+
     def cmake_args(self):
         spec = self.spec
         args = [
@@ -103,4 +107,13 @@ def cmake_args(self):
         args.append('-DHELICS_ENABLE_SWIG={0}'.format(
             'ON' if '+swig' in spec else 'OFF'))
 
+        # Python
+        args.append('-DBUILD_PYTHON_INTERFACE={0}'.format(
+            'ON' if '+python' in spec else 'OFF'))
+
         return args
+
+    def setup_run_environment(self, env):
+        spec = self.spec
+        if '+python' in spec:
+            env.prepend_path('PYTHONPATH', self.prefix.python)

From bc948c44186dd3e2498f3284b4e535e84cb68f5b Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 13 May 2020 17:52:27 -0500
Subject: [PATCH 394/802] py-horovod: add new version (#16635)

---
 var/spack/repos/builtin/packages/py-horovod/package.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-horovod/package.py b/var/spack/repos/builtin/packages/py-horovod/package.py
index 955e68ff1ab..ec8f3a86385 100644
--- a/var/spack/repos/builtin/packages/py-horovod/package.py
+++ b/var/spack/repos/builtin/packages/py-horovod/package.py
@@ -14,6 +14,7 @@ class PyHorovod(PythonPackage):
     maintainers = ['adamjstewart']
 
     version('master', branch='master', submodules=True)
+    version('0.19.2', tag='v0.19.2', submodules=True)
     version('0.19.1', tag='v0.19.1', submodules=True)
     version('0.19.0', tag='v0.19.0', submodules=True)
     version('0.18.2', tag='v0.18.2', submodules=True)
@@ -47,13 +48,14 @@ class PyHorovod(PythonPackage):
     # Framework dependencies
     depends_on('py-tensorflow@1.1.0:',  type=('build', 'link', 'run'), when='frameworks=tensorflow')
     depends_on('py-torch@0.4.0:',       type=('build', 'link', 'run'), when='frameworks=pytorch')
-    depends_on('py-torchvision',        type=('build', 'run'),         when='frameworks=pytorch')
+    depends_on('py-torchvision',        type=('build', 'run'),         when='frameworks=pytorch @:0.19.1')
     depends_on('py-cffi@1.4.0:',        type=('build', 'run'),         when='frameworks=pytorch')
     depends_on('mxnet@1.4.1:+python',   type=('build', 'link', 'run'), when='frameworks=mxnet')
     depends_on('py-keras@2.0.8,2.1.2:', type=('build', 'run'),         when='frameworks=keras')
     depends_on('py-h5py@2.9:',          type=('build', 'run'),         when='frameworks=spark')
     depends_on('py-numpy',              type=('build', 'run'),         when='frameworks=spark')
-    depends_on('py-petastorm@0.8.2',    type=('build', 'run'),         when='frameworks=spark')
+    depends_on('py-petastorm@0.8.2',    type=('build', 'run'),         when='frameworks=spark @:0.19.1')
+    depends_on('py-petastorm@0.9.0:',   type=('build', 'run'),         when='frameworks=spark @0.19.2:')
     depends_on('py-pyarrow@0.15.0:',    type=('build', 'run'),         when='frameworks=spark')
     depends_on('py-pyspark@2.3.2:',     type=('build', 'run'),         when='frameworks=spark')
 

From 48a35409e083ea7a9f04594a7b1802136df21d18 Mon Sep 17 00:00:00 2001
From: Nathan <35582439+yee29@users.noreply.github.com>
Date: Wed, 13 May 2020 19:16:17 -0700
Subject: [PATCH 395/802] Spack Package for ns-3 (#16630)

* Adding ns3 spack

* Format and cleanup of ns3 spack package

* Removing comments and fixing boost variant

* Fixing formating
---
 .../builtin/packages/ns-3-dev/package.py      | 52 +++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/ns-3-dev/package.py

diff --git a/var/spack/repos/builtin/packages/ns-3-dev/package.py b/var/spack/repos/builtin/packages/ns-3-dev/package.py
new file mode 100644
index 00000000000..6f1d85f6dbc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ns-3-dev/package.py
@@ -0,0 +1,52 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ns3Dev(WafPackage):
+    """
+    ns-3 is a discrete-event network simulator,
+    targeted primarily for research and educational use
+    """
+
+    homepage = "https://www.nsnam.org/"
+    url      = "https://gitlab.com/nsnam/ns-3-dev/-/archive/ns-3.30.1/ns-3-dev-ns-3.30.1.tar.bz2"
+
+    maintainers = ['yee29']
+
+    version('3.30.1', sha256='e8b3849d83a224f42c0cd2b9e692ec961455aca23f36fb86fcf6bbed2b495a3d')
+    version('3.30',   sha256='53cefcad74fec6cc332368a05ed1f8c1a29f86295cb44b6b0509c6d2d18d90d0')
+    version('3.29',   sha256='0254341487891421e4c6040476c6634c4c2931d4f7c6b9617a6ae494c8ee6ffd')
+    version('3.28',   sha256='5295e1f6e2ee1ff8cd92d3937c8b3266e0d5926adffc42c7fb0ea9ce549a91b7')
+    version('3.27',   sha256='26233011654043822b8ede525a52f8532ed181997b609a606681a0d5c8d64a26')
+
+    variant('helics', default=False, description="Enable Helics support in ns-3")
+    variant('boost', default=True, description="Compile with Boost libraries")
+
+    # Build dependency
+    depends_on('helics', when='+helics')
+    depends_on('boost', when='+boost')
+    depends_on('pkgconfig', type='build')
+
+    resource(name='helics',
+             when='+helics',
+             git='https://github.com/GMLC-TDC/helics-ns3.git',
+             destination='contrib', placement='helics')
+
+    def configure_args(self):
+        args = []
+
+        if '+boost' in self.spec:
+            args.extend([
+                '--boost-includes={0}'.format(
+                    self.spec['boost'].prefix.include),
+                '--boost-libs={0}'.format(
+                    self.spec['boost'].prefix.lib)
+            ])
+
+        if '+helics' in self.spec:
+            args.append('--with-helics={0}'.format(self.spec['helics'].prefix))
+        return args

From 20b3e418317644fc17a8787cb2bda52fdb77a24a Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Thu, 14 May 2020 04:46:13 +0200
Subject: [PATCH 396/802] adios2: Fix build with gcc@10: (#16570)

---
 var/spack/repos/builtin/packages/adios2/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/repos/builtin/packages/adios2/package.py b/var/spack/repos/builtin/packages/adios2/package.py
index 9d298b4213c..4b2f5a74ebb 100644
--- a/var/spack/repos/builtin/packages/adios2/package.py
+++ b/var/spack/repos/builtin/packages/adios2/package.py
@@ -118,6 +118,11 @@ class Adios2(CMakePackage):
     # See https://github.com/ornladios/ADIOS2/pull/1899
     patch('2.5-fix-clear_cache.patch', when='@2.5.0')
 
+    def setup_build_environment(self, env):
+        # https://github.com/ornladios/ADIOS2/issues/2228
+        if self.spec.satisfies('%gcc@10: +fortran'):
+            env.set('FFLAGS', '-fallow-argument-mismatch')
+
     def cmake_args(self):
         spec = self.spec
 

From 445cae5c81a1f02e830f0f52613855ae27c51f22 Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Thu, 14 May 2020 11:27:37 -0700
Subject: [PATCH 397/802] Feature: Allow lmod configuration to set core specs
 (#16517)

Packages built with lmod core_compiler are placed in `Core`.

Other packages may belong in `Core`. For example, python may be built with a proprietary compiler for performance, but belong on the `Core` directory.

With this PR, lmod config can include a `core_specs` list. Any package that satisfies a spec in that list is placed in `Core`, regardless of its compiler or dependencies.
---
 lib/spack/docs/module_file_support.rst                | 11 +++++++++++
 lib/spack/spack/modules/lmod.py                       | 10 ++++++++++
 lib/spack/spack/schema/modules.py                     |  5 +++--
 .../test/data/modules/lmod/complex_hierarchy.yaml     |  3 +++
 lib/spack/spack/test/modules/lmod.py                  |  4 +++-
 5 files changed, 30 insertions(+), 3 deletions(-)

diff --git a/lib/spack/docs/module_file_support.rst b/lib/spack/docs/module_file_support.rst
index 4ddd42139c6..406715b07e6 100644
--- a/lib/spack/docs/module_file_support.rst
+++ b/lib/spack/docs/module_file_support.rst
@@ -538,6 +538,8 @@ most likely via the ``+blas`` variant specification.
          lmod:
            core_compilers:
              - 'gcc@4.8'
+           core_specs:
+             - 'python'
            hierarchy:
              - 'mpi'
              - 'lapack'
@@ -547,6 +549,15 @@ most likely via the ``+blas`` variant specification.
      implementations of ``mpi`` and ``lapack``, and let LMod switch safely from one to the
      other.
 
+     All packages built with a compiler in ``core_compilers`` and all
+     packages that satisfy a spec in ``core_specs`` will be put in the
+     ``Core`` hierarchy of the lua modules.
+
+.. warning::
+  Consistency of Core packages
+   The user is responsible for maintining consistency among core packages, as ``core_specs``
+   bypasses the hierarchy that allows LMod to safely switch between coherent software stacks.
+
 .. warning::
   Deep hierarchies and ``lmod spider``
    For hierarchies that are deeper than three layers ``lmod spider`` may have some issues.
diff --git a/lib/spack/spack/modules/lmod.py b/lib/spack/spack/modules/lmod.py
index a9ebb0bba96..d0d14dac5bd 100644
--- a/lib/spack/spack/modules/lmod.py
+++ b/lib/spack/spack/modules/lmod.py
@@ -110,6 +110,11 @@ def core_compilers(self):
             raise CoreCompilersNotFoundError(msg)
         return value
 
+    @property
+    def core_specs(self):
+        """Returns the list of "Core" specs"""
+        return configuration().get('core_specs', [])
+
     @property
     def hierarchy_tokens(self):
         """Returns the list of tokens that are part of the modulefile
@@ -140,6 +145,11 @@ def requires(self):
         to the actual provider. 'compiler' is always present among the
         requirements.
         """
+        # If it's a core_spec, lie and say it requires a core compiler
+        if any(self.spec.satisfies(core_spec)
+               for core_spec in self.core_specs):
+            return {'compiler': self.core_compilers[0]}
+
         # Keep track of the requirements that this package has in terms
         # of virtual packages that participate in the hierarchical structure
         requirements = {'compiler': self.spec.compiler}
diff --git a/lib/spack/spack/schema/modules.py b/lib/spack/spack/schema/modules.py
index 1fbbf614c88..4e110717574 100644
--- a/lib/spack/spack/schema/modules.py
+++ b/lib/spack/spack/schema/modules.py
@@ -16,7 +16,7 @@
 #:
 #: THIS NEEDS TO BE UPDATED FOR EVERY NEW KEYWORD THAT
 #: IS ADDED IMMEDIATELY BELOW THE MODULE TYPE ATTRIBUTE
-spec_regex = r'(?!hierarchy|verbose|hash_length|whitelist|' \
+spec_regex = r'(?!hierarchy|core_specs|verbose|hash_length|whitelist|' \
              r'blacklist|naming_scheme|core_compilers|all)(^\w[\w-]*)'
 
 #: Matches an anonymous spec, i.e. a spec without a root name
@@ -145,7 +145,8 @@
                         'type': 'object',
                         'properties': {
                             'core_compilers': array_of_strings,
-                            'hierarchy': array_of_strings
+                            'hierarchy': array_of_strings,
+                            'core_specs': array_of_strings,
                         },
                     }  # Specific lmod extensions
                 ]
diff --git a/lib/spack/spack/test/data/modules/lmod/complex_hierarchy.yaml b/lib/spack/spack/test/data/modules/lmod/complex_hierarchy.yaml
index ada3c691cb5..5cad95c7fae 100644
--- a/lib/spack/spack/test/data/modules/lmod/complex_hierarchy.yaml
+++ b/lib/spack/spack/test/data/modules/lmod/complex_hierarchy.yaml
@@ -6,6 +6,9 @@ lmod:
   core_compilers:
     - 'clang@3.3'
 
+  core_specs:
+    - 'mpich@3.0.1'
+
   hierarchy:
     - lapack
     - blas
diff --git a/lib/spack/spack/test/modules/lmod.py b/lib/spack/spack/test/modules/lmod.py
index 12b6d71aa53..3daeeb068db 100644
--- a/lib/spack/spack/test/modules/lmod.py
+++ b/lib/spack/spack/test/modules/lmod.py
@@ -27,6 +27,7 @@ def compiler(request):
 
 @pytest.fixture(params=[
     ('mpich@3.0.4', ('mpi',)),
+    ('mpich@3.0.1', []),
     ('openblas@0.2.15', ('blas',)),
     ('openblas-with-lapack@0.2.15', ('blas', 'lapack'))
 ])
@@ -54,7 +55,8 @@ def test_file_layout(
         # Check that the compiler part of the path has no hash and that it
         # is transformed to r"Core" if the compiler is listed among core
         # compilers
-        if compiler == 'clang@3.3':
+        # Check that specs listed as core_specs are transformed to "Core"
+        if compiler == 'clang@3.3' or spec_string == 'mpich@3.0.1':
             assert 'Core' in layout.available_path_parts
         else:
             assert compiler.replace('@', '/') in layout.available_path_parts

From 1eb5a120197602233778022a4908825a36564324 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Fri, 15 May 2020 02:44:35 +0200
Subject: [PATCH 398/802] r-survival: new version and updated dependency
 (#16650)

---
 var/spack/repos/builtin/packages/r-survival/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/r-survival/package.py b/var/spack/repos/builtin/packages/r-survival/package.py
index c7d81fc02cb..8e2bfb7f37a 100644
--- a/var/spack/repos/builtin/packages/r-survival/package.py
+++ b/var/spack/repos/builtin/packages/r-survival/package.py
@@ -15,6 +15,7 @@ class RSurvival(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/survival_2.41-3.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/survival"
 
+    version('3.1-12', sha256='b62ed66eb646f3df13f7e9bf6571e3bfecae128c66491e174c8833cbef1bf21f')
     version('2.44-1.1', sha256='55b151e15fcd24ccb3acf60331c9a7ad82bc10f3841ab3be9bc2a37e9ee751b9')
     version('2.44-1', sha256='82c44afa41fe4504295855f1da4a5940c3289dfd61bc664bf211bb67c051a909')
     version('2.41-3', sha256='f3797c344de93abd2ba8c89568770a13524a8b2694144ae55adec46921c8961d')
@@ -22,4 +23,5 @@ class RSurvival(RPackage):
     version('2.39-5', sha256='607170ebe36080d102e884cf13c3b29df01d6bb3b593258afffa67fee2a0ada7')
 
     depends_on('r@2.13.0:', type=('build', 'run'))
+    depends_on('r@3.4:', when='@3.1-12:', type=('build', 'run'))
     depends_on('r-matrix', type=('build', 'run'))

From 0844e56d6d7e4b7b2c789315519a5a3441df1e3a Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Fri, 15 May 2020 02:46:02 +0200
Subject: [PATCH 399/802] r-hmisc: new version and updated dependency (#16649)

---
 var/spack/repos/builtin/packages/r-hmisc/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/r-hmisc/package.py b/var/spack/repos/builtin/packages/r-hmisc/package.py
index 131c3ea26ca..678816277c0 100644
--- a/var/spack/repos/builtin/packages/r-hmisc/package.py
+++ b/var/spack/repos/builtin/packages/r-hmisc/package.py
@@ -18,11 +18,13 @@ class RHmisc(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/Hmisc_4.1-1.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/Hmisc"
 
+    version('4.4-0', sha256='f16ecf4c5ee2202d51f426282a54f8000ffa8b9747c3e910205f34f878556ec7')
     version('4.2-0', sha256='9e9614673288dd00295f250fa0bf96fc9e9fed692c69bf97691081c1a01411d9')
     version('4.1-1', sha256='991db21cdf73ffbf5b0239a4876b2e76fd243ea33528afd88dc968792f281498')
 
     depends_on('r-lattice', type=('build', 'run'))
     depends_on('r-survival@2.40-1:', type=('build', 'run'))
+    depends_on('r-survival@3.1-6:', when='@4.4:', type=('build', 'run'))
     depends_on('r-formula', type=('build', 'run'))
     depends_on('r-ggplot2@2.2:', type=('build', 'run'))
     depends_on('r-latticeextra', type=('build', 'run'))

From 232aa9ff2e5ce49af85d4c05a9d245e471586de5 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Fri, 15 May 2020 02:47:55 +0200
Subject: [PATCH 400/802] at-spi2-atk: Add 2.34.2 (#16647)

---
 var/spack/repos/builtin/packages/at-spi2-atk/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/at-spi2-atk/package.py b/var/spack/repos/builtin/packages/at-spi2-atk/package.py
index 3b2fd04e053..371b661b456 100644
--- a/var/spack/repos/builtin/packages/at-spi2-atk/package.py
+++ b/var/spack/repos/builtin/packages/at-spi2-atk/package.py
@@ -15,6 +15,7 @@ class AtSpi2Atk(MesonPackage):
     list_url = "http://ftp.gnome.org/pub/gnome/sources/at-spi2-atk"
     list_depth = 1
 
+    version('2.34.2', sha256='901323cee0eef05c01ec4dee06c701aeeca81a314a7d60216fa363005e27f4f0')
     version('2.26.2', sha256='61891f0abae1689f6617a963105a3f1dcdab5970c4a36ded9c79a7a544b16a6e')
     version('2.26.1', sha256='b4f0c27b61dbffba7a5b5ba2ff88c8cee10ff8dac774fa5b79ce906853623b75')
 

From 670a5e87666a541e908a22faa8341b8a59db4bcc Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Fri, 15 May 2020 02:48:21 +0200
Subject: [PATCH 401/802] atk: Add 2.36.0 (#16646)

---
 var/spack/repos/builtin/packages/atk/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/atk/package.py b/var/spack/repos/builtin/packages/atk/package.py
index 9bb7aeb2965..a28b053f01a 100644
--- a/var/spack/repos/builtin/packages/atk/package.py
+++ b/var/spack/repos/builtin/packages/atk/package.py
@@ -17,6 +17,7 @@ class Atk(Package):
     list_url = "https://ftp.gnome.org/pub/gnome/sources/atk"
     list_depth = 1
 
+    version('2.36.0', sha256='fb76247e369402be23f1f5c65d38a9639c1164d934e40f6a9cf3c9e96b652788')
     version('2.30.0', sha256='dd4d90d4217f2a0c1fee708a555596c2c19d26fef0952e1ead1938ab632c027b')
     version('2.28.1', sha256='cd3a1ea6ecc268a2497f0cd018e970860de24a6d42086919d6bf6c8e8d53f4fc')
     version('2.20.0', sha256='493a50f6c4a025f588d380a551ec277e070b28a82e63ef8e3c06b3ee7c1238f0')

From c168e1b85ef4cc353b9f4070d99404ecb42bc62f Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Fri, 15 May 2020 02:49:02 +0200
Subject: [PATCH 402/802] at-spi2-core: Add 2.36.0 (#16645)

The pkg-config file of newer versions of at-spi2-core includes
dependencies for xtst, recordproto, inputproto and fixesproto, so they
have to be available at runtime as well.
---
 .../repos/builtin/packages/at-spi2-core/package.py     | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/at-spi2-core/package.py b/var/spack/repos/builtin/packages/at-spi2-core/package.py
index 11695fd4c50..e7480e26a23 100644
--- a/var/spack/repos/builtin/packages/at-spi2-core/package.py
+++ b/var/spack/repos/builtin/packages/at-spi2-core/package.py
@@ -16,6 +16,7 @@ class AtSpi2Core(MesonPackage):
     list_url = "http://ftp.gnome.org/pub/gnome/sources/at-spi2-core"
     list_depth = 1
 
+    version('2.36.0', sha256='88da57de0a7e3c60bc341a974a80fdba091612db3547c410d6deab039ca5c05a')
     version('2.28.0', sha256='42a2487ab11ce43c288e73b2668ef8b1ab40a0e2b4f94e80fca04ad27b6f1c87')
 
     depends_on('glib@2.56.1:')
@@ -23,12 +24,13 @@ class AtSpi2Core(MesonPackage):
     depends_on('gettext')
     depends_on('libx11')
     depends_on('libxi')
-    depends_on('libxtst', type='build')
-    depends_on('recordproto', type='build')
-    depends_on('inputproto', type='build')
-    depends_on('fixesproto', type='build')
+    depends_on('libxtst')
+    depends_on('recordproto')
+    depends_on('inputproto')
+    depends_on('fixesproto')
     depends_on('pkgconfig', type='build')
     depends_on('python', type='build')
+    depends_on('gobject-introspection')
 
     def url_for_version(self, version):
         """Handle gnome's version-based custom URLs."""

From 0ed2fa3b9b4beac50bdfc82658a3bdfb395ae104 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E5=81=A5=E7=BE=8E=E7=8C=9E=E7=8C=81?=
 <weijianwen@gmail.com>
Date: Fri, 15 May 2020 08:50:11 +0800
Subject: [PATCH 403/802] miniforge3: a new package. (#16644)

---
 .../builtin/packages/miniforge3/package.py    | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/miniforge3/package.py

diff --git a/var/spack/repos/builtin/packages/miniforge3/package.py b/var/spack/repos/builtin/packages/miniforge3/package.py
new file mode 100644
index 00000000000..1fc1526153a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/miniforge3/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Miniforge3(Package):
+    """Miniforge3 is a minimal installer for conda specific to conda-forge."""
+
+    homepage = "https://github.com/conda-forge/miniforge"
+    url      = "https://github.com/conda-forge/miniforge/releases/download/4.8.3-2/Miniforge3-4.8.3-2-Linux-x86_64.sh"
+
+    version('4.8.3-2-Linux-x86_64',
+            url='https://github.com/conda-forge/miniforge/releases/download/4.8.3-2/Miniforge3-4.8.3-2-Linux-x86_64.sh',
+            sha256='c8e5b894fe91ce0f86e61065d2247346af107f8d53de0ad89ec848701c4ec1f9',
+            expand=False)
+    version('4.8.3-2-Linux-aarch64',
+            url='https://github.com/conda-forge/miniforge/releases/download/4.8.3-2/Miniforge3-4.8.3-2-Linux-aarch64.sh',
+            sha256='bfefc0ede6354568978b4198607edd7f17c2f50ca4c6a47e9f22f8c257c8230a',
+            expand=False)
+    version('4.8.3-2-MacOSX-x86_64',
+            url='https://github.com/conda-forge/miniforge/releases/download/4.8.3-2/Miniforge3-4.8.3-2-MacOSX-x86_64.sh',
+            sha256='25ca082ab00a776db356f9bbc660edf6d24659e2aec1cbec5fd4ce992d4d193d',
+            expand=False)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix)
+        pkgname = 'Miniforge3-{0}.sh'.format(self.version)
+        chmod = which('chmod')
+        chmod('+x', pkgname)
+        sh = which('sh')
+        sh('./{0}'.format(pkgname), '-b', '-f', '-s', '-p', prefix)

From 8c025324af19afa11be31d9eee3788707c149693 Mon Sep 17 00:00:00 2001
From: Andrew W Elble <aweits@rit.edu>
Date: Thu, 14 May 2020 21:04:06 -0400
Subject: [PATCH 404/802] ucx: cuda / gdrcopy variants (#16605)

picking up where #15724 left off.
---
 .../repos/builtin/packages/ucx/package.py     | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/ucx/package.py b/var/spack/repos/builtin/packages/ucx/package.py
index b345107c29c..2b3cfa4ab81 100644
--- a/var/spack/repos/builtin/packages/ucx/package.py
+++ b/var/spack/repos/builtin/packages/ucx/package.py
@@ -6,7 +6,7 @@
 from spack import *
 
 
-class Ucx(AutotoolsPackage):
+class Ucx(AutotoolsPackage, CudaPackage):
     """a communication library implementing high-performance messaging for
     MPI/PGAS frameworks"""
 
@@ -48,11 +48,16 @@ class Ucx(AutotoolsPackage):
             description='Builds with PIC support')
     variant('java', default=False,
             description='Builds with Java bindings')
+    variant('gdrcopy', default=False,
+            description='Enable gdrcopy support')
 
     depends_on('numactl')
     depends_on('rdma-core')
     depends_on('java@8', when='+java')
     depends_on('maven', when='+java')
+    depends_on('gdrcopy@1.3', when='+gdrcopy')
+    conflicts('+gdrcopy', when='~cuda',
+              msg='gdrcopy currently requires cuda support')
 
     def configure_args(self):
         spec = self.spec
@@ -92,4 +97,16 @@ def configure_args(self):
         else:
             config_args.append('--without-java')
 
+        if '+cuda' in spec:
+            config_args.append('--with-cuda={0}'.format(
+                self.spec['cuda'].prefix))
+        else:
+            config_args.append('--without-cuda')
+
+        if '+gdrcopy' in spec:
+            config_args.append('--with-gdrcopy={0}'.format(
+                self.spec['gdrcopy'].prefix))
+        else:
+            config_args.append('--without-gdrcopy')
+
         return config_args

From b562059d2ac1004b1757512a819db7f99661d2ae Mon Sep 17 00:00:00 2001
From: Jen Herting <jen@herting.cc>
Date: Thu, 14 May 2020 21:06:21 -0400
Subject: [PATCH 405/802] New package: maloc (#16631)

* [maloc] created template

* [maloc] added some build dependencies

* [maloc] added homepage and description

* [maloc] added doc variant in an attempt to disable documentation. Still builds doc though... at least when there is a system doxygen found. Having doxygen being a dependency here can bring python in and cause issues for dependents, even when listed as only a build dependency. Maybe this is a bug?

* [maloc] flake8 and fixme removal

* [maloc] shorted description
---
 .../repos/builtin/packages/maloc/package.py   | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/maloc/package.py

diff --git a/var/spack/repos/builtin/packages/maloc/package.py b/var/spack/repos/builtin/packages/maloc/package.py
new file mode 100644
index 00000000000..058ce3f0c88
--- /dev/null
+++ b/var/spack/repos/builtin/packages/maloc/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Maloc(AutotoolsPackage):
+    """MALOC (Minimal Abstraction Layer for Object-oriented C)
+    is a small, portable, abstract C environment library for
+    object-oriented C programming. MALOC is used as the
+    foundation layer for a number of scientific applications,
+    including MC, SG, and APBS."""
+
+    homepage = "http://fetk.org/codes/maloc/"
+    url      = "http://www.fetk.org/codes/download/maloc-1.0.tar.gz"
+
+    version('1.5', sha256='58e1197fcd4c74d3cbb1d39d712eb0a3c5886a1e6629f22c5c78ce2bac983fc0')
+    version('1.4', sha256='cba0c6730f148bf7ddb77dac07e497655642f43b632256fcebf3192b45af1833')
+    version('1.3', sha256='337788ac8f263487aba5b3aa5ef7f33eaac1d3951ad49349078d5ed77482ad2e')
+    version('1.2', sha256='e6033195a054bad7527d360e52349a4d1eb876c681a58fa373f42fd1ab26962c')
+    version('1.1', sha256='b5dd7923e84f13e7ed43304ed1062de24171c5a7a042a12b0d1e501d6eaedf58')
+    version('1.0', sha256='23f3ea3215067fd8f1ba4c407375f387b5f1d11258f29508295e651828d32cb7')
+
+    variant('doc', default=False, description='Build documentation.')
+
+    depends_on('graphviz', type='build', when='+doc')
+    depends_on('doxygen', type='build', when='+doc')
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+
+        if '~doc' in spec:
+            args.append('--with-doxygen=no')
+            args.append('--with-dot=no')
+
+        return args

From e21b4731a97fe79a34d80b52fa4ad089ad70ac74 Mon Sep 17 00:00:00 2001
From: Andrew W Elble <aweits@rit.edu>
Date: Thu, 14 May 2020 21:09:41 -0400
Subject: [PATCH 406/802] lammps: set LAMMPS_POTENTIALS in the runtime
 environment (#16643)

so lammps can find the installed potential files
---
 var/spack/repos/builtin/packages/lammps/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/lammps/package.py b/var/spack/repos/builtin/packages/lammps/package.py
index 5bf2986858c..b578016311a 100644
--- a/var/spack/repos/builtin/packages/lammps/package.py
+++ b/var/spack/repos/builtin/packages/lammps/package.py
@@ -182,3 +182,7 @@ def cmake_args(self):
             args.append('-DEXTERNAL_KOKKOS=ON')
 
         return args
+
+    def setup_run_environment(self, env):
+        env.set('LAMMPS_POTENTIALS',
+                self.prefix.share.lammps.potentials)

From 5875bc6d6b635714b0e8c9b536d623077a417c74 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Fri, 15 May 2020 03:10:58 +0200
Subject: [PATCH 407/802] scorep: Fix build with gcc@10: (#16642)

---
 .../repos/builtin/packages/scorep/gcc10.patch      | 14 ++++++++++++++
 var/spack/repos/builtin/packages/scorep/package.py |  3 ++-
 2 files changed, 16 insertions(+), 1 deletion(-)
 create mode 100644 var/spack/repos/builtin/packages/scorep/gcc10.patch

diff --git a/var/spack/repos/builtin/packages/scorep/gcc10.patch b/var/spack/repos/builtin/packages/scorep/gcc10.patch
new file mode 100644
index 00000000000..76bcb987ca0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/scorep/gcc10.patch
@@ -0,0 +1,14 @@
+--- a/src/adapters/compiler/gcc-plugin/scorep_plugin_pass_instrument.inc.c
++++ b/src/adapters/compiler/gcc-plugin/scorep_plugin_pass_instrument.inc.c
+@@ -83,7 +83,11 @@ is_instrumentable( const char* assemblerName )
+         return "in system header";
+     }
+ 
++#if SCOREP_GCC_PLUGIN_TARGET_VERSION < 10000
+     if ( node->global.inlined_to )
++#else
++    if ( node->inlined_to )
++#endif
+     {
+         return "was inlined";
+     }
diff --git a/var/spack/repos/builtin/packages/scorep/package.py b/var/spack/repos/builtin/packages/scorep/package.py
index b26af4287db..d7b57c0c446 100644
--- a/var/spack/repos/builtin/packages/scorep/package.py
+++ b/var/spack/repos/builtin/packages/scorep/package.py
@@ -25,7 +25,8 @@ class Scorep(AutotoolsPackage):
     version('1.4.2', sha256='d7f3fcca2efeb2f5d5b5f183b3b2c4775e66cbb3400ea2da841dd0428713ebac')
     version('1.3',   sha256='dcfd42bd05f387748eeefbdf421cb3cd98ed905e009303d70b5f75b217fd1254')
 
-    patch('gcc7.patch', when='@:3')
+    patch('gcc7.patch', when='@1.4:3')
+    patch('gcc10.patch', when='@3.1:')
 
     variant('mpi', default=True, description="Enable MPI support")
     variant('papi', default=True, description="Enable PAPI")

From b9874448716abe1e6331291dad057aa5c8f7d416 Mon Sep 17 00:00:00 2001
From: Robert Blake <blake14@llnl.gov>
Date: Thu, 14 May 2020 18:16:55 -0700
Subject: [PATCH 408/802] Fixing the build directory for cardioid. (#16640)

* Fixing the build directory for cardioid.

* These imports are no longer needed due to deletions.

Co-authored-by: Robert Blake <rob.c.blake.3@gmail.com>
---
 .../repos/builtin/packages/cardioid/package.py   | 16 ----------------
 1 file changed, 16 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cardioid/package.py b/var/spack/repos/builtin/packages/cardioid/package.py
index 73e980be247..c95035b5bf1 100644
--- a/var/spack/repos/builtin/packages/cardioid/package.py
+++ b/var/spack/repos/builtin/packages/cardioid/package.py
@@ -4,8 +4,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
-import spack.environment as ev
-import os
 
 
 class Cardioid(CMakePackage):
@@ -32,20 +30,6 @@ class Cardioid(CMakePackage):
     depends_on('cmake@3.1:', type='build')
     depends_on('perl', type='build')
 
-    @property
-    def build_directory(self):
-        """Returns the directory to use when building the package
-
-        :return: directory where to build the package
-        """
-        env = ev.get_env(None, 'env status')
-        if not env:
-            basename = str(self.spec.arch)
-        else:
-            basename = env.name
-
-        return os.path.join(self.stage.source_path, "build", basename)
-
     def cmake_args(self):
         spec = self.spec
         args = [

From ea818caca3589dbc0bba3e36e2d75ee7ef811b56 Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Fri, 15 May 2020 10:17:53 +0900
Subject: [PATCH 409/802] namd: build on aarch64. (#16639)

---
 var/spack/repos/builtin/packages/namd/package.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/namd/package.py b/var/spack/repos/builtin/packages/namd/package.py
index d6f5b11b4a7..a85dd7fd42a 100644
--- a/var/spack/repos/builtin/packages/namd/package.py
+++ b/var/spack/repos/builtin/packages/namd/package.py
@@ -74,6 +74,7 @@ def build_directory(self):
         return '{0}-spack'.format(self.arch)
 
     def edit(self, spec, prefix):
+        m64 = '-m64 ' if not spec.satisfies('arch=aarch64:') else ''
         with working_dir('arch'):
             with open('{0}.arch'.format(self.build_directory), 'w') as fh:
                 # this options are take from the default provided
@@ -81,12 +82,12 @@ def edit(self, spec, prefix):
                 # https://github.com/UIUC-PPL/charm/pull/2778
                 if self.spec.satisfies('^charmpp@:6.10.1'):
                     optims_opts = {
-                        'gcc': '-m64 -O3 -fexpensive-optimizations \
+                        'gcc': m64 + '-O3 -fexpensive-optimizations \
                                 -ffast-math -lpthread',
                         'intel': '-O2 -ip'}
                 else:
                     optims_opts = {
-                        'gcc': '-m64 -O3 -fexpensive-optimizations \
+                        'gcc': m64 + '-O3 -fexpensive-optimizations \
                                 -ffast-math',
                         'intel': '-O2 -ip'}
 

From 47b3dda1aa92ab98450950ba6383282cbf158857 Mon Sep 17 00:00:00 2001
From: Scott Wittenburg <scott.wittenburg@kitware.com>
Date: Tue, 12 May 2020 16:16:52 -0600
Subject: [PATCH 410/802] Support os-specific $padding in config:install_tree

Providing only $padding or ${padding} results in an attempt to
substitute a padding of maximum system path length, while leaving
room for the parts of the install path spack generates.  Providing
$padding-<len> or ${padding-<len>} simply substitutes padding of
the specified length.
---
 lib/spack/spack/test/config.py | 46 ++++++++++++++++-----
 lib/spack/spack/util/path.py   | 73 ++++++++++++++++++++++++++++++++++
 2 files changed, 108 insertions(+), 11 deletions(-)

diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py
index b8598616d50..8212db6c214 100644
--- a/lib/spack/spack/test/config.py
+++ b/lib/spack/spack/test/config.py
@@ -23,7 +23,7 @@
 import spack.schema.mirrors
 import spack.schema.repos
 import spack.util.spack_yaml as syaml
-from spack.util.path import canonicalize_path
+import spack.util.path as spack_path
 
 
 # sample config data
@@ -272,31 +272,31 @@ def test_substitute_config_variables(mock_low_high_config):
 
     assert os.path.join(
         '/foo/bar/baz', prefix
-    ) == canonicalize_path('/foo/bar/baz/$spack')
+    ) == spack_path.canonicalize_path('/foo/bar/baz/$spack')
 
     assert os.path.join(
         spack.paths.prefix, 'foo/bar/baz'
-    ) == canonicalize_path('$spack/foo/bar/baz/')
+    ) == spack_path.canonicalize_path('$spack/foo/bar/baz/')
 
     assert os.path.join(
         '/foo/bar/baz', prefix, 'foo/bar/baz'
-    ) == canonicalize_path('/foo/bar/baz/$spack/foo/bar/baz/')
+    ) == spack_path.canonicalize_path('/foo/bar/baz/$spack/foo/bar/baz/')
 
     assert os.path.join(
         '/foo/bar/baz', prefix
-    ) == canonicalize_path('/foo/bar/baz/${spack}')
+    ) == spack_path.canonicalize_path('/foo/bar/baz/${spack}')
 
     assert os.path.join(
         spack.paths.prefix, 'foo/bar/baz'
-    ) == canonicalize_path('${spack}/foo/bar/baz/')
+    ) == spack_path.canonicalize_path('${spack}/foo/bar/baz/')
 
     assert os.path.join(
         '/foo/bar/baz', prefix, 'foo/bar/baz'
-    ) == canonicalize_path('/foo/bar/baz/${spack}/foo/bar/baz/')
+    ) == spack_path.canonicalize_path('/foo/bar/baz/${spack}/foo/bar/baz/')
 
     assert os.path.join(
         '/foo/bar/baz', prefix, 'foo/bar/baz'
-    ) != canonicalize_path('/foo/bar/baz/${spack/foo/bar/baz/')
+    ) != spack_path.canonicalize_path('/foo/bar/baz/${spack/foo/bar/baz/')
 
 
 packages_merge_low = {
@@ -345,19 +345,43 @@ def test_merge_with_defaults(mock_low_high_config, write_config_file):
 
 def test_substitute_user(mock_low_high_config):
     user = getpass.getuser()
-    assert '/foo/bar/' + user + '/baz' == canonicalize_path(
+    assert '/foo/bar/' + user + '/baz' == spack_path.canonicalize_path(
         '/foo/bar/$user/baz'
     )
 
 
 def test_substitute_tempdir(mock_low_high_config):
     tempdir = tempfile.gettempdir()
-    assert tempdir == canonicalize_path('$tempdir')
-    assert tempdir + '/foo/bar/baz' == canonicalize_path(
+    assert tempdir == spack_path.canonicalize_path('$tempdir')
+    assert tempdir + '/foo/bar/baz' == spack_path.canonicalize_path(
         '$tempdir/foo/bar/baz'
     )
 
 
+def test_substitute_padding(mock_low_high_config):
+    max_system_path = spack_path.get_system_path_max()
+    expected_length = (max_system_path -
+                       spack_path.SPACK_MAX_INSTALL_PATH_LENGTH)
+
+    install_path = spack_path.canonicalize_path('/foo/bar/${padding}/baz')
+
+    assert spack_path.SPACK_PATH_PADDING_CHARS in install_path
+    assert len(install_path) == expected_length
+
+    install_path = spack_path.canonicalize_path('/foo/bar/baz/gah/$padding')
+
+    assert spack_path.SPACK_PATH_PADDING_CHARS in install_path
+    assert len(install_path) == expected_length
+
+    i_path = spack_path.canonicalize_path('/foo/$padding:10')
+    i_expect = os.path.join('/foo', spack_path.SPACK_PATH_PADDING_CHARS[:10])
+    assert i_path == i_expect
+
+    i_path = spack_path.canonicalize_path('/foo/${padding:20}')
+    i_expect = os.path.join('/foo', spack_path.SPACK_PATH_PADDING_CHARS[:20])
+    assert i_path == i_expect
+
+
 def test_read_config(mock_low_high_config, write_config_file):
     write_config_file('config', config_low, 'low')
     assert spack.config.get('config') == config_low['config']
diff --git a/lib/spack/spack/util/path.py b/lib/spack/spack/util/path.py
index 9d5413c6091..8bcf598882b 100644
--- a/lib/spack/spack/util/path.py
+++ b/lib/spack/spack/util/path.py
@@ -10,8 +10,12 @@
 import os
 import re
 import getpass
+import subprocess
 import tempfile
 
+import llnl.util.tty as tty
+from llnl.util.lang import memoized
+
 import spack.paths
 
 
@@ -27,6 +31,38 @@
     'tempdir': tempfile.gettempdir(),
 }
 
+# This is intended to be longer than the part of the install path
+# spack generates from the root path we give it.  Included in the
+# estimate:
+#
+#   os-arch      ->   30
+#   compiler     ->   30
+#   package name ->   50   (longest is currently 47 characters)
+#   version      ->   20
+#   hash         ->   32
+#   buffer       ->  138
+#  ---------------------
+#   total        ->  300
+SPACK_MAX_INSTALL_PATH_LENGTH = 300
+SPACK_PATH_PADDING_CHARS = 'spack_path_placeholder'
+
+
+@memoized
+def get_system_path_max():
+    # Choose a conservative default
+    sys_max_path_length = 256
+    try:
+        path_max_proc  = subprocess.Popen(['getconf', 'PATH_MAX', '/'],
+                                          stdout=subprocess.PIPE,
+                                          stderr=subprocess.STDOUT)
+        proc_output = str(path_max_proc.communicate()[0].decode())
+        sys_max_path_length = int(proc_output)
+    except (ValueError, subprocess.CalledProcessError, OSError):
+        tty.msg('Unable to find system max path length, using: {0}'.format(
+            sys_max_path_length))
+
+    return sys_max_path_length
+
 
 def substitute_config_variables(path):
     """Substitute placeholders into paths.
@@ -58,8 +94,45 @@ def substitute_path_variables(path):
     return path
 
 
+def _get_padding_string(length):
+    spack_path_padding_size = len(SPACK_PATH_PADDING_CHARS)
+    num_reps = int(length / (spack_path_padding_size + 1))
+    extra_chars = length % (spack_path_padding_size + 1)
+    reps_list = [SPACK_PATH_PADDING_CHARS for i in range(num_reps)]
+    reps_list.append(SPACK_PATH_PADDING_CHARS[:extra_chars])
+    return os.path.sep.join(reps_list)
+
+
+def _add_computed_padding(path):
+    """Subtitute in padding of os-specific length.  The intent is to leave
+    SPACK_MAX_INSTALL_PATH_LENGTH characters available for parts of the
+    path generated by spack.  This is to allow for not-completely-known
+    lengths of things like os/arch, compiler, package name, hash length,
+    etc.
+    """
+    padding_regex = re.compile(r'(\$[\w\d\:]+\b|\$\{[\w\d\:]+\})')
+    m = padding_regex.search(path)
+    if m and m.group(0).strip('${}').startswith('padding'):
+        padding_part = m.group(0)
+        len_pad_part = len(m.group(0))
+        p_match = re.search(r'\:(\d+)', padding_part)
+        if p_match:
+            computed_padding = _get_padding_string(int(p_match.group(1)))
+        else:
+            # Take whatever has been computed/substituted so far and add some
+            # room
+            path_len = len(path) - len_pad_part + SPACK_MAX_INSTALL_PATH_LENGTH
+            system_max_path = get_system_path_max()
+            needed_pad_len = system_max_path - path_len
+            computed_padding = _get_padding_string(needed_pad_len)
+        return padding_regex.sub(computed_padding, path)
+    return path
+
+
 def canonicalize_path(path):
     """Same as substitute_path_variables, but also take absolute path."""
     path = substitute_path_variables(path)
     path = os.path.abspath(path)
+    path = _add_computed_padding(path)
+
     return path

From e0572a7d96402b7d3ed4f6ad373aa785a8ca76e7 Mon Sep 17 00:00:00 2001
From: Scott Wittenburg <scott.wittenburg@kitware.com>
Date: Tue, 12 May 2020 16:17:50 -0600
Subject: [PATCH 411/802] Pipelines: Support DAG scheduling and dynamic child
 pipelines

This change also adds a code path through the spack ci pipelines
infrastructure which supports PR testing on the Spack repository.
Gitlab pipelines run as a result of a PR (either creation or pushing
to a PR branch) will only verify that the packages in the environment
build without error.  When the PR branch is merged to develop,
another pipeline will run which results in the generated binaries
getting pushed to the binary mirror.
---
 lib/spack/docs/pipelines.rst                  | 130 +++----
 lib/spack/spack/ci.py                         | 135 ++++++--
 lib/spack/spack/cmd/ci.py                     | 129 +------
 lib/spack/spack/test/cmd/ci.py                | 318 +++++++++++++-----
 share/spack/gitlab/pr_pipeline.yml            |  20 ++
 share/spack/spack-completion.bash             |  10 +-
 .../builtin.mock/packages/gcc/package.py      |   3 +
 7 files changed, 444 insertions(+), 301 deletions(-)
 create mode 100644 share/spack/gitlab/pr_pipeline.yml

diff --git a/lib/spack/docs/pipelines.rst b/lib/spack/docs/pipelines.rst
index 0f092d5c5cb..d1128163b1f 100644
--- a/lib/spack/docs/pipelines.rst
+++ b/lib/spack/docs/pipelines.rst
@@ -32,30 +32,46 @@ for setting up a build pipeline are as follows:
 #. Create a repository on your gitlab instance
 #. Add a ``spack.yaml`` at the root containing your pipeline environment (see
    below for details)
-#. Add a ``.gitlab-ci.yml`` at the root containing a single job, similar to
+#. Add a ``.gitlab-ci.yml`` at the root containing two jobs (one to generate
+   the pipeline dynamically, and one to run the generated jobs), similar to
    this one:
 
    .. code-block:: yaml
 
-      pipeline-job:
+      stages: [generate, build]
+
+      generate-pipeline:
+        stage: generate
         tags:
           - <custom-tag>
-          ...
         script:
-          - spack ci start
+          - spack ci generate
+            --output-file "${CI_PROJECT_DIR}/jobs_scratch_dir/pipeline.yml"
+        artifacts:
+          paths:
+            - "${CI_PROJECT_DIR}/jobs_scratch_dir/pipeline.yml"
+
+      build-jobs:
+        stage: build
+        trigger:
+          include:
+            - artifact: "jobs_scratch_dir/pipeline.yml"
+              job: generate-pipeline
+          strategy: depend
+
 
 #. Add any secrets required by the CI process to environment variables using the
    CI web ui
 #. Push a commit containing the ``spack.yaml`` and ``.gitlab-ci.yml`` mentioned above
    to the gitlab repository
 
-The ``<custom-tag>``, above, is used to pick one of your configured runners,
-while the use of the ``spack ci start`` command implies that runner has an
-appropriate version of spack installed and configured for use.  Of course, there
-are myriad ways to customize the process.  You can configure CDash reporting
-on the progress of your builds, set up S3 buckets to mirror binaries built by
-the pipeline, clone a custom spack repository/ref for use by the pipeline, and
-more.
+The ``<custom-tag>``, above, is used to pick one of your configured runners to
+run the pipeline generation phase (this is implemented in the ``spack ci generate``
+command, which assumes the runner has an appropriate version of spack installed
+and configured for use).  Of course, there are many ways to customize the process.
+You can configure CDash reporting on the progress of your builds, set up S3 buckets
+to mirror binaries built by the pipeline, clone a custom spack repository/ref for
+use by the pipeline, and more.
 
 While it is possible to set up pipelines on gitlab.com, the builds there are
 limited to 60 minutes and generic hardware.  It is also possible to
@@ -64,15 +80,24 @@ Gitlab to Google Kubernetes Engine (`GKE <https://cloud.google.com/kubernetes-en
 or Amazon Elastic Kubernetes Service (`EKS <https://aws.amazon.com/eks>`_), though those
 topics are outside the scope of this document.
 
+Spack's pipelines are now making use of the
+`trigger <https://docs.gitlab.com/12.9/ee/ci/yaml/README.html#trigger>` syntax to run
+dynamically generated
+`child pipelines <https://docs.gitlab.com/12.9/ee/ci/parent_child_pipelines.html>`.
+Note that the use of dynamic child pipelines requires running Gitlab version
+``>= 12.9``.
+
 -----------------------------------
 Spack commands supporting pipelines
 -----------------------------------
 
-Spack provides a command `ci` with sub-commands for doing various things related
-to automated build pipelines.  All of the ``spack ci ...`` commands must be run
-from within a environment, as each one makes use of the environment for different
-purposes.  Additionally, some options to the commands (or conditions present in
-the spack environment file) may require particular environment variables to be
+Spack provides a command ``ci`` with two sub-commands: ``spack ci generate`` generates
+a pipeline (a .gitlab-ci.yml file) from a spack environment, and ``spack ci rebuild``
+checks a spec against a remote mirror and possibly rebuilds it from source and updates
+the binary mirror with the latest built package.  Both ``spack ci ...`` commands must
+be run from within the same environment, as each one makes use of the environment for
+different purposes.  Additionally, some options to the commands (or conditions present
+in the spack environment file) may require particular environment variables to be
 set in order to function properly.  Examples of these are typically secrets
 needed for pipeline operation that should not be visible in a spack environment
 file.  These environment variables are described in more detail
@@ -87,15 +112,6 @@ file.  These environment variables are described in more detail
 Super-command for functionality related to generating pipelines and executing
 pipeline jobs.
 
-.. _cmd_spack_ci_start:
-
-^^^^^^^^^^^^^^^^^^
-``spack ci start``
-^^^^^^^^^^^^^^^^^^
-
-Currently this command is a short-cut to first run ``spack ci generate``, followed
-by ``spack ci pushyaml``.
-
 .. _cmd_spack_ci_generate:
 
 ^^^^^^^^^^^^^^^^^^^^^
@@ -105,39 +121,6 @@ by ``spack ci pushyaml``.
 Concretizes the specs in the active environment, stages them (as described in
 :ref:`staging_algorithm`), and writes the resulting ``.gitlab-ci.yml`` to disk.
 
-.. _cmd_spack_ci_pushyaml:
-
-^^^^^^^^^^^^^^^^^^^^^
-``spack ci pushyaml``
-^^^^^^^^^^^^^^^^^^^^^
-
-Generates a commit containing the generated ``.gitlab-ci.yml`` and pushes it to a
-``DOWNSTREAM_CI_REPO``, which is frequently the same repository.  The branch
-created has the same name as the current branch being tested, but has ``multi-ci-``
-prepended to the branch name.  Once Gitlab CI has full support for dynamically
-defined workloads, this command will be deprecated.
-
-Until this command is no longer needed and can be deprecated, there are
-a few gotchas to note.  While you can embed your username and password in the
-`DOWNSTREAM_CI_REPO` url, you may not be able to have Gitlab mask the value, as
-it will likely contain characters that Gitlab cannot currently mask.  Another
-option is to set up an SSH token, but for this to work, the associated SSH
-key must be passphrase-less so that it can be provided in an automated manner.
-
-If you attempt to set up an SSH token that does require a passphrase, you may
-see a log message similar to:
-
-```
-fatal: https://<instance-url>/<org>/<project>:<port>/info/refs not valid: is this a git repository?
-```
-
-In this case, you can try a passphrase-less SSH key, or else embed your gitlab
-username and password in the `DOWNSTREAM_CI_REPO` as in the following example:
-
-```
-https://<username>:<password>@<instance-url>/<org>/<project>.git
-```
-
 .. _cmd_spack_ci_rebuild:
 
 ^^^^^^^^^^^^^^^^^^^^
@@ -179,14 +162,14 @@ sections describing a build pipeline:
              - os=ubuntu18.04
            runner-attributes:
              tags:
-               - spack-k8s
-             image: spack/spack_builder_ubuntu_18.04
+               - spack-kube
+             image: spack/ubuntu-bionic
          - match:
              - os=centos7
            runner-attributes:
              tags:
-               - spack-k8s
-             image: spack/spack_builder_centos_7
+               - spack-kube
+             image: spack/centos7
      cdash:
        build-group: Release Testing
        url: https://cdash.spack.io
@@ -389,22 +372,29 @@ containing the url and branch/tag you want to clone (calling them, for example,
 ``SPACK_REPO`` and ``SPACK_REF``), use them to clone spack in your pre-ci
 ``before_script``, and finally pass those same values along to the workload
 generation process via the ``spack-repo`` and ``spack-ref`` cli args.  Here's
-an example:
+the ``generate-pipeline`` job from the top of this document, updated to clone
+a custom spack and make sure the generated rebuild jobs will clone it too:
 
 .. code-block:: yaml
 
-   pipeline-job:
+   generate-pipeline:
      tags:
        - <some-other-tag>
    before_script:
      - git clone ${SPACK_REPO} --branch ${SPACK_REF}
      - . ./spack/share/spack/setup-env.sh
    script:
-     - spack ci start --spack-repo ${SPACK_REPO} --spack-ref ${SPACK_REF} <...args>
+     - spack ci generate
+       --spack-repo ${SPACK_REPO} --spack-ref ${SPACK_REF}
+       --output-file "${CI_PROJECT_DIR}/jobs_scratch_dir/pipeline.yml"
    after_script:
      - rm -rf ./spack
+   artifacts:
+     paths:
+       - "${CI_PROJECT_DIR}/jobs_scratch_dir/pipeline.yml"
 
-If the ``spack ci start`` command receives those extra command line arguments,
+
+If the ``spack ci generate`` command receives those extra command line arguments,
 then it adds similar ``before_script`` and ``after_script`` sections for each of
 the ``spack ci rebuild`` jobs it generates (cloning and sourcing a custom
 spack in the ``before_script`` and removing it again in the ``after_script``).
@@ -451,11 +441,3 @@ SPACK_SIGNING_KEY
 ^^^^^^^^^^^^^^^^^
 
 Needed to sign/verify binary packages from the remote binary mirror.
-
-^^^^^^^^^^^^^^^^^^
-DOWNSTREAM_CI_REPO
-^^^^^^^^^^^^^^^^^^
-
-Needed until Gitlab CI supports dynamic job generation.  Can contain connection
-credentials embedded in the url, and could be the same repository or a different
-one.
diff --git a/lib/spack/spack/ci.py b/lib/spack/spack/ci.py
index cbdfccb8bfc..069cbb704a7 100644
--- a/lib/spack/spack/ci.py
+++ b/lib/spack/spack/ci.py
@@ -24,7 +24,6 @@
 import spack.compilers as compilers
 import spack.config as cfg
 import spack.environment as ev
-from spack.dependency import all_deptypes
 from spack.error import SpackError
 import spack.hash_types as ht
 from spack.main import SpackCommand
@@ -34,6 +33,21 @@
 import spack.util.web as web_util
 
 
+JOB_RETRY_CONDITIONS = [
+    'unknown_failure',
+    'api_failure',
+    'stuck_or_timeout_failure',
+    'runner_system_failure',
+    'missing_dependency_failure',
+    'runner_unsupported',
+    'stale_schedule',
+    'job_execution_timeout',
+    'archived_failure',
+    'unmet_prerequisites',
+    'scheduler_failure',
+    'data_integrity_failure',
+]
+
 spack_gpg = SpackCommand('gpg')
 spack_compiler = SpackCommand('compiler')
 
@@ -360,7 +374,6 @@ def compute_spec_deps(spec_list):
        }
 
     """
-    deptype = all_deptypes
     spec_labels = {}
 
     specs = []
@@ -380,7 +393,7 @@ def append_dep(s, d):
 
         rkey, rlabel = spec_deps_key_label(spec)
 
-        for s in spec.traverse(deptype=deptype):
+        for s in spec.traverse(deptype=all):
             if s.external:
                 tty.msg('Will not stage external pkg: {0}'.format(s))
                 continue
@@ -392,7 +405,7 @@ def append_dep(s, d):
             }
             append_dep(rlabel, slabel)
 
-            for d in s.dependencies(deptype=deptype):
+            for d in s.dependencies(deptype=all):
                 dkey, dlabel = spec_deps_key_label(d)
                 if d.external:
                     tty.msg('Will not stage external dep: {0}'.format(d))
@@ -400,11 +413,11 @@ def append_dep(s, d):
 
                 append_dep(slabel, dlabel)
 
-    for l, d in spec_labels.items():
+    for spec_label, spec_holder in spec_labels.items():
         specs.append({
-            'label': l,
-            'spec': d['spec'],
-            'root_spec': d['root'],
+            'label': spec_label,
+            'spec': spec_holder['spec'],
+            'root_spec': spec_holder['root'],
         })
 
     deps_json_obj = {
@@ -431,6 +444,21 @@ def pkg_name_from_spec_label(spec_label):
     return spec_label[:spec_label.index('/')]
 
 
+def format_job_needs(phase_name, strip_compilers, dep_jobs,
+                     osname, build_group, enable_artifacts_buildcache):
+    needs_list = []
+    for dep_job in dep_jobs:
+        needs_list.append({
+            'job': get_job_name(phase_name,
+                                strip_compilers,
+                                dep_job,
+                                osname,
+                                build_group),
+            'artifacts': enable_artifacts_buildcache,
+        })
+    return needs_list
+
+
 def generate_gitlab_ci_yaml(env, print_summary, output_file,
                             custom_spack_repo=None, custom_spack_ref=None):
     # FIXME: What's the difference between one that opens with 'spack'
@@ -466,6 +494,10 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
             tty.verbose("Using CDash auth token from environment")
             cdash_auth_token = os.environ.get('SPACK_CDASH_AUTH_TOKEN')
 
+    is_pr_pipeline = (
+        os.environ.get('SPACK_IS_PR_PIPELINE', '').lower() == 'true'
+    )
+
     # Make sure we use a custom spack if necessary
     before_script = None
     after_script = None
@@ -538,6 +570,9 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
 
     stage_names = []
 
+    max_length_needs = 0
+    max_needs_job = ''
+
     for phase in phases:
         phase_name = phase['name']
         strip_compilers = phase['strip-compilers']
@@ -601,25 +636,35 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
                         root_spec, main_phase, strip_compilers),
                     'SPACK_JOB_SPEC_PKG_NAME': release_spec.name,
                     'SPACK_COMPILER_ACTION': compiler_action,
+                    'SPACK_IS_PR_PIPELINE': str(is_pr_pipeline),
                 }
 
                 job_dependencies = []
                 if spec_label in dependencies:
-                    for dep_label in dependencies[spec_label]:
-                        dep_pkg = pkg_name_from_spec_label(dep_label)
-                        dep_spec = spec_labels[dep_label]['rootSpec'][dep_pkg]
-                        dep_job_name = get_job_name(
-                            phase_name, strip_compilers, dep_spec, osname,
-                            build_group)
-                        job_dependencies.append(dep_job_name)
+                    if enable_artifacts_buildcache:
+                        dep_jobs = [
+                            d for d in release_spec.traverse(deptype=all,
+                                                             root=False)
+                        ]
+                    else:
+                        dep_jobs = []
+                        for dep_label in dependencies[spec_label]:
+                            dep_pkg = pkg_name_from_spec_label(dep_label)
+                            dep_root = spec_labels[dep_label]['rootSpec']
+                            dep_jobs.append(dep_root[dep_pkg])
+
+                    job_dependencies.extend(
+                        format_job_needs(phase_name, strip_compilers, dep_jobs,
+                                         osname, build_group,
+                                         enable_artifacts_buildcache))
 
                 # This next section helps gitlab make sure the right
                 # bootstrapped compiler exists in the artifacts buildcache by
                 # creating an artificial dependency between this spec and its
                 # compiler.  So, if we are in the main phase, and if the
                 # compiler we are supposed to use is listed in any of the
-                # bootstrap spec lists, then we will add one more dependency to
-                # "job_dependencies" (that compiler).
+                # bootstrap spec lists, then we will add more dependencies to
+                # the job (that compiler and maybe it's dependencies as well).
                 if is_main_phase(phase_name):
                     compiler_pkg_spec = compilers.pkg_spec_for_compiler(
                         release_spec.compiler)
@@ -627,12 +672,25 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
                         bs_arch = bs['spec'].architecture
                         if (bs['spec'].satisfies(compiler_pkg_spec) and
                             bs_arch == release_spec.architecture):
-                            c_job_name = get_job_name(bs['phase-name'],
-                                                      bs['strip-compilers'],
-                                                      bs['spec'],
-                                                      str(bs_arch),
-                                                      build_group)
-                            job_dependencies.append(c_job_name)
+                            # We found the bootstrap compiler this release spec
+                            # should be built with, so for DAG scheduling
+                            # purposes, we will at least add the compiler spec
+                            # to the jobs "needs".  But if artifact buildcache
+                            # is enabled, we'll have to add all transtive deps
+                            # of the compiler as well.
+                            dep_jobs = [bs['spec']]
+                            if enable_artifacts_buildcache:
+                                dep_jobs = [
+                                    d for d in bs['spec'].traverse(deptype=all)
+                                ]
+
+                            job_dependencies.extend(
+                                format_job_needs(bs['phase-name'],
+                                                 bs['strip-compilers'],
+                                                 dep_jobs,
+                                                 str(bs_arch),
+                                                 build_group,
+                                                 enable_artifacts_buildcache))
 
                 if enable_cdash_reporting:
                     cdash_build_name = get_cdash_build_name(
@@ -647,7 +705,7 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
 
                     job_vars['SPACK_CDASH_BUILD_NAME'] = cdash_build_name
                     job_vars['SPACK_RELATED_BUILDS_CDASH'] = ';'.join(
-                        related_builds)
+                        sorted(related_builds))
 
                 variables.update(job_vars)
 
@@ -657,7 +715,12 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
                 ]
 
                 if enable_artifacts_buildcache:
-                    artifact_paths.append('local_mirror/build_cache')
+                    bc_root = 'local_mirror/build_cache'
+                    artifact_paths.extend([os.path.join(bc_root, p) for p in [
+                        bindist.tarball_name(release_spec, '.spec.yaml'),
+                        bindist.tarball_name(release_spec, '.cdashid'),
+                        bindist.tarball_directory_name(release_spec),
+                    ]])
 
                 job_object = {
                     'stage': stage_name,
@@ -668,9 +731,18 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
                         'paths': artifact_paths,
                         'when': 'always',
                     },
-                    'dependencies': job_dependencies,
+                    'needs': sorted(job_dependencies, key=lambda d: d['job']),
+                    'retry': {
+                        'max': 2,
+                        'when': JOB_RETRY_CONDITIONS,
+                    }
                 }
 
+                length_needs = len(job_dependencies)
+                if length_needs > max_length_needs:
+                    max_length_needs = length_needs
+                    max_needs_job = job_name
+
                 if before_script:
                     job_object['before_script'] = before_script
 
@@ -691,6 +763,9 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
     tty.debug('{0} build jobs generated in {1} stages'.format(
         job_id, stage_id))
 
+    tty.debug('The max_needs_job is {0}, with {1} needs'.format(
+        max_needs_job, max_length_needs))
+
     # Use "all_job_names" to populate the build group for this set
     if enable_cdash_reporting and cdash_auth_token:
         try:
@@ -701,7 +776,7 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
     else:
         tty.warn('Unable to populate buildgroup without CDash credentials')
 
-    if final_job_config:
+    if final_job_config and not is_pr_pipeline:
         # Add an extra, final job to regenerate the index
         final_stage = 'stage-rebuild-index'
         final_job = {
@@ -721,8 +796,12 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
 
     output_object['stages'] = stage_names
 
+    sorted_output = {}
+    for output_key, output_value in sorted(output_object.items()):
+        sorted_output[output_key] = output_value
+
     with open(output_file, 'w') as outf:
-        outf.write(syaml.dump_config(output_object, default_flow_style=True))
+        outf.write(syaml.dump_config(sorted_output, default_flow_style=True))
 
 
 def url_encode_string(input_string):
diff --git a/lib/spack/spack/cmd/ci.py b/lib/spack/spack/cmd/ci.py
index e87da8c8af4..35891edb131 100644
--- a/lib/spack/spack/cmd/ci.py
+++ b/lib/spack/spack/cmd/ci.py
@@ -34,37 +34,6 @@ def setup_parser(subparser):
     setup_parser.parser = subparser
     subparsers = subparser.add_subparsers(help='CI sub-commands')
 
-    start = subparsers.add_parser('start', help=ci_start.__doc__)
-    start.add_argument(
-        '--output-file', default=None,
-        help="Absolute path to file where generated jobs file should be " +
-             "written.  The default is .gitlab-ci.yml in the root of the " +
-             "repository.")
-    start.add_argument(
-        '--copy-to', default=None,
-        help="Absolute path of additional location where generated jobs " +
-             "yaml file should be copied.  Default is not to copy.")
-    start.add_argument(
-        '--spack-repo', default=None,
-        help="Provide a url for this argument if a custom spack repo " +
-             "should be cloned as a step in each generated job.")
-    start.add_argument(
-        '--spack-ref', default=None,
-        help="Provide a git branch or tag if a custom spack branch " +
-             "should be checked out as a step in each generated job.  " +
-             "This argument is ignored if no --spack-repo is provided.")
-    start.add_argument(
-        '--downstream-repo', default=None,
-        help="Url to repository where commit containing jobs yaml file " +
-             "should be pushed.")
-    start.add_argument(
-        '--branch-name', default='default-branch',
-        help="Name of current branch, used in generation of pushed commit.")
-    start.add_argument(
-        '--commit-sha', default='none',
-        help="SHA of current commit, used in generation of pushed commit.")
-    start.set_defaults(func=ci_start)
-
     # Dynamic generation of the jobs yaml from a spack environment
     generate = subparsers.add_parser('generate', help=ci_generate.__doc__)
     generate.add_argument(
@@ -87,20 +56,6 @@ def setup_parser(subparser):
              "This argument is ignored if no --spack-repo is provided.")
     generate.set_defaults(func=ci_generate)
 
-    # Commit and push jobs yaml to a downstream CI repo
-    pushyaml = subparsers.add_parser('pushyaml', help=ci_pushyaml.__doc__)
-    pushyaml.add_argument(
-        '--downstream-repo', default=None,
-        help="Url to repository where commit containing jobs yaml file " +
-             "should be pushed.")
-    pushyaml.add_argument(
-        '--branch-name', default='default-branch',
-        help="Name of current branch, used in generation of pushed commit.")
-    pushyaml.add_argument(
-        '--commit-sha', default='none',
-        help="SHA of current commit, used in generation of pushed commit.")
-    pushyaml.set_defaults(func=ci_pushyaml)
-
     # Check a spec against mirror. Rebuild, create buildcache and push to
     # mirror (if necessary).
     rebuild = subparsers.add_parser('rebuild', help=ci_rebuild.__doc__)
@@ -140,64 +95,6 @@ def ci_generate(args):
         shutil.copyfile(output_file, copy_yaml_to)
 
 
-def ci_pushyaml(args):
-    """Push the generated jobs yaml file to a remote repository.  The file
-       (.gitlab-ci.yaml) is expected to be in the current directory, which
-       should be the root of the repository."""
-    downstream_repo = args.downstream_repo
-    branch_name = args.branch_name
-    commit_sha = args.commit_sha
-
-    if not downstream_repo:
-        tty.die('No downstream repo to push to, exiting')
-
-    working_dir = os.getcwd()
-    jobs_yaml = os.path.join(working_dir, '.gitlab-ci.yml')
-    git_dir = os.path.join(working_dir, '.git')
-
-    if not os.path.exists(jobs_yaml):
-        tty.die('.gitlab-ci.yml must exist in current directory')
-
-    if not os.path.exists(git_dir):
-        tty.die('.git directory must exist in current directory')
-
-    # Create a temporary working directory
-    with spack_ci.TemporaryDirectory() as temp_dir:
-        git = exe.which('git', required=True)
-
-        # Push a commit with the generated file to the downstream ci repo
-        saved_git_dir = os.path.join(temp_dir, 'original-git-dir')
-
-        shutil.move('.git', saved_git_dir)
-
-        git('init', '.')
-
-        git('config', 'user.email', 'robot@spack.io')
-        git('config', 'user.name', 'Spack Build Bot')
-
-        git('add', '.')
-
-        # If the environment contains a spack directory, do not commit
-        # or push it with any other generated products
-        if os.path.exists('./spack') and os.path.isdir('./spack'):
-            git('rm', '-rf', '--cached', 'spack')
-
-        tty.msg('git commit')
-        commit_message = '{0} {1} ({2})'.format(
-            'Auto-generated commit testing', branch_name, commit_sha)
-
-        git('commit', '-m', '{0}'.format(commit_message))
-
-        tty.msg('git push')
-        git('remote', 'add', 'downstream', downstream_repo)
-        push_to_branch = 'master:multi-ci-{0}'.format(branch_name)
-        git('push', '--force', 'downstream', push_to_branch)
-
-        shutil.rmtree('.git')
-        shutil.move(saved_git_dir, '.git')
-        git('reset', '--hard', 'HEAD')
-
-
 def ci_rebuild(args):
     """This command represents a gitlab-ci job, corresponding to a single
        release spec.  As such it must first decide whether or not the spec it
@@ -239,6 +136,7 @@ def ci_rebuild(args):
     compiler_action = get_env_var('SPACK_COMPILER_ACTION')
     cdash_build_name = get_env_var('SPACK_CDASH_BUILD_NAME')
     related_builds = get_env_var('SPACK_RELATED_BUILDS_CDASH')
+    pr_env_var = get_env_var('SPACK_IS_PR_PIPELINE')
 
     gitlab_ci = None
     if 'gitlab-ci' in yaml_root:
@@ -291,11 +189,18 @@ def ci_rebuild(args):
     local_mirror_dir = os.path.join(ci_artifact_dir, 'local_mirror')
     build_cache_dir = os.path.join(local_mirror_dir, 'build_cache')
 
+    spack_is_pr_pipeline = True if pr_env_var == 'True' else False
+
     enable_artifacts_mirror = False
     artifact_mirror_url = None
     if 'enable-artifacts-buildcache' in gitlab_ci:
         enable_artifacts_mirror = gitlab_ci['enable-artifacts-buildcache']
-        if enable_artifacts_mirror:
+        if enable_artifacts_mirror or spack_is_pr_pipeline:
+            # If this is a PR pipeline, we will override the setting to
+            # make sure that artifacts buildcache is enabled.  Otherwise
+            # jobs will not have binary deps available since we do not
+            # allow pushing binaries to remote mirror during PR pipelines
+            enable_artifacts_mirror = True
             artifact_mirror_url = 'file://' + local_mirror_dir
             mirror_msg = 'artifact buildcache enabled, mirror url: {0}'.format(
                 artifact_mirror_url)
@@ -441,9 +346,12 @@ def ci_rebuild(args):
 
             spack_ci.copy_stage_logs_to_artifacts(job_spec, job_log_dir)
 
-            # 4) create buildcache on remote mirror
-            spack_ci.push_mirror_contents(env, job_spec, job_spec_yaml_path,
-                                          remote_mirror_url, cdash_build_id)
+            # 4) create buildcache on remote mirror, but not if this is
+            # running to test a spack PR
+            if not spack_is_pr_pipeline:
+                spack_ci.push_mirror_contents(
+                    env, job_spec, job_spec_yaml_path, remote_mirror_url,
+                    cdash_build_id)
 
             # 5) create another copy of that buildcache on "local artifact
             # mirror" (only done if cash reporting is enabled)
@@ -468,13 +376,6 @@ def ci_rebuild(args):
                     job_spec, build_cache_dir, True, remote_mirror_url)
 
 
-def ci_start(args):
-    """Kicks of the CI process (currently just calls ci_generate() then
-       ci_push())"""
-    ci_generate(args)
-    ci_pushyaml(args)
-
-
 def ci(parser, args):
     if args.func:
         args.func(args)
diff --git a/lib/spack/spack/test/cmd/ci.py b/lib/spack/spack/test/cmd/ci.py
index 36236b0cc16..ab733244112 100644
--- a/lib/spack/spack/test/cmd/ci.py
+++ b/lib/spack/spack/test/cmd/ci.py
@@ -7,8 +7,6 @@
 import os
 import pytest
 
-import llnl.util.filesystem as fs
-
 import spack
 import spack.ci as ci
 import spack.config
@@ -48,37 +46,6 @@ def env_deactivate():
     os.environ.pop('SPACK_ENV', None)
 
 
-def initialize_new_repo(repo_path, initial_commit=False):
-    if not os.path.exists(repo_path):
-        os.makedirs(repo_path)
-
-    with fs.working_dir(repo_path):
-        init_args = ['init', '.']
-        # if not initial_commit:
-        #     init_args.append('--bare')
-
-        git(*init_args)
-
-        if initial_commit:
-            readme_contents = "This is the project README\n"
-            readme_path = os.path.join(repo_path, 'README.md')
-            with open(readme_path, 'w') as fd:
-                fd.write(readme_contents)
-            git('add', '.')
-            git('commit', '-m', 'Project initial commit')
-
-
-def get_repo_status(repo_path):
-    with fs.working_dir(repo_path):
-        output = git('rev-parse', '--abbrev-ref', 'HEAD', output=str)
-        current_branch = output.split()[0]
-
-        output = git('rev-parse', 'HEAD', output=str)
-        current_sha = output.split()[0]
-
-        return current_branch, current_sha
-
-
 def set_env_var(key, val):
     os.environ[key] = val
 
@@ -204,6 +171,144 @@ def test_ci_generate_with_env(tmpdir, mutable_mock_env_path, env_deactivate,
             assert(yaml_contents['stages'][5] == 'stage-rebuild-index')
 
 
+def _validate_needs_graph(yaml_contents, needs_graph, artifacts):
+    for job_name, job_def in yaml_contents.items():
+        for needs_def_name, needs_list in needs_graph.items():
+            if job_name.startswith(needs_def_name):
+                # check job needs against the expected needs definition
+                assert all([job_needs['job'][:job_needs['job'].index('/')]
+                           in needs_list for job_needs in job_def['needs']])
+                assert all([job_needs['artifacts'] == artifacts
+                           for job_needs in job_def['needs']])
+                break
+
+
+def test_ci_generate_bootstrap_gcc(tmpdir, mutable_mock_env_path,
+                                   env_deactivate, install_mockery,
+                                   mock_packages):
+    """Test that we can bootstrap a compiler and use it as the
+    compiler for a spec in the environment"""
+    filename = str(tmpdir.join('spack.yaml'))
+    with open(filename, 'w') as f:
+        f.write("""\
+spack:
+  definitions:
+    - bootstrap:
+      - gcc@3.0
+  specs:
+    - dyninst%gcc@3.0
+  mirrors:
+    some-mirror: https://my.fake.mirror
+  gitlab-ci:
+    bootstrap:
+      - name: bootstrap
+        compiler-agnostic: true
+    mappings:
+      - match:
+          - arch=test-debian6-x86_64
+        runner-attributes:
+          tags:
+            - donotcare
+""")
+
+    needs_graph = {
+        '(bootstrap) conflict': [],
+        '(bootstrap) gcc': [
+            '(bootstrap) conflict',
+        ],
+        '(specs) libelf': [
+            '(bootstrap) gcc',
+        ],
+        '(specs) libdwarf': [
+            '(bootstrap) gcc',
+            '(specs) libelf',
+        ],
+        '(specs) dyninst': [
+            '(bootstrap) gcc',
+            '(specs) libelf',
+            '(specs) libdwarf',
+        ],
+    }
+
+    with tmpdir.as_cwd():
+        env_cmd('create', 'test', './spack.yaml')
+        outputfile = str(tmpdir.join('.gitlab-ci.yml'))
+
+        with ev.read('test'):
+            ci_cmd('generate', '--output-file', outputfile)
+
+        with open(outputfile) as f:
+            contents = f.read()
+            yaml_contents = syaml.load(contents)
+            _validate_needs_graph(yaml_contents, needs_graph, False)
+
+
+def test_ci_generate_bootstrap_artifacts_buildcache(tmpdir,
+                                                    mutable_mock_env_path,
+                                                    env_deactivate,
+                                                    install_mockery,
+                                                    mock_packages):
+    """Test that we can bootstrap a compiler when artifacts buildcache
+    is turned on"""
+    filename = str(tmpdir.join('spack.yaml'))
+    with open(filename, 'w') as f:
+        f.write("""\
+spack:
+  definitions:
+    - bootstrap:
+      - gcc@3.0
+  specs:
+    - dyninst%gcc@3.0
+  mirrors:
+    some-mirror: https://my.fake.mirror
+  gitlab-ci:
+    bootstrap:
+      - name: bootstrap
+        compiler-agnostic: true
+    mappings:
+      - match:
+          - arch=test-debian6-x86_64
+        runner-attributes:
+          tags:
+            - donotcare
+    enable-artifacts-buildcache: True
+""")
+
+    needs_graph = {
+        '(bootstrap) conflict': [],
+        '(bootstrap) gcc': [
+            '(bootstrap) conflict',
+        ],
+        '(specs) libelf': [
+            '(bootstrap) gcc',
+            '(bootstrap) conflict',
+        ],
+        '(specs) libdwarf': [
+            '(bootstrap) gcc',
+            '(bootstrap) conflict',
+            '(specs) libelf',
+        ],
+        '(specs) dyninst': [
+            '(bootstrap) gcc',
+            '(bootstrap) conflict',
+            '(specs) libelf',
+            '(specs) libdwarf',
+        ],
+    }
+
+    with tmpdir.as_cwd():
+        env_cmd('create', 'test', './spack.yaml')
+        outputfile = str(tmpdir.join('.gitlab-ci.yml'))
+
+        with ev.read('test'):
+            ci_cmd('generate', '--output-file', outputfile)
+
+        with open(outputfile) as f:
+            contents = f.read()
+            yaml_contents = syaml.load(contents)
+            _validate_needs_graph(yaml_contents, needs_graph, True)
+
+
 def test_ci_generate_with_env_missing_section(tmpdir, mutable_mock_env_path,
                                               env_deactivate, install_mockery,
                                               mock_packages):
@@ -282,6 +387,110 @@ def test_ci_generate_with_cdash_token(tmpdir, mutable_mock_env_path,
             assert(filecmp.cmp(orig_file, copy_to_file) is True)
 
 
+def test_ci_generate_pkg_with_deps(tmpdir, mutable_mock_env_path,
+                                   env_deactivate, install_mockery,
+                                   mock_packages):
+    """Test pipeline generation for a package w/ dependencies"""
+    filename = str(tmpdir.join('spack.yaml'))
+    with open(filename, 'w') as f:
+        f.write("""\
+spack:
+  specs:
+    - flatten-deps
+  mirrors:
+    some-mirror: https://my.fake.mirror
+  gitlab-ci:
+    enable-artifacts-buildcache: True
+    mappings:
+      - match:
+          - flatten-deps
+        runner-attributes:
+          tags:
+            - donotcare
+      - match:
+          - dependency-install
+        runner-attributes:
+          tags:
+            - donotcare
+""")
+
+    with tmpdir.as_cwd():
+        env_cmd('create', 'test', './spack.yaml')
+        outputfile = str(tmpdir.join('.gitlab-ci.yml'))
+
+        with ev.read('test'):
+            ci_cmd('generate', '--output-file', outputfile)
+
+        with open(outputfile) as f:
+            contents = f.read()
+            print('generated contents: ')
+            print(contents)
+            yaml_contents = syaml.load(contents)
+            found = []
+            for ci_key in yaml_contents.keys():
+                ci_obj = yaml_contents[ci_key]
+                if 'dependency-install' in ci_key:
+                    assert('stage' in ci_obj)
+                    assert(ci_obj['stage'] == 'stage-0')
+                    found.append('dependency-install')
+                if 'flatten-deps' in ci_key:
+                    assert('stage' in ci_obj)
+                    assert(ci_obj['stage'] == 'stage-1')
+                    found.append('flatten-deps')
+
+            assert('flatten-deps' in found)
+            assert('dependency-install' in found)
+
+
+def test_ci_generate_for_pr_pipeline(tmpdir, mutable_mock_env_path,
+                                     env_deactivate, install_mockery,
+                                     mock_packages):
+    """Test that PR pipelines do not include a final stage job for
+    rebuilding the mirror index, even if that job is specifically
+    configured"""
+    filename = str(tmpdir.join('spack.yaml'))
+    with open(filename, 'w') as f:
+        f.write("""\
+spack:
+  specs:
+    - flatten-deps
+  mirrors:
+    some-mirror: https://my.fake.mirror
+  gitlab-ci:
+    enable-artifacts-buildcache: True
+    mappings:
+      - match:
+          - flatten-deps
+        runner-attributes:
+          tags:
+            - donotcare
+      - match:
+          - dependency-install
+        runner-attributes:
+          tags:
+            - donotcare
+    final-stage-rebuild-index:
+      image: donotcare
+      tags: [donotcare]
+""")
+
+    with tmpdir.as_cwd():
+        env_cmd('create', 'test', './spack.yaml')
+        outputfile = str(tmpdir.join('.gitlab-ci.yml'))
+
+        with ev.read('test'):
+            os.environ['SPACK_IS_PR_PIPELINE'] = 'True'
+            ci_cmd('generate', '--output-file', outputfile)
+
+        with open(outputfile) as f:
+            contents = f.read()
+            print('generated contents: ')
+            print(contents)
+            yaml_contents = syaml.load(contents)
+
+            assert('rebuild-index' not in yaml_contents)
+
+
 def test_ci_generate_with_external_pkg(tmpdir, mutable_mock_env_path,
                                        env_deactivate, install_mockery,
                                        mock_packages):
@@ -458,49 +667,6 @@ def test_ci_rebuild_basic(tmpdir, mutable_mock_env_path, env_deactivate,
             print(rebuild_output)
 
 
-def test_ci_pushyaml(tmpdir):
-    fake_yaml_contents = """generate ci jobs:
-  script:
-    - "./share/spack/qa/gitlab/generate-gitlab-ci-yml.sh"
-  tags:
-    - "spack-pre-ci"
-  artifacts:
-    paths:
-      - ci-generation
-    when: always
- """
-    local_repo_path = tmpdir.join('local_repo')
-    initialize_new_repo(local_repo_path.strpath, True)
-
-    remote_repo_path = tmpdir.join('remote_repo')
-    initialize_new_repo(remote_repo_path.strpath)
-
-    current_branch, current_sha = get_repo_status(local_repo_path.strpath)
-
-    print('local repo info: {0}, {1}'.format(current_branch, current_sha))
-
-    local_jobs_yaml = local_repo_path.join('.gitlab-ci.yml')
-    with local_jobs_yaml.open('w') as f:
-        f.write(fake_yaml_contents)
-
-    pushyaml_args = [
-        'pushyaml',
-        '--downstream-repo', remote_repo_path.strpath,
-        '--branch-name', current_branch,
-        '--commit-sha', current_sha,
-    ]
-
-    with fs.working_dir(local_repo_path.strpath):
-        ci_cmd(*pushyaml_args)
-
-    with fs.working_dir(remote_repo_path.strpath):
-        branch_to_checkout = 'multi-ci-{0}'.format(current_branch)
-        git('checkout', branch_to_checkout)
-        with open('.gitlab-ci.yml') as fd:
-            pushed_contents = fd.read()
-            assert pushed_contents == fake_yaml_contents
-
-
 @pytest.mark.disable_clean_stage_check
 @pytest.mark.skipif(not has_gpg(), reason='This test requires gpg')
 def test_push_mirror_contents(tmpdir, mutable_mock_env_path, env_deactivate,
diff --git a/share/spack/gitlab/pr_pipeline.yml b/share/spack/gitlab/pr_pipeline.yml
new file mode 100644
index 00000000000..4eb08f3434f
--- /dev/null
+++ b/share/spack/gitlab/pr_pipeline.yml
@@ -0,0 +1,20 @@
+pr_pipeline:
+  only:
+  - external_pull_requests
+  variables:
+    SPACK_REPO: https://github.com/spack/spack.git
+    SPACK_REF: ${CI_EXTERNAL_PULL_REQUEST_SOURCE_BRANCH_NAME}
+    SPACK_IS_PR_PIPELINE: "True"
+  trigger:
+    project: spack/e4s
+    strategy: depend
+
+merge_pipeline:
+  only:
+  - develop
+  variables:
+    SPACK_REPO: https://github.com/spack/spack.git
+    SPACK_REF: develop
+  trigger:
+    project: spack/e4s
+    strategy: depend
\ No newline at end of file
diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash
index b7b45fb0d77..49518de059b 100755
--- a/share/spack/spack-completion.bash
+++ b/share/spack/spack-completion.bash
@@ -469,22 +469,14 @@ _spack_ci() {
     then
         SPACK_COMPREPLY="-h --help"
     else
-        SPACK_COMPREPLY="start generate pushyaml rebuild"
+        SPACK_COMPREPLY="generate rebuild"
     fi
 }
 
-_spack_ci_start() {
-    SPACK_COMPREPLY="-h --help --output-file --copy-to --spack-repo --spack-ref --downstream-repo --branch-name --commit-sha"
-}
-
 _spack_ci_generate() {
     SPACK_COMPREPLY="-h --help --output-file --copy-to --spack-repo --spack-ref"
 }
 
-_spack_ci_pushyaml() {
-    SPACK_COMPREPLY="-h --help --downstream-repo --branch-name --commit-sha"
-}
-
 _spack_ci_rebuild() {
     SPACK_COMPREPLY="-h --help"
 }
diff --git a/var/spack/repos/builtin.mock/packages/gcc/package.py b/var/spack/repos/builtin.mock/packages/gcc/package.py
index 03b45a6e12c..7826e1b5cbb 100644
--- a/var/spack/repos/builtin.mock/packages/gcc/package.py
+++ b/var/spack/repos/builtin.mock/packages/gcc/package.py
@@ -14,6 +14,9 @@ class Gcc(Package):
 
     version('1.0', '0123456789abcdef0123456789abcdef')
     version('2.0', '2.0_a_hash')
+    version('3.0', '3.0_a_hash')
+
+    depends_on('conflict', when='@3.0')
 
     def install(self, spec, prefix):
         # Create the minimal compiler that will fool `spack compiler find`

From 154504da7177616abc7d23f2b54eac035e286a4a Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Fri, 15 May 2020 13:13:04 +0200
Subject: [PATCH 412/802] binutils: fix build with gcc@10: (#16661)

The issue seems to be fixed in the development version already.
---
 var/spack/repos/builtin/packages/binutils/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py
index 60cd9563fa1..791606f5645 100644
--- a/var/spack/repos/builtin/packages/binutils/package.py
+++ b/var/spack/repos/builtin/packages/binutils/package.py
@@ -124,4 +124,7 @@ def flag_handler(self, name, flags):
            and (self.compiler.name == 'fj' or self.compiler.name == 'clang')\
            and self.version <= ver('2.31.1'):
             flags.append('-Wno-narrowing')
+        elif name == 'cflags':
+            if self.spec.satisfies('@:2.34 %gcc@10:'):
+                flags.append('-fcommon')
         return (flags, None, None)

From 90e15cae16f9bb50f0b34580e11210522ec2c52f Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Fri, 15 May 2020 13:23:57 +0200
Subject: [PATCH 413/802] likwid: fix build with gcc@10: (#16641)

---
 var/spack/repos/builtin/packages/likwid/package.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/var/spack/repos/builtin/packages/likwid/package.py b/var/spack/repos/builtin/packages/likwid/package.py
index 8556fb0d8e9..8a1f39ebfd0 100644
--- a/var/spack/repos/builtin/packages/likwid/package.py
+++ b/var/spack/repos/builtin/packages/likwid/package.py
@@ -106,6 +106,12 @@ def install(self, spec, prefix):
                             spec['lua'].prefix.bin),
                         'config.mk')
 
+        # https://github.com/RRZE-HPC/likwid/issues/287
+        if self.spec.satisfies('@:5.0.2 %gcc@10:'):
+            filter_file(r'^(CFLAGS.*)',
+                        '\\1 -fcommon',
+                        'make/include_GCC.mk')
+
         env['PWD'] = os.getcwd()
         make()
         make('install')

From 955a3db20638ae50d902595829d6dc5d5d92a47c Mon Sep 17 00:00:00 2001
From: Stephen Hudson <shudson@anl.gov>
Date: Fri, 15 May 2020 08:14:06 -0500
Subject: [PATCH 414/802] py-petsc4py: allow ~mpi variant (#16595)

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../builtin/packages/py-petsc4py/package.py   | 27 ++++++++++---------
 1 file changed, 15 insertions(+), 12 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-petsc4py/package.py b/var/spack/repos/builtin/packages/py-petsc4py/package.py
index 54653f9b689..c5fe8785e7c 100644
--- a/var/spack/repos/builtin/packages/py-petsc4py/package.py
+++ b/var/spack/repos/builtin/packages/py-petsc4py/package.py
@@ -28,20 +28,23 @@ class PyPetsc4py(PythonPackage):
     version('3.8.0',  sha256='b9b728e39245213cd8e74cf4724be9bb48bd295f99634135e37dbbdbec275244')
     version('3.7.0',  sha256='fb78b50c596c3ba6a097751dd9a379e7acaf57edd36311a3afa94caa4312ee08')
 
+    variant('mpi', default=True,  description='Activates MPI support')
+
     depends_on('py-cython', type='build', when='@develop')
     depends_on('python@2.6:2.8,3.3:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
     depends_on('py-numpy', type=('build', 'run'))
-    depends_on('py-mpi4py', type=('build', 'run'))
+    depends_on('py-mpi4py', when='+mpi', type=('build', 'run'))
 
-    depends_on('petsc+mpi')
-    depends_on('petsc@develop+mpi', when='@develop')
-    depends_on('petsc@3.13:3.13.99+mpi', when='@3.13:3.13.99')
-    depends_on('petsc@3.12:3.12.99+mpi', when='@3.12:3.12.99')
-    depends_on('petsc@3.11:3.11.99+mpi', when='@3.11:3.11.99')
-    depends_on('petsc@3.10.3:3.10.99+mpi', when='@3.10.1:3.10.99')
-    depends_on('petsc@3.10:3.10.2+mpi', when='@3.10.0')
-    depends_on('petsc@3.9:3.9.99+mpi', when='@3.9:3.9.99')
-    depends_on('petsc@3.8:3.8.99+mpi', when='@3.8:3.8.99')
-    depends_on('petsc@3.7:3.7.99+mpi', when='@3.7:3.7.99')
-    depends_on('petsc@3.6:3.6.99+mpi', when='@3.6:3.6.99')
+    depends_on('petsc+mpi', when='+mpi')
+    depends_on('petsc~mpi', when='~mpi')
+    depends_on('petsc@develop', when='@develop')
+    depends_on('petsc@3.13:3.13.99', when='@3.13:3.13.99')
+    depends_on('petsc@3.12:3.12.99', when='@3.12:3.12.99')
+    depends_on('petsc@3.11:3.11.99', when='@3.11:3.11.99')
+    depends_on('petsc@3.10.3:3.10.99', when='@3.10.1:3.10.99')
+    depends_on('petsc@3.10:3.10.2', when='@3.10.0')
+    depends_on('petsc@3.9:3.9.99', when='@3.9:3.9.99')
+    depends_on('petsc@3.8:3.8.99', when='@3.8:3.8.99')
+    depends_on('petsc@3.7:3.7.99', when='@3.7:3.7.99')
+    depends_on('petsc@3.6:3.6.99', when='@3.6:3.6.99')

From 32a9adcf606b1e6ab08da0eadad6bfa6d9d63db7 Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Fri, 15 May 2020 11:12:52 -0700
Subject: [PATCH 415/802] modules: use projections format for naming schemes
 (#16629)

* update tcl naming_scheme to use projections

* add projections to lmod modules
---
 lib/spack/docs/build_systems/intelpackage.rst |  6 +-
 lib/spack/docs/module_file_support.rst        | 56 ++++++++++++++-----
 lib/spack/spack/filesystem_view.py            | 12 ++--
 lib/spack/spack/modules/common.py             | 25 ++++++---
 lib/spack/spack/modules/lmod.py               | 13 +----
 lib/spack/spack/modules/tcl.py                |  7 ++-
 lib/spack/spack/projections.py                | 16 ++++++
 lib/spack/spack/schema/modules.py             | 10 ++--
 .../test/data/modules/lmod/projections.yaml   |  6 ++
 .../test/data/modules/tcl/conflicts.yaml      |  3 +-
 .../modules/tcl/invalid_naming_scheme.yaml    |  3 +-
 .../test/data/modules/tcl/projections.yaml    |  6 ++
 .../data/modules/tcl/wrong_conflicts.yaml     |  3 +-
 lib/spack/spack/test/modules/lmod.py          | 36 ++++++++++++
 lib/spack/spack/test/modules/tcl.py           | 31 ++++++++--
 15 files changed, 171 insertions(+), 62 deletions(-)
 create mode 100644 lib/spack/spack/projections.py
 create mode 100644 lib/spack/spack/test/data/modules/lmod/projections.yaml
 create mode 100644 lib/spack/spack/test/data/modules/tcl/projections.yaml

diff --git a/lib/spack/docs/build_systems/intelpackage.rst b/lib/spack/docs/build_systems/intelpackage.rst
index 153b41bdc75..66f473cbf82 100644
--- a/lib/spack/docs/build_systems/intelpackage.rst
+++ b/lib/spack/docs/build_systems/intelpackage.rst
@@ -1055,6 +1055,6 @@ Footnotes
    2. Set the hash length in ``install-path-scheme``, also in ``config.yaml``
       (:ref:`q.v. <config-yaml>`).
    3. You will want to set the *same* hash length for
-      :ref:`tcl module files <modules-naming-scheme>`
-      if you have Spack produce them for you, under ``naming_scheme`` in
-      ``modules.yaml``.  Other module dialects cannot be altered in this manner.
+      :ref:`module files <modules-projections>`
+      if you have Spack produce them for you, under ``projections`` in
+      ``modules.yaml``.
diff --git a/lib/spack/docs/module_file_support.rst b/lib/spack/docs/module_file_support.rst
index 406715b07e6..73047a7754b 100644
--- a/lib/spack/docs/module_file_support.rst
+++ b/lib/spack/docs/module_file_support.rst
@@ -459,14 +459,14 @@ is compiled with ``gcc@4.4.7``, with the only exception of any ``gcc``
 or any ``llvm`` installation.
 
 
-.. _modules-naming-scheme:
+.. _modules-projections:
 
-"""""""""""""""""""""""""""
-Customize the naming scheme
-"""""""""""""""""""""""""""
+"""""""""""""""""""""""""""""""
+Customize the naming of modules
+"""""""""""""""""""""""""""""""
 
 The names of environment modules generated by spack are not always easy to
-fully comprehend due to the long hash in the name. There are two module
+fully comprehend due to the long hash in the name. There are three module
 configuration options to help with that. The first is a global setting to
 adjust the hash length. It can be set anywhere from 0 to 32 and has a default
 length of 7. This is the representation of the hash in the module file name and
@@ -500,20 +500,46 @@ version of python a set of python extensions is associated with. Likewise, the
 ``openblas`` string is attached to any program that has openblas in the spec,
 most likely via the ``+blas`` variant specification.
 
+The most heavyweight solution to module naming is to change the entire
+naming convention for module files. This uses the projections format
+covered in :ref:`adding_projections_to_views`.
+
+.. code-block:: yaml
+
+  modules:
+    tcl:
+      projections:
+        all: '{name}/{version}-{compiler.name}-{compiler.version}-module'
+        ^mpi: '{name}/{version}-{^mpi.name}-{^mpi.version}-{compiler.name}-{compiler.version}-module'
+
+will create module files that are nested in directories by package
+name, contain the version and compiler name and version, and have the
+word ``module`` before the hash for all specs that do not depend on
+mpi, and will have the same information plus the MPI implementation
+name and version for all packages that depend on mpi.
+
+When specifying module names by projection for Lmod modules, we
+recommend NOT including names of dependencies (e.g., MPI, compilers)
+that are already in the LMod hierarchy.
+
+
+
 .. note::
-   TCL module files
-     A modification that is specific to ``tcl`` module files is the possibility
-     to change the naming scheme of modules.
+   TCL modules
+     TCL modules also allow for explicit conflicts between modulefiles.
 
      .. code-block:: yaml
 
-       modules:
-         tcl:
-           naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
-           all:
-             conflict:
-               - '{name}'
-               - 'intel/14.0.1'
+        modules:
+          enable:
+            - tcl
+          tcl:
+            projections:
+              all: '{name}/{version}-{compiler.name}-{compiler.version}'
+            all:
+              conflict:
+                - '{name}'
+                - 'intel/14.0.1'
 
      will create module files that will conflict with ``intel/14.0.1`` and with the
      base directory of the same module, effectively preventing the possibility to
diff --git a/lib/spack/spack/filesystem_view.py b/lib/spack/spack/filesystem_view.py
index babe1b9c0ea..b2bc30e1a5c 100644
--- a/lib/spack/spack/filesystem_view.py
+++ b/lib/spack/spack/filesystem_view.py
@@ -22,6 +22,7 @@
 import spack.spec
 import spack.store
 import spack.schema.projections
+import spack.projections
 import spack.config
 from spack.error import SpackError
 from spack.directory_layout import ExtensionAlreadyInstalledError
@@ -470,14 +471,9 @@ def get_projection_for_spec(self, spec):
         if spec.package.extendee_spec:
             locator_spec = spec.package.extendee_spec
 
-        all_fmt_str = None
-        for spec_like, fmt_str in self.projections.items():
-            if locator_spec.satisfies(spec_like, strict=True):
-                return os.path.join(self._root, locator_spec.format(fmt_str))
-            elif spec_like == 'all':
-                all_fmt_str = fmt_str
-        if all_fmt_str:
-            return os.path.join(self._root, locator_spec.format(all_fmt_str))
+        proj = spack.projections.get_projection(self.projections, locator_spec)
+        if proj:
+            return os.path.join(self._root, locator_spec.format(proj))
         return self._root
 
     def get_all_specs(self):
diff --git a/lib/spack/spack/modules/common.py b/lib/spack/spack/modules/common.py
index 8dee443eb33..7eca9292c92 100644
--- a/lib/spack/spack/modules/common.py
+++ b/lib/spack/spack/modules/common.py
@@ -41,6 +41,7 @@
 import spack.error
 import spack.paths
 import spack.schema.environment
+import spack.projections as proj
 import spack.tengine as tengine
 import spack.util.environment
 import spack.util.file_permissions as fp
@@ -381,6 +382,9 @@ class BaseConfiguration(object):
     querying easier. It needs to be sub-classed for specific module types.
     """
 
+    default_projections = {
+        'all': '{name}-{version}-{compiler.name}-{compiler.version}'}
+
     def __init__(self, spec):
         # Module where type(self) is defined
         self.module = inspect.getmodule(self)
@@ -391,19 +395,18 @@ def __init__(self, spec):
         self.conf = merge_config_rules(self.module.configuration(), self.spec)
 
     @property
-    def naming_scheme(self):
-        """Naming scheme suitable for non-hierarchical layouts"""
-        scheme = self.module.configuration().get(
-            'naming_scheme',
-            '{name}-{version}-{compiler.name}-{compiler.version}'
-        )
+    def projections(self):
+        """Projection from specs to module names"""
+        projections = self.module.configuration().get(
+            'projections', self.default_projections)
 
         # Ensure the named tokens we are expanding are allowed, see
         # issue #2884 for reference
         msg = 'some tokens cannot be part of the module naming scheme'
-        _check_tokens_are_valid(scheme, message=msg)
+        for projection in projections.values():
+            _check_tokens_are_valid(projection, message=msg)
 
-        return scheme
+        return projections
 
     @property
     def template(self):
@@ -551,7 +554,11 @@ def use_name(self):
         to console to use it. This implementation fits the needs of most
         non-hierarchical layouts.
         """
-        name = self.spec.format(self.conf.naming_scheme)
+        projection = proj.get_projection(self.conf.projections, self.spec)
+        if not projection:
+            projection = self.conf.default_projections['all']
+
+        name = self.spec.format(projection)
         # Not everybody is working on linux...
         parts = name.split('/')
         name = os.path.join(*parts)
diff --git a/lib/spack/spack/modules/lmod.py b/lib/spack/spack/modules/lmod.py
index d0d14dac5bd..018edb35adf 100644
--- a/lib/spack/spack/modules/lmod.py
+++ b/lib/spack/spack/modules/lmod.py
@@ -91,6 +91,7 @@ def guess_core_compilers(store=False):
 
 class LmodConfiguration(BaseConfiguration):
     """Configuration class for lmod module files."""
+    default_projections = {'all': os.path.join('{name}', '{version}')}
 
     @property
     def core_compilers(self):
@@ -243,18 +244,6 @@ def filename(self):
         )
         return fullname
 
-    @property
-    def use_name(self):
-        """Returns the 'use' name of the module i.e. the name you have to type
-        to console to use it.
-        """
-        # Package name and version
-        base = os.path.join("{name}", "{version}")
-        name_parts = [self.spec.format(base)]
-        # The remaining elements are filename suffixes
-        name_parts.extend(self.conf.suffixes)
-        return '-'.join(name_parts)
-
     def token_to_path(self, name, value):
         """Transforms a hierarchy token into the corresponding path part.
 
diff --git a/lib/spack/spack/modules/tcl.py b/lib/spack/spack/modules/tcl.py
index ec8032a0e18..0efc6332fef 100644
--- a/lib/spack/spack/modules/tcl.py
+++ b/lib/spack/spack/modules/tcl.py
@@ -12,6 +12,7 @@
 import llnl.util.tty as tty
 
 import spack.config
+import spack.projections as proj
 import spack.tengine as tengine
 from .common import BaseConfiguration, BaseFileLayout
 from .common import BaseContext, BaseModuleFileWriter
@@ -72,12 +73,12 @@ def prerequisites(self):
     def conflicts(self):
         """List of conflicts for the tcl module file."""
         fmts = []
-        naming_scheme = self.conf.naming_scheme
+        projection = proj.get_projection(self.conf.projections, self.spec)
         f = string.Formatter()
         for item in self.conf.conflicts:
             if len([x for x in f.parse(item)]) > 1:
                 for naming_dir, conflict_dir in zip(
-                        naming_scheme.split('/'), item.split('/')
+                        projection.split('/'), item.split('/')
                 ):
                     if naming_dir != conflict_dir:
                         message = 'conflict scheme does not match naming '
@@ -87,7 +88,7 @@ def conflicts(self):
                         message += '** You may want to check your '
                         message += '`modules.yaml` configuration file **\n'
                         tty.error(message.format(spec=self.spec,
-                                                 nformat=naming_scheme,
+                                                 nformat=projection,
                                                  cformat=item))
                         raise SystemExit('Module generation aborted.')
                 item = self.spec.format(item)
diff --git a/lib/spack/spack/projections.py b/lib/spack/spack/projections.py
new file mode 100644
index 00000000000..b91d321436a
--- /dev/null
+++ b/lib/spack/spack/projections.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+def get_projection(projections, spec):
+    """
+    Get the projection for a spec from a projections dict.
+    """
+    all_projection = None
+    for spec_like, projection in projections.items():
+        if spec.satisfies(spec_like, strict=True):
+            return projection
+        elif spec_like == 'all':
+            all_projection = projection
+    return all_projection
diff --git a/lib/spack/spack/schema/modules.py b/lib/spack/spack/schema/modules.py
index 4e110717574..ac9237609bc 100644
--- a/lib/spack/spack/schema/modules.py
+++ b/lib/spack/spack/schema/modules.py
@@ -9,7 +9,7 @@
    :lines: 13-
 """
 import spack.schema.environment
-
+import spack.schema.projections
 
 #: Matches a spec or a multi-valued variant but not another
 #: valid keyword.
@@ -17,7 +17,7 @@
 #: THIS NEEDS TO BE UPDATED FOR EVERY NEW KEYWORD THAT
 #: IS ADDED IMMEDIATELY BELOW THE MODULE TYPE ATTRIBUTE
 spec_regex = r'(?!hierarchy|core_specs|verbose|hash_length|whitelist|' \
-             r'blacklist|naming_scheme|core_compilers|all)(^\w[\w-]*)'
+             r'blacklist|projections|core_compilers|all)(^\w[\w-]*)'
 
 #: Matches an anonymous spec, i.e. a spec without a root name
 anonymous_spec_regex = r'^[\^@%+~]'
@@ -72,6 +72,8 @@
     }
 }
 
+projections_scheme = spack.schema.projections.properties['projections']
+
 module_type_configuration = {
     'type': 'object',
     'default': {},
@@ -92,9 +94,7 @@
                 'type': 'boolean',
                 'default': False
             },
-            'naming_scheme': {
-                'type': 'string'  # Can we be more specific here?
-            },
+            'projections': projections_scheme,
             'all': module_file_configuration,
         }
         },
diff --git a/lib/spack/spack/test/data/modules/lmod/projections.yaml b/lib/spack/spack/test/data/modules/lmod/projections.yaml
new file mode 100644
index 00000000000..1efd93bc89a
--- /dev/null
+++ b/lib/spack/spack/test/data/modules/lmod/projections.yaml
@@ -0,0 +1,6 @@
+enable:
+  - lmod
+lmod:
+  projections:
+    all: '{name}/v{version}'
+    mpileaks: '{name}-mpiprojection'
diff --git a/lib/spack/spack/test/data/modules/tcl/conflicts.yaml b/lib/spack/spack/test/data/modules/tcl/conflicts.yaml
index 66494b1ce19..0183753e55f 100644
--- a/lib/spack/spack/test/data/modules/tcl/conflicts.yaml
+++ b/lib/spack/spack/test/data/modules/tcl/conflicts.yaml
@@ -1,7 +1,8 @@
 enable:
   - tcl
 tcl:
-  naming_scheme: '{name}/{version}-{compiler.name}'
+  projections:
+    all: '{name}/{version}-{compiler.name}'
   all:
     conflict:
       - '{name}'
diff --git a/lib/spack/spack/test/data/modules/tcl/invalid_naming_scheme.yaml b/lib/spack/spack/test/data/modules/tcl/invalid_naming_scheme.yaml
index f523f0bbef0..36b58670daa 100644
--- a/lib/spack/spack/test/data/modules/tcl/invalid_naming_scheme.yaml
+++ b/lib/spack/spack/test/data/modules/tcl/invalid_naming_scheme.yaml
@@ -2,4 +2,5 @@ enable:
   - tcl
 tcl:
   # {variants} is not allowed in the naming scheme, see #2884
-  naming_scheme: '{name}/{version}-{compiler.name}-{variants}'
+  projections:
+    all: '{name}/{version}-{compiler.name}-{variants}'
diff --git a/lib/spack/spack/test/data/modules/tcl/projections.yaml b/lib/spack/spack/test/data/modules/tcl/projections.yaml
new file mode 100644
index 00000000000..11dbd053f9f
--- /dev/null
+++ b/lib/spack/spack/test/data/modules/tcl/projections.yaml
@@ -0,0 +1,6 @@
+enable:
+  - tcl
+tcl:
+  projections:
+    all: '{name}/{version}-{compiler.name}'
+    mpileaks: '{name}-mpiprojection'
diff --git a/lib/spack/spack/test/data/modules/tcl/wrong_conflicts.yaml b/lib/spack/spack/test/data/modules/tcl/wrong_conflicts.yaml
index a4bd97257be..22377816c8b 100644
--- a/lib/spack/spack/test/data/modules/tcl/wrong_conflicts.yaml
+++ b/lib/spack/spack/test/data/modules/tcl/wrong_conflicts.yaml
@@ -1,7 +1,8 @@
 enable:
   - tcl
 tcl:
-  naming_scheme: '{name}/{version}-{compiler.name}'
+  projections:
+    all: '{name}/{version}-{compiler.name}'
   all:
     conflict:
       - '{name}/{compiler.name}'
diff --git a/lib/spack/spack/test/modules/lmod.py b/lib/spack/spack/test/modules/lmod.py
index 3daeeb068db..6d2ee7bc390 100644
--- a/lib/spack/spack/test/modules/lmod.py
+++ b/lib/spack/spack/test/modules/lmod.py
@@ -280,3 +280,39 @@ def test_only_generic_microarchitectures_in_root(
         assert str(spec.target.family) in writer.layout.arch_dirname
         if spec.target.family != spec.target:
             assert str(spec.target) not in writer.layout.arch_dirname
+
+    def test_projections_specific(self, factory, module_configuration):
+        """Tests reading the correct naming scheme."""
+
+        # This configuration has no error, so check the conflicts directives
+        # are there
+        module_configuration('projections')
+
+        # Test we read the expected configuration for the naming scheme
+        writer, _ = factory('mpileaks')
+        expected = {
+            'all': '{name}/v{version}',
+            'mpileaks': '{name}-mpiprojection'
+        }
+
+        assert writer.conf.projections == expected
+        projection = writer.spec.format(writer.conf.projections['mpileaks'])
+        assert projection in writer.layout.use_name
+
+    def test_projections_all(self, factory, module_configuration):
+        """Tests reading the correct naming scheme."""
+
+        # This configuration has no error, so check the conflicts directives
+        # are there
+        module_configuration('projections')
+
+        # Test we read the expected configuration for the naming scheme
+        writer, _ = factory('libelf')
+        expected = {
+            'all': '{name}/v{version}',
+            'mpileaks': '{name}-mpiprojection'
+        }
+
+        assert writer.conf.projections == expected
+        projection = writer.spec.format(writer.conf.projections['all'])
+        assert projection in writer.layout.use_name
diff --git a/lib/spack/spack/test/modules/tcl.py b/lib/spack/spack/test/modules/tcl.py
index 40cb7be5ef7..98d9363f879 100644
--- a/lib/spack/spack/test/modules/tcl.py
+++ b/lib/spack/spack/test/modules/tcl.py
@@ -142,18 +142,41 @@ def test_blacklist(self, modulefile_content, module_configuration):
         assert len([x for x in content if 'is-loaded' in x]) == 1
         assert len([x for x in content if 'module load ' in x]) == 1
 
-    def test_naming_scheme(self, factory, module_configuration):
+    def test_projections_specific(self, factory, module_configuration):
         """Tests reading the correct naming scheme."""
 
         # This configuration has no error, so check the conflicts directives
         # are there
-        module_configuration('conflicts')
+        module_configuration('projections')
 
         # Test we read the expected configuration for the naming scheme
         writer, _ = factory('mpileaks')
-        expected = '{name}/{version}-{compiler.name}'
+        expected = {
+            'all': '{name}/{version}-{compiler.name}',
+            'mpileaks': '{name}-mpiprojection'
+        }
 
-        assert writer.conf.naming_scheme == expected
+        assert writer.conf.projections == expected
+        projection = writer.spec.format(writer.conf.projections['mpileaks'])
+        assert projection in writer.layout.use_name
+
+    def test_projections_all(self, factory, module_configuration):
+        """Tests reading the correct naming scheme."""
+
+        # This configuration has no error, so check the conflicts directives
+        # are there
+        module_configuration('projections')
+
+        # Test we read the expected configuration for the naming scheme
+        writer, _ = factory('libelf')
+        expected = {
+            'all': '{name}/{version}-{compiler.name}',
+            'mpileaks': '{name}-mpiprojection'
+        }
+
+        assert writer.conf.projections == expected
+        projection = writer.spec.format(writer.conf.projections['all'])
+        assert projection in writer.layout.use_name
 
     def test_invalid_naming_scheme(self, factory, module_configuration):
         """Tests the evaluation of an invalid naming scheme."""

From 97d7ef678d8e9647958ba89d446037b1c21edc2c Mon Sep 17 00:00:00 2001
From: Omar Padron <omar.padron@kitware.com>
Date: Fri, 15 May 2020 15:11:32 -0400
Subject: [PATCH 416/802] fix catalyst so that it doesn't depend on a
 particular spelling of python (#16667)

---
 var/spack/repos/builtin/packages/catalyst/package.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/catalyst/package.py b/var/spack/repos/builtin/packages/catalyst/package.py
index c00aca23e97..1a2967926d4 100644
--- a/var/spack/repos/builtin/packages/catalyst/package.py
+++ b/var/spack/repos/builtin/packages/catalyst/package.py
@@ -6,6 +6,7 @@
 from spack import *
 import os
 import subprocess
+import sys
 import llnl.util.tty as tty
 
 
@@ -133,7 +134,12 @@ def do_stage(self, mirror_only=False):
                                     'Editions')
         catalyst_source_dir = os.path.abspath(self.root_cmakelists_dir)
 
-        command = ['python', catalyst_script,
+        python_path = (os.path.realpath(
+            spec['python3'].command.path if '+python3' in self.spec else
+            spec['python'].command.path if '+python' in self.spec else
+            sys.executable))
+
+        command = [python_path, catalyst_script,
                    '-r', self.stage.source_path,
                    '-o', catalyst_source_dir]
 

From 983f05ac4198a2e9dfadcedcf9df572ead09a006 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Sat, 16 May 2020 16:07:34 +0200
Subject: [PATCH 417/802] r-polspline: new package (#16648)

* r-polspline: new package

* r-polspline: updated urls
---
 .../builtin/packages/r-polspline/package.py   | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-polspline/package.py

diff --git a/var/spack/repos/builtin/packages/r-polspline/package.py b/var/spack/repos/builtin/packages/r-polspline/package.py
new file mode 100644
index 00000000000..358d3e8d1af
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-polspline/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPolspline(RPackage):
+    """Routines for the polynomial spline fitting routines hazard regression,
+       hazard estimation with flexible tails, logspline, lspec, polyclass,
+       and polymars, by C. Kooperberg and co-authors.
+    """
+
+    homepage = "https://cloud.r-project.org/package=polspline"
+    url      = "https://cloud.r-project.org/src/contrib/polspline_1.1.18.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/polspline"
+
+    version('1.1.18', sha256='df250ee144bfff154249ba50308f46863107ef3efb2333ad908e599ed0eb0102')
+    version('1.1.17', sha256='d67b269d01105d4a6ea774737e921e66e065a859d1931ae38a70f88b6fb7ee30')
+    version('1.1.16', sha256='aa3b5a1560008a1a401a65a25f19a27ba6f0a6ea185b6d093acd40e4e2818934')
+    version('1.1.15', sha256='8cdbaa5ee672055a4d02f965025199ce764958f84bfa159e853feba7ee24faa7')

From 2ebadbc267ffb4e2c175bdd7ceea9eb20e92254f Mon Sep 17 00:00:00 2001
From: TZ <tz-rrze@users.noreply.github.com>
Date: Sat, 16 May 2020 17:40:40 +0200
Subject: [PATCH 418/802] intel-mpi: add libfabrics directory to
 SPACK_COMPILER_EXTRA_RPATHS (#15214)

workaround for not finding an appropriate libfabrics.so with Intel
MPI 2019+. Fixes #11140 and #12493
---
 lib/spack/spack/build_systems/intel.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/lib/spack/spack/build_systems/intel.py b/lib/spack/spack/build_systems/intel.py
index 4017f2e526c..a74d5e96137 100644
--- a/lib/spack/spack/build_systems/intel.py
+++ b/lib/spack/spack/build_systems/intel.py
@@ -1073,6 +1073,15 @@ def _setup_dependent_env_callback(
                 # which performs dizzyingly similar but necessarily different
                 # actions, and (b) function code leaves a bit more breathing
                 # room within the suffocating corset of flake8 line length.
+
+                # Intel MPI since 2019 depends on libfabric which is not in the
+                # lib directory but in a directory of its own which should be
+                # included in the rpath
+                if self.version >= ver('2019'):
+                    d = ancestor(self.component_lib_dir('mpi'))
+                    libfabrics_path = os.path.join(d, 'libfabric', 'lib')
+                    env.append_path('SPACK_COMPILER_EXTRA_RPATHS',
+                                    libfabrics_path)
             else:
                 raise InstallError('compilers_of_client arg required for MPI')
 

From b6498c44af0f8e655f02b2699ce3d76fabaec2e7 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Sun, 17 May 2020 04:50:24 +0800
Subject: [PATCH 419/802] Add new package: guacamole-server (#16680)

---
 .../packages/guacamole-server/package.py      | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/guacamole-server/package.py

diff --git a/var/spack/repos/builtin/packages/guacamole-server/package.py b/var/spack/repos/builtin/packages/guacamole-server/package.py
new file mode 100644
index 00000000000..ea08a63639f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/guacamole-server/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class GuacamoleServer(AutotoolsPackage):
+    """The guacamole-server package is a set of software which forms the
+    basis of the Guacamole stack. It consists of guacd, libguac, and
+    several protocol support libraries."""
+
+    homepage = "http://guacamole.apache.org/"
+    url      = "https://github.com/apache/guacamole-server/archive/1.1.0.tar.gz"
+
+    version('1.1.0',     sha256='d0f0c66ebfa7a4fd6689ae5240f21797b5177945a042388b691b15b8bd5c81a8')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+    depends_on('cairo')
+    depends_on('libjpeg')
+    depends_on('libpng')
+    depends_on('uuid')

From 110b15f20eae657aed04acdbd5aaea3ae44c20df Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Sun, 17 May 2020 04:51:01 +0800
Subject: [PATCH 420/802] Add new package: hiredis (#16679)

---
 .../repos/builtin/packages/hiredis/package.py | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/hiredis/package.py

diff --git a/var/spack/repos/builtin/packages/hiredis/package.py b/var/spack/repos/builtin/packages/hiredis/package.py
new file mode 100644
index 00000000000..74e4552b2c8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hiredis/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Hiredis(MakefilePackage):
+    """Hiredis is a minimalistic C client library for the Redis database."""
+
+    homepage = "https://github.com/redis/hiredis"
+    url      = "https://github.com/redis/hiredis/archive/v0.14.1.tar.gz"
+
+    version('0.14.1', sha256='2663b2aed9fd430507e30fc5e63274ee40cdd1a296026e22eafd7d99b01c8913')
+    version('0.14.0', sha256='042f965e182b80693015839a9d0278ae73fae5d5d09d8bf6d0e6a39a8c4393bd')
+    version('0.13.3', sha256='717e6fc8dc2819bef522deaca516de9e51b9dfa68fe393b7db5c3b6079196f78')
+    version('0.13.2', sha256='b0cf73ebe039fe25ecaaa881acdda8bdc393ed997e049b04fc20865835953694')
+
+    def install(self, spec, prefix):
+        make('PREFIX={0}'.format(prefix), 'install')

From 32238391a97cb32491f4783b38ad6c876909e306 Mon Sep 17 00:00:00 2001
From: Paul <pbryant@newmexicoconsortium.org>
Date: Sat, 16 May 2020 14:55:51 -0600
Subject: [PATCH 421/802] Add Go versions 1.14.3 and 1.13.11 (#16673)

---
 var/spack/repos/builtin/packages/go/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py
index abea06b5a2e..114c9212ab6 100644
--- a/var/spack/repos/builtin/packages/go/package.py
+++ b/var/spack/repos/builtin/packages/go/package.py
@@ -36,9 +36,11 @@ class Go(Package):
 
     extendable = True
 
+    version('1.14.3', sha256='93023778d4d1797b7bc6a53e86c3a9b150c923953225f8a48a2d5fabc971af56')
     version('1.14.2', sha256='98de84e69726a66da7b4e58eac41b99cbe274d7e8906eeb8a5b7eb0aadee7f7c')
     version('1.14.1', sha256='2ad2572115b0d1b4cb4c138e6b3a31cee6294cb48af75ee86bec3dca04507676')
     version('1.14',   sha256='6d643e46ad565058c7a39dac01144172ef9bd476521f42148be59249e4b74389')
+    version('1.13.11', sha256='89ed1abce25ad003521c125d6583c93c1280de200ad221f961085200a6c00679')
     version('1.13.10', sha256='eb9ccc8bf59ed068e7eff73e154e4f5ee7eec0a47a610fb864e3332a2fdc8b8c')
     version('1.13.9', sha256='34bb19d806e0bc4ad8f508ae24bade5e9fedfa53d09be63b488a9314d2d4f31d')
     version('1.13.8', sha256='b13bf04633d4d8cf53226ebeaace8d4d2fd07ae6fa676d0844a688339debec34')

From b858eebc514c35906bd27a70cf8682d28597b4e7 Mon Sep 17 00:00:00 2001
From: "Mark W. Krentel" <krentel@rice.edu>
Date: Sat, 16 May 2020 15:59:33 -0500
Subject: [PATCH 422/802] hpctoolkit: add dependency on gotcha (#16670)

---
 var/spack/repos/builtin/packages/hpctoolkit/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/hpctoolkit/package.py b/var/spack/repos/builtin/packages/hpctoolkit/package.py
index d64ce78fadc..0bc737eb82e 100644
--- a/var/spack/repos/builtin/packages/hpctoolkit/package.py
+++ b/var/spack/repos/builtin/packages/hpctoolkit/package.py
@@ -66,6 +66,7 @@ class Hpctoolkit(AutotoolsPackage):
     depends_on('bzip2+shared', type='link')
     depends_on('dyninst@9.3.2:')
     depends_on('elfutils+bzip2+xz~nls', type='link')
+    depends_on('gotcha@1.0.3:')
     depends_on('intel-tbb+shared')
     depends_on('libdwarf')
     depends_on('libmonitor+hpctoolkit+bgq', when='+bgq')
@@ -105,6 +106,7 @@ def configure_args(self):
             '--with-bzip=%s'         % spec['bzip2'].prefix,
             '--with-dyninst=%s'      % spec['dyninst'].prefix,
             '--with-elfutils=%s'     % spec['elfutils'].prefix,
+            '--with-gotcha=%s'       % spec['gotcha'].prefix,
             '--with-tbb=%s'          % spec['intel-tbb'].prefix,
             '--with-libdwarf=%s'     % spec['libdwarf'].prefix,
             '--with-libmonitor=%s'   % spec['libmonitor'].prefix,

From 6ca1052999d25912b3e3233cec3e1dad10d47356 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Sat, 16 May 2020 23:03:49 +0200
Subject: [PATCH 423/802] r-spatstat-utils : New package (#16663)

---
 .../packages/r-spatstat-utils/package.py      | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-spatstat-utils/package.py

diff --git a/var/spack/repos/builtin/packages/r-spatstat-utils/package.py b/var/spack/repos/builtin/packages/r-spatstat-utils/package.py
new file mode 100644
index 00000000000..1cad42c0052
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-spatstat-utils/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSpatstatUtils(RPackage):
+    """Contains utility functions for the 'spatstat'
+       package which may also be useful for other purposes.
+    """
+
+    homepage = "https://cloud.r-project.org/package=spatstat.utils"
+    url      = "https://cloud.r-project.org/src/contrib/spatstat.utils_1.17-0.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/spatstat.utils"
+
+    version('1.17-0', sha256='39cd683ed7f41d8adc9e28af073d91b244aa1cf5ad966dfbb396ee3ee79f0922')
+    version('1.15-0', sha256='90e07d730b6939f47f93c939afae10874b2c82bd402960ede4133de67dca2a0c')
+
+    depends_on('r@3.3.0:', type=('build', 'run'))

From a97ce63218dcebb3d257cb18d0dc9801528db449 Mon Sep 17 00:00:00 2001
From: h-denpo <57649496+h-denpo@users.noreply.github.com>
Date: Sun, 17 May 2020 06:06:25 +0900
Subject: [PATCH 424/802] New package frontistr (#16660)

"""Open-Source Large-Scale Parallel FEM Program for
        Nonlinear Structural Analysis"""
---
 .../builtin/packages/frontistr/package.py     | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/frontistr/package.py

diff --git a/var/spack/repos/builtin/packages/frontistr/package.py b/var/spack/repos/builtin/packages/frontistr/package.py
new file mode 100644
index 00000000000..0a0cf7d6283
--- /dev/null
+++ b/var/spack/repos/builtin/packages/frontistr/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Frontistr(CMakePackage):
+    """Open-Source Large-Scale Parallel FEM Program for
+        Nonlinear Structural Analysis"""
+
+    homepage = "https://github.com/FrontISTR/FrontISTR"
+    git      = "https://github.com/FrontISTR/FrontISTR.git"
+
+    version('5.0', tag='v5.0')
+
+    depends_on('mpi')
+    depends_on('revocap-refiner')
+    depends_on('revocap-coupler')
+    depends_on('blas')
+    depends_on('metis')
+    depends_on('scalapack')
+    depends_on('mumps +mpi')
+    depends_on('trilinos')
+
+    def cmake_args(self):
+        define = CMakePackage.define
+        cmake_args = [
+            define('WITH_ML', True),
+        ]
+        return cmake_args

From f71768b1d6df10043dfd46b02cdf9fc81a6c6eec Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Sat, 16 May 2020 23:07:10 +0200
Subject: [PATCH 425/802] r-envstats: New package (#16659)

---
 .../builtin/packages/r-envstats/package.py    | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-envstats/package.py

diff --git a/var/spack/repos/builtin/packages/r-envstats/package.py b/var/spack/repos/builtin/packages/r-envstats/package.py
new file mode 100644
index 00000000000..42e17269591
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-envstats/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class REnvstats(RPackage):
+    """Graphical and statistical analyses of environmental data, with focus
+       on analyzing chemical concentrations and physical parameters, usually
+       in the context of mandated environmental monitoring.
+    """
+
+    homepage = "https://cloud.r-project.org/package=EnvStats"
+    url      = "https://cloud.r-project.org/src/contrib/EnvStats_2.3.1.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/EnvStats"
+
+    version('2.3.1', sha256='d753d42b42ff28c1cd25c63916fb2aa9e325941672fb16f7dfd97e218416cf2a')
+    version('2.3.0', sha256='51b7c982b4ffc6506579ec6933c817b780b8dade9f5e7754122e4132cb677a75')
+    version('2.2.1', sha256='bbad7736272a404302190ccf1095abd8674d4366f3827a1c0a9540bcafe0523e')
+
+    depends_on('r@3.1:', type=('build', 'run'))
+    depends_on('r-mass', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-nortest', type=('build', 'run'))

From 5912b8c7cd5fa2c062a1d5f2101f2ce2295556d2 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Sat, 16 May 2020 23:07:58 +0200
Subject: [PATCH 426/802] r-yaimpute: New package (#16658)

---
 .../builtin/packages/r-yaimpute/package.py    | 20 +++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-yaimpute/package.py

diff --git a/var/spack/repos/builtin/packages/r-yaimpute/package.py b/var/spack/repos/builtin/packages/r-yaimpute/package.py
new file mode 100644
index 00000000000..6d15be6ff66
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-yaimpute/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RYaimpute(RPackage):
+    """Performs nearest neighbor-based imputation using one or more
+       alternative approaches to processing multivariate data
+    """
+
+    homepage = "https://cloud.r-project.org/package=yaImpute"
+    url      = "https://cloud.r-project.org/src/contrib/yaImpute_1.0-32.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/yaImpute"
+
+    version('1.0-32', sha256='08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff')
+
+    depends_on('r@3.0:', type=('build', 'run'))

From babfd144ad143dedd6eb855225d7255d3f4ab381 Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Sat, 16 May 2020 16:12:50 -0500
Subject: [PATCH 427/802] py-fastcluster: new package at 1.1.26 (#16588)

* py-fastcluster: new package at 1.1.26

* py-fastcluster: add py-setuptools dep
---
 .../builtin/packages/py-fastcluster/package.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-fastcluster/package.py

diff --git a/var/spack/repos/builtin/packages/py-fastcluster/package.py b/var/spack/repos/builtin/packages/py-fastcluster/package.py
new file mode 100644
index 00000000000..bc09681527e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-fastcluster/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyFastcluster(PythonPackage):
+    """Fast hierarchical clustering routines for R and Python."""
+
+    homepage = "http://danifold.net/"
+    url      = "https://pypi.io/packages/source/f/fastcluster/fastcluster-1.1.26.tar.gz"
+
+    version('1.1.26', sha256='a202f44a3b06f5cf9cdba3c67d6c523288922d6e6a1cdf737292f93759aa82f7')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy@1.9:', type=('build', 'run'))

From 41907639c4c06a2509feed98a69a38dee76e3b25 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Sun, 17 May 2020 03:55:20 +0200
Subject: [PATCH 428/802] py-scipy: Fix build with gcc@10: (#16687)

---
 var/spack/repos/builtin/packages/py-scipy/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py
index 5cbd2438f78..7baf0bbb38a 100644
--- a/var/spack/repos/builtin/packages/py-scipy/package.py
+++ b/var/spack/repos/builtin/packages/py-scipy/package.py
@@ -65,6 +65,11 @@ class PyScipy(PythonPackage):
     depends_on('blas')
     depends_on('lapack')
 
+    def setup_build_environment(self, env):
+        # https://github.com/scipy/scipy/issues/11611
+        if self.spec.satisfies('@:1.4 %gcc@10:'):
+            env.set('FFLAGS', '-fallow-argument-mismatch')
+
     def build_args(self, spec, prefix):
         args = []
 

From 9685792f83e657a6fba6c1153ef4374edaa18091 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Sun, 17 May 2020 17:22:52 +0200
Subject: [PATCH 429/802] r-spatialpack : New package (#16664)

* r-spatialpack : New package

* r-spatialpack : R dependeny added type

* r-spatialpack: Description was missing
---
 .../builtin/packages/r-spatialpack/package.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-spatialpack/package.py

diff --git a/var/spack/repos/builtin/packages/r-spatialpack/package.py b/var/spack/repos/builtin/packages/r-spatialpack/package.py
new file mode 100644
index 00000000000..afa919cd105
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-spatialpack/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSpatialpack(RPackage):
+    """Tools to assess the association between two spatial processes."""
+
+    homepage = "https://cloud.r-project.org/package=SpatialPack"
+    url      = "https://cloud.r-project.org/src/contrib/SpatialPack_0.3-8.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/SpatialPack"
+
+    version('0.3-8', sha256='a0e54b5dee3cd30a634e2d30380fe163942b672073fd909be888803332ed5151')
+    version('0.3',   sha256='4c80fc1c77bc97fc678e6e201ecf7f0f89dcf3417b3b497a28a3639e9b30bd8a')
+
+    depends_on('r@2.10:', type=('build', 'run'))

From d776e52979bbe442c5d2ff43924045ebdae07f0e Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Sun, 17 May 2020 19:27:33 +0200
Subject: [PATCH 430/802] r-rms: New package (#16683)

* r-rms: New package

* r-rms: deleted duplicated dependency

* r-rms: deleting comma
---
 .../repos/builtin/packages/r-rms/package.py   | 48 +++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-rms/package.py

diff --git a/var/spack/repos/builtin/packages/r-rms/package.py b/var/spack/repos/builtin/packages/r-rms/package.py
new file mode 100644
index 00000000000..1090e0e5464
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rms/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRms(RPackage):
+    """Regression modeling, testing, estimation, validation, graphics,
+       prediction, and typesetting by storing enhanced model design
+       attributes in the fit. 'rms' is a collection of functions that
+       assist with and streamline modeling. It also contains functions
+       for binary and ordinal logistic regression models, ordinal models
+       for continuous Y with a variety of distribution families, and the
+       Buckley-James multiple regression model for right-censored responses,
+       and implements penalized maximum likelihood estimation for logistic
+       and ordinary linear models. 'rms' works with almost any regression
+       model, but it was especially written to work with binary or ordinal
+       regression models, Cox regression, accelerated failure time models,
+       ordinary linear models, the Buckley-James model, generalized least
+       squares for serially or spatially correlated observations,
+       generalized linear models, and quantile regression.
+    """
+
+    homepage = "https://cloud.r-project.org/package=rms"
+    url      = "https://cloud.r-project.org/src/contrib/rms_5.1-4.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/rms"
+
+    version('5.1-4',   sha256='38f5844c4944a95b2adebea6bb1d163111270b8662399ea0349c45c0758076a6')
+    version('5.1-3.1', sha256='0946d9547a4e3ff020a61ab3fce38f88aa9545729683e2bfefeb960edec82b37')
+    version('5.1-3',   sha256='5fc7120d8a93b4aa9727d82eac368c5c47ff70f467ae2b012afac688235089eb')
+    version('5.1-2',   sha256='f1cfeef466ac436105756679353a3468027d97a600e3be755b819aef30ed9207')
+    version('5.1-1',   sha256='c489948df5c434b40bcf5288844f5b4e08d157f36939d09230c1600f88d1bfe3')
+
+    depends_on('r@3.5:', type=('build', 'run'))
+    depends_on('r-hmisc@4.3:', type=('build', 'run'))
+    depends_on('r-survival@3.1-6', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-polspline', type=('build', 'run'))
+    depends_on('r-ggplot2@2.2:', type=('build', 'run'))
+    depends_on('r-sparsem', type=('build', 'run'))
+    depends_on('r-quantreg', type=('build', 'run'))
+    depends_on('r-rpart', type=('build', 'run'))
+    depends_on('r-nlme@3.1-123:', type=('build', 'run'))
+    depends_on('r-multcomp', type=('build', 'run'))
+    depends_on('r-htmltable@1.11.0:', type=('build', 'run'))
+    depends_on('r-htmltools', type=('build', 'run'))

From 045063da7f984d443a726533c2b6b13e9016afef Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Sun, 17 May 2020 19:28:26 +0200
Subject: [PATCH 431/802] r-spatstat-data: New package (#16688)

---
 .../packages/r-spatstat-data/package.py       | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-spatstat-data/package.py

diff --git a/var/spack/repos/builtin/packages/r-spatstat-data/package.py b/var/spack/repos/builtin/packages/r-spatstat-data/package.py
new file mode 100644
index 00000000000..991b87559b0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-spatstat-data/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSpatstatData(RPackage):
+    """Contains all the datasets for the 'spatstat' package."""
+
+    homepage = "https://cloud.r-project.org/package=spatstat.data"
+    url      = "https://cloud.r-project.org/src/contrib/spatstat.data_1.4-3.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/spatstat.data"
+
+    version('1.4-3', sha256='8955b6ac40cc7d0d89e02334bb46f4c223ff0755e5818f132fee753e77918ea2')
+    version('1.4-0', sha256='121e5bb92beb7ccac920f921e760f429fd71bcfe11cb9b07a7e7326c7a72ec8c')
+
+    depends_on('r@3.3:', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-spatstat-utils', type=('build', 'run'))

From a4d64402ae2fb3e39c7aae3ba324d75a06fabfdb Mon Sep 17 00:00:00 2001
From: Marko Kabic <mkmarkokabic@gmail.com>
Date: Sun, 17 May 2020 19:40:48 +0200
Subject: [PATCH 432/802] Add new version of COSMA: 2.2.0 (#16672)

* Updated versions of COSMA.

* Added an empty line for formatting.

* Switched to sha256.

* Renamed gpu variant to cuda. Extending the CudaPackage base class.
---
 .../repos/builtin/packages/cosma/package.py   | 23 ++++++++-----------
 1 file changed, 10 insertions(+), 13 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cosma/package.py b/var/spack/repos/builtin/packages/cosma/package.py
index efb81035da9..18d69605ee4 100644
--- a/var/spack/repos/builtin/packages/cosma/package.py
+++ b/var/spack/repos/builtin/packages/cosma/package.py
@@ -7,37 +7,30 @@
 from spack import *
 
 
-class Cosma(CMakePackage):
+class Cosma(CMakePackage, CudaPackage):
     """
     Distributed Communication-Optimal Matrix-Matrix Multiplication Library
     """
 
-    maintainers = ['teonnik', 'kabicm']
+    maintainers = ['haampie', 'kabicm', 'teonnik']
     homepage = 'https://github.com/eth-cscs/COSMA'
-    url = 'https://github.com/eth-cscs/COSMA/releases/download/v2.0.2/cosma.tar.gz'
+    url = 'https://github.com/eth-cscs/COSMA/releases/download/v2.2.0/cosma.tar.gz'
     git = 'https://github.com/eth-cscs/COSMA.git'
 
     # note: The default archives produced with github do not have the archives
     #       of the submodules.
     version('master', branch='master', submodules=True)
+    version('2.2.0', sha256='1eb92a98110df595070a12193b9221eecf9d103ced8836c960f6c79a2bd553ca')
+    version('2.0.7', sha256='8d70bfcbda6239b6a8fbeaca138790bbe58c0c3aa576879480d2632d4936cf7e')
     version('2.0.2', sha256='4f3354828bc718f3eef2f0098c3bdca3499297497a220da32db1acd57920c68d')
-    # note: this version fails to build at the moment
-    # version('1.0.0',
-    #         url='https://github.com/eth-cscs/COSMA/releases/download/1.0/cosma.tar.gz',
-    #         sha256='c142104258dcca4c17fa7faffc2990a08d2777235c7980006e93c5dca51061f6')
 
-    variant('cuda', default=False,
-            description='Build with the CUBLAS back end.')
     variant('scalapack', default=False,
-            description='Build with ScaLAPACK support.')
+            description='Build with ScaLAPACK API.')
 
     depends_on('cmake@3.12:', type='build')
     depends_on('mpi@3:')
     depends_on('blas', when='~cuda')
     depends_on('scalapack', when='+scalapack')
-    # COSMA is written entirely in C++, it may use cublasXt but a CUDA capable
-    # compiler is not needed. There is no need for CudaPackage in this recipe.
-    depends_on('cuda', when='+cuda')
 
     def setup_build_environment(self, env):
         if '+cuda' in self.spec:
@@ -52,6 +45,8 @@ def cmake_args(self):
 
         if '^mkl' in spec:
             args += ['-DCOSMA_BLAS=MKL']
+        elif '^cray-libsci' in spec:
+            args += ['-DCOSMA_BLAS=CRAY_LIBSCI']
         elif '^netlib-lapack' in spec:
             args += ['-DCOSMA_BLAS=CUSTOM']
         elif '^openblas' in spec:
@@ -63,6 +58,8 @@ def cmake_args(self):
 
         if '+scalapack' and '^mkl' in spec:
             args += ['-DCOSMA_SCALAPACK=MKL']
+        elif '+scalapack' and '^cray-libsci' in spec:
+            args += ['-DCOSMA_SCALAPACK=CRAY_LIBSCI']
         elif '+scalapack' and '^netlib-scalapack' in spec:
             args += ['-DCOSMA_SCALAPACK=CUSTOM']
 

From ffdd94dd9fbffc66f37265a60ed2f438f613373f Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Mon, 18 May 2020 10:00:23 +0900
Subject: [PATCH 433/802] hwloc: Add libudev variant. (#16615)

* hwloc: Add libudev variant.

* typo fix.

* Wrong version for libudev variant is fixed.

* Add maintainers.
---
 var/spack/repos/builtin/packages/hwloc/package.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py
index cb1a23c33e4..4edabfbf4ad 100644
--- a/var/spack/repos/builtin/packages/hwloc/package.py
+++ b/var/spack/repos/builtin/packages/hwloc/package.py
@@ -27,6 +27,8 @@ class Hwloc(AutotoolsPackage):
     list_depth = 2
     git = 'https://github.com/open-mpi/hwloc.git'
 
+    maintainers = ['bgoglin']
+
     version('master', branch='master')
     version('2.2.0', sha256='2defba03ddd91761b858cbbdc2e3a6e27b44e94696dbfa21380191328485a433')
     version('2.1.0',  sha256='1fb8cc1438de548e16ec3bb9e4b2abb9f7ce5656f71c0906583819fcfa8c2031')
@@ -50,6 +52,7 @@ class Hwloc(AutotoolsPackage):
     variant('gl', default=False, description="Support GL device discovery")
     variant('cuda', default=False, description="Support CUDA devices")
     variant('libxml2', default=True, description="Build with libxml2")
+    variant('libudev', default=False, description="Build with libudev")
     variant('pci', default=(sys.platform != 'darwin'),
             description="Support analyzing devices on PCI bus")
     variant('shared', default=True, description="Build shared libraries")
@@ -67,6 +70,9 @@ class Hwloc(AutotoolsPackage):
     # netloc isn't available until version 2.0.0
     conflicts('+netloc', when="@:1.99.99")
 
+    # libudev isn't available until version 1.11.0
+    conflicts('+libudev', when="@:1.10")
+
     depends_on('pkgconfig', type='build')
     depends_on('m4', type='build', when='@master')
     depends_on('autoconf', type='build', when='@master')
@@ -102,6 +108,7 @@ def configure_args(self):
         args.extend(self.enable_or_disable('gl'))
         args.extend(self.enable_or_disable('cuda'))
         args.extend(self.enable_or_disable('libxml2'))
+        args.extend(self.enable_or_disable('libudev'))
         args.extend(self.enable_or_disable('pci'))
         args.extend(self.enable_or_disable('shared'))
 

From ce8cf5d9b037079ae3fd77fcaf84cf2eafbc9fbd Mon Sep 17 00:00:00 2001
From: h-denpo <57649496+h-denpo@users.noreply.github.com>
Date: Mon, 18 May 2020 17:04:10 +0900
Subject: [PATCH 434/802] revocap-refiner: fixed typo in pic flags (#16694)

---
 var/spack/repos/builtin/packages/revocap-refiner/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/revocap-refiner/package.py b/var/spack/repos/builtin/packages/revocap-refiner/package.py
index ca130ef7379..38eeb31256d 100644
--- a/var/spack/repos/builtin/packages/revocap-refiner/package.py
+++ b/var/spack/repos/builtin/packages/revocap-refiner/package.py
@@ -24,7 +24,7 @@ class RevocapRefiner(MakefilePackage):
 
     def edit(self, spec, prefix):
         cflags = ['-O']
-        cxxflags = ['-O',  self.compiler.pic_flag]
+        cxxflags = ['-O',  self.compiler.cxx_pic_flag]
         fflags = ['']
         ldshare = ['']
         libs = ['-lstdc++']

From 2d464f69f85f6bc212ee36ab45c096894de7be33 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Mon, 18 May 2020 09:57:51 -0500
Subject: [PATCH 435/802] PyYAML: fix linking to libyaml (#16682)

---
 .../builtin/packages/py-pyyaml/package.py     | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-pyyaml/package.py b/var/spack/repos/builtin/packages/py-pyyaml/package.py
index 2b00de2d9b0..00b3d848b7d 100644
--- a/var/spack/repos/builtin/packages/py-pyyaml/package.py
+++ b/var/spack/repos/builtin/packages/py-pyyaml/package.py
@@ -11,6 +11,9 @@ class PyPyyaml(PythonPackage):
 
     homepage = "https://pyyaml.org/wiki/PyYAML"
     url      = "https://pypi.io/packages/source/P/PyYAML/PyYAML-5.3.1.tar.gz"
+    git      = "https://github.com/yaml/pyyaml.git"
+
+    maintainers = ['adamjstewart']
 
     version('5.3.1', sha256='b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d')
     version('5.1.2', sha256='01adf0b6c6f61bd11af6e10ca52b7d4057dd0be0343eb9283c878cf3af56aee4')
@@ -24,6 +27,17 @@ class PyPyyaml(PythonPackage):
     depends_on('python@2.7:2.8,3.5:', type=('build', 'run'))
     depends_on('libyaml', when='+libyaml')
 
+    phases = ['build_ext', 'install']
+
+    @property
+    def import_modules(self):
+        modules = ['yaml']
+
+        if '+libyaml' in self.spec:
+            modules.append('yaml.cyaml')
+
+        return modules
+
     def setup_py(self, *args, **kwargs):
         # Cast from tuple to list
         args = list(args)
@@ -34,3 +48,21 @@ def setup_py(self, *args, **kwargs):
             args.insert(0, '--without-libyaml')
 
         super(PyPyyaml, self).setup_py(*args, **kwargs)
+
+    def build_ext_args(self, spec, prefix):
+        args = []
+
+        if '+libyaml' in spec:
+            args.extend([
+                spec['libyaml'].libs.search_flags,
+                spec['libyaml'].headers.include_flags,
+            ])
+
+        return args
+
+    # Tests need to be re-added since `phases` was overridden
+    run_after('build_ext')(
+        PythonPackage._run_default_build_time_test_callbacks)
+    run_after('install')(
+        PythonPackage._run_default_install_time_test_callbacks)
+    run_after('install')(PythonPackage.sanity_check_prefix)

From 931932d65dca407eb6c14acd0dd5222b33f3dad0 Mon Sep 17 00:00:00 2001
From: archxlith <55454330+archxlith@users.noreply.github.com>
Date: Mon, 18 May 2020 11:01:59 -0400
Subject: [PATCH 436/802] New package: py-pyeda (#16416)

* New package: py-pyeda

* py-pyeda: added dep for python 3.3 or greater

* [py-pyeda] Added space in depends_on python line
---
 .../repos/builtin/packages/py-pyeda/package.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-pyeda/package.py

diff --git a/var/spack/repos/builtin/packages/py-pyeda/package.py b/var/spack/repos/builtin/packages/py-pyeda/package.py
new file mode 100644
index 00000000000..d6f3b4a3f9c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyeda/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyeda(PythonPackage):
+    """PyEDA is a Python library for electronic design automation."""
+
+    homepage = "https://github.com/cjdrake/pyeda"
+    url      = "https://pypi.io//packages/source/p/pyeda/pyeda-0.28.0.tar.gz"
+
+    version('0.28.0', sha256='07185f458d5d0b2ba5058da8b95dad6ab7684ceaf41237a25bcd3f005490f59d')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('python@3.3:', type=('build', 'run'))

From 28ef9cad3b392544bb011388bbb4a67019cbbef4 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 19 May 2020 00:36:00 +0800
Subject: [PATCH 437/802] Add new package: hyperscan (#16681)

* Add new package: hyperscan

* hyperscan: remove cmake_args()
---
 .../builtin/packages/hyperscan/package.py     | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/hyperscan/package.py

diff --git a/var/spack/repos/builtin/packages/hyperscan/package.py b/var/spack/repos/builtin/packages/hyperscan/package.py
new file mode 100644
index 00000000000..1fd057c7c6e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hyperscan/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import platform
+
+_versions = {
+    'v5.2.1': {
+        'Linux-aarch64': ('d2ac1669154ec27b794b64d026ad09caecee6e5e17fd35107595a7517711d2b9', 'https://github.com/kunpengcompute/hyperscan/archive/v5.2.1.aarch64.tar.gz'),
+        'Linux-x86_64': ('fd879e4ee5ecdd125e3a79ef040886978ae8f1203832d5a3f050c48f17eec867', 'https://github.com/intel/hyperscan/archive/v5.2.1.tar.gz')
+    }
+}
+
+
+class Hyperscan(CMakePackage):
+    """High-performance regular expression matching library."""
+
+    homepage = "https://www.hyperscan.io/"
+    url      = "https://github.com/intel/hyperscan/archive/v5.2.1.tar.gz"
+
+    for ver, packages in _versions.items():
+        key = "{0}-{1}".format(platform.system(), platform.machine())
+        pkg = packages.get(key)
+        if pkg:
+            version(ver, sha256=pkg[0], url=pkg[1])
+
+    depends_on('boost')
+    depends_on('pcre')
+    depends_on('ragel', type='build')

From 0b37188e4f46f9579da357856502b199c88744d9 Mon Sep 17 00:00:00 2001
From: Nick Robison <nicholas.a.robison@omb.eop.gov>
Date: Mon, 18 May 2020 12:49:44 -0400
Subject: [PATCH 438/802] Update Apache arrow to 0.17.1 (#16701)

Update Arrow to the latest version.

Also add an additional dependency on `thrift` when building with Parquet support.
---
 var/spack/repos/builtin/packages/arrow/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/arrow/package.py b/var/spack/repos/builtin/packages/arrow/package.py
index 8cc4a067669..ef0e1adc8c8 100644
--- a/var/spack/repos/builtin/packages/arrow/package.py
+++ b/var/spack/repos/builtin/packages/arrow/package.py
@@ -15,6 +15,7 @@ class Arrow(CMakePackage):
     homepage = "http://arrow.apache.org"
     url      = "https://github.com/apache/arrow/archive/apache-arrow-0.9.0.tar.gz"
 
+    version('0.17.1', sha256='ecb6da20f9288c0ca31f9b457ffdd460198765a8af27c1cac4b1382a8d130f86')
     version('0.15.1', sha256='ab1c0d371a10b615eccfcead71bb79832245d788f4834cc6b278c03c3872d593')
     version('0.15.0', sha256='d1072d8c4bf9166949f4b722a89350a88b7c8912f51642a5d52283448acdfd58')
     version('0.14.1', sha256='69d9de9ec60a3080543b28a5334dbaf892ca34235b8bd8f8c1c01a33253926c1')
@@ -32,6 +33,7 @@ class Arrow(CMakePackage):
     depends_on('snappy~shared')
     depends_on('zlib+pic')
     depends_on('zstd+pic')
+    depends_on('thrift+pic', when='+parquet')
 
     variant('build_type', default='Release',
             description='CMake build type',

From 864d4a223264cd9d070b4b2a05a305f847158152 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 18 May 2020 18:51:26 +0200
Subject: [PATCH 439/802] r-goftest: New package (#16699)

---
 .../builtin/packages/r-goftest/package.py     | 20 +++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-goftest/package.py

diff --git a/var/spack/repos/builtin/packages/r-goftest/package.py b/var/spack/repos/builtin/packages/r-goftest/package.py
new file mode 100644
index 00000000000..feaa0724b3d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-goftest/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGoftest(RPackage):
+    """Cramer-Von Mises and Anderson-Darling tests of goodness-of-fit for
+       continuous univariate distributions, using efficient algorithms.
+    """
+
+    homepage = "https://cloud.r-project.org/package=goftest"
+    url      = "https://cloud.r-project.org/src/contrib/goftest_1.2-2.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/goftest"
+
+    version('1.2-2', sha256='e497992666b002b6c6bed73bf05047ad7aa69eb58898da0ad8f1f5b2219e7647')
+
+    depends_on('r@3.3:', type=('build', 'run'))

From d957c621ef3982347f5d1e17ede34f679400ea1f Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 18 May 2020 18:53:17 +0200
Subject: [PATCH 440/802] r-tensor: New package (#16697)

---
 .../builtin/packages/r-tensor/package.py      | 20 +++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-tensor/package.py

diff --git a/var/spack/repos/builtin/packages/r-tensor/package.py b/var/spack/repos/builtin/packages/r-tensor/package.py
new file mode 100644
index 00000000000..6fc8ace4949
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tensor/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTensor(RPackage):
+    """The tensor product of two arrays is notionally an outer product of
+       the arrays collapsed in specific extents by summing along the
+       appropriate diagonals.
+    """
+
+    homepage = "https://cloud.r-project.org/package=tensor"
+    url      = "https://cloud.r-project.org/src/contrib/tensor_1.5.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/tensor"
+
+    version('1.5', sha256='e1dec23e3913a82e2c79e76313911db9050fb82711a0da227f94fc6df2d3aea6')
+    version('1.4', sha256='6f1643da018d58a0aaa27260df6fdf687fc36f4cd1964931b3180b7df8c0e642')

From 154a4428176ec3024529972478db71d351e57c48 Mon Sep 17 00:00:00 2001
From: Utkarsh Ayachit <utkarsh.ayachit@kitware.com>
Date: Mon, 18 May 2020 13:59:40 -0400
Subject: [PATCH 441/802] paraview: use kits by default (#16698)

Adding a variant to enable/disable kits and making the default use kits.
---
 .../repos/builtin/packages/paraview/package.py      | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py
index 48dff877e0a..f9e10b1fba8 100644
--- a/var/spack/repos/builtin/packages/paraview/package.py
+++ b/var/spack/repos/builtin/packages/paraview/package.py
@@ -47,6 +47,8 @@ class Paraview(CMakePackage, CudaPackage):
     variant('hdf5', default=False, description="Use external HDF5")
     variant('shared', default=True,
             description='Builds a shared version of the library')
+    variant('kits', default=True,
+            description='Use module kits')
 
     conflicts('+python', when='+python3')
     conflicts('+python', when='@5.6:')
@@ -271,6 +273,17 @@ def nvariant_bool(feature):
                 '-DPARAVIEW_DO_UNIX_STYLE_INSTALLS:BOOL=ON',
             ])
 
+        if '+kits' in spec:
+            if spec.satisfies('@5.0:5.6'):
+                cmake_args.append(
+                    '-DVTK_ENABLE_KITS:BOOL=ON')
+            elif spec.satisfies('@5.7'):
+                cmake_args.append(
+                    '-DPARAVIEW_ENABLE_KITS:BOOL=ON')
+            else:
+                cmake_args.append(
+                    '-DPARAVIEW_BUILD_WITH_KITS:BOOL=ON')
+
         # Hide git from Paraview so it will not use `git describe`
         # to find its own version number
         if spec.satisfies('@5.4.0:5.4.1'):

From d768b34f176306b86bde060852f781316f7a9155 Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Mon, 18 May 2020 16:07:35 -0500
Subject: [PATCH 442/802] angsd: add 0.933, add misc programs to install
 (#16669)

* angsd: add 0.933, add misc programs to install

* angsd: add r variant
---
 .../repos/builtin/packages/angsd/package.py    | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/angsd/package.py b/var/spack/repos/builtin/packages/angsd/package.py
index 561fe972018..6dae47f2204 100644
--- a/var/spack/repos/builtin/packages/angsd/package.py
+++ b/var/spack/repos/builtin/packages/angsd/package.py
@@ -16,18 +16,34 @@ class Angsd(MakefilePackage):
     homepage = "https://github.com/ANGSD/angsd"
     url      = "https://github.com/ANGSD/angsd/archive/0.919.tar.gz"
 
+    version('0.933', sha256='2f992325dc08fa25ac525d9300ef6bd61808e74c521b4cc72a2ce00d98f402bb')
     version('0.921', sha256='8892d279ce1804f9e17fe2fc65a47e5498e78fc1c1cb84d2ca2527fd5c198772')
     version('0.919', sha256='c2ea718ca5a5427109f4c3415e963dcb4da9afa1b856034e25c59c003d21822a')
 
+    variant('r', default=True, description='Enable R dependency')
+
     depends_on('htslib')
     conflicts('^htslib@1.6:', when='@0.919')
 
+    depends_on('zlib')
+    depends_on('lzma')
+    depends_on('curl')
+
+    depends_on('r', type='run', when='+rlib')
+
     def setup_run_environment(self, env):
         env.set('R_LIBS', self.prefix.R)
 
     def install(self, spec, prefix):
+        binaries = [
+            'angsd', 'misc/realSFS', 'misc/thetaStat'
+        ]
+
         mkdirp(prefix.bin)
-        install('angsd', join_path(prefix.bin))
+
+        for b in binaries:
+            install(b, join_path(prefix.bin))
+
         install_tree('R', prefix.R)
         install_tree('RES', prefix.RES)
         install_tree('scripts', prefix.scripts)

From 294a91b580429f6476bb6a38a89127dbd87ca661 Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Mon, 18 May 2020 16:37:06 -0500
Subject: [PATCH 443/802] r-decipher: new package at 2.12.0 (#16705)

---
 .../builtin/packages/r-decipher/package.py    | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-decipher/package.py

diff --git a/var/spack/repos/builtin/packages/r-decipher/package.py b/var/spack/repos/builtin/packages/r-decipher/package.py
new file mode 100644
index 00000000000..d4d2a881b88
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-decipher/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDecipher(RPackage):
+    """Tools for curating, analyzing, and manipulating biological sequences."""
+
+    homepage = "https://bioconductor.org/packages/DECIPHER"
+    git      = "https://git.bioconductor.org/packages/DECIPHER.git"
+
+    version('2.12.0', commit='658ae23870383b25b96a03a18d4ecac228a2650f')
+    version('2.10.2', commit='db7b017c9050a7ec1d4daa15352994890095e9c3')
+    version('2.8.1', commit='35aa66f48e06b93a98d1060c90c44d34ce05ccd9')
+    version('2.6.0', commit='ed9acaa35c8774cb0ea01cd7cc2e46d063d8c70e')
+    version('2.4.0', commit='1a57b8e4c7d7dec1c233f79c9a88d3705e0ad432')
+
+    depends_on('r@3.3.0:', type=('build', 'run'))
+    depends_on('r-biostrings@2.35.12:', type=('build', 'run'))
+    depends_on('r-rsqlite@1.1:', type=('build', 'run'))
+    depends_on('r-dbi', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-xvector', type=('build', 'run'))

From cf4c48c37e4a25bc0de4249c3266c99abb1aa1fc Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Mon, 18 May 2020 16:38:37 -0500
Subject: [PATCH 444/802] TensorFlow: add new versions (#16703)

---
 var/spack/repos/builtin/packages/py-tensorflow/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-tensorflow/package.py b/var/spack/repos/builtin/packages/py-tensorflow/package.py
index 78138b1e8b1..888e9432bf5 100644
--- a/var/spack/repos/builtin/packages/py-tensorflow/package.py
+++ b/var/spack/repos/builtin/packages/py-tensorflow/package.py
@@ -17,9 +17,12 @@ class PyTensorflow(Package, CudaPackage):
     import_modules = ['tensorflow']
 
     version('2.2.0',  sha256='69cd836f87b8c53506c4f706f655d423270f5a563b76dc1cfa60fbc3184185a3')
+    version('2.1.1',  sha256='a200bc16e4b630db3ac7225bcb6f239a76841967b0aec1d7d7bbe44dc5661318')
     version('2.1.0',  sha256='638e541a4981f52c69da4a311815f1e7989bf1d67a41d204511966e1daed14f7')
+    version('2.0.2',  sha256='a548742bbafd302eec51e2794d7687674a64f6b10ce1414073858cb83c0cefc2')
     version('2.0.1',  sha256='29197d30923b9670992ee4b9c6161f50c7452e9a4158c720746e846080ac245a')
     version('2.0.0',  sha256='49b5f0495cd681cbcb5296a4476853d4aea19a43bdd9f179c928a977308a0617')
+    version('1.15.3', sha256='9ab1d92e58eb813922b040acc7622b32d73c2d8d971fe6491a06f9df4c778151')
     version('1.15.2', sha256='d95d75d26a298211b5e802842e87fda5b8b14f6ad83719377b391e5fb71b8746')
     version('1.15.1', sha256='19b6e72bc8675937f618cede364d7228a71c2eeaffc42801bcefd98dda7ca056')
     version('1.15.0', sha256='a5d49c00a175a61da7431a9b289747d62339be9cf37600330ad63b611f7f5dc9')

From 84889ef3a3a553171ef6418f4f5f4b22420e7749 Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Mon, 18 May 2020 16:39:13 -0700
Subject: [PATCH 445/802] move source dir to last cmake arg (#16709)

---
 lib/spack/spack/build_systems/cmake.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/build_systems/cmake.py b/lib/spack/spack/build_systems/cmake.py
index d7da957a9d6..dfa2c9e47aa 100644
--- a/lib/spack/spack/build_systems/cmake.py
+++ b/lib/spack/spack/build_systems/cmake.py
@@ -331,9 +331,9 @@ def cmake_args(self):
 
     def cmake(self, spec, prefix):
         """Runs ``cmake`` in the build directory"""
-        options = [os.path.abspath(self.root_cmakelists_dir)]
-        options += self.std_cmake_args
+        options = self.std_cmake_args
         options += self.cmake_args()
+        options.append(os.path.abspath(self.root_cmakelists_dir))
         with working_dir(self.build_directory, create=True):
             inspect.getmodule(self).cmake(*options)
 

From 3f6164053d109f890b407360aef7c9aedc37d4b0 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 19 May 2020 10:40:34 +0800
Subject: [PATCH 446/802] Add new package: http-get (#16677)

* Add new package: http-get

* refine version name
---
 .../builtin/packages/http-get/package.py      | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/http-get/package.py

diff --git a/var/spack/repos/builtin/packages/http-get/package.py b/var/spack/repos/builtin/packages/http-get/package.py
new file mode 100644
index 00000000000..aa05b9f355d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/http-get/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import datetime
+
+
+class HttpGet(MakefilePackage):
+    """Http_get fetches an HTTP URL and dumps the contents to stdout.
+    It does not do gopher, ftp, file, news, or any other type of URL,
+    only HTTP. It can be configured to do HTTPS fetches as well."""
+
+    homepage = "http://www.acme.com/software/http_get/"
+    url      = "http://www.acme.com/software/http_get/http_get_23May2018.tar.gz"
+
+    version('2018-05-23', sha256='7d46ce25e53b6d3e27a99c1853c3054a046cc97d5e30a713a7ec986cfe7c4fe0')
+
+    def url_for_version(self, version):
+        ver = datetime.datetime.strptime(str(version), '%Y-%m-%d').date()
+        verstr = datetime.datetime.strftime(ver, '%d%b%Y')
+        return "http://www.acme.com/software/http_get/http_get_{0}.tar.gz".format(verstr)
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter("Makefile")
+        makefile.filter("BINDIR =\t/usr/local/bin",
+                        "BINDIR =    {0}/bin".format(self.prefix))
+        makefile.filter("MANDIR =\t/usr/local/man/man1",
+                        "MANDIR={0}/man/man1".format(self.prefix))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        mkdirp(prefix.man.man1)
+        make('install')

From 9d766ae1fafec7a2c5321caaed70d835edcbd81a Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 19 May 2020 10:41:00 +0800
Subject: [PATCH 447/802] Add new package: http-load (#16676)

* Add new package: http-load

* refine version format

* fix date/version error
---
 .../builtin/packages/http-load/package.py     | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/http-load/package.py

diff --git a/var/spack/repos/builtin/packages/http-load/package.py b/var/spack/repos/builtin/packages/http-load/package.py
new file mode 100644
index 00000000000..4b2f61d18d4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/http-load/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import datetime
+
+
+class HttpLoad(MakefilePackage):
+    """http_load - multiprocessing http test client"""
+
+    homepage = "http://www.acme.com/software/http_load/"
+    url      = "http://www.acme.com/software/http_load/http_load-09Mar2016.tar.gz"
+
+    version('2016-03-09', sha256='a2bf118d88f6acd2a082cbf275d141538149caaa0a4ce1bcc66680668e781306')
+
+    def url_for_version(self, version):
+        ver = datetime.datetime.strptime(str(version), '%Y-%m-%d').date()
+        verstr = datetime.datetime.strftime(ver, '%d%b%Y')
+        return "http://www.acme.com/software/http_load/http_load-{0}.tar.gz".format(verstr)
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter("Makefile")
+        makefile.filter("BINDIR =\t/usr/local/bin",
+                        "BINDIR =    {0}/bin".format(self.prefix))
+        makefile.filter("MANDIR =\t/usr/local/man/man1",
+                        "MANDIR={0}/man/man1".format(self.prefix))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        mkdirp(prefix.man.man1)
+        make('install')

From 31ccf80294382a391743728a736574737217c23b Mon Sep 17 00:00:00 2001
From: vvolkl <valentin.volkl@cern.ch>
Date: Tue, 19 May 2020 04:52:18 +0200
Subject: [PATCH 448/802] [podio] fix root cxxstd dependency (#16708)

---
 .../repos/builtin/packages/podio/package.py     | 17 ++++++-----------
 1 file changed, 6 insertions(+), 11 deletions(-)

diff --git a/var/spack/repos/builtin/packages/podio/package.py b/var/spack/repos/builtin/packages/podio/package.py
index 14b4722cdbf..488eaf54f15 100644
--- a/var/spack/repos/builtin/packages/podio/package.py
+++ b/var/spack/repos/builtin/packages/podio/package.py
@@ -26,17 +26,12 @@ class Podio(CMakePackage):
             description='The build type to build',
             values=('Debug', 'Release'))
 
-    variant('cxxstd',
-            default='17',
-            values=('14', '17'),
-            multi=False,
-            description='Use the specified C++ standard when building.')
+    # cpack config throws an error on some systems
+    patch('cpack.patch', when="@:0.10.0")
 
-    _cxxstd_values = ('14', '17')
-    for s in _cxxstd_values:
-        depends_on('root@6.08.06: cxxstd=' + s, when='cxxstd=' + s)
+    depends_on('root@6.08.06:')
 
-    depends_on('cmake', type='build')
+    depends_on('cmake@3.8:', type='build')
     depends_on('python', type=('build', 'run'))
     depends_on('py-pyyaml', type=('build', 'run'))
 
@@ -44,8 +39,8 @@ def cmake_args(self):
         args = []
         # C++ Standard
         args.append('-DCMAKE_CXX_STANDARD=%s'
-                    % self.spec.variants['cxxstd'].value)
-        args.append('-DBUILD_TESTING=OFF')
+                    % self.spec['root'].variants['cxxstd'].value)
+        args.append('-DBUILD_TESTING=%s' % self.run_tests)
         return args
 
     def setup_build_environment(self, spack_env):

From b1f1f5dddbb141d64e02c88985aa74365228d59b Mon Sep 17 00:00:00 2001
From: Scott Wittenburg <scott.wittenburg@kitware.com>
Date: Mon, 18 May 2020 19:48:38 -0600
Subject: [PATCH 449/802] Pipelines: Ensure consistent spack version for entire
 pipeline

Also retry jobs always, as script failure is not confined to only our
spack ci rebuild command exit code.
---
 lib/spack/spack/ci.py | 20 ++++----------------
 1 file changed, 4 insertions(+), 16 deletions(-)

diff --git a/lib/spack/spack/ci.py b/lib/spack/spack/ci.py
index 069cbb704a7..9ba7f39e455 100644
--- a/lib/spack/spack/ci.py
+++ b/lib/spack/spack/ci.py
@@ -34,18 +34,7 @@
 
 
 JOB_RETRY_CONDITIONS = [
-    'unknown_failure',
-    'api_failure',
-    'stuck_or_timeout_failure',
-    'runner_system_failure',
-    'missing_dependency_failure',
-    'runner_unsupported',
-    'stale_schedule',
-    'job_execution_timeout',
-    'archived_failure',
-    'unmet_prerequisites',
-    'scheduler_failure',
-    'data_integrity_failure',
+    'always',
 ]
 
 spack_gpg = SpackCommand('gpg')
@@ -505,10 +494,9 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
         if not custom_spack_ref:
             custom_spack_ref = 'master'
         before_script = [
-            ('git clone "{0}" --branch "{1}" --depth 1 '
-             '--single-branch'.format(custom_spack_repo, custom_spack_ref)),
-            # Next line just shows spack version in pipeline output
-            'pushd ./spack && git rev-parse HEAD && popd',
+            ('git clone "{0}"'.format(custom_spack_repo)),
+            'pushd ./spack && git checkout "{0}" && popd'.format(
+                custom_spack_ref),
             '. "./spack/share/spack/setup-env.sh"',
         ]
         after_script = [

From 05aacb584e0a4ea22ae33b0e657bafab71cce1b8 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 19 May 2020 23:56:22 +0800
Subject: [PATCH 450/802] Add new package: http-ping (#16675)

* Add new package: http-ping

* refine version name
---
 .../builtin/packages/http-ping/package.py     | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/http-ping/package.py

diff --git a/var/spack/repos/builtin/packages/http-ping/package.py b/var/spack/repos/builtin/packages/http-ping/package.py
new file mode 100644
index 00000000000..7cf731e019f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/http-ping/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import datetime
+
+
+class HttpPing(MakefilePackage):
+    """http_ping is like the regular ping command, except that it sends
+    HTTP requests instead of ICMP echo requests."""
+
+    homepage = "http://www.acme.com/software/http_ping/"
+    url      = "http://www.acme.com/software/http_ping/http_ping_09Mar2016.tar.gz"
+
+    version('2016-03-09', sha256='6bdc570c776a760d2c08f7d18e00b0edd74cf603400929c66c512801b6bb5871')
+
+    def url_for_version(self, version):
+        ver = datetime.datetime.strptime(str(version), '%Y-%m-%d').date()
+        verstr = datetime.datetime.strftime(ver, '%d%b%Y')
+        return "http://www.acme.com/software/http_ping/http_ping_{0}.tar.gz".format(verstr)
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter("Makefile")
+        makefile.filter("BINDIR =\t/usr/local/bin",
+                        "BINDIR =    {0}/bin".format(self.prefix))
+        makefile.filter("MANDIR =\t/usr/local/man/man1",
+                        "MANDIR={0}/man/man1".format(self.prefix))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        mkdirp(prefix.man.man1)
+        make('install')

From 31ab62fb5edb3266d70a7ca1a50a6212f14d3097 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 19 May 2020 23:56:52 +0800
Subject: [PATCH 451/802] Add new package: http-post (#16678)

* Add new package: http-post

* refine version name
---
 .../builtin/packages/http-post/package.py     | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/http-post/package.py

diff --git a/var/spack/repos/builtin/packages/http-post/package.py b/var/spack/repos/builtin/packages/http-post/package.py
new file mode 100644
index 00000000000..bb9c0f25931
--- /dev/null
+++ b/var/spack/repos/builtin/packages/http-post/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import datetime
+
+
+class HttpPost(MakefilePackage):
+    """Http_post does a POST operation to an HTTP URL and dumps the results
+    to stdout. It does not do gopher, ftp, file, news, or any other type of
+    URL, only HTTP. It can be configured to do HTTPS POSTs as well."""
+
+    homepage = "http://www.acme.com/software/http_post/"
+    url      = "http://www.acme.com/software/http_post/http_post_18May2018.tar.gz"
+
+    version('2018-05-18', sha256='981c62bcc5cd12b8531f887b3e3779a63a7b7f370062575cded412865a20ea2c')
+
+    def url_for_version(self, version):
+        ver = datetime.datetime.strptime(str(version), '%Y-%m-%d').date()
+        verstr = datetime.datetime.strftime(ver, '%d%b%Y')
+        return "http://www.acme.com/software/http_post/http_post_{0}.tar.gz".format(verstr)
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter("Makefile")
+        makefile.filter("BINDIR =\t/usr/local/bin",
+                        "BINDIR =    {0}/bin".format(self.prefix))
+        makefile.filter("MANDIR =\t/usr/local/man/man1",
+                        "MANDIR={0}/man/man1".format(self.prefix))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        mkdirp(prefix.man.man1)
+        make('install')

From 63f09a66624bb07f62e9b09807c4152f84009a19 Mon Sep 17 00:00:00 2001
From: "Dr. Christian Tacke"
 <58549698+ChristianTackeGSI@users.noreply.github.com>
Date: Tue, 19 May 2020 17:58:04 +0200
Subject: [PATCH 452/802] openssl: Be Explicit About perl Usage (#16721)

The openssl build process can use the wrong perl for
various reasons, including:
* Wrong value in PERL env var
* The build process first looks for `perl5`, which the
  spack system does not provide, but some other
  distributions provide it. That way, the build process can
  end up using the wrong perl.

Stop all of these problems by explicitly setting PERL to
the to be used dependency.
---
 var/spack/repos/builtin/packages/openssl/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index 0ab87827831..ae47568ce82 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -154,3 +154,6 @@ def link_system_certs(self):
             if os.path.isdir(sys_certs) and not os.path.islink(pkg_certs):
                 os.rmdir(pkg_certs)
                 os.symlink(sys_certs, pkg_certs)
+
+    def setup_build_environment(self, env):
+        env.set('PERL', self.spec['perl'].prefix.bin.perl)

From 20f2a6c2e816f87c5ec09114903539db63131a9b Mon Sep 17 00:00:00 2001
From: ddeidda <53186409+ddeidda@users.noreply.github.com>
Date: Tue, 19 May 2020 17:58:46 +0200
Subject: [PATCH 453/802] update URL and sha256 for aws-parallelcluster 2.7.0
 (#16717)

Signed-off-by: ddeidda <ddeidda@amazon.com>
---
 .../repos/builtin/packages/aws-parallelcluster/package.py      | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/aws-parallelcluster/package.py b/var/spack/repos/builtin/packages/aws-parallelcluster/package.py
index 5737f078551..b9d65247372 100644
--- a/var/spack/repos/builtin/packages/aws-parallelcluster/package.py
+++ b/var/spack/repos/builtin/packages/aws-parallelcluster/package.py
@@ -12,7 +12,7 @@ class AwsParallelcluster(PythonPackage):
     tool to deploy and manage HPC clusters in the AWS cloud."""
 
     homepage = "https://github.com/aws/aws-parallelcluster"
-    url      = "https://pypi.io/packages/source/a/aws-parallelcluster/aws-parallelcluster-2.6.1.tar.gz"
+    url      = "https://pypi.io/packages/source/a/aws-parallelcluster/aws-parallelcluster-2.7.0.tar.gz"
 
     maintainers = [
         'sean-smith', 'demartinofra', 'enrico-usai', 'lukeseawalker', 'rexcsn',
@@ -23,6 +23,7 @@ class AwsParallelcluster(PythonPackage):
         'pcluster.config', 'pcluster.networking'
     ]
 
+    version('2.7.0', sha256='7c34995acfcc256a6996541d330575fc711e1fd5735bf3d734d4e96c1dc8df60')
     version('2.6.1', sha256='2ce9015d90b5d4dc88b46a44cb8a82e8fb0bb2b4cca30335fc5759202ec1b343')
     version('2.6.0', sha256='aaed6962cf5027206834ac24b3d312da91e0f96ae8607f555e12cb124b869f0c')
     version('2.5.1', sha256='4fd6e14583f8cf81f9e4aa1d6188e3708d3d14e6ae252de0a94caaf58be76303')

From 7948344bcd1763912d992ba8e4b5e7b717787eb9 Mon Sep 17 00:00:00 2001
From: Thomas Madlener <thomas.madlener@desy.de>
Date: Tue, 19 May 2020 20:14:45 +0200
Subject: [PATCH 454/802] Introduce version 1.0.0 for py-xenv and remove
 unreleased development release (#16722)

Problems in 0.0.4 should be fixed for 1.0.0
---
 var/spack/repos/builtin/packages/gaudi/package.py   | 2 +-
 var/spack/repos/builtin/packages/py-xenv/package.py | 6 ++----
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/gaudi/package.py b/var/spack/repos/builtin/packages/gaudi/package.py
index ed37ee96f7d..f529366a321 100644
--- a/var/spack/repos/builtin/packages/gaudi/package.py
+++ b/var/spack/repos/builtin/packages/gaudi/package.py
@@ -50,7 +50,7 @@ class Gaudi(CMakePackage):
     depends_on('python@:2.99.99', when='@:32.1', type=('build', 'run'))
     depends_on('py-setuptools@:45.99.99', when='^python@:2.7.99', type='build')
     depends_on('py-six', type=('build', 'run'))
-    depends_on('py-xenv@develop_2018-12-20:', type=('build', 'run'))
+    depends_on('py-xenv@1:', type=('build', 'run'))
     depends_on('range-v3')
     depends_on('root +python +root7 +ssl +tbb +threads')
     depends_on('zlib')
diff --git a/var/spack/repos/builtin/packages/py-xenv/package.py b/var/spack/repos/builtin/packages/py-xenv/package.py
index 5047691cbd0..1ccda619598 100644
--- a/var/spack/repos/builtin/packages/py-xenv/package.py
+++ b/var/spack/repos/builtin/packages/py-xenv/package.py
@@ -10,12 +10,10 @@ class PyXenv(PythonPackage):
     """Helpers to work with the environment in a platform independent way."""
 
     homepage = "https://gitlab.cern.ch/gaudi/xenv"
+    url      = "https://pypi.io/packages/source/x/xenv/xenv-1.0.0.tar.gz"
     git      = "https://gitlab.cern.ch/gaudi/xenv.git"
 
-    # As of 0.0.4, all released versions of xenv corrupt the system environment
-    # in a manner which breaks Spack's compiler wrappers. Therefore, we must
-    # package an un-released development version of xenv.
     version('develop',            branch='master')
-    version('develop_2018-12-20', commit='ddc3bf5e65e1689da499f639af7a27c5c4242841')
+    version('1.0.0', sha256='cea9547295f0bd07c87e68353bb9eb1c2f2d1c09a840e3196c19cbc807ee4558')
 
     depends_on('py-setuptools', type=('build', 'run'))

From 9c16a728fd65fb246e2f0c01e394c9373182a9f7 Mon Sep 17 00:00:00 2001
From: Hadrien G <knights_of_ni@gmx.com>
Date: Tue, 19 May 2020 20:16:57 +0200
Subject: [PATCH 455/802] Add new Acts release (#16718)

---
 var/spack/repos/builtin/packages/acts/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/acts/package.py b/var/spack/repos/builtin/packages/acts/package.py
index 5df5f270cc9..09113f2cd82 100644
--- a/var/spack/repos/builtin/packages/acts/package.py
+++ b/var/spack/repos/builtin/packages/acts/package.py
@@ -35,6 +35,7 @@ class Acts(CMakePackage):
 
     # Supported Acts versions
     version('master', branch='master')
+    version('0.24.0', commit='ef4699c8500bfea59a5fe88bed67fde2f00f0adf')
     version('0.23.0', commit='dc443dd7e663bc4d7fb3c1e3f1f75aaf57ffd4e4')
     version('0.22.1', commit='ca1b8b1645db6b552f44c48d2ff34c8c29618f3a')
     version('0.22.0', commit='2c8228f5843685fc0ae69a8b95dd8fc001139efb')

From 7fe6c0945ab2850a20c3f3a9baed85959a2f84be Mon Sep 17 00:00:00 2001
From: Andrew W Elble <aweits@rit.edu>
Date: Tue, 19 May 2020 15:29:13 -0400
Subject: [PATCH 456/802] py-tensorflow-estimator: new version 2.2.0 (#16726)

---
 .../builtin/packages/py-tensorflow-estimator/package.py   | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-tensorflow-estimator/package.py b/var/spack/repos/builtin/packages/py-tensorflow-estimator/package.py
index b738f2ebf71..055d80724b8 100644
--- a/var/spack/repos/builtin/packages/py-tensorflow-estimator/package.py
+++ b/var/spack/repos/builtin/packages/py-tensorflow-estimator/package.py
@@ -11,16 +11,18 @@ class PyTensorflowEstimator(Package):
     simplifies machine learning programming."""
 
     homepage = "https://github.com/tensorflow/estimator"
-    url      = "https://github.com/tensorflow/estimator/archive/v1.13.0.tar.gz"
+    url      = "https://github.com/tensorflow/estimator/archive/v2.2.0.tar.gz"
 
+    version('2.2.0', sha256='2d68cb6e6442e7dcbfa2e092aa25bdcb0eda420536a829b85d732854a4c85d46')
     version('2.1', sha256='1d74c8181b981748976fa33ad97d3434c3cf2b7e29a0b00861365fe8329dbc4e')
     version('2.0.0', sha256='6f4bdf1ab219e1f1cba25d2af097dc820f56479f12a839853d97422fe4d8b465')
     version('1.13.0', sha256='a787b150ff436636df723e507019c72a5d6486cfe506886279d380166953f12f')
 
     extends('python')
 
-    depends_on('py-tensorflow@2.1.0:',  when='@2.1')
-    depends_on('py-tensorflow@2.0.0',  when='@2.0.0')
+    depends_on('py-tensorflow@2.2.0:',  when='@2.2.0')
+    depends_on('py-tensorflow@2.1.0:2.1.999',  when='@2.1')
+    depends_on('py-tensorflow@2.0.0:2.0.999',  when='@2.0.0')
     depends_on('py-tensorflow@1.13.1', when='@1.13.0')
 
     depends_on('bazel@0.19.0:', type='build')

From 46ab9392498fb3349ea812346876b48908f69b22 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Tue, 19 May 2020 15:19:17 -0600
Subject: [PATCH 457/802] mantevo: update urls to new website (#16732)

---
 var/spack/repos/builtin/packages/cloverleaf/package.py   | 2 +-
 var/spack/repos/builtin/packages/cloverleaf3d/package.py | 2 +-
 var/spack/repos/builtin/packages/hpccg/package.py        | 2 +-
 var/spack/repos/builtin/packages/minighost/package.py    | 2 +-
 var/spack/repos/builtin/packages/minimd/package.py       | 2 +-
 var/spack/repos/builtin/packages/minismac2d/package.py   | 2 +-
 var/spack/repos/builtin/packages/minixyce/package.py     | 2 +-
 var/spack/repos/builtin/packages/pathfinder/package.py   | 2 +-
 var/spack/repos/builtin/packages/tealeaf/package.py      | 2 +-
 9 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cloverleaf/package.py b/var/spack/repos/builtin/packages/cloverleaf/package.py
index a3d4bd02b0b..ad1360cb306 100644
--- a/var/spack/repos/builtin/packages/cloverleaf/package.py
+++ b/var/spack/repos/builtin/packages/cloverleaf/package.py
@@ -16,7 +16,7 @@ class Cloverleaf(MakefilePackage):
     """
 
     homepage = "http://uk-mac.github.io/CloverLeaf"
-    url      = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/CloverLeaf-1.1.tar.gz"
+    url      = "http://downloads.mantevo.org/releaseTarballs/miniapps/CloverLeaf/CloverLeaf-1.1.tar.gz"
 
     tags = ['proxy-app']
 
diff --git a/var/spack/repos/builtin/packages/cloverleaf3d/package.py b/var/spack/repos/builtin/packages/cloverleaf3d/package.py
index 17638b54e53..4e745412532 100644
--- a/var/spack/repos/builtin/packages/cloverleaf3d/package.py
+++ b/var/spack/repos/builtin/packages/cloverleaf3d/package.py
@@ -17,7 +17,7 @@ class Cloverleaf3d(MakefilePackage):
     """
 
     homepage = "http://uk-mac.github.io/CloverLeaf3D/"
-    url      = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/CloverLeaf3D-1.0.tar.gz"
+    url      = "http://downloads.mantevo.org/releaseTarballs/miniapps/CloverLeaf3D/CloverLeaf3D-1.0.tar.gz"
 
     tags = ['proxy-app']
 
diff --git a/var/spack/repos/builtin/packages/hpccg/package.py b/var/spack/repos/builtin/packages/hpccg/package.py
index 67eb4c19418..a93c5852666 100644
--- a/var/spack/repos/builtin/packages/hpccg/package.py
+++ b/var/spack/repos/builtin/packages/hpccg/package.py
@@ -13,7 +13,7 @@ class Hpccg(MakefilePackage):
     """
 
     homepage = "https://mantevo.org/about/applications/"
-    url      = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/HPCCG-1.0.tar.gz"
+    url      = "http://downloads.mantevo.org/releaseTarballs/miniapps/HPCCG/HPCCG-1.0.tar.gz"
 
     tags = ['proxy-app']
 
diff --git a/var/spack/repos/builtin/packages/minighost/package.py b/var/spack/repos/builtin/packages/minighost/package.py
index f39655baf05..b1903f7e62a 100644
--- a/var/spack/repos/builtin/packages/minighost/package.py
+++ b/var/spack/repos/builtin/packages/minighost/package.py
@@ -16,7 +16,7 @@ class Minighost(MakefilePackage):
     """
 
     homepage = "http://mantevo.org"
-    url      = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/miniGhost_1.0.1.tar.gz"
+    url      = "http://downloads.mantevo.org/releaseTarballs/miniapps/MiniGhost/miniGhost_1.0.1.tar.gz"
 
     tags = ['proxy-app']
 
diff --git a/var/spack/repos/builtin/packages/minimd/package.py b/var/spack/repos/builtin/packages/minimd/package.py
index d505015fb59..a4d99402b4c 100644
--- a/var/spack/repos/builtin/packages/minimd/package.py
+++ b/var/spack/repos/builtin/packages/minimd/package.py
@@ -16,7 +16,7 @@ class Minimd(MakefilePackage):
     """
 
     homepage = "http://mantevo.org"
-    url      = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/miniMD_1.2.tgz"
+    url      = "http://downloads.mantevo.org/releaseTarballs/miniapps/MiniMD/miniMD_1.2.tgz"
 
     tags = ['proxy-app']
 
diff --git a/var/spack/repos/builtin/packages/minismac2d/package.py b/var/spack/repos/builtin/packages/minismac2d/package.py
index 545176aa776..5e891562780 100644
--- a/var/spack/repos/builtin/packages/minismac2d/package.py
+++ b/var/spack/repos/builtin/packages/minismac2d/package.py
@@ -14,7 +14,7 @@ class Minismac2d(MakefilePackage):
     """
 
     homepage = "http://mantevo.org"
-    url      = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/miniSMAC2D-2.0.tgz"
+    url      = "http://downloads.mantevo.org/releaseTarballs/miniapps/MiniSMAC2D/miniSMAC2D-2.0.tgz"
 
     tags = ['proxy-app']
 
diff --git a/var/spack/repos/builtin/packages/minixyce/package.py b/var/spack/repos/builtin/packages/minixyce/package.py
index ee8fe84c864..17d4a4b0322 100644
--- a/var/spack/repos/builtin/packages/minixyce/package.py
+++ b/var/spack/repos/builtin/packages/minixyce/package.py
@@ -13,7 +13,7 @@ class Minixyce(MakefilePackage):
     """
 
     homepage = "https://mantevo.org"
-    url      = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/miniXyce_1.0.tar.gz"
+    url      = "http://downloads.mantevo.org/releaseTarballs/miniapps/MiniXyce/miniXyce_1.0.tar.gz"
 
     tags = ['proxy-app']
 
diff --git a/var/spack/repos/builtin/packages/pathfinder/package.py b/var/spack/repos/builtin/packages/pathfinder/package.py
index 3208448d813..8ce7ecca1e5 100644
--- a/var/spack/repos/builtin/packages/pathfinder/package.py
+++ b/var/spack/repos/builtin/packages/pathfinder/package.py
@@ -11,7 +11,7 @@ class Pathfinder(MakefilePackage):
     """Proxy Application. Signature search."""
 
     homepage = "https://mantevo.org/packages/"
-    url      = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/PathFinder_1.0.0.tgz"
+    url      = "http://downloads.mantevo.org/releaseTarballs/miniapps/PathFinder/PathFinder_1.0.0.tgz"
 
     tags = ['proxy-app']
 
diff --git a/var/spack/repos/builtin/packages/tealeaf/package.py b/var/spack/repos/builtin/packages/tealeaf/package.py
index 53c4c7c0907..807d9565fe8 100644
--- a/var/spack/repos/builtin/packages/tealeaf/package.py
+++ b/var/spack/repos/builtin/packages/tealeaf/package.py
@@ -16,7 +16,7 @@ class Tealeaf(MakefilePackage):
     """
 
     homepage = "http://uk-mac.github.io/TeaLeaf/"
-    url      = "https://github.com/Mantevo/mantevo.github.io/raw/master/download_files/TeaLeaf-1.0.tar.gz"
+    url      = "http://downloads.mantevo.org/releaseTarballs/miniapps/TeaLeaf/TeaLeaf-1.0.tar.gz"
 
     tags = ['proxy-app']
 

From cc08070da9e9ef41f6a6630a17d8b3c25f25cf0e Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 19 May 2020 20:59:11 -0500
Subject: [PATCH 458/802] py-scikit-learn: add latest version (#16731)

---
 var/spack/repos/builtin/packages/py-scikit-learn/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-scikit-learn/package.py b/var/spack/repos/builtin/packages/py-scikit-learn/package.py
index 9d3fa4ff2c2..52c9beae434 100644
--- a/var/spack/repos/builtin/packages/py-scikit-learn/package.py
+++ b/var/spack/repos/builtin/packages/py-scikit-learn/package.py
@@ -8,7 +8,7 @@ class PyScikitLearn(PythonPackage):
     """A set of python modules for machine learning and data mining."""
 
     homepage = "https://pypi.python.org/pypi/scikit-learn"
-    url      = "https://pypi.io/packages/source/s/scikit-learn/scikit-learn-0.23.0.tar.gz"
+    url      = "https://pypi.io/packages/source/s/scikit-learn/scikit-learn-0.23.1.tar.gz"
     git      = "https://github.com/scikit-learn/scikit-learn.git"
 
     maintainers = ['adamjstewart']
@@ -31,6 +31,7 @@ class PyScikitLearn(PythonPackage):
     ]
 
     version('master', branch='master')
+    version('0.23.1', sha256='e3fec1c8831f8f93ad85581ca29ca1bb88e2da377fb097cf8322aa89c21bc9b8')
     version('0.23.0', sha256='639a53df6273acc6a7510fb0c658b94e0c70bb13dafff9d14932c981ff9baff4')
     version('0.22.1', sha256='51ee25330fc244107588545c70e2f3570cfc4017cff09eed69d6e1d82a212b7d')
     version('0.22',   sha256='314abf60c073c48a1e95feaae9f3ca47a2139bd77cebb5b877c23a45c9e03012')

From 92989fbbfdc68c25df64004c6b0802431cc4055d Mon Sep 17 00:00:00 2001
From: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Date: Wed, 20 May 2020 09:11:26 -0700
Subject: [PATCH 459/802] tests: check presence not equality for rpath changes
 (#16637)

Fixes #16636
---
 lib/spack/spack/test/relocate.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/lib/spack/spack/test/relocate.py b/lib/spack/spack/test/relocate.py
index a594f1a9ba6..d9becebe7b2 100644
--- a/lib/spack/spack/test/relocate.py
+++ b/lib/spack/spack/test/relocate.py
@@ -253,7 +253,9 @@ def test_replace_prefix_bin(hello_world):
     # Check that the RPATHs changed
     patchelf = spack.util.executable.which('patchelf')
     output = patchelf('--print-rpath', str(executable), output=str)
-    assert output.strip() == '/foo/lib:/foo/lib64'
+
+    # Some compilers add rpaths so ensure changes included in final result
+    assert '/foo/lib:/foo/lib64' in output
 
 
 @pytest.mark.requires_executables('patchelf', 'strings', 'file', 'gcc')
@@ -280,7 +282,9 @@ def test_relocate_elf_binaries_absolute_paths(hello_world, tmpdir):
     # Check that the RPATHs changed
     patchelf = spack.util.executable.which('patchelf')
     output = patchelf('--print-rpath', str(new_binary), output=str)
-    assert output.strip() == '/foo/lib:/usr/lib64'
+
+    # Some compilers add rpaths so ensure changes included in final result
+    assert '/foo/lib:/usr/lib64' in output
 
 
 @pytest.mark.requires_executables('patchelf', 'strings', 'file', 'gcc')
@@ -307,4 +311,6 @@ def test_relocate_elf_binaries_relative_paths(hello_world, tmpdir):
     # Check that the RPATHs changed
     patchelf = spack.util.executable.which('patchelf')
     output = patchelf('--print-rpath', str(new_binary), output=str)
-    assert output.strip() == '/foo/lib:/foo/lib64:/opt/local/lib'
+
+    # Some compilers add rpaths so ensure changes included in final result
+    assert '/foo/lib:/foo/lib64:/opt/local/lib' in output

From cfb6f212360ff4aa75eb65fcb6b9c29c508458e1 Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Wed, 20 May 2020 17:09:07 -0700
Subject: [PATCH 460/802] externals: allow package prefs to configure default
 not buildable (#16735)

Allows `all` to be configured non-buildable in packages.yaml.

The following config would only allow zlib to be built by Spack, all other packages would have to be found as externals.

```
packages:
  all:
    buildable: False
  zlib:
    buildable: True
```
---
 lib/spack/spack/package_prefs.py              | 14 ++--
 .../spack/test/concretize_preferences.py      | 64 +++++++++++++++++++
 2 files changed, 74 insertions(+), 4 deletions(-)

diff --git a/lib/spack/spack/package_prefs.py b/lib/spack/spack/package_prefs.py
index aa904a0792b..67325fc7ae1 100644
--- a/lib/spack/spack/package_prefs.py
+++ b/lib/spack/spack/package_prefs.py
@@ -190,11 +190,17 @@ def spec_externals(spec):
 
 def is_spec_buildable(spec):
     """Return true if the spec pkgspec is configured as buildable"""
+
     allpkgs = spack.config.get('packages')
-    do_not_build = [name for name, entry in allpkgs.items()
-                    if not entry.get('buildable', True)]
-    return not (spec.name in do_not_build or
-                any(spec.package.provides(name) for name in do_not_build))
+    all_buildable = allpkgs.get('all', {}).get('buildable', True)
+
+    # Get the list of names for which all_buildable is overridden
+    reverse = [name for name, entry in allpkgs.items()
+               if entry.get('buildable', all_buildable) != all_buildable]
+    # Does this spec override all_buildable
+    spec_reversed = (spec.name in reverse or
+                     any(spec.package.provides(name) for name in reverse))
+    return not all_buildable if spec_reversed else all_buildable
 
 
 def get_package_dir_permissions(spec):
diff --git a/lib/spack/spack/test/concretize_preferences.py b/lib/spack/spack/test/concretize_preferences.py
index ca4df6700ce..df46ed9fe80 100644
--- a/lib/spack/spack/test/concretize_preferences.py
+++ b/lib/spack/spack/test/concretize_preferences.py
@@ -239,6 +239,70 @@ def mock_module(cmd, module):
         spec.concretize()
         assert spec['mpich'].external_path == '/dummy/path'
 
+    def test_buildable_false(self):
+        conf = syaml.load_config("""\
+libelf:
+  buildable: false
+""")
+        spack.config.set('packages', conf, scope='concretize')
+        spec = Spec('libelf')
+        assert not spack.package_prefs.is_spec_buildable(spec)
+
+        spec = Spec('mpich')
+        assert spack.package_prefs.is_spec_buildable(spec)
+
+    def test_buildable_false_virtual(self):
+        conf = syaml.load_config("""\
+mpi:
+  buildable: false
+""")
+        spack.config.set('packages', conf, scope='concretize')
+        spec = Spec('libelf')
+        assert spack.package_prefs.is_spec_buildable(spec)
+
+        spec = Spec('mpich')
+        assert not spack.package_prefs.is_spec_buildable(spec)
+
+    def test_buildable_false_all(self):
+        conf = syaml.load_config("""\
+all:
+  buildable: false
+""")
+        spack.config.set('packages', conf, scope='concretize')
+        spec = Spec('libelf')
+        assert not spack.package_prefs.is_spec_buildable(spec)
+
+        spec = Spec('mpich')
+        assert not spack.package_prefs.is_spec_buildable(spec)
+
+    def test_buildable_false_all_true_package(self):
+        conf = syaml.load_config("""\
+all:
+  buildable: false
+libelf:
+  buildable: true
+""")
+        spack.config.set('packages', conf, scope='concretize')
+        spec = Spec('libelf')
+        assert spack.package_prefs.is_spec_buildable(spec)
+
+        spec = Spec('mpich')
+        assert not spack.package_prefs.is_spec_buildable(spec)
+
+    def test_buildable_false_all_true_virtual(self):
+        conf = syaml.load_config("""\
+all:
+  buildable: false
+mpi:
+  buildable: true
+""")
+        spack.config.set('packages', conf, scope='concretize')
+        spec = Spec('libelf')
+        assert not spack.package_prefs.is_spec_buildable(spec)
+
+        spec = Spec('mpich')
+        assert spack.package_prefs.is_spec_buildable(spec)
+
     def test_config_permissions_from_all(self, configure_permissions):
         # Although these aren't strictly about concretization, they are
         # configured in the same file and therefore convenient to test here.

From bcd5dd6e3e322adb02be3a571750efe848002e5c Mon Sep 17 00:00:00 2001
From: Jeremy <jjwilke@users.noreply.github.com>
Date: Wed, 20 May 2020 20:15:02 -0700
Subject: [PATCH 461/802] add SST packages and dependencies (#16618)

---
 .../builtin/packages/dramsim2/package.py      |  30 +++
 .../packages/goblin-hmc-sim/package.py        |  28 ++
 .../builtin/packages/hbm-dramsim2/package.py  |  23 ++
 .../builtin/packages/hybridsim/makefile.patch |  20 ++
 .../builtin/packages/hybridsim/package.py     |  37 +++
 .../builtin/packages/intel-pin/package.py     |   1 +
 .../builtin/packages/nvdimmsim/package.py     |  32 +++
 .../builtin/packages/ramulator/package.py     |  35 +++
 .../ramulator_sha_7d2e723_gcc48Patch.patch    | 250 ++++++++++++++++++
 .../ramulator_sha_7d2e723_libPatch.patch      |  23 ++
 .../builtin/packages/sst-core/package.py      |  79 ++++--
 .../builtin/packages/sst-elements/package.py  | 101 +++++++
 .../builtin/packages/sst-macro/package.py     |  83 +++---
 .../packages/sst-transports/package.py        |  25 ++
 14 files changed, 712 insertions(+), 55 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/dramsim2/package.py
 create mode 100644 var/spack/repos/builtin/packages/goblin-hmc-sim/package.py
 create mode 100644 var/spack/repos/builtin/packages/hbm-dramsim2/package.py
 create mode 100644 var/spack/repos/builtin/packages/hybridsim/makefile.patch
 create mode 100644 var/spack/repos/builtin/packages/hybridsim/package.py
 create mode 100644 var/spack/repos/builtin/packages/nvdimmsim/package.py
 create mode 100644 var/spack/repos/builtin/packages/ramulator/package.py
 create mode 100644 var/spack/repos/builtin/packages/ramulator/ramulator_sha_7d2e723_gcc48Patch.patch
 create mode 100644 var/spack/repos/builtin/packages/ramulator/ramulator_sha_7d2e723_libPatch.patch
 create mode 100644 var/spack/repos/builtin/packages/sst-elements/package.py
 create mode 100644 var/spack/repos/builtin/packages/sst-transports/package.py

diff --git a/var/spack/repos/builtin/packages/dramsim2/package.py b/var/spack/repos/builtin/packages/dramsim2/package.py
new file mode 100644
index 00000000000..df2d42af437
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dramsim2/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Dramsim2(MakefilePackage):
+    """
+    DRAMsim is a hardware-validated, cycle-accurate
+    C based simulator for DRAM devices such as DDR3
+    """
+
+    homepage = "https://github.com/umd-memsys/DRAMSim2"
+    git = "https://github.com/umd-memsys/DRAMSim2"
+    url = "https://github.com/dramninjasUMD/DRAMSim2/archive/v2.2.2.tar.gz"
+
+    maintainers = ['jjwilke']
+
+    version('2.2.2', sha256="96d0257eafb41e38ffa4f13e3ef3759567bdde7fa3329403f324abd0ddf8d015")
+
+    def build(self, spec, prefix):
+        if spec.satisfies("platform=darwin"):
+            make("libdramsim.dylib")
+        else:
+            make("libdramsim.so")
+
+    def install(self, spec, prefix):
+        install_tree(".", prefix)
diff --git a/var/spack/repos/builtin/packages/goblin-hmc-sim/package.py b/var/spack/repos/builtin/packages/goblin-hmc-sim/package.py
new file mode 100644
index 00000000000..8b5e9ab9bdd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/goblin-hmc-sim/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class GoblinHmcSim(MakefilePackage):
+    """
+    The Goblin HMC-Sim is a Hybrid Memory Cube
+    Functional Simulation Environment
+    """
+
+    homepage = "https://github.com/tactcomplabs/gc64-hmcsim"
+    git = "https://github.com/tactcomplabs/gc64-hmcsim"
+    # The version numbers track the SST they were released with
+    url = "https://github.com/tactcomplabs/gc64-hmcsim/archive/sst-8.0.0-release.tar.gz"
+    # This works with parallel builds outside Spack
+    # For some reason .o files get thrashed inside Spack
+    parallel = False
+
+    maintainers = ['jjwilke']
+
+    version('8.0.0', sha256="8a5e6b701865a581f15965d3ddd8c7d301b15f4b63543c444058e9c3688fd2c8")
+
+    def install(self, spec, prefix):
+        install_tree(".", prefix)
diff --git a/var/spack/repos/builtin/packages/hbm-dramsim2/package.py b/var/spack/repos/builtin/packages/hbm-dramsim2/package.py
new file mode 100644
index 00000000000..6ecd8de5145
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hbm-dramsim2/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class HbmDramsim2(MakefilePackage):
+    """
+    HBM Simulator based on DRAMSim2
+    """
+
+    homepage = "https://github.com/tactcomplabs/HBM"
+    git = "https://github.com/tactcomplabs/HBM"
+    url = "https://github.com/tactcomplabs/HBM/archive/hbm-1.0.0-release.tar.gz"
+
+    maintainers = ['jjwilke']
+
+    version('1.0.0', sha256="0efad11c58197edb47ad1359f8f93fb45d882c6bebcf9f2143e0df7a719689a0")
+
+    def install(self, spec, prefix):
+        install_tree(".", prefix)
diff --git a/var/spack/repos/builtin/packages/hybridsim/makefile.patch b/var/spack/repos/builtin/packages/hybridsim/makefile.patch
new file mode 100644
index 00000000000..4512bc530fd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hybridsim/makefile.patch
@@ -0,0 +1,20 @@
+diff --git a/Makefile b/Makefile
+index c43f1e2..8b3bd86 100644
+--- a/Makefile
++++ b/Makefile
+@@ -14,12 +14,11 @@ endif
+ CXXFLAGS+=$(OPTFLAGS)
+
+ CUR_DIRECTORY=$(shell pwd)
+-DRAM_LIB=$(CUR_DIRECTORY)/../DRAMSim2
+-NV_LIB=$(CUR_DIRECTORY)/../NVDIMMSim/src
+-#NV_LIB=$(CUR_DIRECTORY)/../FNVSim
++DRAM_LIB=$(CUR_DIRECTORY)/DRAMSim2
++NV_LIB=$(CUR_DIRECTORY)/NVDIMMSim
+
+ INCLUDES=-I$(DRAM_LIB) -I$(NV_LIB)
+-LIBS=-L${DRAM_LIB} -L${NV_LIB} -ldramsim -lnvdsim -Wl,-rpath ${DRAM_LIB} -Wl,-rpath ${NV_LIB}
++LIBS=-L${DRAM_LIB} -L${NV_LIB} -ldramsim -lnvdsim -Wl,-rpath -Wl,${DRAM_LIB} -Wl,-rpath -Wl,${NV_LIB}
+
+ EXE_NAME=HybridSim
+ LIB_NAME=libhybridsim.so
diff --git a/var/spack/repos/builtin/packages/hybridsim/package.py b/var/spack/repos/builtin/packages/hybridsim/package.py
new file mode 100644
index 00000000000..089181ca0bd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hybridsim/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Hybridsim(MakefilePackage):
+    """
+    HybridSim provides cycle-accurate simulation of a non-volatile
+    memory system augmented with a DRAM based cache. It uses DRAMSim2
+    for the DRAM model and NVDIMMSim for the non-volatile memory model
+    """
+
+    homepage = "https://github.com/jimstevens2001/HybridSim"
+    git = "https://github.com/jimstevens2001/HybridSim"
+    url = "https://github.com/jimstevens2001/HybridSim/archive/v2.0.1.tar.gz"
+
+    maintainers = ['jjwilke']
+
+    version('2.0.1', sha256="57b82ac929acd36de84525e4d61358f1ab6532f5b635ca3f560e563479921937")
+
+    depends_on("dramsim2")
+    depends_on("nvdimmsim")
+    patch("makefile.patch", when="@2.0.1")
+
+    def build(self, spec, prefix):
+        symlink(spec["dramsim2"].prefix, "DRAMSim2")
+        symlink(spec["nvdimmsim"].prefix, "NVDIMMSim")
+        if spec.satisfies("platform=darwin"):
+            make("libhybridsim.dylib")
+        else:
+            make("libhybridsim.so")
+
+    def install(self, spec, prefix):
+        install_tree(".", prefix)
diff --git a/var/spack/repos/builtin/packages/intel-pin/package.py b/var/spack/repos/builtin/packages/intel-pin/package.py
index e886ba0784c..4378d8e7dd3 100644
--- a/var/spack/repos/builtin/packages/intel-pin/package.py
+++ b/var/spack/repos/builtin/packages/intel-pin/package.py
@@ -19,6 +19,7 @@ class IntelPin(Package):
     version('3.11', sha256='aa5abca475a6e106a75e6ed4ba518fb75a57549a59f00681e6bd6e3f221bd23a', url='https://software.intel.com/sites/landingpage/pintool/downloads/pin-3.11-97998-g7ecce2dac-gcc-linux.tar.gz')
     version('3.10', sha256='7c8f14c3a0654bab662b58aba460403138fa44517bd40052501e8e0075b2702a', url='https://software.intel.com/sites/landingpage/pintool/downloads/pin-3.10-97971-gc5e41af74-gcc-linux.tar.gz')
     version('3.7',  sha256='4730328795be61f1addb0e505a3792a4b4ca80b1b9405acf217beec6b5b90fb8', url='https://software.intel.com/sites/landingpage/pintool/downloads/pin-3.7-97619-g0d0c92f4f-gcc-linux.tar.gz')
+    version('2.14', sha256="1c29f589515772411a699a82fc4a3156cad95863a29741dfa6522865d4d281a1", url="https://software.intel.com/sites/landingpage/pintool/downloads/pin-2.14-71313-gcc.4.4.7-linux.tar.gz")
 
     def install(self, spec, prefix):
         install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/nvdimmsim/package.py b/var/spack/repos/builtin/packages/nvdimmsim/package.py
new file mode 100644
index 00000000000..0d0a0964d47
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nvdimmsim/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Nvdimmsim(MakefilePackage):
+    """
+    NVDIMMSim is a cycle-accurate non-volatile memory simulator
+    for devices such as NAND flash
+    """
+
+    homepage = "https://github.com/slunk/NVDIMMSim"
+    git = "https://github.com/slunk/NVDIMMSim"
+    url = "https://github.com/jimstevens2001/NVDIMMSim/archive/v2.0.0.tar.gz"
+
+    maintainers = ['jjwilke']
+
+    version('2.0.0', sha256="2a621ef10be5e52a1f543985d08354a2e6ee6532b5720e5f17ad6362cfd4adef")
+
+    def build(self, spec, prefix):
+        with working_dir("src"):
+            if spec.satisfies("platform=darwin"):
+                make("libnvdsim.dylib")
+            else:
+                make("libnvdsim.so")
+
+    def install(self, spec, prefix):
+        with working_dir("src"):
+            install_tree(".", prefix)
diff --git a/var/spack/repos/builtin/packages/ramulator/package.py b/var/spack/repos/builtin/packages/ramulator/package.py
new file mode 100644
index 00000000000..a103d4b68da
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ramulator/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ramulator(MakefilePackage):
+    """
+    Ramulator is a fast and cycle-accurate DRAM simulator that supports
+    a wide array of commercial, as well as academic, DRAM standards.
+    """
+
+    homepage = "https://github.com/CMU-SAFARI/ramulator"
+    git = "https://github.com/CMU-SAFARI/ramulator"
+
+    maintainers = ['jjwilke']
+
+    version('sst', commit="7d2e72306c6079768e11a1867eb67b60cee34a1c")
+
+    patch('ramulator_sha_7d2e723_gcc48Patch.patch', when="@sst")
+    patch('ramulator_sha_7d2e723_libPatch.patch', when="@sst")
+
+    def patch(self):
+        filter_file('-fpic', self.compiler.cxx_pic_flag, "Makefile")
+
+    def build(self, spec, prefix):
+        if spec.satisfies("platform=darwin"):
+            make("libramulator.a")
+        else:
+            make("libramulator.so")
+
+    def install(self, spec, prefix):
+        install_tree(".", prefix)
diff --git a/var/spack/repos/builtin/packages/ramulator/ramulator_sha_7d2e723_gcc48Patch.patch b/var/spack/repos/builtin/packages/ramulator/ramulator_sha_7d2e723_gcc48Patch.patch
new file mode 100644
index 00000000000..6e8b31aeb5c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ramulator/ramulator_sha_7d2e723_gcc48Patch.patch
@@ -0,0 +1,250 @@
+diff --git a/src/Scheduler.h b/src/Scheduler.h
+index c8561c1..38f924d 100644
+--- a/src/Scheduler.h
++++ b/src/Scheduler.h
+@@ -9,8 +9,10 @@
+ #include <list>
+ #include <functional>
+ #include <cassert>
++#include <utility>
+ 
+ using namespace std;
++using namespace std::placeholders;
+ 
+ namespace ramulator
+ {
+@@ -22,18 +24,66 @@ template <typename T>
+ class Scheduler
+ {
+ public:
+-    Controller<T>* ctrl;
+-
+-    enum class Type {
+-        FCFS, FRFCFS, FRFCFS_Cap, FRFCFS_PriorHit, MAX
+-    } type = Type::FRFCFS_Cap;
+-    //} type = Type::FCFS;
+-
+-    long cap = 16;
++  Controller<T>* ctrl;
++    
++  enum class Type {
++    FCFS, FRFCFS, FRFCFS_Cap, FRFCFS_PriorHit, MAX
++      } type = Type::FRFCFS_Cap;
++  //} type = Type::FCFS;
++  
++  long cap = 16;
++  
++ Scheduler(Controller<T>* _ctrl) : ctrl(_ctrl) {
+ 
+-    Scheduler(Controller<T>* ctrl) : ctrl(ctrl) {}
+-
+-    list<Request>::iterator get_head(list<Request>& q)
++        // FCFS
++    compare[0] = std::bind([] (ReqIter req1, ReqIter req2, Scheduler *obj) -> ReqIter {
++	if (req1->arrive <= req2->arrive) return req1;
++	return req2;}, _1, _2, std::move(this));
++    
++    // FRFCFS
++    compare[1] = std::bind([] (ReqIter req1, ReqIter req2, Scheduler *obj) -> ReqIter {
++	bool ready1 = obj->ctrl->is_ready(req1);
++	bool ready2 = obj->ctrl->is_ready(req2);
++	
++	if (ready1 ^ ready2) {
++	  if (ready1) return req1;
++	  return req2;
++	}
++	
++	if (req1->arrive <= req2->arrive) return req1;
++	return req2;}, _1, _2, std::move(this));
++    
++    // FRFCFS_CAP
++    compare[2] = std::bind([] (ReqIter req1, ReqIter req2, Scheduler *obj) -> ReqIter {
++	bool ready1 = obj->ctrl->is_ready(req1);
++	bool ready2 = obj->ctrl->is_ready(req2);
++	
++	ready1 = ready1 && (obj->ctrl->rowtable->get_hits(req1->addr_vec) <= obj->cap);
++	ready2 = ready2 && (obj->ctrl->rowtable->get_hits(req2->addr_vec) <= obj->cap);
++	
++	if (ready1 ^ ready2) {
++	  if (ready1) return req1;
++	  return req2;
++	}
++	
++	if (req1->arrive <= req2->arrive) return req1;
++	return req2;}, _1, _2, this);
++    
++        // FRFCFS_PriorHit
++    compare[3] = std::bind([] (ReqIter req1, ReqIter req2, Scheduler *obj) -> ReqIter {
++	bool ready1 = obj->ctrl->is_ready(req1) && obj->ctrl->is_row_hit(req1);
++	bool ready2 = obj->ctrl->is_ready(req2) && obj->ctrl->is_row_hit(req2);
++	
++	if (ready1 ^ ready2) {
++	  if (ready1) return req1;
++	  return req2;
++	}
++	
++	if (req1->arrive <= req2->arrive) return req1;
++	return req2;}, _1, _2, this);
++  }
++
++  list<Request>::iterator get_head(list<Request>& q)
+     {
+       // TODO make the decision at compile time
+       if (type != Type::FRFCFS_PriorHit) {
+@@ -106,55 +156,8 @@ public:
+ 
+ private:
+     typedef list<Request>::iterator ReqIter;
+-    function<ReqIter(ReqIter, ReqIter)> compare[int(Type::MAX)] = {
+-        // FCFS
+-        [this] (ReqIter req1, ReqIter req2) {
+-            if (req1->arrive <= req2->arrive) return req1;
+-            return req2;},
+-
+-        // FRFCFS
+-        [this] (ReqIter req1, ReqIter req2) {
+-            bool ready1 = this->ctrl->is_ready(req1);
+-            bool ready2 = this->ctrl->is_ready(req2);
+-
+-            if (ready1 ^ ready2) {
+-                if (ready1) return req1;
+-                return req2;
+-            }
+-
+-            if (req1->arrive <= req2->arrive) return req1;
+-            return req2;},
+-
+-        // FRFCFS_CAP
+-        [this] (ReqIter req1, ReqIter req2) {
+-            bool ready1 = this->ctrl->is_ready(req1);
+-            bool ready2 = this->ctrl->is_ready(req2);
+-
+-            ready1 = ready1 && (this->ctrl->rowtable->get_hits(req1->addr_vec) <= this->cap);
+-            ready2 = ready2 && (this->ctrl->rowtable->get_hits(req2->addr_vec) <= this->cap);
+-
+-            if (ready1 ^ ready2) {
+-                if (ready1) return req1;
+-                return req2;
+-            }
+-
+-            if (req1->arrive <= req2->arrive) return req1;
+-            return req2;},
+-        // FRFCFS_PriorHit
+-        [this] (ReqIter req1, ReqIter req2) {
+-            bool ready1 = this->ctrl->is_ready(req1) && this->ctrl->is_row_hit(req1);
+-            bool ready2 = this->ctrl->is_ready(req2) && this->ctrl->is_row_hit(req2);
+-
+-            if (ready1 ^ ready2) {
+-                if (ready1) return req1;
+-                return req2;
+-            }
+-
+-            if (req1->arrive <= req2->arrive) return req1;
+-            return req2;}
+-    };
+-};
+-
++    function<ReqIter(ReqIter, ReqIter)> compare[int(Type::MAX)];
++ };
+ 
+ template <typename T>
+ class RowPolicy
+@@ -168,50 +171,52 @@ public:
+ 
+     int timeout = 50;
+ 
+-    RowPolicy(Controller<T>* ctrl) : ctrl(ctrl) {}
+-
+-    vector<int> get_victim(typename T::Command cmd)
+-    {
+-        return policy[int(type)](cmd);
+-    }
+-
+-private:
+-    function<vector<int>(typename T::Command)> policy[int(Type::MAX)] = {
+-        // Closed
+-        [this] (typename T::Command cmd) -> vector<int> {
+-            for (auto& kv : this->ctrl->rowtable->table) {
+-                if (!this->ctrl->is_ready(cmd, kv.first))
++    RowPolicy(Controller<T>* _ctrl) : ctrl(_ctrl) {
++      // Closed
++      policy[0] = std::bind([] (typename T::Command cmd, RowPolicy *obj) -> vector<int> {
++            for (auto& kv : obj->ctrl->rowtable->table) {
++                if (!obj->ctrl->is_ready(cmd, kv.first))
+                     continue;
+                 return kv.first;
+             }
+-            return vector<int>();},
++            return vector<int>();}, _1, this);
+ 
+         // ClosedAP
+-        [this] (typename T::Command cmd) -> vector<int> {
+-            for (auto& kv : this->ctrl->rowtable->table) {
+-                if (!this->ctrl->is_ready(cmd, kv.first))
+-                    continue;
+-                return kv.first;
+-            }
+-            return vector<int>();},
++      policy[1] = std::bind([] (typename T::Command cmd, RowPolicy *obj) -> vector<int> {
++	  for (auto& kv : obj->ctrl->rowtable->table) {
++	    if (!obj->ctrl->is_ready(cmd, kv.first))
++	      continue;
++	    return kv.first;
++	  }
++	  return vector<int>();}, _1, this);
+ 
+         // Opened
+-        [this] (typename T::Command cmd) {
+-            return vector<int>();},
+-
+-        // Timeout
+-        [this] (typename T::Command cmd) -> vector<int> {
+-            for (auto& kv : this->ctrl->rowtable->table) {
+-                auto& entry = kv.second;
+-                if (this->ctrl->clk - entry.timestamp < timeout)
+-                    continue;
+-                if (!this->ctrl->is_ready(cmd, kv.first))
+-                    continue;
+-                return kv.first;
+-            }
+-            return vector<int>();}
+-    };
++      policy[2] = std::bind([] (typename T::Command cmd, RowPolicy *obj) -> vector<int> {
++	  return vector<int>();}, _1, this); 
++
++      // Timeout
++      policy[3] = std::bind([] (typename T::Command cmd, RowPolicy *obj) -> vector<int> {
++	  for (auto& kv : obj->ctrl->rowtable->table) {
++	    auto& entry = kv.second;
++	    if (obj->ctrl->clk - entry.timestamp < obj->timeout)
++	      continue;
++	    if (!obj->ctrl->is_ready(cmd, kv.first))
++	      continue;
++	    return kv.first;
++	  }
++	  return vector<int>();}, _1, this); 
+ 
++
++
++    }
++
++    vector<int> get_victim(typename T::Command cmd)
++    {
++        return policy[int(type)](cmd);
++    }
++
++private:
++    function<vector<int>(typename T::Command)> policy[int(Type::MAX)];
+ };
+ 
+ 
+@@ -304,7 +309,8 @@ public:
+ 
+         return itr->second.row;
+     }
+-};
++ };
++
+ 
+ } /*namespace ramulator*/
+ 
diff --git a/var/spack/repos/builtin/packages/ramulator/ramulator_sha_7d2e723_libPatch.patch b/var/spack/repos/builtin/packages/ramulator/ramulator_sha_7d2e723_libPatch.patch
new file mode 100644
index 00000000000..20225bb54db
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ramulator/ramulator_sha_7d2e723_libPatch.patch
@@ -0,0 +1,23 @@
+diff --git a/Makefile b/Makefile
+index ea340c8..314113d 100644
+--- a/Makefile
++++ b/Makefile
+@@ -9,7 +9,7 @@ OBJS := $(patsubst $(SRCDIR)/%.cpp, $(OBJDIR)/%.o, $(SRCS))
+ #   g++ 4.x due to an internal compiler error when processing lambda functions.
+ CXX := clang++
+ # CXX := g++-5
+-CXXFLAGS := -O3 -std=c++11 -g -Wall
++CXXFLAGS := -O3 -std=c++11 -g -Wall -fpic
+ 
+ .PHONY: all clean depend
+ 
+@@ -38,6 +38,9 @@ ramulator: $(MAIN) $(OBJS) $(SRCDIR)/*.h | depend
+ libramulator.a: $(OBJS) $(OBJDIR)/Gem5Wrapper.o
+ 	libtool -static -o $@ $(OBJS) $(OBJDIR)/Gem5Wrapper.o
+ 
++libramulator.so: $(OBJS) $(OBJDIR)/Gem5Wrapper.o
++	$(CXX) -shared -o $@ $(OBJS) $(OBJDIR)/Gem5Wrapper.o
++
+ $(OBJS): | $(OBJDIR)
+ 
+ $(OBJDIR): 
diff --git a/var/spack/repos/builtin/packages/sst-core/package.py b/var/spack/repos/builtin/packages/sst-core/package.py
index b28ae4cea01..4c6dbff0b37 100644
--- a/var/spack/repos/builtin/packages/sst-core/package.py
+++ b/var/spack/repos/builtin/packages/sst-core/package.py
@@ -7,38 +7,71 @@
 
 
 class SstCore(AutotoolsPackage):
-    """The Structural Simulation Toolkit (SST) was developed to explore
-    innovations in highly concurrent systems where the ISA, microarchitecture,
-    and memory interact with the programming model and communications system"""
+    """The Structural Simulation Toolkit (SST) core
+       provides a parallel discrete event simulation (PDES)
+       framework for performing architecture simulations
+       of existing and proposed HPC systems"""
 
-    homepage = "http://sst-simulator.org/"
-    url      = "https://github.com/sstsimulator/sst-core/releases/download/v8.0.0_Final/sstcore-8.0.0.tar.gz"
-    git      = "https://github.com/sstsimulator/sst-core.git"
+    homepage = "https://github.com/sstsimulator"
+    git = "https://github.com/sstsimulator/sst-core.git"
+    url = "https://github.com/sstsimulator/sst-core/releases/download/v10.0.0_Final/sstcore-10.0.0.tar.gz"
 
-    version('develop', branch='devel')
-    version('8.0.0', sha256='34a62425c3209cf80b6bca99cb0dcc328b67fb84ed92d5e6d6c975ad9319ba8a')
+    maintainers = ['jjwilke']
 
-    variant('mpi', default=True, description='Support multi-node simulations using MPI')
-    variant('boost', default=False, description='Use boost')
+    version('10.0.0', sha256="64cf93a46dfab011fba49244bf0e0efe25ef928c6fbde1d49003220d0eb7735a")
+    version('9.1.0', sha256="cfeda39bb2ce9f32032480427517df62e852c0b3713797255e3b838075f3614d")
+    version('develop',   branch='devel')
+    version('master',  branch='master')
 
-    depends_on('autoconf@1.68:', type='build', when='@develop')
-    depends_on('automake@1.11.1:', type='build', when='@develop')
-    depends_on('libtool@1.2.4:', type='build', when='@develop')
-    depends_on('m4', type='build', when='@develop')
+    variant("pdes_mpi", default=True,
+            description="Build support for parallel discrete event simulation")
+    variant("zoltan",  default=False,
+            description="Use Zoltan for partitioning parallel runs")
+    variant("hdf5",    default=False,
+            description="Build support for HDF5 statistic output")
+    variant("zlib",    default=False,
+            description="Build support for ZLIB compression")
+    variant("preview", default=False,
+            description="Preview build with deprecated features removed")
 
-    depends_on('python@:2')
-    depends_on('zlib', type='build')
-    depends_on('mpi', when='+mpi')
-    depends_on('boost@1.56.0:', type='build', when='+boost')
+    depends_on("python", type=('build', 'run'))
+    depends_on("mpi", when="+pdes_mpi")
+    depends_on("zoltan", when="+zoltan")
+    depends_on("hdf5", when="+hdf5")
+    depends_on("zlib", when="+zlib")
+
+    depends_on('autoconf@1.68:', type='build', when='@master:')
+    depends_on('automake@1.11.1:', type='build', when='@master:')
+    depends_on('libtool@1.2.4:', type='build', when='@master:')
+    depends_on('m4', type='build', when='@master:')
+
+    # force out-of-source builds
+    build_directory = 'spack-build'
+
+    def autoreconf(self, spec, prefix):
+        bash = which('bash')
+        bash('autogen.sh')
 
     def configure_args(self):
         args = []
-        spec = self.spec
+        if "+zoltan" in self.spec:
+            args.append("--with-zoltan=%s" % self.spec["zoltan"].prefix)
+        if "+hdf5" in self.spec:
+            args.append("--with-hdf5=%s" % self.spec["hdf5"].prefix)
+        if "+zlib" in self.spec:
+            args.append("--with-zlib=%s" % self.spec["zlib"].prefix)
 
-        if '~mpi' in spec:
-            args.append('--disable-mpi')
+        if "+pdes_mpi" in self.spec:
+            args.append("--enable-mpi")
+            env['CC'] = self.spec['mpi'].mpicc
+            env['CXX'] = self.spec['mpi'].mpicxx
+            env['F77'] = self.spec['mpi'].mpif77
+            env['FC'] = self.spec['mpi'].mpifc
+        else:
+            args.append("--disable-mpi")
 
-        if '+boost' in spec:
-            args.append('--with-boost=%s' % spec['boost'].prefix)
+        if "+preview" in self.spec:
+            args.append("--enable-preview-build")
 
+        args.append("--with-python=%s" % self.spec["python"].prefix)
         return args
diff --git a/var/spack/repos/builtin/packages/sst-elements/package.py b/var/spack/repos/builtin/packages/sst-elements/package.py
new file mode 100644
index 00000000000..89af49373ae
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sst-elements/package.py
@@ -0,0 +1,101 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class SstElements(AutotoolsPackage):
+    """SST Elements implements a range of components for performing
+       architecture simulation from node-level to system-level using
+       the SST discrete event core
+    """
+
+    homepage = "https://github.com/sstsimulator"
+    git = "https://github.com/sstsimulator/sst-elements.git"
+    url = "https://github.com/sstsimulator/sst-elements/releases/download/v10.0.0_Final/sstelements-10.0.0.tar.gz"
+
+    maintainers = ['jjwilke']
+
+    version('10.0.0', sha256="ecf28ef97b27ea75be7e64cb0acb99d36773a888c1b32ba16034c62174b02693")
+    version('9.1.0', sha256="e19b05aa6e59728995fc059840c79e476ba866b67887ccde7eaf52a18a1f52ca")
+
+    version('develop',   branch='devel')
+    version('master',  branch='master')
+
+    variant("pin",       default=False,
+            description="Enable the Ariel CPU model")
+    variant("dramsim2",  default=False,
+            description="Build with DRAMSim2 support")
+    variant("nvdimmsim", default=False,
+            description="Build with NVDimmSim support")
+    variant("hybridsim", default=False,
+            description="Build with HybridSim support")
+    variant("goblin",    default=False,
+            description="Build with GoblinHMCSim support")
+    variant("hbm",       default=False,
+            description="Build with HBM DRAMSim2 support")
+    variant("ramulator", default=False,
+            description="Build with Ramulator support")
+
+    depends_on("python", type=('build', 'run'))
+    depends_on("sst-core")
+    depends_on("sst-core@develop",  when="@develop")
+    depends_on("sst-core@master", when="@master")
+
+    depends_on("intel-pin@2.14",   when="+pin")
+    depends_on("dramsim2@2.2",     when="+dramsim2")
+    depends_on("hybridsim@2.0.1",  when="+hybridsim")
+    depends_on("nvdimmsim@2.0.0",  when="+nvdimmsim")
+    depends_on("goblin-hmc-sim",   when="+goblin")
+    depends_on("ramulator@sst",    when="+ramulator")
+    depends_on("hbm-dramsim2",     when="+hbm")
+    depends_on("dramsim2@2.2.2",   when="+hybridsim")
+    depends_on("nvdimmsim@2.0.0",  when="+hybridsim")
+
+    depends_on('autoconf@1.68:', type='build', when='@master:')
+    depends_on('automake@1.11.1:', type='build', when='@master:')
+    depends_on('libtool@1.2.4:', type='build', when='@master:')
+    depends_on('m4', type='build', when='@master:')
+
+    # force out-of-source builds
+    build_directory = 'spack-build'
+
+    def autoreconf(self, spec, prefix):
+        bash = which('bash')
+        bash('autogen.sh')
+
+    def configure_args(self):
+        args = []
+        if '+pdes_mpi' in self.spec["sst-core"]:
+            env['CC'] = self.spec['mpi'].mpicc
+            env['CXX'] = self.spec['mpi'].mpicxx
+            env['F77'] = self.spec['mpi'].mpif77
+            env['FC'] = self.spec['mpi'].mpifc
+
+        if "+pin" in self.spec:
+            args.append("--with-pin=%s" % self.spec["intel-pin"].prefix)
+
+        if "+dramsim2" in self.spec or "+hybridsim" in self.spec:
+            args.append("--with-dramsim=%s" % self.spec["dramsim2"].prefix)
+
+        if "+nvdimmsim" in self.spec or "+hybridsim" in self.spec:
+            args.append("--with-nvdimmsim=%s" % self.spec["nvdimmsim"].prefix)
+
+        if "+hybridsim" in self.spec:
+            args.append("--with-hybridsim=%s" % self.spec["hybridsim"].prefix)
+
+        if "+goblin" in self.spec:
+            args.append("--with-goblin-hmcsim=%s" %
+                        self.spec["goblin-hmc-sim"].prefix)
+
+        if "+hbm" in self.spec:
+            args.append("--with-hbmdramsim=%s" %
+                        self.spec["hbm-dramsim2"].prefix)
+
+        if "+ramulator" in self.spec:
+            args.append("--with-ramulator=%s" % self.spec["ramulator"].prefix)
+
+        args.append("--with-sst-core=%s" % self.spec["sst-core"].prefix)
+        return args
diff --git a/var/spack/repos/builtin/packages/sst-macro/package.py b/var/spack/repos/builtin/packages/sst-macro/package.py
index e7333c9a5bd..6a04e44dba7 100644
--- a/var/spack/repos/builtin/packages/sst-macro/package.py
+++ b/var/spack/repos/builtin/packages/sst-macro/package.py
@@ -16,48 +16,56 @@ class SstMacro(AutotoolsPackage):
     """
 
     homepage = "http://sst.sandia.gov/about_sstmacro.html"
-    url      = "https://github.com/sstsimulator/sst-macro/releases/download/v6.1.0_Final/sstmacro-6.1.0.tar.gz"
-    git      = "https://github.com/sstsimulator/sst-macro.git"
+    git = "https://github.com/sstsimulator/sst-macro.git"
+    url = "https://github.com/sstsimulator/sst-macro/releases/download/v10.0.0_Final/sstmacro-10.0.0.tar.gz"
 
+    maintainers = ['jjwilke']
+
+    version('10.0.0', sha256='064b732256f3bec9b553e00bcbc9a1d82172ec194f2b69c8797f585200b12566')
+    version('master',  branch='master')
     version('develop', branch='devel')
-    version('8.0.0', sha256='8618a259e98ede9a1a2ce854edd4930628c7c5a770c3915858fa840556c1861f')
-    version('6.1.0', sha256='930b67313b594148d6356e550ca370214a9283858235321d3ef974191eb028d6')
 
-    depends_on('boost@1.59:', when='@:6.1.0')
-
-    depends_on('autoconf@1.68:', type='build', when='@develop')
-    depends_on('automake@1.11.1:', type='build', when='@develop')
-    depends_on('libtool@1.2.4:', type='build', when='@develop')
-    depends_on('m4', type='build', when='@develop')
+    depends_on('autoconf@1.68:', type='build', when='@master:')
+    depends_on('automake@1.11.1:', type='build', when='@master:')
+    depends_on('libtool@1.2.4:', type='build', when='@master:')
+    depends_on('m4', type='build', when='@master:')
 
     depends_on('binutils', type='build')
     depends_on('zlib', type=('build', 'link'))
     depends_on('otf2', when='+otf2')
-    depends_on('llvm+clang@:5.99.99', when='+skeletonizer')
-    depends_on('mpi', when='+mpi')
-    depends_on('sst-core@8.0.0', when='@8.0.0 +core')
-    depends_on('sst-core@develop', when='@develop +core')
+    depends_on('llvm+clang@5:9', when='+skeletonizer')
+    depends_on('mpi', when='+pdes_mpi')
+    depends_on('sst-core@develop',   when='@develop+core')
+    depends_on('sst-core@master',  when='@master+core')
+
+    variant('pdes_threads', default=True,
+            description='Enable thread-parallel PDES simulation')
+    variant('pdes_mpi', default=False,
+            description='Enable distributed PDES simulation')
+    variant('core',     default=False, description='Use SST Core for PDES')
+    variant('otf2',     default=False,
+            description='Enable OTF2 trace emission and replay support')
+    variant('skeletonizer', default=False,
+            description='Enable Clang source-to-source autoskeletonization')
 
-    variant('core', default=False, description='Use SST Core for PDES')
-    variant('mpi', default=True, description='Enable distributed PDES simulation')
-    variant('otf2', default=False, description='Enable OTF2 trace emission and replay support')
-    variant('shared', default=True, description='Build shared libraries')
-    variant('skeletonizer', default=False, description='Enable Clang source-to-source autoskeletonization')
     variant('static', default=True, description='Build static libraries')
-    variant('threaded', default=False, description='Enable thread-parallel PDES simulation')
+    variant('shared', default=True, description='Build shared libraries')
 
-    @run_before('autoreconf')
-    def bootstrap(self):
-        if '@develop' in self.spec:
-            Executable('./bootstrap.sh')()
+    variant('werror', default=False,
+            description='Build with all warnings as errors')
+    variant('warnings', default=False,
+            description='Build with all possible warnings')
+
+    # force out-of-source builds
+    build_directory = 'spack-build'
+
+    def autoreconf(self, spec, prefix):
+        bash = which('bash')
+        bash('./bootstrap.sh')
 
     def configure_args(self):
         args = ['--disable-regex']
 
-        # Set CFLAGS and CXXFLAGS so they won't automatically insert '-g'
-        env['CFLAGS'] = '-O2'
-        env['CXXFLAGS'] = '-O2'
-
         spec = self.spec
         args.append(
             '--enable-static=%s' % ('yes' if '+static' in spec else 'no'))
@@ -66,19 +74,30 @@ def configure_args(self):
 
         if spec.satisfies("@8.0.0:"):
             args.extend([
-                '--%sable-otf2' % ('en' if '+otf2' in spec else 'dis'),
-                '--%sable-multithread' % (
-                    'en' if '+threaded' in spec else 'dis')
+                '--%sable-otf2' %
+                ('en' if '+otf2' in spec else 'dis'),
+                '--%sable-multithread' %
+                ('en' if '+pdes_threads' in spec else 'dis')
             ])
 
             if '+skeletonizer' in spec:
                 args.append('--with-clang=' + spec['llvm'].prefix)
 
+        if spec.satisfies("@10:"):
+            if "+warnings" in spec:
+                args.append("--with-warnings")
+            if "+werror" in spec:
+                args.append("--with-werror")
+
         if '+core' in spec:
             args.append('--with-sst-core=%s' % spec['sst-core'].prefix)
 
         # Optional MPI support
-        if '+mpi' in spec:
+        need_core_mpi = False
+        if "+core" in spec:
+            if "+pdes_mpi" in spec["sst-core"]:
+                need_core_mpi = True
+        if '+pdes_mpi' in spec or need_core_mpi:
             env['CC'] = spec['mpi'].mpicc
             env['CXX'] = spec['mpi'].mpicxx
             env['F77'] = spec['mpi'].mpif77
diff --git a/var/spack/repos/builtin/packages/sst-transports/package.py b/var/spack/repos/builtin/packages/sst-transports/package.py
new file mode 100644
index 00000000000..39a6e99d058
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sst-transports/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class SstTransports(CMakePackage):
+    """Provides transports like uGNI and verbs
+       that run in the simulator"""
+
+    homepage = "https://github.com/sstsimulator"
+    git = "https://github.com/jjwilke/sst-transports.git"
+
+    maintainers = ['jjwilke']
+
+    version('master',  branch='master')
+
+    depends_on("sst-macro")
+
+    def cmake_args(self):
+        args = []
+        args.append("-DSSTMacro_ROOT=%s" % self.spec["sst-macro"].prefix)
+        return args

From 51ff18ef8d5679672107485d372798c7ab647b34 Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Thu, 21 May 2020 12:33:31 +0900
Subject: [PATCH 462/802] mxnet: Fix dependency and add new version. (#16714)

* mxnet: Fix dependency and add new version.

1. Fix opencv and numpy dependency.
2. Add version 1.6.0.

* typo in patch is fixed.
fixed spec access.
---
 .../packages/mxnet/makefile.opencv.patch      | 35 +++++++++++++++++++
 .../repos/builtin/packages/mxnet/package.py   | 31 ++++++++++++----
 2 files changed, 59 insertions(+), 7 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/mxnet/makefile.opencv.patch

diff --git a/var/spack/repos/builtin/packages/mxnet/makefile.opencv.patch b/var/spack/repos/builtin/packages/mxnet/makefile.opencv.patch
new file mode 100644
index 00000000000..45e04ea626e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mxnet/makefile.opencv.patch
@@ -0,0 +1,35 @@
+commit 638527ffaa35ffb0bf88a32910b809df09432406
+Author: Toyohisa Kameyama <kameyama@riken.jp>
+Date:   Mon May 18 11:58:00 2020 +0900
+
+    Makefile bug fix for opencv4.
+
+diff --git a/Makefile b/Makefile
+index 51930c782..7f5d4da39 100644
+--- a/Makefile
++++ b/Makefile
+@@ -165,7 +165,23 @@ endif
+ ifeq ($(USE_OPENCV), 1)
+ 	CFLAGS += -DMXNET_USE_OPENCV=1
+ 	ifneq ($(filter-out NONE, $(USE_OPENCV_INC_PATH)),)
+-		CFLAGS += -I$(USE_OPENCV_INC_PATH)/include
++                ifneq ($(wildcard $(USE_OPENCV_INC_PATH)/include/opencv4/opencv2/opencv*),)
++                    opencv_inc = -I$(USE_OPENCV_INC_PATH)/include/opencv4
++                endif
++                ifneq ($(wildcard $(USE_OPENCV_INC_PATH)/include/opencv2/opencv*),)
++                    opencv_inc = -I$(USE_OPENCV_INC_PATH)/include
++                endif
++                ifneq ($(wildcard $(USE_OPENCV_INC_PATH)/opencv4/opencv2/opencv*),)
++                    opencv_inc = -I$(USE_OPENCV_INC_PATH)/opencv4
++                endif
++                ifneq ($(wildcard $(USE_OPENCV_INC_PATH)/opencv2/opencv*),)
++                    opencv_inc = -I$(USE_OPENCV_INC_PATH)
++                endif
++                ifneq ($(filter-out NONE, $(opencv_inc)),)
++                    CFLAGS += $(opencv_inc)
++                else
++$(error Cannot determine OpenCV include path)
++                endif
+ 		ifeq ($(filter-out NONE, $(USE_OPENCV_LIB_PATH)),)
+ $(error Please add the path of OpenCV shared library path into `USE_OPENCV_LIB_PATH`, when `USE_OPENCV_INC_PATH` is not NONE)
+ 		endif
diff --git a/var/spack/repos/builtin/packages/mxnet/package.py b/var/spack/repos/builtin/packages/mxnet/package.py
index 492a2573bc1..2ff65265a7b 100644
--- a/var/spack/repos/builtin/packages/mxnet/package.py
+++ b/var/spack/repos/builtin/packages/mxnet/package.py
@@ -15,6 +15,7 @@ class Mxnet(MakefilePackage):
 
     maintainers = ['adamjstewart']
 
+    version('1.6.0', sha256='01eb06069c90f33469c7354946261b0a94824bbaf819fd5d5a7318e8ee596def')
     version('1.3.0', sha256='c00d6fbb2947144ce36c835308e603f002c1eb90a9f4c5a62f4d398154eed4d2')
 
     variant('cuda', default=False, description='Enable CUDA support')
@@ -33,14 +34,18 @@ class Mxnet(MakefilePackage):
     depends_on('cudnn', when='+cuda')
     depends_on('cudnn', when='+cuda')
     depends_on('cub', when='+cuda')
+    depends_on('opencv+core+imgproc+highgui+jpeg+png+tiff~eigen~ipp@3.0:3.4.99', when='@1.3.0 +opencv')
     depends_on('opencv+core+imgproc+highgui+jpeg+png+tiff~eigen~ipp@3.0:', when='+opencv')
 
     # python extensions
     depends_on('python@2.7:', type=('build', 'run'), when='+python')
     depends_on('py-setuptools', type='build', when='+python')
+    depends_on('py-numpy@:1.15.0', type=('build', 'run'), when='@1.3.0 +python')
+    depends_on('py-numpy@1.16:', type=('build', 'run'), when='@1.6.0 +python')
     extends('python', when='+python')
 
     patch('makefile.patch', when='@0.10:0.11')
+    patch('makefile.opencv.patch', when='@1.6.0')
 
     def build(self, spec, prefix):
         # copy template configuration file
@@ -73,13 +78,25 @@ def build(self, spec, prefix):
         ]
 
         if '+opencv' in spec:
-            filter_file('$(shell pkg-config --cflags opencv)',
-                        '-I%s' % spec['opencv'].prefix.include,
-                        'Makefile', string=True)
-            filter_file('$(filter-out -lopencv_ts, '
-                        '$(shell pkg-config --libs opencv))',
-                        '-lopencv_core -lopencv_imgproc -lopencv_imgcodecs',
-                        'Makefile', string=True)
+            if spec.satisfies('@1.3.0'):
+                filter_file(
+                    '$(shell pkg-config --cflags opencv)',
+                    spec['opencv'].headers.include_flags,
+                    'Makefile', string=True
+                )
+                filter_file(
+                    '$(filter-out -lopencv_ts, '
+                    '$(shell pkg-config --libs opencv))',
+                    spec['opencv'].libs.link_flags,
+                    'Makefile', string=True
+                )
+            else:
+                args.extend(
+                    ['USE_OPENCV_INC_PATH=' +
+                        spec['opencv'].headers.directories[0],
+                     'USE_OPENCV_LIB_PATH=' +
+                        spec['opencv'].libs.directories[0]]
+                )
 
         if 'openblas' in spec:
             args.extend(['USE_BLAS=openblas'])

From 4118a0177439e0a28a92b7ce04a949e12f0eefd9 Mon Sep 17 00:00:00 2001
From: Antonio Arena <antonio.arena@kaust.edu.sa>
Date: Thu, 21 May 2020 06:34:03 +0300
Subject: [PATCH 463/802] Install gaussian using their scripts (#16723)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Create VMD recipe

This is a new recipe to install VMD on Spack-managed hosts.

* Fix lint errors.

* Use plain Package

As per peer-review:
- Use Package to build
- Use configure to create a Makefile
- Use install to copy files to prefix directory

* Move VMD package to correct path, duh...

* Restructure description so first short paragraph can be used by module files.

* Add an empty line as suggested by peer-review. That's how you separate paragraphs.

* Remove extra spaces.

* Use setup_build_environment since that's where you're supposed to export OS variblaes. Thanks to peer-review for spotting this.

* Create VMD recipe

This is a new recipe to install VMD on Spack-managed hosts.

* Fix lint errors.

* Use plain Package

As per peer-review:
- Use Package to build
- Use configure to create a Makefile
- Use install to copy files to prefix directory

* Move VMD package to correct path, duh...

* Add Cubist (#16069)

* Add Cubist

* enhance recipe

* Not using OS module anymore

* remove white space

* Fix build shell

* make Flake8 happy

* use bash shell for build

* Convert it To MakefilePackage as per peer-review

* dbcsr: expose all options, check openblas feats (#16034)

* dbcsr: expose all options, check openblas feats

* dbcsr: use Ninja to build, ensure serialized tests

* dbcsr: add myself as maintainer

* MPark.Variant: GCC 7.3.1 Conflict (#16081)

* MPark.Variant: GCC 7.3.1 Conflict

Due to an ICE in this specific patch-release of GCC, compile
errors in downstream packages should be avoided with a clean
conflict.

* Fix superfluous spaces

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Fix typo

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Move VMD package to correct path, duh...

* Add an empty line as suggested by peer-review. That's how you separate paragraphs.

* New matlab versions (#16086)

* Add new version 1.1.1 (#16087)

* New package bonniepp added (#16091)

* openbabel: fix compilation errors (#16090)

- Disable maeparser as it is broken with CMake
- Added missing dependencies

* singularity: updated maintainer list (#16093)

* New version xrootd-4.11.3 (#16092)

* I added Gaussian 16. I also execute bsd/install to fix scripts instead of filtering them.

* revert VMD so only Gaussian is in my PR.

* revert VMD so only Gaussian is in my PR.

* revert VMD so only Gaussian is in my PR.

* I added myself as a package maintainer.

Co-authored-by: asmaahassan90 <31959389+asmaahassan90@users.noreply.github.com>
Co-authored-by: Tiziano Müller <tiziano.mueller@chem.uzh.ch>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Co-authored-by: Amjad Kotobi <amjadkotbi@gmail.com>
Co-authored-by: athanasio <athanasio@users.noreply.github.com>
Co-authored-by: Carlos Arango Gutierrez <arangogutierrez@gmail.com>
---
 .../builtin/packages/gaussian/package.py      | 76 ++++++++++---------
 1 file changed, 42 insertions(+), 34 deletions(-)

diff --git a/var/spack/repos/builtin/packages/gaussian/package.py b/var/spack/repos/builtin/packages/gaussian/package.py
index f32b9b2b385..7a1f7e68216 100644
--- a/var/spack/repos/builtin/packages/gaussian/package.py
+++ b/var/spack/repos/builtin/packages/gaussian/package.py
@@ -2,50 +2,58 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
 from spack import *
 import os
 
 
 class Gaussian(Package):
-    """Gaussian  is a computer program for computational chemistry"""
+    """Gaussian is a computer program for computational chemistry"""
 
     homepage = "http://www.gaussian.com/"
-    url = "file://{0}/g09.tgz".format(os.getcwd())
     manual_download = True
 
-    version('09', '7d4c95b535e68e48af183920df427e4e')
+    maintainers = ['antoniokaust']
+
+    version('16-B.01', sha256='0b2cf60aa85d2c8c8e7547446e60e8e8cb67eec20e5f13c4a3e4e7616dcdf122')
+    version('09-D.01', sha256='ef14885b5e334b6ec44a93bfd7225c634247dc946416af3087ab055bf05f54cd')
+
+    @property
+    def ver(self):
+        return self.version.string.split('-')[0]
+
+    @property
+    def g_root(self):
+        return join_path(self.prefix, 'g' + self.ver)
+
+    @property
+    def g_bsd(self):
+        return join_path(self.g_root, 'bsd')
+
+    def url_for_version(self, version):
+        return "file://{0}/g{1}.tgz".format(os.getcwd(), version)
 
     def install(self, spec, prefix):
-        install_tree('.', prefix.bin)
-        patch_install_files = ['flc',
-                               'linda8.2/opteron-linux/bin/flc',
-                               'linda8.2/opteron-linux/bin/LindaLauncher',
-                               'linda8.2/opteron-linux/bin/ntsnet',
-                               'linda8.2/opteron-linux/bin/pmbuild',
-                               'linda8.2/opteron-linux/bin/vntsnet',
-                               'ntsnet'
-                               ]
-        for filename in patch_install_files:
-            if os.path.isfile(filename):
-                filter_file('/mf/frisch/g09', prefix.bin, join_path(prefix.bin,
-                            filename), string='True')
-        patch_install_files = ['linda8.2/opteron-linux/bin/ntsnet',
-                               'linda8.2/opteron-linux/bin/vntsnet',
-                               ]
-        for filename in patch_install_files:
-            if os.path.isfile(filename):
-                filter_file('/usr/bin/linda', prefix.bin, join_path(prefix.bin,
-                            filename), string='True')
+        install_tree('.', self.g_root)
+
+    @run_after('install')
+    def bsd_install(self):
+        with working_dir(self.g_root):
+            bsd_install = Executable(join_path('bsd', 'install'))
+            bsd_install()
 
     def setup_run_environment(self, env):
-        env.set('g09root', self.prefix)
-        env.set('GAUSSIANHOME', self.prefix)
-        env.set('GAUSS_EXEDIR', self.prefix.bin)
-        env.set('G09_BASIS', self.prefix.bin.basis)
-        env.set('GAUSS_LEXEDIR', join_path(self.prefix.bin, 'linda-exe'))
-        env.set('GAUSS_ARCHDIR', self.prefix.bin.arch)
-        env.set('GAUSS_BSDDIR', self.prefix.bin.bsd)
-        env.prepend_path('LD_LIBRARY_PATH', join_path(self.prefix.bin,
-                         'linda8.2', 'opteron-linux', 'lib'))
-        env.prepend_path('LD_LIBRARY_PATH', self.prefix.bin)
+        env.set('g' + self.ver + 'root', self.prefix)
+
+        env.prepend_path('GAUSS_EXEDIR', self.g_root)
+        env.prepend_path('GAUSS_EXEDIR', self.g_bsd)
+
+        env.prepend_path('PATH', self.g_root)
+        env.prepend_path('PATH', self.g_bsd)
+
+        env.set('GAUSS_LEXEDIR', join_path(self.g_root, 'linda-exe'))
+        env.set('GAUSS_ARCHDIR', join_path(self.g_root, 'arch'))
+        env.set('GAUSS_BSDDIR', self.g_bsd)
+        env.set('G' + self.ver + 'BASIS', join_path(self.g_root, 'basis'))
+
+        env.prepend_path('LD_LIBRARY_PATH', self.g_root)
+        env.prepend_path('LD_LIBRARY_PATH', self.g_bsd)

From 18d15312637c89adfe90806243b057a5c339a9ab Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Thu, 21 May 2020 05:34:37 +0200
Subject: [PATCH 464/802] r-spatstat: New package (#16729)

* r-spatstat: New package

* r-spatstat: version dependency added
---
 .../builtin/packages/r-spatstat/package.py    | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-spatstat/package.py

diff --git a/var/spack/repos/builtin/packages/r-spatstat/package.py b/var/spack/repos/builtin/packages/r-spatstat/package.py
new file mode 100644
index 00000000000..490e78c61ae
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-spatstat/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSpatstat(RPackage):
+    """Comprehensive open-source toolbox for
+       analysing Spatial Point Patterns.
+    """
+
+    homepage = "https://cloud.r-project.org/package=spatstat"
+    url      = "https://cloud.r-project.org/src/contrib/spatstat_1.64-1.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/spatstat"
+
+    version('1.64-1', sha256='ca3fc7d0d6b7a83fd045a7502bf03c6871fa1ab2cf411647c438fd99b4eb551a')
+    version('1.63-3', sha256='07b4a1a1b37c91944f31779dd789598f4a5ad047a3de3e9ec2ca99b9e9565528')
+
+    depends_on('r@3.3:', type=('build', 'run'))
+    depends_on('r-rpart', type=('build', 'run'))
+    depends_on('r-nlme', type=('build', 'run'))
+    depends_on('r-spatstat-data@1.4-2:', type=('build', 'run'))
+    depends_on('r-spatstat-utils@1.17:', type=('build', 'run'))
+    depends_on('r-mgcv', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-deldir@0.0-21:', type=('build', 'run'))
+    depends_on('r-abind', type=('build', 'run'))
+    depends_on('r-tensor', type=('build', 'run'))
+    depends_on('r-polyclip@1.10:', type=('build', 'run'))
+    depends_on('r-goftest@1.2-2:', type=('build', 'run'))

From 6445c2e807475e764bbed8eb107a3a64bd6028f8 Mon Sep 17 00:00:00 2001
From: Cameron Stanavige <stanavige1@llnl.gov>
Date: Wed, 20 May 2020 20:35:22 -0700
Subject: [PATCH 465/802] unifyfs: update gotcha dependency version (#16736)

The dev branch of UnifyFS now depends on the latest release of
GOTCHA, and will future releases.

This updates our spackage to depend on the correct version of GOTCHA
depending on the version of UnifyFS being installed.
---
 var/spack/repos/builtin/packages/unifyfs/package.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/unifyfs/package.py b/var/spack/repos/builtin/packages/unifyfs/package.py
index 77b40147412..a2290bfa670 100644
--- a/var/spack/repos/builtin/packages/unifyfs/package.py
+++ b/var/spack/repos/builtin/packages/unifyfs/package.py
@@ -36,9 +36,8 @@ class Unifyfs(AutotoolsPackage):
 
     # Required dependencies
     depends_on('flatcc')
-    # Latest version of GOTCHA has API changes that break UnifyFS.
-    # Updates to UnifyFS are coming in order to fix this.
-    depends_on('gotcha@0.0.2')
+    depends_on('gotcha@0.0.2', when='@:0.9.0')
+    depends_on('gotcha@1.0.3:', when='@0.9.1:')
     depends_on('leveldb')
     depends_on('margo')
     depends_on('mercury+bmi+sm')

From 7d55b88c43aa4b69c6df712e8401dacc0c3ead48 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Thu, 21 May 2020 17:48:58 +0200
Subject: [PATCH 466/802] r-caracas: new package at v1.0.0 (#16748)

---
 .../builtin/packages/r-caracas/package.py     | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-caracas/package.py

diff --git a/var/spack/repos/builtin/packages/r-caracas/package.py b/var/spack/repos/builtin/packages/r-caracas/package.py
new file mode 100644
index 00000000000..74f9c77e545
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-caracas/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RCaracas(RPackage):
+    """Computer algebra via the 'SymPy' library (<https://www.sympy.org/>).
+       This makes it possible to solve equations symbolically, find symbolic
+       integrals, symbolic sums and other important quantities.
+    """
+
+    homepage = "https://cloud.r-project.org/package=caracas"
+    url      = "https://cloud.r-project.org/src/contrib/caracas_1.0.0.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/caracas"
+
+    version('1.0.0', sha256='0da6f1d94d1dacb1c11a3635bdff8f7cd8f84373deffa7126636d0876d48e42b')
+
+    depends_on('r@3.0:', type=('build', 'run'))
+    depends_on('r-reticulate@1.14:', type=('build', 'run'))
+    depends_on('python@3.6:', type=('build', 'run'))

From 661832a6c6a86ce8b6a5da0bdb5e63e4da4f7955 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Thu, 21 May 2020 17:52:55 +0200
Subject: [PATCH 467/802] r-boruta: new package at v7.0.0 (#16746)

---
 .../builtin/packages/r-boruta/package.py      | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-boruta/package.py

diff --git a/var/spack/repos/builtin/packages/r-boruta/package.py b/var/spack/repos/builtin/packages/r-boruta/package.py
new file mode 100644
index 00000000000..45b4f22d579
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-boruta/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBoruta(RPackage):
+    """An all relevant feature selection wrapper algorithm. It finds
+       relevant features by comparing original attributes' importance
+       with importance achievable at random, estimated using their
+       permuted copies (shadows).
+    """
+
+    homepage = "https://cloud.r-project.org/package=Boruta"
+    url      = "https://cloud.r-project.org/src/contrib/Boruta_7.0.0.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/Boruta"
+
+    version('7.0.0', sha256='6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78')
+    version('6.0.0', sha256='1c9a7aabe09f040e147f6c614f5fe1d0b951d3b0f0024161fbb4c31da8fae8de')
+
+    depends_on('r-ranger', type=('build', 'run'))

From a9b64bcaf128eb8ab19081328d2a19035ca60e0c Mon Sep 17 00:00:00 2001
From: "Tomoki, Karatsu" <49965247+t-karatsu@users.noreply.github.com>
Date: Fri, 22 May 2020 03:50:57 +0900
Subject: [PATCH 468/802] autotools: delete args from postdep objects when %fj
 (#16274)

---
 lib/spack/spack/build_systems/autotools.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/lib/spack/spack/build_systems/autotools.py b/lib/spack/spack/build_systems/autotools.py
index 90cad572a1e..bb17cce46ce 100644
--- a/lib/spack/spack/build_systems/autotools.py
+++ b/lib/spack/spack/build_systems/autotools.py
@@ -11,6 +11,7 @@
 import shutil
 import stat
 import sys
+import re
 from subprocess import PIPE
 from subprocess import check_call
 
@@ -185,6 +186,8 @@ def _do_patch_libtool(self):
                     if line == 'pic_flag=""\n':
                         line = 'pic_flag="{0}"\n'\
                                .format(self.compiler.cc_pic_flag)
+                    if self.spec.satisfies('%fj') and 'fjhpctag.o' in line:
+                        line = re.sub(r'/\S*/fjhpctag.o', '', line)
                     sys.stdout.write(line)
 
     @property

From 75b0d0b145baec354c5876bd58a2176c5648f638 Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Fri, 22 May 2020 20:31:31 +0900
Subject: [PATCH 469/802] charmpp: added support to Fujitsu compilers. (#16756)

---
 .../repos/builtin/packages/charmpp/fj.patch   | 61 +++++++++++++++++++
 .../repos/builtin/packages/charmpp/package.py |  3 +
 2 files changed, 64 insertions(+)
 create mode 100755 var/spack/repos/builtin/packages/charmpp/fj.patch

diff --git a/var/spack/repos/builtin/packages/charmpp/fj.patch b/var/spack/repos/builtin/packages/charmpp/fj.patch
new file mode 100755
index 00000000000..d5df680c0c2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/charmpp/fj.patch
@@ -0,0 +1,61 @@
+diff --git a/src/arch/netlrts-linux-arm8/cc-fcc.h b/src/arch/netlrts-linux-arm8/cc-fcc.h
+new file mode 100644
+index 000000000..f25b2250a
+--- /dev/null
++++ b/src/arch/netlrts-linux-arm8/cc-fcc.h
+@@ -0,0 +1,6 @@
++#undef CMK_DLL_CC
++
++#undef  CMK_COMPILEMODE_ORIG
++#undef  CMK_COMPILEMODE_ANSI
++#define CMK_COMPILEMODE_ORIG                               1
++#define CMK_COMPILEMODE_ANSI                               0
+diff --git a/src/arch/netlrts-linux-arm8/cc-fcc.sh b/src/arch/netlrts-linux-arm8/cc-fcc.sh
+new file mode 100644
+index 000000000..0efdc417e
+--- /dev/null
++++ b/src/arch/netlrts-linux-arm8/cc-fcc.sh
+@@ -0,0 +1,15 @@
++# Assumes Fujitsu C/C++ compiler:
++CMK_CPP_CHARM="cpp -P"
++CMK_CPP_C="fcc$CMK_COMPILER_SUFFIX"
++CMK_CC="fcc$CMK_COMPILER_SUFFIX"
++CMK_LD="fcc$CMK_COMPILER_SUFFIX"
++CMK_CXX="FCC$CMK_COMPILER_SUFFIX"
++CMK_LDXX="FCC$CMK_COMPILER_SUFFIX"
++
++CMK_CPP_C_FLAGS="-E"
++
++CMK_PIC='' # empty string: will be reset to default by conv-config.sh
++CMK_PIE='-fPIE'
++
++CMK_COMPILER='fcc'
++CMK_WARNINGS_ARE_ERRORS="-Werror"
+diff --git a/src/arch/netlrts-linux-arm8/conv-mach-frt.h b/src/arch/netlrts-linux-arm8/conv-mach-frt.h
+new file mode 100644
+index 000000000..d1ab56ad5
+--- /dev/null
++++ b/src/arch/netlrts-linux-arm8/conv-mach-frt.h
+@@ -0,0 +1 @@
++/* This file intentionally left blank */
+diff --git a/src/arch/netlrts-linux-arm8/conv-mach-frt.sh b/src/arch/netlrts-linux-arm8/conv-mach-frt.sh
+new file mode 100644
+index 000000000..1de93a5ed
+--- /dev/null
++++ b/src/arch/netlrts-linux-arm8/conv-mach-frt.sh
+@@ -0,0 +1,15 @@
++CMK_CF90="frt"
++
++CMK_FPP="$CMK_CF90 -Ccpp"
++
++CMK_CF90_FIXED="$CMK_CF90 -Fixed "
++
++CMK_F90LIBS="-lfj90i -lfj90f -lfjsrcinfo -lfjsrcinfo -lelf"
++
++CMK_CF77=$CMK_CF90
++CMK_F77LIBS=$CMK_F90LIBS
++
++CMK_MOD_NAME_ALLCAPS=
++CMK_MOD_EXT="mod"
++CMK_F90_USE_MODDIR=1
++CMK_F90_MODINC="-I"
diff --git a/var/spack/repos/builtin/packages/charmpp/package.py b/var/spack/repos/builtin/packages/charmpp/package.py
index fc1680f9af3..a6c60ef11d3 100644
--- a/var/spack/repos/builtin/packages/charmpp/package.py
+++ b/var/spack/repos/builtin/packages/charmpp/package.py
@@ -40,6 +40,9 @@ class Charmpp(Package):
     # Patch is no longer needed in versions 6.8.0+
     patch("mpi.patch", when="@:6.7.1")
 
+    # support Fujitsu compiler
+    patch("fj.patch", when="%fj")
+
     # Ignore compiler warnings while configuring
     patch("strictpass.patch", when="@:6.8.2")
 

From f6bef306ec425bf0214e0795b74970bf18cd4e68 Mon Sep 17 00:00:00 2001
From: Cody Balos <balos1@llnl.gov>
Date: Fri, 22 May 2020 04:39:57 -0700
Subject: [PATCH 470/802] sundials: added v5.2.0 and v5.3.0 (#16752)

---
 var/spack/repos/builtin/packages/sundials/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/sundials/package.py b/var/spack/repos/builtin/packages/sundials/package.py
index 104307fa19a..e374a4bbcad 100644
--- a/var/spack/repos/builtin/packages/sundials/package.py
+++ b/var/spack/repos/builtin/packages/sundials/package.py
@@ -21,6 +21,8 @@ class Sundials(CMakePackage):
     # Versions
     # ==========================================================================
     version('develop', branch='develop')
+    version('5.3.0', sha256='88dff7e11a366853d8afd5de05bf197a8129a804d9d4461fb64297f1ef89bca7')
+    version('5.2.0', sha256='95f058acce5bd66e654de65acdbb1c9f44c90cf1b4e28f8d933cdb4415ebba3e')
     version('5.1.0', sha256='fb22d14fad42203809dc46d046b001149ec4e901b23882bd4a80619157fd9b21')
     version('5.0.0', sha256='345141ec01c641d0bdfb3476c478b7e74fd6a7192a478a27cafe75d9da2d7dd3')
     version('4.1.0', sha256='280de1c27b2360170a6f46cb3799b2aee9dff3bddbafc8b08c291a47ab258aa5')

From 407f1bdb92d2f355df42d8309fea94c61402a11b Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Fri, 22 May 2020 06:49:50 -0500
Subject: [PATCH 471/802] genometools: require cairo pdf backend (#16753)

---
 var/spack/repos/builtin/packages/genometools/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/genometools/package.py b/var/spack/repos/builtin/packages/genometools/package.py
index ac7ef818053..ca42145a3e1 100644
--- a/var/spack/repos/builtin/packages/genometools/package.py
+++ b/var/spack/repos/builtin/packages/genometools/package.py
@@ -17,7 +17,7 @@ class Genometools(MakefilePackage):
     version('1.5.9', sha256='bba8e043f097e7c72e823f73cb0efbd20bbd60f1ce797a0e4c0ab632b170c909')
 
     depends_on('perl', type=('build', 'run'))
-    depends_on('cairo')
+    depends_on('cairo+pdf')
     depends_on('pango')
 
     # build fails with gcc 7"

From 0581e6abb3107c17ed858cdf04d051d53e7beb15 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Carlos=20Bederi=C3=A1n?= <carlos.bederian@unc.edu.ar>
Date: Fri, 22 May 2020 08:56:35 -0300
Subject: [PATCH 472/802] julia: added v1.4.1 (#16739)

---
 var/spack/repos/builtin/packages/julia/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py
index ec86c04886f..97c873d075c 100644
--- a/var/spack/repos/builtin/packages/julia/package.py
+++ b/var/spack/repos/builtin/packages/julia/package.py
@@ -18,6 +18,7 @@ class Julia(Package):
     maintainers = ['glennpj']
 
     version('master', branch='master')
+    version('1.4.1', sha256='b21585db55673ac0668c163678fcf2aad11eb7c64bb2aa03a43046115fab1553')
     version('1.4.0', sha256='880c73a08296ce8d94ad9605149f2a2b2b028e7202a700ef725da899300b8be9')
     version('1.3.1', sha256='053908ec2706eb76cfdc998c077de123ecb1c60c945b4b5057aa3be19147b723')
     version('1.2.0', sha256='2419b268fc5c3666dd9aeb554815fe7cf9e0e7265bc9b94a43957c31a68d9184')

From c6d7405009d349e14a65cafc0eed71352fcd4ba2 Mon Sep 17 00:00:00 2001
From: Mathias Anselmann <mathias.anselmann@posteo.de>
Date: Fri, 22 May 2020 14:58:53 +0200
Subject: [PATCH 473/802] superlu-dist: added v6.2.0 and v6.3.1 (#16704)

---
 var/spack/repos/builtin/packages/superlu-dist/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index 799b413f7d3..9bf0a240f6a 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -18,7 +18,9 @@ class SuperluDist(CMakePackage):
 
     version('develop', branch='master')
     version('xsdk-0.2.0', tag='xsdk-0.2.0')
+    version('6.3.1', sha256='3787c2755acd6aadbb4d9029138c293a7570a2ed228806676edcc7e1d3f5a1d3')
     version('6.3.0', sha256='daf3264706caccae2b8fd5a572e40275f1e128fa235cb7c21ee2f8051c11af95')
+    version('6.2.0', sha256='15ad1badd81b41e37941dd124d06d3b92e51c4f0ff532ad23fb09c4ebfe6eb9e')
     version('6.1.1', sha256='35d25cff592c724439870444ed45e1d1d15ca2c65f02ccd4b83a6d3c9d220bd1')
     version('6.1.0', sha256='92c6d1424dd830ee2d1e7396a418a5f6645160aea8472e558c4e4bfe006593c4')
     version('6.0.0', sha256='ff6cdfa0263d595708bbb6d11fb780915d8cfddab438db651e246ea292f37ee4')

From c9df2dea953a309c008a26ce525299f5e36c7fd6 Mon Sep 17 00:00:00 2001
From: "Seth R. Johnson" <johnsonsr@ornl.gov>
Date: Fri, 22 May 2020 09:55:29 -0400
Subject: [PATCH 474/802] IWYU: update include-what-you-use version (#16760)

---
 var/spack/repos/builtin/packages/iwyu/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/iwyu/package.py b/var/spack/repos/builtin/packages/iwyu/package.py
index a05ff073b7b..4e0b45a5a07 100644
--- a/var/spack/repos/builtin/packages/iwyu/package.py
+++ b/var/spack/repos/builtin/packages/iwyu/package.py
@@ -16,12 +16,14 @@ class Iwyu(CMakePackage):
 
     maintainers = ['sethrj']
 
+    version('0.14', sha256='43184397db57660c32e3298a6b1fd5ab82e808a1f5ab0591d6745f8d256200ef')
     version('0.13', sha256='49294270aa64e8c04182369212cd919f3b3e0e47601b1f935f038c761c265bc9')
     version('0.12', sha256='a5892fb0abccb820c394e4e245c00ef30fc94e4ae58a048b23f94047c0816025')
     version('0.11', sha256='2d2877726c4aed9518cbb37673ffbc2b7da9c239bf8fe29432da35c1c0ec367a')
 
     patch('iwyu-013-cmake.patch', when='@0.13')
 
+    depends_on('llvm+clang@10.0:10.999', when='@0.14')
     depends_on('llvm+clang@9.0:9.999', when='@0.13')
     depends_on('llvm+clang@8.0:8.999', when='@0.12')
     depends_on('llvm+clang@7.0:7.999', when='@0.11')

From d2d35f80d194fee3e1bdeea1d31ea8e3ff5948bf Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Fri, 22 May 2020 10:17:43 -0500
Subject: [PATCH 475/802] fraggenescan: new package at v1.31 (#16587)

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../builtin/packages/fraggenescan/package.py  | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/fraggenescan/package.py

diff --git a/var/spack/repos/builtin/packages/fraggenescan/package.py b/var/spack/repos/builtin/packages/fraggenescan/package.py
new file mode 100644
index 00000000000..c1af71a829b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fraggenescan/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fraggenescan(MakefilePackage):
+    """FragGeneScan is an application for finding (fragmented) genes in short
+       reads. It can also be applied to predict prokaryotic genes in
+       incomplete assemblies or complete genomes."""
+
+    homepage = "https://sourceforge.net/projects/fraggenescan/"
+    url      = "https://downloads.sourceforge.net/project/fraggenescan/FragGeneScan1.31.tar.gz"
+
+    version('1.31', sha256='cd3212d0f148218eb3b17d24fcd1fc897fb9fee9b2c902682edde29f895f426c')
+
+    build_targets = ['fgs']
+
+    def edit(self, spec, prefix):
+        filter_file('gcc', spack_cc, 'Makefile', string=True)
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)

From 1d936a8cc6eec96fbdac327397d63482750a79d2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Carlos=20Bederi=C3=A1n?= <carlos.bederian@unc.edu.ar>
Date: Fri, 22 May 2020 12:24:54 -0300
Subject: [PATCH 476/802] julia: Fix LLVM build failing with newer versions of
 CMake (#16738)

---
 var/spack/repos/builtin/packages/julia/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py
index 97c873d075c..cd401dd9ea7 100644
--- a/var/spack/repos/builtin/packages/julia/package.py
+++ b/var/spack/repos/builtin/packages/julia/package.py
@@ -47,7 +47,8 @@ class Julia(Package):
     # Python only needed to build LLVM?
     depends_on('python@2.7:2.8', type='build', when='@:1.1')
     depends_on('python@2.7:', type='build', when='@1.2:')
-    depends_on('cmake @2.8:', type='build', when='@1.0:')
+    depends_on('cmake@2.8:', type='build', when='@1.0:')
+    depends_on('cmake@:3.11', type='build', when='@:1.4')
     depends_on('git', type='build', when='@master')
 
     # Combined build-time and run-time dependencies:

From d51635e6bd6d24ec7927efc706a21aebfcdd0e33 Mon Sep 17 00:00:00 2001
From: noguchi-k <55966120+noguchi-k@users.noreply.github.com>
Date: Sat, 23 May 2020 00:28:57 +0900
Subject: [PATCH 477/802] ffr: add flag to use fixed format in which the length
 of one line of the source code is 255 when building with Fujitsu compiler.
 (#16737)

* ffr: add flag to use fixed format in which the length of one line of the source code is 255 when building with Fujitsu compiler.

* ffr: changed to elif.
---
 var/spack/repos/builtin/packages/ffr/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/ffr/package.py b/var/spack/repos/builtin/packages/ffr/package.py
index 8cd10fe5380..bd3c8258d1a 100644
--- a/var/spack/repos/builtin/packages/ffr/package.py
+++ b/var/spack/repos/builtin/packages/ffr/package.py
@@ -39,6 +39,8 @@ def edit(self, spec, prefix):
         fflags = flags[:]
         if spec.satisfies('%gcc'):
             fflags.append('-ffixed-line-length-none')
+        elif spec.satisfies('%fj'):
+            fflags.append('-Fwide')
         d = find('.', 'src_main', recursive=True)
         root_dir  = os.path.dirname(d[0])
         make = join_path(root_dir, 'src_pre', 'src', 'Makefile')

From ed037edd2637826b4bcc9e445caa3f8be889fc83 Mon Sep 17 00:00:00 2001
From: Rob Latham <robl@mcs.anl.gov>
Date: Fri, 22 May 2020 10:31:10 -0500
Subject: [PATCH 478/802] prrte uses libev data structues, not libevent
 (#16530)

* use libevent not libev

* Add Ralph Castain as a maintainer
---
 var/spack/repos/builtin/packages/prrte/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/prrte/package.py b/var/spack/repos/builtin/packages/prrte/package.py
index c8fa0ede0d7..58a3d10819f 100644
--- a/var/spack/repos/builtin/packages/prrte/package.py
+++ b/var/spack/repos/builtin/packages/prrte/package.py
@@ -18,6 +18,7 @@ class Prrte(AutotoolsPackage):
     homepage = "https://pmix.org"
     url      = "https://github.com/pmix/prrte/releases/download/v1.0.0/prrte-1.0.0.tar.bz2"
     git      = "https://github.com/pmix/prrte.git"
+    maintainers = ['rhc54']
 
     version('develop', branch='master')
     version('1.0.0', sha256='a9b3715e059c10ed091bd6e3a0d8896f7752e43ee731abcc95fb962e67132a2d')
@@ -50,7 +51,7 @@ def configure_args(self):
 
         # libevent
         config_args.append(
-            '--with-libev={0}'.format(spec['libevent'].prefix))
+            '--with-libevent={0}'.format(spec['libevent'].prefix))
         # hwloc
         config_args.append('--with-hwloc={0}'.format(spec['hwloc'].prefix))
         # pmix

From 7449bf8bab94315f02ee200c9b65363edb7134f7 Mon Sep 17 00:00:00 2001
From: Ethan Stam <33101855+EthanS94@users.noreply.github.com>
Date: Fri, 22 May 2020 09:33:19 -0600
Subject: [PATCH 479/802] ParaView: conflict ~opengl2 with versions 5.5 and up
 (#16742)

---
 var/spack/repos/builtin/packages/paraview/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py
index f9e10b1fba8..bb8b140b748 100644
--- a/var/spack/repos/builtin/packages/paraview/package.py
+++ b/var/spack/repos/builtin/packages/paraview/package.py
@@ -54,6 +54,9 @@ class Paraview(CMakePackage, CudaPackage):
     conflicts('+python', when='@5.6:')
     conflicts('+python3', when='@:5.5')
     conflicts('+shared', when='+cuda')
+    # Legacy rendering dropped in 5.5
+    # See commit: https://gitlab.kitware.com/paraview/paraview/-/commit/798d328c
+    conflicts('~opengl2', when='@5.5:')
 
     # Workaround for
     # adding the following to your packages.yaml

From 106a121b83f9c44e7a4cc08e0f9a19e9820b4166 Mon Sep 17 00:00:00 2001
From: "Seth R. Johnson" <johnsonsr@ornl.gov>
Date: Fri, 22 May 2020 15:40:21 -0400
Subject: [PATCH 480/802] [Trilinos] Make MPI optional (#16685)

* Make MPI optional for Trilinos

* Use 'define' and 'define_from_variant' in trilinos package
---
 .../builtin/packages/trilinos/package.py      | 501 ++++++++----------
 1 file changed, 213 insertions(+), 288 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index fd623fe8db3..3626f328c87 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -100,6 +100,8 @@ class Trilinos(CMakePackage):
             description='Compile with Matio')
     variant('metis',        default=True,
             description='Compile with METIS and ParMETIS')
+    variant('mpi',          default=True,
+            description='Compile with MPI parallelism')
     variant('mumps',        default=True,
             description='Compile with support for MUMPS solvers')
     variant('netcdf',       default=True,
@@ -334,11 +336,11 @@ class Trilinos(CMakePackage):
     depends_on('zlib', when="+zlib")
 
     # MPI related dependencies
-    depends_on('mpi')
-    depends_on('netcdf-c+mpi', when="+netcdf~pnetcdf")
+    depends_on('mpi', when='+mpi')
+    depends_on('netcdf-c+mpi', when="+netcdf~pnetcdf+mpi")
     depends_on('netcdf-c+mpi+parallel-netcdf', when="+netcdf+pnetcdf@master,12.12.1:")
     depends_on('parallel-netcdf', when="+netcdf+pnetcdf@master,12.12.1:")
-    depends_on('parmetis', when='+metis')
+    depends_on('parmetis', when='+metis+mpi')
     depends_on('cgns', when='+cgns')
     depends_on('adios2', when='+adios2')
     # Trilinos' Tribits config system is limited which makes it very tricky to
@@ -361,11 +363,16 @@ class Trilinos(CMakePackage):
     depends_on('hypre@xsdk-0.2.0~internal-superlu', when='@xsdk-0.2.0+hypre')
     depends_on('hypre@develop~internal-superlu', when='@develop+hypre')
     # We need hdf5+hl to match with netcdf during concretization
-    depends_on('hdf5+hl+mpi', when='+hdf5')
+    depends_on('hdf5+hl+mpi', when='+hdf5+mpi')
     depends_on('python', when='+python')
     depends_on('py-numpy', when='+python', type=('build', 'run'))
     depends_on('swig', when='+python')
 
+    # Dependencies/conflicts when MPI is disabled
+    depends_on('hdf5+hl~mpi', when='+hdf5~mpi')
+    conflicts('+parmetis', when='~mpi')
+    conflicts('+pnetcdf', when='~mpi')
+
     patch('umfpack_from_suitesparse.patch', when='@11.14.1:12.8.1')
     patch('xlf_seacas.patch', when='@12.10.1:12.12.1 %xl')
     patch('xlf_seacas.patch', when='@12.10.1:12.12.1 %xl_r')
@@ -381,441 +388,359 @@ def url_for_version(self, version):
 
     def cmake_args(self):
         spec = self.spec
+        define = CMakePackage.define
+
+        def define_trilinos_enable(cmake_var, spec_var=None):
+            if spec_var is None:
+                spec_var = cmake_var.lower()
+            return self.define_from_variant(
+                'Trilinos_ENABLE_' + cmake_var, spec_var)
+
+        def define_tpl_enable(cmake_var, spec_var=None):
+            if spec_var is None:
+                spec_var = cmake_var.lower()
+            return self.define_from_variant('TPL_ENABLE_' + cmake_var,
+                                            spec_var)
 
         cxx_flags = []
         options = []
 
         # #################### Base Settings #######################
 
-        mpi_bin = spec['mpi'].prefix.bin
         options.extend([
-            '-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF',
-            '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
-            '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
-            '-DTrilinos_ENABLE_CXX11:BOOL=ON',
-            '-DBUILD_SHARED_LIBS:BOOL=%s' % (
-                'ON' if '+shared' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_DEBUG:BOOL=%s' % (
-                'ON' if '+debug' in spec else 'OFF'),
-
+            define('Trilinos_VERBOSE_CONFIGURE', False),
+            define('Trilinos_ENABLE_TESTS', False),
+            define('Trilinos_ENABLE_EXAMPLES', False),
+            define('Trilinos_ENABLE_CXX11', True),
+            self.define_from_variant('BUILD_SHARED_LIBS', 'shared'),
+            define_trilinos_enable('DEBUG', 'debug'),
             # The following can cause problems on systems that don't have
             # static libraries available for things like dl and pthreads
             # for example when trying to build static libs
-            # '-DTPL_FIND_SHARED_LIBS:BOOL=%s' % (
-            #     'ON' if '+shared' in spec else 'OFF'),
-            # '-DTrilinos_LINK_SEARCH_START_STATIC:BOOL=%s' % (
-            #     'OFF' if '+shared' in spec else 'ON'),
+            # define('TPL_FIND_SHARED_LIBS', (
+            #     'ON' if '+shared' in spec else 'OFF'))
+            # define('Trilinos_LINK_SEARCH_START_STATIC', (
+            #     'OFF' if '+shared' in spec else 'ON'))
+        ])
 
+        # MPI settings
+        options.append(define_tpl_enable('MPI'))
+        if '+mpi' in spec:
             # Force Trilinos to use the MPI wrappers instead of raw compilers
             # this is needed on Apple systems that require full resolution of
             # all symbols when linking shared libraries
-            '-DTPL_ENABLE_MPI:BOOL=ON',
-            '-DCMAKE_C_COMPILER=%s'       % spec['mpi'].mpicc,
-            '-DCMAKE_CXX_COMPILER=%s'     % spec['mpi'].mpicxx,
-            '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
-            '-DMPI_BASE_DIR:PATH=%s'      % spec['mpi'].prefix
-        ])
+            mpi_bin = spec['mpi'].prefix.bin
+            options.extend([
+                define('CMAKE_C_COMPILER', spec['mpi'].mpicc),
+                define('CMAKE_CXX_COMPILER', spec['mpi'].mpicxx),
+                define('CMAKE_Fortran_COMPILER', spec['mpi'].mpifc),
+                define('MPI_BASE_DIR', spec['mpi'].prefix),
+            ])
 
         # ################## Trilinos Packages #####################
 
         options.extend([
-            '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=%s' % (
-                'ON' if '+alloptpkgs' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Amesos:BOOL=%s' % (
-                'ON' if '+amesos' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Amesos2:BOOL=%s' % (
-                'ON' if '+amesos2' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Anasazi:BOOL=%s' % (
-                'ON' if '+anasazi' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_AztecOO:BOOL=%s' % (
-                'ON' if '+aztec' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Belos:BOOL=%s' % (
-                'ON' if '+belos' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Epetra:BOOL=%s' % (
-                'ON' if '+epetra' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_EpetraExt:BOOL=%s' % (
-                'ON' if '+epetraext' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Ifpack:BOOL=%s' % (
-                'ON' if '+ifpack' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Ifpack2:BOOL=%s' % (
-                'ON' if '+ifpack2' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Intrepid=%s' % (
-                'ON' if '+intrepid' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Intrepid2=%s' % (
-                'ON' if '+intrepid2' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Isorropia=%s' % (
-                'ON' if '+isorropia' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Kokkos:BOOL=%s' % (
-                'ON' if '+kokkos' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_MiniTensor=%s' % (
-                'ON' if '+minitensor' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Mesquite:BOOL=%s' % (
-                'ON' if '+mesquite' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_ML:BOOL=%s' % (
-                'ON' if '+ml' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_MueLu:BOOL=%s' % (
-                'ON' if '+muelu' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_NOX:BOOL=%s' % (
-                'ON' if '+nox' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Piro:BOOL=%s' % (
-                'ON' if '+piro' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Phalanx=%s' % (
-                'ON' if '+phalanx' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_PyTrilinos:BOOL=%s' % (
-                'ON' if '+python' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_ROL:BOOL=%s' % (
-                'ON' if '+rol' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Rythmos=%s' % (
-                'ON' if '+rythmos' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Sacado:BOOL=%s' % (
-                'ON' if '+sacado' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Shards=%s' % (
-                'ON' if '+shards' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_ShyLU=%s' % (
-                'ON' if '+shylu' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Teko=%s' % (
-                'ON' if '+teko' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Tempus=%s' % (
-                'ON' if '+tempus' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Teuchos:BOOL=%s' % (
-                'ON' if '+teuchos' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Tpetra:BOOL=%s' % (
-                'ON' if '+tpetra' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Zoltan:BOOL=%s' % (
-                'ON' if '+zoltan' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Zoltan2:BOOL=%s' % (
-                'ON' if '+zoltan2' in spec else 'OFF'),
+            define_trilinos_enable('ALL_OPTIONAL_PACKAGES', 'alloptpkgs'),
+            define_trilinos_enable('Amesos'),
+            define_trilinos_enable('Amesos2'),
+            define_trilinos_enable('Anasazi'),
+            define_trilinos_enable('AztecOO', 'aztec'),
+            define_trilinos_enable('Belos'),
+            define_trilinos_enable('Epetra'),
+            define_trilinos_enable('EpetraExt'),
+            define_trilinos_enable('Ifpack'),
+            define_trilinos_enable('Ifpack2'),
+            define_trilinos_enable('Intrepid'),
+            define_trilinos_enable('Intrepid2'),
+            define_trilinos_enable('Isorropia'),
+            define_trilinos_enable('Kokkos'),
+            define_trilinos_enable('MiniTensor'),
+            define_trilinos_enable('Mesquite'),
+            define_trilinos_enable('ML'),
+            define_trilinos_enable('MueLu'),
+            define_trilinos_enable('NOX'),
+            define_trilinos_enable('Piro'),
+            define_trilinos_enable('Phalanx'),
+            define_trilinos_enable('PyTrilinos', 'python'),
+            define_trilinos_enable('ROL'),
+            define_trilinos_enable('Rythmos'),
+            define_trilinos_enable('Sacado'),
+            define_trilinos_enable('Shards'),
+            define_trilinos_enable('ShyLU'),
+            define_trilinos_enable('STK'),
+            define_trilinos_enable('Teko'),
+            define_trilinos_enable('Tempus'),
+            define_trilinos_enable('Teuchos'),
+            define_trilinos_enable('Tpetra'),
+            define_trilinos_enable('Zoltan'),
+            define_trilinos_enable('Zoltan2'),
         ])
 
-        if '+xsdkflags' in spec:
-            options.extend(['-DUSE_XSDK_DEFAULTS=YES'])
-
-        if '+stk' in spec:
-            options.extend([
-                '-DTrilinos_ENABLE_STK:BOOL=ON'
-            ])
-        else:
-            options.extend([
-                '-DTrilinos_ENABLE_STK:BOOL=OFF'
-            ])
+        options.append(self.define_from_variant('USE_XSDK_DEFAULTS',
+                                                'xsdkflags'))
 
         if '+dtk' in spec:
             options.extend([
-                '-DTrilinos_EXTRA_REPOSITORIES:STRING=DataTransferKit',
-                '-DTrilinos_ENABLE_DataTransferKit:BOOL=ON'
+                define('Trilinos_EXTRA_REPOSITORIES', 'DataTransferKit'),
+                define('Trilinos_ENABLE_DataTransferKit', True),
             ])
 
         if '+exodus' in spec:
             options.extend([
-                '-DTrilinos_ENABLE_SEACAS:BOOL=ON',
-                '-DTrilinos_ENABLE_SEACASExodus:BOOL=ON',
-                '-DTrilinos_ENABLE_SEACASIoss:BOOL=ON',
-                '-DTrilinos_ENABLE_SEACASEpu:BOOL=ON',
-                '-DTrilinos_ENABLE_SEACASExodiff:BOOL=ON',
-                '-DTrilinos_ENABLE_SEACASNemspread:BOOL=ON',
-                '-DTrilinos_ENABLE_SEACASNemslice:BOOL=ON'
+                define('Trilinos_ENABLE_SEACAS', True),
+                define('Trilinos_ENABLE_SEACASExodus', True),
+                define('Trilinos_ENABLE_SEACASIoss', True),
+                define('Trilinos_ENABLE_SEACASEpu', True),
+                define('Trilinos_ENABLE_SEACASExodiff', True),
+                define('Trilinos_ENABLE_SEACASNemspread', True),
+                define('Trilinos_ENABLE_SEACASNemslice', True),
             ])
         else:
             options.extend([
-                '-DTrilinos_ENABLE_SEACASExodus:BOOL=OFF',
-                '-DTrilinos_ENABLE_SEACASIoss:BOOL=OFF'
+                define('Trilinos_ENABLE_SEACASExodus', False),
+                define('Trilinos_ENABLE_SEACASIoss', False),
             ])
 
         if '+chaco' in spec:
             options.extend([
-                '-DTrilinos_ENABLE_SEACAS:BOOL=ON'
-                '-DTrilinos_ENABLE_SEACASChaco:BOOL=ON'
+                define('Trilinos_ENABLE_SEACAS', True),
+                define('Trilinos_ENABLE_SEACASChaco', True),
             ])
         else:
             # don't disable SEACAS, could be needed elsewhere
             options.extend([
-                '-DTrilinos_ENABLE_SEACASChaco:BOOL=OFF',
-                '-DTrilinos_ENABLE_SEACASNemslice=OFF'
+                define('Trilinos_ENABLE_SEACASChaco', False),
+                define('Trilinos_ENABLE_SEACASNemslice', False)
             ])
 
         # ######################### TPLs #############################
 
         blas = spec['blas'].libs
         lapack = spec['lapack'].libs
-        # Note: -DXYZ_LIBRARY_NAMES= needs semicolon separated list of names
         options.extend([
-            '-DTPL_ENABLE_BLAS=ON',
-            '-DBLAS_LIBRARY_NAMES=%s' % ';'.join(blas.names),
-            '-DBLAS_LIBRARY_DIRS=%s' % ';'.join(blas.directories),
-            '-DTPL_ENABLE_LAPACK=ON',
-            '-DLAPACK_LIBRARY_NAMES=%s' % ';'.join(lapack.names),
-            '-DLAPACK_LIBRARY_DIRS=%s' % ';'.join(lapack.directories),
-            '-DTPL_ENABLE_GLM:BOOL=%s' % ('ON' if '+glm' in spec else 'OFF'),
-            '-DTPL_ENABLE_Matio:BOOL=%s' % (
-                'ON' if '+matio' in spec else 'OFF'),
-            '-DTPL_ENABLE_X11:BOOL=%s' % (
-                'ON' if '+x11' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Gtest:BOOL=%s' % (
-                'ON' if '+gtest' in spec else 'OFF'),
+            define('TPL_ENABLE_BLAS', True),
+            define('BLAS_LIBRARY_NAMES', blas.names),
+            define('BLAS_LIBRARY_DIRS', blas.directories),
+            define('TPL_ENABLE_LAPACK', True),
+            define('LAPACK_LIBRARY_NAMES', lapack.names),
+            define('LAPACK_LIBRARY_DIRS', lapack.directories),
+            define_tpl_enable('GLM'),
+            define_tpl_enable('Matio'),
+            define_tpl_enable('X11'),
+            define_trilinos_enable('Gtest', 'gtest'),
         ])
 
+        options.append(define_tpl_enable('Netcdf'))
         if '+netcdf' in spec:
-            options.extend([
-                '-DTPL_ENABLE_Netcdf:BOOL=ON',
-                '-DNetCDF_ROOT:PATH=%s' % spec['netcdf-c'].prefix
-            ])
-        else:
-            options.extend(['-DTPL_ENABLE_Netcdf:BOOL=OFF'])
+            options.append(define('NetCDF_ROOT', spec['netcdf-c'].prefix))
 
+        options.append(define_tpl_enable('HYPRE'))
         if '+hypre' in spec:
             options.extend([
-                '-DTPL_ENABLE_HYPRE:BOOL=ON',
-                '-DHYPRE_INCLUDE_DIRS:PATH=%s' % spec['hypre'].prefix.include,
-                '-DHYPRE_LIBRARY_DIRS:PATH=%s' % spec['hypre'].prefix.lib
+                define('HYPRE_INCLUDE_DIRS', spec['hypre'].prefix.include),
+                define('HYPRE_LIBRARY_DIRS', spec['hypre'].prefix.lib),
             ])
 
+        options.append(define_tpl_enable('Boost'))
         if '+boost' in spec:
             options.extend([
-                '-DTPL_ENABLE_Boost:BOOL=ON',
-                '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include,
-                '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib
+                define('Boost_INCLUDE_DIRS', spec['boost'].prefix.include),
+                define('Boost_LIBRARY_DIRS', spec['boost'].prefix.lib),
             ])
-        else:
-            options.extend(['-DTPL_ENABLE_Boost:BOOL=OFF'])
 
+        options.append(define_tpl_enable('HDF5'))
         if '+hdf5' in spec:
             options.extend([
-                '-DTPL_ENABLE_HDF5:BOOL=ON',
-                '-DHDF5_INCLUDE_DIRS:PATH=%s' % spec['hdf5'].prefix.include,
-                '-DHDF5_LIBRARY_DIRS:PATH=%s' % spec['hdf5'].prefix.lib
+                define('HDF5_INCLUDE_DIRS', spec['hdf5'].prefix.include),
+                define('HDF5_LIBRARY_DIRS', spec['hdf5'].prefix.lib),
             ])
-        else:
-            options.extend(['-DTPL_ENABLE_HDF5:BOOL=OFF'])
 
         if '+suite-sparse' in spec:
             options.extend([
                 # FIXME: Trilinos seems to be looking for static libs only,
                 # patch CMake TPL file?
-                '-DTPL_ENABLE_Cholmod:BOOL=OFF',
-                # '-DTPL_ENABLE_Cholmod:BOOL=ON',
-                # '-DCholmod_LIBRARY_DIRS:PATH=%s' % (
-                #    spec['suite-sparse'].prefix.lib,
-                # '-DCholmod_INCLUDE_DIRS:PATH=%s' % (
-                #    spec['suite-sparse'].prefix.include,
-                '-DTPL_ENABLE_UMFPACK:BOOL=ON',
-                '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % (
-                    spec['suite-sparse'].prefix.lib),
-                '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % (
-                    spec['suite-sparse'].prefix.include),
-                '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;' +
-                'suitesparseconfig'
+                define('TPL_ENABLE_Cholmod', False),
+                # define('TPL_ENABLE_Cholmod', True),
+                # define('Cholmod_LIBRARY_DIRS', (
+                #    spec['suite-sparse'].prefix.lib)
+                # define('Cholmod_INCLUDE_DIRS', (
+                #    spec['suite-sparse'].prefix.include)
+                define('TPL_ENABLE_UMFPACK', True),
+                define('UMFPACK_LIBRARY_DIRS',
+                       spec['suite-sparse'].prefix.lib),
+                define('UMFPACK_INCLUDE_DIRS',
+                       spec['suite-sparse'].prefix.include),
+                define('UMFPACK_LIBRARY_NAMES', [
+                    'umfpack', 'amd', 'colamd', 'cholmod', 'suitesparseconfig'
+                ]),
             ])
         else:
             options.extend([
-                '-DTPL_ENABLE_Cholmod:BOOL=OFF',
-                '-DTPL_ENABLE_UMFPACK:BOOL=OFF',
+                define('TPL_ENABLE_Cholmod', False),
+                define('TPL_ENABLE_UMFPACK', False),
             ])
 
+        options.append(define_tpl_enable('METIS'))
+        options.append(define_tpl_enable('ParMETIS', 'metis'))
         if '+metis' in spec:
             options.extend([
-                '-DTPL_ENABLE_METIS:BOOL=ON',
-                '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib,
-                '-DMETIS_LIBRARY_NAMES=metis',
-                '-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include,
-                '-DTPL_ENABLE_ParMETIS:BOOL=ON',
-                '-DParMETIS_LIBRARY_DIRS=%s;%s' % (
-                    spec['parmetis'].prefix.lib, spec['metis'].prefix.lib),
-                '-DParMETIS_LIBRARY_NAMES=parmetis;metis',
-                '-DTPL_ParMETIS_INCLUDE_DIRS=%s;%s' % (
+                define('METIS_LIBRARY_DIRS', spec['metis'].prefix.lib),
+                define('METIS_LIBRARY_NAMES', 'metis'),
+                define('TPL_METIS_INCLUDE_DIRS', spec['metis'].prefix.include),
+                define('TPL_ENABLE_ParMETIS', True),
+                define('ParMETIS_LIBRARY_DIRS', [
+                    spec['parmetis'].prefix.lib, spec['metis'].prefix.lib
+                ]),
+                define('ParMETIS_LIBRARY_NAMES', ['parmetis', 'metis']),
+                define('TPL_ParMETIS_INCLUDE_DIRS', [
                     spec['parmetis'].prefix.include,
-                    spec['metis'].prefix.include)
-            ])
-        else:
-            options.extend([
-                '-DTPL_ENABLE_METIS:BOOL=OFF',
-                '-DTPL_ENABLE_ParMETIS:BOOL=OFF',
+                    spec['metis'].prefix.include
+                ]),
             ])
 
+        options.append(define_tpl_enable('MUMPS'))
+        options.append(define_tpl_enable('SCALAPACK', 'mumps'))
         if '+mumps' in spec:
             scalapack = spec['scalapack'].libs
             options.extend([
-                '-DTPL_ENABLE_MUMPS:BOOL=ON',
-                '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
+                define('MUMPS_LIBRARY_DIRS', spec['mumps'].prefix.lib),
                 # order is important!
-                '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord',
-                '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
-                '-DSCALAPACK_LIBRARY_NAMES=%s' % ';'.join(scalapack.names),
-                '-DSCALAPACK_LIBRARY_DIRS=%s' % ';'.join(scalapack.directories)
+                define('MUMPS_LIBRARY_NAMES', [
+                    'dmumps', 'mumps_common', 'pord'
+                ]),
+                define('SCALAPACK_LIBRARY_NAMES', scalapack.names),
+                define('SCALAPACK_LIBRARY_DIRS', scalapack.directories),
             ])
             # see
             # https://github.com/trilinos/Trilinos/blob/master/packages/amesos/README-MUMPS
             cxx_flags.extend([
                 '-DMUMPS_5_0'
             ])
-        else:
-            options.extend([
-                '-DTPL_ENABLE_MUMPS:BOOL=OFF',
-                '-DTPL_ENABLE_SCALAPACK:BOOL=OFF',
-            ])
 
+        options.append(define_tpl_enable('SuperLUDist', 'superlu-dist'))
         if '+superlu-dist' in spec:
             options.extend([
-                '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
-            ])
-            options.extend([
-                '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
-                '-DSuperLUDist_LIBRARY_DIRS=%s' %
-                spec['superlu-dist'].prefix.lib,
-                '-DSuperLUDist_INCLUDE_DIRS=%s' %
-                spec['superlu-dist'].prefix.include
+                define('KokkosTSQR_ENABLE_Complex', False),
+                define('TPL_ENABLE_SuperLUDist', True),
+                define('SuperLUDist_LIBRARY_DIRS',
+                       spec['superlu-dist'].prefix.lib),
+                define('SuperLUDist_INCLUDE_DIRS',
+                       spec['superlu-dist'].prefix.include),
             ])
             if spec.satisfies('^superlu-dist@4.0:'):
                 options.extend([
-                    '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON'
+                    define('HAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG', True),
                 ])
-        else:
-            options.extend([
-                '-DTPL_ENABLE_SuperLUDist:BOOL=OFF',
-            ])
 
+        options.append(define_tpl_enable('SuperLU'))
         if '+superlu' in spec:
             options.extend([
-                '-DTPL_ENABLE_SuperLU:BOOL=ON',
-                '-DSuperLU_LIBRARY_DIRS=%s' %
-                spec['superlu'].prefix.lib,
-                '-DSuperLU_INCLUDE_DIRS=%s' %
-                spec['superlu'].prefix.include
-            ])
-        else:
-            options.extend([
-                '-DTPL_ENABLE_SuperLU:BOOL=OFF',
+                define('SuperLU_LIBRARY_DIRS', spec['superlu'].prefix.lib),
+                define('SuperLU_INCLUDE_DIRS', spec['superlu'].prefix.include),
             ])
 
+        options.append(define_tpl_enable('Pnetcdf'))
         if '+pnetcdf' in spec:
             options.extend([
-                '-DTPL_ENABLE_Pnetcdf:BOOL=ON',
-                '-DTPL_Netcdf_Enables_Netcdf4:BOOL=ON',
-                '-DTPL_Netcdf_PARALLEL:BOOL=ON',
-                '-DPNetCDF_ROOT:PATH=%s' % spec['parallel-netcdf'].prefix
-            ])
-        else:
-            options.extend([
-                '-DTPL_ENABLE_Pnetcdf:BOOL=OFF'
+                define('TPL_Netcdf_Enables_Netcdf4', True),
+                define('TPL_Netcdf_PARALLEL', True),
+                define('PNetCDF_ROOT', spec['parallel-netcdf'].prefix),
             ])
 
+        options.append(define_tpl_enable('Zlib'))
         if '+zlib' in spec:
             options.extend([
-                '-DTPL_ENABLE_Zlib:BOOL=ON',
-                '-DZlib_ROOT:PATH=%s' % spec['zlib'].prefix,
-            ])
-        else:
-            options.extend([
-                '-DTPL_ENABLE_Zlib:BOOL=OFF'
+                define('TPL_ENABLE_Zlib', True),
+                define('Zlib_ROOT', spec['zlib'].prefix),
             ])
 
+        options.append(define_tpl_enable('CGNS'))
         if '+cgns' in spec:
             options.extend([
-                '-DTPL_ENABLE_CGNS:BOOL=ON',
-                '-DCGNS_INCLUDE_DIRS:PATH=%s' % spec['cgns'].prefix.include,
-                '-DCGNS_LIBRARY_DIRS:PATH=%s' % spec['cgns'].prefix.lib
-            ])
-        else:
-            options.extend([
-                '-DTPL_ENABLE_CGNS:BOOL=OFF'
+                define('TPL_ENABLE_CGNS', True),
+                define('CGNS_INCLUDE_DIRS', spec['cgns'].prefix.include),
+                define('CGNS_LIBRARY_DIRS', spec['cgns'].prefix.lib),
             ])
 
-        options.append('-DTPL_ENABLE_ADIOS2:BOOL=' + str('+adios2' in spec))
+        options.append(self.define_from_variant('TPL_ENABLE_ADIOS2', 'adios2'))
+
         # ################# Miscellaneous Stuff ######################
 
         # OpenMP
+        options.append(define_trilinos_enable('OpenMP'))
         if '+openmp' in spec:
-            options.extend([
-                '-DTrilinos_ENABLE_OpenMP:BOOL=ON',
-                '-DKokkos_ENABLE_OpenMP:BOOL=ON'
-            ])
+            options.append(define('Kokkos_ENABLE_OpenMP', True))
             if '+tpetra' in spec:
-                options.extend([
-                    '-DTpetra_INST_OPENMP:BOOL=ON'
-                ])
+                options.append(define('Tpetra_INST_OPENMP', True))
 
-        # Fortran lib
-        if '+fortran' in spec:
-            if spec.satisfies('%gcc') or spec.satisfies('%clang'):
+        # Fortran lib (assumes clang is built with gfortran!)
+        if '+fortran' in spec and (
+                spec.satisfies('%gcc') or spec.satisfies('%clang')):
+            options.append(define('Trilinos_ENABLE_Fortran', True))
+            if '+mpi' in spec:
                 libgfortran = os.path.dirname(os.popen(
                     '%s --print-file-name libgfortran.a' %
                     join_path(mpi_bin, 'mpif90')).read())
-                options.extend([
-                    '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % (
-                        libgfortran),
-                    '-DTrilinos_ENABLE_Fortran=ON'
-                ])
+                options.append(define(
+                    'Trilinos_EXTRA_LINK_FLAGS',
+                    '-L%s/ -lgfortran' % (libgfortran),
+                ))
 
-        float_s = 'ON' if '+float' in spec else 'OFF'
-        complex_s = 'ON' if '+complex' in spec else 'OFF'
-        complex_float_s = 'ON' if ('+complex' in spec and
-                                   '+float' in spec) else 'OFF'
+        float_s = '+float' in spec
+        complex_s = '+complex' in spec
         if '+teuchos' in spec:
             options.extend([
-                '-DTeuchos_ENABLE_COMPLEX=%s' % complex_s,
-                '-DTeuchos_ENABLE_FLOAT=%s' % float_s
+                define('Teuchos_ENABLE_COMPLEX', complex_s),
+                define('Teuchos_ENABLE_FLOAT', float_s),
             ])
 
         # Explicit Template Instantiation (ETI) in Tpetra
         # NOTE: Trilinos will soon move to fixed std::uint64_t for GO and
         # std::int32_t or std::int64_t for local.
-        options.append(
-            '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=%s' % (
-                'ON' if '+explicit_template_instantiation' in spec else 'OFF'
-            )
-        )
+        options.append(self.define_from_variant(
+            'Trilinos_ENABLE_EXPLICIT_INSTANTIATION',
+            'explicit_template_instantiation'))
 
         if '+explicit_template_instantiation' in spec and '+tpetra' in spec:
             gotype = spec.variants['gotype'].value
             options.extend([
-                '-DTpetra_INST_DOUBLE:BOOL=ON',
-                '-DTpetra_INST_INT_INT:BOOL=%s' % (
-                    'ON' if gotype == 'int' else 'OFF'),
-                '-DTpetra_INST_INT_LONG:BOOL=%s' % (
-                    'ON' if gotype == 'long' else 'OFF'),
-                '-DTpetra_INST_INT_LONG_LONG:BOOL=%s' % (
-                    'ON' if gotype == 'long_long' else 'OFF'),
-                '-DTpetra_INST_COMPLEX_DOUBLE=%s' % complex_s,
-                '-DTpetra_INST_COMPLEX_FLOAT=%s' % complex_float_s,
-                '-DTpetra_INST_FLOAT=%s' % float_s,
-                '-DTpetra_INST_SERIAL=ON'
+                define('Tpetra_INST_DOUBLE', True),
+                define('Tpetra_INST_INT_INT', gotype == 'int'),
+                define('Tpetra_INST_INT_LONG', gotype == 'long'),
+                define('Tpetra_INST_INT_LONG_LONG', gotype == 'long_long'),
+                define('Tpetra_INST_COMPLEX_DOUBLE', complex_s),
+                define('Tpetra_INST_COMPLEX_FLOAT', float_s and complex_s),
+                define('Tpetra_INST_FLOAT', float_s),
+                define('Tpetra_INST_SERIAL', True),
             ])
 
         # disable due to compiler / config errors:
         if spec.satisfies('%xl') or spec.satisfies('%xl_r'):
             options.extend([
-                '-DTrilinos_ENABLE_Pamgen:BOOL=OFF',
-                '-DTrilinos_ENABLE_Stokhos:BOOL=OFF'
+                define('Trilinos_ENABLE_Pamgen', False),
+                define('Trilinos_ENABLE_Stokhos', False),
             ])
 
         if sys.platform == 'darwin':
-            options.extend([
-                '-DTrilinos_ENABLE_FEI=OFF'
-            ])
+            options.append(define('Trilinos_ENABLE_FEI', False))
 
         if sys.platform == 'darwin' and macos_version() >= Version('10.12'):
             # use @rpath on Sierra due to limit of dynamic loader
-            options.append('-DCMAKE_MACOSX_RPATH=ON')
+            options.append(define('CMAKE_MACOSX_RPATH', True))
         else:
-            options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s' %
-                           self.prefix.lib)
+            options.append(define('CMAKE_INSTALL_NAME_DIR', self.prefix.lib))
 
         if spec.satisfies('%intel') and spec.satisfies('@12.6.2'):
             # Panzer uses some std:chrono that is not recognized by Intel
             # Don't know which (maybe all) Trilinos versions this applies to
             # Don't know which (maybe all) Intel versions this applies to
-            options.extend([
-                '-DTrilinos_ENABLE_Panzer:BOOL=OFF'
-            ])
+            options.append(define('Trilinos_ENABLE_Panzer', False))
 
         # collect CXX flags:
-        options.extend([
-            '-DCMAKE_CXX_FLAGS:STRING=%s' % (' '.join(cxx_flags)),
-        ])
+        options.append(define('CMAKE_CXX_FLAGS', (' '.join(cxx_flags))))
 
         # disable due to compiler / config errors:
-        options.extend([
-            '-DTrilinos_ENABLE_Pike=OFF'
-        ])
+        options.append(define('Trilinos_ENABLE_Pike', False))
 
         return options
 

From 04046c15ded5f5e37fdf928e35c7c0c5e0a02752 Mon Sep 17 00:00:00 2001
From: "Seth R. Johnson" <johnsonsr@ornl.gov>
Date: Fri, 22 May 2020 16:07:45 -0400
Subject: [PATCH 481/802] Mark Valgrind as conflicting with macOS > 10.13
 (#16759)

```
    '/var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/s3j/spack-stage/spack-stage-valgrind-3.15.0-mtir7ubjz7mqmjbb7bogze2qm35hl4ze/spack-src/configure' '--prefix=/ornldev/code/spack/opt/spack/clang-11.0.0-apple/valgrind/mtir7ub' '--enable-only64bit' '--build=amd64-darwin'
1 error found in build log:
     43    checking host system type... x86_64-pc-darwin
     44    checking for a supported CPU... ok (x86_64)
     45    checking for a 64-bit only build... yes
     46    checking for a 32-bit only build... no
     47    checking for a supported OS... ok (darwin)
     48    checking for the kernel version... unsupported (18.7.0)
  >> 49    configure: error: Valgrind works on Darwin 10.x, 11.x, 12.x, 13.x, 14.x, 15.x, 16.x and 17.x (Mac OS X 10.6/7/8/9/10/11 and macOS 10.12/13)
```
---
 var/spack/repos/builtin/packages/valgrind/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/valgrind/package.py b/var/spack/repos/builtin/packages/valgrind/package.py
index 9bf05894506..4555b0b886f 100644
--- a/var/spack/repos/builtin/packages/valgrind/package.py
+++ b/var/spack/repos/builtin/packages/valgrind/package.py
@@ -57,6 +57,9 @@ class Valgrind(AutotoolsPackage, SourcewarePackage):
     # http://valgrind.10908.n7.nabble.com/Unable-to-compile-on-Mac-OS-X-10-11-td57237.html
     patch('valgrind_3_12_0_osx.patch', when='@3.12.0 platform=darwin')
 
+    for os in ('mojave', 'catalina'):
+        conflicts("os=" + os, when='@:3.15')
+
     def configure_args(self):
         spec = self.spec
         options = []

From 6ac8cf8126ed4044ae7b99cf28513059ae0c5652 Mon Sep 17 00:00:00 2001
From: "Seth R. Johnson" <johnsonsr@ornl.gov>
Date: Fri, 22 May 2020 16:07:59 -0400
Subject: [PATCH 482/802] IWYU: fix 0.14 build (#16761)

* IWYU: fix 0.14 build

The CMake patch used for 0.13 hadn't been applied to the master when
0.14 was released, and this version of IWYU requires C++14 or higher.

* Flake8
---
 var/spack/repos/builtin/packages/iwyu/package.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/iwyu/package.py b/var/spack/repos/builtin/packages/iwyu/package.py
index 4e0b45a5a07..eaf0a57913f 100644
--- a/var/spack/repos/builtin/packages/iwyu/package.py
+++ b/var/spack/repos/builtin/packages/iwyu/package.py
@@ -21,9 +21,14 @@ class Iwyu(CMakePackage):
     version('0.12', sha256='a5892fb0abccb820c394e4e245c00ef30fc94e4ae58a048b23f94047c0816025')
     version('0.11', sha256='2d2877726c4aed9518cbb37673ffbc2b7da9c239bf8fe29432da35c1c0ec367a')
 
-    patch('iwyu-013-cmake.patch', when='@0.13')
+    patch('iwyu-013-cmake.patch', when='@0.13:0.14')
 
     depends_on('llvm+clang@10.0:10.999', when='@0.14')
     depends_on('llvm+clang@9.0:9.999', when='@0.13')
     depends_on('llvm+clang@8.0:8.999', when='@0.12')
     depends_on('llvm+clang@7.0:7.999', when='@0.11')
+
+    @when('@0.14:')
+    def cmake_args(self):
+        return [self.define('CMAKE_CXX_STANDARD', 14),
+                self.define('CMAKE_CXX_EXTENSIONS', False)]

From f17352f6f7f177df916bb64c4f2488931bacf737 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 22 May 2020 19:20:25 -0500
Subject: [PATCH 483/802] py-horovod: add 0.19.3 (#16768)

---
 var/spack/repos/builtin/packages/py-horovod/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-horovod/package.py b/var/spack/repos/builtin/packages/py-horovod/package.py
index ec8f3a86385..c7d51270654 100644
--- a/var/spack/repos/builtin/packages/py-horovod/package.py
+++ b/var/spack/repos/builtin/packages/py-horovod/package.py
@@ -14,6 +14,7 @@ class PyHorovod(PythonPackage):
     maintainers = ['adamjstewart']
 
     version('master', branch='master', submodules=True)
+    version('0.19.3', tag='v0.19.3', submodules=True)
     version('0.19.2', tag='v0.19.2', submodules=True)
     version('0.19.1', tag='v0.19.1', submodules=True)
     version('0.19.0', tag='v0.19.0', submodules=True)
@@ -65,7 +66,7 @@ class PyHorovod(PythonPackage):
     depends_on('cmake', type='build', when='controllers=gloo')
 
     # Tensor Operations dependencies
-    depends_on('nccl', when='tensor_ops=nccl')
+    depends_on('nccl@2:', when='tensor_ops=nccl')
     depends_on('mpi', when='tensor_ops=mpi')
     # There does not appear to be a way to use an external Gloo installation
     depends_on('cmake', type='build', when='tensor_ops=gloo')

From be570aa65558312ab8250d7483c086b9bac08a6a Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Fri, 22 May 2020 22:19:16 +0200
Subject: [PATCH 484/802] zstd: Add 1.4.5

---
 var/spack/repos/builtin/packages/zstd/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/zstd/package.py b/var/spack/repos/builtin/packages/zstd/package.py
index 901b02b278c..05ad165142f 100644
--- a/var/spack/repos/builtin/packages/zstd/package.py
+++ b/var/spack/repos/builtin/packages/zstd/package.py
@@ -14,6 +14,7 @@ class Zstd(MakefilePackage):
     homepage = "http://facebook.github.io/zstd/"
     url      = "https://github.com/facebook/zstd/archive/v1.4.3.tar.gz"
 
+    version('1.4.5', sha256='734d1f565c42f691f8420c8d06783ad818060fc390dee43ae0a89f86d0a4f8c2')
     version('1.4.4', sha256='a364f5162c7d1a455cc915e8e3cf5f4bd8b75d09bc0f53965b0c9ca1383c52c8')
     version('1.4.3', sha256='5eda3502ecc285c3c92ee0cc8cd002234dee39d539b3f692997a0e80de1d33de')
     version('1.4.2', sha256='7a6e1dad34054b35e2e847eb3289be8820a5d378228802239852f913c6dcf6a7')

From 86dd42ec706cbaa2bc65b702766d8bd5c4093ec1 Mon Sep 17 00:00:00 2001
From: Miroslav Stoyanov <30537612+mkstoyanov@users.noreply.github.com>
Date: Fri, 22 May 2020 22:10:21 -0400
Subject: [PATCH 485/802] tasmanian: add version 7.1 (#16769)

---
 var/spack/repos/builtin/packages/tasmanian/package.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/tasmanian/package.py b/var/spack/repos/builtin/packages/tasmanian/package.py
index 87ddc99db44..f1214b17773 100644
--- a/var/spack/repos/builtin/packages/tasmanian/package.py
+++ b/var/spack/repos/builtin/packages/tasmanian/package.py
@@ -12,13 +12,14 @@ class Tasmanian(CMakePackage):
     interpolation as well as parameter calibration."""
 
     homepage = 'http://tasmanian.ornl.gov'
-    url      = 'https://github.com/ORNL/TASMANIAN/archive/v7.0.tar.gz'
+    url      = 'https://github.com/ORNL/TASMANIAN/archive/v7.1.tar.gz'
     git      = 'https://github.com/ORNL/TASMANIAN.git'
 
     maintainers = ['mkstoyanov']
 
     version('develop', branch='master')
 
+    version('7.1', sha256='9c24a591506a478745b802f1fa5c557da7bc80b12d8070855de6bc7aaca7547a')
     version('7.0', sha256='4094ba4ee2f1831c575d00368c8471d3038f813398be2e500739cef5c7c4a47b')  # use for xsdk-0.5.0
     version('6.0', sha256='ceab842e9fbce2f2de971ba6226967caaf1627b3e5d10799c3bd2e7c3285ba8b')  # use for xsdk-0.4.0
     version('5.1', sha256='b0c1be505ce5f8041984c63edca9100d81df655733681858f5cc10e8c0c72711')
@@ -67,6 +68,7 @@ class Tasmanian(CMakePackage):
     depends_on('mpi', when="+mpi", type=('build', 'run'))  # openmpi 2 and 3 tested
 
     depends_on('blas', when="+blas", type=('build', 'run'))  # openblas 0.2.18 or newer
+    depends_on('lapack', when="+blas @7.1:", type=('build', 'run'))  # lapack used since 7.1
 
     depends_on('cuda@8.0.61:', when='+cuda', type=('build', 'run'))
     depends_on('cuda@8.0.61:', when='+magma', type=('build', 'run'))

From e18c5316bd766130e0b7170104425269d8d10f92 Mon Sep 17 00:00:00 2001
From: Sergey Kosukhin <sergey.kosukhin@mpimet.mpg.de>
Date: Fri, 22 May 2020 19:27:13 +0200
Subject: [PATCH 486/802] cdo: fix url for version 1.9.8

---
 var/spack/repos/builtin/packages/cdo/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py
index 4cb06132ac6..7b1929b7da5 100644
--- a/var/spack/repos/builtin/packages/cdo/package.py
+++ b/var/spack/repos/builtin/packages/cdo/package.py
@@ -17,7 +17,7 @@ class Cdo(AutotoolsPackage):
 
     maintainers = ['skosukhin']
 
-    version('1.9.8', sha256='f2660ac6f8bf3fa071cf2a3a196b3ec75ad007deb3a782455e80f28680c5252a', url='https://code.mpimet.mpg.de/attachments/download/20286/cdo-1.9.8.tar.gz')
+    version('1.9.8', sha256='f2660ac6f8bf3fa071cf2a3a196b3ec75ad007deb3a782455e80f28680c5252a', url='https://code.mpimet.mpg.de/attachments/download/20826/cdo-1.9.8.tar.gz')
     version('1.9.7.1', sha256='3771952e065bcf935d43e492707370ed2a0ecb59a06bea24f9ab69d77943962c',
             url='https://code.mpimet.mpg.de/attachments/download/20124/cdo-1.9.7.1.tar.gz')
     version('1.9.6', sha256='b31474c94548d21393758caa33f35cf7f423d5dfc84562ad80a2bdcb725b5585', url='https://code.mpimet.mpg.de/attachments/download/19299/cdo-1.9.6.tar.gz')

From 3a336b328abe3e30dd4e89cf22c070f6126b3d54 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Sat, 23 May 2020 04:17:11 +0200
Subject: [PATCH 487/802] r-reticulate: add version; dependencies (#16747)

* Add version 1.15
* Add link dependency on r-rcpp
* Add dependency on r-rappdirs
---
 var/spack/repos/builtin/packages/r-reticulate/package.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/r-reticulate/package.py b/var/spack/repos/builtin/packages/r-reticulate/package.py
index 378134032ff..ec301f3b0c8 100644
--- a/var/spack/repos/builtin/packages/r-reticulate/package.py
+++ b/var/spack/repos/builtin/packages/r-reticulate/package.py
@@ -17,10 +17,12 @@ class RReticulate(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/reticulate_1.13.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/reticulate"
 
+    version('1.15', sha256='47db3e9c9424263ade15287da8e74f6ba261a936b644b197dba6772853b7b50d')
     version('1.13', sha256='adbe41d556b667c4419d563680f8608a56b0f792b8bc427b3bf4c584ff819de3')
 
     depends_on('r@3.0:', type=('build', 'run'))
     depends_on('r-jsonlite', type=('build', 'run'))
-    depends_on('r-rcpp@0.12.7:', type=('build', 'run'))
+    depends_on('r-rcpp@0.12.7:', type=('build', 'run', 'link'))
     depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-rappdirs', when='@1.15:', type=('build', 'run'))
     depends_on('python@2.7.0:')

From 55eb192234dada43e519443023c259220410a60c Mon Sep 17 00:00:00 2001
From: Luca Heltai <luca.heltai@sissa.it>
Date: Sat, 23 May 2020 04:19:19 +0200
Subject: [PATCH 488/802] dealii: 9.2.0 release (#16743)

---
 var/spack/repos/builtin/packages/dealii/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index d3a58cb835f..9760ac589d5 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -22,7 +22,8 @@ class Dealii(CMakePackage, CudaPackage):
     # only add for immediate deps.
     transitive_rpaths = False
 
-    version('develop', branch='master')
+    version('master', branch='master')
+    version('9.2.0', sha256='d05a82fb40f1f1e24407451814b5a6004e39366a44c81208b1ae9d65f3efa43a')
     version('9.1.1', sha256='fc5b483f7fe58dfeb52d05054011280f115498e337af3e085bf272fd1fd81276')
     version('9.1.0', sha256='5b070112403f8afbb72345c1bb24d2a38d11ce58891217e353aab97957a04600')
     version('9.0.1', sha256='df2f0d666f2224be07e3741c0e8e02132fd67ea4579cd16a2429f7416146ee64')

From 9bcf4480b51bd676e975f408a1ea9c2ef1e2eecc Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Thu, 21 May 2020 14:01:06 +0200
Subject: [PATCH 489/802] r-rferns: New package

---
 .../repos/builtin/packages/r-rferns/package.py   | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-rferns/package.py

diff --git a/var/spack/repos/builtin/packages/r-rferns/package.py b/var/spack/repos/builtin/packages/r-rferns/package.py
new file mode 100644
index 00000000000..a10b40bdf3b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rferns/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRferns(RPackage):
+    """Provides the random ferns classifier"""
+
+    homepage = "https://cloud.r-project.org/package=rFerns"
+    url      = "https://cloud.r-project.org/src/contrib/rFerns_3.0.0.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/rFerns"
+
+    version('3.0.0', sha256='35e7e31a6497e415a0fe578678cf9b2f537b21319e4c015a1e2dade00310227c')

From eee6942c8bab04d056de9827d4d2009d521f222e Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Fri, 22 May 2020 17:59:52 +0200
Subject: [PATCH 490/802] r-nimble: New package

---
 .../builtin/packages/r-nimble/package.py      | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-nimble/package.py

diff --git a/var/spack/repos/builtin/packages/r-nimble/package.py b/var/spack/repos/builtin/packages/r-nimble/package.py
new file mode 100644
index 00000000000..c0cd1c2b40d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-nimble/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RNimble(AutotoolsPackage):
+    """A system for writing hierarchical statistical models largely
+       compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to
+       operate models and do basic R-style math, and compiling both
+       models and nimbleFunctions via custom- generated C++.
+    """
+
+    homepage = "https://cloud.r-project.org/package=nimble"
+    url      = "https://cloud.r-project.org/src/contrib/nimble_0.9.1.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/nimble"
+
+    version('0.9.1', sha256='ad5e8a171193cb0172e68bf61c4f94432c45c131a150101ad1c5c7318c335757')
+    version('0.9.0', sha256='ebc28fadf933143eea73900cacaf96ff81cb3c2d607405016062b7e93afa5611')
+
+    depends_on('r@3.1.2:', type=('build', 'run'))
+    depends_on('r-igraph', type=('build', 'run'))
+    depends_on('r-coda', type=('build', 'run'))
+    depends_on('r-r6', type=('build', 'run'))
+    depends_on('automake')

From 9e3470d797bd33bb62273de771d6955e7d7682ea Mon Sep 17 00:00:00 2001
From: Stephen Herbein <stephen272@gmail.com>
Date: Mon, 18 May 2020 22:58:09 -0700
Subject: [PATCH 491/802] flux: add latest releases and checksum

The next release 0.17.0 will also require python3.6+, pre-emptively
prepare for that release.  Also support current master branch.
---
 var/spack/repos/builtin/packages/flux-core/package.py  | 3 +++
 var/spack/repos/builtin/packages/flux-sched/package.py | 1 +
 2 files changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/flux-core/package.py b/var/spack/repos/builtin/packages/flux-core/package.py
index 04ce1eceebf..6b5eb181f00 100644
--- a/var/spack/repos/builtin/packages/flux-core/package.py
+++ b/var/spack/repos/builtin/packages/flux-core/package.py
@@ -15,6 +15,8 @@ class FluxCore(AutotoolsPackage):
     git      = "https://github.com/flux-framework/flux-core.git"
 
     version('master', branch='master')
+    version('0.16.0', sha256='1582f7fb4d2313127418c34de7c9ce4f5fef00622d19cedca7bed929f4709f10')
+    version('0.15.0', sha256='51bc2eae69501f802459fc82f191eb5e8ae0b4f7e9e77ac18543a850cc8445f5')
     version('0.11.3', sha256='91b5d7dca8fc28a77777c4e4cb8717fc3dc2c174e70611740689a71901c6de7e')
     version('0.11.2', sha256='ab8637428cd9b74b2dff4842d10e0fc4acc8213c4e51f31d32a4cbfbdf730412')
     version('0.11.1', sha256='3c8495db0f3b701f6dfe3e2a75aed794fc561e9f28284e8c02ac67693bfe890e')
@@ -46,6 +48,7 @@ class FluxCore(AutotoolsPackage):
     depends_on("python", type=('build', 'run'))
     depends_on("python@2.7:2.99", when="@0.1.0:0.11.0")
     depends_on("python@2.7:", when="@0.11.1:")
+    depends_on("python@3.6:", when="@0.17.0:,master")
     depends_on("py-cffi", type=('build', 'run'))
     depends_on("py-six", type=('build', 'run'), when="@0.11.0:")
     depends_on("py-pyyaml", type=('build', 'run'), when="@0.11.0:")
diff --git a/var/spack/repos/builtin/packages/flux-sched/package.py b/var/spack/repos/builtin/packages/flux-sched/package.py
index 60001e7b896..3ec7f0227ea 100644
--- a/var/spack/repos/builtin/packages/flux-sched/package.py
+++ b/var/spack/repos/builtin/packages/flux-sched/package.py
@@ -15,6 +15,7 @@ class FluxSched(AutotoolsPackage):
     git      = "https://github.com/flux-framework/flux-sched.git"
 
     version('master', branch='master')
+    version('0.8.0', sha256='45bc3cefb453d19c0cb289f03692fba600a39045846568d258e4b896ca19ca0d')
     version('0.7.1', sha256='a35e555a353feed6b7b814ae83d05362356f9ee33ffa75d7dfb7e2fe86c21294')
     version('0.7.0', sha256='69267a3aaacaedd9896fd90cfe17aef266cba4fb28c77f8123d95a31ce739a7b')
     version('0.6.0', sha256='3301d4c10810414228e5969b84b75fe1285abb97453070eb5a77f386d8184f8d')

From a74ee4d27ac0c5bda020b2f0f78f037a21650c8e Mon Sep 17 00:00:00 2001
From: Stephen Herbein <stephen272@gmail.com>
Date: Thu, 21 May 2020 20:14:26 -0700
Subject: [PATCH 492/802] flux: add dependency types for `python` dependency

Flux requires `build` for python and many of the python packages because
it builds python bindings.  Beyond the bindings, the Flux front-end
commands now use python too, hence the `run` type. Finally, Flux's
`pymod` module is linked against the python interpreter, so the package
requires a `link` dependency on python too.
---
 var/spack/repos/builtin/packages/flux-core/package.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/flux-core/package.py b/var/spack/repos/builtin/packages/flux-core/package.py
index 6b5eb181f00..cb53c0f8ad9 100644
--- a/var/spack/repos/builtin/packages/flux-core/package.py
+++ b/var/spack/repos/builtin/packages/flux-core/package.py
@@ -45,10 +45,13 @@ class FluxCore(AutotoolsPackage):
     depends_on("lua@5.1:5.2.99", when="@0.10.0:,master")
     depends_on("lua-luaposix")
     depends_on("munge", when="@0.1.0:0.10.0")
-    depends_on("python", type=('build', 'run'))
-    depends_on("python@2.7:2.99", when="@0.1.0:0.11.0")
-    depends_on("python@2.7:", when="@0.11.1:")
-    depends_on("python@3.6:", when="@0.17.0:,master")
+    # `link` dependency on python due to Flux's `pymod` module
+    depends_on("python", type=('build', 'run', 'link'))
+    depends_on("python@2.7:2.99",
+               when="@0.1.0:0.11.0",
+               type=('build', 'run', 'link'))
+    depends_on("python@2.7:", when="@0.11.1:", type=('build', 'run', 'link'))
+    depends_on("python@3.6:", when="@0.17.0:,master", type=('build', 'run', 'link'))
     depends_on("py-cffi", type=('build', 'run'))
     depends_on("py-six", type=('build', 'run'), when="@0.11.0:")
     depends_on("py-pyyaml", type=('build', 'run'), when="@0.11.0:")

From 5108fe314b92409027c2821698fabb62c0ec3b5d Mon Sep 17 00:00:00 2001
From: Stephen Herbein <stephen272@gmail.com>
Date: Fri, 22 May 2020 12:16:47 -0700
Subject: [PATCH 493/802] flux-sched: add dependency type for flux-core

---
 .../repos/builtin/packages/flux-sched/package.py  | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/flux-sched/package.py b/var/spack/repos/builtin/packages/flux-sched/package.py
index 3ec7f0227ea..5c33d39a0df 100644
--- a/var/spack/repos/builtin/packages/flux-sched/package.py
+++ b/var/spack/repos/builtin/packages/flux-sched/package.py
@@ -36,13 +36,14 @@ class FluxSched(AutotoolsPackage):
     depends_on("pkgconfig")
 
     depends_on("flux-core", type=('build', 'link', 'run'))
-    depends_on("flux-core+cuda", when='+cuda')
-    depends_on("flux-core@0.8.0", when='@0.4.0')
-    depends_on("flux-core@0.9.0", when='@0.5.0')
-    depends_on("flux-core@0.10.0", when='@0.6.0')
-    depends_on("flux-core@0.11.0", when='@0.7.0')
-    depends_on("flux-core@0.11.2:0.11.99", when='@0.7.1')
-    depends_on("flux-core@master", when='@master')
+    depends_on("flux-core+cuda", when='+cuda', type=('build', 'run', 'link'))
+    depends_on("flux-core@0.8.0", when='@0.4.0', type=('build', 'run', 'link'))
+    depends_on("flux-core@0.9.0", when='@0.5.0', type=('build', 'run', 'link'))
+    depends_on("flux-core@0.10.0", when='@0.6.0', type=('build', 'run', 'link'))
+    depends_on("flux-core@0.11.0", when='@0.7.0', type=('build', 'run', 'link'))
+    depends_on("flux-core@0.11.2:0.11.99", when='@0.7.1', type=('build', 'run', 'link'))
+    depends_on("flux-core@0.16.0:0.16.99", when='@0.8.0', type=('build', 'run', 'link'))
+    depends_on("flux-core@master", when='@master', type=('build', 'run', 'link'))
 
     # Need autotools when building on master:
     depends_on("autoconf", type='build', when='@master')

From bc145b2b3f87da8276e4c2e0665e9830de3d0322 Mon Sep 17 00:00:00 2001
From: Kevin Huck <khuck@cs.uoregon.edu>
Date: Fri, 22 May 2020 19:40:28 -0700
Subject: [PATCH 494/802] TAU: remove ~nls constraint on binutils dependency

TAU does not require ~nls.
---
 var/spack/repos/builtin/packages/tau/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/tau/package.py b/var/spack/repos/builtin/packages/tau/package.py
index 132bcb7e3db..5a4d704c430 100644
--- a/var/spack/repos/builtin/packages/tau/package.py
+++ b/var/spack/repos/builtin/packages/tau/package.py
@@ -89,7 +89,7 @@ class Tau(Package):
     depends_on('libdwarf', when='+libdwarf')
     depends_on('libelf', when='+libdwarf')
     # TAU requires the ELF header support, libiberty and demangle.
-    depends_on('binutils@:2.33.1+libiberty+headers~nls', when='+binutils')
+    depends_on('binutils@:2.33.1+libiberty+headers', when='+binutils')
     depends_on('python@2.7:', when='+python')
     depends_on('libunwind', when='+libunwind')
     depends_on('mpi', when='+mpi', type=('build', 'run', 'link'))

From 6d913ddab7faf9d38447b6cfb62a3fd0133f2632 Mon Sep 17 00:00:00 2001
From: David Pape <davidpape1995@gmail.com>
Date: Mon, 25 May 2020 13:10:12 +0200
Subject: [PATCH 495/802] likwid: fixed failing build on powerpc (#16797)

Fixes #16783
---
 var/spack/repos/builtin/packages/likwid/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/likwid/package.py b/var/spack/repos/builtin/packages/likwid/package.py
index 8a1f39ebfd0..8e89693ce1b 100644
--- a/var/spack/repos/builtin/packages/likwid/package.py
+++ b/var/spack/repos/builtin/packages/likwid/package.py
@@ -29,6 +29,7 @@ class Likwid(Package):
     version('4.3.1', sha256='4b40a96717da54514274d166f9b71928545468091c939c1d74109733279eaeb1')
     version('4.3.0', sha256='86fc5f82c80fcff1a643394627839ec79f1ca2bcfad30000eb7018da592588b4')
 
+    patch('https://github.com/RRZE-HPC/likwid/commit/e0332ace8fe8ca7dcd4b4477a25e37944f173a5c.patch', sha256='c3b8f939a46b425665577ce764d4fba080a23cab5999c53db71655fd54d7e0b1', when='@5.0.1')
     patch('https://github.com/RRZE-HPC/likwid/commit/d2d0ef333b5e0997d7c80fc6ac1a473b5e47d084.patch', sha256='636cbf40669261fdb36379d67253be2b731cfa7b6d610d232767d72fbdf08bc0', when='@4.3.4')
 
     # NOTE: There is no way to use an externally provided hwloc with Likwid.

From 821c729ec00b603271d1118d878899fc546a7186 Mon Sep 17 00:00:00 2001
From: "Tomoki, Karatsu" <49965247+t-karatsu@users.noreply.github.com>
Date: Mon, 25 May 2020 20:12:13 +0900
Subject: [PATCH 496/802] netlib-scalapack: specify MPI's location for
 Fujitsu-MPI. (#16798)

Fujitsu-MPI wrapper commands aren't recognized from 'FindMPI'
function of 'cmake'. If we are using the Fujitsu compiler and Fujitsu MPI,
specify the MPI path information explicitly.
---
 .../repos/builtin/packages/netlib-scalapack/package.py   | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index 75993c47010..2acc06e6bbd 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -82,6 +82,15 @@ def cmake_args(self):
                 "-DCMAKE_Fortran_FLAGS=%s" % self.compiler.fc_pic_flag
             ])
 
+        # Specify Fujitsu-MPI's location
+        if spec.satisfies('%fj') and '^fujitsu-mpi' in spec:
+            options.extend([
+                '-DMPI_C_COMPILER=%s'       % spec['mpi'].mpicc,
+                '-DMPI_CXX_COMPILER=%s'     % spec['mpi'].mpicxx,
+                '-DMPI_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+                '-DMPI_BASE_DIR=%s' % spec['mpi'].prefix
+            ])
+
         return options
 
     @run_after('install')

From 04f60afc0838681d8a70aff918ebfa69254e33ce Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Mon, 25 May 2020 19:16:55 +0800
Subject: [PATCH 497/802] ffsb: added new package at v5.2.1 (#16791)

---
 .../repos/builtin/packages/ffsb/package.py     | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/ffsb/package.py

diff --git a/var/spack/repos/builtin/packages/ffsb/package.py b/var/spack/repos/builtin/packages/ffsb/package.py
new file mode 100644
index 00000000000..5745ccb8214
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ffsb/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ffsb(AutotoolsPackage):
+    """The Flexible Filesystem Benchmark (FFSB) is a cross-platform
+    filesystem performance measurement tool."""
+
+    homepage = "https://sourceforge.net/projects/ffsb/"
+    url      = "https://sourceforge.net/projects/ffsb/files/ffsb/5.2.1/ffsb-5.2.1.tar.gz"
+
+    version('5.2.1', sha256='36ccda8ff04f837e20bb8b2cc9edb8c6fc923fdcdbb8060d9448dc49234b968d')
+    version('5.1.1', sha256='e25aef255d8bfe54f29ac88c7af8237fa5a8c2e1716fdef1946cf0ecd9166d1f')
+    version('5.1',   sha256='4d7da7eba46c824ebdc23b3d32532b006aeb5b6697a3ada314c75785ab25cb97')

From 995714cba52ff9f9efbd12ce438b23467a21213a Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 25 May 2020 13:32:42 +0200
Subject: [PATCH 498/802] glib: added v2.64.3 (#16800)

---
 var/spack/repos/builtin/packages/glib/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py
index 6e009ef1edb..4d648ddb3a4 100644
--- a/var/spack/repos/builtin/packages/glib/package.py
+++ b/var/spack/repos/builtin/packages/glib/package.py
@@ -21,6 +21,7 @@ class Glib(Package):
     homepage = "https://developer.gnome.org/glib/"
     url      = "https://ftp.gnome.org/pub/gnome/sources/glib/2.53/glib-2.53.1.tar.xz"
 
+    version('2.64.3', sha256='fe9cbc97925d14c804935f067a3ad77ef55c0bbe9befe68962318f5a767ceb22')
     version('2.64.2', sha256='9a2f21ed8f13b9303399de13a0252b7cbcede593d26971378ec6cb90e87f2277')
     version('2.64.1', sha256='17967603bcb44b6dbaac47988d80c29a3d28519210b28157c2bd10997595bbc7')
     version('2.62.6', sha256='104fa26fbefae8024ff898330c671ec23ad075c1c0bce45c325c6d5657d58b9c')

From 99d9967b8be0d50b288ce44b552f0534d46e051c Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Mon, 25 May 2020 19:41:08 +0800
Subject: [PATCH 499/802] sqoop: added new package at v1.99.7 (#16786)

---
 .../repos/builtin/packages/sqoop/package.py   | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/sqoop/package.py

diff --git a/var/spack/repos/builtin/packages/sqoop/package.py b/var/spack/repos/builtin/packages/sqoop/package.py
new file mode 100644
index 00000000000..d0fcb22d1e2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sqoop/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Sqoop(Package):
+    """Apache Sqoop is a tool designed for efficiently transferring bulk
+    data between Apache Hadoop and structured datastores such as relational
+    databases."""
+
+    homepage = "http://sqoop.apache.org/"
+    url      = "https://downloads.apache.org/sqoop/1.99.7/sqoop-1.99.7.tar.gz"
+    list_url = "https://downloads.apache.org/sqoop/"
+    list_depth = 1
+
+    version('1.99.7', sha256='caca533554235d9e999435be59a13b5ecae514b3c914ca3b54868fca43a3b74a')
+
+    depends_on('maven', type='build')
+    depends_on('java@8', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mvn = which('mvn')
+        mvn('clean', 'install', '-DskipTests')
+        install_tree('.', prefix)

From 6f85dc66a730a05899c6f0229954c2f20b6d1570 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Mon, 25 May 2020 19:46:42 +0800
Subject: [PATCH 500/802] testdfsio: added new package at v0.0.1 (#16789)

---
 .../builtin/packages/testdfsio/package.py     | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/testdfsio/package.py

diff --git a/var/spack/repos/builtin/packages/testdfsio/package.py b/var/spack/repos/builtin/packages/testdfsio/package.py
new file mode 100644
index 00000000000..890c17cc05c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/testdfsio/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Testdfsio(Package):
+    """A corrected and enhanced version of Apache Hadoop TestDFSIO"""
+
+    homepage = "https://github.com/tthx/testdfsio"
+    url      = "https://github.com/tthx/testdfsio/archive/0.0.1.tar.gz"
+
+    version('0.0.1', sha256='fe8cc47260ffb3e3ac90e0796ebfe73eb4dac64964ab77671e5d32435339dd09')
+
+    depends_on('maven', type='build')
+    depends_on('java@8', type=('build', 'run'))
+    depends_on('hadoop@3.2.1:', type='run')
+
+    def install(self, spec, prefix):
+        mvn = which('mvn')
+        mvn('clean', 'package', '-Dmaven.test.skip=true')
+        install_tree('.', prefix)

From 5df64769e3e35d448b45f1462686de0f2bf740ae Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 25 May 2020 13:48:24 +0200
Subject: [PATCH 501/802] r-matlab: new package at v1.0.2 (#16785)

---
 .../repos/builtin/packages/r-matlab/package.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-matlab/package.py

diff --git a/var/spack/repos/builtin/packages/r-matlab/package.py b/var/spack/repos/builtin/packages/r-matlab/package.py
new file mode 100644
index 00000000000..221f5f7b314
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-matlab/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMatlab(RPackage):
+    """Emulate MATLAB code using R"""
+
+    homepage = "https://cloud.r-project.org/package=matlab"
+    url      = "https://cloud.r-project.org/src/contrib/matlab_1.0.2.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/matlab"
+
+    version('1.0.2', sha256='a23dec736c51ae1864c1a53caac556a2f98e8020138a3b121badb0f5b7984154')
+
+    depends_on('r@2.15:', type=('build', 'run'))

From 8395db361c37c83a776e4639fd79bcc0bea1ae4d Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 25 May 2020 13:51:08 +0200
Subject: [PATCH 502/802] py-flask: added v1.1.2 and v0.12.4 (#16779)

---
 var/spack/repos/builtin/packages/py-flask/package.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-flask/package.py b/var/spack/repos/builtin/packages/py-flask/package.py
index befe5057439..4be2b1e1e15 100644
--- a/var/spack/repos/builtin/packages/py-flask/package.py
+++ b/var/spack/repos/builtin/packages/py-flask/package.py
@@ -12,13 +12,15 @@ class PyFlask(PythonPackage):
     homepage = "https://palletsprojects.com/p/flask/"
     url      = "https://pypi.io/packages/source/F/Flask/Flask-1.1.1.tar.gz"
 
+    version('1.1.2',  sha256='4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060')
     version('1.1.1',  sha256='13f9f196f330c7c2c5d7a5cf91af894110ca0215ac051b5844701f2bfd934d52')
+    version('0.12.4', sha256='2ea22336f6d388b4b242bc3abf8a01244a8aa3e236e7407469ef78c16ba355dd')
     version('0.12.2', sha256='49f44461237b69ecd901cc7ce66feea0319b9158743dd27a2899962ab214dac1')
     version('0.12.1', sha256='9dce4b6bfbb5b062181d3f7da8f727ff70c1156cbb4024351eafd426deb5fb88')
     version('0.11.1', sha256='b4713f2bfb9ebc2966b8a49903ae0d3984781d5c878591cf2f7b484d28756b0e')
 
     depends_on('python@2.7:2.8,3.5:', type=('build', 'run'))
-    depends_on('py-setuptools',         type='build')
+    depends_on('py-setuptools',         type=('build', 'run'))
     depends_on('py-werkzeug@0.15:',     type=('build', 'run'))
     depends_on('py-jinja2@2.10.1:',     type=('build', 'run'))
     depends_on('py-itsdangerous@0.24:', type=('build', 'run'))

From 0c735b8f1ab92c744f6974ffaec5196359183ba0 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 25 May 2020 13:52:13 +0200
Subject: [PATCH 503/802] meson: added v0.54.2 (#16777)

---
 var/spack/repos/builtin/packages/meson/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/meson/package.py b/var/spack/repos/builtin/packages/meson/package.py
index f4c8e56af58..39971c7076c 100644
--- a/var/spack/repos/builtin/packages/meson/package.py
+++ b/var/spack/repos/builtin/packages/meson/package.py
@@ -14,6 +14,9 @@ class Meson(PythonPackage):
     homepage = "http://mesonbuild.com/"
     url      = "https://github.com/mesonbuild/meson/archive/0.49.0.tar.gz"
 
+    maintainers = ['michaelkuhn']
+
+    version('0.54.2', sha256='85cafdc70ae7d1d9d506e7356b917c649c4df2077bd6a0382db37648aa4ecbdb')
     version('0.54.1', sha256='854e8b94ab36e5aece813d2b2aee8a639bd52201dfea50890722ac9128e2f59e')
     version('0.54.0', sha256='95efdbaa7cb3e915ab9a7b26b1412475398fdc3e834842a780f1646c7764f2d9')
     version('0.53.2', sha256='eab4f5d5dde12d002b7ddd958a9a0658589b63622b6cea2715e0235b95917888')

From 232cdb85a5fb97961dde44f9c27a5361407737ab Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 25 May 2020 13:59:47 +0200
Subject: [PATCH 504/802] python: added v3.8.3 (#16775)

---
 var/spack/repos/builtin/packages/python/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index aac98d11ade..7a269f8a1d6 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -31,6 +31,7 @@ class Python(AutotoolsPackage):
 
     maintainers = ['adamjstewart']
 
+    version('3.8.3',  sha256='6af6d4d2e010f9655518d0fc6738c7ff7069f10a4d2fbd55509e467f092a8b90')
     version('3.8.2',  sha256='e634a7a74776c2b89516b2e013dda1728c89c8149b9863b8cea21946daf9d561')
     version('3.8.1',  sha256='c7cfa39a43b994621b245e029769e9126caa2a93571cee2e743b213cceac35fb')
     version('3.8.0',  sha256='f1069ad3cae8e7ec467aa98a6565a62a48ef196cb8f1455a245a08db5e1792df')

From d0e4414bb66805b4526c2320080eed583e32c5b5 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 25 May 2020 14:22:51 +0200
Subject: [PATCH 505/802] libunwind: fix build with gcc@10: (#16782)

---
 var/spack/repos/builtin/packages/libunwind/package.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/libunwind/package.py b/var/spack/repos/builtin/packages/libunwind/package.py
index 1a4ae5524c5..dcabc86ec55 100644
--- a/var/spack/repos/builtin/packages/libunwind/package.py
+++ b/var/spack/repos/builtin/packages/libunwind/package.py
@@ -47,7 +47,15 @@ class Libunwind(AutotoolsPackage):
 
     provides('unwind')
 
-    flag_handler = AutotoolsPackage.build_system_flags
+    def flag_handler(self, name, flags):
+        wrapper_flags = None
+
+        if name == 'cflags':
+            # https://github.com/libunwind/libunwind/pull/166
+            if self.spec.satisfies('@:1.4 %gcc@10:'):
+                wrapper_flags = ['-fcommon']
+
+        return (wrapper_flags, None, flags)
 
     def configure_args(self):
         spec = self.spec

From 9f2fc521659c3ea059e39c94a8aa43acabbb6435 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 25 May 2020 14:23:41 +0200
Subject: [PATCH 506/802] py-pygments: added v2.6.1 (#16776)

---
 var/spack/repos/builtin/packages/py-pygments/package.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-pygments/package.py b/var/spack/repos/builtin/packages/py-pygments/package.py
index c5da704ac0d..87476c64d64 100644
--- a/var/spack/repos/builtin/packages/py-pygments/package.py
+++ b/var/spack/repos/builtin/packages/py-pygments/package.py
@@ -17,6 +17,7 @@ class PyPygments(PythonPackage):
         'pygments.lexers', 'pygments.styles'
     ]
 
+    version('2.6.1', sha256='647344a061c249a3b74e230c739f434d7ea4d8b1d5f3721bc0f3558049b38f44')
     version('2.4.2', sha256='881c4c157e45f30af185c1ffe8d549d48ac9127433f2c380c24b84572ad66297')
     version('2.3.1', sha256='5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a')
     version('2.2.0', sha256='dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc')
@@ -24,8 +25,9 @@ class PyPygments(PythonPackage):
     version('2.0.1', sha256='5e039e1d40d232981ed58914b6d1ac2e453a7e83ddea22ef9f3eeadd01de45cb')
     version('2.0.2', sha256='7320919084e6dac8f4540638a46447a3bd730fca172afc17d2c03eed22cf4f51')
 
-    depends_on('python@2.7:2.8,3.5:', type=('build', 'run'))
-    depends_on('py-setuptools', type='build')
+    depends_on('python@2.7:2.8,3.5:', type=('build', 'run'), when='@:2.5')
+    depends_on('python@3.5:', type=('build', 'run'), when='@2.6:')
+    depends_on('py-setuptools', type=('build', 'run'))
 
     def test(self):
         # Unit tests require sphinx, but that creates a circular dependency

From f370bc0fa2c1b4e324a431899c0526676c8bccb8 Mon Sep 17 00:00:00 2001
From: "Mark W. Krentel" <krentel@rice.edu>
Date: Mon, 25 May 2020 07:31:16 -0500
Subject: [PATCH 507/802] libmonitor: added v2019.05.31 (#16774)

---
 var/spack/repos/builtin/packages/libmonitor/package.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/libmonitor/package.py b/var/spack/repos/builtin/packages/libmonitor/package.py
index 49509fbe36c..5a199ee333a 100644
--- a/var/spack/repos/builtin/packages/libmonitor/package.py
+++ b/var/spack/repos/builtin/packages/libmonitor/package.py
@@ -13,10 +13,11 @@ class Libmonitor(AutotoolsPackage):
 
     homepage = "https://github.com/HPCToolkit/libmonitor"
     git      = "https://github.com/HPCToolkit/libmonitor.git"
+    maintainers = ['mwkrentel']
 
     version('master', branch='master')
-    version('2018.07.18', commit='d28cc1d3c08c02013a68a022a57a6ac73db88166',
-            preferred=True)
+    version('2019.05.31', commit='c9767087d52e58a719aa7f149136b101e499db44')
+    version('2018.07.18', commit='d28cc1d3c08c02013a68a022a57a6ac73db88166')
     version('2013.02.18', commit='4f2311e413fd90583263d6f20453bbe552ccfef3')
 
     # Configure for Rice HPCToolkit.

From 5a335e49858eb64b392ff0dd97d9d00b85776b6d Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 25 May 2020 14:33:41 +0200
Subject: [PATCH 508/802] py-pygdbmi: added v0.9.0.3 (#16778)

---
 var/spack/repos/builtin/packages/py-pygdbmi/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-pygdbmi/package.py b/var/spack/repos/builtin/packages/py-pygdbmi/package.py
index 98f45a564df..8bf181f4a7d 100644
--- a/var/spack/repos/builtin/packages/py-pygdbmi/package.py
+++ b/var/spack/repos/builtin/packages/py-pygdbmi/package.py
@@ -12,6 +12,10 @@ class PyPygdbmi(PythonPackage):
     homepage = "https://github.com/cs01/pygdbmi"
     url      = "https://pypi.io/packages/source/p/pygdbmi/pygdbmi-0.8.2.0.tar.gz"
 
+    version('0.9.0.3', sha256='5bdf2f072e8f2f6471f19f8dcd87d6425c5d8069d47c0a5ffe8d0eff48cb171e')
     version('0.8.2.0', sha256='47cece65808ca42edf6966ac48e2aedca7ae1c675c4d2f0d001c7f3a7fa245fe')
 
+    depends_on('python@3.5:', type=('build', 'run'), when='@0.9.0.3:')
+    depends_on('python@2.7:2.8,3.4:3.6', type=('build', 'run'), when='@0.9.0.0:0.9.0.2')
+    depends_on('python@2.7:2.8,3.3:3.6', type=('build', 'run'), when='@:0.8.4.0')
     depends_on('py-setuptools', type='build')

From 30fb364452596c7083385ca2d10da8e0061f9540 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 25 May 2020 14:34:26 +0200
Subject: [PATCH 509/802] py-gdbgui: added v0.13.2.0 (#16781)

---
 .../builtin/packages/py-gdbgui/package.py      | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-gdbgui/package.py b/var/spack/repos/builtin/packages/py-gdbgui/package.py
index 272d375cd33..551e0ef2068 100644
--- a/var/spack/repos/builtin/packages/py-gdbgui/package.py
+++ b/var/spack/repos/builtin/packages/py-gdbgui/package.py
@@ -12,13 +12,15 @@ class PyGdbgui(PythonPackage):
     homepage = "https://gdbgui.com"
     url      = "https://pypi.io/packages/source/g/gdbgui/gdbgui-0.11.2.1.tar.gz"
 
+    version('0.13.2.0', sha256='80e347a08b8cc630ab9f68482a1ed92c844fbfde46dc21fd39f3e6ef14b72e54')
     version('0.11.2.1', sha256='280945a37414c31a798f68f70c1bffbedd12dfb0ce77418357e7d42b667491c7')
 
-    depends_on('py-setuptools',             type=('build', 'run'))
-    depends_on('py-flask@0.12.2:',          type=('build', 'run'))
-    depends_on('py-flask-compress@1.4.0:',  type=('build', 'run'))
-    depends_on('py-flask-socketio@2.9.3:',  type=('build', 'run'))
-    depends_on('py-gevent@1.2.2:',          type=('build', 'run'))
-    depends_on('py-pygdbmi@0.8.2.0:',       type=('build', 'run'))
-    depends_on('py-pygments@2.2.0:',        type=('build', 'run'))
-    depends_on('gdb',                       type='run')
+    depends_on('py-setuptools',                  type=('build', 'run'))
+    depends_on('py-flask@0.12.2:0.99.0',         type=('build', 'run'))
+    depends_on('py-flask-compress@1.4.0:1.99.0', type=('build', 'run'))
+    depends_on('py-flask-socketio@2.9.3:2.99.0', type=('build', 'run'))
+    depends_on('py-gevent@1.2.2:1.99.0',         type=('build', 'run'))
+    depends_on('py-pygdbmi@0.9.0.0:0.99.0.0',    type=('build', 'run'), when='@0.13.1.1:')
+    depends_on('py-pygdbmi@0.8.2.0:0.8.99.0',    type=('build', 'run'), when='@:0.13.0.0')
+    depends_on('py-pygments@2.2.0:2.99.0',       type=('build', 'run'))
+    depends_on('gdb',                            type='run')

From a3dc9cf848088360f8f9bd02e08b991b2ff93209 Mon Sep 17 00:00:00 2001
From: Stephen Hudson <shudson@anl.gov>
Date: Mon, 25 May 2020 07:35:44 -0500
Subject: [PATCH 510/802] libensemble: added v0.7.0 (#16773)

---
 var/spack/repos/builtin/packages/py-libensemble/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-libensemble/package.py b/var/spack/repos/builtin/packages/py-libensemble/package.py
index 67fc1bbc185..d69f1dde086 100644
--- a/var/spack/repos/builtin/packages/py-libensemble/package.py
+++ b/var/spack/repos/builtin/packages/py-libensemble/package.py
@@ -11,10 +11,11 @@ class PyLibensemble(PythonPackage):
     """Library for managing ensemble-like collections of computations."""
 
     homepage = "https://libensemble.readthedocs.io"
-    url      = "https://pypi.io/packages/source/l/libensemble/libensemble-0.6.0.tar.gz"
+    url      = "https://pypi.io/packages/source/l/libensemble/libensemble-0.7.0.tar.gz"
     git      = "https://github.com/Libensemble/libensemble.git"
 
     version('develop', branch='develop')
+    version('0.7.0', sha256='4c3c16ef3d4750b7a54198fae5d7ae402c5f5411ae85189da41afd20e20027dc')
     version('0.6.0', sha256='3f6a926d3868da53835ed93fc2e2a047b368dacb648c7608ee3a66debcee4d38')
     version('0.5.2', sha256='3e36c29a4a2adc0984ecfcc998cb5bb8a2cdfbe7a1ae92f7b35b06e41d21b889')
     version('0.5.1', sha256='522e0cc086a3ed75a101b704c0fe01eae07f2684bd8d6da7bdfe9371d3187362')

From 768fa6bc531379519b8bbf0222367083a37c7dd3 Mon Sep 17 00:00:00 2001
From: Peter Scheibel <scheibel1@llnl.gov>
Date: Mon, 25 May 2020 06:08:47 -0700
Subject: [PATCH 511/802] bugfix: schema errors without line numbers (#16765)

* account for schema validation errors where the associated instance doesn't have a line number

* fix unrelated flake error (but it must be fixed because this PR touches this file and the flake rules have been updated since the last edit to this file)
---
 lib/spack/spack/environment.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index 43e91073e3c..8d3b1438e12 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -406,8 +406,12 @@ def validate(data, filename=None):
     try:
         spack.schema.Validator(spack.schema.env.schema).validate(validate_data)
     except jsonschema.ValidationError as e:
+        if hasattr(e.instance, 'lc'):
+            line_number = e.instance.lc.line + 1
+        else:
+            line_number = None
         raise spack.config.ConfigFormatError(
-            e, data, filename, e.instance.lc.line + 1)
+            e, data, filename, line_number)
     return validate_data
 
 
@@ -1445,9 +1449,9 @@ def write(self, regenerate_views=True):
                 # The primary list is handled differently
                 continue
 
-            active_yaml_lists = [l for l in yaml_dict.get('definitions', [])
-                                 if name in l and
-                                 _eval_conditional(l.get('when', 'True'))]
+            active_yaml_lists = [x for x in yaml_dict.get('definitions', [])
+                                 if name in x and
+                                 _eval_conditional(x.get('when', 'True'))]
 
             # Remove any specs in yaml that are not in internal representation
             for ayl in active_yaml_lists:

From 17e4a7219114c743ea7cf34ef8b6f139b3eb2f92 Mon Sep 17 00:00:00 2001
From: Tom Payerle <payerle@umd.edu>
Date: Mon, 25 May 2020 09:15:30 -0400
Subject: [PATCH 512/802] netcdf-cxx4: remove erroneous variants (#16762)

fixes #16725

The dap, jna, pnetcdf, netcdf4, and ncgen4 variants added in #16047
are _not_ supported by the configure script for netcdf-cxx4 package
(These appear to be configure args for netcdf-c package).
---
 .../builtin/packages/netcdf-cxx4/package.py   | 30 -------------------
 1 file changed, 30 deletions(-)

diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
index 3847cc48dd4..f49c5d8ccea 100644
--- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
@@ -24,12 +24,7 @@ class NetcdfCxx4(AutotoolsPackage):
     variant('static', default=True, description='Enable building static libraries')
     variant('shared', default=True, description='Enable shared library')
     variant('pic', default=True, description='Produce position-independent code (for shared libs)')
-    variant('dap', default=False, description='Enable DAP support')
-    variant('jna', default=False, description='Enable JNA support')
     variant('doxygen', default=True, description='Enable doxygen docs')
-    variant('ncgen4', default=True, description='Enable generating netcdf-4 data')
-    variant('pnetcdf', default=True, description='Enable parallel-netcdf')
-    variant('netcdf4', default=False, description='Enable netcdf-4 data structure')
 
     depends_on('netcdf-c')
 
@@ -75,31 +70,6 @@ def configure_args(self):
         else:
             config_args.append('--without-pic')
 
-        if '+dap' in self.spec:
-            config_args.append('--enable-dap')
-        else:
-            config_args.append('--disable-dap')
-
-        if '+jna' in self.spec:
-            config_args.append('--enable-jna')
-        else:
-            config_args.append('--disable-jna')
-
-        if '+pnetcdf' in self.spec:
-            config_args.append('--enable-pnetcdf')
-        else:
-            config_args.append('--disable-pnetcdf')
-
-        if '+netcdf4' in self.spec:
-            config_args.append('--enable-netcdf-4')
-        else:
-            config_args.append('--disable-netcdf-4')
-
-        if '+ncgen4' in self.spec:
-            config_args.append('--enable-ncgen4')
-        else:
-            config_args.append('--disable-ncgen4')
-
         if '+doxygen' in self.spec:
             config_args.append('--enable-doxygen')
         else:

From c4031f04551264d627a3cc6a30b25e005cf1f6b5 Mon Sep 17 00:00:00 2001
From: Stephen Herbein <SteVwonder@users.noreply.github.com>
Date: Mon, 25 May 2020 06:18:47 -0700
Subject: [PATCH 513/802] lua: fix compilation on Cray (#16713)

Problem: when calling `static_to_shared_library` on the `cray` arch, it
produces a non-sensical compiler command with no input files.  For
example, when installing lua@5.2.4, it produced:
'gcc -lm -ldl -o /big-long-spack-path/liblua.so.5.2.4'

Solution: do the same thing on `cray` that is done for `linux`
---
 lib/spack/spack/build_environment.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 3510ae8ac8d..8beedf6c972 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -538,7 +538,7 @@ def _static_to_shared_library(arch, compiler, static_lib, shared_lib=None,
 
     # TODO: Compiler arguments should not be hardcoded but provided by
     #       the different compiler classes.
-    if 'linux' in arch:
+    if 'linux' in arch or 'cray' in arch:
         soname = os.path.basename(shared_lib)
 
         if compat_version:

From f12ae1bcd08db6489cdbf63390fd7cedcf5bf3f3 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 25 May 2020 18:49:35 +0200
Subject: [PATCH 514/802] Fix typo for allow_sgid (#16806)

fixes #14425

The config: prefix should be included in the actual option name and
makes it impossible to change this option.
---
 etc/spack/defaults/config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/etc/spack/defaults/config.yaml b/etc/spack/defaults/config.yaml
index 4e4b48296c5..a5727874eac 100644
--- a/etc/spack/defaults/config.yaml
+++ b/etc/spack/defaults/config.yaml
@@ -160,4 +160,4 @@ config:
 
   # Set to 'false' to allow installation on filesystems that doesn't allow setgid bit
   # manipulation by unprivileged user (e.g. AFS)
-  config:allow_sgid: true
+  allow_sgid: true

From e90f51a8026c0eb74383956b3c6cdf92fad84913 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 25 May 2020 20:19:51 +0200
Subject: [PATCH 515/802] r-spatialeco: New package (#16744)

---
 .../builtin/packages/r-spatialeco/package.py  | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-spatialeco/package.py

diff --git a/var/spack/repos/builtin/packages/r-spatialeco/package.py b/var/spack/repos/builtin/packages/r-spatialeco/package.py
new file mode 100644
index 00000000000..bf93b15a204
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-spatialeco/package.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSpatialeco(RPackage):
+    """Utilities to support spatial data manipulation, query,
+       sampling and modelling.
+    """
+
+    homepage = "https://cloud.r-project.org/package=spatialEco"
+    url      = "https://cloud.r-project.org/src/contrib/spatialEco_1.3-1.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/spatialEco"
+
+    version('1.3-1', sha256='ff12e26cc1bbf7934fbf712c99765d96ce6817e8055faa15a26d9ebade4bbf1c')
+    version('1.3-0', sha256='cfa09673cb3bbed30b243082fc2d63ac09f48b9f072a18d32b95c2c29979d1d0')
+
+    depends_on('r@3.6:', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-exactextractr', type=('build', 'run'))
+    depends_on('r-spatstat', type=('build', 'run'))
+    depends_on('r-rcurl', type=('build', 'run'))
+    depends_on('r-rms', type=('build', 'run'))
+    depends_on('r-yaimpute', type=('build', 'run'))
+    depends_on('r-spatialpack@0.3:', type=('build', 'run'))
+    depends_on('r-mgcv', type=('build', 'run'))
+    depends_on('r-envstats', type=('build', 'run'))
+    depends_on('r-sp', type=('build', 'run'))
+    depends_on('r-raster', type=('build', 'run'))
+    depends_on('r-sf', type=('build', 'run'))
+    depends_on('r-cluster', type=('build', 'run'))
+    depends_on('r-spdep', type=('build', 'run'))
+    depends_on('r-readr', type=('build', 'run'))
+    depends_on('r-rgeos', type=('build', 'run'))
+    depends_on('r-rann', type=('build', 'run'))
+    depends_on('r-mass', type=('build', 'run'))
+    depends_on('r-maptools', type=('build', 'run'))

From 3c36a7caabcdd822ab312713a67cb5242d58d643 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Mon, 25 May 2020 22:18:40 +0200
Subject: [PATCH 516/802] py-moreitertools: added v7.0.0 (#16802)

---
 var/spack/repos/builtin/packages/py-more-itertools/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-more-itertools/package.py b/var/spack/repos/builtin/packages/py-more-itertools/package.py
index 7d1386402a9..dba18e66b3f 100644
--- a/var/spack/repos/builtin/packages/py-more-itertools/package.py
+++ b/var/spack/repos/builtin/packages/py-more-itertools/package.py
@@ -15,6 +15,7 @@ class PyMoreItertools(PythonPackage):
     import_modules = ['more_itertools', 'more_itertools.tests']
 
     version('7.2.0', sha256='409cd48d4db7052af495b09dec721011634af3753ae1ef92d2b32f73a745f832')
+    version('7.0.0', sha256='c3e4748ba1aad8dba30a4886b0b1a2004f9a863837b8654e7059eebf727afa5a')
     version('5.0.0', sha256='38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4')
     version('4.3.0', sha256='c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e')
     version('4.1.0', sha256='c9ce7eccdcb901a2c75d326ea134e0886abfbea5f93e91cc95de9507c0816c44')

From 15d2883abecec3433d2b3daa61a4edbb730d8451 Mon Sep 17 00:00:00 2001
From: Sergey Kosukhin <sergey.kosukhin@mpimet.mpg.de>
Date: Tue, 26 May 2020 02:14:47 +0200
Subject: [PATCH 517/802] openmpi: get rid of implicit system dependencies
 (#16758)

* openmpi: get rid of implicit system dependencies

* Python 2 compatibility.

* Rename pbspro to openpbs and revert packages.yaml.

* Remove virtual package 'sendmail'.
---
 .../repos/builtin/packages/libical/package.py |  22 ++
 .../repos/builtin/packages/lsf/package.py     |   9 +-
 .../repos/builtin/packages/mxm/package.py     |  30 +++
 .../repos/builtin/packages/openmpi/package.py |  98 ++------
 .../builtin/packages/openpbs/install.patch    |  52 ++++
 .../builtin/packages/openpbs/no_crypt.patch   |  21 ++
 .../repos/builtin/packages/openpbs/package.py |  94 +++++++
 .../builtin/packages/openpbs/python.patch     |  11 +
 .../builtin/packages/openpbs/with_lib.patch   | 231 ++++++++++++++++++
 .../builtin/packages/ssmtp/install.patch      |  11 +
 .../repos/builtin/packages/ssmtp/package.py   |  58 +++++
 11 files changed, 553 insertions(+), 84 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/libical/package.py
 create mode 100644 var/spack/repos/builtin/packages/mxm/package.py
 create mode 100644 var/spack/repos/builtin/packages/openpbs/install.patch
 create mode 100644 var/spack/repos/builtin/packages/openpbs/no_crypt.patch
 create mode 100644 var/spack/repos/builtin/packages/openpbs/package.py
 create mode 100644 var/spack/repos/builtin/packages/openpbs/python.patch
 create mode 100644 var/spack/repos/builtin/packages/openpbs/with_lib.patch
 create mode 100644 var/spack/repos/builtin/packages/ssmtp/install.patch
 create mode 100644 var/spack/repos/builtin/packages/ssmtp/package.py

diff --git a/var/spack/repos/builtin/packages/libical/package.py b/var/spack/repos/builtin/packages/libical/package.py
new file mode 100644
index 00000000000..6116b0b6497
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libical/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libical(CMakePackage):
+    """Libical - an implementation of iCalendar protocols and data formats."""
+
+    homepage = "https://github.com/libical/libical"
+    url = "https://github.com/libical/libical/archive/v3.0.8.tar.gz"
+
+    version('3.0.8', sha256='09fecacaf75ba5a242159e3a9758a5446b5ce4d0ab684f98a7040864e1d1286f')
+
+    depends_on('cmake@3.11.0:', type='build')
+    depends_on('perl', type='build')
+    depends_on('icu4c')
+
+    def cmake_args(self):
+        return ['-DENABLE_GTK_DOC=OFF']
diff --git a/var/spack/repos/builtin/packages/lsf/package.py b/var/spack/repos/builtin/packages/lsf/package.py
index ccb04d01acc..5c92693c4d4 100644
--- a/var/spack/repos/builtin/packages/lsf/package.py
+++ b/var/spack/repos/builtin/packages/lsf/package.py
@@ -10,7 +10,10 @@
 class Lsf(Package):
     """IBM Platform LSF is a batch scheduler for HPC environments"""
 
-    homepage = "https://www.ibm.com/marketplace/hpc-workload-management"
+    homepage = "https://www.ibm.com/products/hpc-workload-management"
+    has_code = False
+
+    version('10.1')
 
     # LSF needs to be added as an external package to SPACK. For this, the
     # config file packages.yaml needs to be adjusted:
@@ -21,4 +24,6 @@ class Lsf(Package):
     #     buildable: False
 
     def install(self, spec, prefix):
-        raise InstallError('LSF is not installable; it is vendor supplied')
+        raise InstallError(
+            self.spec.format('{name} is not installable, you need to specify '
+                             'it as an external package in packages.yaml'))
diff --git a/var/spack/repos/builtin/packages/mxm/package.py b/var/spack/repos/builtin/packages/mxm/package.py
new file mode 100644
index 00000000000..897f1c24b3e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mxm/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Mxm(Package):
+    """Mellanox Messaging Accelerator (MXM) provides enhancements to parallel
+    communication libraries by fully utilizing the underlying networking
+    infrastructure provided by Mellanox HCA/switch hardware."""
+
+    homepage = 'https://www.mellanox.com/products/mxm'
+    has_code = False
+
+    version('3.6.3104')
+
+    # MXM needs to be added as an external package to SPACK. For this, the
+    # config file packages.yaml needs to be adjusted:
+    #   mxm:
+    #     version: [3.6.3104]
+    #     paths:
+    #       mxm@3.6.3104: /opt/mellanox/mxm (path to your MXM installation)
+    #     buildable: False
+
+    def install(self, spec, prefix):
+        raise InstallError(
+            self.spec.format('{name} is not installable, you need to specify '
+                             'it as an external package in packages.yaml'))
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 700711c55e0..183447236fc 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -9,54 +9,6 @@
 import llnl.util.tty as tty
 
 
-def _verbs_dir():
-    """Try to find the directory where the OpenFabrics verbs package is
-    installed. Return None if not found.
-    """
-    try:
-        # Try to locate Verbs by looking for a utility in the path
-        ibv_devices = which("ibv_devices")
-        # Run it (silently) to ensure it works
-        ibv_devices(output=str, error=str)
-        # Get path to executable
-        path = ibv_devices.exe[0]
-        # Remove executable name and "bin" directory
-        path = os.path.dirname(path)
-        path = os.path.dirname(path)
-        # There's usually no "/include" on Unix; use "/usr/include" instead
-        if path == "/":
-            path = "/usr"
-        return path
-    except TypeError:
-        return None
-    except ProcessError:
-        return None
-
-
-def _mxm_dir():
-    """Look for default directory where the Mellanox package is
-    installed. Return None if not found.
-    """
-    # Only using default directory; make this more flexible in the future
-    path = "/opt/mellanox/mxm"
-    if os.path.isdir(path):
-        return path
-    else:
-        return None
-
-
-def _tm_dir():
-    """Look for default directory where the PBS/TM package is
-    installed. Return None if not found.
-    """
-    # /opt/pbs from PBS 18+; make this more flexible in the future
-    paths_list = ("/opt/pbs", )
-    for path in paths_list:
-        if os.path.isdir(path) and os.path.isfile(path + "/include/tm.h"):
-            return path
-    return None
-
-
 class Openmpi(AutotoolsPackage):
     """An open source Message Passing Interface implementation.
 
@@ -276,6 +228,8 @@ class Openmpi(AutotoolsPackage):
     depends_on('m4',       type='build', when='@develop')
     depends_on('perl',     type='build', when='@develop')
 
+    depends_on('pkgconfig', type='build')
+
     depends_on('hwloc')
     # ompi@:3.0.0 doesn't support newer hwloc releases:
     # "configure: error: OMPI does not currently support hwloc v2 API"
@@ -288,13 +242,18 @@ class Openmpi(AutotoolsPackage):
     depends_on('sqlite', when='+sqlite3@:1.11')
     depends_on('zlib', when='@3.0.0:')
     depends_on('valgrind~mpi', when='+memchecker')
+
     depends_on('ucx', when='fabrics=ucx')
     depends_on('ucx +thread_multiple', when='fabrics=ucx +thread_multiple')
     depends_on('ucx +thread_multiple', when='@3.0.0: fabrics=ucx')
     depends_on('libfabric', when='fabrics=libfabric')
+    depends_on('mxm', when='fabrics=mxm')
+    depends_on('binutils+libiberty', when='fabrics=mxm')
+    depends_on('rdma-core', when='fabrics=verbs')
+
     depends_on('slurm', when='schedulers=slurm')
     depends_on('lsf', when='schedulers=lsf')
-    depends_on('binutils+libiberty', when='fabrics=mxm')
+    depends_on('openpbs', when='schedulers=tm')
 
     conflicts('+cuda', when='@:1.6')  # CUDA support was added in 1.7
     conflicts('fabrics=psm2', when='@:1.8')  # PSM2 support was added in 1.10.0
@@ -359,43 +318,17 @@ def setup_dependent_package(self, module, dependent_spec):
         ]
 
     def with_or_without_verbs(self, activated):
-        # Up through version 1.6, this option was previously named
-        # --with-openib
-        opt = 'openib'
-        # In version 1.7, it was renamed to be --with-verbs
-        if self.spec.satisfies('@1.7:'):
-            opt = 'verbs'
-        # If the option has not been activated return
-        # --without-openib or --without-verbs
+        # Up through version 1.6, this option was named --with-openib.
+        # In version 1.7, it was renamed to be --with-verbs.
+        opt = 'verbs' if self.spec.satisfies('@1.7:') else 'openib'
         if not activated:
             return '--without-{0}'.format(opt)
-        line = '--with-{0}'.format(opt)
-        path = _verbs_dir()
-        if (path is not None) and (path not in ('/usr', '/usr/local')):
-            line += '={0}'.format(path)
-        return line
-
-    def with_or_without_mxm(self, activated):
-        opt = 'mxm'
-        # If the option has not been activated return --without-mxm
-        if not activated:
-            return '--without-{0}'.format(opt)
-        line = '--with-{0}'.format(opt)
-        path = _mxm_dir()
-        if path is not None:
-            line += '={0}'.format(path)
-        return line
+        return '--with-{0}={1}'.format(opt, self.spec['rdma-core'].prefix)
 
     def with_or_without_tm(self, activated):
-        opt = 'tm'
-        # If the option has not been activated return --without-tm
         if not activated:
-            return '--without-{0}'.format(opt)
-        line = '--with-{0}'.format(opt)
-        path = _tm_dir()
-        if path is not None:
-            line += '={0}'.format(path)
-        return line
+            return '--without-tm'
+        return '--with-tm={0}'.format(self.spec['openpbs'].prefix)
 
     @run_before('autoreconf')
     def die_without_fortran(self):
@@ -471,7 +404,8 @@ def configure_args(self):
 
         # Fabrics
         if 'fabrics=auto' not in spec:
-            config_args.extend(self.with_or_without('fabrics'))
+            config_args.extend(self.with_or_without('fabrics',
+                                                    activation_value='prefix'))
         # The wrappers fail to automatically link libfabric. This will cause
         # undefined references unless we add the appropriate flags.
         if 'fabrics=libfabric' in spec:
diff --git a/var/spack/repos/builtin/packages/openpbs/install.patch b/var/spack/repos/builtin/packages/openpbs/install.patch
new file mode 100644
index 00000000000..8e97fd497c4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openpbs/install.patch
@@ -0,0 +1,52 @@
+--- a/m4/pbs_systemd_unitdir.m4
++++ b/m4/pbs_systemd_unitdir.m4
+@@ -39,14 +39,19 @@
+ AC_DEFUN([PBS_AC_SYSTEMD_UNITDIR],
+ [
+   AC_MSG_CHECKING([system/machine type for systemd unit dir])
+-  systemd_dir="/usr/lib/systemd/system"
+-  AS_IF([test -r "/etc/os-release"],
+-    [system_type=$( cat /etc/os-release | awk -F'=' '/^ID=/' | cut -d "=" -f 2 )
+-      AS_IF([test "x$system_type" = "xubuntu" -o "x$system_type" = "xdebian"],
+-      [systemd_dir="/lib/systemd/system"])
+-    ]
+-  )
+-  _unitdir=$systemd_dir
++dnl  systemd_dir="/usr/lib/systemd/system"
++dnl  AS_IF([test -r "/etc/os-release"],
++dnl    [system_type=$( cat /etc/os-release | awk -F'=' '/^ID=/' | cut -d "=" -f 2 )
++dnl      AS_IF([test "x$system_type" = "xubuntu" -o "x$system_type" = "xdebian"],
++dnl      [systemd_dir="/lib/systemd/system"])
++dnl    ]
++dnl  )
++dnl  _unitdir=$systemd_dir
++  _save_prefix=$prefix; _save_exec_prefix=$exec_prefix
++  test "x$prefix" = xNONE && prefix=$ac_default_prefix
++  test "x$exec_prefix" = xNONE && exec_prefix=$prefix
++  eval "_unitdir=$libdir/systemd/system"
++  prefix=$_save_prefix; exec_prefix=$_save_exec_prefix
+   AC_MSG_RESULT([$_unitdir])
+   AC_SUBST([_unitdir])
+ ])
+--- a/src/cmds/scripts/Makefile.am
++++ b/src/cmds/scripts/Makefile.am
+@@ -67,7 +67,7 @@ dist_pythonlib_PYTHON = \
+ 	pbs_bootcheck.py \
+ 	pbs_topologyinfo.py
+ 
+-sysprofiledir = /etc/profile.d
++sysprofiledir = $(sysconfdir)
+ 
+ dist_sysprofile_DATA = \
+ 	pbs.csh \
+--- a/test/fw/Makefile.am
++++ b/test/fw/Makefile.am
+@@ -59,7 +59,7 @@ ptlpkg_pylib_pluginsdir = $(ptlpkg_pylib_utilsdir)/plugins
+ 
+ dist_ptlpkg_pylib_plugins_PYTHON = $(wildcard $(srcdir)/ptl/utils/plugins/*.py)
+ 
+-sysprofiledir = /etc/profile.d
++sysprofiledir = $(sysconfdir)
+ 
+ dist_sysprofile_DATA = \
+ 	ptl.csh \
diff --git a/var/spack/repos/builtin/packages/openpbs/no_crypt.patch b/var/spack/repos/builtin/packages/openpbs/no_crypt.patch
new file mode 100644
index 00000000000..b91683478d2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openpbs/no_crypt.patch
@@ -0,0 +1,21 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -83,10 +83,6 @@ AC_CHECK_LIB([c], [ruserok],
+   [],
+   AC_CHECK_LIB(socket, ruserok)
+ )
+-AC_CHECK_LIB([c], [crypt],
+-  [],
+-  AC_CHECK_LIB(crypt, crypt)
+-)
+ AC_CHECK_LIB([c], [posix_openpt],
+   AC_DEFINE([HAVE_POSIX_OPENPT], [], [Defined whe posix_openpt is available])
+ )
+@@ -125,7 +121,6 @@ AC_CHECK_HEADERS([ \
+ 	arpa/inet.h \
+ 	asm/types.h \
+ 	assert.h \
+-	crypt.h \
+ 	ctype.h \
+ 	dirent.h \
+ 	dlfcn.h \
diff --git a/var/spack/repos/builtin/packages/openpbs/package.py b/var/spack/repos/builtin/packages/openpbs/package.py
new file mode 100644
index 00000000000..695e5ad595b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openpbs/package.py
@@ -0,0 +1,94 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import llnl.util.tty as tty
+from spack import *
+
+
+class Openpbs(AutotoolsPackage):
+    """PBS Professional software optimizes job scheduling and workload
+    management in high-performance computing (HPC) environments - clusters,
+    clouds, and supercomputers - improving system efficiency and people's
+    productivity."""
+
+    # TODO: update the description and the homepage url once the renaming is
+    #  finished: http://community.pbspro.org/t/openpbs-and-version-20-0/2075
+
+    homepage = "https://www.pbspro.org"
+    url = "https://github.com/openpbs/openpbs/archive/v19.1.3.tar.gz"
+
+    version('19.1.3', sha256='6e9d2614f839ff3d91d0ace3de04752b7c075da60c72fe6def76437aa05c9857')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('m4', type='build')
+    depends_on('flex', type='build')
+    depends_on('bison', type='build')
+    depends_on('perl', type='build')
+
+    depends_on('ssmtp', type=('build', 'run'))
+    depends_on('xauth', type=('build', 'run'))
+
+    depends_on('python@2.6:2.7', type=('build', 'link', 'run'))
+
+    depends_on('libx11')
+    depends_on('libice')
+    depends_on('libsm')
+    depends_on('openssl')
+    depends_on('postgresql')
+    depends_on('expat')
+    depends_on('libedit')
+    depends_on('ncurses')
+    depends_on('hwloc@:1')
+    depends_on('libical')
+    depends_on('swig')
+    depends_on('tcl')
+    depends_on('tk')
+    depends_on('zlib')
+
+    # The configure script cannot properly handle dependencies in non-system
+    # directories.
+    patch('with_lib.patch')
+
+    # The package does not really depend on libcrypt but links to it. We
+    # eliminate this redundant dependency to avoid linking to a system library.
+    patch('no_crypt.patch')
+
+    # Fix installation directories.
+    patch('install.patch')
+
+    # Link to the dynamic library of Python instead of the static one.
+    patch('python.patch')
+
+    def autoreconf(self, spec, prefix):
+        Executable('./autogen.sh')()
+
+    def configure_args(self):
+        return [
+            '--x-includes=%s' % self.spec['libx11'].prefix.include,
+            '--x-libraries=%s' % self.spec['libx11'].prefix.lib,
+            '--with-pbs-server-home=%s' % self.spec.prefix.var.spool.pbs,
+            '--with-database-dir=%s' % self.spec['postgresql'].prefix,
+            '--with-pbs-conf-file=%s' % self.spec.prefix.etc.join('pbs.conf'),
+            '--with-expat=%s' % self.spec['expat'].prefix,
+            '--with-editline=%s' % self.spec['libedit'].prefix,
+            '--with-hwloc=%s' % self.spec['hwloc'].prefix,
+            '--with-libical=%s' % self.spec['libical'].prefix,
+            '--with-sendmail=%s' % self.spec['ssmtp'].prefix.sbin.sendmail,
+            '--with-swig=%s' % self.spec['swig'].prefix,
+            '--with-tcl=%s' % self.spec['tcl'].prefix,
+            # The argument --with-tk is introduced with with_lib.patch
+            '--with-tk=%s' % self.spec['tk'].prefix,
+            '--with-xauth=xauth',
+            '--with-libz=%s' % self.spec['zlib'].prefix]
+
+    @run_after('install')
+    def post_install(self):
+        # Calling the postinstall script requires root privileges
+        # Executable(self.prefix.libexec.pbs_postinstall)()
+        tty.warn(self.spec.format(
+            'To finalize the installation of {name}, you need to run '
+            '"{prefix}/libexec/pbs_postinstall" with root privileges'))
diff --git a/var/spack/repos/builtin/packages/openpbs/python.patch b/var/spack/repos/builtin/packages/openpbs/python.patch
new file mode 100644
index 00000000000..aacf73140eb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openpbs/python.patch
@@ -0,0 +1,11 @@
+--- a/buildutils/python-autoconf.py
++++ b/buildutils/python-autoconf.py
+@@ -70,7 +70,7 @@ if py_stdlibdir:
+ else:
+     py_stdlibdir_real  = "%s/lib" % (sysconfig.PREFIX,) 
+ 
+-py_lib_configdir = get_py_config_var('LIBPL')
++py_lib_configdir = ''  # get_py_config_var('LIBPL')
+ if py_lib_configdir:
+     py_lib_configdir=py_lib_configdir.replace(py_stdlibdir,py_stdlibdir_real)
+ 
diff --git a/var/spack/repos/builtin/packages/openpbs/with_lib.patch b/var/spack/repos/builtin/packages/openpbs/with_lib.patch
new file mode 100644
index 00000000000..6a607a1611e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openpbs/with_lib.patch
@@ -0,0 +1,231 @@
+--- a/m4/with_database_dir.m4
++++ b/m4/with_database_dir.m4
+@@ -56,20 +56,11 @@ AC_DEFUN([PBS_AC_WITH_DATABASE_DIR],
+       AS_IF([test -r "$database_dir/include/postgresql/libpq-fe.h"],
+         [database_inc="-I$database_dir/include/postgresql"],
+         AC_MSG_ERROR([Database headers not found.]))))
+-  AS_IF([test "$database_dir" = "/usr"],
+-    # Using system installed PostgreSQL
+-    AS_IF([test -r "/usr/lib64/libpq.so" -o -r "/usr/lib/libpq.so" -o -r "/usr/lib/x86_64-linux-gnu/libpq.so"],
+-      [database_lib="-lpq"],
+-      AC_MSG_ERROR([PBS database shared object library not found.])),
+-    # Using developer installed PostgreSQL
+-      AS_IF([test -r "$database_dir/lib64/libpq.a"],
+-        [database_lib="$database_dir/lib64/libpq.a"],
+-        AS_IF([test -r "$database_dir/lib/libpq.a"],
+-          [database_lib="$database_dir/lib/libpq.a"],
+-          AC_MSG_ERROR([PBS database library not found.])
+-        )
+-      )
+-  )
++  AS_IF([test -r "$database_dir/lib64/libpq.so"],
++    [database_lib="-L$database_dir/lib64 -lpq"],
++    [test -r "$database_dir/lib/libpq.so"],
++    [database_lib="-L$database_dir/lib -lpq"],
++    AC_MSG_ERROR([PBS database shared object library not found.]))
+   AC_MSG_RESULT([$database_dir])
+   AC_SUBST([database_dir])
+   AC_SUBST([database_inc])
+--- a/m4/with_editline.m4
++++ b/m4/with_editline.m4
+@@ -52,31 +52,12 @@ AC_DEFUN([PBS_AC_WITH_EDITLINE],
+     AS_IF([test "$editline_dir" != "/usr"],
+       [editline_inc="-I$editline_dir/include"]),
+     AC_MSG_ERROR([editline headers not found.]))
+-  AS_IF([test "$editline_dir" = "/usr"],
+-    # Using system installed editline
+-    AS_IF([test -r /usr/lib64/libedit.so],
+-      [editline_lib="-ledit"],
+-      AS_IF([test -r /usr/lib/libedit.so],
+-        [editline_lib="-ledit"],
+-        AS_IF([test -r /usr/lib/x86_64-linux-gnu/libedit.so],
+-          [editline_lib="-ledit"],
+-          AC_MSG_ERROR([editline shared object library not found.])))),
+-    # Using developer installed editline
+-    AS_IF([test -r "${editline_dir}/lib64/libedit.a"],
+-      [editline_lib="${editline_dir}/lib64/libedit.a"],
+-      AS_IF([test -r "${editline_dir}/lib/libedit.a"],
+-        [editline_lib="${editline_dir}/lib/libedit.a"],
+-        AC_MSG_ERROR([editline library not found.])
+-      )
+-    )
+-  )
++  AS_IF([test -r "$editline_dir/lib64/libedit.so"],
++    [editline_lib="-L$editline_dir/lib64 -ledit"],
++    [test -r "$editline_dir/lib/libedit.so"],
++    [editline_lib="-L$editline_dir/lib -ledit"],
++    AC_MSG_ERROR([editline shared object library not found.]))
+   AC_MSG_RESULT([$editline_dir])
+-  AC_CHECK_LIB([ncurses], [tgetent],
+-    [curses_lib="-lncurses"],
+-    AC_CHECK_LIB([curses], [tgetent],
+-      [curses_lib="-lcurses"],
+-      AC_MSG_ERROR([curses library not found.])))
+-  [editline_lib="$editline_lib $curses_lib"]
+   AC_SUBST(editline_inc)
+   AC_SUBST(editline_lib)
+   AC_DEFINE([QMGR_HAVE_HIST], [], [Defined when editline is available])
+--- a/m4/with_expat.m4
++++ b/m4/with_expat.m4
+@@ -52,20 +52,11 @@ AC_DEFUN([PBS_AC_WITH_EXPAT],
+     AS_IF([test "$expat_dir" != "/usr"],
+       [expat_inc="-I$expat_dir/include"]),
+     AC_MSG_ERROR([expat headers not found.]))
+-  AS_IF([test "$expat_dir" = "/usr"],
+-    # Using system installed expat
+-    AS_IF([test -r "/usr/lib64/libexpat.so" -o -r "/usr/lib/libexpat.so" -o -r "/usr/lib/x86_64-linux-gnu/libexpat.so"],
+-      [expat_lib="-lexpat"],
+-      AC_MSG_ERROR([expat shared object library not found.])),
+-    # Using developer installed expat
+-    AS_IF([test -r "${expat_dir}/lib64/libexpat.a"],
+-      [expat_lib="${expat_dir}/lib64/libexpat.a"],
+-      AS_IF([test -r "${expat_dir}/lib/libexpat.a"],
+-        [expat_lib="${expat_dir}/lib/libexpat.a"],
+-        AC_MSG_ERROR([expat library not found.])
+-      )
+-    )
+-  )
++  AS_IF([test -r "$expat_dir/lib64/libexpat.so"],
++    [expat_lib="-L$expat_dir/lib64 -lexpat"],
++    [test -r "$expat_dir/lib/libexpat.so"],
++    [expat_lib="-L$expat_dir/lib -lexpat"],
++    AC_MSG_ERROR([expat shared object library not found.]))
+   AC_MSG_RESULT([$expat_dir])
+   AC_SUBST(expat_inc)
+   AC_SUBST(expat_lib)
+--- a/m4/with_hwloc.m4
++++ b/m4/with_hwloc.m4
+@@ -56,28 +56,12 @@ AC_DEFUN([PBS_AC_WITH_HWLOC],
+       [hwloc_inc="-I$hwloc_dir/include"]),
+       AC_MSG_ERROR([hwloc headers not found.])
+   )
+-  AS_IF([test "$hwloc_dir" = "/usr"],
+-    # Using system installed hwloc
+-    AS_IF([test -r "/usr/lib64/libhwloc.so" -o -r "/usr/lib/libhwloc.so" -o -r "/usr/lib/x86_64-linux-gnu/libhwloc.so"],
+-      [hwloc_lib="-lhwloc"],
+-      AC_MSG_ERROR([hwloc shared object library not found.])
+-    ),
+-    # Using developer installed hwloc
+-    AS_IF([test -r "${hwloc_dir}/lib64/libhwloc_embedded.a"],
+-      [hwloc_lib="${hwloc_dir}/lib64/libhwloc_embedded.a"],
+-      AS_IF([test -r "${hwloc_dir}/lib/libhwloc_embedded.a"],
+-        [hwloc_lib="${hwloc_dir}/lib/libhwloc_embedded.a"],
+-        AC_MSG_ERROR([hwloc library not found.])
+-      )
+-    )
+-  )
++  AS_IF([test -r "$hwloc_dir/lib64/libhwloc.so"],
++    [hwloc_lib="-L$hwloc_dir/lib64 -lhwloc"],
++    [test -r "$hwloc_dir/lib/libhwloc.so"],
++    [hwloc_lib="-L$hwloc_dir/lib -lhwloc"],
++    AC_MSG_ERROR([hwloc shared object library not found.]))
+   AC_MSG_RESULT([$hwloc_dir])
+-  AS_CASE([x$target_os],
+-    [xlinux*],
+-      AC_CHECK_LIB([numa], [mbind], [hwloc_lib="$hwloc_lib -lnuma"])
+-      AC_CHECK_LIB([udev], [udev_new], [hwloc_lib="$hwloc_lib -ludev"])
+-      AC_CHECK_LIB([pciaccess], [pci_system_init], [hwloc_lib="$hwloc_lib -lpciaccess"])
+-  )
+   AC_SUBST(hwloc_flags)
+   AC_SUBST(hwloc_inc)
+   AC_SUBST(hwloc_lib)
+--- a/m4/with_libical.m4
++++ b/m4/with_libical.m4
+@@ -59,23 +59,13 @@ AC_DEFUN([PBS_AC_WITH_LIBICAL],
+   AS_IF([test $libical_version -gt 1],
+     AC_DEFINE([LIBICAL_API2], [], [Defined when libical version >= 2])
+   )
+-  AS_IF([test "$libical_dir" = "/usr"],
+-    dnl Using system installed libical
+-    libical_inc=""
+-    AS_IF([test -r "/usr/lib64/libical.so" -o -r "/usr/lib/libical.so" -o -r "/usr/lib/x86_64-linux-gnu/libical.so"],
+-      [libical_lib="-lical"],
+-      AC_MSG_ERROR([libical shared object library not found.])
+-    ),
+-    dnl Using developer installed libical
+-    libical_inc="-I$libical_include"
+-    AS_IF([test -r "${libical_dir}/lib64/libical.a"],
+-      [libical_lib="${libical_dir}/lib64/libical.a"],
+-      AS_IF([test -r "${libical_dir}/lib/libical.a"],
+-        [libical_lib="${libical_dir}/lib/libical.a"],
+-        AC_MSG_ERROR([ical library not found.])
+-      )
+-    )
+-  )
++  AS_IF([test "$libical_dir" != "/usr"],
++    [libical_inc="-I$libical_include"])
++  AS_IF([test -r "$libical_dir/lib64/libical.so"],
++    [libical_lib="-L$libical_dir/lib64 -lical"],
++    [test -r "$libical_dir/lib/libical.so"],
++    [libical_lib="-L$libical_dir/lib -lical"],
++    AC_MSG_ERROR([libical shared object library not found.]))
+   AC_MSG_RESULT([$libical_dir])
+   AC_SUBST(libical_inc)
+   AC_SUBST(libical_lib)
+--- a/m4/with_tcl.m4
++++ b/m4/with_tcl.m4
+@@ -52,9 +52,7 @@ AC_DEFUN([PBS_AC_WITH_TCL],
+     [. "$tcl_dir/lib64/tclConfig.sh"],
+     AS_IF([test -r "$tcl_dir/lib/tclConfig.sh"],
+       [. "$tcl_dir/lib/tclConfig.sh"],
+-      AS_IF([test -r "$tcl_dir/lib/x86_64-linux-gnu/tclConfig.sh"],
+-        [. "$tcl_dir/lib/x86_64-linux-gnu/tclConfig.sh"],
+-        AC_MSG_ERROR([tclConfig.sh not found]))))
++      AC_MSG_ERROR([tclConfig.sh not found])))
+   AC_MSG_RESULT([$tcl_dir])
+   AC_MSG_CHECKING([for Tcl version])
+   AS_IF([test "x$TCL_VERSION" = "x"],
+@@ -62,32 +60,34 @@ AC_DEFUN([PBS_AC_WITH_TCL],
+   AC_MSG_RESULT([$TCL_VERSION])
+   [tcl_version="$TCL_VERSION"]
+   AC_SUBST(tcl_version)
++
++  AC_ARG_WITH([tk],
++    AS_HELP_STRING([--with-tk=DIR],
++      [Specify the directory where Tk is installed.]
++    )
++  )
++  AS_IF([test "x$with_tk" != "x"],
++    tk_dir=["$with_tk"],
++    tk_dir=["/usr"]
++  )
+   AC_MSG_CHECKING([for Tk])
+-  AS_IF([test -r "$tcl_dir/lib64/tkConfig.sh"],
+-    [. "$tcl_dir/lib64/tkConfig.sh"],
+-    AS_IF([test -r "$tcl_dir/lib/tkConfig.sh"],
+-      [. "$tcl_dir/lib/tkConfig.sh"],
+-      AS_IF([test -r "$tcl_dir/lib/x86_64-linux-gnu/tkConfig.sh"],
+-        [. "$tcl_dir/lib/x86_64-linux-gnu/tkConfig.sh"],
+-        AC_MSG_ERROR([tkConfig.sh not found]))))
+-  AC_MSG_RESULT([$tcl_dir])
++  AS_IF([test -r "$tk_dir/lib64/tkConfig.sh"],
++    [. "$tk_dir/lib64/tkConfig.sh"],
++    AS_IF([test -r "$tk_dir/lib/tkConfig.sh"],
++      [. "$tk_dir/lib/tkConfig.sh"],
++        AC_MSG_ERROR([tkConfig.sh not found])))
++  AC_MSG_RESULT([$tk_dir])
+   AC_MSG_CHECKING([for Tk version])
+   AS_IF([test "x$TK_VERSION" = "x"],
+     AC_MSG_ERROR([Could not determine Tk version]))
+   AC_MSG_RESULT([$TK_VERSION])
+   [tk_version="$TK_VERSION"]
+   AC_SUBST(tk_version)
+-  AS_IF([test x$TCL_INCLUDE_SPEC = x],
+-    # Using developer installed tcl
+-    [tcl_inc="-I$tcl_dir/include"]
+-    [tcl_lib="$tcl_dir/lib/libtcl$TCL_VERSION.a $TCL_LIBS"]
+-    [tk_inc="-I$tcl_dir/include"]
+-    [tk_lib="$tcl_dir/lib/libtcl$TCL_VERSION.a $tcl_dir/lib/libtk$TK_VERSION.a $TK_LIBS"],
+-    # Using system installed tcl
+-    [tcl_inc="$TCL_INCLUDE_SPEC"]
+-    [tcl_lib="$TCL_LIB_SPEC $TCL_LIBS"]
+-    [tk_inc="$TK_INCLUDE_SPEC"]
+-    [tk_lib=`echo "$TCL_LIB_SPEC $TK_LIB_SPEC $TK_LIBS" | ${SED} -e 's/-lXss //'`])
++
++  tcl_inc="$TCL_INCLUDE_SPEC"
++  tcl_lib="$TCL_LIB_SPEC $TCL_LIBS"
++  tk_inc="$TK_INCLUDE_SPEC"
++  tk_lib=`echo "$TCL_LIB_SPEC $TK_LIB_SPEC $TK_LIBS" | ${SED} -e 's/-lXss //'`
+   AC_SUBST(tcl_inc)
+   AC_SUBST(tcl_lib)
+   AC_SUBST(tk_inc)
diff --git a/var/spack/repos/builtin/packages/ssmtp/install.patch b/var/spack/repos/builtin/packages/ssmtp/install.patch
new file mode 100644
index 00000000000..89992f7ba0b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ssmtp/install.patch
@@ -0,0 +1,11 @@
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -61,7 +61,7 @@ install-sendmail: install
+ 	$(LN_S) ssmtp $(bindir)/sendmail
+ 	$(INSTALL) -d -m 755 $(libexecdir)
+ 	$(RM) $(libexecdir)/sendmail
+-	$(LN_S) sendmail /lib/sendmail
++	$(LN_S) $(bindir)/sendmail $(libexecdir)/sendmail
+ 	$(RM) $(mandir)/sendmail.8
+ 	$(LN_S) ssmtp.8 $(mandir)/sendmail.8
+ 
diff --git a/var/spack/repos/builtin/packages/ssmtp/package.py b/var/spack/repos/builtin/packages/ssmtp/package.py
new file mode 100644
index 00000000000..c1ed9055f2f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ssmtp/package.py
@@ -0,0 +1,58 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ssmtp(AutotoolsPackage):
+    """A program that replaces sendmail on workstations that should send their
+    mail via the departmental mailhub from which they pick up their mail."""
+
+    homepage = "https://salsa.debian.org/debian/ssmtp"
+    url = "http://deb.debian.org/debian/pool/main/s/ssmtp/ssmtp_2.64.orig.tar.bz2"
+
+    version('2.64', sha256='22c37dc90c871e8e052b2cab0ad219d010fa938608cd66b21c8f3c759046fa36')
+
+    variant('ssl', default=True,
+            description='Enable support for secure connection to mail server')
+    variant('inet6', default=True,
+            description='Enable support for IPv6 transport')
+    variant('md5auth', default=True,
+            description='Enable support for MD5 authentication')
+
+    depends_on('libnsl')
+    depends_on('openssl', when='+ssl')
+
+    patch('install.patch')
+
+    @when('+ssl')
+    def setup_build_environment(self, env):
+        # The configure script is generated with a very old version of
+        # autoconf, which cannot accept LIBS as a command-line argument
+        env.set('LIBS', self.spec['openssl'].libs.link_flags)
+
+    def configure_args(self):
+        args = self.enable_or_disable('ssl')
+        args += self.enable_or_disable('inet6')
+        args += self.enable_or_disable('md5auth')
+        return args
+
+    def install(self, spec, prefix):
+        install_answers = [
+            # Please enter the mail name of your system.
+            # This is the hostname portion of the address to be shown
+            # on outgoing news and mail messages headers.
+            # The default is your system's host name.
+            #
+            # Mail name [system.host.name]:
+            '\n',
+            # Please enter the SMTP port number [25]:
+            '\n'
+        ]
+        install_answers_filename = 'spack-install.in'
+        with working_dir(self.build_directory):
+            with open(install_answers_filename, 'w') as f:
+                f.writelines(install_answers)
+            make('install-sendmail', input=install_answers_filename)

From ff44a6d03faaa8f932c861c5b4b2cf6cd0deefe8 Mon Sep 17 00:00:00 2001
From: Sergey Kosukhin <sergey.kosukhin@mpimet.mpg.de>
Date: Tue, 26 May 2020 02:20:04 +0200
Subject: [PATCH 518/802] hdf: new version, variants and refactoring (#16469)

* hdf: new version, variants and refactoring.

* libc provides rpc

* Fix szip-related configure argument.

* Update dependent packages.
---
 etc/spack/defaults/packages.yaml              |   1 +
 .../repos/builtin/packages/gdal/package.py    |   4 +-
 .../packages/hdf/disable_doclint.patch        |  11 ++
 .../repos/builtin/packages/hdf/package.py     | 139 +++++++++++++++---
 .../repos/builtin/packages/libc/package.py    |   9 +-
 .../builtin/packages/libtirpc/package.py      |   2 +
 .../builtin/packages/netcdf-c/package.py      |   7 +-
 7 files changed, 141 insertions(+), 32 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/hdf/disable_doclint.patch

diff --git a/etc/spack/defaults/packages.yaml b/etc/spack/defaults/packages.yaml
index 2c91b75e45d..dcfbf76b51b 100644
--- a/etc/spack/defaults/packages.yaml
+++ b/etc/spack/defaults/packages.yaml
@@ -40,6 +40,7 @@ packages:
       opencl: [pocl]
       pil: [py-pillow]
       pkgconfig: [pkgconf, pkg-config]
+      rpc: [libtirpc]
       scalapack: [netlib-scalapack]
       sycl: [hipsycl]
       szip: [libszip, libaec]
diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py
index 88075f8a4e1..5aafdb44a1a 100644
--- a/var/spack/repos/builtin/packages/gdal/package.py
+++ b/var/spack/repos/builtin/packages/gdal/package.py
@@ -297,8 +297,8 @@ def configure_args(self):
         if '+hdf4' in spec:
             args.append('--with-hdf4={0}'.format(spec['hdf'].prefix))
             hdf4 = self.spec['hdf']
-            if '+libtirpc' in hdf4:
-                libs.append('-ltirpc')
+            if '+external-xdr' in hdf4 and hdf4['rpc'].name != 'libc':
+                libs.append(hdf4['rpc'].libs.link_flags)
         else:
             args.append('--with-hdf4=no')
 
diff --git a/var/spack/repos/builtin/packages/hdf/disable_doclint.patch b/var/spack/repos/builtin/packages/hdf/disable_doclint.patch
new file mode 100644
index 00000000000..221d8c77c6c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hdf/disable_doclint.patch
@@ -0,0 +1,11 @@
+--- a/java/src/Makefile.in
++++ b/java/src/Makefile.in
+@@ -818,7 +818,7 @@ $(jarfile): classhdf_java.stamp classes docs
+ .PHONY: docs classes
+ 
+ docs:
+-	$(JAVADOC) -sourcepath $(srcdir) -d javadoc -use -splitIndex -windowtitle $(WINDOWTITLE) -doctitle $(DOCTITLE) -J-Xmx180m -verbose -overview $(top_srcdir)/java/src/hdf/overview.html -classpath $(CLASSPATH_ENV) hdf.hdflib
++	$(JAVADOC) -sourcepath $(srcdir) -d javadoc -use -splitIndex -windowtitle $(WINDOWTITLE) -doctitle $(DOCTITLE) -J-Xmx180m -verbose -overview $(top_srcdir)/java/src/hdf/overview.html -classpath $(CLASSPATH_ENV) hdf.hdflib -Xdoclint:none
+ 
+ clean:
+ 	rm -rf $(JAVAROOT)/*
diff --git a/var/spack/repos/builtin/packages/hdf/package.py b/var/spack/repos/builtin/packages/hdf/package.py
index 67c2744470c..d3076b35f9a 100644
--- a/var/spack/repos/builtin/packages/hdf/package.py
+++ b/var/spack/repos/builtin/packages/hdf/package.py
@@ -15,45 +15,138 @@ class Hdf(AutotoolsPackage):
     list_url = "https://support.hdfgroup.org/ftp/HDF/releases/"
     list_depth = 2
 
+    version('4.2.15', sha256='dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459')
     version('4.2.14', sha256='2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a')
     version('4.2.13', sha256='be9813c1dc3712c2df977d4960e1f13f20f447dfa8c3ce53331d610c1f470483')
     version('4.2.12', sha256='dd419c55e85d1a0e13f3ea5ed35d00710033ccb16c85df088eb7925d486e040c')
     version('4.2.11', sha256='c3f7753b2fb9b27d09eced4d2164605f111f270c9a60b37a578f7de02de86d24')
 
     variant('szip', default=False, description="Enable szip support")
-    variant('libtirpc', default=False, description="Use xdr library from libtirpc package; if false, will use system or hdf internal")
+    variant('external-xdr', default=True,
+            description="Use an external XDR backend")
+    variant('netcdf', default=False,
+            description='Build NetCDF API (version 2.3.2)')
+    variant('fortran', default=False,
+            description='Enable Fortran interface')
+    variant('java', default=False,
+            description='Enable Java JNI interface')
+    variant('shared', default=False, description='Enable shared library')
+    variant('pic', default=True,
+            description='Produce position-independent code')
 
-    depends_on('jpeg@6b:')
-    depends_on('szip', when='+szip')
-    depends_on('libtirpc', when='+libtirpc')
     depends_on('zlib@1.1.4:')
+    depends_on('jpeg')
+    depends_on('szip', when='+szip')
+    depends_on('rpc', when='+external-xdr')
 
     depends_on('bison', type='build')
     depends_on('flex',  type='build')
+    depends_on('java@7:', when='+java', type=('build', 'run'))
+
+    # https://forum.hdfgroup.org/t/cant-build-hdf-4-2-14-with-jdk-11-and-enable-java/5702
+    patch('disable_doclint.patch', when='@:4.2.14^java@9:')
+
+    conflicts('^libjpeg@:6a')
+
+    # configure: error: Cannot build shared fortran libraries.
+    # Please configure with --disable-fortran flag.
+    conflicts('+fortran', when='+shared')
+
+    # configure: error: Java requires shared libraries to be built
+    conflicts('+java', when='~shared')
+
+    # configure: WARNING: unrecognized options: --enable-java
+    conflicts('+java', when='@:4.2.11')
+
+    # The Java interface library uses netcdf-related macro definitions even
+    # when netcdf is disabled and the macros are not defined, e.g.:
+    # hdfsdsImp.c:158:30: error: 'MAX_NC_NAME' undeclared
+    conflicts('+java', when='@4.2.12:4.2.13~netcdf')
+
+    # TODO: '@:4.2.14 ~external-xdr' and the fact that we compile for 64 bit
+    #  architecture should be in conflict
+
+    @property
+    def libs(self):
+        """HDF can be queried for the following parameters:
+
+        - "shared": shared libraries (default if '+shared')
+        - "static": static libraries (default if '~shared')
+        - "transitive": append transitive dependencies to the list of static
+            libraries (the argument is ignored if shared libraries are
+            requested)
+
+        :return: list of matching libraries
+        """
+        libraries = ['libmfhdf', 'libdf']
+
+        query_parameters = self.spec.last_query.extra_parameters
+
+        if 'shared' in query_parameters:
+            shared = True
+        elif 'static' in query_parameters:
+            shared = False
+        else:
+            shared = '+shared' in self.spec
+
+        libs = find_libraries(
+            libraries, root=self.prefix, shared=shared, recursive=True
+        )
+
+        if not libs:
+            msg = 'Unable to recursively locate {0} {1} libraries in {2}'
+            raise spack.error.NoLibrariesError(
+                msg.format('shared' if shared else 'static',
+                           self.spec.name,
+                           self.spec.prefix))
+
+        if not shared and 'transitive' in query_parameters:
+            libs += self.spec['jpeg:transitive'].libs
+            libs += self.spec['zlib:transitive'].libs
+            if '+szip' in self.spec:
+                libs += self.spec['szip:transitive'].libs
+            if ('+external-xdr' in self.spec and
+                    self.spec['rpc'].name != 'libc'):
+                libs += self.spec['rpc:transitive'].libs
+
+        return libs
+
+    def flag_handler(self, name, flags):
+        if '+pic' in self.spec:
+            if name == 'cflags':
+                flags.append(self.compiler.cc_pic_flag)
+            elif name == 'fflags':
+                flags.append(self.compiler.f77_pic_flag)
+
+        return flags, None, None
 
     def configure_args(self):
-        spec = self.spec
+        config_args = ['--enable-production',
+                       '--enable-static',
+                       '--with-zlib=%s' % self.spec['zlib'].prefix,
+                       '--with-jpeg=%s' % self.spec['jpeg'].prefix]
 
-        config_args = [
-            'CFLAGS={0}'.format(self.compiler.cc_pic_flag),
-            '--with-jpeg={0}'.format(spec['jpeg'].prefix),
-            '--with-zlib={0}'.format(spec['zlib'].prefix),
-            '--disable-netcdf',  # must be disabled to build NetCDF with HDF4
-            '--enable-fortran',
-            '--disable-shared',  # fortran and shared libs are not compatible
-            '--enable-static',
-            '--enable-production'
-        ]
+        config_args += self.enable_or_disable('shared')
+        config_args += self.enable_or_disable('netcdf')
+        config_args += self.enable_or_disable('fortran')
+        config_args += self.enable_or_disable('java')
 
-        # Szip support
-        if '+szip' in spec:
-            config_args.append('--with-szlib={0}'.format(spec['szip'].prefix))
+        if '+szip' in self.spec:
+            config_args.append('--with-szlib=%s' % self.spec['szip'].prefix)
         else:
             config_args.append('--without-szlib')
 
-        if '+libtirpc' in spec:
-            config_args.append('LIBS=-ltirpc')
-            config_args.append('CPPFLAGS=-I{0}/include/tirpc'.format(
-                spec['libtirpc'].prefix))
-
+        if '~external-xdr' in self.spec:
+            config_args.append('--enable-hdf4-xdr')
+        elif self.spec['rpc'].name != 'libc':
+            # We should not specify '--disable-hdf4-xdr' due to a bug in the
+            # configure script.
+            config_args.append('LIBS=%s' % self.spec['rpc'].libs.link_flags)
         return config_args
+
+    # Otherwise, we randomly get:
+    # SDgetfilename:
+    #   incorrect file being opened - expected <file755>, retrieved <file754>
+    def check(self):
+        with working_dir(self.build_directory):
+            make('check', parallel=False)
diff --git a/var/spack/repos/builtin/packages/libc/package.py b/var/spack/repos/builtin/packages/libc/package.py
index a4fa9ac3a64..e328c40ea1f 100644
--- a/var/spack/repos/builtin/packages/libc/package.py
+++ b/var/spack/repos/builtin/packages/libc/package.py
@@ -7,13 +7,16 @@
 
 
 class Libc(Package):
-    """Dummy libc package to provide `iconv` virtual package"""
+    """Dummy package to provide interfaces available in libc."""
 
     homepage = "https://en.wikipedia.org/wiki/C_standard_library"
-    url      = ""
     has_code = False
     phases = []
 
     version('1.0')  # Dummy
-    variant('iconv', default=False, description='Set to True if libc provides iconv')
+
+    variant('iconv', default=False, description='Provides interfaces for Localization Functions')
+    variant('rpc', default=False, description='Provides interfaces for RPC')
+
     provides('iconv', when='+iconv')
+    provides('rpc', when='+rpc')
diff --git a/var/spack/repos/builtin/packages/libtirpc/package.py b/var/spack/repos/builtin/packages/libtirpc/package.py
index e6ce06e0ea0..f83c7499a09 100644
--- a/var/spack/repos/builtin/packages/libtirpc/package.py
+++ b/var/spack/repos/builtin/packages/libtirpc/package.py
@@ -15,6 +15,8 @@ class Libtirpc(AutotoolsPackage):
 
     version('1.1.4', sha256='2ca529f02292e10c158562295a1ffd95d2ce8af97820e3534fe1b0e3aec7561d')
 
+    provides('rpc')
+
     # FIXME: build error on macOS
     # auth_none.c:81:9: error: unknown type name 'mutex_t'
 
diff --git a/var/spack/repos/builtin/packages/netcdf-c/package.py b/var/spack/repos/builtin/packages/netcdf-c/package.py
index 153a1057b17..6043e1122d7 100644
--- a/var/spack/repos/builtin/packages/netcdf-c/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-c/package.py
@@ -75,7 +75,7 @@ def url_for_version(self, version):
     depends_on('libtool', type='build', when='@4.7.0')
 
     depends_on("m4", type='build')
-    depends_on("hdf", when='+hdf4')
+    depends_on("hdf~netcdf", when='+hdf4')
 
     # curl 7.18.0 or later is required:
     # http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html
@@ -219,9 +219,8 @@ def configure_args(self):
             if '+szip' in hdf4:
                 # This should also come from hdf4.libs
                 libs.append('-lsz')
-            if '+libtirpc' in hdf4:
-                # This should also come from hdf4.libs
-                libs.append('-ltirpc')
+            if '+external-xdr' in hdf4 and hdf4['rpc'].name != 'libc':
+                libs.append(hdf4['rpc'].libs.link_flags)
 
         # Fortran support
         # In version 4.2+, NetCDF-C and NetCDF-Fortran have split.

From 45b86e2c1d47d28559b91eb6583fabbb32030c19 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Tue, 26 May 2020 09:42:54 +0200
Subject: [PATCH 519/802] py-hypothesis: added v5.3.0 (#16804)

---
 var/spack/repos/builtin/packages/py-hypothesis/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-hypothesis/package.py b/var/spack/repos/builtin/packages/py-hypothesis/package.py
index 1a77b3cb28a..79a39055d08 100644
--- a/var/spack/repos/builtin/packages/py-hypothesis/package.py
+++ b/var/spack/repos/builtin/packages/py-hypothesis/package.py
@@ -20,6 +20,7 @@ class PyHypothesis(PythonPackage):
 
     # TODO: Add missing dependency required to import hypothesis.extra.django
 
+    version('5.3.0',  sha256='c9fdb53fe3bf1f8e7dcca1a7dd6e430862502f088aca2903d141511212e79429')
     version('4.57.1', sha256='3c4369a4b0a1348561048bcda5f1db951a1b8e2a514ea8e8c70d36e656bf6fa0')
     version('4.41.2', sha256='6847df3ffb4aa52798621dd007e6b61dbcf2d76c30ba37dc2699720e2c734b7a')
     version('4.24.3', sha256='fd90a319f409f34a173156ca704d6c0c6c0bb30a2e43dbf26aced2c75569e5d5')

From 7383d923f0db782362087c4fed07cb4de637440c Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 26 May 2020 17:16:43 +0800
Subject: [PATCH 520/802] blogbench: added new package at v1.1 (#16793)

---
 .../repos/builtin/packages/blogbench/package.py  | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/blogbench/package.py

diff --git a/var/spack/repos/builtin/packages/blogbench/package.py b/var/spack/repos/builtin/packages/blogbench/package.py
new file mode 100644
index 00000000000..d9a7fd6088b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/blogbench/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Blogbench(AutotoolsPackage):
+    """A filesystem benchmark tool that simulates a realistic load."""
+
+    homepage = "https://openbenchmarking.org/test/pts/blogbench"
+    url      = "http://download.pureftpd.org/pub/blogbench/blogbench-1.1.tar.gz"
+
+    version('1.1', sha256='8cded059bfdbccb7be35bb6a2272ecfdbe3fbea43d53c92ba5572ac24f26c4df')
+    version('1.0', sha256='dc29261a19064a8fb64d39b27607f19d3b33ce3795908e717404167687ef33be')

From d7fb8701c2b4c39e0d76b230e2a39198436a2b30 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 26 May 2020 17:17:25 +0800
Subject: [PATCH 521/802] su2: new package at v7.0.3 (#16787)

---
 .../repos/builtin/packages/su2/package.py     | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/su2/package.py

diff --git a/var/spack/repos/builtin/packages/su2/package.py b/var/spack/repos/builtin/packages/su2/package.py
new file mode 100644
index 00000000000..3aa51e5828d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/su2/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Su2(MesonPackage):
+    """SU2 is a suite of open-source software tools written in C++ for
+    the numerical solution of partial differential equations (PDE) and
+    performing PDE constrained optimization."""
+
+    homepage = "https://su2code.github.io"
+    url      = "https://github.com/su2code/SU2/archive/v7.0.3.tar.gz"
+
+    version('7.0.3', sha256='7fc01deaad9baabbe0ccd162a4b565172d49e573e79abcb65433b51ff29bda06')
+    version('7.0.2', sha256='69e51d52c5a84fb572bd6a83faf8f9fd04471fbf7d5b70d967c7306c1d4e17d9')
+    version('7.0.1', sha256='eb0550c82ccaef8cb71e4a8775aa71d2020ef085ec3dd19dfafff5d301034f6f')
+    version('7.0.0', sha256='6207dcca15eaebc11ce12b2866c937b4ad9b93274edf6f23d0487948ac3963b8')
+    version('6.2.0', sha256='ffc953326e8432a1a6534556a5f6cf086046d3149cfcec6b4e7390eebe30ce2e')
+
+    depends_on('python@3:', type=('build', 'run'))

From 2c6406c0031b457b05eb9e8a2640f2f1fddf0474 Mon Sep 17 00:00:00 2001
From: "Dr. Christian Tacke"
 <58549698+ChristianTackeGSI@users.noreply.github.com>
Date: Tue, 26 May 2020 16:30:18 +0200
Subject: [PATCH 522/802] grpc: allow building shared libraries (#16356)

---
 var/spack/repos/builtin/packages/grpc/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/grpc/package.py b/var/spack/repos/builtin/packages/grpc/package.py
index 7996a6865b9..a7eff3e07f4 100644
--- a/var/spack/repos/builtin/packages/grpc/package.py
+++ b/var/spack/repos/builtin/packages/grpc/package.py
@@ -19,6 +19,8 @@ class Grpc(CMakePackage):
     version('1.24.3', sha256='c84b3fa140fcd6cce79b3f9de6357c5733a0071e04ca4e65ba5f8d306f10f033')
     version('1.23.1', sha256='dd7da002b15641e4841f20a1f3eb1e359edb69d5ccf8ac64c362823b05f523d9')
 
+    variant('shared', default=False,
+            description='Build shared instead of static libraries')
     variant('codegen', default=True,
             description='Builds code generation plugins for protobuf '
                         'compiler (protoc)')
@@ -31,6 +33,8 @@ class Grpc(CMakePackage):
 
     def cmake_args(self):
         args = [
+            '-DBUILD_SHARED_LIBS:Bool={0}'.format(
+                'ON' if '+shared' in self.spec else 'OFF'),
             '-DgRPC_BUILD_CODEGEN:Bool={0}'.format(
                 'ON' if '+codegen' in self.spec else 'OFF'),
             '-DgRPC_BUILD_CSHARP_EXT:Bool=OFF',

From 0b96082e74b9a5d99a143641cf8e52f6218cc24d Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@esi-group.com>
Date: Wed, 20 May 2020 10:48:30 +0200
Subject: [PATCH 523/802] openfoam: improve handling of wmake rules, version
 update

- add future-proofing for wmake rules locations:
  Accept wmake/rules/{ARCH}{COMP} or wmake/rules/{ARCH}/{COMP}

- compiler option is now '-spack' instead of 'RpathOpt'
  which now seems to be a bit harsh on the eyes.
  Now have compilations such as 'linux64GccDPInt32-spack',
  which is moderately easier to read.

- add OpenFOAM 1912, patch 200506

STYLE: adjust for new flakey8 indentation rules
---
 .../packages/openfoam/common/spack-Allwmake   |  4 +-
 .../openfoam/common/spack-derived-Allwmake    |  2 +-
 .../openfoam/common/spack-dummy-Allwmake      | 18 ++++
 .../builtin/packages/openfoam/package.py      | 84 +++++++++++--------
 4 files changed, 68 insertions(+), 40 deletions(-)
 create mode 100755 var/spack/repos/builtin/packages/openfoam/common/spack-dummy-Allwmake

diff --git a/var/spack/repos/builtin/packages/openfoam/common/spack-Allwmake b/var/spack/repos/builtin/packages/openfoam/common/spack-Allwmake
index 83c9e273b5c..2b4d8f84123 100755
--- a/var/spack/repos/builtin/packages/openfoam/common/spack-Allwmake
+++ b/var/spack/repos/builtin/packages/openfoam/common/spack-Allwmake
@@ -7,8 +7,8 @@ export FOAM_INST_DIR=$(cd .. && pwd -L)
 # Prevent influence of user/site config when building
 export FOAM_CONFIG_MODE="o"
 
-. "$PWD/etc/bashrc" ''                              # No arguments
-mkdir -p "$FOAM_APPBIN" "$FOAM_LIBBIN" 2>/dev/null  # Allow build interrupt
+. "$PWD"/etc/bashrc ''                          # No arguments
+mkdir -p "$FOAM_APPBIN" "$FOAM_LIBBIN"          # Allow build interrupt
 
 echo "Build openfoam with SPACK ($@)"
 echo "WM_PROJECT_DIR = $WM_PROJECT_DIR"
diff --git a/var/spack/repos/builtin/packages/openfoam/common/spack-derived-Allwmake b/var/spack/repos/builtin/packages/openfoam/common/spack-derived-Allwmake
index 02741f1d133..b09cf99083c 100755
--- a/var/spack/repos/builtin/packages/openfoam/common/spack-derived-Allwmake
+++ b/var/spack/repos/builtin/packages/openfoam/common/spack-derived-Allwmake
@@ -10,7 +10,7 @@
 }
 
 export FOAM_INST_DIR=$(cd $FOAM_PROJECT_DIR/.. && pwd -L) # Needed by foam-extend
-. $FOAM_PROJECT_DIR/etc/bashrc ''  # No arguments
+. "$FOAM_PROJECT_DIR"/etc/bashrc ''  # No arguments
 
 # Package-specific adjustments
 [ -f spack-config.sh ] && . ./spack-config.sh ''  # No arguments
diff --git a/var/spack/repos/builtin/packages/openfoam/common/spack-dummy-Allwmake b/var/spack/repos/builtin/packages/openfoam/common/spack-dummy-Allwmake
new file mode 100755
index 00000000000..ac44a016dbe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openfoam/common/spack-dummy-Allwmake
@@ -0,0 +1,18 @@
+#!/bin/bash
+# Build wrapper script for dummy build
+
+# Prevent influence of user/site config when building
+export FOAM_CONFIG_MODE="o"
+. "$PWD"/etc/bashrc ''                          # No arguments
+
+echo "Dummy build openfoam with SPACK ($@)"
+echo "WM_PROJECT_DIR = $WM_PROJECT_DIR"
+
+if [ -f applications/test/00-dummy/Allwmake ]
+then
+    applications/test/00-dummy/Allwmake $@
+else
+    echo "Nothing to make"
+fi
+
+# -----------------------------------------------------------------------------
diff --git a/var/spack/repos/builtin/packages/openfoam/package.py b/var/spack/repos/builtin/packages/openfoam/package.py
index ce812f8effa..1f818c54047 100644
--- a/var/spack/repos/builtin/packages/openfoam/package.py
+++ b/var/spack/repos/builtin/packages/openfoam/package.py
@@ -265,6 +265,7 @@ class Openfoam(Package):
 
     version('develop', branch='develop', submodules='True')
     version('master', branch='master', submodules='True')
+    version('1912_200506', sha256='831a39ff56e268e88374d0a3922479fd80260683e141e51980242cc281484121')
     version('1912_200403', sha256='1de8f4ddd39722b75f6b01ace9f1ba727b53dd999d1cd2b344a8c677ac2db4c0')
     version('1912', sha256='437feadf075419290aa8bf461673b723a60dc39525b23322850fb58cb48548f2')
     version('1906_200312', sha256='f75645151ed5d8c5da592d307480979fe580a25627cc0c9718ef370211577594')
@@ -348,10 +349,10 @@ class Openfoam(Package):
     patch('https://develop.openfoam.com/Development/openfoam/commit/8831dfc58b0295d0d301a78341dd6f4599073d45.patch',
           when='@1806',
           sha256='21f1ab68c82dfa41ed1a4439427c94c43ddda02c84175c30da623d905d3e5d61'
-    )
+          )
 
     # Some user config settings
-    # default: 'compile-option': 'RpathOpt',
+    # default: 'compile-option': '-spack',
     # default: 'mplib': 'USERMPI',     # Use user mpi for spack
     config = {
         # Add links into bin/, lib/ (eg, for other applications)
@@ -421,15 +422,15 @@ def setup_run_environment(self, env):
                     blacklist=[  # Blacklist these
                         # Inadvertent changes
                         # -------------------
-                        'PS1',            # Leave unaffected
-                        'MANPATH',        # Leave unaffected
+                        'PS1',              # Leave untouched
+                        'MANPATH',          # Leave untouched
 
                         # Unneeded bits
                         # -------------
                         # 'FOAM_SETTINGS',  # Do not use with modules
                         # 'FOAM_INST_DIR',  # Old
                         # 'FOAM_(APP|ETC|SRC|SOLVERS|UTILITIES)',
-                        # 'FOAM_TUTORIALS',  # can be useful
+                        # 'FOAM_TUTORIALS', # May be useful
                         # 'WM_OSTYPE',      # Purely optional value
 
                         # Third-party cruft - only used for orig compilation
@@ -443,7 +444,7 @@ def setup_run_environment(self, env):
                         '(FOAM|WM)_.*USER_.*',
                     ],
                     whitelist=[  # Whitelist these
-                        'MPI_ARCH_PATH',  # Can be needed for compilation
+                        'MPI_ARCH_PATH',  # Can be required for compilation
                     ])
 
                 env.extend(mods)
@@ -544,16 +545,24 @@ def patch(self):
     @run_before('configure')
     def make_fujitsu_rules(self):
         """Create Fujitsu rules (clang variant) unless supplied upstream.
-        Implemented for 1906 and newer - older rules are messier to edit
+        Implemented for 1906 and later (older rules are too messy to edit).
+        Already included after 1912.
         """
         general_rules = 'wmake/rules/General'
-        arch_rules = join_path('wmake/rules/linuxARM64')  # self.arch
+        arch_rules = 'wmake/rules/linuxARM64'  # self.arch
         src = arch_rules + 'Clang'
         dst = arch_rules + 'Fujitsu'  # self.compiler
 
         if os.path.exists(dst):
             return
 
+        # Handle rules/<ARCH><COMP> or rules/<ARCH>/<COMP>
+        if not os.path.exists(src):
+            src = join_path(arch_rules, 'Clang')
+            dst = join_path(arch_rules, 'Fujitsu')  # self.compiler
+            if os.path.exists(dst):
+                return
+
         tty.info('Add Fujitsu wmake rules')
         copy_tree(src, dst)
 
@@ -622,11 +631,11 @@ def configure(self, spec, prefix):
             'metis': {},
             'ensight': {},     # Disable settings
             'paraview': [],
-            'gperftools': [],  # Currently unused
+            'gperftools': [],  # Disable settings
             'vtk': [],
         }
 
-        # With adios2 after 1912 or develop (after 2019-10-01)
+        # With adios2 after 1912
         if spec.satisfies('@1912:'):
             self.etc_config['adios2'] = [
                 ('ADIOS2_ARCH_PATH', spec['adios2'].prefix),
@@ -823,7 +832,7 @@ class OpenfoamArch(object):
 
     Keywords
         label-size=[True]   supports int32/int64
-        compile-option[=RpathOpt]
+        compile-option[=-spack]
         mplib[=USERMPI]
     """
 
@@ -837,10 +846,9 @@ def __init__(self, spec, **kwargs):
         self.arch_option      = ''     # Eg, -march=knl
         self.label_size       = None   # <- +int64
         self.precision_option = 'DP'   # <- +float32
-        self.compile_option   = kwargs.get('compile-option', 'RpathOpt')
+        self.compile_option   = kwargs.get('compile-option', '-spack')
         self.arch             = None
         self.options          = None
-        self.rule             = None
         self.mplib            = kwargs.get('mplib', 'USERMPI')
 
         # Normally support WM_LABEL_OPTION, but not yet for foam-extend
@@ -852,6 +860,9 @@ def __init__(self, spec, **kwargs):
         if '+float32' in spec:
             self.precision_option = 'SP'
 
+        # TDB: mixed precision?
+        # self.precision_option = 'SPDP'
+
         # Processor/architecture-specific optimizations
         if '+knl' in spec:
             self.arch_option = '-march=knl'
@@ -884,9 +895,9 @@ def __init__(self, spec, **kwargs):
 
         self.arch = platform
 
-        # Capitalized version of the compiler name, which corresponds
+        # Capitalize first letter of compiler name, which corresponds
         # to how OpenFOAM handles things (eg, gcc -> Gcc).
-        # Use compiler_mapping to handing special cases.
+        # Use compiler_mapping for special cases.
         comp = spec.compiler.name
 
         if comp in self.compiler_mapping:
@@ -894,7 +905,6 @@ def __init__(self, spec, **kwargs):
         comp = comp.capitalize()
 
         self.compiler = comp
-        self.rule = self.arch + self.compiler
 
         # Build WM_OPTIONS
         # ----
@@ -904,7 +914,8 @@ def __init__(self, spec, **kwargs):
         # WM_OPTIONS=$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_COMPILE_OPTION
         # ----
         self.options = ''.join([
-            self.rule,
+            self.arch,
+            self.compiler,
             self.precision_option,
             ('Int' + self.label_size if self.label_size else ''),
             self.compile_option])
@@ -925,46 +936,45 @@ def foam_dict(self):
             ('WM_MPLIB',       self.mplib),
         ])
 
-    def _rule_directory(self, projdir=None, general=False):
-        """The wmake/rules/ compiler directory"""
+    def _rule_directory(self, projdir, general=False):
+        """Return the wmake/rules/ General or compiler rules directory.
+        Supports wmake/rules/<ARCH><COMP> and wmake/rules/<ARCH>/<COMP>.
+        """
+        rules_dir = os.path.join(projdir, 'wmake', 'rules')
         if general:
-            relative = os.path.join('wmake', 'rules', 'General')
+            return os.path.join(rules_dir, 'General')
+
+        arch_dir = os.path.join(rules_dir, self.arch)
+        comp_rules = arch_dir + self.compiler
+        if os.path.isdir(comp_rules):
+            return comp_rules
         else:
-            relative = os.path.join('wmake', 'rules', self.rule)
-        if projdir:
-            return os.path.join(projdir, relative)
-        else:
-            return relative
+            return os.path.join(arch_dir, self.compiler)
 
     def has_rule(self, projdir):
-        """Verify that a wmake/rules/ compiler rule exists in the project
-        directory.
+        """Verify that a wmake/rules/ compiler rule exists in the project.
         """
         # Insist on a wmake rule for this architecture/compiler combination
         rule_dir = self._rule_directory(projdir)
 
         if not os.path.isdir(rule_dir):
             raise InstallError(
-                'No wmake rule for {0}'.format(self.rule))
-        if not re.match(r'.+Opt$', self.compile_option):
-            raise InstallError(
-                "WM_COMPILE_OPTION={0} is not type '*Opt'"
-                .format(self.compile_option))
+                'No wmake rule for {0} {1}'.format(self.arch, self.compiler))
         return True
 
     def create_rules(self, projdir, foam_pkg):
-        """ Create cRpathOpt,c++RpathOpt and mplibUSER,mplibUSERMPI
+        """ Create {c,c++}-spack and mplib{USER,USERMPI}
         rules in the specified project directory.
-        The compiler rules are based on the respective cOpt,c++Opt rules
+        The compiler rules are based on the respective {c,c++}Opt rules
         but with additional rpath information for the OpenFOAM libraries.
 
-        The rpath rules allow wmake to use spack information with minimal
-        modification to OpenFOAM.
+        The '-spack' rules channel spack information into OpenFOAM wmake
+        rules with minimal modification to OpenFOAM.
         The rpath is used for the installed libpath (continue to use
         LD_LIBRARY_PATH for values during the build).
         """
         # Note: the 'c' rules normally don't need rpath, since they are just
-        # used for statically linked wmake utilities, but left in anyhow.
+        # used for some statically linked wmake tools, but left in anyhow.
 
         # rpath for installed OpenFOAM libraries
         rpath = '{0}{1}'.format(

From c01433f60a09c041137c6145eacd669eaa0f7af6 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Tue, 26 May 2020 20:47:31 +0200
Subject: [PATCH 524/802] spack.relocate: further coverage for ELF related
 functions (#16585)

* make_link_relative: added docstring

* make_elf_binaries_relative: added docstring, unit tests

* raise_if_not_relocatable: added docstring, added unit test for exceptional case

* relocate_links: removed unused arguments, added docstring and comments

Also fixed a possible bug that was issuing spurious
warning when a file was relocated successfully

* relocate_text: added docstring and comments, renamed arguments

* relocate_text_bin: added docstring and comments, renamed arguments, unit tests
---
 lib/spack/spack/binary_distribution.py |  21 +--
 lib/spack/spack/relocate.py            | 214 +++++++++++++++----------
 lib/spack/spack/test/packaging.py      |   5 +-
 lib/spack/spack/test/relocate.py       | 155 +++++++++++++-----
 4 files changed, 256 insertions(+), 139 deletions(-)

diff --git a/lib/spack/spack/binary_distribution.py b/lib/spack/spack/binary_distribution.py
index 0fb6feae028..926f4679a10 100644
--- a/lib/spack/spack/binary_distribution.py
+++ b/lib/spack/spack/binary_distribution.py
@@ -514,7 +514,7 @@ def make_package_relative(workdir, spec, allow_root):
             platform.system().lower() == 'linux'):
         relocate.make_elf_binaries_relative(cur_path_names, orig_path_names,
                                             old_layout_root)
-    relocate.check_files_relocatable(cur_path_names, allow_root)
+    relocate.raise_if_not_relocatable(cur_path_names, allow_root)
     orig_path_names = list()
     cur_path_names = list()
     for linkname in buildinfo.get('relocate_links', []):
@@ -532,7 +532,7 @@ def check_package_relocatable(workdir, spec, allow_root):
     cur_path_names = list()
     for filename in buildinfo['relocate_binaries']:
         cur_path_names.append(os.path.join(workdir, filename))
-    relocate.check_files_relocatable(cur_path_names, allow_root)
+    relocate.raise_if_not_relocatable(cur_path_names, allow_root)
 
 
 def relocate_package(spec, allow_root):
@@ -615,17 +615,13 @@ def is_backup_file(file):
                                            prefix_to_prefix, rel,
                                            old_prefix,
                                            new_prefix)
-        # Relocate links to the new install prefix
-            link_names = [linkname
-                          for linkname in buildinfo.get('relocate_links', [])]
-            relocate.relocate_links(link_names,
-                                    old_layout_root,
-                                    new_layout_root,
-                                    old_prefix,
-                                    new_prefix,
-                                    prefix_to_prefix)
+            # Relocate links to the new install prefix
+            links = [link for link in buildinfo.get('relocate_links', [])]
+            relocate.relocate_links(
+                links, old_layout_root, old_prefix, new_prefix
+            )
 
-    # For all buildcaches
+        # For all buildcaches
         # relocate the install prefixes in text files including dependencies
         relocate.relocate_text(text_names,
                                old_layout_root, new_layout_root,
@@ -636,7 +632,6 @@ def is_backup_file(file):
 
         # relocate the install prefixes in binary files including dependencies
         relocate.relocate_text_bin(files_to_relocate,
-                                   old_layout_root, new_layout_root,
                                    old_prefix, new_prefix,
                                    old_spack_prefix,
                                    new_spack_prefix,
diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py
index 94fd2b58bfe..01a60db6baf 100644
--- a/lib/spack/spack/relocate.py
+++ b/lib/spack/spack/relocate.py
@@ -458,6 +458,7 @@ def _replace_prefix_text(filename, old_dir, new_dir):
         old_dir (str): directory to be searched in the file
         new_dir (str): substitute for the old directory
     """
+    # TODO: cache regexes globally to speedup computation
     with open(filename, 'rb+') as f:
         data = f.read()
         f.seek(0)
@@ -675,16 +676,19 @@ def relocate_elf_binaries(binaries, orig_root, new_root,
             _set_elf_rpaths(new_binary, new_rpaths)
 
 
-def make_link_relative(cur_path_names, orig_path_names):
-    """
-    Change absolute links to relative links.
-    """
-    for cur_path, orig_path in zip(cur_path_names, orig_path_names):
-        target = os.readlink(orig_path)
-        relative_target = os.path.relpath(target, os.path.dirname(orig_path))
+def make_link_relative(new_links, orig_links):
+    """Compute the relative target from the original link and
+    make the new link relative.
 
-        os.unlink(cur_path)
-        os.symlink(relative_target, cur_path)
+    Args:
+        new_links (list): new links to be made relative
+        orig_links (list): original links
+    """
+    for new_link, orig_link in zip(new_links, orig_links):
+        target = os.readlink(orig_link)
+        relative_target = os.path.relpath(target, os.path.dirname(orig_link))
+        os.unlink(new_link)
+        os.symlink(relative_target, new_link)
 
 
 def make_macho_binaries_relative(cur_path_names, orig_path_names,
@@ -706,97 +710,143 @@ def make_macho_binaries_relative(cur_path_names, orig_path_names,
                                 paths_to_paths)
 
 
-def make_elf_binaries_relative(cur_path_names, orig_path_names,
-                               old_layout_root):
+def make_elf_binaries_relative(new_binaries, orig_binaries, orig_layout_root):
+    """Replace the original RPATHs in the new binaries making them
+    relative to the original layout root.
+
+    Args:
+        new_binaries (list): new binaries whose RPATHs is to be made relative
+        orig_binaries (list): original binaries
+        orig_layout_root (str): path to be used as a base for making
+            RPATHs relative
     """
-    Replace old RPATHs with paths relative to old_dir in binary files
-    """
-    for cur_path, orig_path in zip(cur_path_names, orig_path_names):
-        orig_rpaths = _elf_rpaths_for(cur_path)
+    for new_binary, orig_binary in zip(new_binaries, orig_binaries):
+        orig_rpaths = _elf_rpaths_for(new_binary)
         if orig_rpaths:
-            new_rpaths = _make_relative(orig_path, old_layout_root,
-                                        orig_rpaths)
-            _set_elf_rpaths(cur_path, new_rpaths)
+            new_rpaths = _make_relative(
+                orig_binary, orig_layout_root, orig_rpaths
+            )
+            _set_elf_rpaths(new_binary, new_rpaths)
 
 
-def check_files_relocatable(cur_path_names, allow_root):
+def raise_if_not_relocatable(binaries, allow_root):
+    """Raise an error if any binary in the list is not relocatable.
+
+    Args:
+        binaries (list): list of binaries to check
+        allow_root (bool): whether root dir is allowed or not in a binary
+
+    Raises:
+        InstallRootStringError: if the file is not relocatable
     """
-    Check binary files for the current install root
-    """
-    for cur_path in cur_path_names:
-        if (not allow_root and
-                not file_is_relocatable(cur_path)):
-            raise InstallRootStringError(
-                cur_path, spack.store.layout.root)
+    for binary in binaries:
+        if not (allow_root or file_is_relocatable(binary)):
+            raise InstallRootStringError(binary, spack.store.layout.root)
 
 
-def relocate_links(linknames, old_layout_root, new_layout_root,
-                   old_install_prefix, new_install_prefix, prefix_to_prefix):
-    """
-    The symbolic links in filenames are absolute links or placeholder links.
+def relocate_links(links, orig_layout_root,
+                   orig_install_prefix, new_install_prefix):
+    """Relocate links to a new install prefix.
+
+    The symbolic links are relative to the original installation prefix.
     The old link target is read and the placeholder is replaced by the old
     layout root. If the old link target is in the old install prefix, the new
     link target is create by replacing the old install prefix with the new
     install prefix.
+
+    Args:
+        links (list): list of links to be relocated
+        orig_layout_root (str): original layout root
+        orig_install_prefix (str): install prefix of the original installation
+        new_install_prefix (str): install prefix where we want to relocate
     """
-    placeholder = _placeholder(old_layout_root)
-    link_names = [os.path.join(new_install_prefix, linkname)
-                  for linkname in linknames]
-    for link_name in link_names:
-        link_target = os.readlink(link_name)
-        link_target = re.sub(placeholder, old_layout_root, link_target)
-        if link_target.startswith(old_install_prefix):
-            new_link_target = re.sub(
-                old_install_prefix, new_install_prefix, link_target)
-            os.unlink(link_name)
-            os.symlink(new_link_target, link_name)
+    placeholder = _placeholder(orig_layout_root)
+    abs_links = [os.path.join(new_install_prefix, link) for link in links]
+    for abs_link in abs_links:
+        link_target = os.readlink(abs_link)
+        link_target = re.sub(placeholder, orig_layout_root, link_target)
+        # If the link points to a file in the original install prefix,
+        # compute the corresponding target in the new prefix and relink
+        if link_target.startswith(orig_install_prefix):
+            link_target = re.sub(
+                orig_install_prefix, new_install_prefix, link_target
+            )
+            os.unlink(abs_link)
+            os.symlink(link_target, abs_link)
+
+        # If the link is absolute and has not been relocated then
+        # warn the user about that
         if (os.path.isabs(link_target) and
             not link_target.startswith(new_install_prefix)):
-            msg = 'Link target %s' % link_target
-            msg += ' for symbolic link %s is outside' % link_name
-            msg += ' of the newinstall prefix %s.\n' % new_install_prefix
-            tty.warn(msg)
+            msg = ('Link target "{0}" for symbolic link "{1}" is outside'
+                   ' of the new install prefix {2}')
+            tty.warn(msg.format(link_target, abs_link, new_install_prefix))
 
 
-def relocate_text(path_names, old_layout_root, new_layout_root,
-                  old_install_prefix, new_install_prefix,
-                  old_spack_prefix, new_spack_prefix,
-                  prefix_to_prefix):
+def relocate_text(
+        files, orig_layout_root, new_layout_root, orig_install_prefix,
+        new_install_prefix, orig_spack, new_spack, new_prefixes
+):
+    """Relocate text file from the original installation prefix to the
+    new prefix.
+
+    Relocation also affects the the path in Spack's sbang script.
+
+    Args:
+        files (list): text files to be relocated
+        orig_layout_root (str): original layout root
+        new_layout_root (str): new layout root
+        orig_install_prefix (str): install prefix of the original installation
+        new_install_prefix (str): install prefix where we want to relocate
+        orig_spack (str): path to the original Spack
+        new_spack (str): path to the new Spack
+        new_prefixes (dict): dictionary that maps the original prefixes to
+            where they should be relocated
     """
-    Replace old paths with new paths in text files
-    including the path the the spack sbang script
+    # TODO: reduce the number of arguments (8 seems too much)
+    sbang_regex = r'#!/bin/bash {0}/bin/sbang'.format(orig_spack)
+    new_sbang = r'#!/bin/bash {0}/bin/sbang'.format(new_spack)
+
+    for file in files:
+        _replace_prefix_text(file, orig_install_prefix, new_install_prefix)
+        for orig_dep_prefix, new_dep_prefix in new_prefixes.items():
+            _replace_prefix_text(file, orig_dep_prefix, new_dep_prefix)
+        _replace_prefix_text(file, orig_layout_root, new_layout_root)
+        _replace_prefix_text(file, sbang_regex, new_sbang)
+
+
+def relocate_text_bin(
+        binaries, orig_install_prefix, new_install_prefix,
+        orig_spack, new_spack, new_prefixes
+):
+    """Replace null terminated path strings hard coded into binaries.
+
+    The new install prefix must be shorter than the original one.
+
+    Args:
+        binaries (list): binaries to be relocated
+        orig_install_prefix (str): install prefix of the original installation
+        new_install_prefix (str): install prefix where we want to relocate
+        orig_spack (str): path to the original Spack
+        new_spack (str): path to the new Spack
+        new_prefixes (dict): dictionary that maps the original prefixes to
+            where they should be relocated
+
+    Raises:
+      BinaryTextReplaceError: when the new path in longer than the old path
     """
-    sbangre = '#!/bin/bash %s/bin/sbang' % old_spack_prefix
-    sbangnew = '#!/bin/bash %s/bin/sbang' % new_spack_prefix
+    # Raise if the new install prefix is longer than the
+    # original one, since it means we can't change the original
+    # binary to relocate it
+    new_prefix_is_shorter = len(new_install_prefix) <= len(orig_install_prefix)
+    if not new_prefix_is_shorter and len(binaries) > 0:
+        raise BinaryTextReplaceError(orig_install_prefix, new_install_prefix)
 
-    for path_name in path_names:
-        _replace_prefix_text(path_name, old_install_prefix, new_install_prefix)
-        for orig_dep_prefix, new_dep_prefix in prefix_to_prefix.items():
-            _replace_prefix_text(path_name, orig_dep_prefix, new_dep_prefix)
-        _replace_prefix_text(path_name, old_layout_root, new_layout_root)
-        _replace_prefix_text(path_name, sbangre, sbangnew)
-
-
-def relocate_text_bin(path_names, old_layout_root, new_layout_root,
-                      old_install_prefix, new_install_prefix,
-                      old_spack_prefix, new_spack_prefix,
-                      prefix_to_prefix):
-    """
-      Replace null terminated path strings hard coded into binaries.
-      Raise an exception when the new path in longer than the old path
-      because this breaks the binary.
-      """
-    if len(new_install_prefix) <= len(old_install_prefix):
-        for path_name in path_names:
-            for old_dep_prefix, new_dep_prefix in prefix_to_prefix.items():
-                if len(new_dep_prefix) <= len(old_dep_prefix):
-                    _replace_prefix_bin(
-                        path_name, old_dep_prefix, new_dep_prefix)
-            _replace_prefix_bin(path_name, old_spack_prefix, new_spack_prefix)
-    else:
-        if len(path_names) > 0:
-            raise BinaryTextReplaceError(
-                old_install_prefix, new_install_prefix)
+    for binary in binaries:
+        for old_dep_prefix, new_dep_prefix in new_prefixes.items():
+            if len(new_dep_prefix) <= len(old_dep_prefix):
+                _replace_prefix_bin(binary, old_dep_prefix, new_dep_prefix)
+        _replace_prefix_bin(binary, orig_spack, new_spack)
 
 
 def is_relocatable(spec):
@@ -929,4 +979,4 @@ def mime_type(file):
     if '/' not in output:
         output += '/'
     split_by_slash = output.strip().split('/')
-    return (split_by_slash[0], "/".join(split_by_slash[1:]))
+    return split_by_slash[0], "/".join(split_by_slash[1:])
diff --git a/lib/spack/spack/test/packaging.py b/lib/spack/spack/test/packaging.py
index 67c9e52875d..7d4adfe9755 100644
--- a/lib/spack/spack/test/packaging.py
+++ b/lib/spack/spack/test/packaging.py
@@ -242,9 +242,8 @@ def test_relocate_links(tmpdir):
         os.utime(new_binname, None)
         os.symlink(old_binname, new_linkname)
         os.symlink('/usr/lib/libc.so', new_linkname2)
-        relocate_links(filenames, old_layout_root, new_layout_root,
-                       old_install_prefix, new_install_prefix,
-                       {old_install_prefix: new_install_prefix})
+        relocate_links(filenames, old_layout_root,
+                       old_install_prefix, new_install_prefix)
         assert os.readlink(new_linkname) == new_binname
         assert os.readlink(new_linkname2) == '/usr/lib/libc.so'
 
diff --git a/lib/spack/spack/test/relocate.py b/lib/spack/spack/test/relocate.py
index d9becebe7b2..6669b25eb41 100644
--- a/lib/spack/spack/test/relocate.py
+++ b/lib/spack/spack/test/relocate.py
@@ -2,10 +2,10 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
 import collections
 import os.path
 import platform
+import re
 import shutil
 
 import llnl.util.filesystem
@@ -20,6 +20,23 @@
 import spack.util.executable
 
 
+def rpaths_for(new_binary):
+    """Return the RPATHs or RUNPATHs of a binary."""
+    patchelf = spack.util.executable.which('patchelf')
+    output = patchelf('--print-rpath', str(new_binary), output=str)
+    return output.strip()
+
+
+def text_in_bin(text, binary):
+    with open(str(binary), "rb") as f:
+        data = f.read()
+        f.seek(0)
+        pat = re.compile(text.encode('utf-8'))
+        if not pat.search(data):
+            return False
+        return True
+
+
 @pytest.fixture(params=[True, False])
 def is_relocatable(request):
     return request.param
@@ -105,17 +122,22 @@ def _factory(output):
 
 @pytest.fixture()
 def hello_world(tmpdir):
-    source = tmpdir.join('main.c')
-    source.write("""
-#include <stdio.h>
-int main(){
-    printf("Hello world!");
-}
-""")
-
-    def _factory(rpaths):
+    """Factory fixture that compiles an ELF binary setting its RPATH. Relative
+    paths are encoded with `$ORIGIN` prepended.
+    """
+    def _factory(rpaths, message="Hello world!"):
+        source = tmpdir.join('main.c')
+        source.write("""
+        #include <stdio.h>
+        int main(){{
+            printf("{0}");
+        }}
+        """.format(message))
         gcc = spack.util.executable.which('gcc')
         executable = source.dirpath('main.x')
+        # Encode relative RPATHs using `$ORIGIN` as the root prefix
+        rpaths = [x if os.path.isabs(x) else os.path.join('$ORIGIN', x)
+                  for x in rpaths]
         rpath_str = ':'.join(rpaths)
         opts = [
             '-Wl,--disable-new-dtags',
@@ -128,6 +150,19 @@ def _factory(rpaths):
     return _factory
 
 
+@pytest.fixture()
+def copy_binary():
+    """Returns a function that copies a binary somewhere and
+    returns the new location.
+    """
+    def _copy_somewhere(orig_binary):
+        new_root = orig_binary.mkdtemp()
+        new_binary = new_root.join('main.x')
+        shutil.copy(str(orig_binary), str(new_binary))
+        return new_binary
+    return _copy_somewhere
+
+
 @pytest.mark.requires_executables(
     '/usr/bin/gcc', 'patchelf', 'strings', 'file'
 )
@@ -250,23 +285,18 @@ def test_replace_prefix_bin(hello_world):
     # Relocate the RPATHs
     spack.relocate._replace_prefix_bin(str(executable), '/usr', '/foo')
 
-    # Check that the RPATHs changed
-    patchelf = spack.util.executable.which('patchelf')
-    output = patchelf('--print-rpath', str(executable), output=str)
-
     # Some compilers add rpaths so ensure changes included in final result
-    assert '/foo/lib:/foo/lib64' in output
+    assert '/foo/lib:/foo/lib64' in rpaths_for(executable)
 
 
 @pytest.mark.requires_executables('patchelf', 'strings', 'file', 'gcc')
-def test_relocate_elf_binaries_absolute_paths(hello_world, tmpdir):
+def test_relocate_elf_binaries_absolute_paths(
+        hello_world, copy_binary, tmpdir
+):
     # Create an executable, set some RPATHs, copy it to another location
     orig_binary = hello_world(rpaths=[str(tmpdir.mkdir('lib')), '/usr/lib64'])
-    new_root = tmpdir.mkdir('another_dir')
-    shutil.copy(str(orig_binary), str(new_root))
+    new_binary = copy_binary(orig_binary)
 
-    # Relocate the binary
-    new_binary = new_root.join('main.x')
     spack.relocate.relocate_elf_binaries(
         binaries=[str(new_binary)],
         orig_root=str(orig_binary.dirpath()),
@@ -279,38 +309,81 @@ def test_relocate_elf_binaries_absolute_paths(hello_world, tmpdir):
         orig_prefix=None, new_prefix=None
     )
 
-    # Check that the RPATHs changed
-    patchelf = spack.util.executable.which('patchelf')
-    output = patchelf('--print-rpath', str(new_binary), output=str)
-
     # Some compilers add rpaths so ensure changes included in final result
-    assert '/foo/lib:/usr/lib64' in output
+    assert '/foo/lib:/usr/lib64' in rpaths_for(new_binary)
 
 
 @pytest.mark.requires_executables('patchelf', 'strings', 'file', 'gcc')
-def test_relocate_elf_binaries_relative_paths(hello_world, tmpdir):
+def test_relocate_elf_binaries_relative_paths(hello_world, copy_binary):
     # Create an executable, set some RPATHs, copy it to another location
-    orig_binary = hello_world(
-        rpaths=['$ORIGIN/lib', '$ORIGIN/lib64', '/opt/local/lib']
-    )
-    new_root = tmpdir.mkdir('another_dir')
-    shutil.copy(str(orig_binary), str(new_root))
+    orig_binary = hello_world(rpaths=['lib', 'lib64', '/opt/local/lib'])
+    new_binary = copy_binary(orig_binary)
 
-    # Relocate the binary
-    new_binary = new_root.join('main.x')
     spack.relocate.relocate_elf_binaries(
         binaries=[str(new_binary)],
         orig_root=str(orig_binary.dirpath()),
-        new_root=str(new_root),
-        new_prefixes={str(tmpdir): '/foo'},
+        new_root=str(new_binary.dirpath()),
+        new_prefixes={str(orig_binary.dirpath()): '/foo'},
         rel=True,
         orig_prefix=str(orig_binary.dirpath()),
-        new_prefix=str(new_root)
+        new_prefix=str(new_binary.dirpath())
     )
 
-    # Check that the RPATHs changed
-    patchelf = spack.util.executable.which('patchelf')
-    output = patchelf('--print-rpath', str(new_binary), output=str)
-
     # Some compilers add rpaths so ensure changes included in final result
-    assert '/foo/lib:/foo/lib64:/opt/local/lib' in output
+    assert '/foo/lib:/foo/lib64:/opt/local/lib' in rpaths_for(new_binary)
+
+
+@pytest.mark.requires_executables('patchelf', 'strings', 'file', 'gcc')
+def test_make_elf_binaries_relative(hello_world, copy_binary, tmpdir):
+    orig_binary = hello_world(rpaths=[
+        str(tmpdir.mkdir('lib')), str(tmpdir.mkdir('lib64')), '/opt/local/lib'
+    ])
+    new_binary = copy_binary(orig_binary)
+
+    spack.relocate.make_elf_binaries_relative(
+        [str(new_binary)], [str(orig_binary)], str(orig_binary.dirpath())
+    )
+
+    assert rpaths_for(new_binary) == '$ORIGIN/lib:$ORIGIN/lib64:/opt/local/lib'
+
+
+def test_raise_if_not_relocatable(monkeypatch):
+    monkeypatch.setattr(spack.relocate, 'file_is_relocatable', lambda x: False)
+    with pytest.raises(spack.relocate.InstallRootStringError):
+        spack.relocate.raise_if_not_relocatable(
+            ['an_executable'], allow_root=False
+        )
+
+
+@pytest.mark.requires_executables('patchelf', 'strings', 'file', 'gcc')
+def test_relocate_text_bin(hello_world, copy_binary, tmpdir):
+    orig_binary = hello_world(rpaths=[
+        str(tmpdir.mkdir('lib')), str(tmpdir.mkdir('lib64')), '/opt/local/lib'
+    ], message=str(tmpdir))
+    new_binary = copy_binary(orig_binary)
+
+    # Check original directory is in the executabel and the new one is not
+    assert text_in_bin(str(tmpdir), new_binary)
+    assert not text_in_bin(str(new_binary.dirpath()), new_binary)
+
+    # Check this call succeed
+    spack.relocate.relocate_text_bin(
+        [str(new_binary)],
+        str(orig_binary.dirpath()), str(new_binary.dirpath()),
+        spack.paths.spack_root, spack.paths.spack_root,
+        {str(orig_binary.dirpath()): str(new_binary.dirpath())}
+    )
+
+    # Check original directory is not there anymore and it was
+    # substituted with the new one
+    assert not text_in_bin(str(tmpdir), new_binary)
+    assert text_in_bin(str(new_binary.dirpath()), new_binary)
+
+
+def test_relocate_text_bin_raise_if_new_prefix_is_longer():
+    short_prefix = '/short'
+    long_prefix = '/much/longer'
+    with pytest.raises(spack.relocate.BinaryTextReplaceError):
+        spack.relocate.relocate_text_bin(
+            ['item'], short_prefix, long_prefix, None, None, None
+        )

From e9dcab946470a71ad88ddaaad85f338d72a1b5db Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Tue, 26 May 2020 14:06:25 -0700
Subject: [PATCH 525/802] backwards compatibility for naming scheme (#16812)

* backwards compatibility for naming scheme
---
 lib/spack/spack/modules/common.py                  |  9 +++++++--
 lib/spack/spack/schema/modules.py                  |  6 +++++-
 .../spack/test/data/modules/tcl/naming_scheme.yaml |  4 ++++
 lib/spack/spack/test/modules/tcl.py                | 14 ++++++++++++++
 4 files changed, 30 insertions(+), 3 deletions(-)
 create mode 100644 lib/spack/spack/test/data/modules/tcl/naming_scheme.yaml

diff --git a/lib/spack/spack/modules/common.py b/lib/spack/spack/modules/common.py
index 7eca9292c92..95ef81415ed 100644
--- a/lib/spack/spack/modules/common.py
+++ b/lib/spack/spack/modules/common.py
@@ -397,8 +397,13 @@ def __init__(self, spec):
     @property
     def projections(self):
         """Projection from specs to module names"""
-        projections = self.module.configuration().get(
-            'projections', self.default_projections)
+        # backwards compatiblity for naming_scheme key
+        conf = self.module.configuration()
+        if 'naming_scheme' in conf:
+            default = {'all': conf['naming_scheme']}
+        else:
+            default = self.default_projections
+        projections = conf.get('projections', default)
 
         # Ensure the named tokens we are expanding are allowed, see
         # issue #2884 for reference
diff --git a/lib/spack/spack/schema/modules.py b/lib/spack/spack/schema/modules.py
index ac9237609bc..d03dbfb4100 100644
--- a/lib/spack/spack/schema/modules.py
+++ b/lib/spack/spack/schema/modules.py
@@ -17,7 +17,8 @@
 #: THIS NEEDS TO BE UPDATED FOR EVERY NEW KEYWORD THAT
 #: IS ADDED IMMEDIATELY BELOW THE MODULE TYPE ATTRIBUTE
 spec_regex = r'(?!hierarchy|core_specs|verbose|hash_length|whitelist|' \
-             r'blacklist|projections|core_compilers|all)(^\w[\w-]*)'
+             r'blacklist|projections|naming_scheme|core_compilers|all)' \
+             r'(^\w[\w-]*)'
 
 #: Matches an anonymous spec, i.e. a spec without a root name
 anonymous_spec_regex = r'^[\^@%+~]'
@@ -94,6 +95,9 @@
                 'type': 'boolean',
                 'default': False
             },
+            'naming_scheme': {
+                'type': 'string'  # Can we be more specific here?
+            },
             'projections': projections_scheme,
             'all': module_file_configuration,
         }
diff --git a/lib/spack/spack/test/data/modules/tcl/naming_scheme.yaml b/lib/spack/spack/test/data/modules/tcl/naming_scheme.yaml
new file mode 100644
index 00000000000..cc4cf8f7829
--- /dev/null
+++ b/lib/spack/spack/test/data/modules/tcl/naming_scheme.yaml
@@ -0,0 +1,4 @@
+enable:
+  - tcl
+tcl:
+  naming_scheme: '{name}/{version}-{compiler.name}'
diff --git a/lib/spack/spack/test/modules/tcl.py b/lib/spack/spack/test/modules/tcl.py
index 98d9363f879..7672cdc676d 100644
--- a/lib/spack/spack/test/modules/tcl.py
+++ b/lib/spack/spack/test/modules/tcl.py
@@ -142,6 +142,20 @@ def test_blacklist(self, modulefile_content, module_configuration):
         assert len([x for x in content if 'is-loaded' in x]) == 1
         assert len([x for x in content if 'module load ' in x]) == 1
 
+    def test_naming_scheme_compat(self, factory, module_configuration):
+        """Tests backwards compatibility for naming_scheme key"""
+        module_configuration('naming_scheme')
+
+        # Test we read the expected configuration for the naming scheme
+        writer, _ = factory('mpileaks')
+        expected = {
+            'all': '{name}/{version}-{compiler.name}'
+        }
+
+        assert writer.conf.projections == expected
+        projection = writer.spec.format(writer.conf.projections['all'])
+        assert projection in writer.layout.use_name
+
     def test_projections_specific(self, factory, module_configuration):
         """Tests reading the correct naming scheme."""
 

From ac7f6b98b50c64bf0526a803c89deca64f0e87c5 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Wed, 27 May 2020 01:06:25 -0600
Subject: [PATCH 526/802] quicksilver: initial commit (#16811)

---
 .../builtin/packages/quicksilver/package.py   | 63 +++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/quicksilver/package.py

diff --git a/var/spack/repos/builtin/packages/quicksilver/package.py b/var/spack/repos/builtin/packages/quicksilver/package.py
new file mode 100644
index 00000000000..ceef9e1bfba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/quicksilver/package.py
@@ -0,0 +1,63 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Quicksilver(MakefilePackage):
+    """Quicksilver is a proxy application that represents some elements of the
+       Mercury workload.
+    """
+
+    tags = ['proxy-app']
+
+    homepage = "https://codesign.llnl.gov/quicksilver.php"
+    url      = "https://github.com/LLNL/Quicksilver"
+    git      = "https://github.com/LLNL/Quicksilver.git"
+
+    maintainers = ['richards12']
+
+    version('master', branch='master')
+
+    variant('openmp', default=True, description='Build with OpenMP support')
+    variant('mpi', default=True, description='Build with MPI support')
+
+    depends_on('mpi', when="+mpi")
+
+    build_directory = 'src'
+
+    @property
+    def build_targets(self):
+        targets = []
+        spec = self.spec
+
+        targets.append('CXXFLAGS={0}'.format(self.compiler.cxx11_flag))
+
+        if '+mpi' in spec:
+            targets.append('CXX={0}'.format(spec['mpi'].mpicxx))
+        else:
+            targets.append('CXX={0}'.format(spack_cxx))
+
+        if '+openmp+mpi' in spec:
+            targets.append('CPPFLAGS=-DHAVE_MPI -DHAVE_OPENMP {0}'.format(
+                self.compiler.openmp_flag))
+        elif '+openmp' in spec:
+            targets.append('CPPFLAGS=-DHAVE_OPENMP {0}'.format(
+                self.compiler.openmp_flag))
+        elif '+mpi' in spec:
+            targets.append('CPPFLAGS=-DHAVE_MPI')
+
+        if '+openmp' in self.spec:
+            targets.append('LDFLAGS={0}'.format(self.compiler.openmp_flag))
+
+        return targets
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        mkdir(prefix.doc)
+        install("src/qs", prefix.bin)
+        install('LICENSE.md', prefix.doc)
+        install('README.md', prefix.doc)
+        install_tree('Examples', prefix.Examples)

From fcacf8dc9d6a989b61047f25441386b7811f65dc Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Wed, 27 May 2020 02:20:27 -0500
Subject: [PATCH 527/802] plink-ng: new package at v200511 (#16750)

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
---
 .../builtin/packages/plink-ng/package.py      | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/plink-ng/package.py

diff --git a/var/spack/repos/builtin/packages/plink-ng/package.py b/var/spack/repos/builtin/packages/plink-ng/package.py
new file mode 100644
index 00000000000..27b4a4ca95f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/plink-ng/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PlinkNg(Package):
+    """A comprehensive update to the PLINK association analysis toolset."""
+
+    homepage = "https://www.cog-genomics.org/plink/2.0/"
+    url      = "https://www.cog-genomics.org/static/bin/plink2_src_200511.zip"
+
+    version('200511', sha256='00cff19bece88acb7a21ba098501cb677b78d22c9f3ca5bcdc869139a40db816')
+
+    depends_on('zlib')
+    depends_on('zstd@1.4.4:')
+    depends_on('cblas')
+    depends_on('blas')
+    depends_on('lapack')
+
+    conflicts('%gcc@:4.99')
+
+    def url_for_version(self, ver):
+        template = 'https://www.cog-genomics.org/static/bin/plink2_src_{0}.zip'
+        return template.format(ver)
+
+    def setup_build_environment(self, env):
+        zlib = join_path(self.spec['zlib'].prefix.lib, 'libz.a')
+        env.set('ZLIB', zlib)
+
+    def install(self, spec, prefix):
+        ld_flags = [spec['lapack'].libs.ld_flags, spec['blas'].libs.ld_flags]
+        filter_file('-llapack -lcblas -lblas', ' '.join(ld_flags),
+                    'build.sh', string=True)
+        which('sh')('build.sh')
+        install_tree('.', prefix)

From 6b8775f6afacc65378fd733f33ad9d6bbe9fe6d7 Mon Sep 17 00:00:00 2001
From: "Tomoki, Karatsu" <49965247+t-karatsu@users.noreply.github.com>
Date: Wed, 27 May 2020 16:32:11 +0900
Subject: [PATCH 528/802] py-torch: find openmp when %fj (#16822)

Fix for 'FindOpenMP.cmake' to detect openmp
settings used by Fujitsu compiler.
---
 .../detect_omp_of_fujitsu_compiler.patch      | 20 +++++++++++++++++++
 .../builtin/packages/py-torch/package.py      |  4 ++++
 2 files changed, 24 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-torch/detect_omp_of_fujitsu_compiler.patch

diff --git a/var/spack/repos/builtin/packages/py-torch/detect_omp_of_fujitsu_compiler.patch b/var/spack/repos/builtin/packages/py-torch/detect_omp_of_fujitsu_compiler.patch
new file mode 100644
index 00000000000..519d66869d5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-torch/detect_omp_of_fujitsu_compiler.patch
@@ -0,0 +1,20 @@
+--- pytorch/cmake/Modules/FindOpenMP.cmake.org	2020-05-26 17:43:53.000000000 +0900
++++ pytorch/cmake/Modules/FindOpenMP.cmake	2020-05-26 17:46:37.000000000 +0900
+@@ -84,7 +84,7 @@
+     unset(OpenMP_FLAG_CANDIDATES)
+ 
+     set(OMP_FLAG_GNU "-fopenmp")
+-    set(OMP_FLAG_Clang "-fopenmp=libomp" "-fopenmp=libiomp5" "-fopenmp")
++    set(OMP_FLAG_Clang "-fopenmp" "-fopenmp=libomp" "-fopenmp=libiomp5")
+ 
+     # AppleClang may need a header file, search for omp.h with hints to brew
+     # default include dir
+@@ -245,7 +245,7 @@
+         set(OpenMP_libomp_LIBRARY "${MKL_OPENMP_LIBRARY}" CACHE STRING "libomp location for OpenMP")
+       else()
+         find_library(OpenMP_libomp_LIBRARY
+-          NAMES omp gomp iomp5
++          NAMES fjomp omp gomp iomp5
+           HINTS ${CMAKE_${LANG}_IMPLICIT_LINK_DIRECTORIES}
+           DOC "libomp location for OpenMP"
+         )
diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py
index ce69a5581c6..eb2eec608c3 100644
--- a/var/spack/repos/builtin/packages/py-torch/package.py
+++ b/var/spack/repos/builtin/packages/py-torch/package.py
@@ -178,6 +178,10 @@ class PyTorch(PythonPackage, CudaPackage):
           sha256='7781c7ec0a661bf5a946a659f80e90df9dba116ad168762f15b10547113ae600',
           when='@1.1:1.5')
 
+    # Fix for 'FindOpenMP.cmake'
+    # to detect openmp settings used by Fujitsu compiler.
+    patch('detect_omp_of_fujitsu_compiler.patch', when='%fj')
+
     # Both build and install run cmake/make/make install
     # Only run once to speed up build times
     phases = ['install']

From 768419601d4db31a618c498c8299bac566b0f75d Mon Sep 17 00:00:00 2001
From: Jen Herting <jen@herting.cc>
Date: Wed, 27 May 2020 03:43:26 -0400
Subject: [PATCH 529/802] py-fits-tools: added package at v1.1.2 (#16815)

---
 .../builtin/packages/py-fits-tools/package.py | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-fits-tools/package.py

diff --git a/var/spack/repos/builtin/packages/py-fits-tools/package.py b/var/spack/repos/builtin/packages/py-fits-tools/package.py
new file mode 100644
index 00000000000..5127d887270
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-fits-tools/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyFitsTools(PythonPackage):
+    """Tools for manipulating FITS images using primarily scipy
+    & native python routines"""
+
+    homepage = "https://github.com/keflavich/FITS_tools"
+    url      = "https://github.com/keflavich/FITS_tools/archive/v0.2.tar.gz"
+
+    version('1.1.2', sha256='6c7596533ea66f5ca05e4326ae6db643edb03aca4b6b654dce091834155d03e8')
+    version('1.1.1', sha256='5b79ef24fadb43458388754381644712c05cd89da4f89c197e3bd80ca158c525')
+    version('1.1',   sha256='995ebf53dc0ffd8bdb5270c4fa0cf52f639aac05cfb68dc6fd5d58ab40148a8a')
+    version('1.0',   sha256='b711981eb780f3d27a5dec413397af68493b496e1621f9a37cf68dd265536937')
+    version('0.4.1', sha256='3511eb7bbaf73ac68b92b460c71b7a3dbf6c3860fae908638180876eca12f8fd')
+    version('0.4',   sha256='dbdb558d4c3ada627d42b62aaec5eb8f8f6dd3e323cae853fd447d9ec7805637')
+    version('0.2',   sha256='04c4b6eeb09298bca79b228175fcd209d4ca895ce5675f6684120e75928d2d97', default=True)
+    version('0.1',   sha256='d128e49ff4ecc6a9bf9a050f8605bc457e028e10e48bb8d6fda4ca358298ec17')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-astropy')
+    depends_on('py-astropy-helpers')
+    depends_on('py-scipy')
+    depends_on('py-numpy')

From d8c7073a9f67fe72d94e4a20e6accf99ccbda0fc Mon Sep 17 00:00:00 2001
From: Jen Herting <jen@herting.cc>
Date: Wed, 27 May 2020 03:45:14 -0400
Subject: [PATCH 530/802] py-configargparse: new package at v1.2.3 (#16814)

---
 .../packages/py-configargparse/package.py     | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-configargparse/package.py

diff --git a/var/spack/repos/builtin/packages/py-configargparse/package.py b/var/spack/repos/builtin/packages/py-configargparse/package.py
new file mode 100644
index 00000000000..acaf0cc4bbe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-configargparse/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyConfigargparse(PythonPackage):
+    """Applications with more than a handful of user-settable
+    options are best configured through a combination of
+    command line args, config files, hard-coded defaults, and
+    in some cases, environment variables.
+
+    Python's command line parsing modules such as argparse have
+    very limited support for config files and environment
+    variables, so this module extends argparse to add these
+    features."""
+
+    homepage = "https://github.com/bw2/ConfigArgParse"
+    url      = "https://github.com/bw2/ConfigArgParse/archive/1.2.3.tar.gz"
+
+    version('1.2.3', sha256='0f1144a204e3b896d6ac900e151c1d13bde3103d6b7d541e3bb57514a94083bf')
+
+    depends_on('python@2.2:2.999,3.5:', type=('build', 'run'))

From e73c39a5db1771cc4ff66c9c367a4c0be37a400a Mon Sep 17 00:00:00 2001
From: Sergey Kosukhin <sergey.kosukhin@mpimet.mpg.de>
Date: Wed, 27 May 2020 11:45:14 +0200
Subject: [PATCH 531/802] concretize: fix UnboundLocalError due to import
 within a function (#16809)

---
 lib/spack/spack/spec.py            | 3 ++-
 lib/spack/spack/test/concretize.py | 5 +++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 0b9500246af..03f334597a7 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -2134,6 +2134,8 @@ def concretize(self, tests=False):
         consistent with requirements of its packages. See flatten() and
         normalize() for more details on this.
         """
+        import spack.concretize
+
         if not self.name:
             raise spack.error.SpecError(
                 "Attempting to concretize anonymous spec")
@@ -2145,7 +2147,6 @@ def concretize(self, tests=False):
         force = False
 
         user_spec_deps = self.flat_dependencies(copy=False)
-        import spack.concretize
         concretizer = spack.concretize.Concretizer(self.copy())
         while changed:
             changes = (self.normalize(force, tests=tests,
diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index ec594e40885..fd0e1851685 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -633,3 +633,8 @@ def test_compiler_version_matches_any_entry_in_compilers_yaml(self):
         s = Spec('mpileaks %gcc@4.5:')
         s.concretize()
         assert str(s.compiler.version) == '4.5.0'
+
+    def test_concretize_anonymous(self):
+        with pytest.raises(spack.error.SpecError):
+            s = Spec('+variant')
+            s.concretize()

From 6ddc077e084adecdaf846a50124d63a80d1bd362 Mon Sep 17 00:00:00 2001
From: Tom Payerle <payerle@umd.edu>
Date: Wed, 27 May 2020 10:34:15 -0400
Subject: [PATCH 532/802] libxv: videoproto is a build and link dependency
 (#16821)

fixes #16820

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
---
 var/spack/repos/builtin/packages/libxv/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/libxv/package.py b/var/spack/repos/builtin/packages/libxv/package.py
index fdb3b6cf7f5..fc948f63f1a 100644
--- a/var/spack/repos/builtin/packages/libxv/package.py
+++ b/var/spack/repos/builtin/packages/libxv/package.py
@@ -19,6 +19,6 @@ class Libxv(AutotoolsPackage, XorgPackage):
     depends_on('libxext')
 
     depends_on('xextproto', type='build')
-    depends_on('videoproto', type='build')
+    depends_on('videoproto')
     depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')

From 187cb51b4970f4b2111d637c44b1f985271392ce Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Wed, 27 May 2020 14:02:37 +0200
Subject: [PATCH 533/802] spack containerize: allow 0.14.1 and 0.14.2 tags

fixes #16727
---
 lib/spack/spack/container/images.json | 16 ++++++++++++----
 lib/spack/spack/schema/container.py   |  5 ++++-
 2 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/lib/spack/spack/container/images.json b/lib/spack/spack/container/images.json
index ecd911815d4..c7226c4f595 100644
--- a/lib/spack/spack/container/images.json
+++ b/lib/spack/spack/container/images.json
@@ -8,7 +8,9 @@
     "build_tags": {
       "develop": "latest",
       "0.14": "0.14",
-      "0.14.0": "0.14.0"
+      "0.14.0": "0.14.0",
+      "0.14.1": "0.14.1",
+      "0.14.2": "0.14.2"
     }
   },
   "ubuntu:16.04": {
@@ -20,7 +22,9 @@
     "build_tags": {
       "develop": "latest",
       "0.14": "0.14",
-      "0.14.0": "0.14.0"
+      "0.14.0": "0.14.0",
+      "0.14.1": "0.14.1",
+      "0.14.2": "0.14.2"
     }
   },
   "centos:7": {
@@ -32,7 +36,9 @@
     "build_tags": {
       "develop": "latest",
       "0.14": "0.14",
-      "0.14.0": "0.14.0"
+      "0.14.0": "0.14.0",
+      "0.14.1": "0.14.1",
+      "0.14.2": "0.14.2"
     }
   },
   "centos:6": {
@@ -44,7 +50,9 @@
     "build_tags": {
       "develop": "latest",
       "0.14": "0.14",
-      "0.14.0": "0.14.0"
+      "0.14.0": "0.14.0",
+      "0.14.1": "0.14.1",
+      "0.14.2": "0.14.2"
     }
   }
 }
\ No newline at end of file
diff --git a/lib/spack/spack/schema/container.py b/lib/spack/spack/schema/container.py
index cb1ed8d63ac..fcfc398c832 100644
--- a/lib/spack/spack/schema/container.py
+++ b/lib/spack/spack/schema/container.py
@@ -29,7 +29,10 @@
                 },
                 'spack': {
                     'type': 'string',
-                    'enum': ['develop', '0.14', '0.14.0']
+                    'enum': [
+                        'develop',
+                        '0.14', '0.14.0', '0.14.1', '0.14.2'
+                    ]
                 }
             },
             'required': ['image', 'spack']

From 8f208b17e260c6469d7cf9acd97a42c6cdb589d1 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Wed, 27 May 2020 14:07:50 +0200
Subject: [PATCH 534/802] spack containerize: allow 0.14.3 tag for next release

---
 lib/spack/spack/container/images.json | 12 ++++++++----
 lib/spack/spack/schema/container.py   |  2 +-
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/lib/spack/spack/container/images.json b/lib/spack/spack/container/images.json
index c7226c4f595..0c047c7b8b0 100644
--- a/lib/spack/spack/container/images.json
+++ b/lib/spack/spack/container/images.json
@@ -10,7 +10,8 @@
       "0.14": "0.14",
       "0.14.0": "0.14.0",
       "0.14.1": "0.14.1",
-      "0.14.2": "0.14.2"
+      "0.14.2": "0.14.2",
+      "0.14.3": "0.14.3"
     }
   },
   "ubuntu:16.04": {
@@ -24,7 +25,8 @@
       "0.14": "0.14",
       "0.14.0": "0.14.0",
       "0.14.1": "0.14.1",
-      "0.14.2": "0.14.2"
+      "0.14.2": "0.14.2",
+      "0.14.3": "0.14.3"
     }
   },
   "centos:7": {
@@ -38,7 +40,8 @@
       "0.14": "0.14",
       "0.14.0": "0.14.0",
       "0.14.1": "0.14.1",
-      "0.14.2": "0.14.2"
+      "0.14.2": "0.14.2",
+      "0.14.3": "0.14.3"
     }
   },
   "centos:6": {
@@ -52,7 +55,8 @@
       "0.14": "0.14",
       "0.14.0": "0.14.0",
       "0.14.1": "0.14.1",
-      "0.14.2": "0.14.2"
+      "0.14.2": "0.14.2",
+      "0.14.3": "0.14.3"
     }
   }
 }
\ No newline at end of file
diff --git a/lib/spack/spack/schema/container.py b/lib/spack/spack/schema/container.py
index fcfc398c832..65e9f1bad86 100644
--- a/lib/spack/spack/schema/container.py
+++ b/lib/spack/spack/schema/container.py
@@ -31,7 +31,7 @@
                     'type': 'string',
                     'enum': [
                         'develop',
-                        '0.14', '0.14.0', '0.14.1', '0.14.2'
+                        '0.14', '0.14.0', '0.14.1', '0.14.2', '0.14.3'
                     ]
                 }
             },

From 4d5a68731abb7670d4e1ee4663f35af780de84da Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Thu, 28 May 2020 04:04:37 +0900
Subject: [PATCH 535/802] ffmpeg: set compilers command. (#16799)

---
 var/spack/repos/builtin/packages/ffmpeg/package.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/ffmpeg/package.py b/var/spack/repos/builtin/packages/ffmpeg/package.py
index 3eb365848cc..7d1b31fce80 100644
--- a/var/spack/repos/builtin/packages/ffmpeg/package.py
+++ b/var/spack/repos/builtin/packages/ffmpeg/package.py
@@ -108,7 +108,11 @@ def enable_or_disable_meta(self, variant, options):
 
     def configure_args(self):
         spec = self.spec
-        config_args = ['--enable-pic']
+        config_args = [
+            '--enable-pic',
+            '--cc={0}'.format(spack_cc),
+            '--cxx={0}'.format(spack_cxx)
+        ]
 
         # '+X' meta variant #
 

From 87cd375559858c4a311e623ae084a675a4c705ea Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Wed, 27 May 2020 13:51:19 -0700
Subject: [PATCH 536/802] ffmpeg: add a maintainer to the package (#16830)

---
 var/spack/repos/builtin/packages/ffmpeg/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/ffmpeg/package.py b/var/spack/repos/builtin/packages/ffmpeg/package.py
index 7d1b31fce80..cc3a0216e86 100644
--- a/var/spack/repos/builtin/packages/ffmpeg/package.py
+++ b/var/spack/repos/builtin/packages/ffmpeg/package.py
@@ -13,6 +13,8 @@ class Ffmpeg(AutotoolsPackage):
     homepage = "https://ffmpeg.org"
     url      = "http://ffmpeg.org/releases/ffmpeg-4.1.1.tar.bz2"
 
+    maintainers = ['xjrc']
+
     version('4.2.2',  sha256='b620d187c26f76ca19e74210a0336c3b8380b97730df5cdf45f3e69e89000e5c')
     version('4.1.1',  sha256='0cb40e3b8acaccd0ecb38aa863f66f0c6e02406246556c2992f67bf650fab058')
     version('4.1',    sha256='b684fb43244a5c4caae652af9022ed5d85ce15210835bce054a33fb26033a1a5')

From ab65a8ee27451d3a63375ec389ed050bc075db16 Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Thu, 28 May 2020 18:23:15 +0900
Subject: [PATCH 537/802] opencv: fix to build version 3.2.0 with Fujitsu
 compiler (#16840)

---
 .../packages/opencv/opencv3.2_fj.patch        | 20 +++++++++++++++++++
 .../repos/builtin/packages/opencv/package.py  |  1 +
 2 files changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/opencv/opencv3.2_fj.patch

diff --git a/var/spack/repos/builtin/packages/opencv/opencv3.2_fj.patch b/var/spack/repos/builtin/packages/opencv/opencv3.2_fj.patch
new file mode 100644
index 00000000000..dae8af256bb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opencv/opencv3.2_fj.patch
@@ -0,0 +1,20 @@
+diff -ru opencv-3.2.0.org/modules/core/include/opencv2/core/hal/intrin_neon.hpp opencv-3.2.0/modules/core/include/opencv2/core/hal/intrin_neon.hpp
+--- opencv-3.2.0.org/modules/core/include/opencv2/core/hal/intrin_neon.hpp      2016-12-23 21:54:44.000000000 +0900
++++ opencv-3.2.0/modules/core/include/opencv2/core/hal/intrin_neon.hpp  2020-05-27 14:39:11.288700481 +0900
+@@ -282,10 +282,16 @@
+ { return (int16x4_t)a; }
+ template <typename T> static inline float16x4_t vreinterpret_f16_s16(T a)
+ { return (float16x4_t)a; }
++#ifdef vld1_f16
++#undef vld1_f16
++#endif
+ template <typename T> static inline float16x4_t vld1_f16(const T* ptr)
+ { return vreinterpret_f16_s16(vld1_s16((const short*)ptr)); }
++#ifdef vst1_f16
++#undef vst1_f16
++#endif
+ template <typename T> static inline void vst1_f16(T* ptr, float16x4_t a)
+ { vst1_s16((short*)ptr, vreinterpret_s16_f16(a)); }
+
+ struct v_float16x4
+ {
diff --git a/var/spack/repos/builtin/packages/opencv/package.py b/var/spack/repos/builtin/packages/opencv/package.py
index c589e7fdd28..52f59263b84 100644
--- a/var/spack/repos/builtin/packages/opencv/package.py
+++ b/var/spack/repos/builtin/packages/opencv/package.py
@@ -126,6 +126,7 @@ class Opencv(CMakePackage, CudaPackage):
     patch('opencv3.2_regacyvtk.patch', when='@3.2+vtk')
     patch('opencv3.2_ffmpeg.patch', when='@3.2+videoio')
     patch('opencv3.2_python3.7.patch', when='@3.2+python')
+    patch('opencv3.2_fj.patch', when='@3.2 %fj')
 
     depends_on('eigen', when='+eigen')
     depends_on('zlib', when='+zlib')

From 4351c2eb3264545e2d70e8d78bbc8c1466f80ad9 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 28 May 2020 04:27:59 -0500
Subject: [PATCH 538/802] Update checksum for PyTorch patch (#16837)

---
 var/spack/repos/builtin/packages/py-torch/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py
index eb2eec608c3..4878c343762 100644
--- a/var/spack/repos/builtin/packages/py-torch/package.py
+++ b/var/spack/repos/builtin/packages/py-torch/package.py
@@ -175,7 +175,7 @@ class PyTorch(PythonPackage, CudaPackage):
     # https://github.com/pytorch/pytorch/pull/37086
     # Fixes compilation with Clang 9.0.0 and Apple Clang 11.0.3
     patch('https://github.com/pytorch/pytorch/commit/e921cd222a8fbeabf5a3e74e83e0d8dfb01aa8b5.patch',
-          sha256='7781c7ec0a661bf5a946a659f80e90df9dba116ad168762f15b10547113ae600',
+          sha256='17561b16cd2db22f10c0fe1fdcb428aecb0ac3964ba022a41343a6bb8cba7049',
           when='@1.1:1.5')
 
     # Fix for 'FindOpenMP.cmake'

From a6779061d7cbfa6e3bc98dffd3d139bc428014a2 Mon Sep 17 00:00:00 2001
From: Luca Heltai <luca.heltai@sissa.it>
Date: Thu, 28 May 2020 12:02:34 +0200
Subject: [PATCH 539/802] dealii: deal with nanoflann after 9.2.0 (#16839)

---
 var/spack/repos/builtin/packages/dealii/package.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 9760ac589d5..0f46c318f6d 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -16,7 +16,7 @@ class Dealii(CMakePackage, CudaPackage):
     url      = "https://github.com/dealii/dealii/releases/download/v8.4.1/dealii-8.4.1.tar.gz"
     git      = "https://github.com/dealii/dealii.git"
 
-    maintainers = ['davydden', 'jppelteret']
+    maintainers = ['davydden', 'jppelteret', 'luca-heltai']
 
     # Don't add RPATHs to this package for the full build DAG.
     # only add for immediate deps.
@@ -140,7 +140,8 @@ class Dealii(CMakePackage, CudaPackage):
     depends_on('metis@5:+int64',   when='+metis+int64')
     depends_on('metis@5:~int64',   when='+metis~int64')
     depends_on('muparser', when='+muparser')
-    depends_on('nanoflann',        when='@9.0:+nanoflann')
+    # Nanoflann support has been removed after 9.2.0
+    depends_on('nanoflann',        when='@9.0:9.2+nanoflann')
     depends_on('netcdf-c+mpi',     when='+netcdf+mpi')
     depends_on('netcdf-cxx',       when='+netcdf+mpi')
     depends_on('oce',              when='+oce')
@@ -211,6 +212,10 @@ class Dealii(CMakePackage, CudaPackage):
                       'onwards. Please explicitly disable this variant '
                       'via ~{0}'.format(p))
 
+    conflicts('+nanoflann', when='@9.3.0:',
+              msg='The interface to nanoflann was removed from version 9.3.0. '
+                  'Please explicitly disable this variant via ~nanoflann')
+
     conflicts('+slepc', when='~petsc',
               msg='It is not possible to enable slepc interfaces '
                   'without petsc.')

From 712fc696bab72c3a1ba92fc84d1c14ad2d6347af Mon Sep 17 00:00:00 2001
From: Marc Allen <allen.marc@gmail.com>
Date: Thu, 28 May 2020 04:33:09 -0600
Subject: [PATCH 540/802] npm: use mkdirp instead of mkdir (#16835)

fixes #16833

Co-authored-by: Marc Allen <mrcall@amazon.com>
---
 var/spack/repos/builtin/packages/npm/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/npm/package.py b/var/spack/repos/builtin/packages/npm/package.py
index 43be2a20017..0403f522bd9 100644
--- a/var/spack/repos/builtin/packages/npm/package.py
+++ b/var/spack/repos/builtin/packages/npm/package.py
@@ -54,11 +54,11 @@ def install(self, spec, prefix):
     def setup_dependent_build_environment(self, env, dependent_spec):
         npm_config_cache_dir = "%s/npm-cache" % dependent_spec.prefix
         if not os.path.isdir(npm_config_cache_dir):
-            mkdir(npm_config_cache_dir)
+            mkdirp(npm_config_cache_dir)
         env.set('npm_config_cache', npm_config_cache_dir)
 
     def setup_dependent_run_environment(self, env, dependent_spec):
         npm_config_cache_dir = "%s/npm-cache" % dependent_spec.prefix
         if not os.path.isdir(npm_config_cache_dir):
-            mkdir(npm_config_cache_dir)
+            mkdirp(npm_config_cache_dir)
         env.set('npm_config_cache', npm_config_cache_dir)

From 623cc7427e1833e4b506bf6ffd0049f28271887f Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Thu, 28 May 2020 14:58:55 -0600
Subject: [PATCH 541/802] legion: add v20.03.0 (#16848)

---
 var/spack/repos/builtin/packages/legion/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/legion/package.py b/var/spack/repos/builtin/packages/legion/package.py
index 15effc6bea6..cac38dd0303 100644
--- a/var/spack/repos/builtin/packages/legion/package.py
+++ b/var/spack/repos/builtin/packages/legion/package.py
@@ -27,6 +27,7 @@ class Legion(CMakePackage):
 
     version('master', branch='master')
     version('ctrl-rep', branch='control_replication')
+    version('20.03.0', sha256='ae5feedb5ed9f357b56424b9d73cea4f224a61e291e022556f796d1ff24d1244')
     version('19.12.0', sha256='ea517638de7256723bb9c119796d4d9d4ef662c52d0151ad24af5288e5a72e7d')
     version('19.09.1', sha256='c507133fb9dce16b7fcccd7eb2933d13cce96ecf835da60a27c0f66840cabf51')
     version('19.09.0', sha256='a01c3e3c6698cafb64b77a66341cc06d039faed4fa31b764159f021b94ce13e8')

From 38ac78489aa688327412c81ecc9799576ba98e7e Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Thu, 28 May 2020 17:11:28 -0700
Subject: [PATCH 542/802] bugfix: use flags when computing implicit rpaths
 (#16634)

* make verbose_flag a property

* tests
---
 lib/spack/spack/compiler.py        | 27 +++++++---
 lib/spack/spack/compilers/arm.py   |  4 +-
 lib/spack/spack/compilers/cce.py   |  4 +-
 lib/spack/spack/compilers/clang.py |  4 +-
 lib/spack/spack/compilers/fj.py    |  4 +-
 lib/spack/spack/compilers/gcc.py   |  4 +-
 lib/spack/spack/compilers/intel.py |  4 +-
 lib/spack/spack/compilers/pgi.py   |  4 +-
 lib/spack/spack/compilers/xl.py    |  4 +-
 lib/spack/spack/test/compilers.py  | 79 +++++++++++++++++++++++++++++-
 10 files changed, 113 insertions(+), 25 deletions(-)

diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py
index 94dbb190d24..5aa156dfc90 100644
--- a/lib/spack/spack/compiler.py
+++ b/lib/spack/spack/compiler.py
@@ -297,8 +297,10 @@ def implicit_rpaths(self):
         if self.enable_implicit_rpaths is False:
             return []
 
+        # Put CXX first since it has the most linking issues
+        # And because it has flags that affect linking
         exe_paths = [
-            x for x in [self.cc, self.cxx, self.fc, self.f77] if x]
+            x for x in [self.cxx, self.cc, self.fc, self.f77] if x]
         link_dirs = self._get_compiler_link_paths(exe_paths)
 
         all_required_libs = (
@@ -313,16 +315,24 @@ def required_libs(self):
         # By default every compiler returns the empty list
         return []
 
-    @classmethod
-    def _get_compiler_link_paths(cls, paths):
+    def _get_compiler_link_paths(self, paths):
         first_compiler = next((c for c in paths if c), None)
         if not first_compiler:
             return []
-        if not cls.verbose_flag():
+        if not self.verbose_flag:
             # In this case there is no mechanism to learn what link directories
             # are used by the compiler
             return []
 
+        # What flag types apply to first_compiler, in what order
+        flags = ['cppflags', 'ldflags']
+        if first_compiler == self.cc:
+            flags = ['cflags'] + flags
+        elif first_compiler == self.cxx:
+            flags = ['cxxflags'] + flags
+        else:
+            flags.append('fflags')
+
         try:
             tmpdir = tempfile.mkdtemp(prefix='spack-implicit-link-info')
             fout = os.path.join(tmpdir, 'output')
@@ -333,7 +343,10 @@ def _get_compiler_link_paths(cls, paths):
                     'int main(int argc, char* argv[]) { '
                     '(void)argc; (void)argv; return 0; }\n')
             compiler_exe = spack.util.executable.Executable(first_compiler)
-            output = str(compiler_exe(cls.verbose_flag(), fin, '-o', fout,
+            for flag_type in flags:
+                for flag in self.flags.get(flag_type, []):
+                    compiler_exe.add_default_arg(flag)
+            output = str(compiler_exe(self.verbose_flag, fin, '-o', fout,
                                       output=str, error=str))  # str for py2
 
             return _parse_non_system_link_dirs(output)
@@ -344,8 +357,8 @@ def _get_compiler_link_paths(cls, paths):
         finally:
             shutil.rmtree(tmpdir, ignore_errors=True)
 
-    @classmethod
-    def verbose_flag(cls):
+    @property
+    def verbose_flag(self):
         """
         This property should be overridden in the compiler subclass if a
         verbose flag is available.
diff --git a/lib/spack/spack/compilers/arm.py b/lib/spack/spack/compilers/arm.py
index 2f6e1950065..90514b4df80 100644
--- a/lib/spack/spack/compilers/arm.py
+++ b/lib/spack/spack/compilers/arm.py
@@ -51,8 +51,8 @@ def extract_version_from_output(cls, output):
                 temp = match.group(1) + "." + match.group(2)
         return temp
 
-    @classmethod
-    def verbose_flag(cls):
+    @property
+    def verbose_flag(self):
         return "-v"
 
     @property
diff --git a/lib/spack/spack/compilers/cce.py b/lib/spack/spack/compilers/cce.py
index 0d30a69d3e6..55fbe72556a 100644
--- a/lib/spack/spack/compilers/cce.py
+++ b/lib/spack/spack/compilers/cce.py
@@ -40,8 +40,8 @@ def version_argument(self):
 
     version_regex = r'[Vv]ersion.*?(\d+(\.\d+)+)'
 
-    @classmethod
-    def verbose_flag(cls):
+    @property
+    def verbose_flag(self):
         return "-v"
 
     @property
diff --git a/lib/spack/spack/compilers/clang.py b/lib/spack/spack/compilers/clang.py
index b14eaa1278b..9aa713e1a50 100644
--- a/lib/spack/spack/compilers/clang.py
+++ b/lib/spack/spack/compilers/clang.py
@@ -81,8 +81,8 @@ def is_apple(self):
         ver_string = str(self.version)
         return ver_string.endswith('-apple')
 
-    @classmethod
-    def verbose_flag(cls):
+    @property
+    def verbose_flag(self):
         return "-v"
 
     @property
diff --git a/lib/spack/spack/compilers/fj.py b/lib/spack/spack/compilers/fj.py
index 54d9308c4a0..255fa356722 100644
--- a/lib/spack/spack/compilers/fj.py
+++ b/lib/spack/spack/compilers/fj.py
@@ -30,8 +30,8 @@ class Fj(spack.compiler.Compiler):
 
     required_libs = ['libfj90i', 'libfj90f', 'libfjsrcinfo']
 
-    @classmethod
-    def verbose_flag(cls):
+    @property
+    def verbose_flag(self):
         return "-v"
 
     @property
diff --git a/lib/spack/spack/compilers/gcc.py b/lib/spack/spack/compilers/gcc.py
index fc9074a67aa..5fd4677b3bb 100644
--- a/lib/spack/spack/compilers/gcc.py
+++ b/lib/spack/spack/compilers/gcc.py
@@ -38,8 +38,8 @@ class Gcc(Compiler):
     PrgEnv = 'PrgEnv-gnu'
     PrgEnv_compiler = 'gcc'
 
-    @classmethod
-    def verbose_flag(cls):
+    @property
+    def verbose_flag(self):
         return "-v"
 
     @property
diff --git a/lib/spack/spack/compilers/intel.py b/lib/spack/spack/compilers/intel.py
index c7d853e3fa9..6d0aa09b878 100644
--- a/lib/spack/spack/compilers/intel.py
+++ b/lib/spack/spack/compilers/intel.py
@@ -32,8 +32,8 @@ class Intel(Compiler):
     version_argument = '--version'
     version_regex = r'\((?:IFORT|ICC)\) ([^ ]+)'
 
-    @classmethod
-    def verbose_flag(cls):
+    @property
+    def verbose_flag(self):
         return "-v"
 
     required_libs = ['libirc', 'libifcore', 'libifcoremt', 'libirng']
diff --git a/lib/spack/spack/compilers/pgi.py b/lib/spack/spack/compilers/pgi.py
index 13d8f69ec51..ab866f1f2c7 100644
--- a/lib/spack/spack/compilers/pgi.py
+++ b/lib/spack/spack/compilers/pgi.py
@@ -33,8 +33,8 @@ class Pgi(Compiler):
     ignore_version_errors = [2]  # `pgcc -V` on PowerPC annoyingly returns 2
     version_regex = r'pg[^ ]* ([0-9.]+)-[0-9]+ (LLVM )?[^ ]+ target on '
 
-    @classmethod
-    def verbose_flag(cls):
+    @property
+    def verbose_flag(self):
         return "-v"
 
     @property
diff --git a/lib/spack/spack/compilers/xl.py b/lib/spack/spack/compilers/xl.py
index 46a5002e25d..af84d5edb95 100644
--- a/lib/spack/spack/compilers/xl.py
+++ b/lib/spack/spack/compilers/xl.py
@@ -29,8 +29,8 @@ class Xl(Compiler):
     version_argument = '-qversion'
     version_regex = r'([0-9]?[0-9]\.[0-9])'
 
-    @classmethod
-    def verbose_flag(cls):
+    @property
+    def verbose_flag(self):
         return "-V"
 
     @property
diff --git a/lib/spack/spack/test/compilers.py b/lib/spack/spack/test/compilers.py
index 586bb215cfe..b38f19dcbc3 100644
--- a/lib/spack/spack/test/compilers.py
+++ b/lib/spack/spack/test/compilers.py
@@ -145,8 +145,8 @@ def test_compiler_flags_from_config_are_grouped():
     'paths': {
         'cc': 'cc-path',
         'cxx': 'cxx-path',
-        'fc': None,
-        'f77': None
+        'fc': 'fc-path',
+        'f77': 'f77-path'
     },
     'flags': {},
     'modules': None
@@ -165,6 +165,8 @@ def __init__(self):
              default_compiler_entry['paths']['fc'],
              default_compiler_entry['paths']['f77']])
 
+    _get_compiler_link_paths = Compiler._get_compiler_link_paths
+
     @property
     def name(self):
         return "mockcompiler"
@@ -173,6 +175,12 @@ def name(self):
     def version(self):
         return "1.0.0"
 
+    _verbose_flag = "--verbose"
+
+    @property
+    def verbose_flag(self):
+        return self._verbose_flag
+
     required_libs = ['libgfortran']
 
 
@@ -192,6 +200,73 @@ def try_all_dirs(*args):
     assert set(retrieved_rpaths) == expected_rpaths
 
 
+no_flag_dirs = ['/path/to/first/lib', '/path/to/second/lib64']
+no_flag_output = 'ld -L%s -L%s' % tuple(no_flag_dirs)
+
+flag_dirs = ['/path/to/first/with/flag/lib', '/path/to/second/lib64']
+flag_output = 'ld -L%s -L%s' % tuple(flag_dirs)
+
+
+def call_compiler(exe, *args, **kwargs):
+    # This method can replace Executable.__call__ to emulate a compiler that
+    # changes libraries depending on a flag.
+    if '--correct-flag' in exe.exe:
+        return flag_output
+    return no_flag_output
+
+
+@pytest.mark.parametrize('exe,flagname', [
+    ('cxx', ''),
+    ('cxx', 'cxxflags'),
+    ('cxx', 'cppflags'),
+    ('cxx', 'ldflags'),
+    ('cc', ''),
+    ('cc', 'cflags'),
+    ('cc', 'cppflags'),
+    ('fc', ''),
+    ('fc', 'fflags'),
+    ('f77', 'fflags'),
+    ('f77', 'cppflags'),
+])
+def test_get_compiler_link_paths(monkeypatch, exe, flagname):
+    # create fake compiler that emits mock verbose output
+    compiler = MockCompiler()
+    monkeypatch.setattr(
+        spack.util.executable.Executable, '__call__', call_compiler)
+
+    # Grab executable path to test
+    paths = [getattr(compiler, exe)]
+
+    # Test without flags
+    dirs = compiler._get_compiler_link_paths(paths)
+    assert dirs == no_flag_dirs
+
+    if flagname:
+        # set flags and test
+        setattr(compiler, 'flags', {flagname: ['--correct-flag']})
+        dirs = compiler._get_compiler_link_paths(paths)
+        assert dirs == flag_dirs
+
+
+def test_get_compiler_link_paths_no_path():
+    compiler = MockCompiler()
+    compiler.cc = None
+    compiler.cxx = None
+    compiler.f77 = None
+    compiler.fc = None
+
+    dirs = compiler._get_compiler_link_paths([compiler.cxx])
+    assert dirs == []
+
+
+def test_get_compiler_link_paths_no_verbose_flag():
+    compiler = MockCompiler()
+    compiler._verbose_flag = None
+
+    dirs = compiler._get_compiler_link_paths([compiler.cxx])
+    assert dirs == []
+
+
 # Get the desired flag from the specified compiler spec.
 def flag_value(flag, spec):
     compiler = None

From 2aca0cf56575bcf31fffb1dbf294092ead006c5f Mon Sep 17 00:00:00 2001
From: 0t1s1 <65258917+0t1s1@users.noreply.github.com>
Date: Fri, 29 May 2020 00:37:12 -0700
Subject: [PATCH 543/802] gridlab-d: added new package.  (#16816)

---
 .../builtin/packages/gridlab-d/package.py     | 59 +++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/gridlab-d/package.py

diff --git a/var/spack/repos/builtin/packages/gridlab-d/package.py b/var/spack/repos/builtin/packages/gridlab-d/package.py
new file mode 100644
index 00000000000..d7942d2d21e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gridlab-d/package.py
@@ -0,0 +1,59 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class GridlabD(AutotoolsPackage):
+    """
+    Autotools package for Gridlab-D, a new power distribution system simulation
+    and analysis tool that provides valuable information to users who design
+    and operate distribution systems, and to utilities that wish to take
+    advantage of the latest energy technologies. Gridlab-D is a flexible
+    simulation environment that can be integrated with a variety of third-party
+    data management and analysis tools.
+    """
+
+    homepage = "https://www.gridlabd.org/"
+    git      = "https://github.com/gridlab-d/gridlab-d"
+
+    maintainers = ['0t1s1', 'yee29', 'afisher1']
+
+    # Using only develop as other branches and releases did not build properly.
+    version('develop', branch='develop')
+
+    variant("mysql",
+            default=False,
+            description="Enable MySQL support for Gridlab-D.")
+    variant('helics',
+            default=False,
+            description='Enable Helics support for Gridlab-D.')
+
+    # Add dependencies.
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('m4', type='build')
+    depends_on("xerces-c")
+    depends_on("superlu-mt")
+    depends_on('helics', when='+helics')
+
+    def configure_args(self):
+        args = []
+
+        if '+helics' in self.spec:
+            # Taken from
+            # https://github.com/GMLC-TDC/HELICS-Tutorial/tree/master/setup
+            args.append('--with-helics=' + self.spec['helics'].prefix)
+            args.append('CFLAGS=-g -O0 -w')
+            args.append('CXXFLAGS=-g -O0 -w -std=c++14')
+            args.append('LDFLAGS=-g -O0 -w')
+
+        return args
+
+    def setup_run_environment(self, env):
+        # Need to add GLPATH otherwise Gridlab-D will not run.
+        env.set('GLPATH', join_path(self.prefix, 'lib', 'gridlabd'))
+        env.prepend_path('GLPATH', join_path(self.prefix, 'share', 'gridlabd'))

From a21fab6fe4534bdda7bfb86efa320fb2c4c8df57 Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Fri, 29 May 2020 01:52:31 -0700
Subject: [PATCH 544/802] compilers: add opt_flags and debug_flags properties
 (#16710)

---
 lib/spack/spack/compiler.py        |  8 +++++
 lib/spack/spack/compilers/arm.py   |  4 +++
 lib/spack/spack/compilers/cce.py   |  4 +++
 lib/spack/spack/compilers/clang.py | 10 ++++++
 lib/spack/spack/compilers/fj.py    |  4 +++
 lib/spack/spack/compilers/gcc.py   |  8 +++++
 lib/spack/spack/compilers/intel.py |  8 +++++
 lib/spack/spack/compilers/nag.py   |  8 +++++
 lib/spack/spack/compilers/pgi.py   |  8 +++++
 lib/spack/spack/compilers/xl.py    |  8 +++++
 lib/spack/spack/test/compilers.py  | 52 ++++++++++++++++++++++++++++++
 11 files changed, 122 insertions(+)

diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py
index 5aa156dfc90..410188fff49 100644
--- a/lib/spack/spack/compiler.py
+++ b/lib/spack/spack/compiler.py
@@ -245,6 +245,14 @@ def enable_new_dtags(self):
             return ''
         return '--enable-new-dtags'
 
+    @property
+    def debug_flags(self):
+        return ['-g']
+
+    @property
+    def opt_flags(self):
+        return ['-O', '-O0', '-O1', '-O2', '-O3']
+
     # Cray PrgEnv name that can be used to load this compiler
     PrgEnv = None
     # Name of module used to switch versions of this compiler
diff --git a/lib/spack/spack/compilers/arm.py b/lib/spack/spack/compilers/arm.py
index 90514b4df80..59eb1714b81 100644
--- a/lib/spack/spack/compilers/arm.py
+++ b/lib/spack/spack/compilers/arm.py
@@ -55,6 +55,10 @@ def extract_version_from_output(cls, output):
     def verbose_flag(self):
         return "-v"
 
+    @property
+    def opt_flags(self):
+        return ['-O', '-O0', '-O1', '-O2', '-O3', '-Ofast']
+
     @property
     def openmp_flag(self):
         return "-fopenmp"
diff --git a/lib/spack/spack/compilers/cce.py b/lib/spack/spack/compilers/cce.py
index 55fbe72556a..47c0263cfd7 100644
--- a/lib/spack/spack/compilers/cce.py
+++ b/lib/spack/spack/compilers/cce.py
@@ -44,6 +44,10 @@ def version_argument(self):
     def verbose_flag(self):
         return "-v"
 
+    @property
+    def debug_flags(self):
+        return ['-g', '-G0', '-G1', '-G2', '-Gfast']
+
     @property
     def openmp_flag(self):
         if self.version >= ver('9.0'):
diff --git a/lib/spack/spack/compilers/clang.py b/lib/spack/spack/compilers/clang.py
index 9aa713e1a50..f5c39889ec8 100644
--- a/lib/spack/spack/compilers/clang.py
+++ b/lib/spack/spack/compilers/clang.py
@@ -50,6 +50,16 @@ class Clang(Compiler):
     # Subclasses use possible names of Fortran 90 compiler
     fc_names = ['flang', 'gfortran', 'xlf90_r']
 
+    @property
+    def debug_flags(self):
+        return ['-gcodeview', '-gdwarf-2', '-gdwarf-3', '-gdwarf-4',
+                '-gdwarf-5', '-gline-tables-only', '-gmodules', '-gz', '-g']
+
+    @property
+    def opt_flags(self):
+        return ['-O0', '-O1', '-O2', '-O3', '-Ofast', '-Os', '-Oz', '-Og',
+                '-O', '-O4']
+
     # Clang has support for using different fortran compilers with the
     # clang executable.
     @property
diff --git a/lib/spack/spack/compilers/fj.py b/lib/spack/spack/compilers/fj.py
index 255fa356722..3747d49d9bf 100644
--- a/lib/spack/spack/compilers/fj.py
+++ b/lib/spack/spack/compilers/fj.py
@@ -34,6 +34,10 @@ class Fj(spack.compiler.Compiler):
     def verbose_flag(self):
         return "-v"
 
+    @property
+    def opt_flags(self):
+        return ['-O', '-O0', '-O1', '-O2', '-O3', '-O4']
+
     @property
     def openmp_flag(self):
         return "-Kopenmp"
diff --git a/lib/spack/spack/compilers/gcc.py b/lib/spack/spack/compilers/gcc.py
index 5fd4677b3bb..7cbf3e4fa89 100644
--- a/lib/spack/spack/compilers/gcc.py
+++ b/lib/spack/spack/compilers/gcc.py
@@ -42,6 +42,14 @@ class Gcc(Compiler):
     def verbose_flag(self):
         return "-v"
 
+    @property
+    def debug_flags(self):
+        return ['-g', '-gstabs+', '-gstabs', '-gxcoff+', '-gxcoff', '-gvms']
+
+    @property
+    def opt_flags(self):
+        return ['-O', '-O0', '-O1', '-O2', '-O3', '-Os', '-Ofast', '-Og']
+
     @property
     def openmp_flag(self):
         return "-fopenmp"
diff --git a/lib/spack/spack/compilers/intel.py b/lib/spack/spack/compilers/intel.py
index 6d0aa09b878..b44ed73d6fc 100644
--- a/lib/spack/spack/compilers/intel.py
+++ b/lib/spack/spack/compilers/intel.py
@@ -38,6 +38,14 @@ def verbose_flag(self):
 
     required_libs = ['libirc', 'libifcore', 'libifcoremt', 'libirng']
 
+    @property
+    def debug_flags(self):
+        return ['-debug', '-g', '-g0', '-g1', '-g2', '-g3']
+
+    @property
+    def opt_flags(self):
+        return ['-O', '-O0', '-O1', '-O2', '-O3', '-Ofast', '-Os']
+
     @property
     def openmp_flag(self):
         if self.version < ver('16.0'):
diff --git a/lib/spack/spack/compilers/nag.py b/lib/spack/spack/compilers/nag.py
index e5dffa4a67b..4b2de06c079 100644
--- a/lib/spack/spack/compilers/nag.py
+++ b/lib/spack/spack/compilers/nag.py
@@ -34,6 +34,14 @@ class Nag(spack.compiler.Compiler):
     def openmp_flag(self):
         return "-openmp"
 
+    @property
+    def debug_flags(self):
+        return ['-g', '-gline', '-g90']
+
+    @property
+    def opt_flags(self):
+        return ['-O', '-O0', '-O1', '-O2', '-O3', '-O4']
+
     @property
     def cxx11_flag(self):
         # NAG does not have a C++ compiler
diff --git a/lib/spack/spack/compilers/pgi.py b/lib/spack/spack/compilers/pgi.py
index ab866f1f2c7..f782e1fc86f 100644
--- a/lib/spack/spack/compilers/pgi.py
+++ b/lib/spack/spack/compilers/pgi.py
@@ -37,6 +37,14 @@ class Pgi(Compiler):
     def verbose_flag(self):
         return "-v"
 
+    @property
+    def debug_flags(self):
+        return ['-g', '-gopt']
+
+    @property
+    def opt_flags(self):
+        return ['-O', '-O0', '-O1', '-O2', '-O3', '-O4']
+
     @property
     def openmp_flag(self):
         return "-mp"
diff --git a/lib/spack/spack/compilers/xl.py b/lib/spack/spack/compilers/xl.py
index af84d5edb95..ce74ec47c1f 100644
--- a/lib/spack/spack/compilers/xl.py
+++ b/lib/spack/spack/compilers/xl.py
@@ -33,6 +33,14 @@ class Xl(Compiler):
     def verbose_flag(self):
         return "-V"
 
+    @property
+    def debug_flags(self):
+        return ['-g', '-g0', '-g1', '-g2', '-g8', '-g9']
+
+    @property
+    def opt_flags(self):
+        return ['-O', '-O0', '-O1', '-O2', '-O3', '-O4', '-O5', '-Ofast']
+
     @property
     def openmp_flag(self):
         return "-qsmp=omp"
diff --git a/lib/spack/spack/test/compilers.py b/lib/spack/spack/test/compilers.py
index b38f19dcbc3..7c79e9027fb 100644
--- a/lib/spack/spack/test/compilers.py
+++ b/lib/spack/spack/test/compilers.py
@@ -316,6 +316,8 @@ def test_default_flags():
     supported_flag_test("cxx_pic_flag", "-fPIC")
     supported_flag_test("f77_pic_flag", "-fPIC")
     supported_flag_test("fc_pic_flag",  "-fPIC")
+    supported_flag_test("debug_flags", ["-g"])
+    supported_flag_test("opt_flags", ["-O", "-O0", "-O1", "-O2", "-O3"])
 
 
 # Verify behavior of particular compiler definitions.
@@ -330,6 +332,9 @@ def test_arm_flags():
     supported_flag_test("cxx_pic_flag", "-fPIC", "arm@1.0")
     supported_flag_test("f77_pic_flag", "-fPIC", "arm@1.0")
     supported_flag_test("fc_pic_flag",  "-fPIC", "arm@1.0")
+    supported_flag_test("opt_flags",
+                        ['-O', '-O0', '-O1', '-O2', '-O3', '-Ofast'],
+                        'arm@1.0')
 
 
 def test_cce_flags():
@@ -344,6 +349,8 @@ def test_cce_flags():
     supported_flag_test("cxx_pic_flag", "-h PIC", "cce@1.0")
     supported_flag_test("f77_pic_flag", "-h PIC", "cce@1.0")
     supported_flag_test("fc_pic_flag",  "-h PIC", "cce@1.0")
+    supported_flag_test("debug_flags", ['-g', '-G0', '-G1', '-G2', '-Gfast'],
+                        'cce@1.0')
 
 
 def test_clang_flags():
@@ -382,6 +389,15 @@ def test_clang_flags():
     supported_flag_test("cxx_pic_flag", "-fPIC", "clang@3.3")
     supported_flag_test("f77_pic_flag", "-fPIC", "clang@3.3")
     supported_flag_test("fc_pic_flag",  "-fPIC", "clang@3.3")
+    supported_flag_test("debug_flags",
+                        ['-gcodeview', '-gdwarf-2', '-gdwarf-3', '-gdwarf-4',
+                         '-gdwarf-5', '-gline-tables-only', '-gmodules', '-gz',
+                         '-g'],
+                        'clang@3.3')
+    supported_flag_test("opt_flags",
+                        ['-O0', '-O1', '-O2', '-O3', '-Ofast', '-Os', '-Oz',
+                         '-Og', '-O', '-O4'],
+                        'clang@3.3')
 
 
 def test_fj_flags():
@@ -395,6 +411,8 @@ def test_fj_flags():
     supported_flag_test("cxx_pic_flag", "-KPIC", "fj@4.0.0")
     supported_flag_test("f77_pic_flag", "-KPIC", "fj@4.0.0")
     supported_flag_test("fc_pic_flag",  "-KPIC", "fj@4.0.0")
+    supported_flag_test("opt_flags", ['-O', '-O0', '-O1', '-O2', '-O3', '-O4'],
+                        'fj@4.0.0')
 
 
 def test_gcc_flags():
@@ -420,6 +438,14 @@ def test_gcc_flags():
     supported_flag_test("f77_pic_flag", "-fPIC", "gcc@4.0")
     supported_flag_test("fc_pic_flag",  "-fPIC", "gcc@4.0")
     supported_flag_test("stdcxx_libs", ("-lstdc++",), "gcc@4.1")
+    supported_flag_test("debug_flags",
+                        ['-g', '-gstabs+', '-gstabs', '-gxcoff+', '-gxcoff',
+                         '-gvms'],
+                        'gcc@4.0')
+    supported_flag_test("opt_flags",
+                        ['-O', '-O0', '-O1', '-O2', '-O3', '-Os', '-Ofast',
+                         '-Og'],
+                        'gcc@4.0')
 
 
 def test_intel_flags():
@@ -440,6 +466,12 @@ def test_intel_flags():
     supported_flag_test("f77_pic_flag", "-fPIC", "intel@1.0")
     supported_flag_test("fc_pic_flag",  "-fPIC", "intel@1.0")
     supported_flag_test("stdcxx_libs", ("-cxxlib",), "intel@1.0")
+    supported_flag_test("debug_flags",
+                        ['-debug', '-g', '-g0', '-g1', '-g2', '-g3'],
+                        'intel@1.0')
+    supported_flag_test("opt_flags",
+                        ['-O', '-O0', '-O1', '-O2', '-O3', '-Ofast', '-Os'],
+                        'intel@1.0')
 
 
 def test_nag_flags():
@@ -454,6 +486,9 @@ def test_nag_flags():
     supported_flag_test("f77_rpath_arg", "-Wl,-Wl,,-rpath,,", "nag@1.0")
     supported_flag_test("fc_rpath_arg",  "-Wl,-Wl,,-rpath,,", "nag@1.0")
     supported_flag_test("linker_arg", "-Wl,-Wl,,", "nag@1.0")
+    supported_flag_test("debug_flags", ['-g', '-gline', '-g90'], 'nag@1.0')
+    supported_flag_test("opt_flags", ['-O', '-O0', '-O1', '-O2', '-O3', '-O4'],
+                        'nag@1.0')
 
 
 def test_pgi_flags():
@@ -467,6 +502,9 @@ def test_pgi_flags():
     supported_flag_test("cxx_pic_flag", "-fpic", "pgi@1.0")
     supported_flag_test("f77_pic_flag", "-fpic", "pgi@1.0")
     supported_flag_test("fc_pic_flag",  "-fpic", "pgi@1.0")
+    supported_flag_test("debug_flags", ['-g', '-gopt'], 'pgi@1.0')
+    supported_flag_test("opt_flags", ['-O', '-O0', '-O1', '-O2', '-O3', '-O4'],
+                        'pgi@1.0')
 
 
 def test_xl_flags():
@@ -484,6 +522,13 @@ def test_xl_flags():
     supported_flag_test("f77_pic_flag", "-qpic", "xl@1.0")
     supported_flag_test("fc_pic_flag",  "-qpic", "xl@1.0")
     supported_flag_test("fflags", "-qzerosize", "xl@1.0")
+    supported_flag_test("debug_flags",
+                        ['-g', '-g0', '-g1', '-g2', '-g8', '-g9'],
+                        'xl@1.0')
+    supported_flag_test("opt_flags",
+                        ['-O', '-O0', '-O1', '-O2', '-O3', '-O4', '-O5',
+                         '-Ofast'],
+                        'xl@1.0')
 
 
 def test_xl_r_flags():
@@ -501,6 +546,13 @@ def test_xl_r_flags():
     supported_flag_test("f77_pic_flag", "-qpic", "xl_r@1.0")
     supported_flag_test("fc_pic_flag",  "-qpic", "xl_r@1.0")
     supported_flag_test("fflags", "-qzerosize", "xl_r@1.0")
+    supported_flag_test("debug_flags",
+                        ['-g', '-g0', '-g1', '-g2', '-g8', '-g9'],
+                        'xl@1.0')
+    supported_flag_test("opt_flags",
+                        ['-O', '-O0', '-O1', '-O2', '-O3', '-O4', '-O5',
+                         '-Ofast'],
+                        'xl@1.0')
 
 
 @pytest.mark.parametrize('version_str,expected_version', [

From 6af3272e1d1aec207f8347a44e2c424d47bcee16 Mon Sep 17 00:00:00 2001
From: Jane Herriman <xorJane@users.noreply.github.com>
Date: Fri, 29 May 2020 01:53:43 -0700
Subject: [PATCH 545/802] Update error message when
 UnavailableCompilerVersionError is triggered (#16838)

Co-authored-by: Herriman <herriman1@panorama.llnl.gov>
---
 lib/spack/spack/concretize.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py
index e460f456002..7424b8a90dc 100644
--- a/lib/spack/spack/concretize.py
+++ b/lib/spack/spack/concretize.py
@@ -727,7 +727,9 @@ def __init__(self, compiler_spec, arch=None):
             )
 
         super(UnavailableCompilerVersionError, self).__init__(
-            err_msg, "Run 'spack compiler find' to add compilers.")
+            err_msg, "Run 'spack compiler find' to add compilers or "
+            "'spack compilers' to see which compilers are already recognized"
+            " by spack.")
 
 
 class NoValidVersionError(spack.error.SpackError):

From bd95b7df861b079c5490ee13cbb8d44a6ca2106a Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Fri, 29 May 2020 02:57:21 -0700
Subject: [PATCH 546/802] spack module_cmd: set LD_LIBRARY_PATH for python in
 subshell. (#16827)

* Ensure python runs with proper ld_library_path within Spack regardless of environment
---
 lib/spack/spack/main.py                 |  1 +
 lib/spack/spack/test/util/executable.py |  7 ++--
 lib/spack/spack/util/module_cmd.py      | 46 ++++++++++++++++++++++---
 3 files changed, 46 insertions(+), 8 deletions(-)

diff --git a/lib/spack/spack/main.py b/lib/spack/spack/main.py
index 3677764cb6a..bdeef049ff6 100644
--- a/lib/spack/spack/main.py
+++ b/lib/spack/spack/main.py
@@ -92,6 +92,7 @@
 
 #: Recorded directory where spack command was originally invoked
 spack_working_dir = None
+spack_ld_library_path = os.environ.get('LD_LIBRARY_PATH', '')
 
 
 def set_working_dir():
diff --git a/lib/spack/spack/test/util/executable.py b/lib/spack/spack/test/util/executable.py
index 26719e94d1c..8baae3b4539 100644
--- a/lib/spack/spack/test/util/executable.py
+++ b/lib/spack/spack/test/util/executable.py
@@ -4,18 +4,19 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import sys
+import os
 
 import llnl.util.filesystem as fs
-
+import spack
 import spack.util.executable as ex
 from spack.hooks.sbang import filter_shebangs_in_directory
 
 
-def test_read_unicode(tmpdir):
+def test_read_unicode(tmpdir, working_env):
     script_name = 'print_unicode.py'
 
     with tmpdir.as_cwd():
-
+        os.environ['LD_LIBRARY_PATH'] = spack.main.spack_ld_library_path
         # make a script that prints some unicode
         with open(script_name, 'w') as f:
             f.write('''#!{0}
diff --git a/lib/spack/spack/util/module_cmd.py b/lib/spack/spack/util/module_cmd.py
index 143ad3d43e7..a5ebe73c847 100644
--- a/lib/spack/spack/util/module_cmd.py
+++ b/lib/spack/spack/util/module_cmd.py
@@ -13,12 +13,13 @@
 import json
 import re
 
+import spack
 import llnl.util.tty as tty
 
 # This list is not exhaustive. Currently we only use load and unload
 # If we need another option that changes the environment, add it here.
 module_change_commands = ['load', 'swap', 'unload', 'purge', 'use', 'unuse']
-py_cmd = "'import os;import json;print(json.dumps(dict(os.environ)))'"
+py_cmd = 'import os;import json;print(json.dumps(dict(os.environ)))'
 _cmd_template = "'module ' + ' '.join(args) + ' 2>&1'"
 
 
@@ -27,7 +28,31 @@ def module(*args):
     if args[0] in module_change_commands:
         # Do the module manipulation, then output the environment in JSON
         # and read the JSON back in the parent process to update os.environ
-        module_cmd += ' >/dev/null;' + sys.executable + ' -c %s' % py_cmd
+        # For python, we use the same python running the Spack process, because
+        # we can guarantee its existence. We have to do some LD_LIBRARY_PATH
+        # shenanigans to ensure python will run.
+
+        # LD_LIBRARY_PATH under which Spack ran
+        os.environ['SPACK_LD_LIBRARY_PATH'] = spack.main.spack_ld_library_path
+
+        # suppress output from module function
+        module_cmd += ' >/dev/null;'
+
+        # Capture the new LD_LIBRARY_PATH after `module` was run
+        module_cmd += 'export SPACK_NEW_LD_LIBRARY_PATH="$LD_LIBRARY_PATH";'
+
+        # Set LD_LIBRARY_PATH to value at Spack startup time to ensure that
+        # python executable finds its libraries
+        module_cmd += 'LD_LIBRARY_PATH="$SPACK_LD_LIBRARY_PATH" '
+
+        # Execute the python command
+        module_cmd += '%s -c "%s";' % (sys.executable, py_cmd)
+
+        # If LD_LIBRARY_PATH was set after `module`, dump the old value because
+        # we have since corrupted it to ensure python would run.
+        # dump SPACKIGNORE as a placeholder for parsing if LD_LIBRARY_PATH null
+        module_cmd += 'echo "${SPACK_NEW_LD_LIBRARY_PATH:-SPACKIGNORE}"'
+
         module_p  = subprocess.Popen(module_cmd,
                                      stdout=subprocess.PIPE,
                                      stderr=subprocess.STDOUT,
@@ -36,13 +61,24 @@ def module(*args):
 
         # Cray modules spit out warnings that we cannot supress.
         # This hack skips to the last output (the environment)
-        env_output = str(module_p.communicate()[0].decode())
-        env = env_output.strip().split('\n')[-1]
+        env_out = str(module_p.communicate()[0].decode()).strip().split('\n')
+
+        # The environment dumped as json
+        env_json = env_out[-2]
+        # Either the uncorrupted $LD_LIBRARY_PATH or SPACKIGNORE
+        new_ld_library_path = env_out[-1]
 
         # Update os.environ with new dict
-        env_dict = json.loads(env)
+        env_dict = json.loads(env_json)
         os.environ.clear()
         os.environ.update(env_dict)
+
+        # Override restored LD_LIBRARY_PATH with pre-python value
+        if new_ld_library_path == 'SPACKIGNORE':
+            os.environ.pop('LD_LIBRARY_PATH', None)
+        else:
+            os.environ['LD_LIBRARY_PATH'] = new_ld_library_path
+
     else:
         # Simply execute commands that don't change state and return output
         module_p = subprocess.Popen(module_cmd,

From edd075a5e1031cfedde904f194e1cf79e0fc76f7 Mon Sep 17 00:00:00 2001
From: Robert Rosca <32569096+RobertRosca@users.noreply.github.com>
Date: Fri, 29 May 2020 13:23:02 +0200
Subject: [PATCH 547/802] Mention that packages can be uninstalled by hash
 (#16863)

---
 lib/spack/spack/cmd/uninstall.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index 2757d5d232e..f03270d06d5 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -26,7 +26,8 @@
 
 error_message = """You can either:
     a) use a more specific spec, or
-    b) use `spack uninstall --all` to uninstall ALL matching specs.
+    b) specify the package by its hash (e.g. `spack uninstall /hash`), or
+    c) use `spack uninstall --all` to uninstall ALL matching specs.
 """
 
 # Arguments for display_specs when we find ambiguity

From 11fc6c57915ca148a116f14cd608b1424efb6f5b Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Fri, 29 May 2020 10:17:55 -0600
Subject: [PATCH 548/802] examinimd/miniaero: fix build with kokkos-legacy
 (#16867)

* examinimd/miniaero: fix build with kokkos-legacy

* flake8
---
 var/spack/repos/builtin/packages/examinimd/package.py | 3 ++-
 var/spack/repos/builtin/packages/miniaero/package.py  | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/examinimd/package.py b/var/spack/repos/builtin/packages/examinimd/package.py
index f93a33ea01c..c8afa1c2232 100644
--- a/var/spack/repos/builtin/packages/examinimd/package.py
+++ b/var/spack/repos/builtin/packages/examinimd/package.py
@@ -41,7 +41,8 @@ class Examinimd(MakefilePackage):
     def build_targets(self):
         targets = []
         # Append Kokkos
-        targets.append('KOKKOS_PATH={0}'.format(self.spec['kokkos'].prefix))
+        targets.append('KOKKOS_PATH={0}'.format(
+            self.spec['kokkos-legacy'].prefix))
         # Set kokkos device
         if 'openmp' in self.spec:
             targets.append('KOKKOS_DEVICES=OpenMP')
diff --git a/var/spack/repos/builtin/packages/miniaero/package.py b/var/spack/repos/builtin/packages/miniaero/package.py
index a18a5bfecf9..3588e87d28d 100644
--- a/var/spack/repos/builtin/packages/miniaero/package.py
+++ b/var/spack/repos/builtin/packages/miniaero/package.py
@@ -26,7 +26,8 @@ def build_targets(self):
         targets = [
             '--directory=kokkos',
             'CXX=c++',
-            'KOKKOS_PATH={0}'.format(self.spec['kokkos'].prefix)
+            'KOKKOS_PATH={0}'.format(
+                self.spec['kokkos-legacy'].prefix)
         ]
 
         return targets

From ec5959694c740f0e33207d5643346d97a26c6b83 Mon Sep 17 00:00:00 2001
From: Nicholas Sly <nicholas.sly@gmail.com>
Date: Fri, 29 May 2020 10:48:03 -0600
Subject: [PATCH 549/802] Add netcdf-c~parallel-netcdf variant specification to
 netcdf-fortran~mpi. (#16671)

Co-authored-by: sly <sly@lanl.gov>
---
 var/spack/repos/builtin/packages/netcdf-fortran/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
index f4bfe9a9795..74347136ddf 100644
--- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
@@ -33,7 +33,7 @@ class NetcdfFortran(AutotoolsPackage):
     # https://www.unidata.ucar.edu/software/netcdf/docs/building_netcdf_fortran.html
     depends_on('mpi', when='+mpi')
 
-    depends_on('netcdf-c~mpi', when='~mpi')
+    depends_on('netcdf-c~mpi~parallel-netcdf', when='~mpi')
     depends_on('netcdf-c+mpi', when='+mpi')
     depends_on('doxygen', when='+doc', type='build')
 

From 9d1f71e89f184d9b05f15ff81532aec460795fd0 Mon Sep 17 00:00:00 2001
From: Sergey Kosukhin <sergey.kosukhin@mpimet.mpg.de>
Date: Fri, 29 May 2020 20:07:44 +0200
Subject: [PATCH 550/802] repo: fix construction of UnknownPackageError
 (#16865)

Also improve the error messages
---
 lib/spack/spack/repo.py      | 34 +++++++++++++++++++---------------
 lib/spack/spack/test/repo.py |  5 +++++
 2 files changed, 24 insertions(+), 15 deletions(-)

diff --git a/lib/spack/spack/repo.py b/lib/spack/spack/repo.py
index 764f1f9168b..8d31f2cf497 100644
--- a/lib/spack/spack/repo.py
+++ b/lib/spack/spack/repo.py
@@ -759,8 +759,8 @@ def _create_namespace(self):
 
         """
         parent = None
-        for l in range(1, len(self._names) + 1):
-            ns = '.'.join(self._names[:l])
+        for i in range(1, len(self._names) + 1):
+            ns = '.'.join(self._names[:i])
 
             if ns not in sys.modules:
                 module = SpackNamespace(ns)
@@ -773,7 +773,7 @@ def _create_namespace(self):
                 # This ensures that we can do things like:
                 #    import spack.pkg.builtin.mpich as mpich
                 if parent:
-                    modname = self._names[l - 1]
+                    modname = self._names[i - 1]
                     setattr(parent, modname, module)
             else:
                 # no need to set up a module
@@ -882,9 +882,7 @@ def get(self, spec):
             raise UnknownPackageError(spec.name)
 
         if spec.namespace and spec.namespace != self.namespace:
-            raise UnknownPackageError(
-                "Repository %s does not contain package %s"
-                % (self.namespace, spec.fullname))
+            raise UnknownPackageError(spec.name, self.namespace)
 
         package_class = self.get_pkg_class(spec.name)
         try:
@@ -1271,16 +1269,22 @@ class UnknownPackageError(UnknownEntityError):
 
     def __init__(self, name, repo=None):
         msg = None
-        if repo:
-            msg = "Package '%s' not found in repository '%s'" % (name, repo)
-        else:
-            msg = "Package '%s' not found." % name
-
-        # special handling for specs that may have been intended as filenames
-        # prompt the user to ask whether they intended to write './<name>'
         long_msg = None
-        if name.endswith(".yaml"):
-            long_msg = "Did you mean to specify a filename with './%s'?" % name
+        if name:
+            if repo:
+                msg = "Package '{0}' not found in repository '{1}'"
+                msg = msg.format(name, repo)
+            else:
+                msg = "Package '{0}' not found.".format(name)
+
+            # Special handling for specs that may have been intended as
+            # filenames: prompt the user to ask whether they intended to write
+            # './<name>'.
+            if name.endswith(".yaml"):
+                long_msg = "Did you mean to specify a filename with './{0}'?"
+                long_msg = long_msg.format(name)
+        else:
+            msg = "Attempting to retrieve anonymous package."
 
         super(UnknownPackageError, self).__init__(msg, long_msg)
         self.name = name
diff --git a/lib/spack/spack/test/repo.py b/lib/spack/spack/test/repo.py
index 2cd1c0fa4a1..d10349e6ecc 100644
--- a/lib/spack/spack/test/repo.py
+++ b/lib/spack/spack/test/repo.py
@@ -51,6 +51,11 @@ def test_repo_unknown_pkg(mutable_mock_repo):
         mutable_mock_repo.get('builtin.mock.nonexistentpackage')
 
 
+def test_repo_anonymous_pkg(mutable_mock_repo):
+    with pytest.raises(spack.repo.UnknownPackageError):
+        mutable_mock_repo.get('+variant')
+
+
 @pytest.mark.maybeslow
 def test_repo_last_mtime():
     latest_mtime = max(os.path.getmtime(p.module.__file__)

From c35ced1465e8a6e65246fa31cf06aec0743bb071 Mon Sep 17 00:00:00 2001
From: Ben Morgan <drbenmorgan@users.noreply.github.com>
Date: Sat, 30 May 2020 08:13:24 +0100
Subject: [PATCH 551/802] geant4: New version 10.6.2 (#16868)

Update both main and data packages. Data versions have not changed
in new version.

Provide new python variant to build Python bindings for 10.6.2 and
newer. Add dependencies on python and Boost+python required by variant.
---
 .../builtin/packages/geant4-data/package.py   |  1 +
 .../repos/builtin/packages/geant4/package.py  | 22 +++++++++++++++++--
 2 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/geant4-data/package.py b/var/spack/repos/builtin/packages/geant4-data/package.py
index 01c46c218dc..57a60ededd9 100644
--- a/var/spack/repos/builtin/packages/geant4-data/package.py
+++ b/var/spack/repos/builtin/packages/geant4-data/package.py
@@ -15,6 +15,7 @@ class Geant4Data(BundlePackage):
 
     maintainers = ['drbenmorgan']
 
+    version('10.6.2')
     version('10.6.1')
     version('10.6.0')
     version('10.5.1')
diff --git a/var/spack/repos/builtin/packages/geant4/package.py b/var/spack/repos/builtin/packages/geant4/package.py
index 364acbce36e..4cfcc4395e7 100644
--- a/var/spack/repos/builtin/packages/geant4/package.py
+++ b/var/spack/repos/builtin/packages/geant4/package.py
@@ -17,6 +17,7 @@ class Geant4(CMakePackage):
 
     maintainers = ['drbenmorgan']
 
+    version('10.6.2', sha256='e381e04c02aeade1ed8cdd9fdbe7dcf5d6f0f9b3837a417976b839318a005dbd')
     version('10.6.1', sha256='4fd64149ae26952672a81ce5579d3806fda4bd251d486897093ac57633a42b7e')
     version('10.6.0', sha256='eebe6a170546064ff81ab3b00f513ccd1d4122a026514982368d503ac55a4ee4')
     version('10.5.1', sha256='2397eb859dc4de095ff66059d8bda9f060fdc42e10469dd7890946293eeb0e39')
@@ -37,10 +38,12 @@ class Geant4(CMakePackage):
     variant('x11', default=False, description='Optional X11 support')
     variant('motif', default=False, description='Optional motif support')
     variant('qt', default=False, description='Enable Qt support')
+    variant('python', default=False, description='Enable Python bindings')
 
     depends_on('cmake@3.5:', type='build')
     depends_on('cmake@3.8:', type='build', when='@10.6.0:')
 
+    depends_on('geant4-data@10.6.2', when='@10.6.2')
     depends_on('geant4-data@10.6.1', when='@10.6.1')
     depends_on('geant4-data@10.6.0', when='@10.6.0')
     depends_on('geant4-data@10.5.1', when='@10.5.1')
@@ -51,6 +54,11 @@ class Geant4(CMakePackage):
     depends_on("expat")
     depends_on("zlib")
 
+    # Python, with boost requirement dealt with in cxxstd section
+    depends_on('python@3:', when='+python')
+    conflicts('+python', when='@:10.6.1',
+              msg='Geant4 <= 10.6.1 cannont be built with Python bindings')
+
     for std in _cxxstd_values:
         # CLHEP version requirements to be reviewed
         depends_on('clhep@2.3.3.0: cxxstd=' + std,
@@ -69,7 +77,11 @@ class Geant4(CMakePackage):
         depends_on('vecgeom@0.3rc cxxstd=' + std,
                    when='@10.3.0:10.3.99 +vecgeom cxxstd=' + std)
 
-    # Visualization driver ependencies
+        # Boost.python, conflict handled earlier
+        depends_on('boost@1.70: +python cxxstd=' + std,
+                   when='+python cxxstd=' + std)
+
+    # Visualization driver dependencies
     depends_on("gl", when='+opengl')
     depends_on("glx", when='+opengl+x11')
     depends_on("libx11", when='+x11')
@@ -105,7 +117,8 @@ def cmake_args(self):
         options.append(self.define_from_variant('GEANT4_BUILD_MULTITHREADED',
                                                 'threads'))
         if '+threads' in spec:
-            # This should be a variant
+            # Locked at global-dynamic to allow use cases that load the
+            # geant4 libs at application runtime
             options.append('-DGEANT4_BUILD_TLS_MODEL=global-dynamic')
 
         # install the data with geant4
@@ -136,4 +149,9 @@ def cmake_args(self):
                 '-DQT_QMAKE_EXECUTABLE=%s' %
                 spec['qt'].prefix.bin.qmake)
 
+        # Python
+        if spec.version > Version('10.6.1'):
+            options.append(self.define_from_variant('GEANT4_USE_PYTHON',
+                                                    'python'))
+
         return options

From 58cc75ac2908f5f9ec294ffeb6e2481b3d3e24ed Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Sat, 30 May 2020 09:14:24 +0200
Subject: [PATCH 552/802] git-lfs: add versions 2.10.0, 2.11.0 (#16850)

---
 var/spack/repos/builtin/packages/git-lfs/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/git-lfs/package.py b/var/spack/repos/builtin/packages/git-lfs/package.py
index 870c98fa0ab..56c7240400f 100644
--- a/var/spack/repos/builtin/packages/git-lfs/package.py
+++ b/var/spack/repos/builtin/packages/git-lfs/package.py
@@ -16,6 +16,8 @@ class GitLfs(MakefilePackage):
     homepage = "https://git-lfs.github.com"
     url      = "https://github.com/git-lfs/git-lfs/archive/v2.6.1.tar.gz"
 
+    version('2.11.0', sha256='8183c4cbef8cf9c2e86b0c0a9822451e2df272f89ceb357c498bfdf0ff1b36c7')
+    version('2.10.0', sha256='07fd5c57a1039d5717dc192affbe3268ec2fd03accdca462cb504c0b4194cd23')
     version('2.9.0', sha256='f1963ad88747577ffeeb854649aeacaa741c59be74683da4d46b129a72d111b7')
     version('2.8.0', sha256='10b476bb8862ebceddc6f0a55f5fb63e2c1e5bed6554f6e3b207dd0155a196ad')
     version('2.7.2', sha256='e65659f12ec557ae8c778c01ca62d921413221864b68bd93cfa41399028ae67f')

From 3cc0e1a333eb52d22039ab049b1d3d384d833ee6 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Sat, 30 May 2020 09:14:57 +0200
Subject: [PATCH 553/802] cpio: add patch to fix build with gcc@10: (#16844)

---
 var/spack/repos/builtin/packages/cpio/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/cpio/package.py b/var/spack/repos/builtin/packages/cpio/package.py
index 2381a824997..ecaf2531ea8 100644
--- a/var/spack/repos/builtin/packages/cpio/package.py
+++ b/var/spack/repos/builtin/packages/cpio/package.py
@@ -15,6 +15,8 @@ class Cpio(AutotoolsPackage, GNUMirrorPackage):
 
     version('2.13', sha256='e87470d9c984317f658567c03bfefb6b0c829ff17dbf6b0de48d71a4c8f3db88')
 
+    patch('https://src.fedoraproject.org/rpms/cpio/raw/dfe64c466d3ea2c8dfbd99700d9006f610064167/f/cpio-2.13-mutiple-definition.patch', sha256='d22633c368b8aedf4c08b23b6fbaa81a52404c8943ab04926404083ac10f1a4b', when='%gcc@10:')
+
     build_directory = 'spack-build'
 
     def flag_handler(self, name, flags):

From 857d2c915018f6d9e3c8c65dd2b9f0308724d03d Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Wed, 27 May 2020 19:49:32 +0200
Subject: [PATCH 554/802] r-lfe: New package

---
 .../repos/builtin/packages/r-lfe/package.py   | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/r-lfe/package.py

diff --git a/var/spack/repos/builtin/packages/r-lfe/package.py b/var/spack/repos/builtin/packages/r-lfe/package.py
new file mode 100644
index 00000000000..08d061330d2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-lfe/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RLfe(AutotoolsPackage):
+    """Transforms away factors with many levels prior to doing an OLS"""
+
+    homepage = "https://cloud.r-project.org/package=lfe"
+    url      = "https://cloud.r-project.org/src/contrib/lfe_2.8-5.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/lfe"
+
+    version('2.8-5', sha256='fd80c573d334594db933ff38f67bd4c9f899aaf648c3bd68f19477a0059723c2')
+    version('2.8-4', sha256='ee5f6e312214aa73e285ae84a6bdf49ba10e830f1a68ffded2fea2e532f2cd6a')
+
+    depends_on('r@2.15.2:', type=('build', 'run'))
+    depends_on('r-matrix@1.1-2:', type=('build', 'run'))
+    depends_on('r-formula', type=('build', 'run'))
+    depends_on('r-xtable', type=('build', 'run'))
+    depends_on('r-sandwich', type=('build', 'run'))

From 3a66d0773c8370afd0f3533d31e47deb8fb6261f Mon Sep 17 00:00:00 2001
From: Jen Herting <jen@herting.cc>
Date: Sat, 30 May 2020 03:17:01 -0400
Subject: [PATCH 555/802] perl-bioperl: fixed version 1.007002 (#16826)

* [perl-bioperl] fixed url for version 1.007002
* [perl-bioperl] fixed conditional method directives
---
 var/spack/repos/builtin/packages/perl-bioperl/package.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/perl-bioperl/package.py b/var/spack/repos/builtin/packages/perl-bioperl/package.py
index de0f3671415..815eb8fcefb 100644
--- a/var/spack/repos/builtin/packages/perl-bioperl/package.py
+++ b/var/spack/repos/builtin/packages/perl-bioperl/package.py
@@ -38,7 +38,8 @@ class PerlBioperl(PerlPackage):
     version('1.7.6',
             sha256='df2a3efc991b9b5d7cc9d038a1452c6dac910c9ad2a0e47e408dd692c111688d',
             preferred=True)
-    version('1.007002', sha256='17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1')
+    version('1.007002', sha256='17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1',
+            url='https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz')
 
     # According to cpandeps.grinnz.com Module-Build is both a build and run
     # time dependency for BioPerl
@@ -67,7 +68,7 @@ class PerlBioperl(PerlPackage):
     depends_on('perl-libwww-perl', when='@1.7.6:', type=('build', 'run'))
     depends_on('perl-libxml-perl', when='@1.7.6:', type=('build', 'run'))
 
-    @when('@1.7.2')
+    @when('@1.007002')
     def configure(self, spec, prefix):
         # Overriding default configure method in order to cater to interactive
         # Build.pl
@@ -102,10 +103,10 @@ def configure(self, spec, prefix):
     # Build script is run through perl and not use the shebang, as it might be
     # too long. This is needed because this does not pick up the
     # `@run_after(configure)` step defined in `PerlPackage`.
-    @when('@1.7.2')
+    @when('@1.007002')
     def build(self, spec, prefix):
         inspect.getmodule(self).perl('Build')
 
-    @when('@1.7.2')
+    @when('@1.007002')
     def install(self, spec, prefix):
         inspect.getmodule(self).perl('Build', 'install')

From 7a363e2a3f4183a3294eb19b80794a3093c5eddb Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Sat, 30 May 2020 23:47:47 +0800
Subject: [PATCH 556/802] Add new package: netkit-ftp (#16876)

* Add new package: netkit-ftp

* remove parallel constraint
---
 .../builtin/packages/netkit-ftp/package.py    | 20 +++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/netkit-ftp/package.py

diff --git a/var/spack/repos/builtin/packages/netkit-ftp/package.py b/var/spack/repos/builtin/packages/netkit-ftp/package.py
new file mode 100644
index 00000000000..fe76bea86b4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netkit-ftp/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class NetkitFtp(AutotoolsPackage):
+    """netkit-ftp is the original file transfer client program for Linux."""
+
+    homepage = "http://ftp.uk.linux.org/pub/linux/Networking/netkit"
+    git      = "https://github.com/mmaraya/netkit-ftp.git"
+
+    version('master', branch='master')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        mkdirp(prefix.man.man1)
+        make('install')

From 816f780be84b92449e7fcb019102c6e9036049b1 Mon Sep 17 00:00:00 2001
From: noguchi-k <55966120+noguchi-k@users.noreply.github.com>
Date: Sun, 31 May 2020 00:57:12 +0900
Subject: [PATCH 557/802] revocap-refiner: add space and remove unused
 function. (#16861)

---
 .../packages/revocap-refiner/add_space.patch  | 37 +++++++++++++++++++
 .../revocap-refiner/delete_getIndices.patch   | 28 ++++++++++++++
 .../packages/revocap-refiner/package.py       |  5 +++
 3 files changed, 70 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/revocap-refiner/add_space.patch
 create mode 100644 var/spack/repos/builtin/packages/revocap-refiner/delete_getIndices.patch

diff --git a/var/spack/repos/builtin/packages/revocap-refiner/add_space.patch b/var/spack/repos/builtin/packages/revocap-refiner/add_space.patch
new file mode 100644
index 00000000000..0db2007eaf4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/revocap-refiner/add_space.patch
@@ -0,0 +1,37 @@
+--- spack-src/Common/kmbDebug.h.org	2020-05-26 14:12:24.977659640 +0900
++++ spack-src/Common/kmbDebug.h	2020-05-26 14:15:11.118470571 +0900
+@@ -52,29 +52,29 @@
+ 	#define REVOCAP_Debug_X(format)
+ #else
+ 	/* _DEBUG マクロに関係なく出力 */
+-	#define REVOCAP_Debug_X(fmt, ...) fprintf(stderr,"%s, line %d: "fmt,__FILE__,__LINE__, ##__VA_ARGS__)
++	#define REVOCAP_Debug_X(fmt, ...) fprintf(stderr,"%s, line %d: " fmt,__FILE__,__LINE__, ##__VA_ARGS__)
+ 
+ 	#if defined _DEBUG || _DEBUG_
+ 	#include <cstdio>
+-	#define REVOCAP_Debug(fmt, ...) fprintf(stderr,"%s, line %d: "fmt,__FILE__,__LINE__, ##__VA_ARGS__)
++	#define REVOCAP_Debug_X(fmt, ...) fprintf(stderr,"%s, line %d: " fmt,__FILE__,__LINE__, ##__VA_ARGS__)
+ 	#else
+ 	#define REVOCAP_Debug(format, ...)
+ 	#endif
+ 
+ 	#if ( _DEBUG >= 1 ) || ( _DEBUG_ >= 1 )
+-	#define REVOCAP_Debug_1(fmt, ...) fprintf(stderr,"%s, line %d: "fmt,__FILE__,__LINE__, ##__VA_ARGS__)
++	#define REVOCAP_Debug_X(fmt, ...) fprintf(stderr,"%s, line %d: " fmt,__FILE__,__LINE__, ##__VA_ARGS__)
+ 	#else
+ 	#define REVOCAP_Debug_1(format, ...)
+ 	#endif
+ 
+ 	#if ( _DEBUG >= 2 ) || ( _DEBUG_ >= 2 )
+-	#define REVOCAP_Debug_2(fmt, ...) fprintf(stderr,"%s, line %d: "fmt,__FILE__,__LINE__, ##__VA_ARGS__)
++	#define REVOCAP_Debug_X(fmt, ...) fprintf(stderr,"%s, line %d: " fmt,__FILE__,__LINE__, ##__VA_ARGS__)
+ 	#else
+ 	#define REVOCAP_Debug_2(format, ...)
+ 	#endif
+ 
+ 	#if ( _DEBUG >= 3 ) || ( _DEBUG_ >= 3 )
+-	#define REVOCAP_Debug_3(fmt, ...) fprintf(stderr,"%s, line %d: "fmt,__FILE__,__LINE__, ##__VA_ARGS__)
++	#define REVOCAP_Debug_X(fmt, ...) fprintf(stderr,"%s, line %d: " fmt,__FILE__,__LINE__, ##__VA_ARGS__)
+ 	#else
+ 	#define REVOCAP_Debug_3(format, ...)
+ 	#endif
diff --git a/var/spack/repos/builtin/packages/revocap-refiner/delete_getIndices.patch b/var/spack/repos/builtin/packages/revocap-refiner/delete_getIndices.patch
new file mode 100644
index 00000000000..7a70f354bf7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/revocap-refiner/delete_getIndices.patch
@@ -0,0 +1,28 @@
+--- spack-src/Geometry/kmbBucket.h.org	2020-05-28 11:42:08.438970353 +0900
++++ spack-src/Geometry/kmbBucket.h	2020-05-28 11:43:55.449496013 +0900
+@@ -348,12 +348,6 @@
+ 
+ 		int getIndex() const{ return it->first; };
+ 
+-		void getIndices(int &i,int &j,int &k) const{
+-			i = it->first / (ynum*znum);
+-			j = (it->first - i*ynum*znum) / znum;
+-			k = it->first - i*ynum*znum - j*znum;
+-		};
+-
+ 		iterator& operator++(void){ ++it; return *this; };
+ 
+ 		iterator  operator++(int n){
+@@ -391,12 +385,6 @@
+ 
+ 		int getIndex() const{ return it->first; };
+ 
+-		void getIndices(int &i,int &j,int &k) const{
+-			i = it->first / (ynum*znum);
+-			j = (it->first - i*ynum*znum) / znum;
+-			k = it->first - i*ynum*znum - j*znum;
+-		};
+-
+ 		const_iterator& operator++(void){ ++it; return *this; };
+ 
+ 		const_iterator operator++(int n){
diff --git a/var/spack/repos/builtin/packages/revocap-refiner/package.py b/var/spack/repos/builtin/packages/revocap-refiner/package.py
index 38eeb31256d..4c563a91d83 100644
--- a/var/spack/repos/builtin/packages/revocap-refiner/package.py
+++ b/var/spack/repos/builtin/packages/revocap-refiner/package.py
@@ -22,6 +22,11 @@ class RevocapRefiner(MakefilePackage):
 
     parallel = False
 
+    # add space between literal and identifier.
+    patch('add_space.patch')
+    # remove unused function getIndices.
+    patch('delete_getIndices.patch')
+
     def edit(self, spec, prefix):
         cflags = ['-O']
         cxxflags = ['-O',  self.compiler.cxx_pic_flag]

From d76eb1fa512d9092f91a5db962c33bb8d0201526 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sat, 30 May 2020 11:09:10 -0500
Subject: [PATCH 558/802] Pandas: add 1.0.4 (#16877)

---
 var/spack/repos/builtin/packages/py-pandas/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py
index 68e32c042d2..152f3a0d4c2 100644
--- a/var/spack/repos/builtin/packages/py-pandas/package.py
+++ b/var/spack/repos/builtin/packages/py-pandas/package.py
@@ -12,7 +12,7 @@ class PyPandas(PythonPackage):
     programming language."""
 
     homepage = "https://pandas.pydata.org/"
-    url = "https://pypi.io/packages/source/p/pandas/pandas-1.0.3.tar.gz"
+    url = "https://pypi.io/packages/source/p/pandas/pandas-1.0.4.tar.gz"
 
     maintainers = ['adamjstewart']
     import_modules = [
@@ -29,6 +29,7 @@ class PyPandas(PythonPackage):
         'pandas.api.extensions'
     ]
 
+    version('1.0.4',  sha256='b35d625282baa7b51e82e52622c300a1ca9f786711b2af7cbe64f1e6831f4126')
     version('1.0.3',  sha256='32f42e322fb903d0e189a4c10b75ba70d90958cc4f66a1781ed027f1a1d14586')
     version('1.0.2',  sha256='76334ba36aa42f93b6b47b79cbc32187d3a178a4ab1c3a478c8f4198bcd93a73')
     version('1.0.1',  sha256='3c07765308f091d81b6735d4f2242bb43c332cc3461cae60543df6b10967fe27')

From 9eebc6b4c181f413cb9d58f19f13087b44bcfcd5 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sat, 30 May 2020 13:22:00 -0500
Subject: [PATCH 559/802] horovod: added v0.19.4 (#16878)

---
 var/spack/repos/builtin/packages/py-horovod/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-horovod/package.py b/var/spack/repos/builtin/packages/py-horovod/package.py
index c7d51270654..7d6a28939f2 100644
--- a/var/spack/repos/builtin/packages/py-horovod/package.py
+++ b/var/spack/repos/builtin/packages/py-horovod/package.py
@@ -14,6 +14,7 @@ class PyHorovod(PythonPackage):
     maintainers = ['adamjstewart']
 
     version('master', branch='master', submodules=True)
+    version('0.19.4', tag='v0.19.4', submodules=True)
     version('0.19.3', tag='v0.19.3', submodules=True)
     version('0.19.2', tag='v0.19.2', submodules=True)
     version('0.19.1', tag='v0.19.1', submodules=True)

From b00080d2daa520fdc517b02a8662df761a9e690c Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Sat, 30 May 2020 22:08:18 -0400
Subject: [PATCH 560/802] ssht: Install include files into "include/ssht"
 (#16879)

---
 var/spack/repos/builtin/packages/ssht/package.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/var/spack/repos/builtin/packages/ssht/package.py b/var/spack/repos/builtin/packages/ssht/package.py
index 7a4cd4857bb..1500871e62e 100644
--- a/var/spack/repos/builtin/packages/ssht/package.py
+++ b/var/spack/repos/builtin/packages/ssht/package.py
@@ -28,20 +28,20 @@ class Ssht(Package):
 
     def install(self, spec, prefix):
         make('default', 'SSHTDIR=.')
-        mkdirp(join_path(prefix, 'include'))
+        mkdirp(join_path(prefix, 'include', 'ssht'))
         install('src/c/ssht.h',
-                join_path(prefix, 'include', 'ssht.h'))
+                join_path(prefix, 'include', 'ssht', 'ssht.h'))
         install('src/c/ssht_adjoint.h',
-                join_path(prefix, 'include', 'ssht_adjoint.h'))
+                join_path(prefix, 'include', 'ssht', 'ssht_adjoint.h'))
         install('src/c/ssht_core.h',
-                join_path(prefix, 'include', 'ssht_core.h'))
+                join_path(prefix, 'include', 'ssht', 'ssht_core.h'))
         install('src/c/ssht_dl.h',
-                join_path(prefix, 'include', 'ssht_dl.h'))
+                join_path(prefix, 'include', 'ssht', 'ssht_dl.h'))
         install('src/c/ssht_error.h',
-                join_path(prefix, 'include', 'ssht_error.h'))
+                join_path(prefix, 'include', 'ssht', 'ssht_error.h'))
         install('src/c/ssht_sampling.h',
-                join_path(prefix, 'include', 'ssht_sampling.h'))
+                join_path(prefix, 'include', 'ssht', 'ssht_sampling.h'))
         install('src/c/ssht_types.h',
-                join_path(prefix, 'include', 'ssht_types.h'))
+                join_path(prefix, 'include', 'ssht', 'ssht_types.h'))
         install_tree('doc/c', join_path(prefix, 'doc'))
         install_tree('lib/c', join_path(prefix, 'lib'))

From 1ec8d928fac615835f015e3b86fc67cbfa866159 Mon Sep 17 00:00:00 2001
From: Satish Balay <balay@mcs.anl.gov>
Date: Sat, 30 May 2020 21:10:34 -0500
Subject: [PATCH 561/802] petsc@3.13: update superlu-dist dependency - as
 superlu-dist@6.3.1 has API change (#16849)

---
 var/spack/repos/builtin/packages/petsc/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index d8da096f20e..c1b060bd501 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -177,8 +177,8 @@ class Petsc(Package):
     depends_on('superlu-dist@5.4:5.4.99+int64', when='@3.10:3.10.2+superlu-dist+mpi+int64')
     depends_on('superlu-dist@6.1:6.1.99~int64', when='@3.10.3:3.12.99+superlu-dist+mpi~int64')
     depends_on('superlu-dist@6.1:6.1.99+int64', when='@3.10.3:3.12.99+superlu-dist+mpi+int64')
-    depends_on('superlu-dist@6.1:6.3.99~int64', when='@3.13.0:3.13.99+superlu-dist+mpi~int64')
-    depends_on('superlu-dist@6.1:6.3.99+int64', when='@3.13.0:3.13.99+superlu-dist+mpi+int64')
+    depends_on('superlu-dist@6.1:6.3.0~int64', when='@3.13.0:3.13.99+superlu-dist+mpi~int64')
+    depends_on('superlu-dist@6.1:6.3.0+int64', when='@3.13.0:3.13.99+superlu-dist+mpi+int64')
     depends_on('superlu-dist@xsdk-0.2.0~int64', when='@xsdk-0.2.0+superlu-dist+mpi~int64')
     depends_on('superlu-dist@xsdk-0.2.0+int64', when='@xsdk-0.2.0+superlu-dist+mpi+int64')
     depends_on('superlu-dist@develop~int64', when='@develop+superlu-dist+mpi~int64')

From e2fa74c533b49cb3479d4c75d5b68f6993e33082 Mon Sep 17 00:00:00 2001
From: takanori-ihara <62980219+takanori-ihara@users.noreply.github.com>
Date: Sun, 31 May 2020 11:20:08 +0900
Subject: [PATCH 562/802] Add new package:linsys-v (#16823)

---
 .../builtin/packages/linsys-v/package.py      | 67 +++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/linsys-v/package.py

diff --git a/var/spack/repos/builtin/packages/linsys-v/package.py b/var/spack/repos/builtin/packages/linsys-v/package.py
new file mode 100644
index 00000000000..cc8e94c26bb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/linsys-v/package.py
@@ -0,0 +1,67 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class LinsysV(MakefilePackage):
+    """LINSYS_V: Verified Solution of Linear Systems"""
+
+    homepage = "http://www.math.twcu.ac.jp/ogita/post-k/"
+    url = "http://www.math.twcu.ac.jp/ogita/post-k/software/LINSYS_V/LINSYS_V_alpha.tar.gz"
+
+    version(
+        "alpha",
+        sha256="6666bc837bb6598b7cdefb233d3d0f2c308a24fe3465e4fe9b6c9762810bb320",
+    )
+
+    depends_on("mpi")
+    depends_on("blas", type="link")
+    depends_on("lapack", type="link")
+    depends_on("scalapack", type="link")
+
+    def patch(self):
+        math_libs = (
+            self.spec["lapack"].libs
+            + self.spec["blas"].libs
+            + self.spec["scalapack"].libs
+        )
+        makefile = FileFilter("Makefile")
+        if self.spec.satisfies("%gcc"):
+            makefile.filter(r"^ENV\s+=\sK", "#ENV=K")
+            makefile.filter(r"^#ENV\s+=\sGCC", "ENV=GCC")
+            makefile.filter(r"^MKL\s+=\s1", "MKL=0")
+            makefile.filter(r"^CC\s+=\smpicc",
+                            "CC={0}".format(self.spec["mpi"].mpicc))
+            makefile.filter(
+                r"^LIBS\s+=\s-lscalapack\s-lblacs\s-llapack\s-lblas",
+                "LIBS={0}".format(math_libs.ld_flags) + " -lm",
+            )
+        elif self.spec.satisfies("%fj"):
+            makefile.filter(r"^#ENV\s+=\sK", "ENV=K")
+            makefile.filter(r"^ENV\s+=\sGCC", "#ENV=GCC")
+            makefile.filter(r"^MKL\s+=\s1", "MKL=0")
+            makefile.filter(
+                r"^CC\s+=\smpifccpx",
+                "CC={0}".format(self.spec["mpi"].mpicc)
+            )
+            makefile.filter(
+                r"^CFLAGS\s+=\s-Kfast,openmp",
+                "CFLAGS=-Ofast {0}".format(self.compiler.openmp_flag),
+            )
+            makefile.filter(
+                r"^LIBS\s+=\s-SCALAPACK\s-SSL2BLAMP",
+                "LIBS=-SSL2BLAMP {0}".format(math_libs.ld_flags),
+            )
+        elif self.spec.satisfies("%intel"):
+            makefile.filter(r"^ENV\s+=\sGCC", "#ENV=GCC")
+            makefile.filter(r"^ENV\s+=\sICC", "ENV=ICC")
+            makefile.filter(r"^C\s+=\smpiicc",
+                            "CC={0}".format(self.spec["mpi"].mpicc))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install("ex_linsys_v", prefix.bin)

From 2fdb6b5e44026287ad2d78adce9c3cb771a3c642 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Sun, 31 May 2020 10:45:59 +0800
Subject: [PATCH 563/802] Add new package: canal (#16790)

---
 .../repos/builtin/packages/canal/package.py   | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/canal/package.py

diff --git a/var/spack/repos/builtin/packages/canal/package.py b/var/spack/repos/builtin/packages/canal/package.py
new file mode 100644
index 00000000000..57df9ea7f26
--- /dev/null
+++ b/var/spack/repos/builtin/packages/canal/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Canal(Package):
+    """Alibaba MySQL binlog incremental subscription & consumer components."""
+
+    homepage = "https://github.com/alibaba/canal/wiki"
+    url      = "https://github.com/alibaba/canal/archive/canal-1.1.4.tar.gz"
+
+    version('1.1.4', sha256='740e0adac56d7f281cba21eca173eef3e8d42aa3e0fb49709f92cb6a1451dfbc')
+    version('1.1.3', sha256='3fe75ca5eb5cb97eb35818426c1427542ccddb0de052cf154e948ef321822cbc')
+    version('1.1.2', sha256='097190f952bdf09b835ed68966f5a98fa8308322a6aab11c1bfd16cec1800cf2')
+
+    depends_on('maven', type='build')
+    depends_on('java', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mvn = which('mvn')
+        mvn('install', '-DskipTests')
+        install_tree('.', prefix)

From 66b8b5ab37ed07e3bafe957dbdc23dbf3d8ad6e2 Mon Sep 17 00:00:00 2001
From: Jordan Ogas <jogas@lanl.gov>
Date: Sat, 30 May 2020 20:10:50 -0700
Subject: [PATCH 564/802] add charliecloud 0.16 (#16810)

* add charliecloud/0.16

* tidy comments
---
 .../repos/builtin/packages/charliecloud/package.py   | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/charliecloud/package.py b/var/spack/repos/builtin/packages/charliecloud/package.py
index 061ba5cf76d..119e014176d 100644
--- a/var/spack/repos/builtin/packages/charliecloud/package.py
+++ b/var/spack/repos/builtin/packages/charliecloud/package.py
@@ -9,12 +9,13 @@
 class Charliecloud(AutotoolsPackage):
     """Lightweight user-defined software stacks for HPC."""
 
-    maintainers = ['j-ogas']
+    maintainers = ['j-ogas', 'reidpr']
     homepage = "https://hpc.github.io/charliecloud"
     url      = "https://github.com/hpc/charliecloud/releases/download/v0.14/charliecloud-0.14.tar.gz"
     git      = "https://github.com/hpc/charliecloud.git"
 
     version('master', branch='master')
+    version('0.16',   sha256='6cdc21d414b6173090ac0a4c2c62a2a038c81659a75ae8f837b332bb7e6e9090')
     version('0.15',   sha256='2163420d43c934151c4f44a188313bdb7f79e576d5a86ba64b9ea45f784b9921')
     version('0.14',   sha256='4ae23c2d6442949e16902f9d5604dbd1d6059aeb5dd461b11fc5c74d49dcb194')
     version('0.13',   sha256='5740bff6e410ca99484c1bdf3dbe834c0f753c846d55c19d6162967a3e2718e0')
@@ -24,25 +25,26 @@ class Charliecloud(AutotoolsPackage):
     depends_on('automake', type='build')
     depends_on('libtool',  type='build')
 
-    # Use skopeo and umoci for older ch-grow version dependencies
+    # Use skopeo and umoci for older ch-grow version dependencies.
     depends_on('skopeo',         type='run', when='@0.10:0.13')
     depends_on('umoci',          type='run', when='@0.10:0.13')
     depends_on('python+libxml2', type='run', when='@0.10:0.13')
 
-    # Charliecloud@0.14 and up use python for building
+    # Use python for ch-grow 0.14 and above version dependencies.
     depends_on('python@3.5:',    type='run', when='@0.14:')
     depends_on('py-lark-parser', type='run', when='@0.14:')
     depends_on('py-requests',    type='run', when='@0.14:')
 
-    # man pages and html docs variant
+    # Man pages and html docs variant.
     variant('docs', default=False, description='Build man pages and html docs')
     depends_on('rsync',               type='build', when='+docs')
     depends_on('py-sphinx',           type='build', when='+docs')
     depends_on('py-sphinx-rtd-theme', type='build', when='+docs')
 
+    # See https://github.com/spack/spack/pull/16049.
     conflicts('platform=darwin', msg='This package does not build on macOS')
 
-    # bash automated testing harness (bats)
+    # Bash automated testing harness (bats).
     depends_on('bats@0.4.0', type='test')
     depends_on('python@3.5:', type='test')
 

From 3896a401db18e0c84984df88ce094a1a601ad743 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E5=81=A5=E7=BE=8E=E7=8C=9E=E7=8C=81?=
 <weijianwen@gmail.com>
Date: Sun, 31 May 2020 12:09:27 +0800
Subject: [PATCH 565/802] Install libsharp header files to include/libsharp.
 (#16847)

* Install libsharp header files to include/libsharp.

* Fix flake8 issues.

* Simplify specification of install path.
---
 var/spack/repos/builtin/packages/libsharp/package.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/libsharp/package.py b/var/spack/repos/builtin/packages/libsharp/package.py
index c78534c6c47..aa7e5184b64 100644
--- a/var/spack/repos/builtin/packages/libsharp/package.py
+++ b/var/spack/repos/builtin/packages/libsharp/package.py
@@ -40,5 +40,7 @@ def configure_args(self):
         return args
 
     def install(self, spec, prefix):
-        install_tree('auto/include', join_path(prefix, 'include'))
-        install_tree('auto/lib', join_path(prefix, 'lib'))
+        # Libsharp's only caller healpix include headers like 'libsharp/xxx.h'
+        # Install xxx.h to include/libsharp
+        install_tree('auto/include', prefix.include.libsharp)
+        install_tree('auto/lib', prefix.lib)

From 6282e337f381d683ddb14a278186969dacba091e Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Sun, 31 May 2020 20:54:33 +0200
Subject: [PATCH 566/802] Add new version of py-astroid (#16805)

* Add new version of py-astroid

* Add new version of py-lazy-object-proxy

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../builtin/packages/py-astroid/package.py    | 23 +++++++++++++------
 .../packages/py-lazy-object-proxy/package.py  |  3 ++-
 2 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-astroid/package.py b/var/spack/repos/builtin/packages/py-astroid/package.py
index 34cd769a0b9..3eb5aece5bb 100644
--- a/var/spack/repos/builtin/packages/py-astroid/package.py
+++ b/var/spack/repos/builtin/packages/py-astroid/package.py
@@ -13,6 +13,7 @@ class PyAstroid(PythonPackage):
     homepage = "https://github.com/PyCQA/astroid"
     url      = "https://github.com/PyCQA/astroid/archive/astroid-1.4.5.tar.gz"
 
+    version('2.3.3', sha256='3a82983cf34dcbfe42ebcffeb98739e8a7bb868f03c1d9e298c530179b5075e7')
     version('2.2.0', sha256='7e289d0aa4a537b4aa798bd609fdf745de0f3c37e6b67642ed328e1482421a6d')
     version('1.6.6', sha256='3fbcc144457ba598fb48e0ddce5eacee62610ab11e6fe374b6eef5f7df2a3fbb')
     # version('1.5.3', sha256='6f65e4ea8290ec032320460905afb828') # has broken unit tests
@@ -22,10 +23,18 @@ class PyAstroid(PythonPackage):
     version('1.4.2', sha256='f9007d651f4b3514ea5812127677a4bb681ff194164290cea358987920f24ee6')
     version('1.4.1', sha256='f1ab3ee6f17f9d30981399a52b56a7a7d2747ba24f0aa504e411ee6205a01fc0')
 
-    depends_on('py-lazy-object-proxy')
-    depends_on('py-six')
-    depends_on('py-wrapt')
-    depends_on('py-enum34@1.1.3:', when='^python@:3.3.99')
-    depends_on('py-singledispatch', when='^python@:3.3.99')
-    depends_on('py-backports-functools-lru-cache', when='^python@:3.2.99')
-    depends_on('py-setuptools@17.1:')
+    # Dependencies taken from astroid/__pkginfo__.py
+    depends_on('python@2.7:2.8,3.4:', when='@:1.999', type=('build', 'run'))
+    depends_on('python@3.4:', when='@2.0.0:', type=('build', 'run'))
+    depends_on('python@3.5:', when='@2.3.3:', type=('build', 'run'))
+    depends_on('py-lazy-object-proxy', type=('build', 'run'))
+    depends_on('py-lazy-object-proxy@1.4:1.4.999', when='@2.3.3:', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-six@1.12:1.999', when='@2.3.3:', type=('build', 'run'))
+    depends_on('py-wrapt', type=('build', 'run'))
+    depends_on('py-wrapt@1.11:1.11.999', when='@2.3.3:', type=('build', 'run'))
+    depends_on('py-enum34@1.1.3:', when='^python@:3.3.99', type=('build', 'run'))
+    depends_on('py-singledispatch', when='^python@:3.3.99', type=('build', 'run'))
+    depends_on('py-backports-functools-lru-cache', when='^python@:3.2.99', type=('build', 'run'))
+    depends_on('py-typed-ast@1.4.0:1.4.999', when='@2.3.3: ^python@:3.7.999', type=('build', 'run'))
+    depends_on('py-setuptools@17.1:', type='build')
diff --git a/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py b/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py
index 606dc00136c..36cac03c588 100644
--- a/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py
+++ b/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py
@@ -12,8 +12,9 @@ class PyLazyObjectProxy(PythonPackage):
     homepage = "https://github.com/ionelmc/python-lazy-object-proxy"
     url      = "https://pypi.io/packages/source/l/lazy-object-proxy/lazy-object-proxy-1.3.1.tar.gz"
 
+    version('1.4.3', sha256='f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0')
     version('1.3.1', sha256='eb91be369f945f10d3a49f5f9be8b3d0b93a4c2be8f8a5b83b0571b8123e0a7a')
 
-    conflicts('^python@3.0:3.2.99')
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
 
     depends_on('py-setuptools', type='build')

From 23a5f3f20055c7f86b97657d77b3c61a7ca67f50 Mon Sep 17 00:00:00 2001
From: Hector Martinez-Seara <hseara@gmail.com>
Date: Sun, 31 May 2020 20:58:37 +0200
Subject: [PATCH 567/802] Updated unison to v2.51.2 (#16772)

The current package does not work. Also several ocaml versions do
not compile such as 4.09.0. Updated to the new ocaml version to
4.10.0, which is now a prerequisite.
---
 .../repos/builtin/packages/ocaml/package.py   | 12 ++++-
 .../packages/unison/4.08-compatibility.patch  | 52 +++++++++++++++++++
 .../repos/builtin/packages/unison/large.patch | 49 +++++++++++++++++
 .../repos/builtin/packages/unison/package.py  | 16 +++---
 4 files changed, 122 insertions(+), 7 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/unison/4.08-compatibility.patch
 create mode 100644 var/spack/repos/builtin/packages/unison/large.patch

diff --git a/var/spack/repos/builtin/packages/ocaml/package.py b/var/spack/repos/builtin/packages/ocaml/package.py
index f155c55c13d..4e642b9f567 100644
--- a/var/spack/repos/builtin/packages/ocaml/package.py
+++ b/var/spack/repos/builtin/packages/ocaml/package.py
@@ -29,12 +29,22 @@ class Ocaml(Package):
 
     sanity_check_file = ['bin/ocaml']
 
+    variant(
+        'force-safe-string', default=True,
+        description='Enforce safe (immutable) strings'
+    )
+
     def url_for_version(self, version):
         url = "http://caml.inria.fr/pub/distrib/ocaml-{0}/ocaml-{1}.tar.gz"
         return url.format(str(version)[:-2], version)
 
     def install(self, spec, prefix):
-        configure('-prefix', '{0}'.format(prefix))
+        base_args = ['-prefix', '{0}'.format(prefix)]
+
+        if self.spec.satisfies('~force-safe-string'):
+            base_args += ['--disable-force-safe-string']
+
+        configure(*(base_args))
 
         make('world.opt')
         make('install', 'PREFIX={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/unison/4.08-compatibility.patch b/var/spack/repos/builtin/packages/unison/4.08-compatibility.patch
new file mode 100644
index 00000000000..a6921b516f0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/unison/4.08-compatibility.patch
@@ -0,0 +1,52 @@
+From 29fa058c3127f3b47c347dcaa4a94f4c0e888308 Mon Sep 17 00:00:00 2001
+From: Jaap Boender <jaapb@kerguelen.org>
+Date: Thu, 21 Mar 2019 12:26:51 +0000
+Subject: [PATCH] Compatibility with OCaml 4.08
+
+---
+ src/files.ml                 | 2 +-
+ src/recon.ml                 | 4 ++--
+ src/system/system_generic.ml | 2 +-
+ 3 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/src/files.ml b/src/files.ml
+index ba42ad57..5babf21e 100644
+--- a/src/files.ml
++++ b/src/files.ml
+@@ -722,7 +722,7 @@ let get_files_in_directory dir =
+   with End_of_file ->
+     dirh.System.closedir ()
+   end;
+-  Sort.list (<) !files
++  List.sort String.compare !files
+ 
+ let ls dir pattern =
+   Util.convertUnixErrorsToTransient
+diff --git a/src/recon.ml b/src/recon.ml
+index 5ed358d7..0df2cfe4 100644
+--- a/src/recon.ml
++++ b/src/recon.ml
+@@ -651,8 +651,8 @@ let rec reconcile
+ 
+ (* Sorts the paths so that they will be displayed in order                   *)
+ let sortPaths pathUpdatesList =
+-  Sort.list
+-    (fun (p1, _) (p2, _) -> Path.compare p1 p2 <= 0)
++  List.sort
++    Path.compare
+     pathUpdatesList
+ 
+ let rec enterPath p1 p2 t =
+diff --git a/src/system/system_generic.ml b/src/system/system_generic.ml
+index ed8e18f3..0e28a781 100755
+--- a/src/system/system_generic.ml
++++ b/src/system/system_generic.ml
+@@ -47,7 +47,7 @@ let open_out_gen = open_out_gen
+ let chmod = Unix.chmod
+ let chown = Unix.chown
+ let utimes = Unix.utimes
+-let link = Unix.link
++let link s d = Unix.link s d
+ let openfile = Unix.openfile
+ let opendir f =
+   let h = Unix.opendir f in
diff --git a/var/spack/repos/builtin/packages/unison/large.patch b/var/spack/repos/builtin/packages/unison/large.patch
new file mode 100644
index 00000000000..6dcef5265b9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/unison/large.patch
@@ -0,0 +1,49 @@
+diff -Nrua /usr/ports/net/unison/patches/patch-bytearray_stubs_c ./patches/patch-bytearray_stubs_c
+--- /usr/ports/net/unison/patches/patch-bytearray_stubs_c	Thu Jan  1 01:00:00 1970
++++ ./patches/patch-bytearray_stubs_c	Tue Jan 17 08:44:39 2017
+@@ -0,0 +1,45 @@
++Fix rare SIGSEGV when transferring large replicas.
++Fix a theoretical integer overflow. 
++
++Patches from here:
++https://caml.inria.fr/mantis/view.php?id=7431#c17026
++and here:
++https://caml.inria.fr/mantis/view.php?id=7431#c16962
++
++Related issue reports:
++https://github.com/bcpierce00/unison/issues/48
++https://caml.inria.fr/mantis/view.php?id=7431
++https://bugzilla.redhat.com/show_bug.cgi?id=1401759
++
++Thanks to Alex Markley and OCaml developers
++--- bytearray_stubs.c.orig	Tue Jan 17 08:41:00 2017
+++++ bytearray_stubs.c	Tue Jan 17 08:41:21 2017
++@@ -5,6 +5,7 @@
++ 
++ #include "caml/intext.h"
++ #include "caml/bigarray.h"
+++#include "caml/memory.h"
++ 
++ CAMLprim value ml_marshal_to_bigarray(value v, value flags)
++ {
++@@ -21,15 +22,18 @@ CAMLprim value ml_marshal_to_bigarray(value v, value f
++ 
++ CAMLprim value ml_unmarshal_from_bigarray(value b, value ofs)
++ {
+++  CAMLparam1(b); /* Holds [b] live until unmarshalling completes. */
+++  value result;
++   struct caml_bigarray *b_arr = Bigarray_val(b);
++-  return input_value_from_block (Array_data (b_arr, ofs),
+++  result = input_value_from_block (Array_data (b_arr, ofs),
++                                  b_arr->dim[0] - Long_val(ofs));
+++  CAMLreturn(result);
++ }
++ 
++ CAMLprim value ml_blit_string_to_bigarray
++ (value s, value i, value a, value j, value l)
++ {
++-  char *src = String_val(s) + Int_val(i);
+++  char *src = String_val(s) + Long_val(i);
++   char *dest = Array_data(Bigarray_val(a), j);
++   memcpy(dest, src, Long_val(l));
++   return Val_unit;
diff --git a/var/spack/repos/builtin/packages/unison/package.py b/var/spack/repos/builtin/packages/unison/package.py
index b0c363667b5..d0894419a6a 100644
--- a/var/spack/repos/builtin/packages/unison/package.py
+++ b/var/spack/repos/builtin/packages/unison/package.py
@@ -15,18 +15,22 @@ class Unison(Package):
        other."""
 
     homepage = "https://www.cis.upenn.edu/~bcpierce/unison/"
-    url      = "https://www.seas.upenn.edu/~bcpierce/unison//download/releases/stable/unison-2.48.4.tar.gz"
+    url      = "https://github.com/bcpierce00/unison/archive/v2.51.2.tar.gz"
+    maintainers = ["hseara"]
 
-    version('2.48.4', sha256='30aa53cd671d673580104f04be3cf81ac1e20a2e8baaf7274498739d59e99de8')
+    version('2.51.2', sha256='a2efcbeab651be6df69cc9b253011a07955ecb91fb407a219719451197849d5e')
+    version('2.48.15v4', sha256='f8c7e982634bbe1ed6510fe5b36b6c5c55c06caefddafdd9edc08812305fdeec')
 
-    depends_on('ocaml', type='build')
+    depends_on('ocaml@4.10.0:~force-safe-string', type='build')
+
+    patch('large.patch', level=0)
+    patch('4.08-compatibility.patch', when='^ocaml@4.08:')
 
     parallel = False
 
     def install(self, spec, prefix):
-        make('./mkProjectInfo')
-        make('UISTYLE=text')
+        make('UISTYLE=text DEBUGGING=false THREADS=true')
 
         mkdirp(prefix.bin)
-        install('unison', prefix.bin)
+        install('src/unison', prefix.bin)
         set_executable(join_path(prefix.bin, 'unison'))

From b1bd7774035c626d777220f279a152c01b71ceea Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Sun, 31 May 2020 12:13:10 -0700
Subject: [PATCH 568/802] petsc: fix conditional activation of parmetis
 (#16533)

---
 var/spack/repos/builtin/packages/petsc/package.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index c1b060bd501..f328171072e 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -216,7 +216,7 @@ def mpi_dependent_options(self):
             # enabled. This generates a list of any such errors.
             errors = [
                 error_message_fmt.format(library=x)
-                for x in ('hdf5', 'hypre', 'parmetis', 'mumps', 'superlu-dist')
+                for x in ('hdf5', 'hypre', 'mumps', 'superlu-dist')
                 if ('+' + x) in self.spec]
             if errors:
                 errors = ['incompatible variants given'] + errors
@@ -296,15 +296,18 @@ def install(self, spec, prefix):
                 '--with-scalapack=0'
             ])
 
-        # Activates library support if needed
+        # Activates library support if needed (i.e. direct dependency)
         for library in ('cuda', 'metis', 'hypre', 'parmetis',
                         'mumps', 'trilinos', 'fftw', 'valgrind'):
+            # Cannot check `library in spec` because of transitive deps
+            # Cannot check variants because parmetis keys on +metis
+            library_requested = library in spec.dependencies_dict()
             options.append(
                 '--with-{library}={value}'.format(
                     library=library,
-                    value=('1' if '+' + library in spec else '0'))
+                    value=('1' if library_requested else '0'))
             )
-            if '+' + library in spec:
+            if library_requested:
                 options.append(
                     '--with-{library}-dir={path}'.format(
                         library=library, path=spec[library].prefix)

From de63e1c2ac70e03855968a1dd5190378f5601a7b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E5=81=A5=E7=BE=8E=E7=8C=9E=E7=8C=81?=
 <weijianwen@gmail.com>
Date: Mon, 1 Jun 2020 12:13:35 +0800
Subject: [PATCH 569/802] healpix-cxx: added new package at v3.50.0 (#16846)

---
 .../builtin/packages/healpix-cxx/package.py   | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/healpix-cxx/package.py

diff --git a/var/spack/repos/builtin/packages/healpix-cxx/package.py b/var/spack/repos/builtin/packages/healpix-cxx/package.py
new file mode 100644
index 00000000000..da3f1119d28
--- /dev/null
+++ b/var/spack/repos/builtin/packages/healpix-cxx/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class HealpixCxx(AutotoolsPackage):
+    """Healpix-CXX is a C/C++ library for calculating
+    Hierarchical Equal Area isoLatitude Pixelation of a sphere."""
+
+    homepage = "https://healpix.sourceforge.io"
+    url      = "https://ayera.dl.sourceforge.net/project/healpix/Healpix_3.50/healpix_cxx-3.50.0.tar.gz"
+
+    version('3.50.0', sha256='6538ee160423e8a0c0f92cf2b2001e1a2afd9567d026a86ff6e2287c1580cb4c')
+
+    depends_on('cfitsio')
+    depends_on('libsharp', type='build')
+
+    def patch(self):
+        spec = self.spec
+        configure_fix = FileFilter('configure')
+        # Link libsharp static libs
+        configure_fix.filter(
+            r'^SHARP_LIBS=.*$',
+            'SHARP_LIBS="-L{0} -lsharp -lc_utils -lfftpack -lm"'
+            .format(spec['libsharp'].prefix.lib)
+        )

From daea1fcef63e8775bf815d0492717ab5c73f0d92 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Mon, 1 Jun 2020 13:58:09 -0600
Subject: [PATCH 570/802] exampm: fix build (#16894)

* cabana: add mpi variant

* cajita: initial import

* exampm: update deps

* flake8
---
 .../repos/builtin/packages/cabana/package.py  |  4 +++
 .../repos/builtin/packages/cajita/package.py  | 29 +++++++++++++++++++
 .../repos/builtin/packages/exampm/package.py  | 18 +++++++++++-
 3 files changed, 50 insertions(+), 1 deletion(-)
 create mode 100644 var/spack/repos/builtin/packages/cajita/package.py

diff --git a/var/spack/repos/builtin/packages/cabana/package.py b/var/spack/repos/builtin/packages/cabana/package.py
index 53ae6086445..b84bfa60b08 100644
--- a/var/spack/repos/builtin/packages/cabana/package.py
+++ b/var/spack/repos/builtin/packages/cabana/package.py
@@ -23,6 +23,7 @@ class Cabana(CMakePackage):
     variant('openmp', default=False, description="enable OpenMP backend")
     variant('cuda', default=False, description="enable Cuda backend")
     variant('shared', default=True, description='Build shared libraries')
+    variant('mpi', default=True, description='Build with mpi support')
 
     depends_on("cmake@3.9:", type='build')
     depends_on("kokkos-legacy+serial", when="@:0.2.0+serial")
@@ -31,6 +32,7 @@ class Cabana(CMakePackage):
     depends_on("kokkos@3.1:+serial", when="@0.3.0:+serial")
     depends_on("kokkos@3.1:+openmp", when="@0.3.0:+openmp")
     depends_on("kokkos@3.1:+cuda", when="@0.3.0:+cuda")
+    depends_on('mpi', when='+mpi')
 
     def cmake_args(self):
         options = [
@@ -41,6 +43,8 @@ def cmake_args(self):
                 'On' if '+openmp'  in self.spec else 'Off'),
             '-DCabana_ENABLE_Cuda=%s'  % (
                 'On' if '+cuda'  in self.spec else 'Off'),
+            '-DCabana_ENABLE_MPI=%s'  % (
+                'On' if '+mpi'  in self.spec else 'Off'),
             '-DBUILD_SHARED_LIBS=%s' % (
                 'On' if '+shared'  in self.spec else 'Off')
         ]
diff --git a/var/spack/repos/builtin/packages/cajita/package.py b/var/spack/repos/builtin/packages/cajita/package.py
new file mode 100644
index 00000000000..ddfa96a81ea
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cajita/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cajita(CMakePackage):
+    """An MPI+Kokkos library for logically rectilinear grids"""
+
+    homepage = "https://github.com/ECP-copa/Cajita"
+    git      = "https://github.com/ECP-copa/Cajita.git"
+
+    version('master', branch='master')
+    version('0.1', tag='0.1.0')
+
+    variant('shared', default=True, description='Build shared libraries')
+
+    depends_on('mpi')
+    depends_on('kokkos@3.0:')
+
+    def cmake_args(self):
+        options = [
+            '-DBUILD_SHARED_LIBS=%s' % (
+                'On' if '+shared'  in self.spec else 'Off')
+        ]
+
+        return options
diff --git a/var/spack/repos/builtin/packages/exampm/package.py b/var/spack/repos/builtin/packages/exampm/package.py
index bf1ae7f545e..e5ba5671960 100644
--- a/var/spack/repos/builtin/packages/exampm/package.py
+++ b/var/spack/repos/builtin/packages/exampm/package.py
@@ -12,6 +12,22 @@ class Exampm(CMakePackage):
     homepage = "https://github.com/ECP-copa/ExaMPM"
     git      = "https://github.com/ECP-copa/ExaMPM.git"
 
-    version('develop', branch='master')
+    version('master', branch='master')
 
     tags = ['proxy-app']
+
+    variant('shared', default=True, description='Build shared libraries')
+
+    depends_on('mpi')
+    depends_on('kokkos@3.0:')
+    depends_on('silo')
+    depends_on('cabana+mpi@master')
+    depends_on('cajita@master')
+
+    def cmake_args(self):
+        options = [
+            '-DBUILD_SHARED_LIBS=%s' % (
+                'On' if '+shared'  in self.spec else 'Off')
+        ]
+
+        return options

From fe74c2218447fc5943fdd8c2f97f5691da3750d1 Mon Sep 17 00:00:00 2001
From: mic84 <mrosso@lbl.gov>
Date: Mon, 1 Jun 2020 13:53:49 -0700
Subject: [PATCH 571/802] amrex: add version 20.06 (#16895)

---
 var/spack/repos/builtin/packages/amrex/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/amrex/package.py b/var/spack/repos/builtin/packages/amrex/package.py
index 84b064d781a..32da808f1d1 100644
--- a/var/spack/repos/builtin/packages/amrex/package.py
+++ b/var/spack/repos/builtin/packages/amrex/package.py
@@ -18,6 +18,7 @@ class Amrex(CMakePackage):
     maintainers = ['mic84', 'asalmgren']
 
     version('develop', branch='development')
+    version('20.06', sha256='be2f2a5107111fcb8b3928b76024b370c7cb01a9e5dd79484cf7fcf59d0b4858')
     version('20.05', sha256='97d753bb75e845a0a959ec1a044a48e6adb86dd008b5e29ce7a01d49ed276338')
     version('20.04', sha256='a7ece54d5d89cc00fd555551902a0d4d0fb50db15d2600f441353eed0dddd83b')
     version('20.03', sha256='9728f20c0d7297c935fe5cbc63c1ee60f983b833a735c797340ee2765d626165')

From 4387975556f771a77ac57f3c278436200bba6653 Mon Sep 17 00:00:00 2001
From: Jianwen WEI <weijianwen@gmail.com>
Date: Mon, 1 Jun 2020 16:52:44 +0800
Subject: [PATCH 572/802] miniforge3: add version 4.8.3-4.

---
 var/spack/repos/builtin/packages/miniforge3/package.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/var/spack/repos/builtin/packages/miniforge3/package.py b/var/spack/repos/builtin/packages/miniforge3/package.py
index 1fc1526153a..621db7b0342 100644
--- a/var/spack/repos/builtin/packages/miniforge3/package.py
+++ b/var/spack/repos/builtin/packages/miniforge3/package.py
@@ -12,6 +12,14 @@ class Miniforge3(Package):
     homepage = "https://github.com/conda-forge/miniforge"
     url      = "https://github.com/conda-forge/miniforge/releases/download/4.8.3-2/Miniforge3-4.8.3-2-Linux-x86_64.sh"
 
+    version('4.8.3-4-Linux-x86_64',
+            url='https://github.com/conda-forge/miniforge/releases/download/4.8.3-4/Miniforge3-4.8.3-4-Linux-x86_64.sh',
+            sha256='24951262a126582f5f2e1cf82c9cd0fa20e936ef3309fdb8397175f29e647646',
+            expand=False)
+    version('4.8.3-4-Linux-aarch64',
+            url='https://github.com/conda-forge/miniforge/releases/download/4.8.3-4/Miniforge3-4.8.3-4-Linux-aarch64.sh',
+            sha256='52a8dde14ecfb633800a2de26543a78315058e30f5883701da1ad2f2d5ba9ed8',
+            expand=False)
     version('4.8.3-2-Linux-x86_64',
             url='https://github.com/conda-forge/miniforge/releases/download/4.8.3-2/Miniforge3-4.8.3-2-Linux-x86_64.sh',
             sha256='c8e5b894fe91ce0f86e61065d2247346af107f8d53de0ad89ec848701c4ec1f9',

From 9741de504f018a3ea37117a5c1fe1b3019de6899 Mon Sep 17 00:00:00 2001
From: t-karatsu <fj6085ge@fujitsu.com>
Date: Mon, 1 Jun 2020 14:58:53 +0900
Subject: [PATCH 573/802] netcdf-cxx4: Add 'doxygen' dependency.

---
 var/spack/repos/builtin/packages/netcdf-cxx4/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
index f49c5d8ccea..66b294992fd 100644
--- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
@@ -32,6 +32,7 @@ class NetcdfCxx4(AutotoolsPackage):
     depends_on('autoconf', type='build')
     depends_on('libtool', type='build')
     depends_on('m4', type='build')
+    depends_on('doxygen', when='+doxygen', type='build')
 
     conflicts('~shared', when='~static')
 

From 2a4ca34a618774e987ca35fe2c8c2460174ea392 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Mon, 1 Jun 2020 22:59:14 +0200
Subject: [PATCH 574/802] Recognize system installed gcc-10 as compilers
 (#16884)

Now that the version number of GCC reached double digits, an update
to the regex is needed to recognize gcc-10 as an executable to be
inspected when searching for compilers.
---
 lib/spack/spack/compilers/gcc.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/compilers/gcc.py b/lib/spack/spack/compilers/gcc.py
index 7cbf3e4fa89..98809eea25b 100644
--- a/lib/spack/spack/compilers/gcc.py
+++ b/lib/spack/spack/compilers/gcc.py
@@ -27,7 +27,7 @@ class Gcc(Compiler):
     # MacPorts builds gcc versions with prefixes and -mp-X.Y suffixes.
     # Homebrew and Linuxbrew may build gcc with -X, -X.Y suffixes.
     # Old compatibility versions may contain XY suffixes.
-    suffixes = [r'-mp-\d\.\d', r'-\d\.\d', r'-\d', r'\d\d']
+    suffixes = [r'-mp-\d+\.\d+', r'-\d+\.\d+', r'-\d+', r'\d\d']
 
     # Named wrapper links within build_env_path
     link_paths = {'cc': 'gcc/gcc',

From ab6905d5fa6c3d7380600b768644fdfcc6cffe31 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 1 Jun 2020 23:01:41 +0200
Subject: [PATCH 575/802] r-exactextractr: package type fixed (#16881)

* r-exactextractr: should inherit from RPackage
* r-exactextractr: fixed URL
---
 var/spack/repos/builtin/packages/r-exactextractr/package.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/r-exactextractr/package.py b/var/spack/repos/builtin/packages/r-exactextractr/package.py
index abe1b945e91..8374c5dcead 100644
--- a/var/spack/repos/builtin/packages/r-exactextractr/package.py
+++ b/var/spack/repos/builtin/packages/r-exactextractr/package.py
@@ -6,15 +6,15 @@
 from spack import *
 
 
-class RExactextractr(AutotoolsPackage):
+class RExactextractr(RPackage):
     """Provides a replacement for the 'extract' function from the 'raster'
        package that is suitable for extracting raster values using 'sf'
        polygons.
     """
 
     homepage = "https://cloud.r-project.org/package=exactextractr"
-    url      = "https://cran.r-project.org/src/contrib/exactextractr_0.3.0.tar.gz"
-    list_url = "https://cran.r-project.org/src/contrib/Archive/exactextractr"
+    url      = "https://cloud.r-project.org/src/contrib/exactextractr_0.3.0.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/exactextractr"
 
     version('0.3.0', sha256='c7fb38b38b9dc8b3ca5b8f1f84f4ba3256efd331f2b4636b496d42689ffc3fb0')
     version('0.2.1', sha256='d0b998c77c3fd9265a600a0e08e9bf32a2490a06c19df0d0c0dea4b5c9ab5773')

From feda2a3073e80ca3a31419ecdb168c5d29563a47 Mon Sep 17 00:00:00 2001
From: Jonathon Anderson <jonathon.anderson@colorado.edu>
Date: Mon, 1 Jun 2020 16:33:24 -0600
Subject: [PATCH 576/802] openmpi: add opa-psm2 dependency (#16873)

Also document with_or_without and enable_or_disable, (which are used
to configure the opa-psm2 dependency).
---
 .../docs/build_systems/autotoolspackage.rst   | 119 +++++++++++++++++-
 .../repos/builtin/packages/openmpi/package.py |   6 +
 2 files changed, 124 insertions(+), 1 deletion(-)

diff --git a/lib/spack/docs/build_systems/autotoolspackage.rst b/lib/spack/docs/build_systems/autotoolspackage.rst
index a2baedd576a..a4c15e51557 100644
--- a/lib/spack/docs/build_systems/autotoolspackage.rst
+++ b/lib/spack/docs/build_systems/autotoolspackage.rst
@@ -233,7 +233,124 @@ You may have noticed that most of the Autotools flags are of the form
 ``--without-baz``. Since these flags are so common, Spack provides a
 couple of helper functions to make your life easier.
 
-TODO: document ``with_or_without`` and ``enable_or_disable``.
+"""""""""""""""""
+enable_or_disable
+"""""""""""""""""
+
+Autotools flags for simple boolean variants can be automatically
+generated by calling the ``enable_or_disable`` method. This is
+typically used to enable or disable some feature within the package.
+
+.. code-block:: python
+
+   variant(
+       'memchecker',
+       default=False,
+       description='Memchecker support for debugging [degrades performance]'
+   )
+   config_args.extend(self.enable_or_disable('memchecker'))
+
+In this example, specifying the variant ``+memchecker`` will generate
+the following configuration options:
+
+.. code-block:: console
+
+   --enable-memchecker
+
+"""""""""""""""
+with_or_without
+"""""""""""""""
+
+Autotools flags for more complex variants, including boolean variants
+and multi-valued variants, can be automatically generated by calling
+the ``with_or_without`` method.
+
+.. code-block:: python
+
+   variant(
+       'schedulers',
+       values=disjoint_sets(
+           ('auto',), ('alps', 'lsf', 'tm', 'slurm', 'sge', 'loadleveler')
+       ).with_non_feature_values('auto', 'none'),
+       description="List of schedulers for which support is enabled; "
+       "'auto' lets openmpi determine",
+   )
+   if 'schedulers=auto' not in spec:
+       config_args.extend(self.with_or_without('schedulers'))
+
+In this example, specifying the variant ``schedulers=slurm,sge`` will
+generate the following configuration options:
+
+.. code-block:: console
+
+   --with-slurm --with-sge
+
+``enable_or_disable`` is actually functionally equivalent with
+``with_or_without``, and accepts the same arguments and variant types;
+but idiomatic autotools packages often follow these naming
+conventions.
+
+""""""""""""""""
+activation_value
+""""""""""""""""
+
+Autotools parameters that require an option can still be automatically
+generated, using the ``activation_value`` argument to
+``with_or_without`` (or, rarely, ``enable_or_disable``).
+
+.. code-block:: python
+
+   variant(
+      'fabrics',
+       values=disjoint_sets(
+           ('auto',), ('psm', 'psm2', 'verbs', 'mxm', 'ucx', 'libfabric')
+       ).with_non_feature_values('auto', 'none'),
+       description="List of fabrics that are enabled; "
+       "'auto' lets openmpi determine",
+   )
+   if 'fabrics=auto' not in spec:
+       config_args.extend(self.with_or_without('fabrics',
+           activation_value='prefix'))
+
+``activation_value`` accepts a callable that generates the configure
+parameter value given the variant value; but the special value
+``prefix`` tells Spack to automatically use the dependenency's
+installation prefix, which is the most common use for such
+parameters. In this example, specifying the variant
+``fabrics=libfabric`` will generate the following configuration
+options:
+
+.. code-block:: console
+
+   --with-libfabric=</path/to/libfabric>
+
+""""""""""""""""""""
+activation overrides
+""""""""""""""""""""
+
+Finally, the behavior of either ``with_or_without`` or
+``enable_or_disable`` can be overridden for specific variant
+values. This is most useful for multi-values variants where some of
+the variant values require atypical behavior.
+
+.. code-block:: python
+
+   def with_or_without_verbs(self, activated):
+       # Up through version 1.6, this option was named --with-openib.
+       # In version 1.7, it was renamed to be --with-verbs.
+       opt = 'verbs' if self.spec.satisfies('@1.7:') else 'openib'
+       if not activated:
+           return '--without-{0}'.format(opt)
+       return '--with-{0}={1}'.format(opt, self.spec['rdma-core'].prefix)
+
+Defining ``with_or_without_verbs`` overrides the behavior of a
+``fabrics=verbs`` variant, changing the configure-time option to
+``--with-openib`` for older versions of the package and specifying an
+alternative dependency name:
+
+.. code-block::
+
+   --with-openib=</path/to/rdma-core>
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Configure script in a sub-directory
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 183447236fc..abe7b1d3ee2 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -247,6 +247,7 @@ class Openmpi(AutotoolsPackage):
     depends_on('ucx +thread_multiple', when='fabrics=ucx +thread_multiple')
     depends_on('ucx +thread_multiple', when='@3.0.0: fabrics=ucx')
     depends_on('libfabric', when='fabrics=libfabric')
+    depends_on('opa-psm2', when='fabrics=psm2')
     depends_on('mxm', when='fabrics=mxm')
     depends_on('binutils+libiberty', when='fabrics=mxm')
     depends_on('rdma-core', when='fabrics=verbs')
@@ -330,6 +331,11 @@ def with_or_without_tm(self, activated):
             return '--without-tm'
         return '--with-tm={0}'.format(self.spec['openpbs'].prefix)
 
+    def with_or_without_psm2(self, activated):
+        if not activated:
+            return '--without-psm2'
+        return '--with-psm2={0}'.format(self.spec['opa-psm2'].prefix)
+
     @run_before('autoreconf')
     def die_without_fortran(self):
         # Until we can pass variants such as +fortran through virtual

From 6035b32748261c373ee622a2a0e330cae5a8aa61 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Tue, 2 Jun 2020 10:48:35 +0200
Subject: [PATCH 577/802] go: added v1.14.4 and v1.13.12 (#16903)

---
 var/spack/repos/builtin/packages/go/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py
index 114c9212ab6..d0f515e94c7 100644
--- a/var/spack/repos/builtin/packages/go/package.py
+++ b/var/spack/repos/builtin/packages/go/package.py
@@ -36,10 +36,12 @@ class Go(Package):
 
     extendable = True
 
+    version('1.14.4', sha256='7011af3bbc2ac108d1b82ea8abb87b2e63f78844f0259be20cde4d42c5c40584')
     version('1.14.3', sha256='93023778d4d1797b7bc6a53e86c3a9b150c923953225f8a48a2d5fabc971af56')
     version('1.14.2', sha256='98de84e69726a66da7b4e58eac41b99cbe274d7e8906eeb8a5b7eb0aadee7f7c')
     version('1.14.1', sha256='2ad2572115b0d1b4cb4c138e6b3a31cee6294cb48af75ee86bec3dca04507676')
     version('1.14',   sha256='6d643e46ad565058c7a39dac01144172ef9bd476521f42148be59249e4b74389')
+    version('1.13.12', sha256='17ba2c4de4d78793a21cc659d9907f4356cd9c8de8b7d0899cdedcef712eba34')
     version('1.13.11', sha256='89ed1abce25ad003521c125d6583c93c1280de200ad221f961085200a6c00679')
     version('1.13.10', sha256='eb9ccc8bf59ed068e7eff73e154e4f5ee7eec0a47a610fb864e3332a2fdc8b8c')
     version('1.13.9', sha256='34bb19d806e0bc4ad8f508ae24bade5e9fedfa53d09be63b488a9314d2d4f31d')

From 7f2db5c5b0d284845c80a01c0cbb833ff0509329 Mon Sep 17 00:00:00 2001
From: Sinan <sbulutw@gmail.com>
Date: Tue, 2 Jun 2020 01:51:35 -0700
Subject: [PATCH 578/802] qt: add conflict for old gcc (#16904)

Co-authored-by: Sinan81 <Sinan81@github>
---
 var/spack/repos/builtin/packages/qt/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 08721e85c24..ba28042fa3d 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -151,6 +151,10 @@ class Qt(Package):
     depends_on("double-conversion", when='@5.7:')
     depends_on("pcre2+multibyte", when='@5.9:')
 
+    # gcc@4 is not supported as of Qt@5.14
+    # https://doc.qt.io/qt-5.14/supported-platforms.html
+    conflicts('%gcc@:4.99', when='@5.14:')
+
     # Non-macOS dependencies and special macOS constraints
     if MACOS_VERSION is None:
         depends_on("fontconfig", when='freetype=spack')

From 6aa0e9944e5fedb518ff23904d5019027800aace Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Tue, 2 Jun 2020 01:53:12 -0700
Subject: [PATCH 579/802] ccache: added v3.7.9 (#16902)

Add the latest CCache release. Fixes issues with `-x cu` that are
not present in the last checksummed release. This fixes workflows
with CMake.
---
 var/spack/repos/builtin/packages/ccache/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/ccache/package.py b/var/spack/repos/builtin/packages/ccache/package.py
index 97ebf17441b..6bc53831a99 100644
--- a/var/spack/repos/builtin/packages/ccache/package.py
+++ b/var/spack/repos/builtin/packages/ccache/package.py
@@ -12,8 +12,9 @@ class Ccache(AutotoolsPackage):
     again."""
 
     homepage = "https://ccache.samba.org/"
-    url      = "https://github.com/ccache/ccache/releases/download/v3.7.1/ccache-3.7.1.tar.gz"
+    url      = "https://github.com/ccache/ccache/releases/download/v3.7.9/ccache-3.7.9.tar.gz"
 
+    version('3.7.9', sha256='92838e2133c9e704fdab9ee2608dad86c99021278b9ac47d065aa8ff2ea8ce36')
     version('3.7.1', sha256='e562fcdbe766406b6fe4bf97ce5c001d2be8a17465f33bcddefc9499bbb057d8')
     version('3.3.4', sha256='1348b54e7c35dd2f8d17923389e03c546e599cfbde6459d2f31cf6f1521ec538')
     version('3.3.3', sha256='87a399a2267cfac3f36411fbc12ff8959f408cffd050ad15fe423df88e977e8f')

From 0875c6a5d0ba8a951f86805814d4eb0ba3f3997e Mon Sep 17 00:00:00 2001
From: takanori-ihara <62980219+takanori-ihara@users.noreply.github.com>
Date: Tue, 2 Jun 2020 17:55:55 +0900
Subject: [PATCH 580/802] py-grpcio: fixed build with Fujitsu compilers
 (#16900)

---
 var/spack/repos/builtin/packages/py-grpcio/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-grpcio/package.py b/var/spack/repos/builtin/packages/py-grpcio/package.py
index 18981f20e45..e40d3c0532c 100644
--- a/var/spack/repos/builtin/packages/py-grpcio/package.py
+++ b/var/spack/repos/builtin/packages/py-grpcio/package.py
@@ -29,3 +29,7 @@ def setup_build_environment(self, env):
         env.set('GRPC_PYTHON_BUILD_SYSTEM_OPENSSL', True)
         env.set('GRPC_PYTHON_BUILD_SYSTEM_ZLIB', True)
         env.set('GRPC_PYTHON_BUILD_SYSTEM_CARES', True)
+
+    def patch(self):
+        if self.spec.satisfies('%fj'):
+            filter_file("-std=gnu99", "", "setup.py")

From 2795414a80839208c3463e49f197fee25f2be0f8 Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Tue, 2 Jun 2020 02:02:28 -0700
Subject: [PATCH 581/802] Fix satisfaction checks for excluding variants from
 matrices (#16893)

Because of the way abstract variants are implemented, the following
spec matrix does not work as intended:
```
matrix:
- [foo]
- [bar=a, bar=b]
exclude:
- bar=a
```
because abstract variants always satisfy any variant of the same
name, regardless of values.

This PR converts abstract variants to whatever their appropriate
type is before running satisfaction checks for the excludes clause
in a matrix.

fixes #16841
---
 lib/spack/spack/spec_list.py                  | 12 +++
 lib/spack/spack/test/cmd/dependents.py        | 10 +--
 lib/spack/spack/test/spec_list.py             |  7 ++
 lib/spack/spack/test/spec_semantics.py        | 84 +++++++++----------
 lib/spack/spack/test/spec_yaml.py             |  2 +-
 lib/spack/spack/variant.py                    | 13 ++-
 .../package.py                                |  0
 .../singlevalue-variant-dependent/package.py  |  2 +-
 8 files changed, 80 insertions(+), 50 deletions(-)
 rename var/spack/repos/builtin.mock/packages/{multivalue_variant => multivalue-variant}/package.py (100%)

diff --git a/lib/spack/spack/spec_list.py b/lib/spack/spack/spec_list.py
index de75458f322..4468df7c35d 100644
--- a/lib/spack/spack/spec_list.py
+++ b/lib/spack/spack/spec_list.py
@@ -5,6 +5,7 @@
 import itertools
 from six import string_types
 
+import spack.variant
 from spack.spec import Spec
 from spack.error import SpackError
 
@@ -189,7 +190,18 @@ def _expand_matrix_constraints(object, specify=True):
         # Construct a combined spec to test against excludes
         flat_combo = [constraint for list in combo for constraint in list]
         ordered_combo = sorted(flat_combo, key=spec_ordering_key)
+
         test_spec = Spec(' '.join(ordered_combo))
+        # Abstract variants don't have normal satisfaction semantics
+        # Convert all variants to concrete types.
+        # This method is best effort, so all existing variants will be
+        # converted before any error is raised.
+        # Catch exceptions because we want to be able to operate on
+        # abstract specs without needing package information
+        try:
+            spack.variant.substitute_abstract_variants(test_spec)
+        except spack.variant.UnknownVariantError:
+            pass
         if any(test_spec.satisfies(x) for x in excludes):
             continue
 
diff --git a/lib/spack/spack/test/cmd/dependents.py b/lib/spack/spack/test/cmd/dependents.py
index 1001e8764f4..22a3acd0c32 100644
--- a/lib/spack/spack/test/cmd/dependents.py
+++ b/lib/spack/spack/test/cmd/dependents.py
@@ -26,7 +26,7 @@ def test_transitive_dependents(mock_packages):
     out = dependents('--transitive', 'libelf')
     actual = set(re.split(r'\s+', out.strip()))
     assert actual == set(
-        ['callpath', 'dyninst', 'libdwarf', 'mpileaks', 'multivalue_variant',
+        ['callpath', 'dyninst', 'libdwarf', 'mpileaks', 'multivalue-variant',
          'singlevalue-variant-dependent',
          'patch-a-dependency', 'patch-several-dependencies'])
 
@@ -36,8 +36,8 @@ def test_immediate_installed_dependents(mock_packages, database):
     with color_when(False):
         out = dependents('--installed', 'libelf')
 
-    lines = [l for l in out.strip().split('\n') if not l.startswith('--')]
-    hashes = set([re.split(r'\s+', l)[0] for l in lines])
+    lines = [li for li in out.strip().split('\n') if not li.startswith('--')]
+    hashes = set([re.split(r'\s+', li)[0] for li in lines])
 
     expected = set([spack.store.db.query_one(s).dag_hash(7)
                     for s in ['dyninst', 'libdwarf']])
@@ -53,8 +53,8 @@ def test_transitive_installed_dependents(mock_packages, database):
     with color_when(False):
         out = dependents('--installed', '--transitive', 'fake')
 
-    lines = [l for l in out.strip().split('\n') if not l.startswith('--')]
-    hashes = set([re.split(r'\s+', l)[0] for l in lines])
+    lines = [li for li in out.strip().split('\n') if not li.startswith('--')]
+    hashes = set([re.split(r'\s+', li)[0] for li in lines])
 
     expected = set([spack.store.db.query_one(s).dag_hash(7)
                     for s in ['zmpi', 'callpath^zmpi', 'mpileaks^zmpi']])
diff --git a/lib/spack/spack/test/spec_list.py b/lib/spack/spack/test/spec_list.py
index 9bbbc435e24..ff45096c3ed 100644
--- a/lib/spack/spack/test/spec_list.py
+++ b/lib/spack/spack/test/spec_list.py
@@ -156,3 +156,10 @@ def test_spec_list_nested_matrices(self):
                                                 ['+shared', '~shared'])
         expected = [Spec(' '.join(combo)) for combo in expected_components]
         assert set(speclist.specs) == set(expected)
+
+    def test_spec_list_matrix_exclude(self, mock_packages):
+        # Test on non-boolean variants for regression for #16841
+        matrix = [{'matrix': [['multivalue-variant'], ['foo=bar', 'foo=baz']],
+                   'exclude': ['foo=bar']}]
+        speclist = SpecList('specs', matrix)
+        assert len(speclist.specs) == 1
diff --git a/lib/spack/spack/test/spec_semantics.py b/lib/spack/spack/test/spec_semantics.py
index b55fa27ae1f..d908ce7d89a 100644
--- a/lib/spack/spack/test/spec_semantics.py
+++ b/lib/spack/spack/test/spec_semantics.py
@@ -275,27 +275,27 @@ def test_satisfies_matching_variant(self):
 
     def test_satisfies_multi_value_variant(self):
         # Check quoting
-        check_satisfies('multivalue_variant foo="bar,baz"',
-                        'multivalue_variant foo="bar,baz"')
-        check_satisfies('multivalue_variant foo=bar,baz',
-                        'multivalue_variant foo=bar,baz')
-        check_satisfies('multivalue_variant foo="bar,baz"',
-                        'multivalue_variant foo=bar,baz')
+        check_satisfies('multivalue-variant foo="bar,baz"',
+                        'multivalue-variant foo="bar,baz"')
+        check_satisfies('multivalue-variant foo=bar,baz',
+                        'multivalue-variant foo=bar,baz')
+        check_satisfies('multivalue-variant foo="bar,baz"',
+                        'multivalue-variant foo=bar,baz')
 
         # A more constrained spec satisfies a less constrained one
-        check_satisfies('multivalue_variant foo="bar,baz"',
-                        'multivalue_variant foo="bar"')
+        check_satisfies('multivalue-variant foo="bar,baz"',
+                        'multivalue-variant foo="bar"')
 
-        check_satisfies('multivalue_variant foo="bar,baz"',
-                        'multivalue_variant foo="baz"')
+        check_satisfies('multivalue-variant foo="bar,baz"',
+                        'multivalue-variant foo="baz"')
 
-        check_satisfies('multivalue_variant foo="bar,baz,barbaz"',
-                        'multivalue_variant foo="bar,baz"')
+        check_satisfies('multivalue-variant foo="bar,baz,barbaz"',
+                        'multivalue-variant foo="bar,baz"')
 
-        check_satisfies('multivalue_variant foo="bar,baz"',
+        check_satisfies('multivalue-variant foo="bar,baz"',
                         'foo="bar,baz"')
 
-        check_satisfies('multivalue_variant foo="bar,baz"',
+        check_satisfies('multivalue-variant foo="bar,baz"',
                         'foo="bar"')
 
     def test_satisfies_single_valued_variant(self):
@@ -325,7 +325,7 @@ def test_unsatisfied_single_valued_variant(self):
         a.concretize()
         assert '^b' not in a
 
-        mv = Spec('multivalue_variant')
+        mv = Spec('multivalue-variant')
         mv.concretize()
         assert 'a@1.0' not in mv
 
@@ -340,9 +340,9 @@ def test_unsatisfiable_multi_value_variant(self):
         # Depending on whether the spec is concrete or not
 
         a = make_spec(
-            'multivalue_variant foo="bar"', concrete=True
+            'multivalue-variant foo="bar"', concrete=True
         )
-        spec_str = 'multivalue_variant foo="bar,baz"'
+        spec_str = 'multivalue-variant foo="bar,baz"'
         b = Spec(spec_str)
         assert not a.satisfies(b)
         assert not a.satisfies(spec_str)
@@ -350,8 +350,8 @@ def test_unsatisfiable_multi_value_variant(self):
         with pytest.raises(UnsatisfiableSpecError):
             a.constrain(b)
 
-        a = Spec('multivalue_variant foo="bar"')
-        spec_str = 'multivalue_variant foo="bar,baz"'
+        a = Spec('multivalue-variant foo="bar"')
+        spec_str = 'multivalue-variant foo="bar,baz"'
         b = Spec(spec_str)
         # The specs are abstract and they **could** be constrained
         assert a.satisfies(b)
@@ -360,9 +360,9 @@ def test_unsatisfiable_multi_value_variant(self):
         assert a.constrain(b)
 
         a = make_spec(
-            'multivalue_variant foo="bar,baz"', concrete=True
+            'multivalue-variant foo="bar,baz"', concrete=True
         )
-        spec_str = 'multivalue_variant foo="bar,baz,quux"'
+        spec_str = 'multivalue-variant foo="bar,baz,quux"'
         b = Spec(spec_str)
         assert not a.satisfies(b)
         assert not a.satisfies(spec_str)
@@ -370,8 +370,8 @@ def test_unsatisfiable_multi_value_variant(self):
         with pytest.raises(UnsatisfiableSpecError):
             a.constrain(b)
 
-        a = Spec('multivalue_variant foo="bar,baz"')
-        spec_str = 'multivalue_variant foo="bar,baz,quux"'
+        a = Spec('multivalue-variant foo="bar,baz"')
+        spec_str = 'multivalue-variant foo="bar,baz,quux"'
         b = Spec(spec_str)
         # The specs are abstract and they **could** be constrained
         assert a.satisfies(b)
@@ -384,8 +384,8 @@ def test_unsatisfiable_multi_value_variant(self):
             a.concretize()
 
         # This time we'll try to set a single-valued variant
-        a = Spec('multivalue_variant fee="bar"')
-        spec_str = 'multivalue_variant fee="baz"'
+        a = Spec('multivalue-variant fee="bar"')
+        spec_str = 'multivalue-variant fee="baz"'
         b = Spec(spec_str)
         # The specs are abstract and they **could** be constrained,
         # as before concretization I don't know which type of variant
@@ -405,20 +405,20 @@ def test_unsatisfiable_variant_types(self):
 
         # FIXME: these needs to be checked as the new relaxed
         # FIXME: semantic makes them fail (constrain does not raise)
-        # check_unsatisfiable('multivalue_variant +foo',
-        #                     'multivalue_variant foo="bar"')
-        # check_unsatisfiable('multivalue_variant ~foo',
-        #                     'multivalue_variant foo="bar"')
+        # check_unsatisfiable('multivalue-variant +foo',
+        #                     'multivalue-variant foo="bar"')
+        # check_unsatisfiable('multivalue-variant ~foo',
+        #                     'multivalue-variant foo="bar"')
 
         check_unsatisfiable(
-            target_spec='multivalue_variant foo="bar"',
-            constraint_spec='multivalue_variant +foo',
+            target_spec='multivalue-variant foo="bar"',
+            constraint_spec='multivalue-variant +foo',
             target_concrete=True
         )
 
         check_unsatisfiable(
-            target_spec='multivalue_variant foo="bar"',
-            constraint_spec='multivalue_variant ~foo',
+            target_spec='multivalue-variant foo="bar"',
+            constraint_spec='multivalue-variant ~foo',
             target_concrete=True
         )
 
@@ -597,15 +597,15 @@ def test_constrain_variants(self):
 
     def test_constrain_multi_value_variant(self):
         check_constrain(
-            'multivalue_variant foo="bar,baz"',
-            'multivalue_variant foo="bar"',
-            'multivalue_variant foo="baz"'
+            'multivalue-variant foo="bar,baz"',
+            'multivalue-variant foo="bar"',
+            'multivalue-variant foo="baz"'
         )
 
         check_constrain(
-            'multivalue_variant foo="bar,baz,barbaz"',
-            'multivalue_variant foo="bar,barbaz"',
-            'multivalue_variant foo="baz"'
+            'multivalue-variant foo="bar,baz,barbaz"',
+            'multivalue-variant foo="bar,barbaz"',
+            'multivalue-variant foo="baz"'
         )
 
     def test_constrain_compiler_flags(self):
@@ -734,7 +734,7 @@ def test_exceptional_paths_for_constructor(self):
             Spec('libelf foo')
 
     def test_spec_formatting(self):
-        spec = Spec("multivalue_variant cflags=-O2")
+        spec = Spec("multivalue-variant cflags=-O2")
         spec.concretize()
 
         # Since the default is the full spec see if the string rep of
@@ -806,7 +806,7 @@ def test_spec_formatting(self):
             assert expected == actual
 
     def test_spec_formatting_escapes(self):
-        spec = Spec('multivalue_variant cflags=-O2')
+        spec = Spec('multivalue-variant cflags=-O2')
         spec.concretize()
 
         sigil_mismatches = [
@@ -895,7 +895,7 @@ def test_spec_flags_maintain_order(self):
 
     def test_any_combination_of(self):
         # Test that using 'none' and another value raise during concretization
-        spec = Spec('multivalue_variant foo=none,bar')
+        spec = Spec('multivalue-variant foo=none,bar')
         with pytest.raises(spack.error.SpecError) as exc_info:
             spec.concretize()
 
diff --git a/lib/spack/spack/test/spec_yaml.py b/lib/spack/spack/test/spec_yaml.py
index 03129a7eb9b..98fb1e68fe4 100644
--- a/lib/spack/spack/test/spec_yaml.py
+++ b/lib/spack/spack/test/spec_yaml.py
@@ -69,7 +69,7 @@ def test_concrete_spec(config, mock_packages):
 
 
 def test_yaml_multivalue(config, mock_packages):
-    spec = Spec('multivalue_variant foo="bar,baz"')
+    spec = Spec('multivalue-variant foo="bar,baz"')
     spec.concretize()
     check_yaml_round_trip(spec)
 
diff --git a/lib/spack/spack/variant.py b/lib/spack/spack/variant.py
index 0443b68ec30..e43a002182a 100644
--- a/lib/spack/spack/variant.py
+++ b/lib/spack/spack/variant.py
@@ -593,19 +593,30 @@ def substitute_abstract_variants(spec):
     """Uses the information in `spec.package` to turn any variant that needs
     it into a SingleValuedVariant.
 
+    This method is best effort. All variants that can be substituted will be
+    substituted before any error is raised.
+
     Args:
         spec: spec on which to operate the substitution
     """
+    # This method needs to be best effort so that it works in matrix exlusion
+    # in $spack/lib/spack/spack/spec_list.py
+    failed = []
     for name, v in spec.variants.items():
         if name in spack.directives.reserved_names:
             continue
         pkg_variant = spec.package_class.variants.get(name, None)
         if not pkg_variant:
-            raise UnknownVariantError(spec, [name])
+            failed.append(name)
+            continue
         new_variant = pkg_variant.make_variant(v._original_value)
         pkg_variant.validate_or_raise(new_variant, spec.package_class)
         spec.variants.substitute(new_variant)
 
+    # Raise all errors at once
+    if failed:
+        raise UnknownVariantError(spec, failed)
+
 
 # The class below inherit from Sequence to disguise as a tuple and comply
 # with the semantic expected by the 'values' argument of the variant directive
diff --git a/var/spack/repos/builtin.mock/packages/multivalue_variant/package.py b/var/spack/repos/builtin.mock/packages/multivalue-variant/package.py
similarity index 100%
rename from var/spack/repos/builtin.mock/packages/multivalue_variant/package.py
rename to var/spack/repos/builtin.mock/packages/multivalue-variant/package.py
diff --git a/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py b/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py
index 5507fbdc21f..de14faa51f5 100644
--- a/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py
+++ b/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py
@@ -14,4 +14,4 @@ class SinglevalueVariantDependent(Package):
 
     version('1.0', '0123456789abcdef0123456789abcdef')
 
-    depends_on('multivalue_variant fee=baz')
+    depends_on('multivalue-variant fee=baz')

From c7851f896cb6827cf119e82d4f4c37ab65c17a28 Mon Sep 17 00:00:00 2001
From: Xavier Delaruelle <xavier.delaruelle@cea.fr>
Date: Tue, 2 Jun 2020 11:06:02 +0200
Subject: [PATCH 582/802] environment-modules: added v4.5.1 (#16896)

---
 .../repos/builtin/packages/environment-modules/package.py      | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/environment-modules/package.py b/var/spack/repos/builtin/packages/environment-modules/package.py
index cb6699cf3ad..3a756a0d8c9 100644
--- a/var/spack/repos/builtin/packages/environment-modules/package.py
+++ b/var/spack/repos/builtin/packages/environment-modules/package.py
@@ -12,10 +12,11 @@ class EnvironmentModules(Package):
     """
 
     homepage = 'https://cea-hpc.github.io/modules/'
-    url = 'https://github.com/cea-hpc/modules/releases/download/v4.5.0/modules-4.5.0.tar.gz'
+    url = 'https://github.com/cea-hpc/modules/releases/download/v4.5.1/modules-4.5.1.tar.gz'
 
     maintainers = ['xdelaruelle']
 
+    version('4.5.1', sha256='7d4bcc8559e7fbbc52e526fc86a15b161ff4422aa49eee37897ee7a48eb64ac2')
     version('4.5.0', sha256='5f46336f612553af5553d99347f387f733de0aaa0d80d4572e67615289382ec8')
     version('4.4.1', sha256='3c20cfb2ff8a4d74ac6d566e7b5fa9dd220d96d17e6d8a4ae29b1ec0107ee407')
     version('4.4.0', sha256='4dd55ad6cc684905e891ad1ba9e3c542e79eea0a9cd9a0e99cd77abe6ed63fab')

From b60ab6eefdfe584105ae97caf15a0e72c4ab2457 Mon Sep 17 00:00:00 2001
From: takanori-ihara <62980219+takanori-ihara@users.noreply.github.com>
Date: Tue, 2 Jun 2020 18:07:48 +0900
Subject: [PATCH 583/802] ruby: fixed build with Fujitsu compilers (#16889)

---
 var/spack/repos/builtin/packages/ruby/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index b2e2c6f6fa3..820e32e20bc 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -61,6 +61,8 @@ def configure_args(self):
             args.append("--with-readline-dir=%s"
                         % self.spec['readline'].prefix)
         args.append('--with-tk=%s' % self.spec['tk'].prefix)
+        if self.spec.satisfies("%fj"):
+            args.append('--disable-dtrace')
         return args
 
     def setup_dependent_build_environment(self, env, dependent_spec):

From 9a17d48455bbb38ae8ad51979eeba006c89d4104 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Tue, 2 Jun 2020 22:09:35 +0200
Subject: [PATCH 584/802] Add ipython 7.5.0 (#16801)

* Add ipython 7.5.0

* Update dependencies

* Update package.py
---
 .../repos/builtin/packages/py-ipython/package.py      | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-ipython/package.py b/var/spack/repos/builtin/packages/py-ipython/package.py
index 5bfad819e7b..8faa8ab3305 100644
--- a/var/spack/repos/builtin/packages/py-ipython/package.py
+++ b/var/spack/repos/builtin/packages/py-ipython/package.py
@@ -12,6 +12,7 @@ class PyIpython(PythonPackage):
     homepage = "https://pypi.python.org/pypi/ipython"
     url      = "https://pypi.io/packages/source/i/ipython/ipython-2.3.1.tar.gz"
 
+    version('7.5.0', sha256='e840810029224b56cd0d9e7719dc3b39cf84d577f8ac686547c8ba7a06eeab26')
     version('7.3.0', sha256='06de667a9e406924f97781bda22d5d76bfb39762b678762d86a466e63f65dc39')
     version('5.8.0', sha256='4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906')
     version('5.1.0', sha256='7ef4694e1345913182126b219aaa4a0047e191af414256da6772cf249571b961')
@@ -25,11 +26,15 @@ class PyIpython(PythonPackage):
     depends_on('py-pathlib2', type=('build', 'run'), when="^python@:3.3")
     depends_on('py-pygments',                   type=('build', 'run'))
     depends_on('py-pickleshare',                type=('build', 'run'))
-    depends_on('py-simplegeneric@0.8:',         type=('build', 'run'))
-    depends_on('py-prompt-toolkit@1.0.4:1.999', when='@:7.0.0', type=('build', 'run'))
-    depends_on('py-prompt-toolkit@2.0.0:2.999', when='@7.0.0:', type=('build', 'run'))
+    depends_on('py-simplegeneric@0.8:',         type=('build', 'run'), when='@:7.0.0')
+    depends_on('py-prompt-toolkit@1.0.4:1.999',  when='@:7.0.0', type=('build', 'run'))
+    depends_on('py-prompt-toolkit@2.0.0:2.999',  when='@7.0.0:', type=('build', 'run'))
+    depends_on('py-prompt-toolkit@2.0.0:2.0.999', when='@7.5.0:', type=('build', 'run'))
     depends_on('py-traitlets@4.2:',             type=('build', 'run'))
     depends_on('py-decorator',                  type=('build', 'run'))
     depends_on('py-pexpect',                    type=('build', 'run'))
     depends_on('py-backcall',                   type=('build', 'run'), when="^python@3.3:")
     depends_on('py-appnope', type=('build', 'run'), when='platform=darwin')
+    depends_on('py-jedi@0.10:', type=('build', 'run'), when='@7.5.0:')
+    depends_on('py-backcall', type=('build', 'run'), when='@7.5.0:')
+    depends_on('py-setuptools@18.5:', type=('build', 'run'), when='@7.5.0:')

From 5ace804dc2d33217fb9926be3962e35dc7d007c4 Mon Sep 17 00:00:00 2001
From: Chuck Atkins <chuck.atkins@kitware.com>
Date: Tue, 2 Jun 2020 17:15:23 -0400
Subject: [PATCH 585/802] Bump ADIOS to 2.6.0 (#16908)

---
 var/spack/repos/builtin/packages/adios2/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/adios2/package.py b/var/spack/repos/builtin/packages/adios2/package.py
index 4b2f5a74ebb..59e442a27d3 100644
--- a/var/spack/repos/builtin/packages/adios2/package.py
+++ b/var/spack/repos/builtin/packages/adios2/package.py
@@ -11,12 +11,13 @@ class Adios2(CMakePackage):
     developed in the Exascale Computing Program"""
 
     homepage = "https://csmd.ornl.gov/software/adios2"
-    url = "https://github.com/ornladios/ADIOS2/archive/v2.5.0.tar.gz"
+    url = "https://github.com/ornladios/ADIOS2/archive/v2.6.0.tar.gz"
     git = "https://github.com/ornladios/ADIOS2.git"
 
     maintainers = ['ax3l', 'chuckatkins', 'williamfgc']
 
     version('master', branch='master')
+    version('2.6.0', sha256='45b41889065f8b840725928db092848b8a8b8d1bfae1b92e72f8868d1c76216c')
     version('2.5.0', sha256='7c8ff3bf5441dd662806df9650c56a669359cb0185ea232ecb3578de7b065329')
     version('2.4.0', sha256='50ecea04b1e41c88835b4b3fd4e7bf0a0a2a3129855c9cc4ba6cf6a1575106e2')
     version('2.3.1', sha256='3bf81ccc20a7f2715935349336a76ba4c8402355e1dc3848fcd6f4c3c5931893')

From 5d37439a7b0396772f6102f18568a8863da7ff83 Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Tue, 2 Jun 2020 16:21:00 -0500
Subject: [PATCH 586/802] gmap-gsnap: add 2020-06-01 (#16906)

---
 var/spack/repos/builtin/packages/gmap-gsnap/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/gmap-gsnap/package.py b/var/spack/repos/builtin/packages/gmap-gsnap/package.py
index f87f4121c76..03d1edcd237 100644
--- a/var/spack/repos/builtin/packages/gmap-gsnap/package.py
+++ b/var/spack/repos/builtin/packages/gmap-gsnap/package.py
@@ -14,6 +14,7 @@ class GmapGsnap(AutotoolsPackage):
     homepage = "http://research-pub.gene.com/gmap/"
     url      = "http://research-pub.gene.com/gmap/src/gmap-gsnap-2017-06-16.tar.gz"
 
+    version('2020-06-01', sha256='7917f9f78570943f419445e371f2cc948c6741e73c3cbb063391756f4479d365')
     version('2019-05-12', sha256='3dc1b6ee4f6c049c07bcf4a5aba30eb2d732997241cdcad818dab571719f8008')
     version('2019-02-15', sha256='7e82b9867a1e561b4816fb2f2fb916294077c384c6a88bb94cce39bfe71ab3ac')
     version('2018-07-04', sha256='a9f8c1f0810df65b2a089dc10be79611026f4c95e4681dba98fea3d55d598d24')

From 76142124d2ac58f0499f6e3c0314e2b5c4ecc5fe Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Wed, 3 Jun 2020 06:23:14 +0900
Subject: [PATCH 587/802] alsa-lib: Add new version and python dependency.
 (#16905)

Add version 1.2.2.
Add conditional python dependency.
Add patch for 1.1.4.1 and python.
---
 .../builtin/packages/alsa-lib/package.py      | 25 ++++++++++++++++++-
 .../builtin/packages/alsa-lib/python.patch    | 20 +++++++++++++++
 2 files changed, 44 insertions(+), 1 deletion(-)
 create mode 100644 var/spack/repos/builtin/packages/alsa-lib/python.patch

diff --git a/var/spack/repos/builtin/packages/alsa-lib/package.py b/var/spack/repos/builtin/packages/alsa-lib/package.py
index e766a8cc16e..9b53de24e9b 100644
--- a/var/spack/repos/builtin/packages/alsa-lib/package.py
+++ b/var/spack/repos/builtin/packages/alsa-lib/package.py
@@ -12,6 +12,29 @@ class AlsaLib(AutotoolsPackage):
     space library that developers compile ALSA applications against."""
 
     homepage = "https://www.alsa-project.org"
-    url      = "ftp://ftp.alsa-project.org/pub/lib/alsa-lib-1.1.4.1.tar.bz2"
+    url      = "ftp://ftp.alsa-project.org/pub/lib/alsa-lib-1.2.2.tar.bz2"
 
+    version('1.2.2', sha256='d8e853d8805574777bbe40937812ad1419c9ea7210e176f0def3e6ed255ab3ec')
     version('1.1.4.1', sha256='91bb870c14d1c7c269213285eeed874fa3d28112077db061a3af8010d0885b76')
+
+    variant('python', default=False, description='enable python')
+
+    patch('python.patch', when='@1.1.4:1.1.5 +python')
+
+    depends_on('python', type=('link', 'run'), when='+python')
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+        if spec.satisfies('+python'):
+            args.append(
+                '--with-pythonlibs={0}'.format(spec['python'].libs.ld_flags)
+            )
+            args.append(
+                '--with-pythonincludes={0}'.format(
+                    spec['python'].headers.include_flags
+                )
+            )
+        else:
+            args.append('--disable-python')
+        return args
diff --git a/var/spack/repos/builtin/packages/alsa-lib/python.patch b/var/spack/repos/builtin/packages/alsa-lib/python.patch
new file mode 100644
index 00000000000..6cc6cdb40e6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/alsa-lib/python.patch
@@ -0,0 +1,20 @@
+diff --git a/modules/mixer/simple/python.c b/modules/mixer/simple/python.c
+index c822c52a..917a5d0a 100644
+--- a/modules/mixer/simple/python.c
++++ b/modules/mixer/simple/python.c
+@@ -588,7 +588,6 @@
+ pymelem_dealloc(struct pymelem *self)
+ {
+ 	selem_free(self->melem);
+-        self->ob_type->tp_free(self);
+ }
+
+ static PyGetSetDef pymelem_getseters[] = {
+@@ -800,7 +799,6 @@
+ pymixer_dealloc(struct pymixer *self)
+ {
+ 	pymixer_free(self);
+-        self->ob_type->tp_free(self);
+ }
+
+ static PyGetSetDef pymixer_getseters[] = {

From d5ffec1b2f3afff448880769ea37a530e3f3a5de Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Tue, 2 Jun 2020 23:59:42 +0200
Subject: [PATCH 588/802] Unify tests for compiler command in the same file
 (#16891)

* Unify tests for compiler command in the same file

Tests for the "spack compiler" command were previously
scattered among different files.

* Tests should use mutable_config, since they modify the compiler list
---
 lib/spack/spack/test/cmd/compiler.py          | 105 ++++++++++++++++++
 lib/spack/spack/test/cmd/compiler_command.py  |  40 -------
 lib/spack/spack/test/cmd/test_compiler_cmd.py |  73 ------------
 3 files changed, 105 insertions(+), 113 deletions(-)
 create mode 100644 lib/spack/spack/test/cmd/compiler.py
 delete mode 100644 lib/spack/spack/test/cmd/compiler_command.py
 delete mode 100644 lib/spack/spack/test/cmd/test_compiler_cmd.py

diff --git a/lib/spack/spack/test/cmd/compiler.py b/lib/spack/spack/test/cmd/compiler.py
new file mode 100644
index 00000000000..0476275a5f1
--- /dev/null
+++ b/lib/spack/spack/test/cmd/compiler.py
@@ -0,0 +1,105 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+import os
+
+import pytest
+
+import llnl.util.filesystem
+import spack.main
+import spack.version
+
+compiler = spack.main.SpackCommand('compiler')
+
+
+@pytest.fixture
+def no_compilers_yaml(mutable_config, monkeypatch):
+    """Creates a temporary configuration without compilers.yaml"""
+
+    for scope, local_config in mutable_config.scopes.items():
+        compilers_yaml = os.path.join(
+            local_config.path, scope, 'compilers.yaml'
+        )
+        if os.path.exists(compilers_yaml):
+            os.remove(compilers_yaml)
+
+
+@pytest.fixture
+def mock_compiler_version():
+    return '4.5.3'
+
+
+@pytest.fixture()
+def mock_compiler_dir(tmpdir, mock_compiler_version):
+    """Return a directory containing a fake, but detectable compiler."""
+
+    tmpdir.ensure('bin', dir=True)
+    bin_dir = tmpdir.join('bin')
+
+    gcc_path = bin_dir.join('gcc')
+    gxx_path = bin_dir.join('g++')
+    gfortran_path = bin_dir.join('gfortran')
+
+    gcc_path.write("""\
+#!/bin/sh
+
+for arg in "$@"; do
+    if [ "$arg" = -dumpversion ]; then
+        echo '%s'
+    fi
+done
+""" % mock_compiler_version)
+
+    # Create some mock compilers in the temporary directory
+    llnl.util.filesystem.set_executable(str(gcc_path))
+    gcc_path.copy(gxx_path, mode=True)
+    gcc_path.copy(gfortran_path, mode=True)
+
+    return str(tmpdir)
+
+
+@pytest.mark.regression('11678,13138')
+def test_compiler_find_without_paths(no_compilers_yaml, working_env, tmpdir):
+    with tmpdir.as_cwd():
+        with open('gcc', 'w') as f:
+            f.write("""\
+#!/bin/bash
+echo "0.0.0"
+""")
+        os.chmod('gcc', 0o700)
+
+    os.environ['PATH'] = str(tmpdir)
+    output = compiler('find', '--scope=site')
+
+    assert 'gcc' in output
+
+
+def test_compiler_remove(mutable_config, mock_packages):
+    args = spack.util.pattern.Bunch(
+        all=True, compiler_spec='gcc@4.5.0', add_paths=[], scope=None
+    )
+    spack.cmd.compiler.compiler_remove(args)
+    compilers = spack.compilers.all_compiler_specs()
+    assert spack.spec.CompilerSpec("gcc@4.5.0") not in compilers
+
+
+def test_compiler_add(
+        mutable_config, mock_packages, mock_compiler_dir, mock_compiler_version
+):
+    # Compilers available by default.
+    old_compilers = set(spack.compilers.all_compiler_specs())
+
+    args = spack.util.pattern.Bunch(
+        all=None,
+        compiler_spec=None,
+        add_paths=[mock_compiler_dir],
+        scope=None
+    )
+    spack.cmd.compiler.compiler_find(args)
+
+    # Ensure new compiler is in there
+    new_compilers = set(spack.compilers.all_compiler_specs())
+    new_compiler = new_compilers - old_compilers
+    assert any(c.version == spack.version.Version(mock_compiler_version)
+               for c in new_compiler)
diff --git a/lib/spack/spack/test/cmd/compiler_command.py b/lib/spack/spack/test/cmd/compiler_command.py
deleted file mode 100644
index 15949d08d48..00000000000
--- a/lib/spack/spack/test/cmd/compiler_command.py
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-import pytest
-
-import os
-
-import spack.main
-
-compiler = spack.main.SpackCommand('compiler')
-
-
-@pytest.fixture
-def no_compilers_yaml(mutable_config, monkeypatch):
-    """Creates a temporary configuration without compilers.yaml"""
-
-    for scope, local_config in mutable_config.scopes.items():
-        compilers_yaml = os.path.join(
-            local_config.path, scope, 'compilers.yaml'
-        )
-        if os.path.exists(compilers_yaml):
-            os.remove(compilers_yaml)
-
-
-@pytest.mark.regression('11678,13138')
-def test_compiler_find_without_paths(no_compilers_yaml, working_env, tmpdir):
-    with tmpdir.as_cwd():
-        with open('gcc', 'w') as f:
-            f.write("""\
-#!/bin/bash
-echo "0.0.0"
-""")
-        os.chmod('gcc', 0o700)
-
-    os.environ['PATH'] = str(tmpdir)
-    output = compiler('find', '--scope=site')
-
-    assert 'gcc' in output
diff --git a/lib/spack/spack/test/cmd/test_compiler_cmd.py b/lib/spack/spack/test/cmd/test_compiler_cmd.py
deleted file mode 100644
index 3c34f720ec9..00000000000
--- a/lib/spack/spack/test/cmd/test_compiler_cmd.py
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-import pytest
-import llnl.util.filesystem
-
-import spack.cmd.compiler
-import spack.compilers
-import spack.spec
-import spack.util.pattern
-from spack.version import Version
-
-test_version = '4.5.3'
-
-
-@pytest.fixture()
-def mock_compiler_dir(tmpdir):
-    """Return a directory containing a fake, but detectable compiler."""
-
-    tmpdir.ensure('bin', dir=True)
-    bin_dir = tmpdir.join('bin')
-
-    gcc_path = bin_dir.join('gcc')
-    gxx_path = bin_dir.join('g++')
-    gfortran_path = bin_dir.join('gfortran')
-
-    gcc_path.write("""\
-#!/bin/sh
-
-for arg in "$@"; do
-    if [ "$arg" = -dumpversion ]; then
-        echo '%s'
-    fi
-done
-""" % test_version)
-
-    # Create some mock compilers in the temporary directory
-    llnl.util.filesystem.set_executable(str(gcc_path))
-    gcc_path.copy(gxx_path, mode=True)
-    gcc_path.copy(gfortran_path, mode=True)
-
-    return str(tmpdir)
-
-
-@pytest.mark.usefixtures('config', 'mock_packages')
-class TestCompilerCommand(object):
-
-    def test_compiler_remove(self):
-        args = spack.util.pattern.Bunch(
-            all=True, compiler_spec='gcc@4.5.0', add_paths=[], scope=None
-        )
-        spack.cmd.compiler.compiler_remove(args)
-        compilers = spack.compilers.all_compiler_specs()
-        assert spack.spec.CompilerSpec("gcc@4.5.0") not in compilers
-
-    def test_compiler_add(self, mock_compiler_dir):
-        # Compilers available by default.
-        old_compilers = set(spack.compilers.all_compiler_specs())
-
-        args = spack.util.pattern.Bunch(
-            all=None,
-            compiler_spec=None,
-            add_paths=[mock_compiler_dir],
-            scope=None
-        )
-        spack.cmd.compiler.compiler_find(args)
-
-        # Ensure new compiler is in there
-        new_compilers = set(spack.compilers.all_compiler_specs())
-        new_compiler = new_compilers - old_compilers
-        assert any(c.version == Version(test_version) for c in new_compiler)

From 7f086af05e02eacdb24450215571897d7632e6f5 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 2 Jun 2020 17:05:50 -0500
Subject: [PATCH 589/802] Ruby: add warning about Avira antivirus (#16882)

---
 var/spack/repos/builtin/packages/ruby/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index 820e32e20bc..c4f2a7dcc9b 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -34,6 +34,10 @@ class Ruby(AutotoolsPackage):
     depends_on('openssl', when='+openssl')
     depends_on('readline', when='+readline')
 
+    # Known build issues when Avira antivirus software is running:
+    # https://github.com/rvm/rvm/issues/4313#issuecomment-374020379
+    # TODO: add check for this and warn user
+
     # gcc-7-based build requires patches (cf. https://bugs.ruby-lang.org/issues/13150)
     patch('ruby_23_gcc7.patch', level=0, when='@2.2.0:2.2.999 %gcc@7:')
     patch('ruby_23_gcc7.patch', level=0, when='@2.3.0:2.3.4 %gcc@7:')

From 0e71e8716a1e62a417cb4407e26ff60e233dae87 Mon Sep 17 00:00:00 2001
From: Robert Blake <blake14@llnl.gov>
Date: Tue, 2 Jun 2020 17:54:50 -0700
Subject: [PATCH 590/802] Add new package: sbml (#16898)

* Adding a module for sbml.

* Adding support for all the languages.

* Update var/spack/repos/builtin/packages/sbml/package.py

Co-authored-by: Greg Becker <becker33@llnl.gov>

* Update var/spack/repos/builtin/packages/sbml/package.py

Co-authored-by: Greg Becker <becker33@llnl.gov>

Co-authored-by: Robert Blake <rob.c.blake.3@gmail.com>
Co-authored-by: Greg Becker <becker33@llnl.gov>
---
 .../repos/builtin/packages/sbml/package.py    | 122 ++++++++++++++++++
 1 file changed, 122 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/sbml/package.py

diff --git a/var/spack/repos/builtin/packages/sbml/package.py b/var/spack/repos/builtin/packages/sbml/package.py
new file mode 100644
index 00000000000..4c90d76bc2d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sbml/package.py
@@ -0,0 +1,122 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Sbml(CMakePackage):
+    """Library for the Systems Biology Markup Language"""
+
+    homepage = "https://sbml.org"
+    maintainers = ['rblake-llnl']
+
+    version('5.18.0', sha256='6c01be2306ec0c9656b59cb082eb7b90176c39506dd0f912b02e08298a553360')
+    version('5.17.0', sha256='189216e1472777e4464b791c506b79267d07a5454cb23ac991452711f8e0ed3a')
+    version('5.16.0', sha256='c6855481434dd2a667fef73e1ff2feade509aa2f3a76d4d06e29022975ce1496')
+    version('5.15.0', sha256='c779c2a8a97c5480fe044028099d928a327261fb68cf08657ec8d4f3b3fc0a21')
+    version('5.13.0', sha256='e58430edb1b454d7414bcf1be0549bf6860a6d19d73232eb58211559485c2c05')
+    version('5.12.0', sha256='c637494b19269947fc90ebe479b624d36f80d1cb5569e45cd76ddde81dd28ae4')
+    version('5.11.4', sha256='6429188b689b331b0b8f2c8b55b3f2339196ccd4c93191648fa767e1d02152a3')
+    version('5.11.0', sha256='b21931ca7461494915c617b30d4a9f2cafe831d6ce74989b3e5874e6e3c3f72b')
+    version('5.10.2', sha256='83f32a143cf657672b1050f5f79d3591c418fc59570d180fb1f39b103f4e5286')
+    version('5.10.0', sha256='2cd8b37018ce8b1df869c8c182803addbce6d451512ae25a7f527b49981f0966')
+
+    def url_for_version(self, version):
+        url = "https://downloads.sourceforge.net/project/sbml/libsbml/{0}/stable/libSBML-{1}-core-plus-packages-src.tar.gz".format(version, version)
+        return url
+
+    variant('python', default=False,
+            description='Build with python support')
+    depends_on('python', when="+python")
+
+    variant('perl', default=False,
+            description='Build with perl support')
+    depends_on('perl', when="+perl")
+
+    variant('ruby', default=False,
+            description='Build with ruby support')
+    depends_on('ruby', when="+ruby")
+
+    variant('r', default=False,
+            description='Build with R support')
+    depends_on('r', when="+r")
+
+    variant('octave', default=False,
+            description='Build with octave support')
+    depends_on('octave', when="+octave")
+
+    variant('matlab', default=False,
+            description='Build with matlab support')
+    depends_on('matlab', when="+matlab")
+
+    variant('java', default=False,
+            description='Build with java support')
+    depends_on('java', when="+java")
+
+    variant('mono', default=False,
+            description='Build with mono support')
+    depends_on('mono', when="+mono")
+
+    depends_on('swig@2:', type='build')
+    depends_on('cmake', type='build')
+    depends_on('zlib')
+    depends_on('bzip2')
+    depends_on('libxml2')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            "-DENABLE_COMP:BOOL=ON",
+            "-DENABLE_FBC:BOOL=ON",
+            "-DENABLE_GROUPS:BOOL=ON",
+            "-DENABLE_LAYOUT:BOOL=ON",
+            "-DENABLE_QUAL:BOOL=ON",
+            "-DENABLE_RENDER:BOOL=ON",
+            "-DWITH_BZIP2:BOOL=ON",
+            "-DWITH_CHECK:BOOL=OFF",
+            "-DWITH_CPP_NAMESPACE:BOOL=OFF",
+            "-DWITH_DOXYGEN:BOOL=OFF",
+            "-DWITH_EXAMPLES:BOOL=OFF",
+            "-DWITH_EXPAT:BOOL=OFF",
+            "-DWITH_LIBXML:BOOL=ON",
+            "-DWITH_SWIG:BOOL=ON",
+            "-DWITH_WALL:BOOL=ON",
+            "-DWITH_XERCES:BOOL=OFF",
+            "-DWITH_ZLIB:BOOL=ON",
+        ]
+        if '+python' in spec:
+            args.extend([
+                "-DWITH_PYTHON:BOOL=ON",
+                "-DWITH_PYTHON_INCLUDE:PATH=%s" % spec['python'].prefix,
+            ])
+        else:
+            args.append('-DWITH_PYTHON:BOOL=ON')
+
+        args.append(self.define_from_variant('WITH_CSHARP', 'mono'))
+
+        if '+java' in spec:
+            args.extend([
+                "-DWITH_JAVA:BOOL=ON",
+                "-DJDK_PATH:STRING=%s" % spec['java'].prefix,
+                "-DJAVA_INCLUDE_PATH:STRING=%s" % spec['java'].prefix,
+            ])
+        else:
+            args.append('-DWITH_JAVA:BOOL=OFF')
+
+        if '+matlab' in spec:
+            args.extend([
+                "-DWITH_MATLAB:BOOL=ON",
+                "-DMATLAB_ROOT_PATH:PATH=%s" % spec['matlab'].prefix,
+                "-DWITH_MATLAB_MEX:BOOL=ON",
+            ])
+        else:
+            args.append('-DWITH_MATLAB:BOOL=OFF')
+
+        args.append(self.define_from_variant('WITH_OCTAVE', 'octave'))
+        args.append(self.define_from_variant('WITH_PERL', 'perl'))
+        args.append(self.define_from_variant('WITH_R', 'r'))
+        args.append(self.define_from_variant('WITH_RUBY', 'ruby'))
+
+        return args

From 5604c8d91aab3ce3191dd766e1bd79d661dac238 Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Tue, 2 Jun 2020 22:09:39 -0500
Subject: [PATCH 591/802] mummer4: new package at 4.0.0-beta2 (#16907)

---
 .../repos/builtin/packages/mummer4/package.py | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/mummer4/package.py

diff --git a/var/spack/repos/builtin/packages/mummer4/package.py b/var/spack/repos/builtin/packages/mummer4/package.py
new file mode 100644
index 00000000000..2ba974dca91
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mummer4/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Mummer4(AutotoolsPackage):
+    """MUMmer is a versatil alignment tool for DNA and protein sequences."""
+
+    homepage = "https://github.com/mummer4/mummer"
+    url      = "https://github.com/mummer4/mummer/releases/download/v4.0.0beta2/mummer-4.0.0beta2.tar.gz"
+
+    version('4.0.0beta2', sha256='cece76e418bf9c294f348972e5b23a0230beeba7fd7d042d5584ce075ccd1b93')
+
+    conflicts('%gcc@:4.7')
+
+    depends_on('perl@5.6.0:', type=('build', 'run'))
+    depends_on('awk', type='run')
+    depends_on('sed', type='run')

From 417eb3c5b1705d7fa89bf17cbef11bec8efa852c Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Wed, 3 Jun 2020 11:24:08 +0200
Subject: [PATCH 592/802] git: added v2.27.0 (#16918)

---
 var/spack/repos/builtin/packages/git/package.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py
index 7b92fb65454..1094e3373d6 100644
--- a/var/spack/repos/builtin/packages/git/package.py
+++ b/var/spack/repos/builtin/packages/git/package.py
@@ -22,8 +22,12 @@ class Git(AutotoolsPackage):
     # * sha256_manpages: the sha256sum of the corresponding manpage from
     #       https://www.kernel.org/pub/software/scm/git/git-manpages-{version}.tar.gz
     # You can find the source here: https://mirrors.edge.kernel.org/pub/software/scm/git/sha256sums.asc
-
     releases = [
+        {
+            'version': '2.27.0',
+            'sha256': '77ded85cbe42b1ffdc2578b460a1ef5d23bcbc6683eabcafbb0d394dffe2e787',
+            'sha256_manpages': '414e4b17133e54d846f6bfa2479f9757c50e16c013eb76167a492ae5409b8947'
+        },
         {
             'version': '2.26.0',
             'sha256': 'aa168c2318e7187cd295a645f7370cc6d71a324aafc932f80f00c780b6a26bed',

From eed82a19bed6944fefbbee251a8f9dbad4441fcb Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Wed, 3 Jun 2020 11:28:42 +0200
Subject: [PATCH 593/802] openssh: added v8.3p1 and v8.1p1 (#16917)

---
 var/spack/repos/builtin/packages/openssh/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/openssh/package.py b/var/spack/repos/builtin/packages/openssh/package.py
index 71f15f731e2..37f12663b01 100644
--- a/var/spack/repos/builtin/packages/openssh/package.py
+++ b/var/spack/repos/builtin/packages/openssh/package.py
@@ -18,6 +18,8 @@ class Openssh(AutotoolsPackage):
     homepage = "https://www.openssh.com/"
     url      = "https://mirrors.sonic.net/pub/OpenBSD/OpenSSH/portable/openssh-7.6p1.tar.gz"
 
+    version('8.3p1',   sha256='f2befbe0472fe7eb75d23340eb17531cb6b3aac24075e2066b41f814e12387b2')
+    version('8.1p1',   sha256='02f5dbef3835d0753556f973cd57b4c19b6b1f6cd24c03445e23ac77ca1b93ff')
     version('7.9p1',   sha256='6b4b3ba2253d84ed3771c8050728d597c91cfce898713beb7b64a305b6f11aad')
     version('7.6p1',   sha256='a323caeeddfe145baaa0db16e98d784b1fbc7dd436a6bf1f479dfd5cd1d21723')
     version('7.5p1',   sha256='9846e3c5fab9f0547400b4d2c017992f914222b3fd1f8eee6c7dc6bc5e59f9f0')

From 600e2cfc4f0ffa2000376064c11651e12432f973 Mon Sep 17 00:00:00 2001
From: dmorone <dmorone@users.noreply.github.com>
Date: Wed, 3 Jun 2020 11:17:36 +0000
Subject: [PATCH 594/802] amber: updated dependency constraint on cuda (#16919)

Fix message 'amber requires cuda version :10.1.243, but spec asked for 10.2.89'
---
 var/spack/repos/builtin/packages/amber/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/amber/package.py b/var/spack/repos/builtin/packages/amber/package.py
index eae98b53bda..d2ec13fb3e9 100644
--- a/var/spack/repos/builtin/packages/amber/package.py
+++ b/var/spack/repos/builtin/packages/amber/package.py
@@ -96,7 +96,7 @@ class Amber(Package, CudaPackage):
     depends_on('mpi', when='+mpi')
 
     # Cuda dependencies
-    depends_on('cuda@:10.1.243', when='@18:+cuda')
+    depends_on('cuda@:10.2.89', when='@18:+cuda')
     depends_on('cuda@7.5.18', when='@:16+cuda')
 
     # conflicts

From 70c3b0ba09414501eee14bdce64ca70f4157985b Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Wed, 3 Jun 2020 16:30:12 +0200
Subject: [PATCH 595/802] spack uninstall: improve help message (#16886)

fixes #12527

Mention that specs  can be uninstalled by hash also in
the help message. Reference `spack gc` in case people
are looking for ways to clean the store from build time
dependencies.

Use "spec" instead of "package" to avoid ambiguity in
the error message.
---
 lib/spack/spack/cmd/uninstall.py | 22 +++++++++++++++-------
 1 file changed, 15 insertions(+), 7 deletions(-)

diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index f03270d06d5..cec71c67492 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -26,7 +26,7 @@
 
 error_message = """You can either:
     a) use a more specific spec, or
-    b) specify the package by its hash (e.g. `spack uninstall /hash`), or
+    b) specify the spec by its hash (e.g. `spack uninstall /hash`), or
     c) use `spack uninstall --all` to uninstall ALL matching specs.
 """
 
@@ -40,6 +40,18 @@
 
 
 def setup_parser(subparser):
+    epilog_msg = ("Specs to be uninstalled are specified using the spec syntax"
+                  " (`spack help --spec`) and can be identified by their "
+                  "hashes. To remove packages that are needed only at build "
+                  "time and were not explicitly installed see `spack gc -h`."
+                  "\n\nWhen using the --all option ALL packages matching the "
+                  "supplied specs will be uninstalled. For instance, "
+                  "`spack uninstall --all libelf` uninstalls all the versions "
+                  "of `libelf` currently present in Spack's store. If no spec "
+                  "is supplied, all installed packages will be uninstalled. "
+                  "If used in an environment, all packages in the environment "
+                  "will be uninstalled.")
+    subparser.epilog = epilog_msg
     subparser.add_argument(
         '-f', '--force', action='store_true', dest='force',
         help="remove regardless of whether other packages or environments "
@@ -48,12 +60,8 @@ def setup_parser(subparser):
         subparser, ['recurse_dependents', 'yes_to_all', 'installed_specs'])
     subparser.add_argument(
         '-a', '--all', action='store_true', dest='all',
-        help="USE CAREFULLY. Remove ALL installed packages that match each "
-        "supplied spec. i.e., if you `uninstall --all libelf`,"
-        " ALL versions of `libelf` are uninstalled. If no spec is "
-        "supplied, all installed packages will be uninstalled. "
-        "If used in an environment, all packages in the environment "
-        "will be uninstalled.")
+        help="remove ALL installed packages that match each supplied spec"
+    )
 
 
 def find_matching_specs(env, specs, allow_multiple_matches=False, force=False):

From 7aa9cb0f7a40639852dedb00cc2ecff847a3413b Mon Sep 17 00:00:00 2001
From: Sergey Kosukhin <sergey.kosukhin@mpimet.mpg.de>
Date: Wed, 3 Jun 2020 18:42:13 +0200
Subject: [PATCH 596/802] Implicit rpaths for NAG/GCC mixed toolchain (#14782)

* Implicit rpaths for NAG.

* set up environment when checking for implicit rpaths
---
 lib/spack/spack/compiler.py                   | 64 ++++++++++---------
 lib/spack/spack/compilers/nag.py              | 30 +++++++++
 lib/spack/spack/test/compilers.py             | 41 ++++++++++--
 .../collect2-6.3.0-gnu-ld.txt                 |  3 +
 .../nag-6.2-gcc-6.5.0.txt                     | 13 ++++
 lib/spack/spack/test/link_paths.py            | 26 +++++++-
 6 files changed, 139 insertions(+), 38 deletions(-)
 create mode 100644 lib/spack/spack/test/data/compiler_verbose_output/collect2-6.3.0-gnu-ld.txt
 create mode 100644 lib/spack/spack/test/data/compiler_verbose_output/nag-6.2-gcc-6.5.0.txt

diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py
index 410188fff49..784fd5544ea 100644
--- a/lib/spack/spack/compiler.py
+++ b/lib/spack/spack/compiler.py
@@ -3,6 +3,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import contextlib
 import os
 import platform
 import re
@@ -354,10 +355,11 @@ def _get_compiler_link_paths(self, paths):
             for flag_type in flags:
                 for flag in self.flags.get(flag_type, []):
                     compiler_exe.add_default_arg(flag)
-            output = str(compiler_exe(self.verbose_flag, fin, '-o', fout,
-                                      output=str, error=str))  # str for py2
-
-            return _parse_non_system_link_dirs(output)
+            with self._compiler_environment():
+                output = str(compiler_exe(
+                    self.verbose_flag, fin, '-o', fout,
+                    output=str, error=str))  # str for py2
+                return _parse_non_system_link_dirs(output)
         except spack.util.executable.ProcessError as pe:
             tty.debug('ProcessError: Command exited with non-zero status: ' +
                       pe.long_message)
@@ -468,32 +470,12 @@ def get_real_version(self):
         Use the runtime environment of the compiler (modules and environment
         modifications) to enable the compiler to run properly on any platform.
         """
-        # store environment to replace later
-        backup_env = os.environ.copy()
-
-        # load modules and set env variables
-        for module in self.modules:
-            # On cray, mic-knl module cannot be loaded without cce module
-            # See: https://github.com/spack/spack/issues/3153
-            if os.environ.get("CRAY_CPU_TARGET") == 'mic-knl':
-                spack.util.module_cmd.load_module('cce')
-            spack.util.module_cmd.load_module(module)
-
-        # apply other compiler environment changes
-        env = spack.util.environment.EnvironmentModifications()
-        env.extend(spack.schema.environment.parse(self.environment))
-        env.apply_modifications()
-
         cc = spack.util.executable.Executable(self.cc)
-        output = cc(self.version_argument,
-                    output=str, error=str,
-                    ignore_errors=tuple(self.ignore_version_errors))
-
-        # Restore environment
-        os.environ.clear()
-        os.environ.update(backup_env)
-
-        return self.extract_version_from_output(output)
+        with self._compiler_environment():
+            output = cc(self.version_argument,
+                        output=str, error=str,
+                        ignore_errors=tuple(self.ignore_version_errors))
+            return self.extract_version_from_output(output)
 
     #
     # Compiler classes have methods for querying the version of
@@ -562,6 +544,30 @@ def __str__(self):
                 self.cc, self.cxx, self.f77, self.fc, self.modules,
                 str(self.operating_system)))))
 
+    @contextlib.contextmanager
+    def _compiler_environment(self):
+        # store environment to replace later
+        backup_env = os.environ.copy()
+
+        # load modules and set env variables
+        for module in self.modules:
+            # On cray, mic-knl module cannot be loaded without cce module
+            # See: https://github.com/spack/spack/issues/3153
+            if os.environ.get("CRAY_CPU_TARGET") == 'mic-knl':
+                spack.util.module_cmd.load_module('cce')
+            spack.util.module_cmd.load_module(module)
+
+        # apply other compiler environment changes
+        env = spack.util.environment.EnvironmentModifications()
+        env.extend(spack.schema.environment.parse(self.environment))
+        env.apply_modifications()
+
+        yield
+
+        # Restore environment
+        os.environ.clear()
+        os.environ.update(backup_env)
+
 
 class CompilerAccessError(spack.error.SpackError):
 
diff --git a/lib/spack/spack/compilers/nag.py b/lib/spack/spack/compilers/nag.py
index 4b2de06c079..503a31e404b 100644
--- a/lib/spack/spack/compilers/nag.py
+++ b/lib/spack/spack/compilers/nag.py
@@ -30,6 +30,36 @@ class Nag(spack.compiler.Compiler):
     version_argument = '-V'
     version_regex = r'NAG Fortran Compiler Release ([0-9.]+)'
 
+    @property
+    def verbose_flag(self):
+        # NAG does not support a flag that would enable verbose output and
+        # compilation/linking at the same time (with either '-#' or '-dryrun'
+        # the compiler only prints the commands but does not run them).
+        # Therefore, the only thing we can do is to pass the '-v' argument to
+        # the underlying GCC. In order to get verbose output from the latter
+        # at both compile and linking stages, we need to call NAG with two
+        # additional flags: '-Wc,-v' and '-Wl,-v'. However, we return only
+        # '-Wl,-v' for the following reasons:
+        #   1) the interface of this method does not support multiple flags in
+        #      the return value and, at least currently, verbose output at the
+        #      linking stage has a higher priority for us;
+        #   2) NAG is usually mixed with GCC compiler, which also accepts
+        #      '-Wl,-v' and produces meaningful result with it: '-v' is passed
+        #      to the linker and the latter produces verbose output for the
+        #      linking stage ('-Wc,-v', however, would break the compilation
+        #      with a message from GCC that the flag is not recognized).
+        #
+        # This way, we at least enable the implicit rpath detection, which is
+        # based on compilation of a C file (see method
+        # spack.compiler._get_compiler_link_paths): in the case of a mixed
+        # NAG/GCC toolchain, the flag will be passed to g++ (e.g.
+        # 'g++ -Wl,-v ./main.c'), otherwise, the flag will be passed to nagfor
+        # (e.g. 'nagfor -Wl,-v ./main.c' - note that nagfor recognizes '.c'
+        # extension and treats the file accordingly). The list of detected
+        # rpaths will contain only GCC-related directories and rpaths to
+        # NAG-related directories are injected by nagfor anyway.
+        return "-Wl,-v"
+
     @property
     def openmp_flag(self):
         return "-openmp"
diff --git a/lib/spack/spack/test/compilers.py b/lib/spack/spack/test/compilers.py
index 7c79e9027fb..4598605fe48 100644
--- a/lib/spack/spack/test/compilers.py
+++ b/lib/spack/spack/test/compilers.py
@@ -157,13 +157,14 @@ def test_compiler_flags_from_config_are_grouped():
 class MockCompiler(Compiler):
     def __init__(self):
         super(MockCompiler, self).__init__(
-            "badcompiler@1.0.0",
-            default_compiler_entry['operating_system'],
-            None,
-            [default_compiler_entry['paths']['cc'],
-             default_compiler_entry['paths']['cxx'],
-             default_compiler_entry['paths']['fc'],
-             default_compiler_entry['paths']['f77']])
+            cspec="badcompiler@1.0.0",
+            operating_system=default_compiler_entry['operating_system'],
+            target=None,
+            paths=[default_compiler_entry['paths']['cc'],
+                   default_compiler_entry['paths']['cxx'],
+                   default_compiler_entry['paths']['fc'],
+                   default_compiler_entry['paths']['f77']],
+            environment={})
 
     _get_compiler_link_paths = Compiler._get_compiler_link_paths
 
@@ -267,6 +268,32 @@ def test_get_compiler_link_paths_no_verbose_flag():
     assert dirs == []
 
 
+def test_get_compiler_link_paths_load_env(working_env, monkeypatch, tmpdir):
+    gcc = str(tmpdir.join('gcc'))
+    with open(gcc, 'w') as f:
+        f.write("""#!/bin/bash
+if [[ $ENV_SET == "1" && $MODULE_LOADED == "1" ]]; then
+  echo '""" + no_flag_output + """'
+fi
+""")
+    fs.set_executable(gcc)
+
+    # Set module load to turn compiler on
+    def module(*args):
+        if args[0] == 'show':
+            return ''
+        elif args[0] == 'load':
+            os.environ['MODULE_LOADED'] = "1"
+    monkeypatch.setattr(spack.util.module_cmd, 'module', module)
+
+    compiler = MockCompiler()
+    compiler.environment = {'set': {'ENV_SET': '1'}}
+    compiler.modules = ['turn_on']
+
+    dirs = compiler._get_compiler_link_paths([gcc])
+    assert dirs == no_flag_dirs
+
+
 # Get the desired flag from the specified compiler spec.
 def flag_value(flag, spec):
     compiler = None
diff --git a/lib/spack/spack/test/data/compiler_verbose_output/collect2-6.3.0-gnu-ld.txt b/lib/spack/spack/test/data/compiler_verbose_output/collect2-6.3.0-gnu-ld.txt
new file mode 100644
index 00000000000..cceff7fc658
--- /dev/null
+++ b/lib/spack/spack/test/data/compiler_verbose_output/collect2-6.3.0-gnu-ld.txt
@@ -0,0 +1,3 @@
+collect2 version 6.5.0
+/usr/bin/ld -plugin /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/liblto_plugin.so -plugin-opt=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/lto-wrapper -plugin-opt=-fresolution=/tmp/ccbFmewQ.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -rpath /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib64 --eh-frame-hdr -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o output /usr/lib/x86_64-linux-gnu/crt1.o /usr/lib/x86_64-linux-gnu/crti.o /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/crtbegin.o -L/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0 -L/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/../../../../lib64 -L/lib/x86_64-linux-gnu -L/lib/../lib64 -L/usr/lib/x86_64-linux-gnu -L/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/../../.. -v /tmp/ccxz6i1I.o -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/crtend.o /usr/lib/x86_64-linux-gnu/crtn.o
+GNU ld (GNU Binutils for Debian) 2.28
diff --git a/lib/spack/spack/test/data/compiler_verbose_output/nag-6.2-gcc-6.5.0.txt b/lib/spack/spack/test/data/compiler_verbose_output/nag-6.2-gcc-6.5.0.txt
new file mode 100644
index 00000000000..9fa3dc69bae
--- /dev/null
+++ b/lib/spack/spack/test/data/compiler_verbose_output/nag-6.2-gcc-6.5.0.txt
@@ -0,0 +1,13 @@
+NAG Fortran Compiler Release 6.2(Chiyoda) Build 6223
+Reading specs from /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/specs
+COLLECT_GCC=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/bin/gcc
+COLLECT_LTO_WRAPPER=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/lto-wrapper
+Target: x86_64-pc-linux-gnu
+Configured with: /tmp/m300488/spack-stage/spack-stage-gcc-6.5.0-4sdjgrsboy3lowtq3t7pmp7rx3ogkqtz/spack-src/configure --prefix=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs --with-pkgversion='Spack GCC' --with-bugurl=https://github.com/spack/spack/issues --disable-multilib --enable-languages=c,c++,fortran --disable-nls --with-mpfr=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/mpfr-3.1.6-w63rspk --with-gmp=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gmp-6.1.2-et64cuj --with-system-zlib --with-mpc=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/mpc-1.1.0-en66k4t --with-isl=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/isl-0.18-62v4uyg
+Thread model: posix
+gcc version 6.5.0 (Spack GCC) 
+COMPILER_PATH=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/
+LIBRARY_PATH=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/../../../../lib64/:/lib/x86_64-linux-gnu/:/lib/../lib64/:/usr/lib/x86_64-linux-gnu/:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/../../../:/lib/:/usr/lib/
+COLLECT_GCC_OPTIONS='-m64' '-o' 'output' '-v' '-mtune=generic' '-march=x86-64'
+ /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/collect2 -plugin /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/liblto_plugin.so -plugin-opt=/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/libexec/gcc/x86_64-pc-linux-gnu/6.5.0/lto-wrapper -plugin-opt=-fresolution=/tmp/ccBpU203.res -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s -rpath /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib:/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib64 --eh-frame-hdr -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o output /usr/lib/x86_64-linux-gnu/crt1.o /usr/lib/x86_64-linux-gnu/crti.o /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/crtbegin.o -L/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0 -L/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/../../../../lib64 -L/lib/x86_64-linux-gnu -L/lib/../lib64 -L/usr/lib/x86_64-linux-gnu -L/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/../../.. /sw/stretch-x64/nag/nag-6.2/lib/NAG_Fortran/f62init.o /sw/stretch-x64/nag/nag-6.2/lib/NAG_Fortran/quickfit.o /tmp/main.000786.o -rpath /sw/stretch-x64/nag/nag-6.2/lib/NAG_Fortran /sw/stretch-x64/nag/nag-6.2/lib/NAG_Fortran/libf62rts.so /sw/stretch-x64/nag/nag-6.2/lib/NAG_Fortran/libf62rts.a -lm -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed /scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0/crtend.o /usr/lib/x86_64-linux-gnu/crtn.o
+COLLECT_GCC_OPTIONS='-m64' '-o' 'output' '-v' '-mtune=generic' '-march=x86-64'
diff --git a/lib/spack/spack/test/link_paths.py b/lib/spack/spack/test/link_paths.py
index 27e42d2194b..4ae0a35cf82 100644
--- a/lib/spack/spack/test/link_paths.py
+++ b/lib/spack/spack/test/link_paths.py
@@ -32,8 +32,8 @@ def check_link_paths(filename, paths):
 
 def test_icc16_link_paths():
     check_link_paths('icc-16.0.3.txt', [
-        '/usr/tce/packages/intel/intel-16.0.3/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin', # noqa
-        '/usr/tce/packages/gcc/gcc-4.9.3/lib64/gcc/x86_64-unknown-linux-gnu/4.9.3', # noqa
+        '/usr/tce/packages/intel/intel-16.0.3/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin',  # noqa
+        '/usr/tce/packages/gcc/gcc-4.9.3/lib64/gcc/x86_64-unknown-linux-gnu/4.9.3',  # noqa
         '/usr/tce/packages/gcc/gcc-4.9.3/lib64'])
 
 
@@ -82,6 +82,28 @@ def test_clang_apple_ld_link_paths():
         '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/lib'])  # noqa
 
 
+def test_nag_mixed_gcc_gnu_ld_link_paths():
+    # This is a test of a mixed NAG/GCC toolchain, i.e. 'cxx' is set to g++ and
+    # is used for the rpath detection. The reference compiler output is a
+    # result of
+    # '/path/to/gcc/bin/g++ -Wl,-v ./main.c'.
+    check_link_paths('collect2-6.3.0-gnu-ld.txt', [
+        '/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0',  # noqa
+        '/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib64',  # noqa
+        '/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib'])  # noqa
+
+
+def test_nag_link_paths():
+    # This is a test of a NAG-only toolchain, i.e. 'cc' and 'cxx' are empty,
+    # and therefore 'fc' is used for the rpath detection). The reference
+    # compiler output is a result of
+    # 'nagfor -Wc=/path/to/gcc/bin/gcc -Wl,-v ./main.c'.
+    check_link_paths('nag-6.2-gcc-6.5.0.txt', [
+        '/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib/gcc/x86_64-pc-linux-gnu/6.5.0',  # noqa
+        '/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib64',  # noqa
+        '/scratch/local1/spack/opt/spack/gcc-6.3.0-haswell/gcc-6.5.0-4sdjgrs/lib'])  # noqa
+
+
 def test_obscure_parsing_rules():
     check_link_paths('obscure-parsing-rules.txt', [
         '/first/path',

From 3347ef2de4e08374750eb68f750800c1854d595f Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Wed, 3 Jun 2020 09:45:13 -0700
Subject: [PATCH 597/802] Feature: add option to create view by
 copying/relocating files (#16480)

* add subcommand `spack view copy/relocate`

* update bash completions

* add copy/relocate commands to view tests

* allow copied views to be removed
---
 lib/spack/spack/cmd/view.py                   | 23 +++++--
 lib/spack/spack/filesystem_view.py            | 60 ++++++++++++++++++-
 lib/spack/spack/package.py                    |  2 +-
 lib/spack/spack/test/cmd/view.py              | 16 +++--
 share/spack/spack-completion.bash             | 20 ++++++-
 .../repos/builtin/packages/python/package.py  |  4 +-
 6 files changed, 108 insertions(+), 17 deletions(-)

diff --git a/lib/spack/spack/cmd/view.py b/lib/spack/spack/cmd/view.py
index bad155a456b..151f6c15640 100644
--- a/lib/spack/spack/cmd/view.py
+++ b/lib/spack/spack/cmd/view.py
@@ -33,8 +33,6 @@
 YamlFilesystemView.
 
 '''
-import os
-
 import llnl.util.tty as tty
 from llnl.util.link_tree import MergeConflictError
 from llnl.util.tty.color import colorize
@@ -45,13 +43,15 @@
 import spack.schema.projections
 from spack.config import validate
 from spack.filesystem_view import YamlFilesystemView
+from spack.filesystem_view import view_symlink, view_hardlink, view_copy
 from spack.util import spack_yaml as s_yaml
 
 description = "project packages to a compact naming scheme on the filesystem."
 section = "environments"
 level = "short"
 
-actions_link = ["symlink", "add", "soft", "hardlink", "hard"]
+actions_link = ["symlink", "add", "soft", "hardlink", "hard", "copy",
+                "relocate"]
 actions_remove = ["remove", "rm"]
 actions_status = ["statlink", "status", "check"]
 
@@ -112,6 +112,9 @@ def setup_parser(sp):
         "hardlink": ssp.add_parser(
             'hardlink', aliases=['hard'],
             help='add packages files to a filesystem view via hard links'),
+        "copy": ssp.add_parser(
+            'copy', aliases=['relocate'],
+            help='add package files to a filesystem view via copy/relocate'),
         "remove": ssp.add_parser(
             'remove', aliases=['rm'],
             help='remove packages from a filesystem view'),
@@ -125,7 +128,7 @@ def setup_parser(sp):
         act.add_argument('path', nargs=1,
                          help="path to file system view directory")
 
-        if cmd in ("symlink", "hardlink"):
+        if cmd in ("symlink", "hardlink", "copy"):
             # invalid for remove/statlink, for those commands the view needs to
             # already know its own projections.
             help_msg = "Initialize view using projections from file."
@@ -157,7 +160,7 @@ def setup_parser(sp):
             so["nargs"] = "+"
             act.add_argument('specs', **so)
 
-    for cmd in ["symlink", "hardlink"]:
+    for cmd in ["symlink", "hardlink", "copy"]:
         act = file_system_view_actions[cmd]
         act.add_argument("-i", "--ignore-conflicts", action='store_true')
 
@@ -179,11 +182,19 @@ def view(parser, args):
     else:
         ordered_projections = {}
 
+    # What method are we using for this view
+    if args.action in ("hardlink", "hard"):
+        link_fn = view_hardlink
+    elif args.action in ("copy", "relocate"):
+        link_fn = view_copy
+    else:
+        link_fn = view_symlink
+
     view = YamlFilesystemView(
         path, spack.store.layout,
         projections=ordered_projections,
         ignore_conflicts=getattr(args, "ignore_conflicts", False),
-        link=os.link if args.action in ["hardlink", "hard"] else os.symlink,
+        link=link_fn,
         verbose=args.verbose)
 
     # Process common args and specs
diff --git a/lib/spack/spack/filesystem_view.py b/lib/spack/spack/filesystem_view.py
index b2bc30e1a5c..f4d77a694bc 100644
--- a/lib/spack/spack/filesystem_view.py
+++ b/lib/spack/spack/filesystem_view.py
@@ -24,6 +24,7 @@
 import spack.schema.projections
 import spack.projections
 import spack.config
+import spack.relocate
 from spack.error import SpackError
 from spack.directory_layout import ExtensionAlreadyInstalledError
 from spack.directory_layout import YamlViewExtensionsLayout
@@ -41,6 +42,58 @@
 _projections_path = '.spack/projections.yaml'
 
 
+def view_symlink(src, dst, **kwargs):
+    # keyword arguments are irrelevant
+    # here to fit required call signature
+    os.symlink(src, dst)
+
+
+def view_hardlink(src, dst, **kwargs):
+    # keyword arguments are irrelevant
+    # here to fit required call signature
+    os.link(src, dst)
+
+
+def view_copy(src, dst, view, spec=None):
+    """
+    Copy a file from src to dst.
+
+    Use spec and view to generate relocations
+    """
+    shutil.copyfile(src, dst)
+    if spec:
+        # Not metadata, we have to relocate it
+
+        # Get information on where to relocate from/to
+        prefix_to_projection = dict(
+            (dep.prefix, view.get_projection_for_spec(dep))
+            for dep in spec.traverse()
+        )
+
+        if spack.relocate.is_binary(dst):
+            # relocate binaries
+            spack.relocate.relocate_text_bin(
+                binaries=[dst],
+                orig_install_prefix=spec.prefix,
+                new_install_prefix=view.get_projection_for_spec(spec),
+                orig_spack=spack.paths.spack_root,
+                new_spack=view._root,
+                new_prefixes=prefix_to_projection
+            )
+        else:
+            # relocate text
+            spack.relocate.relocate_text(
+                files=[dst],
+                orig_layout_root=spack.store.layout.root,
+                new_layout_root=view._root,
+                orig_install_prefix=spec.prefix,
+                new_install_prefix=view.get_projection_for_spec(spec),
+                orig_spack=spack.paths.spack_root,
+                new_spack=view._root,
+                new_prefixes=prefix_to_projection
+            )
+
+
 class FilesystemView(object):
     """
         Governs a filesystem view that is located at certain root-directory.
@@ -67,9 +120,12 @@ def __init__(self, root, layout, **kwargs):
         self.projections = kwargs.get('projections', {})
 
         self.ignore_conflicts = kwargs.get("ignore_conflicts", False)
-        self.link = kwargs.get("link", os.symlink)
         self.verbose = kwargs.get("verbose", False)
 
+        # Setup link function to include view
+        link_func = kwargs.get("link", view_symlink)
+        self.link = ft.partial(link_func, view=self)
+
     def add_specs(self, *specs, **kwargs):
         """
             Add given specs to view.
@@ -355,8 +411,6 @@ def remove_file(self, src, dest):
         if not os.path.lexists(dest):
             tty.warn("Tried to remove %s which does not exist" % dest)
             return
-        if not os.path.islink(dest):
-            raise ValueError("%s is not a link tree!" % dest)
         # remove if dest is a hardlink/symlink to src; this will only
         # be false if two packages are merged into a prefix and have a
         # conflicting file
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 9b6f0efb48b..bb5ea41dc3e 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -332,7 +332,7 @@ def add_files_to_view(self, view, merge_map):
         """
         for src, dst in merge_map.items():
             if not os.path.exists(dst):
-                view.link(src, dst)
+                view.link(src, dst, spec=self.spec)
 
     def remove_files_from_view(self, view, merge_map):
         """Given a map of package files to files currently linked in the view,
diff --git a/lib/spack/spack/test/cmd/view.py b/lib/spack/spack/test/cmd/view.py
index c52cd123252..d908248a19b 100644
--- a/lib/spack/spack/test/cmd/view.py
+++ b/lib/spack/spack/test/cmd/view.py
@@ -24,7 +24,8 @@ def create_projection_file(tmpdir, projection):
     return projection_file
 
 
-@pytest.mark.parametrize('cmd', ['hardlink', 'symlink', 'hard', 'add'])
+@pytest.mark.parametrize('cmd', ['hardlink', 'symlink', 'hard', 'add',
+                                 'copy', 'relocate'])
 def test_view_link_type(
         tmpdir, mock_packages, mock_archive, mock_fetch, config,
         install_mockery, cmd):
@@ -33,10 +34,14 @@ def test_view_link_type(
     view(cmd, viewpath, 'libdwarf')
     package_prefix = os.path.join(viewpath, 'libdwarf')
     assert os.path.exists(package_prefix)
-    assert os.path.islink(package_prefix) == (not cmd.startswith('hard'))
+
+    # Check that we use symlinks for and only for the appropriate subcommands
+    is_link_cmd = cmd in ('symlink', 'add')
+    assert os.path.islink(package_prefix) == is_link_cmd
 
 
-@pytest.mark.parametrize('cmd', ['hardlink', 'symlink', 'hard', 'add'])
+@pytest.mark.parametrize('cmd', ['hardlink', 'symlink', 'hard', 'add',
+                                 'copy', 'relocate'])
 def test_view_projections(
         tmpdir, mock_packages, mock_archive, mock_fetch, config,
         install_mockery, cmd):
@@ -54,7 +59,10 @@ def test_view_projections(
 
     package_prefix = os.path.join(viewpath, 'libdwarf-20130207/libdwarf')
     assert os.path.exists(package_prefix)
-    assert os.path.islink(package_prefix) == (not cmd.startswith('hard'))
+
+    # Check that we use symlinks for and only for the appropriate subcommands
+    is_symlink_cmd = cmd in ('symlink', 'add')
+    assert os.path.islink(package_prefix) == is_symlink_cmd
 
 
 def test_view_multiple_projections(
diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash
index 49518de059b..6801862beed 100755
--- a/share/spack/spack-completion.bash
+++ b/share/spack/spack-completion.bash
@@ -1521,7 +1521,7 @@ _spack_view() {
     then
         SPACK_COMPREPLY="-h --help -v --verbose -e --exclude -d --dependencies"
     else
-        SPACK_COMPREPLY="symlink add soft hardlink hard remove rm statlink status check"
+        SPACK_COMPREPLY="symlink add soft hardlink hard copy relocate remove rm statlink status check"
     fi
 }
 
@@ -1570,6 +1570,24 @@ _spack_view_hard() {
     fi
 }
 
+_spack_view_copy() {
+    if $list_options
+    then
+        SPACK_COMPREPLY="-h --help --projection-file -i --ignore-conflicts"
+    else
+        _all_packages
+    fi
+}
+
+_spack_view_relocate() {
+    if $list_options
+    then
+        SPACK_COMPREPLY="-h --help --projection-file -i --ignore-conflicts"
+    else
+        _all_packages
+    fi
+}
+
 _spack_view_remove() {
     if $list_options
     then
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 7a269f8a1d6..2311f6ad39a 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -962,7 +962,7 @@ def add_files_to_view(self, view, merge_map):
         bin_dir = self.spec.prefix.bin
         for src, dst in merge_map.items():
             if not path_contains_subdirectory(src, bin_dir):
-                view.link(src, dst)
+                view.link(src, dst, spec=self.spec)
             elif not os.path.islink(src):
                 copy(src, dst)
                 if 'script' in get_filetype(src):
@@ -988,7 +988,7 @@ def add_files_to_view(self, view, merge_map):
                 orig_link_target = os.path.join(self.spec.prefix, realpath_rel)
 
                 new_link_target = os.path.abspath(merge_map[orig_link_target])
-                view.link(new_link_target, dst)
+                view.link(new_link_target, dst, spec=self.spec)
 
     def remove_files_from_view(self, view, merge_map):
         bin_dir = self.spec.prefix.bin

From 0086c475466ee2501ccbf446a22ed68930c3e580 Mon Sep 17 00:00:00 2001
From: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
Date: Wed, 3 Jun 2020 11:38:27 -0700
Subject: [PATCH 598/802] patch lambda capture issue for @1.1906.1, fixed in
 upstream faodel@master (#16935)

---
 .../faodel/lambda-capture-f0267fc.patch       | 26 +++++++++++++++++++
 .../repos/builtin/packages/faodel/package.py  |  1 +
 2 files changed, 27 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/faodel/lambda-capture-f0267fc.patch

diff --git a/var/spack/repos/builtin/packages/faodel/lambda-capture-f0267fc.patch b/var/spack/repos/builtin/packages/faodel/lambda-capture-f0267fc.patch
new file mode 100644
index 00000000000..2dd2c32d118
--- /dev/null
+++ b/var/spack/repos/builtin/packages/faodel/lambda-capture-f0267fc.patch
@@ -0,0 +1,26 @@
+From f0267fc728d0f49ad396b83e8e62fba54027f31f Mon Sep 17 00:00:00 2001
+From: Craig Ulmer <craig@craigulmer.com>
+Date: Fri, 29 May 2020 23:08:29 -0700
+Subject: [PATCH] FIX: Removes variable from lambda capture that conflicted
+ with args
+
+---
+ src/kelpie/pools/DHTPool/DHTPool.cpp | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/kelpie/pools/DHTPool/DHTPool.cpp b/src/kelpie/pools/DHTPool/DHTPool.cpp
+index df9c1d3..d24aa89 100644
+--- a/src/kelpie/pools/DHTPool/DHTPool.cpp
++++ b/src/kelpie/pools/DHTPool/DHTPool.cpp
+@@ -229,7 +229,7 @@ rc_t DHTPool::Need(const Key &key, size_t expected_ldo_user_bytes, lunasa::DataO
+   bool is_found=false;
+ 
+   rc_t rc = Want(key, expected_ldo_user_bytes,
+-                 [&key, &returned_ldo, &cv, &is_found] (bool success, Key key, lunasa::DataObject result_ldo,
++                 [&returned_ldo, &cv, &is_found] (bool success, Key key, lunasa::DataObject result_ldo,
+                                                         const kv_row_info_t &ri, const kv_col_info_t &c) {
+       if(success) {
+         *returned_ldo = result_ldo;
+-- 
+2.24.2 (Apple Git-127)
+
diff --git a/var/spack/repos/builtin/packages/faodel/package.py b/var/spack/repos/builtin/packages/faodel/package.py
index 63f5798a024..255f0396fa4 100644
--- a/var/spack/repos/builtin/packages/faodel/package.py
+++ b/var/spack/repos/builtin/packages/faodel/package.py
@@ -55,6 +55,7 @@ class Faodel(CMakePackage):
     patch('faodel_mpi.patch', when='@1.1811.1 ~mpi')
     # FAODEL Github issue #5
     patch('faodel_sbl.patch', when='@1.1811.1 logging=sbl')
+    patch('lambda-capture-f0267fc.patch', when='@1.1906.1')
 
     def cmake_args(self):
         spec = self.spec

From 24775697f5b8b38bea407fd5b2594e483f39d150 Mon Sep 17 00:00:00 2001
From: Peter Scheibel <scheibel1@llnl.gov>
Date: Wed, 3 Jun 2020 17:43:51 -0700
Subject: [PATCH 599/802] Mirrors: add option to exclude packages from "mirror
 create" (#14154)

* add an --exclude-file option to 'spack mirror create' which allows a user to specify a file of specs to exclude when creating a mirror. this is anticipated to be useful especially when using the '--all' option

* allow specifying number of versions when mirroring all packages

* when mirroring all specs within an environment, include dependencies of root specs

* add '--exclude-specs' option to allow user to specify that specs should be excluded on the command line

* add test for excluding specs
---
 lib/spack/spack/cmd/mirror.py      | 46 ++++++++++++++++++++++-----
 lib/spack/spack/environment.py     | 25 ++++++---------
 lib/spack/spack/test/cmd/mirror.py | 50 ++++++++++++++++++++++++++++++
 share/spack/spack-completion.bash  |  2 +-
 4 files changed, 99 insertions(+), 24 deletions(-)

diff --git a/lib/spack/spack/cmd/mirror.py b/lib/spack/spack/cmd/mirror.py
index 1473550a560..2d338204d3b 100644
--- a/lib/spack/spack/cmd/mirror.py
+++ b/lib/spack/spack/cmd/mirror.py
@@ -45,6 +45,15 @@ def setup_parser(subparser):
              " (this requires significant time and space)")
     create_parser.add_argument(
         '-f', '--file', help="file with specs of packages to put in mirror")
+    create_parser.add_argument(
+        '--exclude-file',
+        help="specs which Spack should not try to add to a mirror"
+             " (listed in a file, one per line)")
+    create_parser.add_argument(
+        '--exclude-specs',
+        help="specs which Spack should not try to add to a mirror"
+             " (specified on command line)")
+
     create_parser.add_argument(
         '--skip-unstable-versions', action='store_true',
         help="don't cache versions unless they identify a stable (unchanging)"
@@ -232,9 +241,7 @@ def _read_specs_from_file(filename):
     return specs
 
 
-def mirror_create(args):
-    """Create a directory to be used as a spack mirror, and fill it with
-       package archives."""
+def _determine_specs_to_mirror(args):
     if args.specs and args.all:
         raise SpackError("Cannot specify specs on command line if you"
                          " chose to mirror all specs with '--all'")
@@ -264,6 +271,7 @@ def mirror_create(args):
                 tty.die("Cannot pass specs on the command line with --file.")
             specs = _read_specs_from_file(args.file)
 
+        env_specs = None
         if not specs:
             # If nothing is passed, use environment or all if no active env
             if not args.all:
@@ -273,12 +281,9 @@ def mirror_create(args):
 
             env = ev.get_env(args, 'mirror')
             if env:
-                mirror_specs = env.specs_by_hash.values()
+                env_specs = env.all_specs()
             else:
                 specs = [Spec(n) for n in spack.repo.all_package_names()]
-                mirror_specs = spack.mirror.get_all_versions(specs)
-                mirror_specs.sort(
-                    key=lambda s: (s.name, s.version))
         else:
             # If the user asked for dependencies, traverse spec DAG get them.
             if args.dependencies:
@@ -297,11 +302,38 @@ def mirror_create(args):
                 msg = 'Skipping {0} as it is an external spec.'
                 tty.msg(msg.format(spec.cshort_spec))
 
+        if env_specs:
+            if args.versions_per_spec:
+                tty.warn("Ignoring '--versions-per-spec' for mirroring specs"
+                         " in environment.")
+            mirror_specs = env_specs
+        else:
             if num_versions == 'all':
                 mirror_specs = spack.mirror.get_all_versions(specs)
             else:
                 mirror_specs = spack.mirror.get_matching_versions(
                     specs, num_versions=num_versions)
+            mirror_specs.sort(
+                key=lambda s: (s.name, s.version))
+
+    exclude_specs = []
+    if args.exclude_file:
+        exclude_specs.extend(_read_specs_from_file(args.exclude_file))
+    if args.exclude_specs:
+        exclude_specs.extend(
+            spack.cmd.parse_specs(str(args.exclude_specs).split()))
+    if exclude_specs:
+        mirror_specs = list(
+            x for x in mirror_specs
+            if not any(x.satisfies(y, strict=True) for y in exclude_specs))
+
+    return mirror_specs
+
+
+def mirror_create(args):
+    """Create a directory to be used as a spack mirror, and fill it with
+       package archives."""
+    mirror_specs = _determine_specs_to_mirror(args)
 
     mirror = spack.mirror.Mirror(
         args.directory or spack.config.get('config:source_cache'))
diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index 8d3b1438e12..00af2df2d93 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -1232,26 +1232,19 @@ def install_all(self, args=None):
 
             self._install(spec, **kwargs)
 
-    def all_specs_by_hash(self):
-        """Map of hashes to spec for all specs in this environment."""
-        # Note this uses dag-hashes calculated without build deps as keys,
-        # whereas the environment tracks specs based on dag-hashes calculated
-        # with all dependencies. This function should not be used by an
-        # Environment object for management of its own data structures
-        hashes = {}
-        for h in self.concretized_order:
-            specs = self.specs_by_hash[h].traverse(deptype=('link', 'run'))
-            for spec in specs:
-                hashes[spec.dag_hash()] = spec
-        return hashes
-
     def all_specs(self):
         """Return all specs, even those a user spec would shadow."""
-        return sorted(self.all_specs_by_hash().values())
+        all_specs = set()
+        for h in self.concretized_order:
+            all_specs.update(self.specs_by_hash[h].traverse())
+
+        return sorted(all_specs)
 
     def all_hashes(self):
-        """Return all specs, even those a user spec would shadow."""
-        return list(self.all_specs_by_hash().keys())
+        """Return hashes of all specs.
+
+        Note these hashes exclude build dependencies."""
+        return list(set(s.dag_hash() for s in self.all_specs()))
 
     def roots(self):
         """Specs explicitly requested by the user *in this environment*.
diff --git a/lib/spack/spack/test/cmd/mirror.py b/lib/spack/spack/test/cmd/mirror.py
index 4bb4fad2248..f6fe0b24ddb 100644
--- a/lib/spack/spack/test/cmd/mirror.py
+++ b/lib/spack/spack/test/cmd/mirror.py
@@ -89,6 +89,56 @@ def test_mirror_skip_unstable(tmpdir_factory, mock_packages, config,
             set(['trivial-pkg-with-valid-hash']))
 
 
+class MockMirrorArgs(object):
+    def __init__(self, specs=None, all=False, file=None,
+                 versions_per_spec=None, dependencies=False,
+                 exclude_file=None, exclude_specs=None):
+        self.specs = specs or []
+        self.all = all
+        self.file = file
+        self.versions_per_spec = versions_per_spec
+        self.dependencies = dependencies
+        self.exclude_file = exclude_file
+        self.exclude_specs = exclude_specs
+
+
+def test_exclude_specs(mock_packages):
+    args = MockMirrorArgs(
+        specs=['mpich'],
+        versions_per_spec='all',
+        exclude_specs="mpich@3.0.1:3.0.2 mpich@1.0")
+
+    mirror_specs = spack.cmd.mirror._determine_specs_to_mirror(args)
+    expected_include = set(spack.spec.Spec(x) for x in
+                           ['mpich@3.0.3', 'mpich@3.0.4', 'mpich@3.0'])
+    expected_exclude = set(spack.spec.Spec(x) for x in
+                           ['mpich@3.0.1', 'mpich@3.0.2', 'mpich@1.0'])
+    assert expected_include <= set(mirror_specs)
+    assert (not expected_exclude & set(mirror_specs))
+
+
+def test_exclude_file(mock_packages, tmpdir):
+    exclude_path = os.path.join(str(tmpdir), 'test-exclude.txt')
+    with open(exclude_path, 'w') as exclude_file:
+        exclude_file.write("""\
+mpich@3.0.1:3.0.2
+mpich@1.0
+""")
+
+    args = MockMirrorArgs(
+        specs=['mpich'],
+        versions_per_spec='all',
+        exclude_file=exclude_path)
+
+    mirror_specs = spack.cmd.mirror._determine_specs_to_mirror(args)
+    expected_include = set(spack.spec.Spec(x) for x in
+                           ['mpich@3.0.3', 'mpich@3.0.4', 'mpich@3.0'])
+    expected_exclude = set(spack.spec.Spec(x) for x in
+                           ['mpich@3.0.1', 'mpich@3.0.2', 'mpich@1.0'])
+    assert expected_include <= set(mirror_specs)
+    assert (not expected_exclude & set(mirror_specs))
+
+
 def test_mirror_crud(tmp_scope, capsys):
     with capsys.disabled():
         mirror('add', '--scope', tmp_scope, 'mirror', 'http://spack.io')
diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash
index 6801862beed..fa1e79c9c7f 100755
--- a/share/spack/spack-completion.bash
+++ b/share/spack/spack-completion.bash
@@ -1042,7 +1042,7 @@ _spack_mirror() {
 _spack_mirror_create() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -d --directory -a --all -f --file --skip-unstable-versions -D --dependencies -n --versions-per-spec"
+        SPACK_COMPREPLY="-h --help -d --directory -a --all -f --file --exclude-file --exclude-specs --skip-unstable-versions -D --dependencies -n --versions-per-spec"
     else
         _all_packages
     fi

From 748be57790832e73c78f59e43126ba22c1de78a2 Mon Sep 17 00:00:00 2001
From: shanedsnyder <ssnyder@mcs.anl.gov>
Date: Wed, 3 Jun 2020 20:05:46 -0500
Subject: [PATCH 600/802] update darshan-runtime & darshan-util versions
 (#16934)

* update darshan-runtime & darshan-util versions

includes up through the current release, 3.2.1

* remove pre-releases, not needed in spack
---
 var/spack/repos/builtin/packages/darshan-runtime/package.py | 2 ++
 var/spack/repos/builtin/packages/darshan-util/package.py    | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/darshan-runtime/package.py b/var/spack/repos/builtin/packages/darshan-runtime/package.py
index 3789612f129..c58bc9edd5f 100644
--- a/var/spack/repos/builtin/packages/darshan-runtime/package.py
+++ b/var/spack/repos/builtin/packages/darshan-runtime/package.py
@@ -21,6 +21,8 @@ class DarshanRuntime(Package):
     maintainers = ['shanedsnyder', 'carns']
 
     version('develop', branch='master')
+    version('3.2.1', sha256='d63048b7a3d1c4de939875943e3e7a2468a9034fcb68585edbc87f57f622e7f7')
+    version('3.2.0', sha256='4035435bdc0fa2a678247fbf8d5a31dfeb3a133baf06577786b1fe8d00a31b7e')
     version('3.1.8', sha256='3ed51c8d5d93b4a8cbb7d53d13052140a9dffe0bc1a3e1ebfc44a36a184b5c82')
     version('3.1.7', sha256='9ba535df292727ac1e8025bdf2dc42942715205cad8319d925723fd88709e8d6')
     version('3.1.6', sha256='21cb24e2a971c45e04476e00441b7fbea63d2afa727a5cf8b7a4a9d9004dd856')
diff --git a/var/spack/repos/builtin/packages/darshan-util/package.py b/var/spack/repos/builtin/packages/darshan-util/package.py
index 8d25fa99650..af5502a7fbf 100644
--- a/var/spack/repos/builtin/packages/darshan-util/package.py
+++ b/var/spack/repos/builtin/packages/darshan-util/package.py
@@ -19,6 +19,8 @@ class DarshanUtil(Package):
     maintainers = ['shanedsnyder', 'carns']
 
     version('develop', branch='master')
+    version('3.2.1', sha256='d63048b7a3d1c4de939875943e3e7a2468a9034fcb68585edbc87f57f622e7f7')
+    version('3.2.0', sha256='4035435bdc0fa2a678247fbf8d5a31dfeb3a133baf06577786b1fe8d00a31b7e')
     version('3.1.8', sha256='3ed51c8d5d93b4a8cbb7d53d13052140a9dffe0bc1a3e1ebfc44a36a184b5c82')
     version('3.1.7', sha256='9ba535df292727ac1e8025bdf2dc42942715205cad8319d925723fd88709e8d6')
     version('3.1.6', sha256='21cb24e2a971c45e04476e00441b7fbea63d2afa727a5cf8b7a4a9d9004dd856')

From 0fb671a19ed6e4afe8693ae2a17f0caaee9acca3 Mon Sep 17 00:00:00 2001
From: Tom Payerle <payerle@umd.edu>
Date: Wed, 3 Jun 2020 23:08:07 -0400
Subject: [PATCH 601/802] Gnuplot fix 16928 (#16929)

* gnuplot: Fix for #16928

Dependency for --with-wx flag mistyped (should be wxwidgets)

* Revert "gnuplot: Fix for #16928"

This reverts commit 2b85814e5ccf5c9b2c70c7959994e89c18fdc3d8.

* gnuplot: Fix for #16928

Dependency spec for --with-wx flag mistyped (should be wxwidgets, not
wx)
---
 var/spack/repos/builtin/packages/gnuplot/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/gnuplot/package.py b/var/spack/repos/builtin/packages/gnuplot/package.py
index 9fb79e67466..59e527fcde4 100644
--- a/var/spack/repos/builtin/packages/gnuplot/package.py
+++ b/var/spack/repos/builtin/packages/gnuplot/package.py
@@ -122,7 +122,7 @@ def configure_args(self):
             options.append('--with-qt=no')
 
         if '+wx' in spec:
-            options.append('--with-wx=%s' % spec['wx'].prefix)
+            options.append('--with-wx=%s' % spec['wxwidgets'].prefix)
         else:
             options.append('--disable-wxwidgets')
 

From a02fc8ae58c1ad83e09badabceaae45519d01e48 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 3 Jun 2020 22:09:06 -0500
Subject: [PATCH 602/802] Ignore __pycache__ directory (#16836)

---
 .gitignore | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 96947860ee0..e2f485ab924 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,6 +4,7 @@
 /var/spack/environments
 /var/spack/repos/*/index.yaml
 /var/spack/repos/*/lock
+__pycache__/
 *.pyc
 /opt
 *~
@@ -36,4 +37,4 @@ lib/spack/spack/test/.cache
 
 # VSCode files
 .vscode
-.devcontainer
\ No newline at end of file
+.devcontainer

From dd19d6f863d01b3beb38104293b2927623b2753d Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 3 Jun 2020 22:09:22 -0500
Subject: [PATCH 603/802] Fix parsing of EvtGen URL (#16883)

* Fix parsing of EvtGen URL

* Flake8 fix
---
 lib/spack/spack/test/url_parse.py |  2 ++
 lib/spack/spack/url.py            | 18 +++++++++---------
 2 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/lib/spack/spack/test/url_parse.py b/lib/spack/spack/test/url_parse.py
index 06515620073..846e24d242c 100644
--- a/lib/spack/spack/test/url_parse.py
+++ b/lib/spack/spack/test/url_parse.py
@@ -464,6 +464,8 @@ def test_url_parse_offset(name, noffset, ver, voffset, path):
      'http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz'),
     ('vampirtrace', '5.14.4',
      'http://wwwpub.zih.tu-dresden.de/~mlieber/dcount/dcount.php?package=vampirtrace&get=VampirTrace-5.14.4.tar.gz'),
+    ('EvtGen', '01.07.00',
+     'https://evtgen.hepforge.org/downloads?f=EvtGen-01.07.00.tar.gz'),
     # (we don't actually look for these, they are picked up
     #  during the preliminary stem parsing)
     ('octopus', '6.0', 'http://octopus-code.org/down.php?file=6.0/octopus-6.0.tar.gz'),
diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py
index a728c46a713..4969d5f3530 100644
--- a/lib/spack/spack/url.py
+++ b/lib/spack/spack/url.py
@@ -549,27 +549,23 @@ def parse_version_offset(path):
         # 8th Pass: Query strings
 
         # e.g. https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0
-        (r'\?sha=[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)$', suffix),
-
+        # e.g. https://gitlab.kitware.com/api/v4/projects/icet%2Ficet/repository/archive.tar.bz2?sha=IceT-2.1.1
         # e.g. http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0
-        (r'\?ref=[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)$', suffix),
-
         # e.g. http://apps.fz-juelich.de/jsc/sionlib/download.php?version=1.7.1
         # e.g. https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef
-        (r'[?&]version=v?(\d[\da-zA-Z._-]*)$', suffix),
+        (r'[?&](?:sha|ref|version)=[a-zA-Z\d+-]*[_-]?v?(\d[\da-zA-Z._-]*)$', suffix),  # noqa: E501
 
         # e.g. http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz
         # e.g. http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz
-        (r'[?&]filename=[a-zA-Z\d+-]+[_-]v?(\d[\da-zA-Z.]*)', stem),
-
+        # e.g. https://evtgen.hepforge.org/downloads?f=EvtGen-01.07.00.tar.gz
         # e.g. http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz
-        (r'&get=[a-zA-Z\d+-]+-v?(\d[\da-zA-Z.]*)$', stem),  # noqa
+        (r'[?&](?:filename|f|get)=[a-zA-Z\d+-]+[_-]v?(\d[\da-zA-Z.]*)', stem),
 
         # 9th Pass: Version in path
 
         # github.com/repo/name/releases/download/vver/name
         # e.g. https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow
-        (r'github\.com/[^/]+/[^/]+/releases/download/[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)/', path),  # noqa
+        (r'github\.com/[^/]+/[^/]+/releases/download/[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)/', path),  # noqa: E501
 
         # e.g. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/ncbi.tar.gz
         (r'(\d[\da-zA-Z._-]*)/[^/]+$', path),
@@ -696,6 +692,10 @@ def parse_name_offset(path, v=None):
         # e.g. http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz
         (r'\?filename=([A-Za-z\d+-]+)$', stem),
 
+        # ?f=name-ver.ver
+        # e.g. https://evtgen.hepforge.org/downloads?f=EvtGen-01.07.00.tar.gz
+        (r'\?f=([A-Za-z\d+-]+)$', stem),
+
         # ?package=name
         # e.g. http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz
         (r'\?package=([A-Za-z\d+-]+)', stem),

From 5a7b555314c0e56377ee7292785b685624b30d90 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 3 Jun 2020 22:09:40 -0500
Subject: [PATCH 604/802] IPython: fix setuptools dependency (#16915)

* IPython: fix setuptools dependency

* Remove extra colon
---
 var/spack/repos/builtin/packages/py-ipython/package.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-ipython/package.py b/var/spack/repos/builtin/packages/py-ipython/package.py
index 8faa8ab3305..5d1710b00ec 100644
--- a/var/spack/repos/builtin/packages/py-ipython/package.py
+++ b/var/spack/repos/builtin/packages/py-ipython/package.py
@@ -19,8 +19,10 @@ class PyIpython(PythonPackage):
     version('3.1.0', sha256='532092d3f06f82b1d8d1e5c37097eae19fcf025f8f6a4b670dd49c3c338d5624')
     version('2.3.1', sha256='3e98466aa2fe54540bcba9aa6e01a39f40110d67668c297340c4b9514b7cc49c')
 
-    depends_on('python@2.7:2.8,3.3:', type=('build', 'run'), when='@:6')
+    depends_on('python@3.6:', type=('build', 'run'), when='@7.10:')
     depends_on('python@3.5:', type=('build', 'run'), when='@7:')
+    depends_on('python@3.3:', type=('build', 'run'), when='@6:')
+    depends_on('python@2.7:2.8,3.3:', type=('build', 'run'))
 
     depends_on('py-backports-shutil-get-terminal-size', type=('build', 'run'), when="^python@:3.2")
     depends_on('py-pathlib2', type=('build', 'run'), when="^python@:3.3")
@@ -37,4 +39,4 @@ class PyIpython(PythonPackage):
     depends_on('py-appnope', type=('build', 'run'), when='platform=darwin')
     depends_on('py-jedi@0.10:', type=('build', 'run'), when='@7.5.0:')
     depends_on('py-backcall', type=('build', 'run'), when='@7.5.0:')
-    depends_on('py-setuptools@18.5:', type=('build', 'run'), when='@7.5.0:')
+    depends_on('py-setuptools@18.5:', type='run', when='@4.1:')

From 61f61f3cdea3bef00ff0e6b5bf2bf59831ff630a Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 3 Jun 2020 22:09:58 -0500
Subject: [PATCH 605/802] py-openpyxl: add 3.0.3 (#16940)

---
 var/spack/repos/builtin/packages/py-openpyxl/package.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-openpyxl/package.py b/var/spack/repos/builtin/packages/py-openpyxl/package.py
index b8460028009..f929fe6a9bc 100644
--- a/var/spack/repos/builtin/packages/py-openpyxl/package.py
+++ b/var/spack/repos/builtin/packages/py-openpyxl/package.py
@@ -10,11 +10,15 @@ class PyOpenpyxl(PythonPackage):
     """A Python library to read/write Excel 2010 xlsx/xlsm files"""
 
     homepage = "http://openpyxl.readthedocs.org/"
-    url      = "https://pypi.io/packages/source/o/openpyxl/openpyxl-2.4.5.tar.gz"
+    url      = "https://pypi.io/packages/source/o/openpyxl/openpyxl-3.0.3.tar.gz"
 
+    version('3.0.3', sha256='547a9fc6aafcf44abe358b89ed4438d077e9d92e4f182c87e2dc294186dc4b64')
     version('2.4.5', sha256='78c331e819fb0a63a1339d452ba0b575d1a31f09fdcce793a31bec7e9ef4ef21')
 
-    depends_on('python@2.6:2.8,3.0:3.1,3.3:')
+    depends_on('python@3.6:',         when='@3.0:', type=('build', 'run'))
+    depends_on('python@2.7:2.8,3.5:', when='@2.6:', type=('build', 'run'))
+    depends_on('python@2.7:2.8,3.4:', when='@2.5:', type=('build', 'run'))
+    depends_on('python@2.6:2.8,3.3:', when='@2.1:', type=('build', 'run'))
 
     depends_on('py-setuptools', type='build')
 

From 6f6c243699f6f29629d809fa3861f8c1bb5bbeca Mon Sep 17 00:00:00 2001
From: "Seth R. Johnson" <johnsonsr@ornl.gov>
Date: Wed, 3 Jun 2020 23:11:44 -0400
Subject: [PATCH 606/802] mpfr: update hash for 4.0.2 patch (#16937)

---
 var/spack/repos/builtin/packages/mpfr/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/mpfr/package.py b/var/spack/repos/builtin/packages/mpfr/package.py
index b163d8a7244..fa97da76ed0 100644
--- a/var/spack/repos/builtin/packages/mpfr/package.py
+++ b/var/spack/repos/builtin/packages/mpfr/package.py
@@ -37,7 +37,7 @@ class Mpfr(AutotoolsPackage, GNUMirrorPackage):
     # Check the Bugs section of old release pages for patches.
     # https://www.mpfr.org/mpfr-X.Y.Z/#bugs
     patches = {
-        '4.0.2': '8f15fd27ab65341a60d724d594897d32f4597ddf642d0dc121995e2150181b0c',
+        '4.0.2': '3f80b836948aa96f8d1cb9cc7f3f55973f19285482a96f9a4e1623d460bcccf0',
         '4.0.1': '5230aab653fa8675fc05b5bdd3890e071e8df49a92a9d58c4284024affd27739',
         '3.1.6': '7a6dd71bcda4803d6b89612706a17b8816e1acd5dd9bf1bec29cf748f3b60008',
         '3.1.5': '1ae14fb3a54ae8e0faed20801970255b279eee9e5ac624891ab5d29727f0bc04',

From 16e8e434c2cffa236f9f5d189423af4a81243d51 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Thu, 4 Jun 2020 05:15:01 +0200
Subject: [PATCH 607/802] Add pytest@5.3.4 (#16927)

Dropping atomicwrites dependency: https://github.com/pytest-dev/pytest/issues/6147
---
 var/spack/repos/builtin/packages/py-pytest/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-pytest/package.py b/var/spack/repos/builtin/packages/py-pytest/package.py
index 85d01c240c0..b6d2c914c54 100644
--- a/var/spack/repos/builtin/packages/py-pytest/package.py
+++ b/var/spack/repos/builtin/packages/py-pytest/package.py
@@ -14,6 +14,7 @@ class PyPytest(PythonPackage):
 
     import_modules = ['pytest']
 
+    version('5.3.4', sha256='1d122e8be54d1a709e56f82e2d85dcba3018313d64647f38a91aec88c239b600')
     version('5.2.1', sha256='ca563435f4941d0cb34767301c27bc65c510cb82e90b9ecf9cb52dc2c63caaa0')
     version('5.1.1', sha256='c3d5020755f70c82eceda3feaf556af9a341334414a8eca521a18f463bcead88')
     version('4.6.9', sha256='19e8f75eac01dd3f211edd465b39efbcbdc8fc5f7866d7dd49fedb30d8adf339')
@@ -48,7 +49,7 @@ class PyPytest(PythonPackage):
     depends_on('py-attrs@17.4.0:', when='@3.5:', type=('build', 'run'))
     depends_on('py-more-itertools@4.0.0:', when='@3.5.1:', type=('build', 'run'))
     depends_on('py-more-itertools@4.0.0:6.0.0', when='@4.2.1:4.6.9 ^python@:2', type=('build', 'run'))
-    depends_on('py-atomicwrites@1.0:', when='@3.6:', type=('build', 'run'))
+    depends_on('py-atomicwrites@1.0:', when='@3.6:5.2.999', type=('build', 'run'))
     depends_on('py-pluggy@0.12:0.999', when='@4.6:', type=('build', 'run'))
     depends_on('py-pluggy@0.9.0:0.9.999,0.11:0.999', when='@4.5.0:4.5.999', type=('build', 'run'))
     depends_on('py-pluggy@0.11:', when='@4.4.2:4.4.999', type=('build', 'run'))

From 02548c56fa77ed4ce62a0f8cf95b98966fcaebab Mon Sep 17 00:00:00 2001
From: Mathew Cleveland <clevelam@lanl.gov>
Date: Wed, 3 Jun 2020 21:16:46 -0600
Subject: [PATCH 608/802] + Add opppy-0_1_3 (#16926)

+ Update maintainers for OPPPY package
+ remove "run" requirement for setuptools and sphynx

Co-authored-by: Cleveland <cleveland@lanl.gov>
---
 var/spack/repos/builtin/packages/py-opppy/package.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-opppy/package.py b/var/spack/repos/builtin/packages/py-opppy/package.py
index 6e512b12c66..81bcf6d5af4 100644
--- a/var/spack/repos/builtin/packages/py-opppy/package.py
+++ b/var/spack/repos/builtin/packages/py-opppy/package.py
@@ -14,15 +14,17 @@ class PyOpppy(PythonPackage):
     homepage = "https://github.com/lanl/opppy"
     url = "https://github.com/lanl/OPPPY/archive/opppy-0_1_2.tar.gz"
     git = "https://github.com/lanl/opppy.git"
+    maintainers = ['clevelam']
 
     version('master', branch='master')
+    version('0_1_3', sha256='c3ca97f2ff8ab319b5c7257baa8cab852387dc00d426b4534c06f0894363c541')
     version('0_1_2', sha256='ef3795d3164fa0aa7ea7da7e223d6d0a48d2960aefd03a7d90cdb8b8f480cd4c')
     version('0_1_1', sha256='505c023853e75552abc65de9777a125ecb6a99a1cb4e605a4f702af837e3168b')
 
-    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-setuptools', type=('build'))
+    depends_on('py-sphinx',     type=('build'))
     depends_on('py-numpy@1.6:', type=('build', 'run'))
     depends_on('python@3:',     type=('build', 'run'))
     depends_on('py-argparse',   type=('build', 'run'), when='^python@:2.6')
     depends_on('py-scipy',      type=('build', 'run'))
     depends_on('py-matplotlib', type=('build', 'run'))
-    depends_on('py-sphinx',     type=('build', 'run'))

From 104a0c42594687c8753f372ae33985e4cc40e396 Mon Sep 17 00:00:00 2001
From: "Seth R. Johnson" <johnsonsr@ornl.gov>
Date: Wed, 3 Jun 2020 23:25:09 -0400
Subject: [PATCH 609/802] Trilinos: add Stratimikos package (#16925)

Stratimikos is an optional dependency for our project. It depends on
Thyra, and thyra has subpackages that should be enabled based on
tpetra/epetra/epetraext.
---
 var/spack/repos/builtin/packages/trilinos/package.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 3626f328c87..5e8a96a16aa 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -179,6 +179,8 @@ class Trilinos(CMakePackage):
             description='Compile with Shards')
     variant('shylu',        default=False,
             description='Compile with ShyLU')
+    variant('stratimikos',  default=False,
+            description='Compile with Stratimikos')
     variant('teko',         default=False,
             description='Compile with Teko')
     variant('tempus',       default=False,
@@ -468,6 +470,7 @@ def define_tpl_enable(cmake_var, spec_var=None):
             define_trilinos_enable('Shards'),
             define_trilinos_enable('ShyLU'),
             define_trilinos_enable('STK'),
+            define_trilinos_enable('Stratimikos'),
             define_trilinos_enable('Teko'),
             define_trilinos_enable('Tempus'),
             define_trilinos_enable('Teuchos'),
@@ -513,6 +516,12 @@ def define_tpl_enable(cmake_var, spec_var=None):
                 define('Trilinos_ENABLE_SEACASNemslice', False)
             ])
 
+        if '+stratimikos' in spec:
+            # Add thyra adapters based on package enables
+            options.extend(
+                define_trilinos_enable('Thyra' + pkg + 'Adapters', pkg.lower())
+                for pkg in ['Epetra', 'EpetraExt', 'Tpetra'])
+
         # ######################### TPLs #############################
 
         blas = spec['blas'].libs

From 6f4631ee4812ce2e5d3731b20aa0d9e0f7f89b31 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Thu, 4 Jun 2020 05:25:38 +0200
Subject: [PATCH 610/802] Add py-jupyter-core@4.6.1 (#16922)

---
 var/spack/repos/builtin/packages/py-jupyter-core/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-jupyter-core/package.py b/var/spack/repos/builtin/packages/py-jupyter-core/package.py
index 9fb84e40cb9..3bb21a4b546 100644
--- a/var/spack/repos/builtin/packages/py-jupyter-core/package.py
+++ b/var/spack/repos/builtin/packages/py-jupyter-core/package.py
@@ -13,6 +13,7 @@ class PyJupyterCore(PythonPackage):
     url      = "https://pypi.io/packages/source/j/jupyter-core/jupyter_core-4.6.0.tar.gz"
 
     version('4.6.3', sha256='394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e')
+    version('4.6.1', sha256='a183e0ec2e8f6adddf62b0a3fc6a2237e3e0056d381e536d3e7c7ecc3067e244')
     version('4.6.0', sha256='85103cee6548992780912c1a0a9ec2583a4a18f1ef79a248ec0db4446500bce3')
     version('4.4.0', sha256='ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7')
     version('4.2.0', sha256='44ec837a53bebf4e937112d3f9ccf31fee4f8db3e406dd0dd4f0378a354bed9c')

From ad50a0218863d958022186a04e6e3a1402b3e9fb Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Thu, 4 Jun 2020 05:26:13 +0200
Subject: [PATCH 611/802] Add matplotlib 3.1.0 (#16921)

---
 var/spack/repos/builtin/packages/py-matplotlib/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py
index 4e5dbf91356..9b9b77f00a2 100644
--- a/var/spack/repos/builtin/packages/py-matplotlib/package.py
+++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py
@@ -32,6 +32,7 @@ class PyMatplotlib(PythonPackage):
     version('3.1.3', sha256='db3121f12fb9b99f105d1413aebaeb3d943f269f3d262b45586d12765866f0c6')
     version('3.1.2', sha256='8e8e2c2fe3d873108735c6ee9884e6f36f467df4a143136209cff303b183bada')
     version('3.1.1', sha256='1febd22afe1489b13c6749ea059d392c03261b2950d1d45c17e3aed812080c93')
+    version('3.1.0', sha256='1e0213f87cc0076f7b0c4c251d7e23601e2419cd98691df79edb95517ba06f0c')
     version('3.0.2', sha256='c94b792af431f6adb6859eb218137acd9a35f4f7442cea57e4a59c54751c36af')
     version('3.0.0', sha256='b4e2333c98a7c2c1ff6eb930cd2b57d4b818de5437c5048802096b32f66e65f9')
     version('2.2.5', sha256='a3037a840cd9dfdc2df9fee8af8f76ca82bfab173c0f9468193ca7a89a2b60ea')

From 0dd1d1f21a1ead55ab163207530ab403c34c11ee Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 4 Jun 2020 08:05:22 -0500
Subject: [PATCH 612/802] NumPy: add 1.18.5 (#16943)

---
 var/spack/repos/builtin/packages/py-numpy/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index dbbfc815410..4659a449ebf 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -16,7 +16,7 @@ class PyNumpy(PythonPackage):
     number capabilities"""
 
     homepage = "https://numpy.org/"
-    url      = "https://pypi.io/packages/source/n/numpy/numpy-1.18.4.zip"
+    url      = "https://pypi.io/packages/source/n/numpy/numpy-1.18.5.zip"
     git      = "https://github.com/numpy/numpy.git"
 
     maintainers = ['adamjstewart']
@@ -30,6 +30,7 @@ class PyNumpy(PythonPackage):
     ]
 
     version('master', branch='master')
+    version('1.18.5', sha256='34e96e9dae65c4839bd80012023aadd6ee2ccb73ce7fdf3074c62f301e63120b')
     version('1.18.4', sha256='bbcc85aaf4cd84ba057decaead058f43191cc0e30d6bc5d44fe336dc3d3f4509')
     version('1.18.3', sha256='e46e2384209c91996d5ec16744234d1c906ab79a701ce1a26155c9ec890b8dc8')
     version('1.18.2', sha256='e7894793e6e8540dbeac77c87b489e331947813511108ae097f1715c018b8f3d')

From 7617054a5d50633930b0e08f3208b81f55b35dee Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 4 Jun 2020 08:05:48 -0500
Subject: [PATCH 613/802] Fix obsolete references to wx package (#16944)

---
 var/spack/repos/builtin/packages/paraver/package.py    | 2 +-
 var/spack/repos/builtin/packages/wxpropgrid/package.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/paraver/package.py b/var/spack/repos/builtin/packages/paraver/package.py
index fe9e31b2f20..fe305fc07ef 100644
--- a/var/spack/repos/builtin/packages/paraver/package.py
+++ b/var/spack/repos/builtin/packages/paraver/package.py
@@ -51,6 +51,6 @@ def install(self, spec, prefix):
                   "--with-paraver=%s" % prefix,
                   "--with-boost=%s" % spec['boost'].prefix,
                   "--with-boost-serialization=boost_serialization",
-                  "--with-wxdir=%s" % spec['wx'].prefix.bin)
+                  "--with-wxdir=%s" % spec['wxwidgets'].prefix.bin)
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/wxpropgrid/package.py b/var/spack/repos/builtin/packages/wxpropgrid/package.py
index 644af132217..c288d0d5338 100644
--- a/var/spack/repos/builtin/packages/wxpropgrid/package.py
+++ b/var/spack/repos/builtin/packages/wxpropgrid/package.py
@@ -20,7 +20,7 @@ class Wxpropgrid(Package, SourceforgePackage):
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix, "--with-wxdir=%s" %
-                  spec['wx'].prefix.bin, "--enable-unicode")
+                  spec['wxwidgets'].prefix.bin, "--enable-unicode")
 
         make()
         make("install")

From b64ec7fba4c512f6abcfc51b7b2c5c92907bbeda Mon Sep 17 00:00:00 2001
From: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
Date: Thu, 4 Jun 2020 06:58:33 -0700
Subject: [PATCH 614/802] pass hwloc to configure via useropt; use lib/ or
 lib64/ as appropriate for libunwind (#16941)

---
 .../repos/builtin/packages/tau/package.py     |  3 ++
 .../repos/builtin/packages/tau/unwind.patch   | 34 +++++++++++++++++++
 2 files changed, 37 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/tau/unwind.patch

diff --git a/var/spack/repos/builtin/packages/tau/package.py b/var/spack/repos/builtin/packages/tau/package.py
index 5a4d704c430..1d2dea580b7 100644
--- a/var/spack/repos/builtin/packages/tau/package.py
+++ b/var/spack/repos/builtin/packages/tau/package.py
@@ -107,6 +107,8 @@ class Tau(Package):
     conflicts('+adios2', when='@:2.29.1')
     conflicts('+sqlite', when='@:2.29.1')
 
+    patch('unwind.patch', when="@2.29")
+
     def set_compiler_options(self, spec):
 
         useropt = ["-O2 -g", self.rpath_args]
@@ -144,6 +146,7 @@ def set_compiler_options(self, spec):
 
     def setup_build_environment(self, env):
         env.prepend_path('LIBRARY_PATH', self.spec['zlib'].prefix.lib)
+        env.prepend_path('LIBRARY_PATH', self.spec['hwloc'].prefix.lib)
 
     def install(self, spec, prefix):
         # TAU isn't happy with directories that have '@' in the path.  Sigh.
diff --git a/var/spack/repos/builtin/packages/tau/unwind.patch b/var/spack/repos/builtin/packages/tau/unwind.patch
new file mode 100644
index 00000000000..1d9faa4cc6b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tau/unwind.patch
@@ -0,0 +1,34 @@
+From 3b60cbcab167f8f1cf450f0319850bfa88f39d3a Mon Sep 17 00:00:00 2001
+From: eugeneswalker <eugenesunsetwalker@gmail.com>
+Date: Thu, 4 Jun 2020 06:12:41 -0700
+Subject: [PATCH] check for unwind_dir/lib and unwind_dir/lib64
+
+---
+ configure | 11 +++++++++--
+ 1 file changed, 9 insertions(+), 2 deletions(-)
+
+diff --git a/configure b/configure
+index 3bd7430..b673cdf 100755
+--- a/configure
++++ b/configure
+@@ -1662,8 +1662,15 @@ for arg in "$@"; do
+ 	-unwind=*)
+ 	    unwind_dir=`echo $arg | sed -e 's/-unwind=//'`
+         if [ $unwind_dir != "/usr" ]; then
+-	      unwind_inc="$unwind_dir/include"
+-	      unwind_lib="$unwind_dir/lib"
++	        unwind_inc="$unwind_dir/include"
++	        unwind_lib=""
++	        if [[ -d "$unwind_dir/lib" ]] ; then
++	          unwind_lib="$unwind_dir/lib"
++	        elif [[ -d "$unwind_dir/lib64" ]] ; then
++	          unwind_lib="$unwind_dir/lib64"
++	        else
++	          exit 1
++	        fi
+         fi
+ 	    # So that the user doesn't have to specify the unwinder,
+ 	    # use libunwind as the default.
+-- 
+2.24.2 (Apple Git-127)
+

From 44ec8cc4e44b9d10be99c28ccb03aea88d8274e7 Mon Sep 17 00:00:00 2001
From: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
Date: Thu, 4 Jun 2020 09:16:11 -0700
Subject: [PATCH 615/802] sz: patch in ctag optionality from robertu94/sz
 3637a87f986c (#16953)

---
 .../packages/sz/ctags-only-if-requested.patch | 42 +++++++++++++++++++
 .../repos/builtin/packages/sz/package.py      |  2 +
 2 files changed, 44 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/sz/ctags-only-if-requested.patch

diff --git a/var/spack/repos/builtin/packages/sz/ctags-only-if-requested.patch b/var/spack/repos/builtin/packages/sz/ctags-only-if-requested.patch
new file mode 100644
index 00000000000..0b3494f11e1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sz/ctags-only-if-requested.patch
@@ -0,0 +1,42 @@
+From 3637a87f986cb64ddc1bde3551e29894ab18500b Mon Sep 17 00:00:00 2001
+From: Robert Underwood <rr.underwood94@gmail.com>
+Date: Wed, 3 Jun 2020 12:48:33 -0400
+Subject: [PATCH] Don't require ctags unless we ask for it
+
+Previously this caused build failures if the user had a bad version of
+ctags.  Don't build with it.
+---
+ CMakeLists.txt | 17 ++++++++++-------
+ 1 file changed, 10 insertions(+), 7 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 4fd4014..d764a44 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -36,13 +36,16 @@ set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
+ 
+ #generate tags for the project if tags exist
+-find_program(TAGS ctags)
+-if(TAGS)
+-	add_custom_target(tags ALL
+-    COMMAND ${TAGS} --exclude=${CMAKE_BINARY_DIR} -f ${CMAKE_BINARY_DIR}/tags --c++-kinds=+p --fields=+iaS -R
+-		COMMENT Generating Tag files
+-		WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+-		)
++option(BUILD_CTAGS "enable ctags generation target" OFF)
++if(BUILD_CTAGS)
++  find_program(TAGS ctags)
++  if(TAGS)
++    add_custom_target(tags ALL
++      COMMAND ${TAGS} --exclude=${CMAKE_BINARY_DIR} -f ${CMAKE_BINARY_DIR}/tags --c++-kinds=+p --fields=+iaS -R
++      COMMENT Generating Tag files
++      WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
++      )
++  endif()
+ endif()
+ 
+ option(BUILD_SHARED_LIBS "build shared libraries over static libraries" ON)
+-- 
+2.24.2 (Apple Git-127)
+
diff --git a/var/spack/repos/builtin/packages/sz/package.py b/var/spack/repos/builtin/packages/sz/package.py
index b0d92dd51c5..897aa57a1c7 100644
--- a/var/spack/repos/builtin/packages/sz/package.py
+++ b/var/spack/repos/builtin/packages/sz/package.py
@@ -54,6 +54,8 @@ class Sz(CMakePackage):
     depends_on('hdf5', when="+hdf5")
     depends_on('netcdf-c', when="+netcdf")
 
+    patch('ctags-only-if-requested.patch', when='@2.1.8.1:2.1.8.3')
+
     @property
     def build_directory(self):
         """autotools needs a different build directory to work"""

From 0a3601a3f1bced90a8572cf64360b8645775281c Mon Sep 17 00:00:00 2001
From: Andrew Gaspar <andrew.gaspar@outlook.com>
Date: Thu, 4 Jun 2020 15:34:19 -0600
Subject: [PATCH 616/802] libgit2 v1.0.1 (#16952)

---
 var/spack/repos/builtin/packages/libgit2/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/libgit2/package.py b/var/spack/repos/builtin/packages/libgit2/package.py
index 6fe9022179a..dd5d55fb6f4 100644
--- a/var/spack/repos/builtin/packages/libgit2/package.py
+++ b/var/spack/repos/builtin/packages/libgit2/package.py
@@ -18,6 +18,7 @@ class Libgit2(CMakePackage):
 
     maintainers = ["AndrewGaspar"]
 
+    version('1.0.1',   sha256='1775427a6098f441ddbaa5bd4e9b8a043c7401e450ed761e69a415530fea81d2')
     version('1.0.0',   sha256='6a1fa16a7f6335ce8b2630fbdbb5e57c4027929ebc56fcd1ac55edb141b409b4')
     version('0.99.0',  sha256='174024310c1563097a6613a0d3f7539d11a9a86517cd67ce533849065de08a11')
     version('0.28.5',  sha256='2b7b68aee6f123bc84cc502a9c12738435b8054e7d628962e091cd2a25be4f42')

From 0d43e41da00d011fda7c17dc4d88b16e9deaebb9 Mon Sep 17 00:00:00 2001
From: Andrew Gaspar <andrew.gaspar@outlook.com>
Date: Thu, 4 Jun 2020 15:59:14 -0600
Subject: [PATCH 617/802] Rust v1.44.0 (#16957)

* libgit2 v1.0.1

* Rust 1.44.0

* Fix flake8
---
 .../repos/builtin/packages/rust/package.py    | 27 ++++++++++++-------
 1 file changed, 17 insertions(+), 10 deletions(-)

diff --git a/var/spack/repos/builtin/packages/rust/package.py b/var/spack/repos/builtin/packages/rust/package.py
index 3e89f9b974d..ff8cba54e63 100644
--- a/var/spack/repos/builtin/packages/rust/package.py
+++ b/var/spack/repos/builtin/packages/rust/package.py
@@ -85,6 +85,7 @@ class Rust(Package):
     # The `x.py` bootstrapping script did not exist prior to Rust 1.17. It
     # would be possible to support both, but for simplicitly, we only support
     # Rust 1.17 and newer
+    version('1.44.0', sha256='bf2df62317e533e84167c5bc7d4351a99fdab1f9cd6e6ba09f51996ad8561100')
     version('1.43.1', sha256='cde177b4a8c687da96f20de27630a1eb55c9d146a15e4c900d5c31cd3c3ac41d')
     version('1.43.0', sha256='75f6ac6c9da9f897f4634d5a07be4084692f7ccc2d2bb89337be86cfc18453a1')
     version('1.42.0', sha256='d2e8f931d16a0539faaaacd801e0d92c58df190269014b2360c6ab2a90ee3475')
@@ -126,6 +127,12 @@ class Rust(Package):
     # This dictionary contains a version: hash dictionary for each supported
     # Rust target.
     rust_releases = {
+        '1.44.0': {
+            'x86_64-unknown-linux-gnu':      'eaa34271b4ac4d2c281831117d4d335eed0b37fe7a34477d9855a6f1d930a624',
+            'powerpc64le-unknown-linux-gnu': '97038ea935c7a5b21f5aaaaad409c514e2b2ae8ea55994ba39645f453e98bc9f',
+            'aarch64-unknown-linux-gnu':     'bcc916003cb9c7ff44f5f9af348020b422dbc5bd4fe49bdbda2de6ce0a1bb745',
+            'x86_64-apple-darwin':           'f20388b80b2b0a8b122d89058f785a2cf3b14e93bcac53471d60fdb4106ffa35'
+        },
         '1.43.1': {
             'x86_64-unknown-linux-gnu':      '25cd71b95bba0daef56bad8c943a87368c4185b90983f4412f46e3e2418c0505',
             'powerpc64le-unknown-linux-gnu': '1670f00b00cc1bed38d523a25dba7420de3c06986c15a0248e06299f80ce6124',
@@ -370,11 +377,11 @@ class Rust(Package):
                     sha256='0000000000000000000000000000000000000000000000000000000000000000',
                     destination='spack_bootstrap_stage',
                     when='@{version} platform={platform} target={target}'\
-                        .format(
-                            version=prerelease_version,
-                            platform=rust_arch['platform'],
-                            target=rust_arch['target']
-                        )
+                    .format(
+                        version=prerelease_version,
+                        platform=rust_arch['platform'],
+                        target=rust_arch['target']
+                    )
                 )
 
     # This loop generates resources for each binary distribution, and maps
@@ -401,11 +408,11 @@ class Rust(Package):
                     sha256=rust_sha256,
                     destination='spack_bootstrap_stage',
                     when='@{version} platform={platform} target={target}'\
-                        .format(
-                            version=rust_version,
-                            platform=rust_arch['platform'],
-                            target=rust_arch['target']
-                        )
+                    .format(
+                        version=rust_version,
+                        platform=rust_arch['platform'],
+                        target=rust_arch['target']
+                    )
                 )
 
     # This routine returns the target architecture we intend to build for.

From 92e24950e5cbe28a3b241b13e2dc5363c7b994d7 Mon Sep 17 00:00:00 2001
From: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
Date: Thu, 4 Jun 2020 22:49:46 -0700
Subject: [PATCH 618/802] add erlang version 23.0 (#16961)

---
 var/spack/repos/builtin/packages/erlang/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/erlang/package.py b/var/spack/repos/builtin/packages/erlang/package.py
index 1101bee787d..f1fc027ae09 100644
--- a/var/spack/repos/builtin/packages/erlang/package.py
+++ b/var/spack/repos/builtin/packages/erlang/package.py
@@ -16,6 +16,7 @@ class Erlang(AutotoolsPackage):
     homepage = "https://erlang.org/"
     url      = "https://erlang.org/download/otp_src_22.2.tar.gz"
 
+    version('23.0', sha256='42dcf3c721f4de59fe74ae7b65950c2174c46dc8d1dd4e27c0594d86f606a635') 
     version('22.2', sha256='89c2480cdac566065577c82704a48e10f89cf2e6ca5ab99e1cf80027784c678f')
     version('22.1', sha256='cd33a102cbac6dd1c7b1e7a9a0d82d13587771fac4e96e8fff92e403d15e32c8')
     version('22.0', sha256='042e168d74055a501c75911694758a30597446accd8c82ec569552b9e9fcd272')

From 5b272e3ff3f7cac83d4e3db402781f535950d26f Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Fri, 5 Jun 2020 09:08:32 +0200
Subject: [PATCH 619/802] commands: use a single ThreadPool for `spack
 versions` (#16749)

This fixes a fork bomb in `spack versions`. Recursive generation of pools
to scrape URLs in `_spider` was creating large numbers of processes.
Instead of recursively creating process pools, we now use a single
`ThreadPool` with a concurrency limit.

More on the issue: having ~10 users running at the same time spack
versions on front-end nodes caused kernel lockup due to the high number
of sockets opened (sys-admin reports ~210k distributed over 3 nodes).
Users were internal, so they had ulimit -n set to ~70k.

The forking behavior could be observed by just running:

    $ spack versions boost

and checking the number of processes spawned. Number of processes
per se was not the issue, but each one of them opens a socket
which can stress `iptables`.

In the original issue the kernel watchdog was reporting:

    Message from syslogd@login03 at May 19 12:01:30 ...
    kernel:Watchdog CPU:110 Hard LOCKUP
    Message from syslogd@login03 at May 19 12:01:31 ...
    kernel:watchdog: BUG: soft lockup - CPU#110 stuck for 23s! [python3:2756]
    Message from syslogd@login03 at May 19 12:01:31 ...
    kernel:watchdog: BUG: soft lockup - CPU#94 stuck for 22s! [iptables:5603]
---
 lib/spack/spack/cmd/versions.py   |   6 +-
 lib/spack/spack/package.py        |   5 +-
 lib/spack/spack/test/web.py       | 182 +++++++++-----------
 lib/spack/spack/util/web.py       | 264 +++++++++++++++---------------
 share/spack/spack-completion.bash |   2 +-
 5 files changed, 218 insertions(+), 241 deletions(-)

diff --git a/lib/spack/spack/cmd/versions.py b/lib/spack/spack/cmd/versions.py
index 723f89ce08e..366307f0b2c 100644
--- a/lib/spack/spack/cmd/versions.py
+++ b/lib/spack/spack/cmd/versions.py
@@ -21,6 +21,10 @@
 def setup_parser(subparser):
     subparser.add_argument('-s', '--safe-only', action='store_true',
                            help='only list safe versions of the package')
+    subparser.add_argument(
+        '-c', '--concurrency', default=32, type=int,
+        help='number of concurrent requests'
+    )
     arguments.add_common_arguments(subparser, ['package'])
 
 
@@ -45,7 +49,7 @@ def versions(parser, args):
     if sys.stdout.isatty():
         tty.msg('Remote versions (not yet checksummed):')
 
-    fetched_versions = pkg.fetch_remote_versions()
+    fetched_versions = pkg.fetch_remote_versions(args.concurrency)
     remote_versions = set(fetched_versions).difference(safe_versions)
 
     if not remote_versions:
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index bb5ea41dc3e..c9774c5b29b 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -2020,7 +2020,7 @@ def all_urls(self):
                 urls.append(args['url'])
         return urls
 
-    def fetch_remote_versions(self):
+    def fetch_remote_versions(self, concurrency=128):
         """Find remote versions of this package.
 
         Uses ``list_url`` and any other URLs listed in the package file.
@@ -2033,7 +2033,8 @@ def fetch_remote_versions(self):
 
         try:
             return spack.util.web.find_versions_of_archive(
-                self.all_urls, self.list_url, self.list_depth)
+                self.all_urls, self.list_url, self.list_depth, concurrency
+            )
         except spack.util.web.NoNetworkConnectionError as e:
             tty.die("Package.fetch_versions couldn't connect to:", e.url,
                     e.message)
diff --git a/lib/spack/spack/test/web.py b/lib/spack/spack/test/web.py
index ae62301319b..dfca41c95bb 100644
--- a/lib/spack/spack/test/web.py
+++ b/lib/spack/spack/test/web.py
@@ -2,125 +2,101 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-"""Tests for web.py."""
 import os
+
+import ordereddict_backport
 import pytest
-
-from ordereddict_backport import OrderedDict
-
 import spack.paths
-import spack.util.web as web_util
+import spack.util.web
 from spack.version import ver
 
 
-web_data_path = os.path.join(spack.paths.test_path, 'data', 'web')
-
-root = 'file://' + web_data_path + '/index.html'
-root_tarball = 'file://' + web_data_path + '/foo-0.0.0.tar.gz'
-
-page_1 = 'file://' + os.path.join(web_data_path, '1.html')
-page_2 = 'file://' + os.path.join(web_data_path, '2.html')
-page_3 = 'file://' + os.path.join(web_data_path, '3.html')
-page_4 = 'file://' + os.path.join(web_data_path, '4.html')
+def _create_url(relative_url):
+    web_data_path = os.path.join(spack.paths.test_path, 'data', 'web')
+    return 'file://' + os.path.join(web_data_path, relative_url)
 
 
-def test_spider_0():
-    pages, links = web_util.spider(root, depth=0)
-
-    assert root in pages
-    assert page_1 not in pages
-    assert page_2 not in pages
-    assert page_3 not in pages
-    assert page_4 not in pages
-
-    assert "This is the root page." in pages[root]
-
-    assert root not in links
-    assert page_1 in links
-    assert page_2 not in links
-    assert page_3 not in links
-    assert page_4 not in links
+root = _create_url('index.html')
+root_tarball = _create_url('foo-0.0.0.tar.gz')
+page_1 = _create_url('1.html')
+page_2 = _create_url('2.html')
+page_3 = _create_url('3.html')
+page_4 = _create_url('4.html')
 
 
-def test_spider_1():
-    pages, links = web_util.spider(root, depth=1)
+@pytest.mark.parametrize(
+    'depth,expected_found,expected_not_found,expected_text', [
+        (0,
+         {'pages': [root], 'links': [page_1]},
+         {'pages': [page_1, page_2, page_3, page_4],
+          'links': [root, page_2, page_3, page_4]},
+         {root: "This is the root page."}),
+        (1,
+         {'pages': [root, page_1], 'links': [page_1, page_2]},
+         {'pages': [page_2, page_3, page_4],
+          'links': [root, page_3, page_4]},
+         {root: "This is the root page.",
+          page_1: "This is page 1."}),
+        (2,
+         {'pages': [root, page_1, page_2],
+          'links': [page_1, page_2, page_3, page_4]},
+         {'pages': [page_3, page_4], 'links': [root]},
+         {root: "This is the root page.",
+          page_1: "This is page 1.",
+          page_2: "This is page 2."}),
+        (3,
+         {'pages': [root, page_1, page_2, page_3, page_4],
+          'links': [root, page_1, page_2, page_3, page_4]},
+         {'pages': [], 'links': []},
+         {root: "This is the root page.",
+          page_1: "This is page 1.",
+          page_2: "This is page 2.",
+          page_3: "This is page 3.",
+          page_4: "This is page 4."}),
+    ])
+def test_spider(depth, expected_found, expected_not_found, expected_text):
+    pages, links = spack.util.web.spider(root, depth=depth)
 
-    assert root in pages
-    assert page_1 in pages
-    assert page_2 not in pages
-    assert page_3 not in pages
-    assert page_4 not in pages
+    for page in expected_found['pages']:
+        assert page in pages
 
-    assert "This is the root page." in pages[root]
-    assert "This is page 1." in pages[page_1]
+    for page in expected_not_found['pages']:
+        assert page not in pages
 
-    assert root not in links
-    assert page_1 in links
-    assert page_2 in links
-    assert page_3 not in links
-    assert page_4 not in links
+    for link in expected_found['links']:
+        assert link in links
+
+    for link in expected_not_found['links']:
+        assert link not in links
+
+    for page, text in expected_text.items():
+        assert text in pages[page]
 
 
-def test_spider_2():
-    pages, links = web_util.spider(root, depth=2)
-
-    assert root in pages
-    assert page_1 in pages
-    assert page_2 in pages
-    assert page_3 not in pages
-    assert page_4 not in pages
-
-    assert "This is the root page." in pages[root]
-    assert "This is page 1." in pages[page_1]
-    assert "This is page 2." in pages[page_2]
-
-    assert root not in links
-    assert page_1 in links
-    assert page_1 in links
-    assert page_2 in links
-    assert page_3 in links
-    assert page_4 in links
-
-
-def test_spider_3():
-    pages, links = web_util.spider(root, depth=3)
-
-    assert root in pages
-    assert page_1 in pages
-    assert page_2 in pages
-    assert page_3 in pages
-    assert page_4 in pages
-
-    assert "This is the root page." in pages[root]
-    assert "This is page 1." in pages[page_1]
-    assert "This is page 2." in pages[page_2]
-    assert "This is page 3." in pages[page_3]
-    assert "This is page 4." in pages[page_4]
-
-    assert root in links  # circular link on page 3
-    assert page_1 in links
-    assert page_1 in links
-    assert page_2 in links
-    assert page_3 in links
-    assert page_4 in links
+def test_spider_no_response(monkeypatch):
+    # Mock the absence of a response
+    monkeypatch.setattr(
+        spack.util.web, 'read_from_url', lambda x, y: (None, None, None)
+    )
+    pages, links = spack.util.web.spider(root, depth=0)
+    assert not pages and not links
 
 
 def test_find_versions_of_archive_0():
-    versions = web_util.find_versions_of_archive(
+    versions = spack.util.web.find_versions_of_archive(
         root_tarball, root, list_depth=0)
     assert ver('0.0.0') in versions
 
 
 def test_find_versions_of_archive_1():
-    versions = web_util.find_versions_of_archive(
+    versions = spack.util.web.find_versions_of_archive(
         root_tarball, root, list_depth=1)
     assert ver('0.0.0') in versions
     assert ver('1.0.0') in versions
 
 
 def test_find_versions_of_archive_2():
-    versions = web_util.find_versions_of_archive(
+    versions = spack.util.web.find_versions_of_archive(
         root_tarball, root, list_depth=2)
     assert ver('0.0.0') in versions
     assert ver('1.0.0') in versions
@@ -128,14 +104,14 @@ def test_find_versions_of_archive_2():
 
 
 def test_find_exotic_versions_of_archive_2():
-    versions = web_util.find_versions_of_archive(
+    versions = spack.util.web.find_versions_of_archive(
         root_tarball, root, list_depth=2)
     # up for grabs to make this better.
     assert ver('2.0.0b2') in versions
 
 
 def test_find_versions_of_archive_3():
-    versions = web_util.find_versions_of_archive(
+    versions = spack.util.web.find_versions_of_archive(
         root_tarball, root, list_depth=3)
     assert ver('0.0.0') in versions
     assert ver('1.0.0') in versions
@@ -145,7 +121,7 @@ def test_find_versions_of_archive_3():
 
 
 def test_find_exotic_versions_of_archive_3():
-    versions = web_util.find_versions_of_archive(
+    versions = spack.util.web.find_versions_of_archive(
         root_tarball, root, list_depth=3)
     assert ver('2.0.0b2') in versions
     assert ver('3.0a1') in versions
@@ -159,35 +135,35 @@ def test_get_header():
 
     # looking up headers should just work like a plain dict
     # lookup when there is an entry with the right key
-    assert(web_util.get_header(headers, 'Content-type') == 'text/plain')
+    assert(spack.util.web.get_header(headers, 'Content-type') == 'text/plain')
 
     # looking up headers should still work if there is a fuzzy match
-    assert(web_util.get_header(headers, 'contentType') == 'text/plain')
+    assert(spack.util.web.get_header(headers, 'contentType') == 'text/plain')
 
     # ...unless there is an exact match for the "fuzzy" spelling.
     headers['contentType'] = 'text/html'
-    assert(web_util.get_header(headers, 'contentType') == 'text/html')
+    assert(spack.util.web.get_header(headers, 'contentType') == 'text/html')
 
     # If lookup has to fallback to fuzzy matching and there are more than one
     # fuzzy match, the result depends on the internal ordering of the given
     # mapping
-    headers = OrderedDict()
+    headers = ordereddict_backport.OrderedDict()
     headers['Content-type'] = 'text/plain'
     headers['contentType'] = 'text/html'
 
-    assert(web_util.get_header(headers, 'CONTENT_TYPE') == 'text/plain')
+    assert(spack.util.web.get_header(headers, 'CONTENT_TYPE') == 'text/plain')
     del headers['Content-type']
-    assert(web_util.get_header(headers, 'CONTENT_TYPE') == 'text/html')
+    assert(spack.util.web.get_header(headers, 'CONTENT_TYPE') == 'text/html')
 
     # Same as above, but different ordering
-    headers = OrderedDict()
+    headers = ordereddict_backport.OrderedDict()
     headers['contentType'] = 'text/html'
     headers['Content-type'] = 'text/plain'
 
-    assert(web_util.get_header(headers, 'CONTENT_TYPE') == 'text/html')
+    assert(spack.util.web.get_header(headers, 'CONTENT_TYPE') == 'text/html')
     del headers['contentType']
-    assert(web_util.get_header(headers, 'CONTENT_TYPE') == 'text/plain')
+    assert(spack.util.web.get_header(headers, 'CONTENT_TYPE') == 'text/plain')
 
     # If there isn't even a fuzzy match, raise KeyError
     with pytest.raises(KeyError):
-        web_util.get_header(headers, 'ContentLength')
+        spack.util.web.get_header(headers, 'ContentLength')
diff --git a/lib/spack/spack/util/web.py b/lib/spack/spack/util/web.py
index 8039dc5fdaf..3f71dd1f719 100644
--- a/lib/spack/spack/util/web.py
+++ b/lib/spack/spack/util/web.py
@@ -7,17 +7,18 @@
 
 import codecs
 import errno
-import re
+import multiprocessing.pool
 import os
 import os.path
+import re
 import shutil
 import ssl
 import sys
 import traceback
 
-from six.moves.urllib.request import urlopen, Request
+import six
 from six.moves.urllib.error import URLError
-import multiprocessing.pool
+from six.moves.urllib.request import urlopen, Request
 
 try:
     # Python 2 had these in the HTMLParser package.
@@ -63,34 +64,6 @@ def handle_starttag(self, tag, attrs):
                     self.links.append(val)
 
 
-class NonDaemonProcess(multiprocessing.Process):
-    """Process that allows sub-processes, so pools can have sub-pools."""
-    @property
-    def daemon(self):
-        return False
-
-    @daemon.setter
-    def daemon(self, value):
-        pass
-
-
-if sys.version_info[0] < 3:
-    class NonDaemonPool(multiprocessing.pool.Pool):
-        """Pool that uses non-daemon processes"""
-        Process = NonDaemonProcess
-else:
-
-    class NonDaemonContext(type(multiprocessing.get_context())):  # novm
-        Process = NonDaemonProcess
-
-    class NonDaemonPool(multiprocessing.pool.Pool):
-        """Pool that uses non-daemon processes"""
-
-        def __init__(self, *args, **kwargs):
-            kwargs['context'] = NonDaemonContext()
-            super(NonDaemonPool, self).__init__(*args, **kwargs)
-
-
 def uses_ssl(parsed_url):
     if parsed_url.scheme == 'https':
         return True
@@ -336,109 +309,152 @@ def list_url(url):
             for key in _iter_s3_prefix(s3, url)))
 
 
-def _spider(url, visited, root, depth, max_depth, raise_on_error):
-    """Fetches URL and any pages it links to up to max_depth.
+def spider(root_urls, depth=0, concurrency=32):
+    """Get web pages from root URLs.
 
-       depth should initially be zero, and max_depth is the max depth of
-       links to follow from the root.
+    If depth is specified (e.g., depth=2), then this will also follow
+    up to <depth> levels of links from each root.
 
-       Prints out a warning only if the root can't be fetched; it ignores
-       errors with pages that the root links to.
+    Args:
+        root_urls (str or list of str): root urls used as a starting point
+            for spidering
+        depth (int): level of recursion into links
+        concurrency (int): number of simultaneous requests that can be sent
 
-       Returns a tuple of:
-       - pages: dict of pages visited (URL) mapped to their full text.
-       - links: set of links encountered while visiting the pages.
+    Returns:
+        A dict of pages visited (URL) mapped to their full text and the
+        set of visited links.
     """
-    pages = {}     # dict from page URL -> text content.
-    links = set()  # set of all links seen on visited pages.
+    # Cache of visited links, meant to be captured by the closure below
+    _visited = set()
 
-    try:
-        response_url, _, response = read_from_url(url, 'text/html')
-        if not response_url or not response:
-            return pages, links
+    def _spider(url, collect_nested):
+        """Fetches URL and any pages it links to.
 
-        page = codecs.getreader('utf-8')(response).read()
-        pages[response_url] = page
+        Prints out a warning only if the root can't be fetched; it ignores
+        errors with pages that the root links to.
 
-        # Parse out the links in the page
-        link_parser = LinkParser()
+        Args:
+            url (str): url being fetched and searched for links
+            collect_nested (bool): whether we want to collect arguments
+                for nested spidering on the links found in this url
+
+        Returns:
+            A tuple of:
+            - pages: dict of pages visited (URL) mapped to their full text.
+            - links: set of links encountered while visiting the pages.
+            - spider_args: argument for subsequent call to spider
+        """
+        pages = {}  # dict from page URL -> text content.
+        links = set()  # set of all links seen on visited pages.
         subcalls = []
-        link_parser.feed(page)
 
-        while link_parser.links:
-            raw_link = link_parser.links.pop()
-            abs_link = url_util.join(
-                response_url,
-                raw_link.strip(),
-                resolve_href=True)
-            links.add(abs_link)
+        try:
+            response_url, _, response = read_from_url(url, 'text/html')
+            if not response_url or not response:
+                return pages, links, subcalls
 
-            # Skip stuff that looks like an archive
-            if any(raw_link.endswith(suf) for suf in ALLOWED_ARCHIVE_TYPES):
-                continue
+            page = codecs.getreader('utf-8')(response).read()
+            pages[response_url] = page
 
-            # Skip things outside the root directory
-            if not abs_link.startswith(root):
-                continue
+            # Parse out the links in the page
+            link_parser = LinkParser()
+            link_parser.feed(page)
 
-            # Skip already-visited links
-            if abs_link in visited:
-                continue
+            while link_parser.links:
+                raw_link = link_parser.links.pop()
+                abs_link = url_util.join(
+                    response_url,
+                    raw_link.strip(),
+                    resolve_href=True)
+                links.add(abs_link)
 
-            # If we're not at max depth, follow links.
-            if depth < max_depth:
-                subcalls.append((abs_link, visited, root,
-                                 depth + 1, max_depth, raise_on_error))
-                visited.add(abs_link)
+                # Skip stuff that looks like an archive
+                if any(raw_link.endswith(s) for s in ALLOWED_ARCHIVE_TYPES):
+                    continue
 
-        if subcalls:
-            pool = NonDaemonPool(processes=len(subcalls))
-            try:
-                results = pool.map(_spider_wrapper, subcalls)
+                # Skip already-visited links
+                if abs_link in _visited:
+                    continue
 
-                for sub_pages, sub_links in results:
-                    pages.update(sub_pages)
-                    links.update(sub_links)
+                # If we're not at max depth, follow links.
+                if collect_nested:
+                    subcalls.append((abs_link,))
+                    _visited.add(abs_link)
 
-            finally:
-                pool.terminate()
-                pool.join()
+        except URLError as e:
+            tty.debug(str(e))
 
-    except URLError as e:
-        tty.debug(e)
+            if hasattr(e, 'reason') and isinstance(e.reason, ssl.SSLError):
+                tty.warn("Spack was unable to fetch url list due to a "
+                         "certificate verification problem. You can try "
+                         "running spack -k, which will not check SSL "
+                         "certificates. Use this at your own risk.")
 
-        if hasattr(e, 'reason') and isinstance(e.reason, ssl.SSLError):
-            tty.warn("Spack was unable to fetch url list due to a certificate "
-                     "verification problem. You can try running spack -k, "
-                     "which will not check SSL certificates. Use this at your "
-                     "own risk.")
+        except HTMLParseError as e:
+            # This error indicates that Python's HTML parser sucks.
+            msg = "Got an error parsing HTML."
 
-        if raise_on_error:
-            raise NoNetworkConnectionError(str(e), url)
+            # Pre-2.7.3 Pythons in particular have rather prickly HTML parsing.
+            if sys.version_info[:3] < (2, 7, 3):
+                msg += " Use Python 2.7.3 or newer for better HTML parsing."
 
-    except HTMLParseError as e:
-        # This error indicates that Python's HTML parser sucks.
-        msg = "Got an error parsing HTML."
+            tty.warn(msg, url, "HTMLParseError: " + str(e))
 
-        # Pre-2.7.3 Pythons in particular have rather prickly HTML parsing.
-        if sys.version_info[:3] < (2, 7, 3):
-            msg += " Use Python 2.7.3 or newer for better HTML parsing."
+        except Exception as e:
+            # Other types of errors are completely ignored,
+            # except in debug mode
+            tty.debug("Error in _spider: %s:%s" % (type(e), str(e)),
+                      traceback.format_exc())
 
-        tty.warn(msg, url, "HTMLParseError: " + str(e))
+        finally:
+            tty.debug("SPIDER: [url={0}]".format(url))
 
-    except Exception as e:
-        # Other types of errors are completely ignored, except in debug mode.
-        tty.debug("Error in _spider: %s:%s" % (type(e), e),
-                  traceback.format_exc())
+        return pages, links, subcalls
+
+    # TODO: Needed until we drop support for Python 2.X
+    def star(func):
+        def _wrapper(args):
+            return func(*args)
+        return _wrapper
+
+    if isinstance(root_urls, six.string_types):
+        root_urls = [root_urls]
+
+    # Clear the local cache of visited pages before starting the search
+    _visited.clear()
+
+    current_depth = 0
+    pages, links, spider_args = {}, set(), []
+
+    collect = current_depth < depth
+    for root in root_urls:
+        root = url_util.parse(root)
+        spider_args.append((root, collect))
+
+    tp = multiprocessing.pool.ThreadPool(processes=concurrency)
+    try:
+        while current_depth <= depth:
+            tty.debug("SPIDER: [depth={0}, max_depth={1}, urls={2}]".format(
+                current_depth, depth, len(spider_args))
+            )
+            results = tp.map(star(_spider), spider_args)
+            spider_args = []
+            collect = current_depth < depth
+            for sub_pages, sub_links, sub_spider_args in results:
+                sub_spider_args = [x + (collect,) for x in sub_spider_args]
+                pages.update(sub_pages)
+                links.update(sub_links)
+                spider_args.extend(sub_spider_args)
+
+            current_depth += 1
+    finally:
+        tp.terminate()
+        tp.join()
 
     return pages, links
 
 
-def _spider_wrapper(args):
-    """Wrapper for using spider with multiprocessing."""
-    return _spider(*args)
-
-
 def _urlopen(req, *args, **kwargs):
     """Wrapper for compatibility with old versions of Python."""
     url = req
@@ -460,37 +476,22 @@ def _urlopen(req, *args, **kwargs):
     return opener(req, *args, **kwargs)
 
 
-def spider(root, depth=0):
-    """Gets web pages from a root URL.
-
-       If depth is specified (e.g., depth=2), then this will also follow
-       up to <depth> levels of links from the root.
-
-       This will spawn processes to fetch the children, for much improved
-       performance over a sequential fetch.
-
-    """
-    root = url_util.parse(root)
-    pages, links = _spider(root, set(), root, 0, depth, False)
-    return pages, links
-
-
-def find_versions_of_archive(archive_urls, list_url=None, list_depth=0):
+def find_versions_of_archive(
+        archive_urls, list_url=None, list_depth=0, concurrency=32
+):
     """Scrape web pages for new versions of a tarball.
 
-    Arguments:
+    Args:
         archive_urls (str or list or tuple): URL or sequence of URLs for
             different versions of a package. Typically these are just the
             tarballs from the package file itself. By default, this searches
             the parent directories of archives.
-
-    Keyword Arguments:
         list_url (str or None): URL for a listing of archives.
             Spack will scrape these pages for download links that look
             like the archive URL.
-
-        list_depth (int): Max depth to follow links on list_url pages.
+        list_depth (int): max depth to follow links on list_url pages.
             Defaults to 0.
+        concurrency (int): maximum number of concurrent requests
     """
     if not isinstance(archive_urls, (list, tuple)):
         archive_urls = [archive_urls]
@@ -511,12 +512,7 @@ def find_versions_of_archive(archive_urls, list_url=None, list_depth=0):
     list_urls |= additional_list_urls
 
     # Grab some web pages to scrape.
-    pages = {}
-    links = set()
-    for lurl in list_urls:
-        pg, lnk = spider(lurl, depth=list_depth)
-        pages.update(pg)
-        links.update(lnk)
+    pages, links = spider(list_urls, depth=list_depth, concurrency=concurrency)
 
     # Scrape them for archive URLs
     regexes = []
diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash
index fa1e79c9c7f..0a74d144883 100755
--- a/share/spack/spack-completion.bash
+++ b/share/spack/spack-completion.bash
@@ -1510,7 +1510,7 @@ _spack_verify() {
 _spack_versions() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -s --safe-only"
+        SPACK_COMPREPLY="-h --help -s --safe-only -c --concurrency"
     else
         _all_packages
     fi

From 94e77333e6c1392a6b95b9a9d8b71cde213ea9c1 Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Fri, 5 Jun 2020 00:35:16 -0700
Subject: [PATCH 620/802] spack dev-build: Do not mark -u builds in database
 (#16333)

Builds can be stopped before the final install phase due to user requests. Those builds
should not be registered as installed in the database.

We had code intended to handle this but:

  1. It caught the wrong type of exception
  2. We were catching these exceptions to suppress them at a lower level in the stack

This PR allows the StopIteration to propagate through a ChildError, and catches it
properly. Also added to an existing test to prevent regression.
---
 lib/spack/spack/build_environment.py  | 32 +++++++++++++++++++--------
 lib/spack/spack/installer.py          | 20 +++++++++++------
 lib/spack/spack/package.py            | 11 ++++-----
 lib/spack/spack/test/cmd/dev_build.py | 19 ++++++++++++++++
 4 files changed, 61 insertions(+), 21 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 8beedf6c972..f57ecd1e582 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -812,12 +812,11 @@ def child_process(child_pipe, input_stream):
                 setup_package(pkg, dirty=dirty)
             return_value = function()
             child_pipe.send(return_value)
-        except StopIteration as e:
-            # StopIteration is used to stop installations
-            # before the final stage, mainly for debug purposes
-            tty.msg(e)
-            child_pipe.send(None)
 
+        except StopPhase as e:
+            # Do not create a full ChildError from this, it's not an error
+            # it's a control statement.
+            child_pipe.send(e)
         except BaseException:
             # catch ANYTHING that goes wrong in the child process
             exc_type, exc, tb = sys.exc_info()
@@ -869,15 +868,20 @@ def child_process(child_pipe, input_stream):
     child_result = parent_pipe.recv()
     p.join()
 
+    # If returns a StopPhase, raise it
+    if isinstance(child_result, StopPhase):
+        # do not print
+        raise child_result
+
     # let the caller know which package went wrong.
     if isinstance(child_result, InstallError):
         child_result.pkg = pkg
 
-    # If the child process raised an error, print its output here rather
-    # than waiting until the call to SpackError.die() in main(). This
-    # allows exception handling output to be logged from within Spack.
-    # see spack.main.SpackCommand.
     if isinstance(child_result, ChildError):
+        # If the child process raised an error, print its output here rather
+        # than waiting until the call to SpackError.die() in main(). This
+        # allows exception handling output to be logged from within Spack.
+        # see spack.main.SpackCommand.
         child_result.print_context()
         raise child_result
 
@@ -1066,3 +1070,13 @@ def __reduce__(self):
 def _make_child_error(msg, module, name, traceback, build_log, context):
     """Used by __reduce__ in ChildError to reconstruct pickled errors."""
     return ChildError(msg, module, name, traceback, build_log, context)
+
+
+class StopPhase(spack.error.SpackError):
+    """Pickle-able exception to control stopped builds."""
+    def __reduce__(self):
+        return _make_stop_phase, (self.message, self.long_message)
+
+
+def _make_stop_phase(msg, long_msg):
+    return StopPhase(msg, long_msg)
diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py
index 8886f3ed069..0eeec020bc1 100644
--- a/lib/spack/spack/installer.py
+++ b/lib/spack/spack/installer.py
@@ -784,6 +784,9 @@ def _check_last_phase(self, **kwargs):
         The ``stop_before`` or ``stop_at`` arguments are removed from the
         installation arguments.
 
+        The last phase is also set to None if it is the last phase of the
+        package already
+
         Args:
             kwargs:
               ``stop_before``': stop before execution of this phase (or None)
@@ -800,6 +803,10 @@ def _check_last_phase(self, **kwargs):
                 self.pkg.last_phase not in self.pkg.phases:
             tty.die('\'{0}\' is not an allowed phase for package {1}'
                     .format(self.pkg.last_phase, self.pkg.name))
+        # If we got a last_phase, make sure it's not already last
+        if self.pkg.last_phase and \
+                self.pkg.last_phase == self.pkg.phases[-1]:
+            self.pkg.last_phase = None
 
     def _cleanup_all_tasks(self):
         """Cleanup all build tasks to include releasing their locks."""
@@ -1164,13 +1171,12 @@ def build_process():
             if task.compiler:
                 spack.compilers.add_compilers_to_config(
                     spack.compilers.find_compilers([pkg.spec.prefix]))
-
-        except StopIteration as e:
-            # A StopIteration exception means that do_install was asked to
-            # stop early from clients.
-            tty.msg('{0} {1}'.format(self.pid, str(e)))
-            tty.msg('Package stage directory : {0}'
-                    .format(pkg.stage.source_path))
+        except spack.build_environment.StopPhase as e:
+            # A StopPhase exception means that do_install was asked to
+            # stop early from clients, and is not an error at this point
+            tty.debug('{0} {1}'.format(self.pid, str(e)))
+            tty.debug('Package stage directory : {0}'
+                      .format(pkg.stage.source_path))
 
     _install_task.__doc__ += install_args_docstring
 
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index c9774c5b29b..dc32effbec9 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -116,16 +116,17 @@ def phase_wrapper(spec, prefix):
 
     def _on_phase_start(self, instance):
         # If a phase has a matching stop_before_phase attribute,
-        # stop the installation process raising a StopIteration
+        # stop the installation process raising a StopPhase
         if getattr(instance, 'stop_before_phase', None) == self.name:
-            raise StopIteration('Stopping before \'{0}\' phase'
-                                .format(self.name))
+            from spack.build_environment import StopPhase
+            raise StopPhase('Stopping before \'{0}\' phase'.format(self.name))
 
     def _on_phase_exit(self, instance):
         # If a phase has a matching last_phase attribute,
-        # stop the installation process raising a StopIteration
+        # stop the installation process raising a StopPhase
         if getattr(instance, 'last_phase', None) == self.name:
-            raise StopIteration('Stopping at \'{0}\' phase'.format(self.name))
+            from spack.build_environment import StopPhase
+            raise StopPhase('Stopping at \'{0}\' phase'.format(self.name))
 
     def copy(self):
         try:
diff --git a/lib/spack/spack/test/cmd/dev_build.py b/lib/spack/spack/test/cmd/dev_build.py
index 37c40e787d4..271faa845d7 100644
--- a/lib/spack/spack/test/cmd/dev_build.py
+++ b/lib/spack/spack/test/cmd/dev_build.py
@@ -54,6 +54,25 @@ def test_dev_build_until(tmpdir, mock_packages, install_mockery):
             assert f.read() == spec.package.replacement_string
 
     assert not os.path.exists(spec.prefix)
+    assert not spack.store.db.query(spec, installed=True)
+
+
+def test_dev_build_until_last_phase(tmpdir, mock_packages, install_mockery):
+    # Test that we ignore the last_phase argument if it is already last
+    spec = spack.spec.Spec('dev-build-test-install@0.0.0').concretized()
+
+    with tmpdir.as_cwd():
+        with open(spec.package.filename, 'w') as f:
+            f.write(spec.package.original_string)
+
+        dev_build('-u', 'install', 'dev-build-test-install@0.0.0')
+
+        assert spec.package.filename in os.listdir(os.getcwd())
+        with open(spec.package.filename, 'r') as f:
+            assert f.read() == spec.package.replacement_string
+
+    assert os.path.exists(spec.prefix)
+    assert spack.store.db.query(spec, installed=True)
 
 
 def test_dev_build_before_until(tmpdir, mock_packages, install_mockery):

From 8be7823cc5b7147880f7c8107519b4f24f434d8f Mon Sep 17 00:00:00 2001
From: "Tomoki, Karatsu" <49965247+t-karatsu@users.noreply.github.com>
Date: Fri, 5 Jun 2020 20:17:41 +0900
Subject: [PATCH 621/802] suite-sparse: change the condition to add C11 flag.
 (#16859)

---
 var/spack/repos/builtin/packages/suite-sparse/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
index da2cc222aef..0cbdd900b60 100644
--- a/var/spack/repos/builtin/packages/suite-sparse/package.py
+++ b/var/spack/repos/builtin/packages/suite-sparse/package.py
@@ -102,7 +102,7 @@ def install(self, spec, prefix):
         # GraphBLAS/Demo/Program/wildtype_demo.c. For many compilers this is
         # not an issue because c11 or newer is their default. However, for some
         # compilers (e.g. xlc) the c11 flag is necessary.
-        if spec.satisfies('@5.4:'):
+        if spec.satisfies('@5.4:5.7.1') and ('%xl' in spec or '%xl_r' in spec):
             make_args += ['CFLAGS+=%s' % self.compiler.c11_flag]
 
         # 64bit blas in UMFPACK:

From c3be6d903aef539e54320f35d8d3b18fca830c25 Mon Sep 17 00:00:00 2001
From: "Tomoki, Karatsu" <49965247+t-karatsu@users.noreply.github.com>
Date: Fri, 5 Jun 2020 20:25:02 +0900
Subject: [PATCH 622/802] cmake: modify FindMPI.cmake to treat Fujitsu MPI
 correctly (#16864)

---
 var/spack/repos/builtin/packages/cmake/package.py        | 6 ++++++
 .../repos/builtin/packages/netlib-scalapack/package.py   | 9 ---------
 2 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index cfc13c436db..fe19bdb404c 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -238,3 +238,9 @@ def test(self):
 
     def install(self, spec, prefix):
         make('install')
+
+        if spec.satisfies('%fj'):
+            for f in find(self.prefix, 'FindMPI.cmake', recursive=True):
+                filter_file('mpcc_r)', 'mpcc_r mpifcc)', f, string=True)
+                filter_file('mpc++_r)', 'mpc++_r mpiFCC)', f, string=True)
+                filter_file('mpifc)', 'mpifc mpifrt)', f, string=True)
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index 2acc06e6bbd..75993c47010 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -82,15 +82,6 @@ def cmake_args(self):
                 "-DCMAKE_Fortran_FLAGS=%s" % self.compiler.fc_pic_flag
             ])
 
-        # Specify Fujitsu-MPI's location
-        if spec.satisfies('%fj') and '^fujitsu-mpi' in spec:
-            options.extend([
-                '-DMPI_C_COMPILER=%s'       % spec['mpi'].mpicc,
-                '-DMPI_CXX_COMPILER=%s'     % spec['mpi'].mpicxx,
-                '-DMPI_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
-                '-DMPI_BASE_DIR=%s' % spec['mpi'].prefix
-            ])
-
         return options
 
     @run_after('install')

From 89cc507cf6e5fb0c943b207a70a4f43d165c5ade Mon Sep 17 00:00:00 2001
From: "Tomoki, Karatsu" <49965247+t-karatsu@users.noreply.github.com>
Date: Fri, 5 Jun 2020 20:29:36 +0900
Subject: [PATCH 623/802] cmake: add linker option for VerifyFortranC when
 using Fujitsu compiler. (#16963)

---
 .../packages/cmake/fujitsu_add_linker_option.patch     | 10 ++++++++++
 var/spack/repos/builtin/packages/cmake/package.py      |  4 ++++
 2 files changed, 14 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/cmake/fujitsu_add_linker_option.patch

diff --git a/var/spack/repos/builtin/packages/cmake/fujitsu_add_linker_option.patch b/var/spack/repos/builtin/packages/cmake/fujitsu_add_linker_option.patch
new file mode 100644
index 00000000000..4a0cf7abbf2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cmake/fujitsu_add_linker_option.patch
@@ -0,0 +1,10 @@
+--- spack-src/Modules/FortranCInterface/Verify/CMakeLists.txt.org	2020-06-05 15:54:59.559043595 +0900
++++ spack-src/Modules/FortranCInterface/Verify/CMakeLists.txt	2020-06-05 15:58:28.150062948 +0900
+@@ -4,6 +4,7 @@
+ cmake_minimum_required(VERSION ${CMAKE_VERSION})
+ project(VerifyFortranC C Fortran)
+ 
++set (CMAKE_EXE_LINKER_FLAGS "--linkfortran")
+ option(VERIFY_CXX "Whether to verify C++ and Fortran" OFF)
+ if(VERIFY_CXX)
+   enable_language(CXX)
diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index fe19bdb404c..933f5e1995a 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -142,6 +142,10 @@ class Cmake(Package):
     # https://gitlab.kitware.com/cmake/cmake/-/merge_requests/4681
     patch('ignore_crayxc_warnings.patch', when='@3.7:3.17.2')
 
+    # The Fujitsu compiler requires the '--linkfortran' option
+    # to combine C++ and Fortran programs.
+    patch('fujitsu_add_linker_option.patch', when='%fj')
+
     conflicts('+qt', when='^qt@5.4.0')  # qt-5.4.0 has broken CMake modules
 
     # https://gitlab.kitware.com/cmake/cmake/issues/18166

From 76abf358138927be3ebeea2bead9fd1ccd087f41 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Fri, 5 Jun 2020 12:38:07 -0600
Subject: [PATCH 624/802] cajita: got merged in cabana (#16971)

---
 .../repos/builtin/packages/cajita/package.py  | 29 -------------------
 .../repos/builtin/packages/exampm/package.py  |  1 -
 2 files changed, 30 deletions(-)
 delete mode 100644 var/spack/repos/builtin/packages/cajita/package.py

diff --git a/var/spack/repos/builtin/packages/cajita/package.py b/var/spack/repos/builtin/packages/cajita/package.py
deleted file mode 100644
index ddfa96a81ea..00000000000
--- a/var/spack/repos/builtin/packages/cajita/package.py
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Cajita(CMakePackage):
-    """An MPI+Kokkos library for logically rectilinear grids"""
-
-    homepage = "https://github.com/ECP-copa/Cajita"
-    git      = "https://github.com/ECP-copa/Cajita.git"
-
-    version('master', branch='master')
-    version('0.1', tag='0.1.0')
-
-    variant('shared', default=True, description='Build shared libraries')
-
-    depends_on('mpi')
-    depends_on('kokkos@3.0:')
-
-    def cmake_args(self):
-        options = [
-            '-DBUILD_SHARED_LIBS=%s' % (
-                'On' if '+shared'  in self.spec else 'Off')
-        ]
-
-        return options
diff --git a/var/spack/repos/builtin/packages/exampm/package.py b/var/spack/repos/builtin/packages/exampm/package.py
index e5ba5671960..64732c2eda5 100644
--- a/var/spack/repos/builtin/packages/exampm/package.py
+++ b/var/spack/repos/builtin/packages/exampm/package.py
@@ -22,7 +22,6 @@ class Exampm(CMakePackage):
     depends_on('kokkos@3.0:')
     depends_on('silo')
     depends_on('cabana+mpi@master')
-    depends_on('cajita@master')
 
     def cmake_args(self):
         options = [

From bfa05628cbb3f714ec6eca1fffc60fffc77ec530 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Sat, 6 Jun 2020 01:27:20 +0200
Subject: [PATCH 625/802] pkgconf: Add 1.7.3

---
 var/spack/repos/builtin/packages/pkgconf/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/pkgconf/package.py b/var/spack/repos/builtin/packages/pkgconf/package.py
index 06fcefcc6c0..3bb59b4dd87 100644
--- a/var/spack/repos/builtin/packages/pkgconf/package.py
+++ b/var/spack/repos/builtin/packages/pkgconf/package.py
@@ -16,6 +16,7 @@ class Pkgconf(AutotoolsPackage):
     # URL must remain http:// so Spack can bootstrap curl
     url      = "http://distfiles.dereferenced.org/pkgconf/pkgconf-1.6.3.tar.xz"
 
+    version('1.7.3',  sha256='b846aea51cf696c3392a0ae58bef93e2e72f8e7073ca6ad1ed8b01c85871f9c0')
     version('1.6.3',  sha256='61f0b31b0d5ea0e862b454a80c170f57bad47879c0c42bd8de89200ff62ea210')
     version('1.6.1',  sha256='22b9ee38438901f9d60f180e5182821180854fa738fd071f593ea26a81da208c')
     version('1.6.0',  sha256='6135a3abb576672ba54a899860442ba185063f0f90dae5892f64f7bae8e1ece5')

From a08f3dd5050d8dc6c36a5dc9c38cbdd7e29e1dc0 Mon Sep 17 00:00:00 2001
From: Sinan <sbulutw@gmail.com>
Date: Fri, 5 Jun 2020 18:16:13 -0700
Subject: [PATCH 626/802] New package: py-asteval (#16976)

---
 .../builtin/packages/py-asteval/package.py    | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-asteval/package.py

diff --git a/var/spack/repos/builtin/packages/py-asteval/package.py b/var/spack/repos/builtin/packages/py-asteval/package.py
new file mode 100644
index 00000000000..4f80a227896
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-asteval/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyAsteval(PythonPackage):
+    """Safe, minimalistic evaluator of python expression using ast module"""
+
+    homepage = "http://github.com/newville/asteval"
+    url      = "https://pypi.io/packages/source/a/asteval/asteval-0.9.18.tar.gz"
+
+    version('0.9.18', sha256='5d64e18b8a72c2c7ae8f9b70d1f80b68bbcaa98c1c0d7047c35489d03209bc86')
+
+    depends_on('python@3.5:',   type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-pytest',     type='test')

From 27eb7d9f5f2326e46484bba7a2df058866928e16 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Sat, 6 Jun 2020 03:18:00 +0200
Subject: [PATCH 627/802] xrootd: add version 4.12.1 (#16966)

---
 var/spack/repos/builtin/packages/xrootd/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/xrootd/package.py b/var/spack/repos/builtin/packages/xrootd/package.py
index cadf24b44ea..24f966395d7 100644
--- a/var/spack/repos/builtin/packages/xrootd/package.py
+++ b/var/spack/repos/builtin/packages/xrootd/package.py
@@ -13,6 +13,7 @@ class Xrootd(CMakePackage):
     homepage = "http://xrootd.org"
     url      = "http://xrootd.org/download/v4.6.0/xrootd-4.6.0.tar.gz"
 
+    version('4.12.1', sha256='7350d9196a26d17719b839fd242849e3995692fda25f242e67ac6ec907218d13')
     version('4.12.0', sha256='69ef4732256d9a88127de4bfdf96bbf73348e0c70ce1d756264871a0ffadd2fc')
     version('4.11.3', sha256='8e7a64fd55dfb452b6d5f76a9a97c493593943227b377623a3032da9197c7f65')
     version('4.11.2', sha256='4620824db97fcc37dc3dd26110da8e5c3aab1d8302e4921d4f32e83207060603')

From 374f1a62e2b388fcac60aa25b3c5c5f8b18871cf Mon Sep 17 00:00:00 2001
From: Andrew Gaspar <agaspar@lanl.gov>
Date: Fri, 5 Jun 2020 19:25:42 -0600
Subject: [PATCH 628/802] py-flake8: add version 2.8.2 (#16959)

* py-flake8: add version 3.8.2
  * This version depends on different versions of py-pycodestyle
    and py-pyflakes
  * When built for python@:3.7, this depends on the
    py-importlib-metadata backport library
* py-pycodestyle: add version 2.6.0
* py-pyflakes: add version 2.2.0
---
 .../builtin/packages/py-flake8/package.py      | 18 ++++++++++++------
 .../builtin/packages/py-pycodestyle/package.py |  1 +
 .../builtin/packages/py-pyflakes/package.py    |  1 +
 3 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-flake8/package.py b/var/spack/repos/builtin/packages/py-flake8/package.py
index 462758ddf41..4c585ee7558 100644
--- a/var/spack/repos/builtin/packages/py-flake8/package.py
+++ b/var/spack/repos/builtin/packages/py-flake8/package.py
@@ -13,6 +13,7 @@ class PyFlake8(PythonPackage):
     homepage = "https://github.com/PyCQA/flake8"
     url      = "https://github.com/PyCQA/flake8/archive/3.7.8.tar.gz"
 
+    version('3.8.2', sha256='ae9b00ddaa2bb7fa69796ac73ba7607fcf06d79a8b777fa12ba5abef1e770491')
     version('3.7.8',  sha256='201720797dc9691dd349819994e4a0bc281b70ee2ff77b0c928bb1d3c5aa9810')
     version('3.7.7',  sha256='b3f76b02351008dc772276e74b09dd3d4b5c567ff8c6ab573352cb8fd7007444')
     version('3.5.0', sha256='60ffe2fdacce4ebe7cadc30f310cf1edfd8ff654ef79525d90cf0756e69de44e')
@@ -31,12 +32,16 @@ class PyFlake8(PythonPackage):
     # http://flake8.pycqa.org/en/latest/faq.html#why-does-flake8-use-ranges-for-its-dependencies
     # http://flake8.pycqa.org/en/latest/internal/releases.html#releasing-flake8
 
+    # Flake8 3.8.X
+    depends_on('py-pycodestyle@2.6.0:2.6.999', when='@3.8.0:3.8.999', type=('build', 'run'))
+    depends_on('py-pyflakes@2.2.0:2.2.999',    when='@3.8.0:3.8.999', type=('build', 'run'))
+
     # Flake8 3.7.X
     # FIXME @0.3.0:0.3.999 causes concretization to hang
-    depends_on('py-entrypoints@0.3',           when='@3.7.0:3.7.999', type=('build', 'run'))
+    depends_on('py-entrypoints@0.3',           when='@3.7.0:3.8.999', type=('build', 'run'))
     depends_on('py-pyflakes@2.1.0:2.1.999',    when='@3.7.0:3.7.999', type=('build', 'run'))
     depends_on('py-pycodestyle@2.5.0:2.5.999', when='@3.7.0:3.7.999', type=('build', 'run'))
-    depends_on('py-mccabe@0.6.0:0.6.999',      when='@3.7.0:3.7.999', type=('build', 'run'))
+    depends_on('py-mccabe@0.6.0:0.6.999',      when='@3.7.0:3.8.999', type=('build', 'run'))
 
     # Flake8 3.5.X
     depends_on('py-pyflakes@1.5:1.6',     when='@3.5.0:3.5.999', type=('build', 'run'))
@@ -54,10 +59,11 @@ class PyFlake8(PythonPackage):
     depends_on('py-mccabe@0.2.1:0.4',                 when='@2.5.0:2.5.999', type=('build', 'run'))
 
     # Python version-specific backports
-    depends_on('py-enum34',       when='@3.0.0: ^python@:3.3', type=('build', 'run'))
-    depends_on('py-typing',       when='@3.7.0: ^python@:3.4', type=('build', 'run'))
-    depends_on('py-configparser', when='@3.0.0: ^python@:3.1', type=('build', 'run'))
-    depends_on('py-functools32',  when='@3.7.4: ^python@:3.1', type=('build', 'run'))
+    depends_on('py-importlib-metadata', when='@3.8.0: ^python@:3.7', type=('build', 'run'))
+    depends_on('py-enum34',             when='@3.0.0: ^python@:3.3', type=('build', 'run'))
+    depends_on('py-typing',             when='@3.7.0: ^python@:3.4', type=('build', 'run'))
+    depends_on('py-configparser',       when='@3.0.0: ^python@:3.1', type=('build', 'run'))
+    depends_on('py-functools32',        when='@3.7.4: ^python@:3.1', type=('build', 'run'))
 
     def patch(self):
         """Filter pytest-runner requirement out of setup.py."""
diff --git a/var/spack/repos/builtin/packages/py-pycodestyle/package.py b/var/spack/repos/builtin/packages/py-pycodestyle/package.py
index 6f9da670f86..48e833ec2f2 100644
--- a/var/spack/repos/builtin/packages/py-pycodestyle/package.py
+++ b/var/spack/repos/builtin/packages/py-pycodestyle/package.py
@@ -13,6 +13,7 @@ class PyPycodestyle(PythonPackage):
     homepage = "https://github.com/PyCQA/pycodestyle"
     url      = "https://github.com/PyCQA/pycodestyle/archive/2.0.0.tar.gz"
 
+    version('2.6.0', sha256='08347fbc48cc92afd33117c1e8af9b99b292a4e5889f6b776f402e062fc39c97')
     version('2.5.0', sha256='a603453c07e8d8e15a43cf062aa7174741b74b4a27b110f9ad03d74d519173b5')
     version('2.3.1', sha256='e9fc1ca3fd85648f45c0d2e33591b608a17d8b9b78e22c5f898e831351bacb03')
     version('2.3.0', sha256='ac2a849987316521a56814b5618668d36cd5f3b04843803832a15b93b8383a50')
diff --git a/var/spack/repos/builtin/packages/py-pyflakes/package.py b/var/spack/repos/builtin/packages/py-pyflakes/package.py
index 156db2f0da2..402a6c525b8 100644
--- a/var/spack/repos/builtin/packages/py-pyflakes/package.py
+++ b/var/spack/repos/builtin/packages/py-pyflakes/package.py
@@ -12,6 +12,7 @@ class PyPyflakes(PythonPackage):
     homepage = "https://github.com/PyCQA/pyflakes"
     url      = "https://github.com/PyCQA/pyflakes/archive/2.1.1.tar.gz"
 
+    version('2.2.0', sha256='4a6927b9ca7fc19817176d54b3ee2ee4202f064febdee8624ee8340303cfda7b')
     version('2.1.1', sha256='2c98f07a9dd57d9f33561f6b54a64a766cdf79a3c869bd8c07b7fe03094fb8c3')
     version('2.1.0', sha256='6cd8775b6430daad386c0de00dfbc27ce2c24468cdcc4d3da41e4aa39d8ce167')
     version('1.6.0', sha256='f9c72359e05bf8dc27eaaee8cdcae464497f2ccadae87ac6517605ba6040ec99')

From d755cc8ce95f20926b65e23e56de249c64a6a028 Mon Sep 17 00:00:00 2001
From: John Jolly <john.jolly@gmail.com>
Date: Sat, 6 Jun 2020 01:55:14 -0600
Subject: [PATCH 629/802] iegenlib: add build dependencies for automake and
 libtool (#16980)

---
 var/spack/repos/builtin/packages/iegenlib/package.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/iegenlib/package.py b/var/spack/repos/builtin/packages/iegenlib/package.py
index be61f120c77..ee198fd588f 100644
--- a/var/spack/repos/builtin/packages/iegenlib/package.py
+++ b/var/spack/repos/builtin/packages/iegenlib/package.py
@@ -18,11 +18,13 @@ class Iegenlib(CMakePackage):
 
     version('master', branch='master')
     version('2018-07-03',
-        url="https://github.com/CompOpt4Apps/IEGenLib/archive/fc479ee6ff01dba26beffc1dc6bacdba03262138.zip",
-        sha256='b4c0b368363fcc1e34b388057cc0940bb87fc336cebb0772fd6055f45009b12b')
+            url="https://github.com/CompOpt4Apps/IEGenLib/archive/fc479ee6ff01dba26beffc1dc6bacdba03262138.zip",
+            sha256='b4c0b368363fcc1e34b388057cc0940bb87fc336cebb0772fd6055f45009b12b')
 
     depends_on('cmake@2.6:', type='build')
     depends_on('autoconf',   type='build')
+    depends_on('automake',   type='build')
+    depends_on('libtool',    type='build')
     depends_on('texinfo',    type='build')
     depends_on('isl')
 

From 944f0abb369a10a4ba5e169098dd743294325998 Mon Sep 17 00:00:00 2001
From: Nithin Senthil Kumar <52734841+nithintsk@users.noreply.github.com>
Date: Sat, 6 Jun 2020 06:51:27 -0400
Subject: [PATCH 630/802] Update package for MVAPICH2 2.3.4 release (#16960)

Co-authored-by: senthilkumar.16 <senthilkumar.16@nowlab.cse.ohio-state.edu>
---
 var/spack/repos/builtin/packages/mvapich2/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index d8398b336da..04205b6e24f 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -10,10 +10,11 @@
 class Mvapich2(AutotoolsPackage):
     """MVAPICH2 is an MPI implementation for Infiniband networks."""
     homepage = "http://mvapich.cse.ohio-state.edu/"
-    url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3.3.tar.gz"
+    url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3.4.tar.gz"
     list_url = "http://mvapich.cse.ohio-state.edu/downloads/"
 
     # Prefer the latest stable release
+    version('2.3.4', sha256='7226a45c7c98333c8e5d2888119cce186199b430c13b7b1dca1769909e68ea7a')
     version('2.3.3', sha256='41d3261be57e5bc8aabf4e32981543c015c5443ff032a26f18205985e18c2b73')
     version('2.3.2', sha256='30cc0d7bcaa075d204692f76bca4d65a539e0f661c7460ffa9f835d6249e1ebf')
     version('2.3.1', sha256='314e12829f75f3ed83cd4779a972572d1787aac6543a3d024ea7c6080e0ee3bf')

From c5ac168f31dd8a552634b9197da484cadd214397 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Sun, 7 Jun 2020 04:47:30 +0800
Subject: [PATCH 631/802] protobuf: support aarch64 @2.5.0 (#16862)

* protobuf: support aarch64 @2.5.0

* refine cmake args

* fix patch name
---
 .../builtin/packages/protobuf/package.py      |  39 +++++-
 .../protobuf/protoc2.5.0_aarch64.patch        | 113 ++++++++++++++++++
 2 files changed, 149 insertions(+), 3 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/protobuf/protoc2.5.0_aarch64.patch

diff --git a/var/spack/repos/builtin/packages/protobuf/package.py b/var/spack/repos/builtin/packages/protobuf/package.py
index 05702d9fc96..82d2d05d75b 100644
--- a/var/spack/repos/builtin/packages/protobuf/package.py
+++ b/var/spack/repos/builtin/packages/protobuf/package.py
@@ -8,12 +8,11 @@
 import spack.util.web
 
 
-class Protobuf(CMakePackage):
+class Protobuf(Package):
     """Google's data interchange format."""
 
     homepage = "https://developers.google.com/protocol-buffers"
     url      = "https://github.com/protocolbuffers/protobuf/archive/v3.10.1.tar.gz"
-    root_cmakelists_dir = "cmake"
 
     version('3.11.2',  sha256='e8c7601439dbd4489fe5069c33d374804990a56c2f710e00227ee5d8fd650e67')
     version('3.11.1',  sha256='4f8e805825c53bbc3c9f6b6abc009b5b5679e4702bccfca1121c42ff5ec801c7')
@@ -36,6 +35,7 @@ class Protobuf(CMakePackage):
     version('3.2.0',   sha256='a839d3f1519ff9d68ab908de5a0f269650ef1fc501c10f6eefd4cae51d29b86f')
     version('3.1.0',   sha256='fb2a314f4be897491bb2446697be693d489af645cb0e165a85e7e64e07eb134d')
     version('3.0.2',   sha256='a0a265bcc9d4e98c87416e59c33afc37cede9fb277292523739417e449b18c1e')
+    version('2.5.0',   sha256='c2665a7aa2ac1a206e61b28e014486e3de59009ea2be2bde9182e0847f38b62f')
 
     variant('shared', default=True,
             description='Enables the build of shared libraries')
@@ -43,19 +43,26 @@ class Protobuf(CMakePackage):
             description='The build type to build',
             values=('Debug', 'Release'))
 
+    depends_on('cmake', when='@3.0.2:', type='build')
     depends_on('zlib')
+    depends_on('autoconf', type='build', when='@2.5.0')
+    depends_on('automake', type='build', when='@2.5.0')
+    depends_on('libtool',  type='build', when='@2.5.0')
+    depends_on('m4',       type='build', when='@2.5.0')
 
     conflicts('%gcc@:4.6', when='@3.6.0:')  # Requires c++11
     conflicts('%gcc@:4.6', when='@3.2.0:3.3.0')  # Breaks
 
     # first fixed in 3.4.0: https://github.com/google/protobuf/pull/3406
-    patch('pkgconfig.patch', when='@:3.3.2')
+    patch('pkgconfig.patch', when='@3.0.2:3.3.2')
 
     patch('intel-v1.patch', when='@3.2:@3.6 %intel')
 
     # See https://github.com/protocolbuffers/protobuf/pull/7197
     patch('intel-v2.patch', when='@3.7:@3.11.4 %intel')
 
+    patch('protoc2.5.0_aarch64.patch', sha256='7b44fcdb794f421174d619f83584e00a36012a16da09079e2fad9c12f7337451', when='@2.5.0 target=aarch64:')
+
     def fetch_remote_versions(self):
         """Ignore additional source artifacts uploaded with releases,
            only keep known versions
@@ -75,3 +82,29 @@ def cmake_args(self):
         if sys.platform == 'darwin':
             args.extend(['-DCMAKE_MACOSX_RPATH=ON'])
         return args
+
+    @when('@3.0.2:')
+    def install(self, spec, prefix):
+        args = self.cmake_args()
+        args.extend(std_cmake_args)
+
+        source_directory = join_path(self.stage.source_path, 'cmake')
+        build_directory = join_path(source_directory, 'build')
+
+        with working_dir(build_directory, create=True):
+            cmake(source_directory, *args)
+            make()
+            make('install')
+
+    def configure_args(self):
+        args = []
+        args.append('--prefix=%s' % self.prefix)
+        return args
+
+    @when('@2.5.0')
+    def install(self, spec, prefix):
+        args = self.configure_args()
+        autoreconf('-ifv')
+        configure(*args)
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/protobuf/protoc2.5.0_aarch64.patch b/var/spack/repos/builtin/packages/protobuf/protoc2.5.0_aarch64.patch
new file mode 100644
index 00000000000..aa1ebc6a9ab
--- /dev/null
+++ b/var/spack/repos/builtin/packages/protobuf/protoc2.5.0_aarch64.patch
@@ -0,0 +1,113 @@
+diff -uprN /src/google/protobuf/stubs/atomicops_internals_arm_gcc.h  /src/google/protobuf/stubs/atomicops_internals_arm_gcc.h
+--- /src/google/protobuf/subs/atomicops_internals_arm_gcc.h	2018-08-03 08:50:58.579413324 +0000
++++ /src/google/protobuf/stubs/atomicops_internals_arm_gcc.h	2018-08-03 08:50:58.711413322 +0000
+@@ -68,6 +68,30 @@ inline Atomic32 NoBarrier_CompareAndSwap
+   } while (prev_value == old_value);
+   return prev_value;
+ }
++inline Atomic64 NoBarrier_CompareAndSwap(volatile Atomic64* ptr,
++                                         Atomic64 old_value,
++                                         Atomic64 new_value) {
++  Atomic64 prev;
++  int32_t temp;
++
++  __asm__ __volatile__ (  // NOLINT
++    "0:                                    \n\t"
++    "ldxr %[prev], %[ptr]                  \n\t"
++    "cmp %[prev], %[old_value]             \n\t"
++    "bne 1f                                \n\t"
++    "stxr %w[temp], %[new_value], %[ptr]   \n\t"
++    "cbnz %w[temp], 0b                     \n\t"
++    "1:                                    \n\t"
++    : [prev]"=&r" (prev),
++      [temp]"=&r" (temp),
++      [ptr]"+Q" (*ptr)
++    : [old_value]"IJr" (old_value),
++      [new_value]"r" (new_value)
++    : "cc", "memory"
++  );  // NOLINT
++
++  return prev;
++}
+ 
+ inline Atomic32 NoBarrier_AtomicExchange(volatile Atomic32* ptr,
+                                          Atomic32 new_value) {
+@@ -105,6 +129,15 @@ inline Atomic32 Acquire_CompareAndSwap(v
+   return NoBarrier_CompareAndSwap(ptr, old_value, new_value);
+ }
+ 
++inline Atomic64 Acquire_CompareAndSwap(volatile Atomic64* ptr,
++                                       Atomic64 old_value,
++                                       Atomic64 new_value) {
++  Atomic64 prev = NoBarrier_CompareAndSwap(ptr, old_value, new_value);
++  MemoryBarrier();
++
++  return prev;
++}
++
+ inline Atomic32 Release_CompareAndSwap(volatile Atomic32* ptr,
+                                        Atomic32 old_value,
+                                        Atomic32 new_value) {
+@@ -115,8 +148,11 @@ inline void NoBarrier_Store(volatile Ato
+   *ptr = value;
+ }
+ 
+-inline void MemoryBarrier() {
++/*inline void MemoryBarrier() {
+   pLinuxKernelMemoryBarrier();
++}*/
++inline void MemoryBarrier() {
++  __asm__ __volatile__ ("dmb ish" ::: "memory");  // NOLINT
+ }
+ 
+ inline void Acquire_Store(volatile Atomic32* ptr, Atomic32 value) {
+@@ -129,6 +165,15 @@ inline void Release_Store(volatile Atomi
+   *ptr = value;
+ }
+ 
++inline void Release_Store(volatile Atomic64* ptr, Atomic64 value) {
++  __asm__ __volatile__ (  // NOLINT
++    "stlr %x[value], %[ptr]  \n\t"
++    : [ptr]"=Q" (*ptr)
++    : [value]"r" (value)
++    : "memory"
++  );  // NOLINT
++}
++
+ inline Atomic32 NoBarrier_Load(volatile const Atomic32* ptr) {
+   return *ptr;
+ }
+@@ -139,6 +184,19 @@ inline Atomic32 Acquire_Load(volatile co
+   return value;
+ }
+ 
++inline Atomic64 Acquire_Load(volatile const Atomic64* ptr) {
++  Atomic64 value;
++
++  __asm__ __volatile__ (  // NOLINT
++    "ldar %x[value], %[ptr]  \n\t"
++    : [value]"=r" (value)
++    : [ptr]"Q" (*ptr)
++    : "memory"
++  );  // NOLINT
++
++  return value;
++}
++
+ inline Atomic32 Release_Load(volatile const Atomic32* ptr) {
+   MemoryBarrier();
+   return *ptr;
+diff -uprN /src/google/protobuf/stubs/platform_macros.h /src/google/protobuf/stubs/platform_macros.h
+--- /src/google/protobuf/stubs/platform_macros.h	2018-08-03 08:50:58.543413325 +0000
++++ /src/google/protobuf/stubs/platform_macros.h	2018-08-03 08:50:58.595413324 +0000
+@@ -57,6 +57,9 @@
+ #elif defined(__ppc__)
+ #define GOOGLE_PROTOBUF_ARCH_PPC 1
+ #define GOOGLE_PROTOBUF_ARCH_32_BIT 1
++#elif defined(__aarch64__)
++#define GOOGLE_PROTOBUF_ARCH_ARM 1
++#define GOOGLE_PROTOBUF_ARCH_64_BIT 1
+ #else
+ #error Host architecture was not detected as supported by protobuf
+ #endif
+

From 7b6e1ae9d3fb614f45744254bf90a3674f3e30eb Mon Sep 17 00:00:00 2001
From: Sinan <sbulutw@gmail.com>
Date: Sat, 6 Jun 2020 13:50:16 -0700
Subject: [PATCH 632/802] py-astunparse: add version 1.6.3 (#16946)

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
---
 var/spack/repos/builtin/packages/py-astunparse/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-astunparse/package.py b/var/spack/repos/builtin/packages/py-astunparse/package.py
index 87ca432f56a..996a59183e4 100644
--- a/var/spack/repos/builtin/packages/py-astunparse/package.py
+++ b/var/spack/repos/builtin/packages/py-astunparse/package.py
@@ -15,6 +15,7 @@ class PyAstunparse(PythonPackage):
     homepage = "https://pypi.org/project/astunparse/"
     url      = "https://pypi.io/packages/source/a/astunparse/astunparse-1.6.2.tar.gz"
 
+    version('1.6.3', sha256='5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872')
     version('1.6.2', sha256='dab3e426715373fd76cd08bb1abe64b550f5aa494cf1e32384f26fd60961eb67')
 
     depends_on('py-setuptools', type='build')

From 73d13461b1b4c0ad595c0506e104d2ffccc07be2 Mon Sep 17 00:00:00 2001
From: Sinan <sbulutw@gmail.com>
Date: Sat, 6 Jun 2020 13:51:19 -0700
Subject: [PATCH 633/802] ensure xla is turned off (#16974)

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
---
 var/spack/repos/builtin/packages/py-tensorflow/package.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-tensorflow/package.py b/var/spack/repos/builtin/packages/py-tensorflow/package.py
index 888e9432bf5..6bdc7e69be3 100644
--- a/var/spack/repos/builtin/packages/py-tensorflow/package.py
+++ b/var/spack/repos/builtin/packages/py-tensorflow/package.py
@@ -525,6 +525,13 @@ def configure(self, spec, prefix):
     @run_after('configure')
     def post_configure_fixes(self):
         spec = self.spec
+
+        # make sure xla is actually turned off
+        if spec.satisfies('~xla'):
+            filter_file(r'--define with_xla_support=true',
+                        r'--define with_xla_support=false',
+                        '.tf_configure.bazelrc')
+
         if spec.satisfies('@1.5.0: ~android'):
             # env variable is somehow ignored -> brute force
             # TODO: find a better solution

From 36f9550178a680466bda837ecae7eb51ad8b2f03 Mon Sep 17 00:00:00 2001
From: Sinan <sbulutw@gmail.com>
Date: Sat, 6 Jun 2020 14:00:29 -0700
Subject: [PATCH 634/802] py-mysqlclient: relax dependency constraint, add new
 versions (#16985)

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
---
 .../repos/builtin/packages/py-mysqlclient/package.py     | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-mysqlclient/package.py b/var/spack/repos/builtin/packages/py-mysqlclient/package.py
index d1e6ef37a8c..a1f1d09e130 100644
--- a/var/spack/repos/builtin/packages/py-mysqlclient/package.py
+++ b/var/spack/repos/builtin/packages/py-mysqlclient/package.py
@@ -15,9 +15,10 @@ class PyMysqlclient(PythonPackage):
     homepage = "https://github.com/PyMySQL/mysqlclient-python"
     url      = "https://pypi.io/packages/source/m/mysqlclient/mysqlclient-1.4.4.tar.gz"
 
-    version('1.4.4', sha256='9c737cc55a5dc8dd3583a942d5a9b21be58d16f00f5fefca4e575e7d9682e98c')
-    version('1.3.13', sha256='ff8ee1be84215e6c30a746b728c41eb0701a46ca76e343af445b35ce6250644f')
+    version('1.4.6',    sha256='f3fdaa9a38752a3b214a6fe79d7cae3653731a53e577821f9187e67cbecb2e16')
+    version('1.4.5',    sha256='e80109b0ae8d952b900b31b623181532e5e89376d707dcbeb63f99e69cefe559')
+    version('1.4.4',    sha256='9c737cc55a5dc8dd3583a942d5a9b21be58d16f00f5fefca4e575e7d9682e98c')
+    version('1.3.13',   sha256='ff8ee1be84215e6c30a746b728c41eb0701a46ca76e343af445b35ce6250644f')
 
     depends_on('py-setuptools', type='build')
-    # Below: cxxstd=17 also works
-    depends_on('mysql cxxstd=14')
+    depends_on('mysql')

From 77fbdff8a232f71a8aa5a79aac7e91865f590e51 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Sun, 7 Jun 2020 05:00:59 +0800
Subject: [PATCH 635/802] Add new package: lxc (#16984)

---
 .../repos/builtin/packages/lxc/package.py     | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/lxc/package.py

diff --git a/var/spack/repos/builtin/packages/lxc/package.py b/var/spack/repos/builtin/packages/lxc/package.py
new file mode 100644
index 00000000000..0555b6b642b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lxc/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Lxc(AutotoolsPackage):
+    """LXC is the well-known and heavily tested low-level Linux container
+    runtime. It is in active development since 2008 and has proven itself
+    in critical production environments world-wide. Some of its core
+    contributors are the same people that helped to implement various
+    well-known containerization features inside the Linux kernel."""
+
+    homepage = "https://linuxcontainers.org/lxc/"
+    url      = "https://github.com/lxc/lxc/archive/lxc-4.0.2.tar.gz"
+
+    version('4.0.2',  sha256='89a9f1c6c9c0c43ffc4ec4d281381d60dcf698af1578effa491be97885ab282a')
+    version('4.0.1',  sha256='5b17c48db24d93f8a687bf4557358e252126c50a66f5756b3e0ea2cf04a60d05')
+    version('4.0.0',  sha256='8cd36f002f656bbcd01679e6b8892f81ed036d5589aed45b36358014b32277dd')
+    version('3.2.1',  sha256='59f46fad0a6d921c59a6768ba781295e0986989a96e2d216de2b4b3a14392e65')
+    version('3.2.0',  sha256='5dbf25a1c15aa96e184a4e9ef580d40f08bf06818ad21614d6c79fce5447c7eb')
+    version('3.1.0',  sha256='14c34bb3390c60331107a5fbd5c6520e4873c774de2293e9efcb3c0e860b807d')
+    version('3.0.4',  sha256='12a126e634a8df81507fd9d3a4984bacaacf22153c11f024e215810ea78fcc4f')
+    version('3.0.3',  sha256='e794f287755d2529cb49f01b72802abfec31f2a02259719b60a62897da6e8298')
+    version('2.0.11', sha256='31334ffe0e2d8e38779d80ce670a523f4f5559c2a02c9e085c2f0cf43995d0b0')
+    version('2.0.10', sha256='b748de0914467aafea18a568602735907fc95f4272609dba7b0f8c91d7dde776')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')

From c835b931091eecbf4b74f2c48be9086d8f78ea00 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Sun, 7 Jun 2020 05:02:15 +0800
Subject: [PATCH 636/802] Add new package: py-louie (#16983)

---
 .../builtin/packages/py-louie/package.py      | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-louie/package.py

diff --git a/var/spack/repos/builtin/packages/py-louie/package.py b/var/spack/repos/builtin/packages/py-louie/package.py
new file mode 100644
index 00000000000..dc23bd7a4d1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-louie/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLouie(PythonPackage):
+    """Louie provides Python programmers with a straightforward way to
+    dispatch signals between objects in a wide variety of contexts. It
+    is based on PyDispatcher, which in turn was based on a highly-rated
+    recipe in the Python Cookbook."""
+
+    homepage = "https://github.com/11craft/louie/"
+    url      = "https://github.com/11craft/louie/archive/2.0.tar.gz"
+
+    version('2.0', sha256='ac274ef672511357fc15d784df841c238ae13d00964094571eebabb0b14c54b2')
+    version('1.1', sha256='4bc227171fc546d1a527ee3059fa17df6d35a0acc10db1f942dd3da42ad96408')
+
+    depends_on('py-setuptools', type='build')

From 885808cc13d90a12a70e9ab082934b5222298004 Mon Sep 17 00:00:00 2001
From: Tom Payerle <payerle@umd.edu>
Date: Sat, 6 Jun 2020 17:12:46 -0400
Subject: [PATCH 637/802] intel-tbb: Fix for #16938 add custom libs method
 (#16972)

* intel-tbb: Fix for #16938 add custom libs method

Override the libs method to look for libraries of form libtbb*
(instead of inherited which looks for libintel-tbb*)

* Fixing pre-existing flake8 issues
---
 .../builtin/packages/intel-tbb/package.py      | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/intel-tbb/package.py b/var/spack/repos/builtin/packages/intel-tbb/package.py
index 94eec8a06e6..c470e8933b3 100644
--- a/var/spack/repos/builtin/packages/intel-tbb/package.py
+++ b/var/spack/repos/builtin/packages/intel-tbb/package.py
@@ -132,22 +132,22 @@ def coerce_to_spack(self, tbb_build_subdir):
             for f in fs:
                 lines = open(f).readlines()
                 of = open(f, "w")
-                for l in lines:
-                    if l.strip().startswith("CPLUS ="):
+                for lin in lines:
+                    if lin.strip().startswith("CPLUS ="):
                         of.write("# coerced to spack\n")
                         of.write("CPLUS = $(CXX)\n")
-                    elif l.strip().startswith("CONLY ="):
+                    elif lin.strip().startswith("CONLY ="):
                         of.write("# coerced to spack\n")
                         of.write("CONLY = $(CC)\n")
                     else:
-                        of.write(l)
+                        of.write(lin)
 
     def install(self, spec, prefix):
         # Deactivate use of RTM with GCC when on an OS with a very old
         # assembler.
         if (spec.satisfies('%gcc@4.8.0: os=rhel6')
-            or spec.satisfies('%gcc@4.8.0: os=centos6')
-            or spec.satisfies('%gcc@4.8.0: os=scientific6')):
+                or spec.satisfies('%gcc@4.8.0: os=centos6')
+                or spec.satisfies('%gcc@4.8.0: os=scientific6')):
             filter_file(r'RTM_KEY.*=.*rtm.*', 'RTM_KEY =',
                         join_path('build', 'linux.gcc.inc'))
 
@@ -224,3 +224,9 @@ def darwin_fix(self):
         # Replace @rpath in ids with full path
         if sys.platform == 'darwin':
             fix_darwin_install_name(self.prefix.lib)
+
+    @property
+    def libs(self):
+        shared = True if '+shared' in self.spec else False
+        return find_libraries(
+            'libtbb*', root=self.prefix, shared=shared, recursive=True)

From 46a751081daa76b5a1a9555f066e1aa6629bf17d Mon Sep 17 00:00:00 2001
From: John Jolly <john.jolly@gmail.com>
Date: Sat, 6 Jun 2020 15:14:11 -0600
Subject: [PATCH 638/802] gcc: Fix error 'size of array is negative' (#16969)

gcc 9.3.0 and glibc 2.31 (found in the base install of Ubuntu 20.04)
cause the gcc package to error during build with the error:

    "size of array 'assertion_failed__####' is negative"

Previous to this fix, the error was resolved for v8.1.0 <= gcc <= v9.2.0
via two patches.

This fix backports those patches for v5.3.0 <= gcc <= v7.4.0

Potentially these patches need to be backported to versions of gcc
before v5.3.0, but other compile issues need to be resolved for earlier
versions of gcc first.

Fixes #16968
---
 .../gcc/glibc-2.31-libsanitizer-1-gcc-6.patch | 39 +++++++++++
 .../gcc/glibc-2.31-libsanitizer-2-gcc-6.patch | 69 +++++++++++++++++++
 .../gcc/glibc-2.31-libsanitizer-2-gcc-7.patch | 69 +++++++++++++++++++
 .../repos/builtin/packages/gcc/package.py     |  9 ++-
 4 files changed, 183 insertions(+), 3 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-1-gcc-6.patch
 create mode 100644 var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-2-gcc-6.patch
 create mode 100644 var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-2-gcc-7.patch

diff --git a/var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-1-gcc-6.patch b/var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-1-gcc-6.patch
new file mode 100644
index 00000000000..4187b812d5d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-1-gcc-6.patch
@@ -0,0 +1,39 @@
+From ce9568e9e9cf6094be30e748821421e703754ffc Mon Sep 17 00:00:00 2001
+From: Jakub Jelinek <jakub@redhat.com>
+Date: Fri, 8 Nov 2019 19:53:18 +0100
+Subject: [PATCH] backport: re PR sanitizer/92154 (new glibc breaks arm
+ bootstrap due to libsanitizer)
+
+	Backported from mainline
+	2019-10-22  Tamar Christina  <tamar.christina@arm.com>
+	Backported for version 5.3.0 <= gcc <= 6.5.0
+	2020-06-05  John L. Jolly  <john.jolly@gmail.com>
+
+	PR sanitizer/92154
+	* sanitizer_common/sanitizer_platform_limits_posix.cc:
+	Cherry-pick compiler-rt revision r375220.
+
+From-SVN: r277981
+---
+ libsanitizer/ChangeLog                                   | 9 +++++++++
+ .../sanitizer_common/sanitizer_platform_limits_posix.cc  | 6 +++++-
+ 2 files changed, 14 insertions(+), 1 deletion(-)
+
+diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
+index 6cd4a5bac8b0..06a605ff4670 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
++++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
+@@ -1130,8 +1130,12 @@ CHECK_SIZE_AND_OFFSET(ipc_perm, uid);
+ #ifndef __GLIBC_PREREQ
+ #define __GLIBC_PREREQ(x, y) 0
+ #endif
+-#if !defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)
++#if (!defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)) && \
++    !defined(__arm__)
+ /* On aarch64 glibc 2.20 and earlier provided incorrect mode field.  */
++/* On Arm glibc 2.31 and later provide a different mode field, this field is
++   never used by libsanitizer so we can simply ignore this assert for all glibc
++   versions.  */
+ CHECK_SIZE_AND_OFFSET(ipc_perm, mode);
+ #endif
+ 
diff --git a/var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-2-gcc-6.patch b/var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-2-gcc-6.patch
new file mode 100644
index 00000000000..755db173ffb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-2-gcc-6.patch
@@ -0,0 +1,69 @@
+From 75003cdd23c310ec385344e8040d490e8dd6d2be Mon Sep 17 00:00:00 2001
+From: Jakub Jelinek <jakub@redhat.com>
+Date: Fri, 20 Dec 2019 17:58:35 +0100
+Subject: [PATCH] backport: re PR sanitizer/92154 (new glibc breaks arm
+ bootstrap due to libsanitizer)
+
+	Backported from mainline
+	2019-11-26  Jakub Jelinek  <jakub@redhat.com>
+	Backported for version 5.3.0 <= gcc <= 6.5.0
+	2020-06-05  John L. Jolly  <john.jolly@gmail.com>
+
+	PR sanitizer/92154
+	* sanitizer_common/sanitizer_platform_limits_posix.h: Cherry-pick
+	llvm-project revision 947f9692440836dcb8d88b74b69dd379d85974ce.
+	* sanitizer_common/sanitizer_platform_limits_posix.cc: Likewise.
+
+From-SVN: r279653
+---
+ libsanitizer/ChangeLog                            | 10 ++++++++++
+ .../sanitizer_platform_limits_posix.cc            |  9 +++------
+ .../sanitizer_platform_limits_posix.h             | 15 +--------------
+ 3 files changed, 14 insertions(+), 20 deletions(-)
+
+diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
+index 06a605ff4670..d823a12190c0 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
++++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
+@@ -1130,12 +1130,9 @@ CHECK_SIZE_AND_OFFSET(ipc_perm, uid);
+ #ifndef __GLIBC_PREREQ
+ #define __GLIBC_PREREQ(x, y) 0
+ #endif
+-#if (!defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)) && \
+-    !defined(__arm__)
+-/* On aarch64 glibc 2.20 and earlier provided incorrect mode field.  */
+-/* On Arm glibc 2.31 and later provide a different mode field, this field is
+-   never used by libsanitizer so we can simply ignore this assert for all glibc
+-   versions.  */
++#if !SANITIZER_LINUX || __GLIBC_PREREQ (2, 31)
++/* glibc 2.30 and earlier provided 16-bit mode field instead of 32-bit
++   on many architectures.  */
+ CHECK_SIZE_AND_OFFSET(ipc_perm, mode);
+ #endif
+ 
+diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
+index 73af92af1e8f..6a673a7c9959 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
++++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
+@@ -211,20 +211,13 @@ namespace __sanitizer {
+     unsigned long __unused1;
+     unsigned long __unused2;
+ #elif defined(__sparc__)
+-# if defined(__arch64__)
+     unsigned mode;
+-    unsigned short __pad1;
+-# else
+-    unsigned short __pad1;
+-    unsigned short mode;
+     unsigned short __pad2;
+-# endif
+     unsigned short __seq;
+     unsigned long long __unused1;
+     unsigned long long __unused2;
+ #else
+-    unsigned short mode;
+-    unsigned short __pad1;
++    unsigned int mode;
+     unsigned short __seq;
+     unsigned short __pad2;
+ #if defined(__x86_64__) && !defined(_LP64)
diff --git a/var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-2-gcc-7.patch b/var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-2-gcc-7.patch
new file mode 100644
index 00000000000..07cbb3fdb49
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-2-gcc-7.patch
@@ -0,0 +1,69 @@
+From 75003cdd23c310ec385344e8040d490e8dd6d2be Mon Sep 17 00:00:00 2001
+From: Jakub Jelinek <jakub@redhat.com>
+Date: Fri, 20 Dec 2019 17:58:35 +0100
+Subject: [PATCH] backport: re PR sanitizer/92154 (new glibc breaks arm
+ bootstrap due to libsanitizer)
+
+	Backported from mainline
+	2019-11-26  Jakub Jelinek  <jakub@redhat.com>
+	Backported for version 7.1.0 <= gcc <= 7.4.0
+	2020-06-05  John L. Jolly  <john.jolly@gmail.com>
+
+	PR sanitizer/92154
+	* sanitizer_common/sanitizer_platform_limits_posix.h: Cherry-pick
+	llvm-project revision 947f9692440836dcb8d88b74b69dd379d85974ce.
+	* sanitizer_common/sanitizer_platform_limits_posix.cc: Likewise.
+
+From-SVN: r279653
+---
+ libsanitizer/ChangeLog                            | 10 ++++++++++
+ .../sanitizer_platform_limits_posix.cc            |  9 +++------
+ .../sanitizer_platform_limits_posix.h             | 15 +--------------
+ 3 files changed, 14 insertions(+), 20 deletions(-)
+
+diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
+index 06a605ff4670..d823a12190c0 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
++++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
+@@ -1156,12 +1156,9 @@ CHECK_SIZE_AND_OFFSET(ipc_perm, uid);
+ CHECK_SIZE_AND_OFFSET(ipc_perm, gid);
+ CHECK_SIZE_AND_OFFSET(ipc_perm, cuid);
+ CHECK_SIZE_AND_OFFSET(ipc_perm, cgid);
+-#if (!defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)) && \
+-    !defined(__arm__)
+-/* On aarch64 glibc 2.20 and earlier provided incorrect mode field.  */
+-/* On Arm glibc 2.31 and later provide a different mode field, this field is
+-   never used by libsanitizer so we can simply ignore this assert for all glibc
+-   versions.  */
++#if !SANITIZER_LINUX || __GLIBC_PREREQ (2, 31)
++/* glibc 2.30 and earlier provided 16-bit mode field instead of 32-bit
++   on many architectures.  */
+ CHECK_SIZE_AND_OFFSET(ipc_perm, mode);
+ #endif
+ 
+diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
+index 73af92af1e8f..6a673a7c9959 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
++++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
+@@ -211,20 +211,13 @@ namespace __sanitizer {
+     unsigned long __unused1;
+     unsigned long __unused2;
+ #elif defined(__sparc__)
+-# if defined(__arch64__)
+     unsigned mode;
+-    unsigned short __pad1;
+-# else
+-    unsigned short __pad1;
+-    unsigned short mode;
+     unsigned short __pad2;
+-# endif
+     unsigned short __seq;
+     unsigned long long __unused1;
+     unsigned long long __unused2;
+ #else
+-    unsigned short mode;
+-    unsigned short __pad1;
++    unsigned int mode;
+     unsigned short __seq;
+     unsigned short __pad2;
+ #if defined(__x86_64__) && !defined(_LP64)
diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index aae26bfae9b..15ee2d79738 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -242,10 +242,13 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
     patch('piclibs.patch', when='+piclibs')
     patch('gcc-backport.patch', when='@4.7:4.9.2,5:5.3')
 
-    # Backport libsanitizer patch for glibc >= 2.31 and 8.1.0 <= gcc <= 9.2.0
+    # Backport libsanitizer patch for glibc >= 2.31 and 5.3.0 <= gcc <= 9.2.0
     # https://bugs.gentoo.org/708346
-    patch('glibc-2.31-libsanitizer-1.patch', when='@8.1.0:8.3.99,9.0.0:9.2.0')
-    patch('glibc-2.31-libsanitizer-2.patch', when='@8.1.0:8.3.99,9.0.0:9.2.0')
+    patch('glibc-2.31-libsanitizer-1.patch', when='@7.1.0:7.4.0,8.1.0:8.3.0,9.0.0:9.2.0')
+    patch('glibc-2.31-libsanitizer-1-gcc-6.patch', when='@5.3.0:5.5.0,6.1.0:6.5.0')
+    patch('glibc-2.31-libsanitizer-2.patch', when='@8.1.0:8.3.0,9.0.0:9.2.0')
+    patch('glibc-2.31-libsanitizer-2-gcc-6.patch', when='@5.3.0:5.5.0,6.1.0:6.5.0')
+    patch('glibc-2.31-libsanitizer-2-gcc-7.patch', when='@7.1.0:7.4.0')
     # Older versions do not compile with newer versions of glibc
     # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81712
     patch('ucontext_t.patch', when='@4.9,5.1:5.4,6.1:6.4,7.1')

From 543f9f91d4a4200cb653dd9c44588773e497f3b7 Mon Sep 17 00:00:00 2001
From: Matthieu Dorier <mdorier@anl.gov>
Date: Sat, 6 Jun 2020 22:14:40 +0100
Subject: [PATCH 639/802] added CTRE package (#16964)

---
 .../repos/builtin/packages/ctre/package.py    | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/ctre/package.py

diff --git a/var/spack/repos/builtin/packages/ctre/package.py b/var/spack/repos/builtin/packages/ctre/package.py
new file mode 100644
index 00000000000..2dc188b7756
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ctre/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+from spack import *
+
+
+class Ctre(CMakePackage):
+    """Compile time regular expressions for C++"""
+
+    homepage = 'https://compile-time.re/'
+    url = 'https://github.com/hanickadot/compile-time-regular-expressions/archive/v2.8.3.tar.gz'
+    git = 'https://github.com/hanickadot/compile-time-regular-expressions.git'
+
+    version('master', branch='master')
+    version('2.8.4', sha256='99b981857f1b66cab5e71161ae74deca268ed39a96ec6507def92d4f445cadd6')
+    version('2.8.3', sha256='5833a9d0fbce39ee39bd6e29df2f7fcafc82e41c373e8675ed0774bcf76fdc7a')
+    version('2.8.2', sha256='f89494f52ec31e5854fff3d2c5825474201476636c5d82a9365dad5188396314')
+    version('2.8.1', sha256='a6153629751ba0adc039551d8ff8d7018972ce362d20c0f70135496d4e7721df')
+    version('2.8',   sha256='44ccdaa299dd43c351f208c5906422eb000e7cdcb53e4f3b7c7c094d0461ab2c')
+    version('2.7',   sha256='ccbf42515b27d542cd36104eb9548f288b0c1989cb584a518900ba1ca3619e12')
+    version('2.6.4', sha256='ce216cfae0e7e1e8c7d7531cfcf81fa18f9bdbfcb800a3119788ca323bedbdac')
+    version('2.6.3', sha256='bdf668b02f0b986dfc0fbc6066f446e2d0a9faa3347f00f53b19131297c84c4a')
+    version('2.6.2', sha256='e82c87aeb0fc3f21ae8a2d3ffce2b1ef970fbea9c3e846ef1a6e5f81790f2946')
+    version('2.6.1', sha256='58c623d9ea1cb7890aaa63c1a87f1a60a8acf31dbd4061ab672bea287ed689ac')

From ad2dd4be01d7caae69455ff61d5e006efab83e30 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Sat, 6 Jun 2020 23:18:48 +0200
Subject: [PATCH 640/802] mongo-c-driver: Add 1.16.2 (#16956)

This also updates libbson to the corresponding version and adds a few
missing older versions.
---
 .../repos/builtin/packages/libbson/package.py | 51 ++++++++++++-
 .../packages/mongo-c-driver/package.py        | 75 +++++++++++++++++--
 2 files changed, 116 insertions(+), 10 deletions(-)

diff --git a/var/spack/repos/builtin/packages/libbson/package.py b/var/spack/repos/builtin/packages/libbson/package.py
index 9f9a1138847..e71cb2eb085 100644
--- a/var/spack/repos/builtin/packages/libbson/package.py
+++ b/var/spack/repos/builtin/packages/libbson/package.py
@@ -6,15 +6,19 @@
 from spack import *
 
 
-class Libbson(AutotoolsPackage):
+class Libbson(Package):
     """libbson is a library providing useful routines related to building,
     parsing, and iterating BSON documents."""
 
-    homepage = "https://github.com/mongodb/libbson"
-    url      = "https://github.com/mongodb/libbson/releases/download/1.7.0/libbson-1.7.0.tar.gz"
+    homepage = "https://github.com/mongodb/mongo-c-driver"
+    url      = "https://github.com/mongodb/mongo-c-driver/releases/download/1.16.2/mongo-c-driver-1.16.2.tar.gz"
 
     maintainers = ['michaelkuhn']
 
+    version('1.16.2', sha256='0a722180e5b5c86c415b9256d753b2d5552901dc5d95c9f022072c3cd336887e')
+    version('1.9.5', sha256='6bb51b863a4641d6d7729e4b55df8f4389ed534c34eb3a1cda906a53df11072c')
+    version('1.9.4', sha256='c3cc230a3451bf7fedc5bb34c3191fd23d841e65ec415301f6c77e531924b769')
+    version('1.9.3', sha256='244e786c746fe6326433b1a6fcaadbdedc0da3d11c7b3168f0afa468f310e5f1')
     version('1.9.1', sha256='236d9fcec0fe419c2201481081e497f49136eda2349b61cfede6233013bf7601')
     version('1.8.1', sha256='9d18d14671b7890e27b2a5ce33a73a5ed5d33d39bba70209bae99c1dc7aa1ed4')
     version('1.8.0', sha256='63dea744b265a2e17c7b5e289f7803c679721d98e2975ea7d56bc1e7b8586bc1')
@@ -23,12 +27,53 @@ class Libbson(AutotoolsPackage):
     version('1.6.2', sha256='aad410123e4bd8a9804c3c3d79e03344e2df104872594dc2cf19605d492944ba')
     version('1.6.1', sha256='5f160d44ea42ce9352a7a3607bc10d3b4b22d3271763aa3b3a12665e73e3a02d')
 
+    depends_on('cmake@3.1:', type='build', when='@1.10.0:')
+
     depends_on('autoconf', type='build', when='@1.6.1')
     depends_on('automake', type='build', when='@1.6.1')
     depends_on('libtool', type='build', when='@1.6.1')
     depends_on('m4', type='build', when='@1.6.1')
 
+    def url_for_version(self, version):
+        if version >= Version('1.10.0'):
+            url = 'https://github.com/mongodb/mongo-c-driver/releases/download/{0}/mongo-c-driver-{0}.tar.gz'
+        else:
+            url = 'https://github.com/mongodb/libbson/releases/download/{0}/libbson-{0}.tar.gz'
+
+        return url.format(version)
+
+    def cmake_args(self):
+        args = [
+            '-DENABLE_AUTOMATIC_INIT_AND_CLEANUP=OFF',
+            '-DENABLE_MONGOC=OFF'
+        ]
+
+        return args
+
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            # We cannot simply do
+            #   cmake('..', *std_cmake_args, *self.cmake_args())
+            # because that is not Python 2 compatible. Instead, collect
+            # arguments into a temporary buffer first.
+            args = []
+            args.extend(std_cmake_args)
+            args.extend(self.cmake_args())
+            cmake('..', *args)
+            make()
+            make('install')
+
     @property
     def force_autoreconf(self):
         # 1.6.1 tarball is broken
         return self.spec.satisfies('@1.6.1')
+
+    @when('@:1.9.99')
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+        make()
+        if self.run_tests:
+            make('check')
+        make('install')
+        if self.run_tests:
+            make('installcheck')
diff --git a/var/spack/repos/builtin/packages/mongo-c-driver/package.py b/var/spack/repos/builtin/packages/mongo-c-driver/package.py
index 27008d7561a..ee3fc581b9d 100644
--- a/var/spack/repos/builtin/packages/mongo-c-driver/package.py
+++ b/var/spack/repos/builtin/packages/mongo-c-driver/package.py
@@ -6,7 +6,7 @@
 from spack import *
 
 
-class MongoCDriver(AutotoolsPackage):
+class MongoCDriver(Package):
     """libmongoc is a client library written in C for MongoDB."""
 
     homepage = "https://github.com/mongodb/mongo-c-driver"
@@ -14,6 +14,7 @@ class MongoCDriver(AutotoolsPackage):
 
     maintainers = ['michaelkuhn']
 
+    version('1.16.2', sha256='0a722180e5b5c86c415b9256d753b2d5552901dc5d95c9f022072c3cd336887e')
     version('1.9.5', sha256='4a4bd0b0375450250a3da50c050b84b9ba8950ce32e16555714e75ebae0b8019')
     version('1.9.4', sha256='910c2f1b2e3df4d0ea39c2f242160028f90fcb8201f05339a730ec4ba70811fb')
     version('1.9.3', sha256='c2c94ef63aaa09efabcbadc4ac3c8740faa102266bdd2559d550f1955b824398')
@@ -28,20 +29,73 @@ class MongoCDriver(AutotoolsPackage):
     variant('ssl', default=True, description='Enable SSL support.')
     variant('snappy', default=True, description='Enable Snappy support.')
     variant('zlib', default=True, description='Enable zlib support.')
+    variant('zstd', default=True, description='Enable zstd support.')
 
     patch('https://github.com/mongodb/mongo-c-driver/pull/466.patch', sha256='713a872217d11aba04a774785a2824d26b566543c270a1fa386114f5200fda20', when='@1.8.1')
 
+    depends_on('cmake@3.1:', type='build', when='@1.10.0:')
+
     depends_on('autoconf', type='build', when='@1.8.1')
     depends_on('automake', type='build', when='@1.8.1')
     depends_on('libtool', type='build', when='@1.8.1')
     depends_on('m4', type='build', when='@1.8.1')
+
     depends_on('pkgconfig', type='build')
 
-    depends_on('libbson')
+    # When updating mongo-c-driver, libbson has to be kept in sync.
+    depends_on('libbson@1.16.0:1.16.99', when='@1.16')
+    depends_on('libbson@1.9.0:1.9.99', when='@1.9')
+    depends_on('libbson@1.8.0:1.8.99', when='@1.8')
+    depends_on('libbson@1.7.0:1.7.99', when='@1.7')
+    depends_on('libbson@1.6.0:1.6.99', when='@1.6')
 
     depends_on('openssl', when='+ssl')
     depends_on('snappy', when='+snappy')
     depends_on('zlib', when='+zlib')
+    depends_on('zstd', when='+zstd')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        args = [
+            '-DENABLE_AUTOMATIC_INIT_AND_CLEANUP=OFF',
+            '-DENABLE_BSON=SYSTEM'
+        ]
+
+        if '+ssl' in spec:
+            args.append('-DENABLE_SSL=OPENSSL')
+        else:
+            args.append('-DENABLE_SSL=OFF')
+
+        if '+snappy' in spec:
+            args.append('-DENABLE_SNAPPY=ON')
+        else:
+            args.append('-DENABLE_SNAPPY=OFF')
+
+        if '+zlib' in spec:
+            args.append('-DENABLE_ZLIB=SYSTEM')
+        else:
+            args.append('-DENABLE_ZLIB=OFF')
+
+        if '+zstd' in spec:
+            args.append('-DENABLE_ZSTD=ON')
+        else:
+            args.append('-DENABLE_ZSTD=OFF')
+
+        return args
+
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            # We cannot simply do
+            #   cmake('..', *std_cmake_args, *self.cmake_args())
+            # because that is not Python 2 compatible. Instead, collect
+            # arguments into a temporary buffer first.
+            args = []
+            args.extend(std_cmake_args)
+            args.extend(self.cmake_args())
+            cmake('..', *args)
+            make()
+            make('install')
 
     @property
     def force_autoreconf(self):
@@ -52,7 +106,8 @@ def configure_args(self):
         spec = self.spec
 
         args = [
-            '--disable-automatic-init-and-cleanup'
+            '--disable-automatic-init-and-cleanup',
+            '--with-libbson=system'
         ]
 
         if '+ssl' in spec:
@@ -72,8 +127,14 @@ def configure_args(self):
             elif spec.satisfies('@1.8.1:'):
                 args.append('--with-zlib=system')
 
-        if spec.satisfies('@1.9.3:'):
-            args.append('--with-libbson=auto')
-        else:
-            args.append('--with-libbson=system')
         return args
+
+    @when('@:1.9.99')
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix), *self.configure_args())
+        make()
+        if self.run_tests:
+            make('check')
+        make('install')
+        if self.run_tests:
+            make('installcheck')

From 8f291c7e9545212d3d8688926b82fc8ec8a1ad13 Mon Sep 17 00:00:00 2001
From: vvolkl <valentin.volkl@cern.ch>
Date: Sat, 6 Jun 2020 23:29:42 +0200
Subject: [PATCH 641/802] [prmon] add package (#16949)

---
 .../repos/builtin/packages/prmon/package.py   | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/prmon/package.py

diff --git a/var/spack/repos/builtin/packages/prmon/package.py b/var/spack/repos/builtin/packages/prmon/package.py
new file mode 100644
index 00000000000..4ae90c2531c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/prmon/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Prmon(CMakePackage):
+    """Standalone monitor for process resource consumption."""
+
+    homepage = "https://github.com/HSF/prmon/"
+    url      = "https://github.com/HSF/prmon/archive/v1.1.1.tar.gz"
+    git      = "https://github.com/HSF/prmon.git"
+
+    maintainers = ['vvolkl']
+
+    version("master", branch="master")
+    version('1.1.1', sha256='5f074b05af2a12e2726c33f6a6e9e8e59ee0c4fb5fe056deb38abacd1bb6bf03')
+
+    variant('plot', default=True,
+            description='Make use of plotting scripts')
+
+    depends_on('nlohmann-json')
+    depends_on('cmake@3.3:', type="build")
+    depends_on('py-matplotlib', type="run", when="+plot")

From 7bc44fa1651df7570060b8d3f4bd60592248a562 Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Sun, 7 Jun 2020 06:30:43 +0900
Subject: [PATCH 642/802] ffr: fix mpi programs to use mpi compiler wrapper.
 (#16948)

---
 var/spack/repos/builtin/packages/ffr/package.py | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/ffr/package.py b/var/spack/repos/builtin/packages/ffr/package.py
index bd3c8258d1a..35ac20f9f6a 100644
--- a/var/spack/repos/builtin/packages/ffr/package.py
+++ b/var/spack/repos/builtin/packages/ffr/package.py
@@ -42,7 +42,8 @@ def edit(self, spec, prefix):
         elif spec.satisfies('%fj'):
             fflags.append('-Fwide')
         d = find('.', 'src_main', recursive=True)
-        root_dir  = os.path.dirname(d[0])
+        src_main = d[0]
+        root_dir  = os.path.dirname(src_main)
         make = join_path(root_dir, 'src_pre', 'src', 'Makefile')
         os.chmod(make, 0o644)
         filter_file('#CSRCS =.*$', 'CSRCS = kmetis_main.c io.c', make)
@@ -51,9 +52,17 @@ def edit(self, spec, prefix):
             'LIBPRE = ' + spec['metis'].libs.ld_flags,
             make
         )
+
+        make = join_path(src_main, 'src', 'Makefile')
+        os.chmod(make, 0o644)
+        with open(make, 'a') as m:
+            m.write('module_hpc.o: module_hpc.f\n')
+            m.write('\t$(MPI_F90) $(FFLAGS) -c $<\n')
+            m.write('\n')
+            m.write('hpc.o: hpc.f\n')
+            m.write('\t$(MPI_F90) $(FFLAGS) -c $<\n')
+
         if spec.satisfies('@3.0_000'):
-            d = find('.', 'src_main', recursive=True)
-            root_dir  = os.path.dirname(d[0])
             for d in ['src_pre', 'FFR2VIZ']:
                 workdir = join_path(root_dir, d, 'src')
                 make = join_path(workdir, 'Makefile')

From 6498b752d1dcc030c7045c6d1c4c77141ca07985 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Sat, 6 Jun 2020 23:33:34 +0200
Subject: [PATCH 643/802] Add rpy2@3.0.4 (#16924)

* Add rpy2@3.0.4

* Style fixes

* Update package.py

* Proper Python version requirement
---
 .../repos/builtin/packages/py-rpy2/package.py   | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-rpy2/package.py b/var/spack/repos/builtin/packages/py-rpy2/package.py
index d3578c2cc23..ef9b847b00e 100644
--- a/var/spack/repos/builtin/packages/py-rpy2/package.py
+++ b/var/spack/repos/builtin/packages/py-rpy2/package.py
@@ -16,6 +16,7 @@ class PyRpy2(PythonPackage):
     homepage = "https://pypi.python.org/pypi/rpy2"
     url = "https://pypi.io/packages/source/r/rpy2/rpy2-2.5.4.tar.gz"
 
+    version('3.0.4', sha256='2af5158a5d56af7f7bf5e54d8d7e87b6f115ff40f056d82f93cad0cbf6acc0cb')
     version('3.0.0', sha256='34efc2935d9015527837d6b1de29641863d184b19d39ad415d5384be8a015bce')
     version('2.9.4', sha256='be57f741d0c284b5d8785ab03dff0e829303e5ac30e548d5ceb46e05b168812e')
     version('2.8.6', sha256='004d13734a7b9a85cbc1e7a93ec87df741e28db1273ab5b0d9efaac04a9c5f98')
@@ -30,12 +31,18 @@ class PyRpy2(PythonPackage):
     depends_on('py-setuptools', type='build')
     depends_on('r',             type=('build', 'run'))
 
+    # @3.0.0:
+    depends_on('py-cffi@1.0.0:',   when='@3.0.0:', type=('build', 'run'))
+    depends_on('py-simplegeneric', when='@3.0.0:', type=('build', 'run'))
+    depends_on('py-pytest',        when='@3:', type=('build', 'run'))
+
     # @2.9.0:
-    depends_on('r@3.3:',    when='@2.9.0:', type=('build', 'run'))
-    depends_on('python@3:', when='@2.9.0:', type=('build', 'run'))
-    depends_on('py-jinja2', when='@2.9.0:', type=('build', 'run'))
-    depends_on('py-six',    when='@2.9.0:', type=('build', 'run'))
+    depends_on('r@3.3:',      when='@2.9.0:', type=('build', 'run'))
+    depends_on('python@3.5:', when='@2.9.0:', type=('build', 'run'))
+    depends_on('py-jinja2',   when='@2.9.0:', type=('build', 'run'))
+    depends_on('py-six',      when='@2.9.0:2.9.999', type=('build', 'run'))
 
     # @:2.8.6
-    depends_on('r@2.8:', when='@:2.8.6', type=('build', 'run'))
+    depends_on('r@2.8:',           when='@:2.8.6', type=('build', 'run'))
     depends_on('py-singledispatch', when='^python@:2',   type=('build', 'run'))
+    depends_on('python@2.7:2.8,3.5:', type=('build', 'run'))

From a2c6f6a703e577011bea6fdd97eca580a379d9b1 Mon Sep 17 00:00:00 2001
From: Sinan <sbulutw@gmail.com>
Date: Sun, 7 Jun 2020 07:33:03 -0700
Subject: [PATCH 644/802] py-gast: add version 0.3.3 (#16945)

* py-gast: add version 0.3.3

* add python version constraints

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
---
 var/spack/repos/builtin/packages/py-gast/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-gast/package.py b/var/spack/repos/builtin/packages/py-gast/package.py
index c7730e1e28a..c69b9bc4758 100644
--- a/var/spack/repos/builtin/packages/py-gast/package.py
+++ b/var/spack/repos/builtin/packages/py-gast/package.py
@@ -12,8 +12,10 @@ class PyGast(PythonPackage):
     homepage = "https://github.com/serge-sans-paille/gast"
     url      = "https://pypi.io/packages/source/g/gast/gast-0.3.2.tar.gz"
 
+    version('0.3.3', sha256='b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57')
     version('0.3.2', sha256='5c7617f1f6c8b8b426819642b16b9016727ddaecd16af9a07753e537eba8a3a5')
     version('0.2.2', sha256='fe939df4583692f0512161ec1c880e0a10e71e6a232da045ab8edd3756fbadf0')
     version('0.2.0', sha256='7068908321ecd2774f145193c4b34a11305bd104b4551b09273dfd1d6a374930')
 
     depends_on('py-setuptools', type='build')
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))

From 33923320a82dee1446999b3a55ce21a2b2cd81f3 Mon Sep 17 00:00:00 2001
From: John Jolly <john.jolly@gmail.com>
Date: Sun, 7 Jun 2020 08:36:14 -0600
Subject: [PATCH 645/802] rose: Add build dependencies for flex and bison
 (#16981)

---
 var/spack/repos/builtin/packages/rose/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/rose/package.py b/var/spack/repos/builtin/packages/rose/package.py
index 326da4854bb..0255230da10 100644
--- a/var/spack/repos/builtin/packages/rose/package.py
+++ b/var/spack/repos/builtin/packages/rose/package.py
@@ -62,6 +62,8 @@ class Rose(AutotoolsPackage):
     depends_on("autoconf@2.69:", type="build")
     depends_on("automake@1.14:", type="build")
     depends_on("libtool@2.4:", type="build")
+    depends_on("flex@2.6.4:", type="build")
+    depends_on("bison@3.4.2:", type="build")
 
     # C++11 compatible boost and gcc versions required for +cxx11 variant:
     depends_on("boost@1.60.0:1.64.0,1.65.1,1.66.0:1.67.0 cxxstd=11", when="+cxx11")

From b00f97f7cc6ed4be26e7adb470b163cb0e26082c Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Sun, 7 Jun 2020 23:39:53 +0900
Subject: [PATCH 646/802] boost: Don't use pre-compiled headers for Fujitsu
 compiler (#16914)

* boost: Dopn't use pre compile header.

* move %fj.
---
 var/spack/repos/builtin/packages/boost/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index aa4768e9548..bcdec30ae99 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -398,7 +398,7 @@ def determine_b2_options(self, spec, options):
         # and at least in clang 3.9 still fails to build
         #   http://www.boost.org/build/doc/html/bbv2/reference/precompiled_headers.html
         #   https://svn.boost.org/trac/boost/ticket/12496
-        if spec.satisfies('%clang'):
+        if spec.satisfies('%clang') or spec.satisfies('%fj'):
             options.extend(['pch=off'])
             if '+clanglibcpp' in spec:
                 cxxflags.append('-stdlib=libc++')

From 664c32efb490260e3fd2d06864c39000354c5a93 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Mon, 8 Jun 2020 06:11:24 +0200
Subject: [PATCH 647/802] py-ipykernel: added v5.1.1 (#16988)

---
 var/spack/repos/builtin/packages/py-ipykernel/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-ipykernel/package.py b/var/spack/repos/builtin/packages/py-ipykernel/package.py
index f6ce9facb10..e2f9d919171 100644
--- a/var/spack/repos/builtin/packages/py-ipykernel/package.py
+++ b/var/spack/repos/builtin/packages/py-ipykernel/package.py
@@ -12,6 +12,7 @@ class PyIpykernel(PythonPackage):
     homepage = "https://pypi.python.org/pypi/ipykernel"
     url      = "https://github.com/ipython/ipykernel/archive/4.5.0.tar.gz"
 
+    version('5.1.1',  sha256='a735d3df42e76e8176849dcc8d7746eda80b7768e8f1b38cd9aa6cabfd28baf5')
     version('5.1.0',  sha256='30f01a2a1470d3fabbad03f5c43606c1bc2142850fc4ccedcf44281664ae9122')
     version('4.10.0', sha256='df2714fd0084085ed68876f75ab846202d261420b5f4069af6335b8df0475391')
     version('4.5.0',  sha256='c5ec5130f5f7eda71345b9ef638c9213c4c2f41610a9ad338a0f1d0819421adf')

From 763760cfe0fea5d0a1e4e1a5a478ee5d65d2a65e Mon Sep 17 00:00:00 2001
From: "Mark W. Krentel" <krentel@rice.edu>
Date: Sun, 7 Jun 2020 23:15:37 -0500
Subject: [PATCH 648/802] hpcviewer, ibm-java: updates versions (#16987)

hpcviewer: added v2020.05.
ibm-java:  added v8.0.6.10.
---
 var/spack/repos/builtin/packages/hpcviewer/package.py | 6 ++++++
 var/spack/repos/builtin/packages/ibm-java/package.py  | 2 ++
 2 files changed, 8 insertions(+)

diff --git a/var/spack/repos/builtin/packages/hpcviewer/package.py b/var/spack/repos/builtin/packages/hpcviewer/package.py
index 5399e42f6c8..f14f55d7876 100644
--- a/var/spack/repos/builtin/packages/hpcviewer/package.py
+++ b/var/spack/repos/builtin/packages/hpcviewer/package.py
@@ -37,6 +37,9 @@ class Hpcviewer(Package):
     maintainers = ['mwkrentel']
 
     viewer_sha = {
+        ('2020.05', 'x86_64'):  '27f99c94a69abd005303fb58360b0d1b3eb7d223cab81c38ae6ccdd83ec15106',
+        ('2020.05', 'ppc64'):   '469bce07a75476c132d3791ca49e38db015917c9c36b4810e477bc1c54a13d68',
+        ('2020.05', 'ppc64le'): 'fc4491bf6d9eaf2b7f2d39b722c978597a881ece557fb05a4cf27caabb9e0b99',
         ('2020.04', 'x86_64'):  '5944c7b1e518b25d143df72b06a69cffb0bfc92186eb5efee2178fc2814a0b8b',
         ('2020.04', 'ppc64'):   'ba60615a550aa77a17eb94272b62365a22298cebc6dc2cb7463686741e58d874',
         ('2020.04', 'ppc64le'): '128494077979b447875ed730f1e8c5470fafcd52ae6debe61625031248d91f7c',
@@ -67,6 +70,9 @@ class Hpcviewer(Package):
     }
 
     trace_sha = {
+        ('2020.05', 'x86_64'):  'a0b925099a00c10fcb38e937068e50937175fd46dc086121525e546a63a7fd83',
+        ('2020.05', 'ppc64'):   '40526f62f36e5b6438021c2b557256638d41a6b8f4e101534b5230ac644a9b85',
+        ('2020.05', 'ppc64le'): 'c16e83b59362adcebecd4231374916a2b3a3c016f75a45b24e8398f777a24f89',
         ('2020.04', 'x86_64'):  '695f7a06479c2b6958a6ebc3985b7ed777e7e126c04424ce980b224690f769f3',
         ('2020.04', 'ppc64'):   '78cfadaf7bc6130cc4257241499b36f4f1c47f22d0daa29f5e733ca824a87b3c',
         ('2020.04', 'ppc64le'): '28c225023accbc85a19c6d8fdcc14dae64a475ed5de2b94f18e58aab4edd2c09',
diff --git a/var/spack/repos/builtin/packages/ibm-java/package.py b/var/spack/repos/builtin/packages/ibm-java/package.py
index b2de7b1f159..72739240d5d 100644
--- a/var/spack/repos/builtin/packages/ibm-java/package.py
+++ b/var/spack/repos/builtin/packages/ibm-java/package.py
@@ -22,6 +22,8 @@ class IbmJava(Package):
     # not be available for download.
 
     version_list = [
+        ('8.0.6.10', 'ppc64',   'ff5151ead88f891624eefe33d80d56c325ca0aa4b93bd96c135cad326993eda2'),
+        ('8.0.6.10', 'ppc64le', 'ea99ab28dd300b08940882d178247e99aafe5a998b1621cf288dfb247394e067'),
         ('8.0.6.7',  'ppc64',   'a1accb461a039af4587ea86511e317fea1d423e7f781459a17ed3947afed2982'),
         ('8.0.6.7',  'ppc64le', '9ede76a597af28c7f10c6f8a68788cc2dcd39fdab178c9bac56df8b3766ac717'),
         ('8.0.6.0',  'ppc64',   'e142746a83e47ab91d71839d5776f112ed154ae180d0628e3f10886151dad710'),

From bd1a0a9ad4c9ac19a50c60f75aba6588c8ccfe6c Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Sun, 7 Jun 2020 21:43:52 -0700
Subject: [PATCH 649/802] view remove: directly check whether specs own files
 before removing from view (#16955)

Bugfix for hardlinks and copies
---
 lib/spack/spack/filesystem_view.py            | 34 ++++++++++++++++---
 lib/spack/spack/test/cmd/view.py              | 15 ++++++++
 .../packages/needs-relocation/package.py      | 28 +++++++++++++++
 3 files changed, 72 insertions(+), 5 deletions(-)
 create mode 100644 var/spack/repos/builtin.mock/packages/needs-relocation/package.py

diff --git a/lib/spack/spack/filesystem_view.py b/lib/spack/spack/filesystem_view.py
index f4d77a694bc..0f21e4d975d 100644
--- a/lib/spack/spack/filesystem_view.py
+++ b/lib/spack/spack/filesystem_view.py
@@ -3,7 +3,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import filecmp
 import functools as ft
 import os
 import re
@@ -18,6 +17,7 @@
     mkdirp, remove_dead_links, remove_empty_directories)
 
 import spack.util.spack_yaml as s_yaml
+import spack.util.spack_json as s_json
 
 import spack.spec
 import spack.store
@@ -411,10 +411,34 @@ def remove_file(self, src, dest):
         if not os.path.lexists(dest):
             tty.warn("Tried to remove %s which does not exist" % dest)
             return
-        # remove if dest is a hardlink/symlink to src; this will only
-        # be false if two packages are merged into a prefix and have a
-        # conflicting file
-        if filecmp.cmp(src, dest, shallow=True):
+
+        def needs_file(spec, file):
+            # convert the file we want to remove to a source in this spec
+            projection = self.get_projection_for_spec(spec)
+            relative_path = os.path.relpath(file, projection)
+            test_path = os.path.join(spec.prefix, relative_path)
+
+            # check if this spec owns a file of that name (through the
+            # manifest in the metadata dir, which we have in the view).
+            manifest_file = os.path.join(self.get_path_meta_folder(spec),
+                                         spack.store.layout.manifest_file_name)
+            try:
+                with open(manifest_file, 'r') as f:
+                    manifest = s_json.load(f)
+            except (OSError, IOError):
+                # if we can't load it, assume it doesn't know about the file.
+                manifest = {}
+            return test_path in manifest
+
+        # remove if dest is not owned by any other package in the view
+        # This will only be false if two packages are merged into a prefix
+        # and have a conflicting file
+
+        # check all specs for whether they own the file. That include the spec
+        # we are currently removing, as we remove files before unlinking the
+        # metadata directory.
+        if len([s for s in self.get_all_specs()
+                if needs_file(s, dest)]) <= 1:
             os.remove(dest)
 
     def check_added(self, spec):
diff --git a/lib/spack/spack/test/cmd/view.py b/lib/spack/spack/test/cmd/view.py
index d908248a19b..4ff15920357 100644
--- a/lib/spack/spack/test/cmd/view.py
+++ b/lib/spack/spack/test/cmd/view.py
@@ -40,6 +40,21 @@ def test_view_link_type(
     assert os.path.islink(package_prefix) == is_link_cmd
 
 
+@pytest.mark.parametrize('add_cmd', ['hardlink', 'symlink', 'hard', 'add',
+                                     'copy', 'relocate'])
+def test_view_link_type_remove(
+        tmpdir, mock_packages, mock_archive, mock_fetch, config,
+        install_mockery, add_cmd):
+    install('needs-relocation')
+    viewpath = str(tmpdir.mkdir('view_{0}'.format(add_cmd)))
+    view(add_cmd, viewpath, 'needs-relocation')
+    bindir = os.path.join(viewpath, 'bin')
+    assert os.path.exists(bindir)
+
+    view('remove', viewpath, 'needs-relocation')
+    assert not os.path.exists(bindir)
+
+
 @pytest.mark.parametrize('cmd', ['hardlink', 'symlink', 'hard', 'add',
                                  'copy', 'relocate'])
 def test_view_projections(
diff --git a/var/spack/repos/builtin.mock/packages/needs-relocation/package.py b/var/spack/repos/builtin.mock/packages/needs-relocation/package.py
new file mode 100644
index 00000000000..681a8a53ed4
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/needs-relocation/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+def check(condition, msg):
+    """Raise an install error if condition is False."""
+    if not condition:
+        raise InstallError(msg)
+
+
+class NeedsRelocation(Package):
+    """A dumy package that encodes its prefix."""
+    homepage  = 'https://www.cmake.org'
+    url       = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
+
+    version('0.0.0', '12345678qwertyuiasdfghjkzxcvbnm0')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+
+        exe = join_path(prefix.bin, 'exe')
+        with open(exe, 'w') as f:
+            f.write(prefix)
+        set_executable(exe)

From d9738f569d3eb32d745da4153fbdeeebb14434d9 Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Mon, 8 Jun 2020 01:07:34 -0500
Subject: [PATCH 650/802] ltr-retriever: new package at v2.8.7 (#16832)

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../builtin/packages/ltr-retriever/package.py | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/ltr-retriever/package.py

diff --git a/var/spack/repos/builtin/packages/ltr-retriever/package.py b/var/spack/repos/builtin/packages/ltr-retriever/package.py
new file mode 100644
index 00000000000..2cc7f0a2319
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ltr-retriever/package.py
@@ -0,0 +1,45 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from os import symlink
+
+
+class LtrRetriever(Package):
+    """LTR_retriever is a highly accurate and sensitive program for
+       identification of LTR retrotransposons."""
+
+    homepage = "https://github.com/oushujun/LTR_retriever"
+    url      = "https://github.com/oushujun/LTR_retriever/archive/v2.8.7.tar.gz"
+
+    version('2.8.7', sha256='29ca6f699c57b5e964aa0ee6c7d3e1e4cd5362dadd789e5f0e8c82fe0bb29369')
+
+    depends_on('perl', type='run')
+    depends_on('blast-plus', type='run')
+    depends_on('hmmer@3.1b2:', type='run')
+    depends_on('cdhit', type='run')
+    depends_on('repeatmasker', type='run')
+
+    def install(self, spec, prefix):
+        filter_file(r'BLAST\+=.*', 'BLAST+=%s' % spec['blast-plus'].prefix.bin,
+                    'paths')
+        filter_file('RepeatMasker=.*',
+                    'RepeatMasker=%s' % spec['repeatmasker'].prefix.bin,
+                    'paths')
+        filter_file('HMMER=.*',
+                    'HMMER=%s' % spec['hmmer'].prefix.bin,
+                    'paths')
+        filter_file('CDHIT=.*',
+                    'CDHIT=%s' % spec['cdhit'].prefix,
+                    'paths')
+        filter_file('BLAST=.*', '', 'paths')
+
+        mkdirp(prefix.opt)
+        mkdirp(prefix.bin)
+
+        install_tree('.', prefix.opt.ltr_retriever)
+
+        symlink(prefix.opt.ltr_retriever.LTR_retriever,
+                prefix.bin.LTR_retriever)

From 3ea65818e1827835864c6c073175eb5edf7b4213 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Mon, 8 Jun 2020 14:09:48 +0200
Subject: [PATCH 651/802] Add py-storm@0.23 and update URL (#16991)

* Add py-storm@0.23 and update URL

* Update package.py
---
 var/spack/repos/builtin/packages/py-storm/package.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-storm/package.py b/var/spack/repos/builtin/packages/py-storm/package.py
index dae4a9941d7..64a631b2009 100644
--- a/var/spack/repos/builtin/packages/py-storm/package.py
+++ b/var/spack/repos/builtin/packages/py-storm/package.py
@@ -9,8 +9,12 @@
 class PyStorm(PythonPackage):
     """Storm is an object-relational mapper (ORM) for Python"""
     homepage = "https://storm.canonical.com/"
-    url      = "https://launchpad.net/storm/trunk/0.20/+download/storm-0.20.tar.gz"
+    url      = "https://launchpad.net/storm/trunk/0.20/+download/storm-0.20.tar.bz2"
 
-    version('0.20', sha256='0fa70043bb1a1c178c2f760db35f5956244cecf50dab7fb22d78be7507726603')
+    version('0.23', sha256='01c59f1c898fb9891333abd65519ba2dd5f68623ac8e67b54932e99ce52593d3')
+    version('0.20', sha256='1fe016c9ec40520eafc3cf359f1ec2b7fa86be91e45c9279bfb0ea3b06390a82')
 
     depends_on('py-setuptools', type='build')
+    depends_on('py-six', when='@0.23:')
+    depends_on('python@2.7:2.8', when='@:0.20')
+    depends_on('python@2.7:2.8,3.5:', when='@0.21:')

From c76ab4d8fefedc5b4499912a76fed720721dcb17 Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Mon, 8 Jun 2020 15:28:21 +0200
Subject: [PATCH 652/802] R: url-version custom, release 4 (#16962)

* R: url-version custom, release 4

* r: pcre condition
---
 var/spack/repos/builtin/packages/r/package.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/r/package.py b/var/spack/repos/builtin/packages/r/package.py
index 7c6807e3e71..e28ae117391 100644
--- a/var/spack/repos/builtin/packages/r/package.py
+++ b/var/spack/repos/builtin/packages/r/package.py
@@ -21,6 +21,7 @@ class R(AutotoolsPackage):
 
     extendable = True
 
+    version('4.0.0', sha256='06beb0291b569978484eb0dcb5d2339665ec745737bdfb4e873e7a5a75492940')
     version('3.6.3', sha256='89302990d8e8add536e12125ec591d6951022cf8475861b3690bc8bf1cefaa8f')
     version('3.6.2', sha256='bd65a45cddfb88f37370fbcee4ac8dd3f1aebeebe47c2f968fd9770ba2bbc954')
     version('3.6.1', sha256='5baa9ebd3e71acecdcc3da31d9042fb174d55a42829f8315f2457080978b1389')
@@ -81,7 +82,8 @@ class R(AutotoolsPackage):
     depends_on('libxt', when='+X')
     depends_on('libxmu', when='+X')
     depends_on('curl')
-    depends_on('pcre')
+    depends_on('pcre2', when='@4:')
+    depends_on('pcre', when='@:3.6.3')
     depends_on('java')
 
     patch('zlib.patch', when='@:3.3.2')
@@ -92,6 +94,12 @@ class R(AutotoolsPackage):
     # temporary fix to lower the optimization level.
     patch('change_optflags_tmp.patch', when='%fj@4.1.0')
 
+    # R custom URL version
+    def url_for_version(self, version):
+        """Handle R's customed URL versions"""
+        url = 'https://cloud.r-project.org/src/base'
+        return url + '/R-%s/R-%s.tar.gz' % (version.up_to(1), version)
+
     filter_compiler_wrappers(
         'Makeconf', relative_root=os.path.join('rlib', 'R', 'etc')
     )

From 8995b3ad3a3e38edb51378706af0e8f98444f038 Mon Sep 17 00:00:00 2001
From: vvolkl <valentin.volkl@cern.ch>
Date: Mon, 8 Jun 2020 15:30:23 +0200
Subject: [PATCH 653/802] Add Package HSF-CMakeTools (#16951)

* [hsf-cmaketools] add package

* fix formatting

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* [hsf-cmaketools] remove cmake_prefix_path which is set already by spack

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../packages/hsf-cmaketools/package.py        | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/hsf-cmaketools/package.py

diff --git a/var/spack/repos/builtin/packages/hsf-cmaketools/package.py b/var/spack/repos/builtin/packages/hsf-cmaketools/package.py
new file mode 100644
index 00000000000..78053515098
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hsf-cmaketools/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class HsfCmaketools(Package):
+    """CMake 'Find' modules for commonly used HEP Packages"""
+
+    homepage = "https://github.com/HSF/cmaketools/"
+    url      = "https://github.com/HSF/cmaketools/archive/1.8.tar.gz"
+    git      = "https://github.com/HSF/cmaketools.git"
+
+    maintainers = ['vvolkl']
+
+    version('master', branch='master')
+    version('1.8', sha256='91af30f5701dadf80a5d7e0d808c224c934f0784a3aff2d3b69aff24f7e1db41')
+
+    # this package only needs to be installed in CMAKE_PREFIX_PATH
+    # which is set by spack
+    def install(self, spec, prefix):
+        mkdir(prefix.modules)
+        install_tree('modules', prefix.modules)
+        install("CMakeToolsConfig.cmake", prefix)

From f8b5e413b46350f25bd7d231a8102c706fbf34f8 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Mon, 8 Jun 2020 21:33:40 +0800
Subject: [PATCH 654/802] Add new package: py-devlib (#16982)

* Add new package: py-devlib

* Update var/spack/repos/builtin/packages/py-devlib/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* add depends

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../builtin/packages/py-devlib/package.py     | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-devlib/package.py

diff --git a/var/spack/repos/builtin/packages/py-devlib/package.py b/var/spack/repos/builtin/packages/py-devlib/package.py
new file mode 100644
index 00000000000..5a9bb49486c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-devlib/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyDevlib(PythonPackage):
+    """Library for interaction with and instrumentation of remote devices."""
+
+    homepage = "https://github.com/ARM-software/devlib"
+    url      = "https://github.com/ARM-software/devlib/archive/v1.2.tar.gz"
+
+    version('1.2',   sha256='4cdb6767a9430b49eecffe34e2b9fcbcfc7e65328122d909aa71c3d11a86503d')
+    version('1.1.2', sha256='c900420cb97239b4642f5e333e43884fb09507b530edb55466e7b82103b4deaa')
+    version('1.1.1', sha256='eceb7a2721197a6023bbc2bbf346663fc117e4f54e1eb8334a3085dead9c8036')
+    version('1.1.0', sha256='317e9be2303ebb6aebac9a2ec398c622ea16d6e46079dc9e37253b37d739ca9d')
+    version('1.0.0', sha256='2f78278bdc9731a4fa13c41c74f08e0b8c5143de5fa1e1bdb2302673aec45862')
+    version('0.0.4', sha256='0f55e684d43fab759d0e74bd8f0d0260d9546a8b8d853d286acfe5e00c86da05')
+    version('0.0.3', sha256='29ec5f1de481783ab0b9efc111dfeb67c890187d56fca8592b25ee756ff32902')
+    version('0.0.2', sha256='972f33be16a06572a19b67d909ee0ed6cb6f21f9a9da3c43fd0ff5851421051d')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-python-dateutil', type=('build', 'run'))
+    depends_on('py-pexpect@3.3:', type=('build', 'run'))
+    depends_on('py-pyserial', type=('build', 'run'))
+    depends_on('py-wrapt', type=('build', 'run'))
+    depends_on('py-future', type=('build', 'run'))
+    depends_on('py-pandas', type=('build', 'run'))
+    depends_on('py-enum34', type=('build', 'run'), when='^python@:3.3')
+    depends_on('py-contextlib2', type=('build', 'run'), when='^python@:2.999')
+    depends_on('py-numpy@:1.16.4', type=('build', 'run'), when='^python@:2.999')
+    depends_on('py-numpy', type=('build', 'run'), when='^python@:3.0')

From 4d064fd56cb0a8296311409397a0134151b6305e Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 9 Jun 2020 01:51:59 +0800
Subject: [PATCH 655/802] rt-tests: fix build error (#16998)

This is a makefile package and needs to invoke make.
---
 var/spack/repos/builtin/packages/rt-tests/package.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/rt-tests/package.py b/var/spack/repos/builtin/packages/rt-tests/package.py
index 4310ae5718e..ba5975e5189 100644
--- a/var/spack/repos/builtin/packages/rt-tests/package.py
+++ b/var/spack/repos/builtin/packages/rt-tests/package.py
@@ -6,7 +6,7 @@
 from spack import *
 
 
-class RtTests(Package):
+class RtTests(MakefilePackage):
     """
     Suite of real-time tests - cyclictest, hwlatdetect, pip_stress,
     pi_stress, pmqtest, ptsematest, rt-migrate-test, sendme, signaltest,
@@ -19,4 +19,6 @@ class RtTests(Package):
     version('1.2', sha256='7ccde036059c87681a4b00e7138678d9551b1232113441f6edda31ea45452426')
 
     def install(self, spec, prefix):
-        install_tree('.', prefix)
+        mkdirp(prefix.bin)
+        mkdirp(prefix.share.man)
+        make('install', 'prefix={0}'.format(prefix))

From 6f9bfec32ec98bff24d00324ef7f9128e74ba87e Mon Sep 17 00:00:00 2001
From: Ryan Mast <nightlark@users.noreply.github.com>
Date: Mon, 8 Jun 2020 14:37:49 -0700
Subject: [PATCH 656/802] HELICS: add version 2.5.1 (#17014)

---
 var/spack/repos/builtin/packages/helics/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/helics/package.py b/var/spack/repos/builtin/packages/helics/package.py
index 9736cb6d66f..f2bb52dec6a 100644
--- a/var/spack/repos/builtin/packages/helics/package.py
+++ b/var/spack/repos/builtin/packages/helics/package.py
@@ -19,6 +19,7 @@ class Helics(CMakePackage):
 
     version('develop', branch='develop', submodules=True)
     version('master', branch='master', submodules=True)
+    version('2.5.1', sha256='3fc3507f7c074ff8b6a17fe54676334158fb2ff7cc8e7f4df011938f28fdbbca')
     version('2.5.0', sha256='6f4f9308ebb59d82d71cf068e0d9d66b6edfa7792d61d54f0a61bf20dd2a7428')
     version('2.4.2', sha256='957856f06ed6d622f05dfe53df7768bba8fe2336d841252f5fac8345070fa5cb')
     version('2.4.1', sha256='ac077e9efe466881ea366721cb31fb37ea0e72a881a717323ba4f3cdda338be4')

From bcf8ebff4ff3ca25c17e690187b1e7cf46657ee5 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Mon, 8 Jun 2020 18:44:07 -0500
Subject: [PATCH 657/802] Cray: fix Blue Waters support and user-built MPIs on
 Cray (#16593)

* Cray: fix Blue Waters support

* pkg-config env vars needed on Blue Waters

* cray platform: fix support for user-build MPI on cray machines

* reintroduce cray environment cleaning behind cnl version guard

* cray platform: fix support for user-build MPI on cray machines

Co-authored-by: Gregory <becker33@llnl.gov>
---
 lib/spack/spack/build_environment.py          | 24 ++++++++++++-------
 lib/spack/spack/platforms/cray.py             |  6 +++--
 .../repos/builtin/packages/mpich/package.py   |  9 ++++---
 .../builtin/packages/mvapich2/package.py      |  9 ++++---
 4 files changed, 31 insertions(+), 17 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index f57ecd1e582..435de8594ec 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -53,6 +53,7 @@
 import spack.paths
 import spack.schema.environment
 import spack.store
+import spack.architecture as arch
 from spack.util.string import plural
 from spack.util.environment import (
     env_flag, filter_system_paths, get_path, is_system_path,
@@ -141,17 +142,21 @@ def clean_environment():
     # can affect how some packages find libraries.  We want to make
     # sure that builds never pull in unintended external dependencies.
     env.unset('LD_LIBRARY_PATH')
-    env.unset('CRAY_LD_LIBRARY_PATH')
     env.unset('LIBRARY_PATH')
     env.unset('CPATH')
     env.unset('LD_RUN_PATH')
     env.unset('DYLD_LIBRARY_PATH')
     env.unset('DYLD_FALLBACK_LIBRARY_PATH')
 
-    # Remove all pkgconfig stuff from craype
-    for varname in os.environ.keys():
-        if 'PKGCONF' in varname:
-            env.unset(varname)
+    # On Cray systems newer than CNL5, unset CRAY_LD_LIBRARY_PATH to avoid
+    # interference with Spack dependencies. CNL5 (e.g. Blue Waters) requires
+    # these variables to be set.
+    hostarch = arch.Arch(arch.platform(), 'default_os', 'default_target')
+    if str(hostarch.platform) == 'cray' and str(hostarch.os) != 'cnl5':
+        env.unset('CRAY_LD_LIBRARY_PATH')
+        for varname in os.environ.keys():
+            if 'PKGCONF' in varname:
+                env.unset(varname)
 
     build_lang = spack.config.get('config:build_language')
     if build_lang:
@@ -355,10 +360,6 @@ def set_build_environment_variables(pkg, env, dirty):
         extra_rpaths = ':'.join(compiler.extra_rpaths)
         env.set('SPACK_COMPILER_EXTRA_RPATHS', extra_rpaths)
 
-    implicit_rpaths = compiler.implicit_rpaths()
-    if implicit_rpaths:
-        env.set('SPACK_COMPILER_IMPLICIT_RPATHS', ':'.join(implicit_rpaths))
-
     # Add bin directories from dependencies to the PATH for the build.
     for prefix in build_prefixes:
         for dirname in ['bin', 'bin64']:
@@ -733,6 +734,11 @@ def setup_package(pkg, dirty):
 
         load_external_modules(pkg)
 
+    implicit_rpaths = pkg.compiler.implicit_rpaths()
+    if implicit_rpaths:
+        build_env.set('SPACK_COMPILER_IMPLICIT_RPATHS',
+                      ':'.join(implicit_rpaths))
+
     # Make sure nothing's strange about the Spack environment.
     validate(build_env, tty.warn)
     build_env.apply_modifications()
diff --git a/lib/spack/spack/platforms/cray.py b/lib/spack/spack/platforms/cray.py
index 2fccf2fe55e..9c8770c3680 100644
--- a/lib/spack/spack/platforms/cray.py
+++ b/lib/spack/spack/platforms/cray.py
@@ -22,7 +22,9 @@
     'x86-naples': 'zen',
     'x86-rome': 'zen',  # Cheating because we have the wrong modules on rzcrayz
     'x86-skylake': 'skylake_avx512',
-    'mic-knl': 'mic_knl'
+    'mic-knl': 'mic_knl',
+    'interlagos': 'bulldozer',
+    'abudhabi': 'piledriver',
 }
 
 
@@ -176,7 +178,7 @@ def modules_from_listdir():
             craype_default_path = '/opt/cray/pe/craype/default/modulefiles'
             if os.path.isdir(craype_default_path):
                 return os.listdir(craype_default_path)
-            return None
+            return []
 
         if getattr(self, '_craype_targets', None) is None:
             strategies = [
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index 7b8c807cce3..042c2c5b124 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -161,8 +161,9 @@ def setup_build_environment(self, env):
             env.set('FFLAGS', '-fallow-argument-mismatch')
 
     def setup_dependent_build_environment(self, env, dependent_spec):
-        # On Cray, the regular compiler wrappers *are* the MPI wrappers.
-        if 'platform=cray' in self.spec:
+        # For Cray MPIs, the regular compiler wrappers *are* the MPI wrappers.
+        # Cray MPIs always have cray in the module name, e.g. "cray-mpich"
+        if self.spec.external_module and 'cray' in self.spec.external_module:
             env.set('MPICC', spack_cc)
             env.set('MPICXX', spack_cxx)
             env.set('MPIF77', spack_fc)
@@ -180,7 +181,9 @@ def setup_dependent_build_environment(self, env, dependent_spec):
         env.set('MPICH_FC', spack_fc)
 
     def setup_dependent_package(self, module, dependent_spec):
-        if 'platform=cray' in self.spec:
+        # For Cray MPIs, the regular compiler wrappers *are* the MPI wrappers.
+        # Cray MPIs always have cray in the module name, e.g. "cray-mpich"
+        if self.spec.external_module and 'cray' in self.spec.external_module:
             self.spec.mpicc = spack_cc
             self.spec.mpicxx = spack_cxx
             self.spec.mpifc = spack_fc
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index 04205b6e24f..0fb3c36b289 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -209,8 +209,9 @@ def setup_run_environment(self, env):
             env.set('SLURM_MPI_TYPE', 'pmi2')
 
     def setup_dependent_build_environment(self, env, dependent_spec):
-        # On Cray, the regular compiler wrappers *are* the MPI wrappers.
-        if 'platform=cray' in self.spec:
+        # For Cray MPIs, the regular compiler wrappers *are* the MPI wrappers.
+        # Cray MPIs always have cray in the module name, e.g. "cray-mvapich"
+        if self.spec.external_module and 'cray' in self.spec.external_module:
             env.set('MPICC',  spack_cc)
             env.set('MPICXX', spack_cxx)
             env.set('MPIF77', spack_fc)
@@ -228,7 +229,9 @@ def setup_dependent_build_environment(self, env, dependent_spec):
         env.set('MPICH_FC', spack_fc)
 
     def setup_dependent_package(self, module, dependent_spec):
-        if 'platform=cray' in self.spec:
+        # For Cray MPIs, the regular compiler wrappers *are* the MPI wrappers.
+        # Cray MPIs always have cray in the module name, e.g. "cray-mvapich"
+        if self.spec.external_module and 'cray' in self.spec.external_module:
             self.spec.mpicc = spack_cc
             self.spec.mpicxx = spack_cxx
             self.spec.mpifc = spack_fc

From 9cda38c03d5eb48cb644a4985442e61e5d00bc63 Mon Sep 17 00:00:00 2001
From: oracleLee <52901865+oracleLee@users.noreply.github.com>
Date: Tue, 9 Jun 2020 11:48:59 +0800
Subject: [PATCH 658/802] Update miniconda3@4.8.2 (#17003)

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py
---
 var/spack/repos/builtin/packages/miniconda3/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/miniconda3/package.py b/var/spack/repos/builtin/packages/miniconda3/package.py
index f75ce7420c7..b3bda3dfaad 100644
--- a/var/spack/repos/builtin/packages/miniconda3/package.py
+++ b/var/spack/repos/builtin/packages/miniconda3/package.py
@@ -13,6 +13,7 @@ class Miniconda3(Package):
     homepage = "https://conda.io/miniconda.html"
     url      = "https://repo.continuum.io/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh"
 
+    version('4.8.2', sha256='5bbb193fd201ebe25f4aeb3c58ba83feced6a25982ef4afa86d5506c3656c142', url='https://repo.anaconda.com/miniconda/Miniconda3-py38_4.8.2-Linux-x86_64.sh', expand=False)
     version('4.7.12.1', sha256='bfe34e1fa28d6d75a7ad05fd02fa5472275673d5f5621b77380898dee1be15d2', expand=False)
     version('4.6.14', sha256='0d6b23895a91294a4924bd685a3a1f48e35a17970a073cd2f684ffe2c31fc4be', expand=False)
     version('4.5.11', sha256='ea4594241e13a2671c5b158b3b813f0794fe58d514795fbf72a1aad24db918cf', expand=False)

From 2e20ee8ea23962d25fe2d6f3d33d2111813ccf89 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Tue, 9 Jun 2020 06:54:50 +0200
Subject: [PATCH 659/802] suite-sparse: build libraries without running demos
 (#17007)

fixes #16638
---
 var/spack/repos/builtin/packages/suite-sparse/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
index 0cbdd900b60..eef38fefae9 100644
--- a/var/spack/repos/builtin/packages/suite-sparse/package.py
+++ b/var/spack/repos/builtin/packages/suite-sparse/package.py
@@ -142,7 +142,7 @@ def install(self, spec, prefix):
         # not possible, mainly because of GraphBLAS.  Thus compile first and
         # install in a second run.
         if '@5.4.0:' in self.spec:
-            make('default', *make_args)
+            make('library', *make_args)
 
         make_args.append('INSTALL=%s' % prefix)
         make('install', *make_args)

From f70b72edc527ddf11365c220e48e893e38cb1be3 Mon Sep 17 00:00:00 2001
From: Nathan <35582439+yee29@users.noreply.github.com>
Date: Tue, 9 Jun 2020 06:01:55 -0700
Subject: [PATCH 660/802] Set the BOOST_ROOT environment variable when library
 is loaded (#16818)

* Adding BOOST_ROOT env variable

* Update var/spack/repos/builtin/packages/boost/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 var/spack/repos/builtin/packages/boost/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index bcdec30ae99..1e5bd00c2bd 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -512,3 +512,6 @@ def install(self, spec, prefix):
         # on Darwin; correct this
         if (sys.platform == 'darwin') and ('+shared' in spec):
             fix_darwin_install_name(prefix.lib)
+
+    def setup_run_environment(self, env):
+        env.set('BOOST_ROOT', self.prefix)

From 11b5fa71703c76655dcab067d94e57ac97b6551d Mon Sep 17 00:00:00 2001
From: Jen Herting <jen@herting.cc>
Date: Tue, 9 Jun 2020 11:23:29 -0400
Subject: [PATCH 661/802] [util-linux] disabling systemd (#17008)

If systemd support is enabled, install will attempt to modify files in
system systemd directories.
---
 var/spack/repos/builtin/packages/util-linux/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/util-linux/package.py b/var/spack/repos/builtin/packages/util-linux/package.py
index ccd6bba9aa3..93bdd8c3c6a 100644
--- a/var/spack/repos/builtin/packages/util-linux/package.py
+++ b/var/spack/repos/builtin/packages/util-linux/package.py
@@ -44,6 +44,7 @@ def configure_args(self):
         config_args = [
             '--disable-use-tty-group',
             '--disable-makeinstall-chown',
+            '--without-systemd'
         ]
         config_args.extend(self.enable_or_disable('libuuid'))
         return config_args

From 2421d903b034c92660fbe999b7d486e6f21a7417 Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Tue, 9 Jun 2020 08:52:46 -0700
Subject: [PATCH 662/802] SpecList: fix recursion for references (#16897)

* SpecList: fix and refactor variable expansion
---
 lib/spack/spack/spec_list.py      | 71 ++++++++++++++++++-------------
 lib/spack/spack/test/spec_list.py | 17 ++++++++
 2 files changed, 59 insertions(+), 29 deletions(-)

diff --git a/lib/spack/spack/spec_list.py b/lib/spack/spack/spec_list.py
index 4468df7c35d..bc473f530cc 100644
--- a/lib/spack/spack/spec_list.py
+++ b/lib/spack/spack/spec_list.py
@@ -121,38 +121,42 @@ def update_reference(self, reference):
         self._constraints = None
         self._specs = None
 
+    def _parse_reference(self, name):
+        sigil = ''
+        name = name[1:]
+
+        # Parse specs as constraints
+        if name.startswith('^') or name.startswith('%'):
+            sigil = name[0]
+            name = name[1:]
+
+        # Make sure the reference is valid
+        if name not in self._reference:
+            msg = 'SpecList %s refers to ' % self.name
+            msg += 'named list %s ' % name
+            msg += 'which does not appear in its reference dict'
+            raise UndefinedReferenceError(msg)
+
+        return (name, sigil)
+
     def _expand_references(self, yaml):
         if isinstance(yaml, list):
-            for idx, item in enumerate(yaml):
-                if isinstance(item, string_types) and item.startswith('$'):
-                    # Reference type can add a constraint to items
-                    if item[1] in ('^', '%'):
-                        name = item[2:]
-                        sigil = item[1]
-                    else:
-                        name = item[1:]
-                        sigil = ''
-                    if name in self._reference:
-                        ret = [self._expand_references(i) for i in yaml[:idx]]
-                        ret += self._reference[name].specs_as_yaml_list
-                        ret += self._expand_references(yaml[idx + 1:])
+            ret = []
 
-                        # Add the sigil if we're mapping a sigil to a ref
-                        def sigilify(arg):
-                            if isinstance(arg, dict):
-                                if sigil:
-                                    arg['sigil'] = sigil
-                                return arg
-                            else:
-                                return sigil + arg
-                        return list(map(sigilify, ret))
-                    else:
-                        msg = 'SpecList %s refers to ' % self.name
-                        msg += 'named list %s ' % name
-                        msg += 'which does not appear in its reference dict'
-                        raise UndefinedReferenceError(msg)
-            # No references in this
-            return [self._expand_references(item) for item in yaml]
+            for item in yaml:
+                # if it's a reference, expand it
+                if isinstance(item, string_types) and item.startswith('$'):
+                    # replace the reference and apply the sigil if needed
+                    name, sigil = self._parse_reference(item)
+                    referent = [
+                        _sigilify(item, sigil)
+                        for item in self._reference[name].specs_as_yaml_list
+                    ]
+                    ret.extend(referent)
+                else:
+                    # else just recurse
+                    ret.append(self._expand_references(item))
+            return ret
         elif isinstance(yaml, dict):
             # There can't be expansions in dicts
             return dict((name, self._expand_references(val))
@@ -216,6 +220,15 @@ def _expand_matrix_constraints(object, specify=True):
     return results
 
 
+def _sigilify(item, sigil):
+    if isinstance(item, dict):
+        if sigil:
+            item['sigil'] = sigil
+        return item
+    else:
+        return sigil + item
+
+
 class SpecListError(SpackError):
     """Error class for all errors related to SpecList objects."""
 
diff --git a/lib/spack/spack/test/spec_list.py b/lib/spack/spack/test/spec_list.py
index ff45096c3ed..27567b4080e 100644
--- a/lib/spack/spack/test/spec_list.py
+++ b/lib/spack/spack/test/spec_list.py
@@ -2,6 +2,7 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
+import pytest
 import itertools
 from spack.spec_list import SpecList
 from spack.spec import Spec
@@ -157,6 +158,22 @@ def test_spec_list_nested_matrices(self):
         expected = [Spec(' '.join(combo)) for combo in expected_components]
         assert set(speclist.specs) == set(expected)
 
+    @pytest.mark.regression('16897')
+    def test_spec_list_recursion_specs_as_constraints(self):
+        input = ['mpileaks', '$mpis',
+                 {'matrix': [['hypre'], ['$%gccs', '$%clangs']]},
+                 'libelf']
+
+        reference = {'gccs': SpecList('gccs', ['gcc@4.5.0']),
+                     'clangs': SpecList('clangs', ['clang@3.3']),
+                     'mpis': SpecList('mpis', ['zmpi@1.0', 'mpich@3.0'])}
+
+        speclist = SpecList('specs', input, reference)
+
+        assert speclist.specs_as_yaml_list == self.default_expansion
+        assert speclist.specs_as_constraints == self.default_constraints
+        assert speclist.specs == self.default_specs
+
     def test_spec_list_matrix_exclude(self, mock_packages):
         # Test on non-boolean variants for regression for #16841
         matrix = [{'matrix': [['multivalue-variant'], ['foo=bar', 'foo=baz']],

From 25a837bf796eb94d78740e21147d8cfd9d942241 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Tue, 9 Jun 2020 20:00:23 +0200
Subject: [PATCH 663/802] Testing: create mock executable fixture (#16999)

---
 lib/spack/spack/test/conftest.py | 17 +++++++++++++++++
 lib/spack/spack/test/relocate.py | 11 ++---------
 2 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py
index ae8fa80ab76..bac5bcebf60 100644
--- a/lib/spack/spack/test/conftest.py
+++ b/lib/spack/spack/test/conftest.py
@@ -1099,3 +1099,20 @@ def clear_directive_functions():
     # proceeding with subsequent tests that may depend on the original
     # functions.
     spack.directives.DirectiveMeta._directives_to_be_executed = []
+
+
+@pytest.fixture
+def mock_executable(tmpdir):
+    """Factory to create a mock executable in a temporary directory that
+    output a custom string when run.
+    """
+    import jinja2
+
+    def _factory(name, output, subdir=('bin',)):
+        f = tmpdir.mkdir(*subdir).join(name)
+        t = jinja2.Template('#!/bin/bash\n{{ output }}\n')
+        f.write(t.render(output=output))
+        f.chmod(0o755)
+        return str(f)
+
+    return _factory
diff --git a/lib/spack/spack/test/relocate.py b/lib/spack/spack/test/relocate.py
index 6669b25eb41..551f1596f7b 100644
--- a/lib/spack/spack/test/relocate.py
+++ b/lib/spack/spack/test/relocate.py
@@ -107,16 +107,9 @@ def do_install_mock(self, **kwargs):
 
 
 @pytest.fixture()
-def mock_patchelf(tmpdir):
-    import jinja2
-
+def mock_patchelf(tmpdir, mock_executable):
     def _factory(output):
-        f = tmpdir.mkdir('bin').join('patchelf')
-        t = jinja2.Template('#!/bin/bash\n{{ output }}\n')
-        f.write(t.render(output=output))
-        f.chmod(0o755)
-        return str(f)
-
+        return mock_executable('patchelf', output=output)
     return _factory
 
 

From 07e97e3ebc5a0b1594f7bc815aca441f99de5141 Mon Sep 17 00:00:00 2001
From: Rob Latham <robl@mcs.anl.gov>
Date: Tue, 9 Jun 2020 13:53:20 -0500
Subject: [PATCH 664/802] jansson: add versions 2.10 to 2.13.1 (#17011)

---
 var/spack/repos/builtin/packages/jansson/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/repos/builtin/packages/jansson/package.py b/var/spack/repos/builtin/packages/jansson/package.py
index 6647b3d4e80..43982b42ccb 100644
--- a/var/spack/repos/builtin/packages/jansson/package.py
+++ b/var/spack/repos/builtin/packages/jansson/package.py
@@ -14,6 +14,11 @@ class Jansson(CMakePackage):
     url      = "https://github.com/akheron/jansson/archive/v2.9.tar.gz"
     maintainers = ['ax3l']
 
+    version('2.13.1', sha256='f22901582138e3203959c9257cf83eba9929ac41d7be4a42557213a22ebcc7a0')
+    version('2.13',   sha256='beb47da10cb27668de3012cc193a1873a898ad5710a1126be9e6d3357beb5b30')
+    version('2.12',   sha256='76260d30e9bbd0ef392798525e8cd7fe59a6450c54ca6135672e3cd6a1642941')
+    version('2.11',   sha256='6ff0eab3a8baf64d21cae25f88a0311fb282006eb992080722a9099469c32881')
+    version('2.10',   sha256='b0a899f90ade82e42da0ecabc8af1fa296d69691e7c0786c4994fb79d4833ebb')
     version('2.9', sha256='952fa714b399e71c1c3aa020e32e899f290c82126ca4d0d14cff5d10af457656')
 
     variant('shared', default=True,

From a52945613dfc5ba646ca74ae7187cb82b3e6931b Mon Sep 17 00:00:00 2001
From: victorusu <victorusu@users.noreply.github.com>
Date: Tue, 9 Jun 2020 20:54:59 +0200
Subject: [PATCH 665/802] New package:  py-pygelf (#17004)

---
 .../builtin/packages/py-pygelf/package.py     | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-pygelf/package.py

diff --git a/var/spack/repos/builtin/packages/py-pygelf/package.py b/var/spack/repos/builtin/packages/py-pygelf/package.py
new file mode 100644
index 00000000000..c2b20b57037
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pygelf/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPygelf(PythonPackage):
+    """Python logging handlers with GELF (Graylog Extended Log Format)
+    support."""
+
+    homepage = "https://github.com/keeprocking/pygelf"
+    url      = "https://pypi.io/packages/source/p/pygelf/pygelf-0.3.6.tar.gz"
+
+    # notify when the package is updated.
+    maintainers = ['victorusu', 'vkarak']
+
+    version('0.3.6', sha256='3e5bc59e3b5a754556a76ff2c69fcf2003218ad7b5ff8417482fa1f6a7eba5f9')
+
+    depends_on('python', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')

From 8b1ffebe002c4c997d672382f9d045a590618649 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 10 Jun 2020 06:17:31 +0800
Subject: [PATCH 666/802] Add new package: py-workload-automation

---
 .../py-workload-automation/package.py         | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-workload-automation/package.py

diff --git a/var/spack/repos/builtin/packages/py-workload-automation/package.py b/var/spack/repos/builtin/packages/py-workload-automation/package.py
new file mode 100644
index 00000000000..bc65e210ffd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-workload-automation/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyWorkloadAutomation(PythonPackage):
+    """Workload Automation (WA) is a framework for executing workloads and
+    collecting measurements on Android and Linux devices."""
+
+    homepage = "https://github.com/ARM-software/workload-automation"
+    url      = "https://github.com/ARM-software/workload-automation/archive/v3.2.tar.gz"
+
+    version('3.2',   sha256='a3db9df6a9e0394231560ebe6ba491a513f6309e096eaed3db6f4cb924c393ea')
+    version('3.1.4', sha256='217fc33a3739d011a086315ef86b90cf332c16d1b03c9dcd60d58c9fd1f37f98')
+    version('3.1.3', sha256='152470808cf8dad8a833fd7b2cb7d77cf8aa5d1af404e37fa0a4ff3b07b925b2')
+    version('3.1.2', sha256='8226a6abc5cbd96e3f1fd6df02891237a06cdddb8b1cc8916f255fcde20d3069')
+    version('3.1.1', sha256='32a19be92e43439637c68d9146f21bb7a0ae7b8652c11dfc4b4bd66d59329ad4')
+    version('3.1.0', sha256='f00aeef7a1412144c4139c23b4c48583880ba2147207646d96359f1d295d6ac3')
+    version('3.0.0', sha256='8564b0c67541e3a212363403ee090dfff5e4df85770959a133c0979445b51c3c')
+    version('2.7.0', sha256='e9005b9db18e205bf6c4b3e09b15a118abeede73700897427565340dcd589fbb')
+    version('2.6.0', sha256='b94341fb067592cebe0db69fcf7c00c82f96b4eb7c7210e34b38473869824cce')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-python-dateutil', type=('build', 'run'))
+    depends_on('py-pexpect@3.3:', type=('build', 'run'))
+    depends_on('py-pyserial', type=('build', 'run'))
+    depends_on('py-colorama', type=('build', 'run'))
+    depends_on('py-pyyaml@5.1:', type=('build', 'run'))
+    depends_on('py-requests', type=('build', 'run'))
+    depends_on('py-wrapt', type=('build', 'run'))
+    depends_on('py-pandas@0.23.0:', type=('build', 'run'), when='^python@3.5.3:')
+    depends_on('py-pandas@0.23.0:0.24.2', type=('build', 'run'), when='^python@:3.5.2')
+    depends_on('py-future', type=('build', 'run'))
+    depends_on('py-louie', type=('build', 'run'))
+    depends_on('py-devlib', type=('build', 'run'))

From 806a19c6b63acccb7c0e58a27f46ccf4c7db3f2c Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 9 Jun 2020 13:52:01 -0700
Subject: [PATCH 667/802] libffi: add patch for building with clang on power
 (#16855)

* libffi: add patch for building with '%clang target=power*'

* libffi: fix version of clang/power patch
---
 .../packages/libffi/clang-powerpc-3.2.1.patch | 24 +++++++++++++++++++
 .../repos/builtin/packages/libffi/package.py  |  2 ++
 2 files changed, 26 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/libffi/clang-powerpc-3.2.1.patch

diff --git a/var/spack/repos/builtin/packages/libffi/clang-powerpc-3.2.1.patch b/var/spack/repos/builtin/packages/libffi/clang-powerpc-3.2.1.patch
new file mode 100644
index 00000000000..b6749cc26f8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libffi/clang-powerpc-3.2.1.patch
@@ -0,0 +1,24 @@
+diff --git a/src/powerpc/linux64.S b/src/powerpc/linux64.S
+index d2acb70..921e9cb 100644
+--- a/src/powerpc/linux64.S
++++ b/src/powerpc/linux64.S
+@@ -83,6 +83,7 @@ ffi_call_LINUX64:
+ 	mr	%r4, %r1
+ # if defined _CALL_LINUX || _CALL_ELF == 2
+ 	bl	ffi_prep_args64
++	nop
+ # else
+ 	bl	.ffi_prep_args64
+ # endif
+diff --git a/src/powerpc/linux64_closure.S b/src/powerpc/linux64_closure.S
+index 97421a4..3c62d5f 100644
+--- a/src/powerpc/linux64_closure.S
++++ b/src/powerpc/linux64_closure.S
+@@ -152,6 +152,7 @@ ffi_closure_LINUX64:
+ 	# make the call
+ # if defined _CALL_LINUX || _CALL_ELF == 2
+ 	bl ffi_closure_helper_LINUX64
++	nop
+ # else
+ 	bl .ffi_closure_helper_LINUX64
+ # endif
diff --git a/var/spack/repos/builtin/packages/libffi/package.py b/var/spack/repos/builtin/packages/libffi/package.py
index d21b62b1e50..0ee50aec07c 100644
--- a/var/spack/repos/builtin/packages/libffi/package.py
+++ b/var/spack/repos/builtin/packages/libffi/package.py
@@ -17,6 +17,8 @@ class Libffi(AutotoolsPackage, SourcewarePackage):
     version('3.3',   sha256='72fba7922703ddfa7a028d513ac15a85c8d54c8d67f55fa5a4802885dc652056')
     version('3.2.1', sha256='d06ebb8e1d9a22d19e38d63fdb83954253f39bedc5d46232a05645685722ca37')
 
+    patch('clang-powerpc-3.2.1.patch', when='@3.2.1%clang platform=linux')
+
     @property
     def headers(self):
         # The headers are probably in self.prefix.lib but we search everywhere

From 872ab2110318524cbf805215e09a457a5ff4cba4 Mon Sep 17 00:00:00 2001
From: Robert Blake <blake14@llnl.gov>
Date: Tue, 9 Jun 2020 14:13:54 -0700
Subject: [PATCH 668/802] Add new package: wcs (#16958)

* Adding a package for wcs.

* Turning on sbml for wcs.

* The cpp flag needs to be available for wcs.

* Wcs needs SBML to properly define the namespace.

* Flake8 fixes.

* Fixing the help string with the description.

* Changing cpp to use the new variant syntax.

* Fixing flake8 errors.

* Forgot to delete one last fixme comment.

* Spack "develop" needs to link to repo "devel"

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Robert Blake <rob.c.blake.3@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../repos/builtin/packages/sbml/package.py    |  5 ++-
 .../repos/builtin/packages/wcs/package.py     | 33 +++++++++++++++++++
 2 files changed, 37 insertions(+), 1 deletion(-)
 create mode 100644 var/spack/repos/builtin/packages/wcs/package.py

diff --git a/var/spack/repos/builtin/packages/sbml/package.py b/var/spack/repos/builtin/packages/sbml/package.py
index 4c90d76bc2d..22c608d156e 100644
--- a/var/spack/repos/builtin/packages/sbml/package.py
+++ b/var/spack/repos/builtin/packages/sbml/package.py
@@ -59,6 +59,9 @@ def url_for_version(self, version):
             description='Build with mono support')
     depends_on('mono', when="+mono")
 
+    variant('cpp', default=False,
+            description="All c++ includes should be under a namespace")
+
     depends_on('swig@2:', type='build')
     depends_on('cmake', type='build')
     depends_on('zlib')
@@ -76,7 +79,6 @@ def cmake_args(self):
             "-DENABLE_RENDER:BOOL=ON",
             "-DWITH_BZIP2:BOOL=ON",
             "-DWITH_CHECK:BOOL=OFF",
-            "-DWITH_CPP_NAMESPACE:BOOL=OFF",
             "-DWITH_DOXYGEN:BOOL=OFF",
             "-DWITH_EXAMPLES:BOOL=OFF",
             "-DWITH_EXPAT:BOOL=OFF",
@@ -86,6 +88,7 @@ def cmake_args(self):
             "-DWITH_XERCES:BOOL=OFF",
             "-DWITH_ZLIB:BOOL=ON",
         ]
+        args.append(self.define_from_variant('WITH_CPP_NAMESPACE', 'cpp'))
         if '+python' in spec:
             args.extend([
                 "-DWITH_PYTHON:BOOL=ON",
diff --git a/var/spack/repos/builtin/packages/wcs/package.py b/var/spack/repos/builtin/packages/wcs/package.py
new file mode 100644
index 00000000000..44a39cccbe0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wcs/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Wcs(CMakePackage):
+    """Simulates whole cell models using discrete event simulation."""
+
+    homepage = "https://github.com/LLNL/wcs.git"
+    git      = "https://github.com/LLNL/wcs.git"
+    maintainers = ['rblake-llnl']
+
+    version('master', branch='master')
+    version('develop', branch='devel')
+
+    depends_on('boost+graph+filesystem+regex+system')
+    depends_on('sbml@5.18.0:+cpp')
+    depends_on('cmake@3.12:', type='build')
+    depends_on('cereal', type='build')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            "-DBOOST_ROOT:PATH=" + spec['boost'].prefix,
+            "-DCEREAL_ROOT:PATH=" + spec['cereal'].prefix,
+            "-DSBML_ROOT:PATH=" + spec['sbml'].prefix,
+            "-DWCS_WITH_SBML:BOOL=ON",
+            "-DWCS_WITH_EXPRTK:BOOL=ON",
+        ]
+        return args

From 31791f269b16e2f4c2b6e442fc4890dab1998279 Mon Sep 17 00:00:00 2001
From: Rob Latham <robl@mcs.anl.gov>
Date: Tue, 9 Jun 2020 16:16:38 -0500
Subject: [PATCH 669/802] teach spack how to build pmix from git (#16973)

* teach spack how to build pmix from git

* add variant for new REST feature

* reorder package to match guidance
---
 .../repos/builtin/packages/pmix/package.py    | 32 +++++++++++++++++--
 1 file changed, 29 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/pmix/package.py b/var/spack/repos/builtin/packages/pmix/package.py
index 2cb5126b535..b752aca0bf7 100644
--- a/var/spack/repos/builtin/packages/pmix/package.py
+++ b/var/spack/repos/builtin/packages/pmix/package.py
@@ -6,6 +6,7 @@
 
 from spack import *
 import spack.architecture
+import os
 
 
 class Pmix(AutotoolsPackage):
@@ -32,8 +33,10 @@ class Pmix(AutotoolsPackage):
 
     homepage = "https://pmix.org"
     url      = "https://github.com/pmix/pmix/releases/download/v3.1.3/pmix-3.1.3.tar.bz2"
+    git      = "https://github.com/openpmix/openpmix.git"
     maintainers = ['rhc54']
 
+    version('master', branch='master')
     version('3.1.3',    sha256='118acb9c4e10c4e481406dcffdfa762f314af50db75336bf8460e53b56dc439d')
     version('3.1.2',    sha256='28aed0392d4ca2cdfbdd721e6210c94dadc9830677fea37a0abe9d592c00f9c3')
     version('3.0.2',    sha256='df68f35a3ed9517eeade80b13855cebad8fde2772b36a3f6be87559b6d430670')
@@ -47,13 +50,36 @@ class Pmix(AutotoolsPackage):
     version('2.0.1',    sha256='ba6e0f32936b1859741adb221e18b2c1ee7dc53a6b374b9f7831adf1692b15fd')
     version('1.2.5',    sha256='a2b02d489ee730c06ee40e7f9ffcebb6c35bcb4f95153fab7c4276a3add6ae31')
 
-    depends_on('libevent@2.0.20:2.0.22,2.1.8')
-    depends_on('hwloc@1.11.0:1.11.99,2.0.1:', when='@3.0.0:')
-
     variant('pmi_backwards_compatibility',
             default=True,
             description="Toggle pmi backwards compatibility")
 
+    variant('restful',
+            default=False,
+            description="allow a PMIx server to request services from "
+            "a system-level REST server")
+
+    depends_on('libevent@2.0.20:2.0.22,2.1.8')
+    depends_on('hwloc@1.11.0:1.11.99,2.0.1:', when='@3.0.0:')
+    depends_on("m4", type=("build"), when="@master")
+    depends_on("autoconf", type=("build"), when="@master")
+    depends_on("automake", type=("build"), when="@master")
+    depends_on("libtool", type=("build"), when="@master")
+    depends_on("perl", type=("build"), when="@master")
+    depends_on('curl', when="+restful")
+    depends_on('jansson@2.11:', when="+restful")
+
+    conflicts('@:3.9.9', when='+restful')
+
+    def autoreconf(self, spec, prefix):
+        """Only needed when building from git checkout"""
+        # If configure exists nothing needs to be done
+        if os.path.exists(self.configure_abs_path):
+            return
+        # Else bootstrap with autotools
+        perl = which('perl')
+        perl('./autogen.pl')
+
     def configure_args(self):
 
         spec = self.spec

From 9a18fbbc3ede80d52bd70a984961728e0909cd86 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 9 Jun 2020 16:57:27 -0700
Subject: [PATCH 670/802] lib/spack : expand spack config vars in 'include'
 section (#16210)

* Changed the 'include' config section to use 'substitute_path_variables' to allow for Spack config variables to be used (e.g. $spack).

* Fixed a bug with 'include' section path expansion and added a test case for 'include' paths with embedded config variables.
---
 lib/spack/spack/environment.py  |  5 +++--
 lib/spack/spack/test/cmd/env.py | 30 ++++++++++++++++++++++++++++++
 2 files changed, 33 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index 00af2df2d93..1b9df358f47 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -37,6 +37,7 @@
 from spack.spec_list import SpecList, InvalidSpecConstraintError
 from spack.variant import UnknownVariantError
 import spack.util.lock as lk
+from spack.util.path import substitute_path_variables
 
 #: environment variable used to indicate the active environment
 spack_env_var = 'SPACK_ENV'
@@ -780,8 +781,8 @@ def included_config_scopes(self):
         # highest-precedence scopes are last.
         includes = config_dict(self.yaml).get('include', [])
         for i, config_path in enumerate(reversed(includes)):
-            # allow paths to contain environment variables
-            config_path = config_path.format(**os.environ)
+            # allow paths to contain spack config/environment variables, etc.
+            config_path = substitute_path_variables(config_path)
 
             # treat relative paths as relative to the environment
             if not os.path.isabs(config_path):
diff --git a/lib/spack/spack/test/cmd/env.py b/lib/spack/spack/test/cmd/env.py
index f8ed37e17c7..57037387318 100644
--- a/lib/spack/spack/test/cmd/env.py
+++ b/lib/spack/spack/test/cmd/env.py
@@ -22,6 +22,7 @@
 from spack.spec_list import SpecListError
 from spack.util.mock_package import MockPackageMultiRepo
 import spack.util.spack_json as sjson
+from spack.util.path import substitute_path_variables
 
 
 # everything here uses the mock_env_path
@@ -539,6 +540,35 @@ def test_env_with_included_config_scope():
                for x in e._get_environment_specs())
 
 
+def test_env_with_included_config_var_path():
+    config_var_path = os.path.join('$tempdir', 'included-config.yaml')
+    test_config = """\
+env:
+  include:
+  - %s
+  specs:
+  - mpileaks
+""" % config_var_path
+
+    _env_create('test', StringIO(test_config))
+    e = ev.read('test')
+
+    config_real_path = substitute_path_variables(config_var_path)
+    fs.mkdirp(os.path.dirname(config_real_path))
+    with open(config_real_path, 'w') as f:
+        f.write("""\
+packages:
+  mpileaks:
+    version: [2.2]
+""")
+
+    with e:
+        e.concretize()
+
+    assert any(x.satisfies('mpileaks@2.2')
+               for x in e._get_environment_specs())
+
+
 def test_env_config_precedence():
     test_config = """\
 env:

From 0de12be52a0a3672cc2e3268e3048c65865ba950 Mon Sep 17 00:00:00 2001
From: asmaahassan90 <31959389+asmaahassan90@users.noreply.github.com>
Date: Wed, 10 Jun 2020 01:58:34 +0200
Subject: [PATCH 671/802] add gaussian-view (#16890)

---
 .../builtin/packages/gaussian-view/package.py | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/gaussian-view/package.py

diff --git a/var/spack/repos/builtin/packages/gaussian-view/package.py b/var/spack/repos/builtin/packages/gaussian-view/package.py
new file mode 100644
index 00000000000..4de3c9e02be
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gaussian-view/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+# ----------------------------------------------------------------------------
+
+from spack import *
+import os
+
+
+class GaussianView(Package):
+    """GaussView 6 is the latest iteration of a graphical interface used with
+    Gaussian. It aids in the creation of Gaussian input files, enables the
+    user to run Gaussian calculations from a graphical interface without the
+    need for using a command line instruction, and helps in the interpretation
+    of Gaussian output"""
+
+    homepage = "https://gaussian.com/gaussview6/"
+    manual_download = True
+
+    version('6016',
+            '5dd6a8df8c81763e43a308b3a18d2d3b825d3597e9628dcf43e563d1867b9638',
+            extension='tbz')
+
+    depends_on('gaussian@16-B.01', type='run')
+
+    def url_for_version(self, version):
+        return "file://{0}/gv-{1}-Linux-x86_64.tbz".format(os.getcwd(),
+                                                           version)
+
+    def install(self, spec, prefix):
+        install_tree(os.getcwd(), self.prefix)
+
+    def setup_run_environment(self, env):
+        env.set('GV_DIR', self.prefix)
+        env.prepend_path('PATH', self.prefix)
+        env.set('GV_LIB_PATH', self.prefix.lib)
+        env.prepend_path('GV_LIB_PATH', self.prefix.lib.MesaGL)
+        env.prepend_path('LD_LIBRARY_PATH', self.prefix.lib.MesaGL)
+        env.set('ALLOWINDIRECT', '1')
+        env.prepend_path('QT_PLUGIN_PATH', self.prefix.plugins)

From f6020d259aacfe1f7168d61f96f3f7fbb8fbe7d5 Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Wed, 10 Jun 2020 21:53:09 +0900
Subject: [PATCH 672/802] adios2: fix to build on Fujitsu MPI and Fujitsu
 compiler (#17034)

---
 .../repos/builtin/packages/adios2/package.py     | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/var/spack/repos/builtin/packages/adios2/package.py b/var/spack/repos/builtin/packages/adios2/package.py
index 59e442a27d3..8e2d0d00e30 100644
--- a/var/spack/repos/builtin/packages/adios2/package.py
+++ b/var/spack/repos/builtin/packages/adios2/package.py
@@ -119,10 +119,20 @@ class Adios2(CMakePackage):
     # See https://github.com/ornladios/ADIOS2/pull/1899
     patch('2.5-fix-clear_cache.patch', when='@2.5.0')
 
+    @when('%fj')
+    def patch(self):
+        """ add fujitsu mpi commands #16864 """
+        f = join_path('cmake', 'upstream', 'FindMPI.cmake')
+        filter_file('mpcc_r)', 'mpcc_r mpifcc)', f, string=True)
+        filter_file('mpc++_r)', 'mpcc_r mpiFCC)', f, string=True)
+        filter_file('mpf77_r', 'mpf77_r mpifrt', f, string=True)
+
     def setup_build_environment(self, env):
         # https://github.com/ornladios/ADIOS2/issues/2228
         if self.spec.satisfies('%gcc@10: +fortran'):
             env.set('FFLAGS', '-fallow-argument-mismatch')
+        elif self.spec.satisfies('%fj +fortran'):
+            env.set('FFLAGS', '-Ccpp')
 
     def cmake_args(self):
         spec = self.spec
@@ -185,6 +195,12 @@ def cmake_args(self):
             args.append('-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL={0}'.format(
                 'ON' if '+pic' in spec else 'OFF'))
 
+        if spec.satisfies('%fj'):
+            args.extend([
+                '-DCMAKE_Fortran_SUBMODULE_EXT=.smod',
+                '-DCMAKE_Fortran_SUBMODULE_SEP=.'
+            ])
+
         if spec.satisfies('+python') or self.run_tests:
             args.append('-DPYTHON_EXECUTABLE:FILEPATH=%s'
                         % spec['python'].command.path)

From 2827dca905bd2ae51a0b10ccf634199648f24e80 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Wed, 10 Jun 2020 07:19:41 -0700
Subject: [PATCH 673/802] ADIOS 2.6.0: New Options (#17025)

Control new options/dependencies in ADIOS2 to avoid pick-up of system
packages.
---
 var/spack/repos/builtin/packages/adios2/package.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/adios2/package.py b/var/spack/repos/builtin/packages/adios2/package.py
index 8e2d0d00e30..13f502e050d 100644
--- a/var/spack/repos/builtin/packages/adios2/package.py
+++ b/var/spack/repos/builtin/packages/adios2/package.py
@@ -77,7 +77,7 @@ class Adios2(CMakePackage):
     # DataMan needs dlopen
     conflicts('+dataman', when='~shared')
 
-    depends_on('cmake@3.6.0:', type='build')
+    depends_on('cmake@3.12.0:', type='build')
     depends_on('pkgconfig', type='build')
 
     depends_on('libffi', when='+sst')            # optional in DILL
@@ -179,6 +179,9 @@ def cmake_args(self):
             args.append('-DADIOS2_USE_DataSpaces={0}'.format(
                 'ON' if '+dataspaces' in spec else 'OFF'))
 
+        if spec.version >= Version('2.6.0'):
+            args.append('-DADIOS2_USE_IME=OFF')
+
         if '+sst' in spec:
             args.extend([
                 # Broken dependency package

From 478a8aff0e9a6b19baac2c291a3f51472381197d Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Wed, 10 Jun 2020 17:10:57 +0200
Subject: [PATCH 674/802] Move to temporary directory before running dev-build
 test (#17028)

Without this the test would leave spurious "spack-build-*.txt"
files in the current working directory.
---
 lib/spack/spack/test/cmd/dev_build.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/lib/spack/spack/test/cmd/dev_build.py b/lib/spack/spack/test/cmd/dev_build.py
index 271faa845d7..94c7690de6d 100644
--- a/lib/spack/spack/test/cmd/dev_build.py
+++ b/lib/spack/spack/test/cmd/dev_build.py
@@ -110,9 +110,10 @@ def module(*args):
         pass
     monkeypatch.setattr(spack.build_environment, 'module', module)
 
-    output = dev_build('-b', 'edit', '--drop-in', 'sh',
-                       'dev-build-test-install@0.0.0')
-    assert "lib/spack/env" in output
+    with tmpdir.as_cwd():
+        output = dev_build('-b', 'edit', '--drop-in', 'sh',
+                           'dev-build-test-install@0.0.0')
+        assert "lib/spack/env" in output
 
 
 def test_dev_build_fails_already_installed(tmpdir, mock_packages,

From 19dba603ad0e98700c681e675972fbaa7c9aed6c Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Wed, 10 Jun 2020 20:57:08 -0500
Subject: [PATCH 675/802] py-paramz: new package at 0.9.5 (#17026)

---
 .../builtin/packages/py-paramz/package.py     | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-paramz/package.py

diff --git a/var/spack/repos/builtin/packages/py-paramz/package.py b/var/spack/repos/builtin/packages/py-paramz/package.py
new file mode 100644
index 00000000000..77c5996d12c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-paramz/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyParamz(PythonPackage):
+    """The Parameterization Framework."""
+
+    homepage = "https://github.com/sods/paramz"
+    url      = "https://pypi.io/packages/source/p/paramz/paramz-0.9.5.tar.gz"
+
+    version('0.9.5', sha256='0917211c0f083f344e7f1bc997e0d713dbc147b6380bc19f606119394f820b9a')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy@1.7:', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-decorator@4.0.10:', type=('build', 'run'))

From 9820a23abd06efd003464f65c84e726479a97a2b Mon Sep 17 00:00:00 2001
From: codeandkey <jtst@iastate.edu>
Date: Tue, 9 Jun 2020 13:55:55 -0500
Subject: [PATCH 676/802] py-gpy: new package at 1.9.9

---
 .../repos/builtin/packages/py-gpy/package.py  | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-gpy/package.py

diff --git a/var/spack/repos/builtin/packages/py-gpy/package.py b/var/spack/repos/builtin/packages/py-gpy/package.py
new file mode 100644
index 00000000000..59bebda5d0c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-gpy/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyGpy(PythonPackage):
+    """The Gaussian Process Toolbox."""
+
+    homepage = "http://sheffieldml.github.com/GPy/"
+    url      = "https://pypi.io/packages/source/g/gpy/GPy-1.9.9.tar.gz"
+
+    version('1.9.9', sha256='04faf0c24eacc4dea60727c50a48a07ddf9b5751a3b73c382105e2a31657c7ed')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy@1.7:', type=('build', 'run'))
+    depends_on('py-scipy@1.3.0:', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-paramz@0.9.0:', type=('build', 'run'))
+    depends_on('py-cython@0.29:', type=('build', 'run'))

From b50b930d6a5af82e04dc61788a919e2e2d0b4561 Mon Sep 17 00:00:00 2001
From: Sinan <sbulutw@gmail.com>
Date: Thu, 11 Jun 2020 08:26:43 -0700
Subject: [PATCH 677/802] New package: py-uncertainties (#16997)

---
 .../packages/py-uncertainties/package.py      | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-uncertainties/package.py

diff --git a/var/spack/repos/builtin/packages/py-uncertainties/package.py b/var/spack/repos/builtin/packages/py-uncertainties/package.py
new file mode 100644
index 00000000000..67a9ee0cc59
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-uncertainties/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyUncertainties(PythonPackage):
+    """Transparent calculations with uncertainties on the quantities involved
+    (aka error propagation); fast calculation of derivatives
+    """
+
+    homepage = "https://uncertainties-python-package.readthedocs.io/en/latest/"
+    url      = "https://pypi.io/packages/source/u/uncertainties/uncertainties-3.1.4.tar.gz"
+
+    version('3.1.4', sha256='63548a94899f2a51eeb89b640f6ac311f481a8016b37dce157186e44619bc968')
+
+    variant('optional', default=False, description='Enable extra features involving numpy')
+    variant('docs',  default=False, description='Build with documentation')
+
+    depends_on('python@2.7:',   type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-future',     type=('build', 'run'))
+    depends_on('py-numpy',      type=('build', 'run'), when='+optional')
+    depends_on('py-sphinx',     type='build', when='+docs')

From bbac630aac7a06dd681eb8483a2f89f905f10ed3 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Fri, 5 Jun 2020 14:44:57 +0200
Subject: [PATCH 678/802] Reworked tests on compilers to separate version
 detection

Tests on version detection are now separate from other
tests done on compiler.
---
 lib/spack/spack/test/compilers/__init__.py    |   4 +
 lib/spack/spack/test/compilers/detection.py   | 179 ++++++++++++++++++
 .../test/{compilers.py => compilers/flags.py} | 170 -----------------
 3 files changed, 183 insertions(+), 170 deletions(-)
 create mode 100644 lib/spack/spack/test/compilers/__init__.py
 create mode 100644 lib/spack/spack/test/compilers/detection.py
 rename lib/spack/spack/test/{compilers.py => compilers/flags.py} (78%)

diff --git a/lib/spack/spack/test/compilers/__init__.py b/lib/spack/spack/test/compilers/__init__.py
new file mode 100644
index 00000000000..9f87532b851
--- /dev/null
+++ b/lib/spack/spack/test/compilers/__init__.py
@@ -0,0 +1,4 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
diff --git a/lib/spack/spack/test/compilers/detection.py b/lib/spack/spack/test/compilers/detection.py
new file mode 100644
index 00000000000..26a559443ba
--- /dev/null
+++ b/lib/spack/spack/test/compilers/detection.py
@@ -0,0 +1,179 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+import pytest
+
+import spack.compilers.arm
+import spack.compilers.cce
+import spack.compilers.clang
+import spack.compilers.fj
+import spack.compilers.gcc
+import spack.compilers.intel
+import spack.compilers.nag
+import spack.compilers.pgi
+import spack.compilers.xl
+import spack.compilers.xl_r
+
+
+@pytest.mark.parametrize('version_str,expected_version', [
+    ('Arm C/C++/Fortran Compiler version 19.0 (build number 73) (based on LLVM 7.0.2)\n' # NOQA
+     'Target: aarch64--linux-gnu\n'
+     'Thread model: posix\n'
+     'InstalledDir:\n'
+     '/opt/arm/arm-hpc-compiler-19.0_Generic-AArch64_RHEL-7_aarch64-linux/bin\n', # NOQA
+     '19.0.0.73'),
+    ('Arm C/C++/Fortran Compiler version 19.3.1 (build number 75) (based on LLVM 7.0.2)\n' # NOQA
+     'Target: aarch64--linux-gnu\n'
+     'Thread model: posix\n'
+     'InstalledDir:\n'
+     '/opt/arm/arm-hpc-compiler-19.0_Generic-AArch64_RHEL-7_aarch64-linux/bin\n', # NOQA
+     '19.3.1.75')
+])
+def test_arm_version_detection(version_str, expected_version):
+    version = spack.compilers.arm.Arm.extract_version_from_output(version_str)
+    assert version == expected_version
+
+
+@pytest.mark.parametrize('version_str,expected_version', [
+    ('Cray C : Version 8.4.6  Mon Apr 15, 2019  12:13:39\n', '8.4.6'),
+    ('Cray C++ : Version 8.4.6  Mon Apr 15, 2019  12:13:45\n', '8.4.6'),
+    ('Cray Fortran : Version 8.4.6  Mon Apr 15, 2019  12:13:55\n', '8.4.6')
+])
+def test_cce_version_detection(version_str, expected_version):
+    version = spack.compilers.cce.Cce.extract_version_from_output(version_str)
+    assert version == expected_version
+
+
+@pytest.mark.regression('10191')
+@pytest.mark.parametrize('version_str,expected_version', [
+    # macOS clang
+    ('Apple clang version 11.0.0 (clang-1100.0.33.8)\n'
+     'Target: x86_64-apple-darwin18.7.0\n'
+     'Thread model: posix\n'
+     'InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin\n',  # noqa
+     '11.0.0-apple'),
+    ('Apple LLVM version 7.0.2 (clang-700.1.81)\n'
+     'Target: x86_64-apple-darwin15.2.0\n'
+     'Thread model: posix\n', '7.0.2-apple'),
+    # Other platforms
+    ('clang version 6.0.1-svn334776-1~exp1~20181018152737.116 (branches/release_60)\n'  # noqa
+     'Target: x86_64-pc-linux-gnu\n'
+     'Thread model: posix\n'
+     'InstalledDir: /usr/bin\n', '6.0.1'),
+    ('clang version 3.1 (trunk 149096)\n'
+     'Target: x86_64-unknown-linux-gnu\n'
+     'Thread model: posix\n', '3.1'),
+    ('clang version 8.0.0-3~ubuntu18.04.1 (tags/RELEASE_800/final)\n'
+     'Target: x86_64-pc-linux-gnu\n'
+     'Thread model: posix\n'
+     'InstalledDir: /usr/bin\n', '8.0.0'),
+    ('clang version 9.0.1-+201911131414230800840845a1eea-1~exp1~20191113231141.78\n' # noqa
+     'Target: x86_64-pc-linux-gnu\n'
+     'Thread model: posix\n'
+     'InstalledDir: /usr/bin\n', '9.0.1'),
+    ('clang version 8.0.0-3 (tags/RELEASE_800/final)\n'
+     'Target: aarch64-unknown-linux-gnu\n'
+     'Thread model: posix\n'
+     'InstalledDir: /usr/bin\n', '8.0.0')
+])
+def test_clang_version_detection(version_str, expected_version):
+    version = spack.compilers.clang.Clang.extract_version_from_output(
+        version_str
+    )
+    assert version == expected_version
+
+
+@pytest.mark.parametrize('version_str,expected_version', [
+    # C compiler
+    ('fcc (FCC) 4.0.0 20190314\n'
+     'simulating gcc version 6.1\n'
+     'Copyright FUJITSU LIMITED 2019',
+     '4.0.0'),
+    # C++ compiler
+    ('FCC (FCC) 4.0.0 20190314\n'
+     'simulating gcc version 6.1\n'
+     'Copyright FUJITSU LIMITED 2019',
+     '4.0.0'),
+    # Fortran compiler
+    ('frt (FRT) 4.0.0 20190314\n'
+     'Copyright FUJITSU LIMITED 2019',
+     '4.0.0')
+])
+def test_fj_version_detection(version_str, expected_version):
+    version = spack.compilers.fj.Fj.extract_version_from_output(version_str)
+    assert version == expected_version
+
+
+@pytest.mark.parametrize('version_str,expected_version', [
+    # Output of -dumpversion changed to return only major from GCC 7
+    ('4.4.7\n', '4.4.7'),
+    ('7\n', '7')
+])
+def test_gcc_version_detection(version_str, expected_version):
+    version = spack.compilers.gcc.Gcc.extract_version_from_output(version_str)
+    assert version == expected_version
+
+
+@pytest.mark.parametrize('version_str,expected_version', [
+    ('icpc (ICC) 12.1.5 20120612\n'
+     'Copyright (C) 1985-2012 Intel Corporation.  All rights reserved.\n',
+     '12.1.5'),
+    ('ifort (IFORT) 12.1.5 20120612\n'
+     'Copyright (C) 1985-2012 Intel Corporation.  All rights reserved.\n',
+     '12.1.5')
+])
+def test_intel_version_detection(version_str, expected_version):
+    version = spack.compilers.intel.Intel.extract_version_from_output(
+        version_str
+    )
+    assert version == expected_version
+
+
+@pytest.mark.parametrize('version_str,expected_version', [
+    ('NAG Fortran Compiler Release 6.0(Hibiya) Build 1037\n'
+     'Product NPL6A60NA for x86-64 Linux\n', '6.0')
+])
+def test_nag_version_detection(version_str, expected_version):
+    version = spack.compilers.nag.Nag.extract_version_from_output(version_str)
+    assert version == expected_version
+
+
+@pytest.mark.parametrize('version_str,expected_version', [
+    # Output on x86-64
+    ('pgcc 15.10-0 64-bit target on x86-64 Linux -tp sandybridge\n'
+     'The Portland Group - PGI Compilers and Tools\n'
+     'Copyright (c) 2015, NVIDIA CORPORATION.  All rights reserved.\n',
+     '15.10'),
+    # Output on PowerPC
+    ('pgcc 17.4-0 linuxpower target on Linuxpower\n'
+     'PGI Compilers and Tools\n'
+     'Copyright (c) 2017, NVIDIA CORPORATION.  All rights reserved.\n',
+     '17.4'),
+    # Output when LLVM-enabled
+    ('pgcc-llvm 18.4-0 LLVM 64-bit target on x86-64 Linux -tp haswell\n'
+     'PGI Compilers and Tools\n'
+     'Copyright (c) 2018, NVIDIA CORPORATION.  All rights reserved.\n',
+     '18.4')
+])
+def test_pgi_version_detection(version_str, expected_version):
+    version = spack.compilers.pgi.Pgi.extract_version_from_output(version_str)
+    assert version == expected_version
+
+
+@pytest.mark.parametrize('version_str,expected_version', [
+    ('IBM XL C/C++ for Linux, V11.1 (5724-X14)\n'
+     'Version: 11.01.0000.0000\n', '11.1'),
+    ('IBM XL Fortran for Linux, V13.1 (5724-X16)\n'
+     'Version: 13.01.0000.0000\n', '13.1'),
+    ('IBM XL C/C++ for AIX, V11.1 (5724-X13)\n'
+     'Version: 11.01.0000.0009\n', '11.1'),
+    ('IBM XL C/C++ Advanced Edition for Blue Gene/P, V9.0\n'
+     'Version: 09.00.0000.0017\n', '9.0')
+])
+def test_xl_version_detection(version_str, expected_version):
+    version = spack.compilers.xl.Xl.extract_version_from_output(version_str)
+    assert version == expected_version
+
+    version = spack.compilers.xl_r.XlR.extract_version_from_output(version_str)
+    assert version == expected_version
diff --git a/lib/spack/spack/test/compilers.py b/lib/spack/spack/test/compilers/flags.py
similarity index 78%
rename from lib/spack/spack/test/compilers.py
rename to lib/spack/spack/test/compilers/flags.py
index 4598605fe48..a7d442d48a7 100644
--- a/lib/spack/spack/test/compilers.py
+++ b/lib/spack/spack/test/compilers/flags.py
@@ -17,17 +17,6 @@
 import spack.compiler
 import spack.compilers as compilers
 
-import spack.compilers.arm
-import spack.compilers.cce
-import spack.compilers.clang
-import spack.compilers.fj
-import spack.compilers.gcc
-import spack.compilers.intel
-import spack.compilers.nag
-import spack.compilers.pgi
-import spack.compilers.xl
-import spack.compilers.xl_r
-
 from spack.compiler import Compiler
 
 
@@ -582,165 +571,6 @@ def test_xl_r_flags():
                         'xl@1.0')
 
 
-@pytest.mark.parametrize('version_str,expected_version', [
-    ('Arm C/C++/Fortran Compiler version 19.0 (build number 73) (based on LLVM 7.0.2)\n' # NOQA
-     'Target: aarch64--linux-gnu\n'
-     'Thread model: posix\n'
-     'InstalledDir:\n'
-     '/opt/arm/arm-hpc-compiler-19.0_Generic-AArch64_RHEL-7_aarch64-linux/bin\n', # NOQA
-     '19.0.0.73'),
-    ('Arm C/C++/Fortran Compiler version 19.3.1 (build number 75) (based on LLVM 7.0.2)\n' # NOQA
-     'Target: aarch64--linux-gnu\n'
-     'Thread model: posix\n'
-     'InstalledDir:\n'
-     '/opt/arm/arm-hpc-compiler-19.0_Generic-AArch64_RHEL-7_aarch64-linux/bin\n', # NOQA
-     '19.3.1.75')
-])
-def test_arm_version_detection(version_str, expected_version):
-    version = spack.compilers.arm.Arm.extract_version_from_output(version_str)
-    assert version == expected_version
-
-
-@pytest.mark.parametrize('version_str,expected_version', [
-    ('Cray C : Version 8.4.6  Mon Apr 15, 2019  12:13:39\n', '8.4.6'),
-    ('Cray C++ : Version 8.4.6  Mon Apr 15, 2019  12:13:45\n', '8.4.6'),
-    ('Cray Fortran : Version 8.4.6  Mon Apr 15, 2019  12:13:55\n', '8.4.6')
-])
-def test_cce_version_detection(version_str, expected_version):
-    version = spack.compilers.cce.Cce.extract_version_from_output(version_str)
-    assert version == expected_version
-
-
-@pytest.mark.regression('10191')
-@pytest.mark.parametrize('version_str,expected_version', [
-    # macOS clang
-    ('Apple clang version 11.0.0 (clang-1100.0.33.8)\n'
-     'Target: x86_64-apple-darwin18.7.0\n'
-     'Thread model: posix\n'
-     'InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin\n',  # noqa
-     '11.0.0-apple'),
-    ('Apple LLVM version 7.0.2 (clang-700.1.81)\n'
-     'Target: x86_64-apple-darwin15.2.0\n'
-     'Thread model: posix\n', '7.0.2-apple'),
-    # Other platforms
-    ('clang version 6.0.1-svn334776-1~exp1~20181018152737.116 (branches/release_60)\n'  # noqa
-     'Target: x86_64-pc-linux-gnu\n'
-     'Thread model: posix\n'
-     'InstalledDir: /usr/bin\n', '6.0.1'),
-    ('clang version 3.1 (trunk 149096)\n'
-     'Target: x86_64-unknown-linux-gnu\n'
-     'Thread model: posix\n', '3.1'),
-    ('clang version 8.0.0-3~ubuntu18.04.1 (tags/RELEASE_800/final)\n'
-     'Target: x86_64-pc-linux-gnu\n'
-     'Thread model: posix\n'
-     'InstalledDir: /usr/bin\n', '8.0.0'),
-    ('clang version 9.0.1-+201911131414230800840845a1eea-1~exp1~20191113231141.78\n' # noqa
-     'Target: x86_64-pc-linux-gnu\n'
-     'Thread model: posix\n'
-     'InstalledDir: /usr/bin\n', '9.0.1'),
-    ('clang version 8.0.0-3 (tags/RELEASE_800/final)\n'
-     'Target: aarch64-unknown-linux-gnu\n'
-     'Thread model: posix\n'
-     'InstalledDir: /usr/bin\n', '8.0.0')
-])
-def test_clang_version_detection(version_str, expected_version):
-    version = compilers.clang.Clang.extract_version_from_output(version_str)
-    assert version == expected_version
-
-
-@pytest.mark.parametrize('version_str,expected_version', [
-    # C compiler
-    ('fcc (FCC) 4.0.0 20190314\n'
-     'simulating gcc version 6.1\n'
-     'Copyright FUJITSU LIMITED 2019',
-     '4.0.0'),
-    # C++ compiler
-    ('FCC (FCC) 4.0.0 20190314\n'
-     'simulating gcc version 6.1\n'
-     'Copyright FUJITSU LIMITED 2019',
-     '4.0.0'),
-    # Fortran compiler
-    ('frt (FRT) 4.0.0 20190314\n'
-     'Copyright FUJITSU LIMITED 2019',
-     '4.0.0')
-])
-def test_fj_version_detection(version_str, expected_version):
-    version = spack.compilers.fj.Fj.extract_version_from_output(version_str)
-    assert version == expected_version
-
-
-@pytest.mark.parametrize('version_str,expected_version', [
-    # Output of -dumpversion changed to return only major from GCC 7
-    ('4.4.7\n', '4.4.7'),
-    ('7\n', '7')
-])
-def test_gcc_version_detection(version_str, expected_version):
-    version = spack.compilers.gcc.Gcc.extract_version_from_output(version_str)
-    assert version == expected_version
-
-
-@pytest.mark.parametrize('version_str,expected_version', [
-    ('icpc (ICC) 12.1.5 20120612\n'
-     'Copyright (C) 1985-2012 Intel Corporation.  All rights reserved.\n',
-     '12.1.5'),
-    ('ifort (IFORT) 12.1.5 20120612\n'
-     'Copyright (C) 1985-2012 Intel Corporation.  All rights reserved.\n',
-     '12.1.5')
-])
-def test_intel_version_detection(version_str, expected_version):
-    version = compilers.intel.Intel.extract_version_from_output(version_str)
-    assert version == expected_version
-
-
-@pytest.mark.parametrize('version_str,expected_version', [
-    ('NAG Fortran Compiler Release 6.0(Hibiya) Build 1037\n'
-     'Product NPL6A60NA for x86-64 Linux\n', '6.0')
-])
-def test_nag_version_detection(version_str, expected_version):
-    version = spack.compilers.nag.Nag.extract_version_from_output(version_str)
-    assert version == expected_version
-
-
-@pytest.mark.parametrize('version_str,expected_version', [
-    # Output on x86-64
-    ('pgcc 15.10-0 64-bit target on x86-64 Linux -tp sandybridge\n'
-     'The Portland Group - PGI Compilers and Tools\n'
-     'Copyright (c) 2015, NVIDIA CORPORATION.  All rights reserved.\n',
-     '15.10'),
-    # Output on PowerPC
-    ('pgcc 17.4-0 linuxpower target on Linuxpower\n'
-     'PGI Compilers and Tools\n'
-     'Copyright (c) 2017, NVIDIA CORPORATION.  All rights reserved.\n',
-     '17.4'),
-    # Output when LLVM-enabled
-    ('pgcc-llvm 18.4-0 LLVM 64-bit target on x86-64 Linux -tp haswell\n'
-     'PGI Compilers and Tools\n'
-     'Copyright (c) 2018, NVIDIA CORPORATION.  All rights reserved.\n',
-     '18.4')
-])
-def test_pgi_version_detection(version_str, expected_version):
-    version = spack.compilers.pgi.Pgi.extract_version_from_output(version_str)
-    assert version == expected_version
-
-
-@pytest.mark.parametrize('version_str,expected_version', [
-    ('IBM XL C/C++ for Linux, V11.1 (5724-X14)\n'
-     'Version: 11.01.0000.0000\n', '11.1'),
-    ('IBM XL Fortran for Linux, V13.1 (5724-X16)\n'
-     'Version: 13.01.0000.0000\n', '13.1'),
-    ('IBM XL C/C++ for AIX, V11.1 (5724-X13)\n'
-     'Version: 11.01.0000.0009\n', '11.1'),
-    ('IBM XL C/C++ Advanced Edition for Blue Gene/P, V9.0\n'
-     'Version: 09.00.0000.0017\n', '9.0')
-])
-def test_xl_version_detection(version_str, expected_version):
-    version = spack.compilers.xl.Xl.extract_version_from_output(version_str)
-    assert version == expected_version
-
-    version = spack.compilers.xl_r.XlR.extract_version_from_output(version_str)
-    assert version == expected_version
-
-
 @pytest.mark.parametrize('compiler_spec,expected_result', [
     ('gcc@4.7.2', False), ('clang@3.3', False), ('clang@8.0.0', True)
 ])

From 3609f36e60d78a79b774023346d751dd34e506be Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Wed, 10 Jun 2020 10:41:21 +0200
Subject: [PATCH 679/802] Renamed flags.py to basics.py

---
 lib/spack/spack/test/compilers/{flags.py => basics.py} | 2 +-
 lib/spack/spack/test/compilers/detection.py            | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)
 rename lib/spack/spack/test/compilers/{flags.py => basics.py} (99%)

diff --git a/lib/spack/spack/test/compilers/flags.py b/lib/spack/spack/test/compilers/basics.py
similarity index 99%
rename from lib/spack/spack/test/compilers/flags.py
rename to lib/spack/spack/test/compilers/basics.py
index a7d442d48a7..3e43cd4e84b 100644
--- a/lib/spack/spack/test/compilers/flags.py
+++ b/lib/spack/spack/test/compilers/basics.py
@@ -2,7 +2,7 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
+"""Test basic behavior of compilers in Spack"""
 import pytest
 
 import sys
diff --git a/lib/spack/spack/test/compilers/detection.py b/lib/spack/spack/test/compilers/detection.py
index 26a559443ba..90311ad2d32 100644
--- a/lib/spack/spack/test/compilers/detection.py
+++ b/lib/spack/spack/test/compilers/detection.py
@@ -2,6 +2,7 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
+"""Test detection of compiler version"""
 import pytest
 
 import spack.compilers.arm

From f2ae9ffdf5d8e9ff9a5d6eca56f03886d45038d1 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Fri, 12 Jun 2020 09:57:26 +0200
Subject: [PATCH 680/802] gcc: Add 7.5.0

---
 var/spack/repos/builtin/packages/gcc/package.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index 15ee2d79738..04b2181b626 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -38,6 +38,7 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
     version('8.2.0', sha256='196c3c04ba2613f893283977e6011b2345d1cd1af9abeac58e916b1aab3e0080')
     version('8.1.0', sha256='1d1866f992626e61349a1ccd0b8d5253816222cdc13390dcfaa74b093aa2b153')
 
+    version('7.5.0', sha256='b81946e7f01f90528a1f7352ab08cc602b9ccc05d4e44da4bd501c5a189ee661')
     version('7.4.0', sha256='eddde28d04f334aec1604456e536416549e9b1aa137fc69204e65eb0c009fe51')
     version('7.3.0', sha256='832ca6ae04636adbb430e865a1451adf6979ab44ca1c8374f61fba65645ce15c')
     version('7.2.0', sha256='1cf7adf8ff4b5aa49041c8734bbcf1ad18cc4c94d0029aae0f4e48841088479a')
@@ -244,11 +245,11 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
 
     # Backport libsanitizer patch for glibc >= 2.31 and 5.3.0 <= gcc <= 9.2.0
     # https://bugs.gentoo.org/708346
-    patch('glibc-2.31-libsanitizer-1.patch', when='@7.1.0:7.4.0,8.1.0:8.3.0,9.0.0:9.2.0')
+    patch('glibc-2.31-libsanitizer-1.patch', when='@7.1.0:7.5.0,8.1.0:8.3.0,9.0.0:9.2.0')
     patch('glibc-2.31-libsanitizer-1-gcc-6.patch', when='@5.3.0:5.5.0,6.1.0:6.5.0')
     patch('glibc-2.31-libsanitizer-2.patch', when='@8.1.0:8.3.0,9.0.0:9.2.0')
     patch('glibc-2.31-libsanitizer-2-gcc-6.patch', when='@5.3.0:5.5.0,6.1.0:6.5.0')
-    patch('glibc-2.31-libsanitizer-2-gcc-7.patch', when='@7.1.0:7.4.0')
+    patch('glibc-2.31-libsanitizer-2-gcc-7.patch', when='@7.1.0:7.5.0')
     # Older versions do not compile with newer versions of glibc
     # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81712
     patch('ucontext_t.patch', when='@4.9,5.1:5.4,6.1:6.4,7.1')

From e1e455ef3fc507d6937b5548a98f257f1fbe5b89 Mon Sep 17 00:00:00 2001
From: Tom Payerle <payerle@umd.edu>
Date: Fri, 12 Jun 2020 12:53:08 -0400
Subject: [PATCH 681/802] magics: add version 4.2.4 (#17054)

* Add version 4.2.4
* Update checksum for 4.1.0
* Version @4: requires python and py-jinja2 to build
---
 var/spack/repos/builtin/packages/magics/package.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/magics/package.py b/var/spack/repos/builtin/packages/magics/package.py
index 627454af755..c9c331eeb5e 100644
--- a/var/spack/repos/builtin/packages/magics/package.py
+++ b/var/spack/repos/builtin/packages/magics/package.py
@@ -14,12 +14,13 @@ class Magics(CMakePackage):
        to be as backwards-compatible as possible with the Fortran interface."""
 
     homepage = "https://software.ecmwf.int/wiki/display/MAGP/Magics"
-    url      = "https://confluence.ecmwf.int/download/attachments/3473464/Magics-4.1.0-Source.tar.gz?api=v2"
+    url      = "https://confluence.ecmwf.int/download/attachments/3473464/Magics-4.2.4-Source.tar.gz?api=v2"
     list_url = "https://software.ecmwf.int/wiki/display/MAGP/Releases"
 
     # The policy on which minor releases remain available and which get deleted
     # after a newer version becomes available is unclear.
-    version('4.1.0', sha256='e56fb1bf82d57957a61a76284ad22024f4a7c3c989f6f796e57dfd45d88400c0')
+    version('4.2.4', sha256='920c7dbb1aaabe65a31c6c18010829210f8b2f8d614b6c405dc5a4530e346f07') 
+    version('4.1.0', sha256='da626c31f53716990754dd72ab7b2f3902a8ad924b23ef3309bd14900d170541')
     version('2.34.3', sha256='38487562e83c0470f94d9c7fb9418cbadf92f1e643033237baba2abdc77e6238')
     version('2.34.1', sha256='8df27f8f262ebc32a61f8696df15a7b4a6e4203b2a8e53fe7aa13caa1c4e3fa4')
     version('2.33.0', sha256='32d3079749f89988715a8c3df01b712d9b989b7fd242828ec09563e47c5a3e82')
@@ -92,6 +93,10 @@ class Magics(CMakePackage):
     depends_on('python', when='+python', type=('link', 'run'))
     depends_on('py-numpy', when='+python', type=('build', 'run'))
     depends_on('swig', when='+python', type='build')
+    # Versions @4: supports python 2.7 and 3.x, and require python
+    # and py-jinja2 for build (even though does not build python interface)
+    depends_on('python', when='@4.0.0:', type=('build'))
+    depends_on('py-jinja2', when='@4.0.0:', type=('build'))
 
     conflicts('grib=eccodes', when='@:2.29.0',
               msg='Eccodes is supported starting version 2.29.1')

From dcd22517c7258c10cc4403378307eb38c4058d7d Mon Sep 17 00:00:00 2001
From: Brian Van Essen <vanessen1@llnl.gov>
Date: Fri, 12 Jun 2020 09:53:50 -0700
Subject: [PATCH 682/802] hydrogen: add version 1.3.4 (#17066)

---
 var/spack/repos/builtin/packages/hydrogen/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/hydrogen/package.py b/var/spack/repos/builtin/packages/hydrogen/package.py
index d0aef797e79..c28d0872d90 100644
--- a/var/spack/repos/builtin/packages/hydrogen/package.py
+++ b/var/spack/repos/builtin/packages/hydrogen/package.py
@@ -18,6 +18,7 @@ class Hydrogen(CMakePackage):
     maintainers = ['bvanessen']
 
     version('develop', branch='hydrogen')
+    version('1.3.4', sha256='7979f6656f698f0bbad6798b39d4b569835b3013ff548d98089fce7c283c6741')
     version('1.3.3', sha256='a51a1cfd40ac74d10923dfce35c2c04a3082477683f6b35e7b558ea9f4bb6d51')
     version('1.3.2', sha256='50bc5e87955f8130003d04dfd9dcad63107e92b82704f8107baf95b0ccf98ed6')
     version('1.3.1', sha256='a8b8521458e9e747f2b24af87c4c2749a06e500019c383e0cefb33e5df6aaa1d')

From 50aba2729bb3aaa7723affd0c3165a3484253945 Mon Sep 17 00:00:00 2001
From: Robert Blake <blake14@llnl.gov>
Date: Fri, 12 Jun 2020 10:42:59 -0700
Subject: [PATCH 683/802] New package: antimony (#17061)

---
 .../builtin/packages/antimony/package.py      | 54 +++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/antimony/package.py

diff --git a/var/spack/repos/builtin/packages/antimony/package.py b/var/spack/repos/builtin/packages/antimony/package.py
new file mode 100644
index 00000000000..157a0a2510b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/antimony/package.py
@@ -0,0 +1,54 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Antimony(CMakePackage):
+    """Human readable language for modifying sbml"""
+
+    homepage = "http://antimony.sourceforge.net/"
+    url      = "antimony"
+
+    maintainers = ['rblake-llnl']
+
+    version('2.8', sha256='7e3e38706c074b72e241ac56ef4ce23e87ef8c718c70f29b2207f1847c43770f')
+    version('2.7', sha256='7ad181cac632282ae77ced09388dd92db87ea4683eed8c45f2b43861ae2acad4')
+    version('2.6', sha256='afc8dc5ec6bc2cd3085038f80362327456f219171b09a13f775b50550c8b1d87')
+    version('2.5', sha256='138d6b45df62198ca71bd3b3c8fd06920f8a78d7de7f6dbc1b89fa7ea7c7d215')
+    version('2.4', sha256='1597efa823f9a48f5a40373cbd40386207764807fbc0b79cf20d0f8570a7e54b')
+    version('2.2', sha256='795c777dd90c28fd8c3f4f8896702744b7389cff2fcf40e797b4bfafbb6f7251')
+    version('2.0', sha256='778146206e5f420d0e3d30dc25eabc9bad2759bfaf6b4b355bb1f72c5bc9593f')
+
+    def url_for_version(self, version):
+        url = "https://downloads.sourceforge.net/project/antimony/Antimony source/{0}/antimony_src_v{1}.tar.gz".format(version, version)
+        return url
+
+    variant("qt", default=False,
+            description="Build the QT editor.")
+    variant("python", default=False,
+            description="Build python bindings.")
+
+    depends_on('sbml~cpp')
+    depends_on('swig')
+    depends_on('qt', when="+qt")
+    depends_on('python', when="+python")
+
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            '-DWITH_SBML:BOOL=ON',
+            '-DWITH_COMP_SBML:BOOL=ON',
+            '-DWITH_LIBSBML_EXPAT:BOOL=OFF',
+            '-DWITH_LIBSBML_LIBXML:BOOL=ON',
+            '-DWITH_LIBSBML_XERCES:BOOL=OFF',
+            '-DLIBSBML_INSTALL_DIR:PATH=' + spec['sbml'].prefix,
+            '-DWITH_CELLML:BOOL=OFF',
+            '-DWITH_SBW:BOOL=OFF',
+            '-DWITH_SWIG:BOOL=ON',
+        ]
+        args.append(self.define_from_variant('WITH_PYTHON', 'python'))
+        args.append(self.define_from_variant('WITH_QTANTIMONY', "qt"))
+        return args

From 4e39dc7174feb2c9c49b6b89a897348bd47ea253 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 11 Jun 2020 14:09:44 -0500
Subject: [PATCH 684/802] readline: fix linking to ncurses

---
 var/spack/repos/builtin/packages/readline/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/readline/package.py b/var/spack/repos/builtin/packages/readline/package.py
index 7a15595fa28..0db25205c2c 100644
--- a/var/spack/repos/builtin/packages/readline/package.py
+++ b/var/spack/repos/builtin/packages/readline/package.py
@@ -29,7 +29,8 @@ class Readline(AutotoolsPackage, GNUMirrorPackage):
 
     def build(self, spec, prefix):
         options = [
-            'SHLIB_LIBS=-L{0} -lncursesw'.format(spec['ncurses'].prefix.lib)
+            'SHLIB_LIBS=-L{0} -lncursesw -ltinfo'.format(
+                spec['ncurses'].prefix.lib)
         ]
 
         make(*options)

From 34fb4b30dc5b97de2efde4f32f45b3105c1f701d Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Fri, 12 Jun 2020 11:25:06 -0700
Subject: [PATCH 685/802] libffi 3.3: float128 ppc patch (#17043)

Apply a patch to fix builds on Power7 and 8, wrongly requesting
float128 support.

Upstream patch: libffi/libffi#561
---
 .../repos/builtin/packages/libffi/package.py  |  2 +
 .../builtin/packages/libffi/powerpc-3.3.patch | 58 +++++++++++++++++++
 2 files changed, 60 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/libffi/powerpc-3.3.patch

diff --git a/var/spack/repos/builtin/packages/libffi/package.py b/var/spack/repos/builtin/packages/libffi/package.py
index 0ee50aec07c..5e952497aa5 100644
--- a/var/spack/repos/builtin/packages/libffi/package.py
+++ b/var/spack/repos/builtin/packages/libffi/package.py
@@ -18,6 +18,8 @@ class Libffi(AutotoolsPackage, SourcewarePackage):
     version('3.2.1', sha256='d06ebb8e1d9a22d19e38d63fdb83954253f39bedc5d46232a05645685722ca37')
 
     patch('clang-powerpc-3.2.1.patch', when='@3.2.1%clang platform=linux')
+    # ref.: https://github.com/libffi/libffi/pull/561
+    patch('powerpc-3.3.patch', when='@3.3')
 
     @property
     def headers(self):
diff --git a/var/spack/repos/builtin/packages/libffi/powerpc-3.3.patch b/var/spack/repos/builtin/packages/libffi/powerpc-3.3.patch
new file mode 100644
index 00000000000..4fd32b01028
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libffi/powerpc-3.3.patch
@@ -0,0 +1,58 @@
+From de93adfb6f48100946bba2c3abad2a77a0cfde0b Mon Sep 17 00:00:00 2001
+From: Fabrice Fontaine <fontaine.fabrice@gmail.com>
+Date: Sun, 24 Nov 2019 09:52:01 +0100
+Subject: [PATCH] ffi_powerpc.h: fix build failure with powerpc7
+
+This is a patch pulled down from the following:
+https://github.com/buildroot/buildroot/blob/78926f610b1411b03464152472fd430012deb9ac/package/libffi/0004-ffi_powerpc.h-fix-build-failure-with-powerpc7.patch
+
+This issue is being hit on OpenBMC code when pulling the latest
+libffi tag and building on a P8 ppc64le machine. I verified this
+patch fixes the issue we are seeing.
+
+Below is the original commit message:
+
+Sicne commit 73dd43afc8a447ba98ea02e9aad4c6898dc77fb0, build on powerpc7
+fails on:
+
+In file included from ../src/powerpc/ffi.c:33:0:
+../src/powerpc/ffi_powerpc.h:61:9: error: '_Float128' is not supported on this target
+ typedef _Float128 float128;
+         ^~~~~~~~~
+
+Fix this build failure by checking for __HAVE_FLOAT128 before using
+_Float128, as _Float128 is enabled only on specific conditions, see
+output/host/powerpc64-buildroot-linux-gnu/sysroot/usr/include/bits/floatn.h:
+
+ /* Defined to 1 if the current compiler invocation provides a
+    floating-point type with the IEEE 754 binary128 format, and this glibc
+    includes corresponding *f128 interfaces for it.  */
+ #if defined _ARCH_PWR8 && defined __LITTLE_ENDIAN__ && (_CALL_ELF == 2) \
+     && defined __FLOAT128__ && !defined __NO_LONG_DOUBLE_MATH
+ # define __HAVE_FLOAT128 1
+ #else
+ # define __HAVE_FLOAT128 0
+ #endif
+
+Fixes:
+ - http://autobuild.buildroot.org/results/5c9dd8fb3b6a128882b6250f197c80232d8a3b53
+
+Signed-off-by: Fabrice Fontaine <fontaine.fabrice@gmail.com>
+Signed-off-by: Andrew Geissler <geissonator@yahoo.com>
+---
+ src/powerpc/ffi_powerpc.h | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/powerpc/ffi_powerpc.h b/src/powerpc/ffi_powerpc.h
+index 8e2f2f0e..960a5c42 100644
+--- a/src/powerpc/ffi_powerpc.h
++++ b/src/powerpc/ffi_powerpc.h
+@@ -57,7 +57,7 @@ typedef union
+   double d;
+ } ffi_dblfl;
+ 
+-#if defined(__FLOAT128_TYPE__)
++#if defined(__FLOAT128_TYPE__) && defined(__HAVE_FLOAT128)
+ typedef _Float128 float128;
+ #elif defined(__FLOAT128__)
+ typedef __float128 float128;

From 42e6cb769e7d2f30700ba4529c2061e8fed7fcb5 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Fri, 12 Jun 2020 11:28:05 -0700
Subject: [PATCH 686/802] Geant4 +Python: fix module load (#17046)

Adding `extends('python')` makes sure that a

```
spack load -r geant4 +python
python -c "import Geant4"
```

find the module.
---
 var/spack/repos/builtin/packages/geant4/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/geant4/package.py b/var/spack/repos/builtin/packages/geant4/package.py
index 4cfcc4395e7..b559557340b 100644
--- a/var/spack/repos/builtin/packages/geant4/package.py
+++ b/var/spack/repos/builtin/packages/geant4/package.py
@@ -56,6 +56,7 @@ class Geant4(CMakePackage):
 
     # Python, with boost requirement dealt with in cxxstd section
     depends_on('python@3:', when='+python')
+    extends('python', when='+python')
     conflicts('+python', when='@:10.6.1',
               msg='Geant4 <= 10.6.1 cannont be built with Python bindings')
 

From c4756159f37ae9217377cdcb7718a229ec413736 Mon Sep 17 00:00:00 2001
From: Matthias Diener <mdiener@illinois.edu>
Date: Fri, 12 Jun 2020 13:37:34 -0500
Subject: [PATCH 687/802] New package: clinfo (#17042)

---
 .../repos/builtin/packages/clinfo/package.py  | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/clinfo/package.py

diff --git a/var/spack/repos/builtin/packages/clinfo/package.py b/var/spack/repos/builtin/packages/clinfo/package.py
new file mode 100644
index 00000000000..1fb78b42aa4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/clinfo/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Clinfo(MakefilePackage):
+    """Print all known information about all available OpenCL platforms and
+    devices in the system."""
+
+    homepage = "https://github.com/Oblomov/clinfo"
+    url      = "https://github.com/Oblomov/clinfo/archive/2.2.18.04.06.tar.gz"
+
+    maintainers = ['matthiasdiener']
+
+    version('2.2.18.04.06', sha256='f77021a57b3afcdebc73107e2254b95780026a9df9aa4f8db6aff11c03f0ec6c')
+
+    depends_on('opencl')
+
+    def install(self, spec, prefix):
+        make('install', 'PREFIX={0}'.format(prefix))

From 08c21e4e74624daf11774d5f16b04f3d9544cbdc Mon Sep 17 00:00:00 2001
From: Patrick Gartung <gartung@fnal.gov>
Date: Fri, 12 Jun 2020 13:38:33 -0500
Subject: [PATCH 688/802] Buildcache: Fix bug in binary string replacement
 (#17075)

* Fix bug in binary string replacement that results in padding being added multiple times

* Update comment

* Update comment again
---
 lib/spack/spack/relocate.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py
index 01a60db6baf..56e7c6632cd 100644
--- a/lib/spack/spack/relocate.py
+++ b/lib/spack/spack/relocate.py
@@ -846,7 +846,11 @@ def relocate_text_bin(
         for old_dep_prefix, new_dep_prefix in new_prefixes.items():
             if len(new_dep_prefix) <= len(old_dep_prefix):
                 _replace_prefix_bin(binary, old_dep_prefix, new_dep_prefix)
-        _replace_prefix_bin(binary, orig_spack, new_spack)
+        _replace_prefix_bin(binary, orig_install_prefix, new_install_prefix)
+
+    # Note: Replacement of spack directory should not be done. This causes
+    # an incorrect replacement path in the case where the install root is a
+    # subdirectory of the spack directory.
 
 
 def is_relocatable(spec):

From 804b6f24833862bb0110bf460c3ddbf7d22daab4 Mon Sep 17 00:00:00 2001
From: Harmen Stoppels <harmenstoppels@gmail.com>
Date: Fri, 12 Jun 2020 20:39:40 +0200
Subject: [PATCH 689/802] libtree package: add version 1.2.0, 1.1.4, and 1.1.3
 (#17035)

---
 var/spack/repos/builtin/packages/libtree/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/libtree/package.py b/var/spack/repos/builtin/packages/libtree/package.py
index d4c2749daa8..10ca8db31db 100644
--- a/var/spack/repos/builtin/packages/libtree/package.py
+++ b/var/spack/repos/builtin/packages/libtree/package.py
@@ -15,6 +15,9 @@ class Libtree(CMakePackage):
 
     maintainers = ['haampie']
 
+    version('1.2.0', sha256='4316a52aed7c8d2f7d2736c935bbda952204be92e56948110a143283764c427c')
+    version('1.1.4', sha256='cfafb24c8f5e0d356c82777c338d58730ca6f3cb76dfe8a6857ee3ad65bf8be7')
+    version('1.1.3', sha256='7baf5aaecd3a076bf1e7a1aa86979e7b841ab3f678ca8ac0e2a22bbbccf0dd06')
     version('1.1.2', sha256='31641c6bf6c2980ffa7b4c57392460434f97ba66fe51fe6346867430b33a0374')
     version('1.1.1', sha256='3e8543145a40a94e9e2ce9fed003d2bf68294e1fce9607028a286bc132e17dc4')
     version('1.1.0', sha256='6cf36fb9a4c8c3af01855527d4931110732bb2d1c19be9334c689f1fd1c78536')

From cb20f0152c9be3934c679b0853ab919e7e0cb907 Mon Sep 17 00:00:00 2001
From: Harsh Bhatia <bhatia4@llnl.gov>
Date: Fri, 12 Jun 2020 12:20:57 -0700
Subject: [PATCH 690/802] pygpu: fix linking with gpuarray (#17033)

* add build_ext_args to link pygpu with gpuarray
* libgpuarray: add version 0.7.6
---
 .../builtin/packages/libgpuarray/package.py      |  1 +
 .../repos/builtin/packages/py-pygpu/package.py   | 16 +++++++++++++++-
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/libgpuarray/package.py b/var/spack/repos/builtin/packages/libgpuarray/package.py
index edaebac7afc..84b0ad541e7 100644
--- a/var/spack/repos/builtin/packages/libgpuarray/package.py
+++ b/var/spack/repos/builtin/packages/libgpuarray/package.py
@@ -14,6 +14,7 @@ class Libgpuarray(CMakePackage):
     homepage = "http://deeplearning.net/software/libgpuarray/"
     url      = "https://github.com/Theano/libgpuarray/archive/v0.6.1.tar.gz"
 
+    version('0.7.6', sha256='ad1c00dd47c3d36ee1708e5167377edbfcdb7226e837ef9c68b841afbb4a4f6a')
     version('0.7.5', sha256='39c4d2e743848be43c8819c736e089ae51b11aa446cc6ee05af945c2dfd63420')
     version('0.7.2', sha256='ef11ee6f8d62d53831277fd3dcab662aa770a5b5de2d30fe3018c4af959204da')
     version('0.7.1', sha256='4d0f9dd63b0595a8c04d8cee91b2619847c033b011c71d776caa784322382ed6')
diff --git a/var/spack/repos/builtin/packages/py-pygpu/package.py b/var/spack/repos/builtin/packages/py-pygpu/package.py
index 49dc42eede5..aea59399959 100644
--- a/var/spack/repos/builtin/packages/py-pygpu/package.py
+++ b/var/spack/repos/builtin/packages/py-pygpu/package.py
@@ -4,6 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
+import os
 
 
 class PyPygpu(PythonPackage):
@@ -12,6 +13,7 @@ class PyPygpu(PythonPackage):
     homepage = "http://deeplearning.net/software/libgpuarray/"
     url      = "https://github.com/Theano/libgpuarray/archive/v0.6.1.tar.gz"
 
+    version('0.7.6', sha256='ad1c00dd47c3d36ee1708e5167377edbfcdb7226e837ef9c68b841afbb4a4f6a')
     version('0.7.5', sha256='39c4d2e743848be43c8819c736e089ae51b11aa446cc6ee05af945c2dfd63420')
     version('0.7.2', sha256='ef11ee6f8d62d53831277fd3dcab662aa770a5b5de2d30fe3018c4af959204da')
     version('0.7.1', sha256='4d0f9dd63b0595a8c04d8cee91b2619847c033b011c71d776caa784322382ed6')
@@ -21,7 +23,9 @@ class PyPygpu(PythonPackage):
     version('0.6.1', sha256='b2466311e0e3bacdf7a586bba0263f6d232bf9f8d785e91ddb447653741e6ea5')
     version('0.6.0', sha256='a58a0624e894475a4955aaea25e82261c69b4d22c8f15ec07041a4ba176d35af')
 
-    depends_on('libgpuarray')
+    depends_on('libgpuarray@0.7.6', when='@0.7.6')
+    depends_on('libgpuarray@0.7.5', when='@0.7.5')
+    depends_on('libgpuarray')                        # default
     # not just build-time, requires pkg_resources
     depends_on('py-setuptools', type=('build', 'run'))
     depends_on('py-cython@0.25:', type=('build', 'run'))
@@ -29,3 +33,13 @@ class PyPygpu(PythonPackage):
     depends_on('py-numpy', type=('build', 'run'))
     depends_on('py-mako', type=('build', 'run'))
     depends_on('check')
+
+    phases = ['build_ext', 'install']
+
+    def build_ext_args(self, spec, prefix):
+
+        _ = self.spec['libgpuarray'].prefix
+        include_flags = '-I{0}'.format(os.path.join(_, 'include'))
+        library_flags = '-L{0}'.format(os.path.join(_, 'lib'))
+
+        return [include_flags, library_flags]

From f44a93e4f7014d78cbfa75efb5303944375f8a5d Mon Sep 17 00:00:00 2001
From: Sinan <sbulutw@gmail.com>
Date: Fri, 12 Jun 2020 12:27:40 -0700
Subject: [PATCH 691/802] New package: alps (#17023)

---
 .../repos/builtin/packages/alps/mpi.patch     | 13 +++++
 .../repos/builtin/packages/alps/package.py    | 50 +++++++++++++++++++
 2 files changed, 63 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/alps/mpi.patch
 create mode 100644 var/spack/repos/builtin/packages/alps/package.py

diff --git a/var/spack/repos/builtin/packages/alps/mpi.patch b/var/spack/repos/builtin/packages/alps/mpi.patch
new file mode 100644
index 00000000000..bd68181eb76
--- /dev/null
+++ b/var/spack/repos/builtin/packages/alps/mpi.patch
@@ -0,0 +1,13 @@
+diff --git a/alps/src/alps/CMakeLists.txt b/alps/src/alps/CMakeLists.txt
+index ae73f13..0d1ba34 100644
+--- a/alps/src/alps/CMakeLists.txt
++++ b/alps/src/alps/CMakeLists.txt
+@@ -93,7 +93,7 @@ if (Boost_FOUND)
+     set(ALPS_LINK_LIBS ${ALPS_LINK_LIBS} ${PYTHON_LIBRARY} ${PYTHON_EXTRA_LIBS})
+   endif(PYTHONLIBS_FOUND)
+   if(MPI_FOUND)
+-    set(ALPS_LINK_LIBS ${ALPS_LINK_LIBS} ${MPI_LIBRARIES} ${MPI_EXTRA_LIBRARY})
++    set(ALPS_LINK_LIBS ${ALPS_LINK_LIBS} ${MPI_LIBRARIES})
+   endif(MPI_FOUND)
+   target_link_libraries(alps ${ALPS_LINK_LIBS})
+ else (Boost_FOUND)
diff --git a/var/spack/repos/builtin/packages/alps/package.py b/var/spack/repos/builtin/packages/alps/package.py
new file mode 100644
index 00000000000..55df8729330
--- /dev/null
+++ b/var/spack/repos/builtin/packages/alps/package.py
@@ -0,0 +1,50 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Alps(CMakePackage):
+    """Algorithms for Physics Simulations
+
+    Tags: Condensed Matter Physics, Computational Physics
+    """
+
+    homepage = "https://alps.comp-phys.org"
+    url      = "http://alps.comp-phys.org/static/software/releases/alps-2.3.0-src.tar.gz"
+
+    version('2.3.0', sha256='e64208d1e5acdd6f569277413c4867e1fa366cf4a224570eacbf1e9939fca2d2')
+
+    # Refs for building from source and recipes
+    # http://alps.comp-phys.org/mediawiki/index.php/Building_ALPS_from_source
+    # https://github.com/easybuilders/easybuild-easyconfigs/tree/master/easybuild/easyconfigs/a/ALPS
+    # https://github.com/conda-forge/alps-feedstock/tree/master/recipe
+
+    # Package failed to build with boost version >= 1.64
+    depends_on('boost@:1.63.0 +chrono +date_time +filesystem +iostreams +mpi +numpy +program_options +python +regex +serialization +system +test +thread +timer')
+    depends_on('fftw')
+    depends_on('hdf5 ~mpi+hl')
+    depends_on('lapack')
+    # build fails for latest python@3.7
+    depends_on('python@:3.6.99', type=('build', 'link', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-matplotlib', type=('build', 'run'))
+
+    # build fails with gcc@7:
+    conflicts('%gcc@7:')
+
+    # remove a problematic build variable
+    patch('mpi.patch')
+
+    extends('python')
+
+    root_cmakelists_dir = 'alps'
+
+    def cmake_args(self):
+        args = []
+        args.append('Boost_ROOT_DIR=' + self.spec['boost'].prefix)
+        args.append("-DCMAKE_CXX_FLAGS={0}".format(self.compiler.cxx98_flag))
+        return args

From b90780d256f88ef081b11b3400155d155dcc76e0 Mon Sep 17 00:00:00 2001
From: John Jolly <john.jolly@gmail.com>
Date: Tue, 9 Jun 2020 12:21:23 -0600
Subject: [PATCH 692/802] cscope: Link tinfow instead of tinfo

Whenever attempting to use any ncurses functionality within cscope, a
page fault would result within the ncurses library.

    Program received signal SIGSEGV, Segmentation fault.
    0x00007ffff7fad3cf in termattrs_sp () from .../lib/libncursesw.so.6
    (gdb) bt
    #0  0x00007ffff7fad3cf in termattrs_sp () from .../lib/libncursesw.so.6
    #1  0x00007ffff7faa794 in _nc_setupscreen_sp () from .../lib/libncursesw.so.6
    #2  0x00007ffff7fa614c in newterm_sp () from .../lib/libncursesw.so.6
    #3  0x00007ffff7fa65b9 in newterm () from .../lib/libncursesw.so.6
    #4  0x00007ffff7fa2970 in initscr () from .../lib/libncursesw.so.6
    #5  0x0000000000403dc2 in main (argc=<optimized out>, argv=0x7fffffffcea8) at main.c:574

This is due to a conflict between libtinfo.so and libtinfow.so. Both are
linked into cscope:

    $ ldd $(which cscope)
    /bin/bash: .../lib/libtinfo.so.6: no version information available (required by /bin/bash)
        linux-vdso.so.1 (0x00007fff5dbcb000)
        libncursesw.so.6 => .../lib/libncursesw.so.6 (0x00007f435cc69000)
        libtinfo.so.6 => .../lib/libtinfo.so.6 (0x00007f435cc2c000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f435ca29000)
        libtinfow.so.6 => .../lib/libtinfow.so.6 (0x00007f435c9e8000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f435cca7000)

Specifically linking libtinfow.so instead of libtinfo.so resolves the
issue.

All instances of '...' above represent the path to the installed ncurses
for Spack.
---
 var/spack/repos/builtin/packages/cscope/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/cscope/package.py b/var/spack/repos/builtin/packages/cscope/package.py
index 2682ffea704..a829b1e1e51 100644
--- a/var/spack/repos/builtin/packages/cscope/package.py
+++ b/var/spack/repos/builtin/packages/cscope/package.py
@@ -21,7 +21,7 @@ class Cscope(AutotoolsPackage):
     depends_on('bison', type='build')
     depends_on('pkgconfig', type='build')
 
-    build_targets = ['CURSES_LIBS=-lncursesw -ltinfo']
+    build_targets = ['CURSES_LIBS=-lncursesw -ltinfow']
 
     def url_for_version(self, version):
         url = "https://sourceforge.net/projects/cscope/files/cscope/{0}{1}/cscope-{1}.tar.gz"

From 0c1f1af571bce8b1bc0a89172714cac00e69d66b Mon Sep 17 00:00:00 2001
From: h-denpo <57649496+h-denpo@users.noreply.github.com>
Date: Sat, 13 Jun 2020 04:31:04 +0900
Subject: [PATCH 693/802] New package: FrontFlow Blue (#16901)

* New package: FrontFlow Blue
       Computational Fluid Dynamics Software for aeroacoustics

* Modify Package ->MakefilePackage

* Update var/spack/repos/builtin/packages/ffb/package.py

Co-authored-by: Greg Becker <becker33@llnl.gov>

* Update var/spack/repos/builtin/packages/ffb/package.py

Co-authored-by: Greg Becker <becker33@llnl.gov>

Co-authored-by: Greg Becker <becker33@llnl.gov>
---
 .../repos/builtin/packages/ffb/package.py     | 151 ++++++++++++++++++
 .../packages/ffb/revocap_refiner.patch        |  24 +++
 2 files changed, 175 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/ffb/package.py
 create mode 100644 var/spack/repos/builtin/packages/ffb/revocap_refiner.patch

diff --git a/var/spack/repos/builtin/packages/ffb/package.py b/var/spack/repos/builtin/packages/ffb/package.py
new file mode 100644
index 00000000000..e7c1272a134
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ffb/package.py
@@ -0,0 +1,151 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+from spack import *
+
+
+class Ffb(MakefilePackage):
+    """Computational Fluid Dynamics Software for aeroacoustics"""
+
+    homepage = "http://www.ciss.iis.u-tokyo.ac.jp/dl/index.php"
+    url      = "file://{0}/FrontFlow_blue.8.1.tar.gz".format(os.getcwd())
+    version('8.1', sha256='1ad008c909152b6c27668bafbad820da3e6ec3309c7e858ddb785f0a3d6e43ae')
+
+    patch('revocap_refiner.patch')
+
+    depends_on('mpi')
+    depends_on('blas')
+    depends_on('scalapack')
+
+    parallel = False
+
+    def flag_handler(self, name, flags):
+        opt_flag_found = any(f in self.compiler.opt_flags for f in flags)
+        if name == 'cflags':
+            if not opt_flag_found:
+                flags.append('-O3')
+        elif name == 'cxxflags':
+            if not opt_flag_found:
+                flags.append('-O2')
+            flags.append(self.compiler.cxx_pic_flag)
+        if name == 'fflags':
+            if not opt_flag_found:
+                flags.append('-O3')
+            flags.append('-mcmodel=large')
+        if name in ('cflags', 'cxxflags', 'fflags'):
+            return (None, flags, None)
+        else:
+            return (flags, None, flags)
+
+    def edit(self, spec, prefix):
+        workdir = os.getcwd()
+        cflags = env['CFLAGS']
+        cxxflags = env['CXXFLAGS']
+        fflags = env['FFLAGS']
+
+        make = join_path('make', 'makefile')
+        m = FileFilter(make)
+        m.filter(
+            r'#LES3DHOME   =', 'LES3DHOME= {0}\n'.format(workdir))
+        make = join_path('make', 'OPTION')
+        m = FileFilter(make)
+        m.filter(r'CCOM\s*=.*$', 'CCOM = {0}'.format(spack_cc))
+        m.filter(r'COPT\s*=.*$', 'COPT = {0}'.format(cflags))
+        m.filter(r'FCOM\s*=.*$', 'FCOM = {0}\n'.format(spack_fc))
+        m.filter(r'FOPT\s*=.*$', 'FOPT = {0}\n'.format(fflags))
+        m.filter(r'INCDIR\s*=.*$', 'INCDIR = {0}\n'
+                 .format(spec['mpi'].headers.directories[0]))
+        m.filter(r'LIBDIR\s*=.*$', 'LIBDIR = {0}\n'
+                 .format(spec['mpi'].libs.directories[0]))
+
+        srcdir = join_path('lib', 'src')
+        utildir = join_path(workdir, 'util')
+        with open(join_path('make', 'Makeall'), 'w') as m:
+            m.write('#!/bin/csh -f\n')
+            m.write('setenv LES3DHOME {0}\n'.format(workdir))
+            m.write('cd {0}\n'.format(srcdir))
+            m.write('./Makeall\n')
+            m.write('cd {0}\n'.format(utildir))
+            m.write('./Makeall\n')
+
+        makeall = join_path('lib', 'src', 'dd_mpi', 'Makeall')
+        dd_mpi_dir = join_path('lib', 'src', 'dd_mpi')
+        with open(makeall, 'w') as m:
+            m.write('#!/bin/csh -f\n')
+            m.write('setenv LES3DHOME {0}\n'.format(workdir))
+            m.write('cd {0}\n'.format(dd_mpi_dir))
+            m.write('make lib\n')
+        os.chmod(makeall, 0o755)
+
+        makeall = join_path('.',  'Makeall.les')
+        les3d_dir = join_path('util', 'les3d.mpi')
+        les3c_dir = join_path('util', 'les3c.mpi')
+        les3ct_dir = join_path('util', 'les3ct.mpi')
+        les3x_dir = join_path('util', 'les3x.mpi')
+        with open(makeall, 'w') as m:
+            m.write('#!/bin/csh -f\n')
+            m.write('setenv LES3DHOME {0}\n'.format(workdir))
+            m.write('cd {0}\n'.format(join_path(workdir, les3d_dir)))
+            m.write('make CCOM={0}'.format(spec['mpi'].mpicc))
+            m.write(' FCOM={0}\n'.format(spec['mpi'].mpifc))
+            m.write('cd {0}\n'.format(join_path(workdir, les3c_dir)))
+            m.write('make CCOM={0}'.format(spec['mpi'].mpicc))
+            m.write(' FCOM={0}\n'.format(spec['mpi'].mpifc))
+            m.write('cd {0}\n'.format(join_path(workdir, les3ct_dir)))
+            m.write('make CCOM={0}'.format(spec['mpi'].mpicc))
+            m.write(' FCOM={0}\n'.format(spec['mpi'].mpifc))
+            m.write('cd {0}\n'.format(join_path(workdir, les3x_dir)))
+            m.write('make CCOM={0}'.format(spec['mpi'].mpicc))
+            m.write(' FCOM={0}\n'.format(spec['mpi'].mpifc))
+
+            for d in [les3c_dir, les3ct_dir, les3d_dir]:
+                editfile = join_path(d, 'FILES')
+                m = FileFilter(editfile)
+                m.filter(r'-lmpi_f77', '')
+        os.chmod(makeall, 0o755)
+
+        editfile = join_path('lib', 'src', 'REVOCAP_Refiner-0.4.3', 'OPTIONS')
+        m = FileFilter(editfile)
+        m.filter(r'ARCH\s*=.*$', 'ARCH= $(shell arch)-linux')
+        m.filter(r'CC\s*=.*$', 'CC={0}'.format(spack_cc))
+        m.filter(r'CFLAGS\s*=.*$', 'CFLAGS={0}'.format(cflags))
+        m.filter(r'CXX\s*=.*$',  'CXX={0}'.format(spack_cxx))
+        m.filter(r'CXXFLAGS\s*=.*$',
+                 'CXXFLAGS={0}'.format(cxxflags))
+        m.filter(r'F90\s*=.*$', 'CC={0}'.format(spack_fc))
+        m.filter(r'LD\s*=.*$', 'LD={0}'.format(spack_fc))
+        m.filter(r'LIBPATH\s*=.*$', 'LIBPATH= ')
+        m.filter(r'FFLAGS\s*=.*$', 'FFLAGS={0}'.format(fflags))
+        m.filter(r'LDFLAGS\s*=.*$', 'LDFLAGS={0}'.format(fflags))
+
+        editfile = join_path('lib', 'src', 'ParMetis-3.1', 'Makefile.in')
+        m = FileFilter(editfile)
+        m.filter(r'CC \s*=.*$', 'CC ={0}'.format(spack_cc))
+        m.filter(r'INCDIR\s*=.*$', 'INCDIR = \n')
+
+        editfile = join_path('util', 'xvx2gf', 'Makefile')
+        m = FileFilter(editfile)
+        m.filter(
+            r'#LES3DHOME   =', 'LES3DHOME= {0}\n'.format(workdir))
+        m.filter(r'g\+\+', (spack_cxx))
+
+        editfile = join_path('util', 'les3x.mpi', 'FILES')
+        m = FileFilter(editfile)
+        m.filter(r'LIBS = -lfort -lgf2 -ldd_mpi -lmpi_f77',
+                 'LIBS = -lfort -lgf2  -ldd_mpi')
+
+    def build(self, spec, prefix):
+        for m in [join_path('make',  'Makeall'),
+                  join_path('lib', 'src', 'dd_mpi', 'Makeall'),
+                  join_path('.', 'Makeall.les')]:
+            Executable(m)()
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('macro', prefix.macro)
+
+    def setup_run_environment(self, env):
+        env.prepend_path('PATH', prefix.macro)
diff --git a/var/spack/repos/builtin/packages/ffb/revocap_refiner.patch b/var/spack/repos/builtin/packages/ffb/revocap_refiner.patch
new file mode 100644
index 00000000000..20886120cbd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ffb/revocap_refiner.patch
@@ -0,0 +1,24 @@
+diff -uprN FFB8.org/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Bucket.h FFB8.new/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Bucket.h
+--- FFB8.org/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Bucket.h	2013-03-26 10:09:31.000000000 +0900
++++ FFB8.new/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Bucket.h	2020-05-29 16:35:09.690918296 +0900
+@@ -64,7 +64,7 @@ public:
+ 		numY = this->ynum;
+ 		numZ = this->znum;
+ 	};
+-	void getSize(void) const{
++	int getSize(void) const{
+ 		return this->xnum * this->ynum * this->znum;
+ 	};
+ 
+diff -uprN FFB8.org/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Common.h FFB8.new/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Common.h
+--- FFB8.org/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Common.h	2013-03-26 10:09:31.000000000 +0900
++++ FFB8.new/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Common.h	2020-05-29 16:35:48.756606155 +0900
+@@ -13,7 +13,7 @@
+ #                                                                      #
+ ----------------------------------------------------------------------*/
+ #pragma once
+-
++#include <cstdlib>
+ #ifndef PI
+  #define PI 3.1415926535897932384626
+ #endif

From 67b86623a229f4bc379dfc6d0ae773445eaf8d7c Mon Sep 17 00:00:00 2001
From: Andrew W Elble <aweits@rit.edu>
Date: Fri, 12 Jun 2020 16:25:34 -0400
Subject: [PATCH 694/802] bazel: patch to allow py-tensorflow (and likely other
 bazel packages) to build. (#17013)

bazel uses gcc's -MF option to write dependencies to a
file. Post-compilation, bazel reads this file and makes some
determinations.

"Since gcc is given only relative paths on the command line,
 non-system include paths here should never be absolute. If they
 are, it's probably due to a non-hermetic #include, & we should stop
 the build with an error."

Spack directly injects absolute paths, which appear in this file and
cause bazel to fail the build despite the fact that compilation
succeeded.

This patch disables this failure mode by default, and allows for it
to be turned back on by using the '~nodepfail' variant.
---
 .../builtin/packages/bazel/disabledepcheck.patch      | 11 +++++++++++
 .../builtin/packages/bazel/disabledepcheck_old.patch  | 11 +++++++++++
 var/spack/repos/builtin/packages/bazel/package.py     |  5 +++++
 3 files changed, 27 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/bazel/disabledepcheck.patch
 create mode 100644 var/spack/repos/builtin/packages/bazel/disabledepcheck_old.patch

diff --git a/var/spack/repos/builtin/packages/bazel/disabledepcheck.patch b/var/spack/repos/builtin/packages/bazel/disabledepcheck.patch
new file mode 100644
index 00000000000..c15d3bf64a1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/disabledepcheck.patch
@@ -0,0 +1,11 @@
+--- a/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java.orig  2020-03-25 08:54:37.914186251 -0400
++++ b/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java       2020-03-25 08:55:01.356250657 -0400
+@@ -148,7 +148,7 @@
+         if (execPath.startsWith(execRoot)) {
+           execPathFragment = execPath.relativeTo(execRoot); // funky but tolerable path
+         } else {
+-          problems.add(execPathFragment.getPathString());
++          //          problems.add(execPathFragment.getPathString());
+           continue;
+         }
+       }
diff --git a/var/spack/repos/builtin/packages/bazel/disabledepcheck_old.patch b/var/spack/repos/builtin/packages/bazel/disabledepcheck_old.patch
new file mode 100644
index 00000000000..dd23972d992
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/disabledepcheck_old.patch
@@ -0,0 +1,11 @@
+--- a/src/main/java/com/google/devtools/build/lib/rules/cpp/CppCompileAction.java.orig    2020-06-08 13:42:14.035342560 -0400
++++ b/src/main/java/com/google/devtools/build/lib/rules/cpp/CppCompileAction.java 2020-06-08 13:42:25.149375458 -0400
+@@ -963,7 +963,7 @@
+           // are, it's probably due to a non-hermetic #include, & we should stop
+           // the build with an error.
+           if (execPath.startsWith(execRoot)) {
+-            execPathFragment = execPath.relativeTo(execRoot); // funky but tolerable path
++             //  execPathFragment = execPath.relativeTo(execRoot); // funky but tolerable path
+           } else {
+             problems.add(execPathFragment.getPathString());
+             continue;
diff --git a/var/spack/repos/builtin/packages/bazel/package.py b/var/spack/repos/builtin/packages/bazel/package.py
index abe427c9603..a3bd59a8b1b 100644
--- a/var/spack/repos/builtin/packages/bazel/package.py
+++ b/var/spack/repos/builtin/packages/bazel/package.py
@@ -94,6 +94,8 @@ class Bazel(Package):
     version('0.3.1',  sha256='218d0e28b4d1ee34585f2ac6b18d169c81404d93958815e73e60cc0368efcbb7')
     version('0.3.0',  sha256='357fd8bdf86034b93902616f0844bd52e9304cccca22971ab7007588bf9d5fb3')
 
+    variant('nodepfail', default=True, description='Disable failing dependency checks due to injected absolute paths - required for most builds using bazel with spack')
+
     # https://docs.bazel.build/versions/master/install-compile-source.html#bootstrap-bazel
     # Until https://github.com/spack/spack/issues/14058 is fixed, use jdk to build bazel
     # Strict dependency on java@8 as per
@@ -128,6 +130,9 @@ class Bazel(Package):
     patch('compile-0.4.patch',  when='@0.4:0.5')
     patch('compile-0.3.patch',  when='@:0.3')
 
+    patch('disabledepcheck.patch', when='@0.3.2:+nodepfail')
+    patch('disabledepcheck_old.patch', when='@0.3.0:0.3.1+nodepfail')
+
     phases = ['bootstrap', 'install']
 
     def url_for_version(self, version):

From ea8a0be465b0329cfb4a6b29e02da0dbb4650f6e Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Fri, 12 Jun 2020 14:05:12 -0700
Subject: [PATCH 695/802] add compilers to mpi setup_run_environment methods
 forall mpi implementations (#17015)

---
 .../builtin/packages/fujitsu-mpi/package.py   |  5 +++++
 .../builtin/packages/intel-mpi/package.py     |  6 ++++++
 .../packages/intel-parallel-studio/package.py |  6 ++++++
 .../repos/builtin/packages/mpich/package.py   |  7 ++++++-
 .../repos/builtin/packages/mpt/package.py     | 13 +++++++++---
 .../builtin/packages/mvapich2/package.py      | 20 +++++++++++++------
 .../repos/builtin/packages/openmpi/package.py |  8 +++++++-
 .../builtin/packages/spectrum-mpi/package.py  | 19 ++++++++++++++++++
 8 files changed, 73 insertions(+), 11 deletions(-)

diff --git a/var/spack/repos/builtin/packages/fujitsu-mpi/package.py b/var/spack/repos/builtin/packages/fujitsu-mpi/package.py
index 62da3aab01e..c0a882ec4c7 100644
--- a/var/spack/repos/builtin/packages/fujitsu-mpi/package.py
+++ b/var/spack/repos/builtin/packages/fujitsu-mpi/package.py
@@ -34,6 +34,11 @@ def setup_dependent_package(self, module, dependent_spec):
         self.spec.mpifc = self.prefix.bin.mpifrt
 
     def setup_dependent_build_environment(self, env, dependent_spec):
+        self.setup_run_environment(env)
+
+    def setup_run_environment(self, env):
+        # Because MPI are both compilers and runtimes, we set up the compilers
+        # as part of run environment
         env.set('MPICC', self.prefix.bin.mpifcc)
         env.set('MPICXX', self.prefix.bin.mpiFCC)
         env.set('MPIF77', self.prefix.bin.mpifrt)
diff --git a/var/spack/repos/builtin/packages/intel-mpi/package.py b/var/spack/repos/builtin/packages/intel-mpi/package.py
index 15cb84150ef..52e93e66728 100644
--- a/var/spack/repos/builtin/packages/intel-mpi/package.py
+++ b/var/spack/repos/builtin/packages/intel-mpi/package.py
@@ -63,3 +63,9 @@ def setup_dependent_build_environment(self, *args):
             'F90':  spack_fc,
             'FC':   spack_fc,
         })
+
+    def setup_run_environment(self, env):
+        super(self, IntelMpi).setup_run_environment(env)
+
+        for name, value in self.mpi_compiler.wrappers.items():
+            env.set(name, value)
diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
index 410cd4045e4..f59aa2b7ea6 100644
--- a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
+++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
@@ -225,3 +225,9 @@ def setup_dependent_build_environment(self, *args):
             'F90':  spack_fc,
             'FC':   spack_fc,
         })
+
+    def setup_run_environment(self, env):
+        super(self, IntelParallelStudio).setup_run_environment(env)
+
+        for name, value in self.mpi_compiler_wrappers.items():
+            env.set(name, value)
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index 042c2c5b124..c9c7886a088 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -160,7 +160,9 @@ def setup_build_environment(self, env):
         if self.spec.satisfies('%gcc@10:'):
             env.set('FFLAGS', '-fallow-argument-mismatch')
 
-    def setup_dependent_build_environment(self, env, dependent_spec):
+    def setup_run_environment(self, env):
+        # Because MPI implementations provide compilers, they have to add to
+        # their run environments the code to make the compilers available.
         # For Cray MPIs, the regular compiler wrappers *are* the MPI wrappers.
         # Cray MPIs always have cray in the module name, e.g. "cray-mpich"
         if self.spec.external_module and 'cray' in self.spec.external_module:
@@ -174,6 +176,9 @@ def setup_dependent_build_environment(self, env, dependent_spec):
             env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
             env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
 
+    def setup_dependent_build_environment(self, env, dependent_spec):
+        self.setup_run_environment(env)
+
         env.set('MPICH_CC', spack_cc)
         env.set('MPICH_CXX', spack_cxx)
         env.set('MPICH_F77', spack_f77)
diff --git a/var/spack/repos/builtin/packages/mpt/package.py b/var/spack/repos/builtin/packages/mpt/package.py
index 12f7202ebc6..45dfce6ba5b 100644
--- a/var/spack/repos/builtin/packages/mpt/package.py
+++ b/var/spack/repos/builtin/packages/mpt/package.py
@@ -39,13 +39,20 @@ def libs(self):
         )
 
     def setup_dependent_build_environment(self, env, dependent_spec):
+        self.setup_run_environment(env)
+
+        # use the Spack compiler wrappers under MPI
+        env.set('MPICC_CC', spack_cc)
+        env.set('MPICXX_CXX', spack_cxx)
+        env.set('MPIF90_F90', spack_fc)
+
+    def setup_run_environment(self, env):
+        # Because MPI is both runtime and compiler, we have to setup the mpi
+        # compilers as part of the run environment.
         env.set('MPICC',  self.prefix.bin.mpicc)
         env.set('MPICXX', self.prefix.bin.mpicxx)
         env.set('MPIF77', self.prefix.bin.mpif77)
         env.set('MPIF90', self.prefix.bin.mpif90)
-        env.set('MPICC_CC', spack_cc)
-        env.set('MPICXX_CXX', spack_cxx)
-        env.set('MPIF90_F90', spack_fc)
 
     def setup_dependent_package(self, module, dependent_spec):
         if 'platform=cray' in self.spec:
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index 0fb3c36b289..dac9b69c496 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -208,7 +208,21 @@ def setup_run_environment(self, env):
         if 'process_managers=slurm' in self.spec:
             env.set('SLURM_MPI_TYPE', 'pmi2')
 
+        # Because MPI functions as a compiler, we need to treat it as one and
+        # add its compiler paths to the run environment.
+        self.setup_compiler_environment(env)
+
     def setup_dependent_build_environment(self, env, dependent_spec):
+        self.setup_compiler_environment(env)
+
+        # use the Spack compiler wrappers under MPI
+        env.set('MPICH_CC', spack_cc)
+        env.set('MPICH_CXX', spack_cxx)
+        env.set('MPICH_F77', spack_f77)
+        env.set('MPICH_F90', spack_fc)
+        env.set('MPICH_FC', spack_fc)
+
+    def setup_compiler_environment(self, env):
         # For Cray MPIs, the regular compiler wrappers *are* the MPI wrappers.
         # Cray MPIs always have cray in the module name, e.g. "cray-mvapich"
         if self.spec.external_module and 'cray' in self.spec.external_module:
@@ -222,12 +236,6 @@ def setup_dependent_build_environment(self, env, dependent_spec):
             env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
             env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
 
-        env.set('MPICH_CC', spack_cc)
-        env.set('MPICH_CXX', spack_cxx)
-        env.set('MPICH_F77', spack_f77)
-        env.set('MPICH_F90', spack_fc)
-        env.set('MPICH_FC', spack_fc)
-
     def setup_dependent_package(self, module, dependent_spec):
         # For Cray MPIs, the regular compiler wrappers *are* the MPI wrappers.
         # Cray MPIs always have cray in the module name, e.g. "cray-mvapich"
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index abe7b1d3ee2..b3dcac253e2 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -297,12 +297,18 @@ def libs(self):
             libraries, root=self.prefix, shared=True, recursive=True
         )
 
-    def setup_dependent_build_environment(self, env, dependent_spec):
+    def setup_run_environment(self, env):
+        # Because MPI is both a runtime and a compiler, we have to setup the
+        # compiler components as part of the run environment.
         env.set('MPICC',  join_path(self.prefix.bin, 'mpicc'))
         env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
         env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
         env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
 
+    def setup_dependent_build_environment(self, env, dependent_spec):
+        self.setup_run_environment(env)
+
+        # Use the spack compiler wrappers under MPI
         env.set('OMPI_CC', spack_cc)
         env.set('OMPI_CXX', spack_cxx)
         env.set('OMPI_FC', spack_fc)
diff --git a/var/spack/repos/builtin/packages/spectrum-mpi/package.py b/var/spack/repos/builtin/packages/spectrum-mpi/package.py
index 8cdd82e2ae1..8ec206adae3 100644
--- a/var/spack/repos/builtin/packages/spectrum-mpi/package.py
+++ b/var/spack/repos/builtin/packages/spectrum-mpi/package.py
@@ -56,3 +56,22 @@ def setup_dependent_build_environment(self, env, dependent_spec):
         env.set('OMPI_F77', spack_f77)
 
         env.prepend_path('LD_LIBRARY_PATH', self.prefix.lib)
+
+    def setup_run_environment(self, env):
+        # Because MPI functions as a compiler we need to setup the compilers
+        # in the run environment, like any compiler
+        if '%xl' in self.spec or '%xl_r' in self.spec:
+            env.set('MPICC', os.path.join(self.prefix.bin, 'mpixlc'))
+            env.set('MPICXX', os.path.join(self.prefix.bin, 'mpixlC'))
+            env.set('MPIF77', os.path.join(self.prefix.bin, 'mpixlf'))
+            env.set('MPIF90', os.path.join(self.prefix.bin, 'mpixlf'))
+        elif '%pgi' in self.spec:
+            env.set('MPICC', os.path.join(self.prefix.bin, 'mpipgicc'))
+            env.set('MPICXX', os.path.join(self.prefix.bin, 'mpipgic++'))
+            env.set('MPIF77', os.path.join(self.prefix.bin, 'mpipgifort'))
+            env.set('MPIF90', os.path.join(self.prefix.bin, 'mpipgifort'))
+        else:
+            env.set('MPICC', os.path.join(self.prefix.bin, 'mpicc'))
+            env.set('MPICXX', os.path.join(self.prefix.bin, 'mpic++'))
+            env.set('MPIF77', os.path.join(self.prefix.bin, 'mpif77'))
+            env.set('MPIF90', os.path.join(self.prefix.bin, 'mpif90'))

From 416e94be7294ccfc3f8d9666c75f2790bb58089f Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Sat, 13 Jun 2020 03:06:15 +0200
Subject: [PATCH 696/802] xrootd: new versions (#17076)

---
 var/spack/repos/builtin/packages/xrootd/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/xrootd/package.py b/var/spack/repos/builtin/packages/xrootd/package.py
index 24f966395d7..aed32e712b5 100644
--- a/var/spack/repos/builtin/packages/xrootd/package.py
+++ b/var/spack/repos/builtin/packages/xrootd/package.py
@@ -13,6 +13,8 @@ class Xrootd(CMakePackage):
     homepage = "http://xrootd.org"
     url      = "http://xrootd.org/download/v4.6.0/xrootd-4.6.0.tar.gz"
 
+    version('4.12.3', sha256='6f2ca1accc8d49d605706bb556777c753860bf46d845b1ee11393a5cb5987f15')
+    version('4.12.2', sha256='29f7bc3ea51b9d5d310eabd177152245d4160223325933c67f938ed5120f67bb')
     version('4.12.1', sha256='7350d9196a26d17719b839fd242849e3995692fda25f242e67ac6ec907218d13')
     version('4.12.0', sha256='69ef4732256d9a88127de4bfdf96bbf73348e0c70ce1d756264871a0ffadd2fc')
     version('4.11.3', sha256='8e7a64fd55dfb452b6d5f76a9a97c493593943227b377623a3032da9197c7f65')

From 2b58b3a1bfc5c30f8640601f3bfd2db8b723eb3a Mon Sep 17 00:00:00 2001
From: Peter Scheibel <scheibel1@llnl.gov>
Date: Fri, 12 Jun 2020 18:12:35 -0700
Subject: [PATCH 697/802] replace 'no' with 'none' as possible value of
 'threads' variant (#17063)

---
 .../repos/builtin/packages/libflame/package.py    | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/libflame/package.py b/var/spack/repos/builtin/packages/libflame/package.py
index 1a8de4b47a4..7d7a9837d34 100644
--- a/var/spack/repos/builtin/packages/libflame/package.py
+++ b/var/spack/repos/builtin/packages/libflame/package.py
@@ -30,9 +30,9 @@ class Libflame(AutotoolsPackage):
             ' to their corresponding native C implementations'
             ' in libflame.')
 
-    variant('threads', default='no',
+    variant('threads', default='none',
             description='Multithreading support',
-            values=('pthreads', 'openmp', 'no'),
+            values=('pthreads', 'openmp', 'none'),
             multi=False)
 
     variant('static', default=True,
@@ -70,6 +70,12 @@ def flag_handler(self, name, flags):
             flags.append('-std=gnu99')
         return (flags, None, None)
 
+    def enable_or_disable_threads(self, variant, options):
+        opt_val = self.spec.variants['threads'].value
+        if variant_val == 'none':
+            opt_val = 'no'
+        return ['--enable-multithreading={0}'.format(opt_val)]
+
     def configure_args(self):
         # Libflame has a secondary dependency on BLAS,
         # but doesn't know which library name to expect:
@@ -96,10 +102,9 @@ def configure_args(self):
         else:
             config_args.append("--disable-debug")
 
-        config_args.append('--enable-multithreading='
-                           + self.spec.variants['threads'].value)
+        config_args.extend(self.enable_or_disable('threads'))
 
-        if 'no' != self.spec.variants['threads'].value:
+        if 'none' != self.spec.variants['threads'].value:
             config_args.append("--enable-supermatrix")
         else:
             config_args.append("--disable-supermatrix")

From 405303638819fbc8a16714a91ed36e344131dee0 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Sat, 13 Jun 2020 09:18:38 +0800
Subject: [PATCH 698/802] fix depends issue and support for aarch64 (#17045)

---
 .../repos/builtin/packages/mysql/package.py     | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/mysql/package.py b/var/spack/repos/builtin/packages/mysql/package.py
index 7501d57cbd0..80b49865b6f 100644
--- a/var/spack/repos/builtin/packages/mysql/package.py
+++ b/var/spack/repos/builtin/packages/mysql/package.py
@@ -22,6 +22,7 @@ class Mysql(CMakePackage):
     version('8.0.13', sha256='d85eb7f98b6aa3e2c6fe38263bf40b22acb444a4ce1f4668473e9e59fb98d62e')
     version('8.0.12', sha256='69f16e20834dbc60cb28d6df7351deda323330b9de685d22415f135bcedd1b20')
     version('8.0.11', sha256='3bde3e30d5d4afcedfc6db9eed5c984237ac7db9480a9cc3bddc026d50700bf9')
+    version('5.7.27', sha256='f8b65872a358d6f5957de86715c0a3ef733b60451dad8d64a8fd1a92bf091bba')
     version('5.7.26', sha256='5f01d579a20199e06fcbc28f0801c3cb545a54a2863ed8634f17fe526480b9f1')
     version('5.7.25', sha256='53751c6243806103114567c1a8b6a3ec27f23c0e132f377a13ce1eb56c63723f')
     version('5.7.24', sha256='05bf0c92c6a97cf85b67fff1ac83ca7b3467aea2bf306374d727fa4f18431f87')
@@ -77,11 +78,16 @@ class Mysql(CMakePackage):
 
     # Each version of MySQL requires a specific version of boost
     # See BOOST_PACKAGE_NAME in cmake/boost.cmake
-    # 8.0.16+
-    depends_on('boost@1.69.0 cxxstd=98', type='build', when='@8.0.16: cxxstd=98')
-    depends_on('boost@1.69.0 cxxstd=11', type='build', when='@8.0.16: cxxstd=11')
-    depends_on('boost@1.69.0 cxxstd=14', type='build', when='@8.0.16: cxxstd=14')
-    depends_on('boost@1.69.0 cxxstd=17', type='build', when='@8.0.16: cxxstd=17')
+    # 8.0.19+
+    depends_on('boost@1.70.0 cxxstd=98', type='build', when='@8.0.19: cxxstd=98')
+    depends_on('boost@1.70.0 cxxstd=11', type='build', when='@8.0.19: cxxstd=11')
+    depends_on('boost@1.70.0 cxxstd=11', type='build', when='@8.0.19: cxxstd=14')
+    depends_on('boost@1.70.0 cxxstd=17', type='build', when='@8.0.19: cxxstd=17')
+    # 8.0.16--8.0.18
+    depends_on('boost@1.69.0 cxxstd=98', type='build', when='@8.0.16:8.0.18 cxxstd=98')
+    depends_on('boost@1.69.0 cxxstd=11', type='build', when='@8.0.16:8.0.18 cxxstd=11')
+    depends_on('boost@1.69.0 cxxstd=14', type='build', when='@8.0.16:8.0.18 cxxstd=14')
+    depends_on('boost@1.69.0 cxxstd=17', type='build', when='@8.0.16:8.0.18 cxxstd=17')
     # 8.0.14--8.0.15
     depends_on('boost@1.68.0 cxxstd=98', type='build', when='@8.0.14:8.0.15 cxxstd=98')
     depends_on('boost@1.68.0 cxxstd=11', type='build', when='@8.0.14:8.0.15 cxxstd=11')
@@ -103,6 +109,7 @@ class Mysql(CMakePackage):
     depends_on('boost@1.59.0 cxxstd=14', when='@5.7.0:5.7.999 cxxstd=14')
     depends_on('boost@1.59.0 cxxstd=17', when='@5.7.0:5.7.999 cxxstd=17')
 
+    depends_on('rpcsvc-proto')
     depends_on('ncurses')
     depends_on('openssl')
     depends_on('libtirpc', when='@5.7.0:')

From a69a213b9b5dad7c5853e964edc77adfc05768c8 Mon Sep 17 00:00:00 2001
From: Ross Miller <rgmiller@ornl.gov>
Date: Fri, 12 Jun 2020 21:19:28 -0400
Subject: [PATCH 699/802] New recipe for building the Log4C package (#17038)

* New recipe for building the Log4C package

* Update Copyright notice
---
 .../repos/builtin/packages/log4c/package.py     | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/log4c/package.py

diff --git a/var/spack/repos/builtin/packages/log4c/package.py b/var/spack/repos/builtin/packages/log4c/package.py
new file mode 100644
index 00000000000..afc9da054a2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/log4c/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Log4c(AutotoolsPackage):
+    """Library for writing log messages from C programs"""
+
+    homepage = "http://log4c.sourceforge.net/"
+    url      = "https://downloads.sourceforge.net/project/log4c/log4c/1.2.4/log4c-1.2.4.tar.gz"
+
+    version('1.2.4', sha256='5991020192f52cc40fa852fbf6bbf5bd5db5d5d00aa9905c67f6f0eadeed48ea')
+
+    depends_on('expat@1.95.1:')

From 50a50875f9d3165885683aa9a463e9bc5f56c600 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E5=81=A5=E7=BE=8E=E7=8C=9E=E7=8C=81?=
 <weijianwen@gmail.com>
Date: Sat, 13 Jun 2020 09:36:24 +0800
Subject: [PATCH 700/802] py-healpy: a new package. (#17001)

* py-healpy: a new package.

* Use internal libraries within py-healpy.

* Fix python dependencies.

* Fix python dependency.
---
 .../builtin/packages/py-healpy/package.py     | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-healpy/package.py

diff --git a/var/spack/repos/builtin/packages/py-healpy/package.py b/var/spack/repos/builtin/packages/py-healpy/package.py
new file mode 100644
index 00000000000..d1781d13a17
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-healpy/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyHealpy(PythonPackage):
+    """healpy is a Python package to handle pixelated data on the sphere."""
+
+    homepage = "https://healpy.readthedocs.io/"
+    url      = "https://pypi.python.org/packages/source/h/healpy/healpy-1.13.0.tar.gz"
+
+    version('1.13.0', sha256='d0ae02791c2404002a09c643e9e50bc58e3d258f702c736dc1f39ce1e6526f73')
+    version('1.7.4', sha256='3cca7ed7786ffcca70e2f39f58844667ffb8521180ac890d4da651b459f51442')
+
+    depends_on('python', type=('build', 'run'))
+    depends_on('py-setuptools@3.2:', type='build')
+    depends_on('py-numpy@1.13:', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-astropy', type=('build', 'run'))
+    depends_on('py-matplotlib', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))

From 82f84fb61b5914a3f9d0cff60b8fb1943643cf8a Mon Sep 17 00:00:00 2001
From: victorusu <victorusu@users.noreply.github.com>
Date: Sat, 13 Jun 2020 03:38:17 +0200
Subject: [PATCH 701/802] Reframe 3.0 (#17005)

* Add pygelf Python package

* Update ReFrame package version

* Address styling remarks

* Update var/spack/repos/builtin/packages/reframe/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/reframe/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/reframe/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/reframe/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/reframe/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Address PR remarks

* Remove setuptools runtime dependency

* Address PR remarks

* Address PR remarks

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 .../repos/builtin/packages/reframe/package.py | 30 ++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/reframe/package.py b/var/spack/repos/builtin/packages/reframe/package.py
index 14a307e6e44..ff7581f4c08 100644
--- a/var/spack/repos/builtin/packages/reframe/package.py
+++ b/var/spack/repos/builtin/packages/reframe/package.py
@@ -4,6 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
+import shutil
 
 
 class Reframe(Package):
@@ -22,13 +23,40 @@ class Reframe(Package):
     maintainers = ['victorusu', 'vkarak']
 
     version('master',   branch='master')
+    version('3.0',       sha256='c4fe84a92d961546e4d0e33ca3476ba0d4cebc908eb4e33897f646bd1fd5205b')
     version('2.21',      sha256='f35d4fda2f9672c87d3ef664d9a2d6eb0c01c88218a31772a6645c32c8934c4d')
     version('2.20',      sha256='310c18d705858bbe6bd9a2dc4d382b254c1f093b0671d72363f2111e8c162ba4')
     version('2.17.3',    sha256='dc8dfb2ccb9a966303879b7cdcd188c47063e9b7999cbd5d6255223b066bf357')
     version('2.17.2',    sha256='092241cdc15918040aacb922c806aecb59c5bdc3ff7db034a4f355d39aecc101')
     version('2.17.1',    sha256='0b0d32a892607840a7d668f5dcea6f03f7022a26b23e5042a0faf5b8c41cb146')
 
-    depends_on('python@3.5:', type=('run'))
+    variant("docs", default=False,
+            description="Build ReFrame's man page documentation")
+    variant("gelf", default=False,
+            description="Add graylog handler support")
+
+    depends_on('python@3.5:', when='@2.0:2.999', type='run')
+    depends_on('python@3.6:', when='@3.0:', type='run')
+    depends_on('py-jsonschema', type='run')
+    depends_on('py-setuptools', type='build')
+    depends_on("py-pygelf", when="+gelf", type="run")
+    depends_on("py-sphinx", when="+docs", type="build")
+    depends_on("py-sphinx-rtd-theme", when="+docs", type="build")
 
     def install(self, spec, prefix):
+        if spec.version >= Version('3.0'):
+            if "+docs" in spec:
+                with working_dir("docs"):
+                    make("man")
+                    make("html")
+                    with working_dir("man"):
+                        mkdir('man1')
+                        shutil.move('reframe.1', 'man1')
+                        mkdir('man8')
+                        shutil.move('reframe.settings.8', 'man8')
         install_tree(self.stage.source_path, self.prefix)
+
+    def setup_run_environment(self, env):
+        if spec.version >= Version('3.0'):
+            if "+docs" in spec:
+                env.prepend_path('MANPATH',  self.prefix.docs.man)

From b9cf50d571271be6572339669ac4b507caf9b845 Mon Sep 17 00:00:00 2001
From: Sinan <sbulutw@gmail.com>
Date: Fri, 12 Jun 2020 19:23:55 -0700
Subject: [PATCH 702/802] New package: ocl-icd (#17078)

* new package: ocl-icd

* flake8

Co-authored-by: Sinan81 <Sinan81@github>
---
 .../repos/builtin/packages/ocl-icd/package.py | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/ocl-icd/package.py

diff --git a/var/spack/repos/builtin/packages/ocl-icd/package.py b/var/spack/repos/builtin/packages/ocl-icd/package.py
new file mode 100644
index 00000000000..fa49bab56a7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ocl-icd/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class OclIcd(AutotoolsPackage):
+    """This package aims at creating an Open Source alternative to vendor specific
+OpenCL ICD loaders."""
+
+    homepage = "https://github.com/OCL-dev/ocl-icd"
+    url      = "https://github.com/OCL-dev/ocl-icd/archive/v2.2.12.tar.gz"
+
+    version('2.2.12', sha256='17500e5788304eef5b52dbe784cec197bdae64e05eecf38317840d2d05484272')
+    version('2.2.11', sha256='c1865ef7701b8201ebc6930ed3ac757c7e5cb30f3aa4c1e742a6bc022f4f2292')
+    version('2.2.10', sha256='d0459fa1421e8d86aaf0a4df092185ea63bc4e1a7682d3af261ae5d3fae063c7')
+    version('2.2.9',  sha256='88da749bc2bd75149f0bb6e72eb4a9d74401a54f4508bc730f13cc03c57a17ed')
+    version('2.2.8',  sha256='8a8a405c7d659b905757a358dc467f4aa3d7e4dff1d1624779065764d962a246')
+    version('2.2.7',  sha256='b8e68435904e1a95661c385f24d6924ed28f416985c6db5a3c7448698ad5fea2')
+    version('2.2.6',  sha256='4567cae92f58c1d6ecfc771c456fa95f206d8a5c7c5d6c9010ec688a9fd83750')
+    version('2.2.5',  sha256='50bf51f4544f83e69a5a2f564732a2adca63fbe9511430aba12f8d6f3a53ae59')
+    version('2.2.4',  sha256='92853137ffff393cc74f829357fdd80ac46a82b46c970e80195db86164cca316')
+    version('2.2.3',  sha256='46b8355d90f8cc240555e4e077f223c47b950abeadf3e1af52d6e68d2efc2ff3')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')

From 58332d028e58f568d2080318c374c6087ec9881d Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Sat, 13 Jun 2020 06:31:24 -0700
Subject: [PATCH 703/802] clang: add 'version_argument', remove redundant
 method (#17071)

---
 lib/spack/spack/compilers/clang.py       | 22 ++--------------------
 lib/spack/spack/test/compilers/basics.py |  1 +
 2 files changed, 3 insertions(+), 20 deletions(-)

diff --git a/lib/spack/spack/compilers/clang.py b/lib/spack/spack/compilers/clang.py
index f5c39889ec8..846c3609dc8 100644
--- a/lib/spack/spack/compilers/clang.py
+++ b/lib/spack/spack/compilers/clang.py
@@ -50,6 +50,8 @@ class Clang(Compiler):
     # Subclasses use possible names of Fortran 90 compiler
     fc_names = ['flang', 'gfortran', 'xlf90_r']
 
+    version_argument = '--version'
+
     @property
     def debug_flags(self):
         return ['-gcodeview', '-gdwarf-2', '-gdwarf-3', '-gdwarf-4',
@@ -201,26 +203,6 @@ def fc_pic_flag(self):
 
     required_libs = ['libclang']
 
-    @classmethod
-    @llnl.util.lang.memoized
-    def default_version(cls, comp):
-        """The ``--version`` option works for clang compilers.
-        On most platforms, output looks like this::
-
-            clang version 3.1 (trunk 149096)
-            Target: x86_64-unknown-linux-gnu
-            Thread model: posix
-
-        On macOS, it looks like this::
-
-            Apple LLVM version 7.0.2 (clang-700.1.81)
-            Target: x86_64-apple-darwin15.2.0
-            Thread model: posix
-        """
-        compiler = Executable(comp)
-        output = compiler('--version', output=str, error=str)
-        return cls.extract_version_from_output(output)
-
     @classmethod
     @llnl.util.lang.memoized
     def extract_version_from_output(cls, output):
diff --git a/lib/spack/spack/test/compilers/basics.py b/lib/spack/spack/test/compilers/basics.py
index 3e43cd4e84b..faf18e38715 100644
--- a/lib/spack/spack/test/compilers/basics.py
+++ b/lib/spack/spack/test/compilers/basics.py
@@ -389,6 +389,7 @@ def test_clang_flags():
     supported_flag_test("fc_pic_flag",  "-fPIC", "clang@2.0.0-apple")
 
     # non-Apple Clang.
+    supported_flag_test("version_argument", "--version", "clang@foo.bar")
     supported_flag_test("openmp_flag", "-fopenmp", "clang@3.3")
     unsupported_flag_test("cxx11_flag", "clang@3.2")
     supported_flag_test("cxx11_flag", "-std=c++11", "clang@3.3")

From 59e4caad1d618956c8b56d3b62389adc23309bfa Mon Sep 17 00:00:00 2001
From: Sinan <sbulutw@gmail.com>
Date: Sat, 13 Jun 2020 07:00:46 -0700
Subject: [PATCH 704/802] add dependency for icd variant, or else build fails
 (#17079)

Co-authored-by: Sinan81 <Sinan81@github>
---
 var/spack/repos/builtin/packages/pocl/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/pocl/package.py b/var/spack/repos/builtin/packages/pocl/package.py
index da707344f5d..121b240e288 100644
--- a/var/spack/repos/builtin/packages/pocl/package.py
+++ b/var/spack/repos/builtin/packages/pocl/package.py
@@ -71,6 +71,8 @@ class Pocl(CMakePackage):
     variant("icd", default=False,
             description="Support a system-wide ICD loader")
 
+    depends_on('ocl-icd', when='+icd')
+
     def url_for_version(self, version):
         if version >= Version('1.0'):
             url = "https://github.com/pocl/pocl/archive/v{0}.tar.gz"

From aa50c2c7d05ff8b42b22f814e593ae235235eb75 Mon Sep 17 00:00:00 2001
From: "Mark W. Krentel" <krentel@rice.edu>
Date: Sat, 13 Jun 2020 09:01:42 -0500
Subject: [PATCH 705/802] hpctoolkit: add version 2020.06.12 (#17081)

Add versions 2020.06.12 and develop.
Switch default for variant papi to true.
---
 var/spack/repos/builtin/packages/hpctoolkit/package.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/hpctoolkit/package.py b/var/spack/repos/builtin/packages/hpctoolkit/package.py
index 0bc737eb82e..9de2184d92f 100644
--- a/var/spack/repos/builtin/packages/hpctoolkit/package.py
+++ b/var/spack/repos/builtin/packages/hpctoolkit/package.py
@@ -18,7 +18,9 @@ class Hpctoolkit(AutotoolsPackage):
     git      = "https://github.com/HPCToolkit/hpctoolkit.git"
     maintainers = ['mwkrentel']
 
-    version('master', branch='master')
+    version('develop', branch='develop')
+    version('master',  branch='master')
+    version('2020.06.12', commit='ac6ae1156e77d35596fea743ed8ae768f7222f19')
     version('2020.03.01', commit='94ede4e6fa1e05e6f080be8dc388240ea027f769')
     version('2019.12.28', commit='b4e1877ff96069fd8ed0fdf0e36283a5b4b62240')
     version('2019.08.14', commit='6ea44ed3f93ede2d0a48937f288a2d41188a277c')
@@ -44,7 +46,7 @@ class Hpctoolkit(AutotoolsPackage):
     # We can't build with both PAPI and perfmon for risk of segfault
     # from mismatched header files (unless PAPI installs the perfmon
     # headers).
-    variant('papi', default=False,
+    variant('papi', default=True,
             description='Use PAPI instead of perfmon for access to '
             'the hardware performance counters.')
 
@@ -60,7 +62,7 @@ class Hpctoolkit(AutotoolsPackage):
         ' +graph +regex +shared +multithreaded visibility=global'
     )
 
-    depends_on('binutils+libiberty~nls', type='link', when='@master')
+    depends_on('binutils+libiberty~nls', type='link', when='@2020.04.00:')
     depends_on('binutils@:2.33.1+libiberty~nls', type='link', when='@:2020.03.99')
     depends_on('boost' + boost_libs)
     depends_on('bzip2+shared', type='link')

From 1501de59ed74802f48e32b0657fc6c95997b264a Mon Sep 17 00:00:00 2001
From: Sinan <sbulutw@gmail.com>
Date: Sun, 14 Jun 2020 06:36:10 -0700
Subject: [PATCH 706/802] Package/py-lmfit: add new version (#16975)

* save edits

* tidy up

* Update var/spack/repos/builtin/packages/py-lmfit/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* add python version constraints

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Sinan81 <Sinan81@github>
---
 .../repos/builtin/packages/py-lmfit/package.py  | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-lmfit/package.py b/var/spack/repos/builtin/packages/py-lmfit/package.py
index 4c798622b02..9f70b89aa03 100644
--- a/var/spack/repos/builtin/packages/py-lmfit/package.py
+++ b/var/spack/repos/builtin/packages/py-lmfit/package.py
@@ -12,8 +12,17 @@ class PyLmfit(PythonPackage):
     homepage = "http://lmfit.github.io/lmfit-py/"
     url      = "https://pypi.io/packages/source/l/lmfit/lmfit-0.9.5.tar.gz"
 
-    version('0.9.5', sha256='eebc3c34ed9f3e51bdd927559a5482548c423ad5a0690c6fdcc414bfb5be6667')
+    version('1.0.1',  sha256='d249eb756899360f4d2a544c9458f47fc8f765ac22c09e099530585fd64e286e')
+    version('0.9.15', sha256='cd7bdf47c09a3d49f30dff9a1c7f778973d15d1e1b5dc642f14c22f6630eaf2f')
+    version('0.9.5',  sha256='eebc3c34ed9f3e51bdd927559a5482548c423ad5a0690c6fdcc414bfb5be6667')
 
-    depends_on('py-numpy@1.5:',  type=('build', 'run'))
-    depends_on('py-scipy@0.14:', type=('build', 'run'))
-    depends_on('py-setuptools',  type='build')
+    depends_on('python@3.5:',               type=('build', 'run'), when='@1:')
+    depends_on('python@2.7:2.8,3.5:',       type=('build', 'run'), when='@0.9.15')
+    depends_on('py-asteval@0.9.16',         type=('build', 'run'), when='@0.9.15:')
+    depends_on('py-numpy@1.5:',             type=('build', 'run'), when='@0.9.5:')
+    depends_on('py-numpy@1.16:',            type=('build', 'run'), when='@0.9.15:')
+    depends_on('py-scipy@0.14:',            type=('build', 'run'), when='@0.9.5')
+    depends_on('py-scipy@1.2:',             type=('build', 'run'), when='@0.9.15:')
+    depends_on('py-setuptools',             type='build')
+    depends_on('py-six@1.11:',              type=('build', 'run'), when='@0.9.15')
+    depends_on('py-uncertainties@3.0.1:',   type=('build', 'run'), when='@0.9.15:')

From 6c2e14dfcaf3a2edec0ab36f0d60fd6bdb9c0688 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Mon, 15 Jun 2020 21:56:29 +0800
Subject: [PATCH 707/802] grafana: added new package at v6.7.3 (#16788)

---
 .../repos/builtin/packages/grafana/package.py | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/grafana/package.py

diff --git a/var/spack/repos/builtin/packages/grafana/package.py b/var/spack/repos/builtin/packages/grafana/package.py
new file mode 100644
index 00000000000..c323b942525
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grafana/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Grafana(Package):
+    """The tool for beautiful monitoring and metric analytics & dashboards
+    for Graphite, InfluxDB & Prometheus & More"""
+
+    homepage = "https://grafana.com"
+    url      = "https://github.com/grafana/grafana/archive/v6.7.3.tar.gz"
+
+    version('6.7.3', sha256='2477b70bfc8770ab844ee683f72b5efe8a47324b9779663d8e5259ffb9ddb8d8')
+    version('6.7.2', sha256='dc81cdb77c1c0ae99ae3302a0ef8b3d577f4a717208a90df65da8fcb282122fc')
+    version('6.7.1', sha256='5750d286273069a195679d5586e810b0ca8cdd08ee07dcdd9b52cfaac8c62b89')
+    version('6.7.0', sha256='7f4e3f0d42b8188a334e97062c3bf63ff43af273095ba10147b299e3c1c5a7b7')
+    version('6.6.2', sha256='e11e5971d08e45e277b55e060c0ce3cf25ca0ba144367c53b4836f2d133ed9b8')
+
+    depends_on('go', type='build')
+
+    def install(self, spec, prefix):
+        go = which('go')
+        go('run', 'build.go', 'build')
+        install_tree('bin', prefix.bin)

From 5fc88a7c65a2ab1255e2524a6a000c16129aee67 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Mon, 15 Jun 2020 20:24:56 +0200
Subject: [PATCH 708/802] Skip failing test on MacOS (#17072)

* Skip failing test on MacOS

* Update setup-python action and unpin coverage
---
 .github/workflows/macos_unit_tests.yaml | 4 ++--
 lib/spack/spack/test/llnl/util/lock.py  | 2 ++
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/macos_unit_tests.yaml b/.github/workflows/macos_unit_tests.yaml
index da970edc7ac..71e59a7b143 100644
--- a/.github/workflows/macos_unit_tests.yaml
+++ b/.github/workflows/macos_unit_tests.yaml
@@ -20,13 +20,13 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Setup Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install Python packages
       run: |
           pip install --upgrade pip six setuptools
-          pip install --upgrade codecov coverage==4.5.4
+          pip install --upgrade codecov coverage
           pip install --upgrade flake8 pep8-naming
     - name: Setup Homebrew packages
       run: |
diff --git a/lib/spack/spack/test/llnl/util/lock.py b/lib/spack/spack/test/llnl/util/lock.py
index b2b7cf85acc..a959ea0c73a 100644
--- a/lib/spack/spack/test/llnl/util/lock.py
+++ b/lib/spack/spack/test/llnl/util/lock.py
@@ -1143,6 +1143,8 @@ def read():
                     assert vals['read'] == 1
 
 
+@pytest.mark.skipif('macos' in os.environ.get('GITHUB_WORKFLOW', ''),
+                    reason="Skip failing test for GA on MacOS")
 def test_lock_debug_output(lock_path):
     host = socket.getfqdn()
 

From eb26b4666fffd33625e69d7ebd6a42d6fc93c0b7 Mon Sep 17 00:00:00 2001
From: Itaru Kitayama <ikitayama@users.noreply.github.com>
Date: Tue, 16 Jun 2020 05:21:35 +0900
Subject: [PATCH 709/802] Add 4.5 release to cubelib (#17090)

---
 var/spack/repos/builtin/packages/cubelib/package.py | 1 +
 var/spack/repos/builtin/packages/cubew/package.py   | 1 +
 2 files changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/cubelib/package.py b/var/spack/repos/builtin/packages/cubelib/package.py
index 42b756648d8..7d6181c7c12 100644
--- a/var/spack/repos/builtin/packages/cubelib/package.py
+++ b/var/spack/repos/builtin/packages/cubelib/package.py
@@ -12,6 +12,7 @@ class Cubelib(AutotoolsPackage):
     homepage = "http://www.scalasca.org/software/cube-4.x/download.html"
     url = "http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/cubelib-4.4.tar.gz"
 
+    version('4.5', sha256='98f66837b4a834b1aacbcd4480a242d7a8c4a1b8dd44e02e836b8c7a4f0ffd98')
     version('4.4.4', sha256='adb8216ee3b7701383884417374e7ff946edb30e56640307c65465187dca7512')
     version('4.4.3', sha256='bcd4fa81a5ba37194e590a5d7c3e6c44b448f5e156a175837b77c21206847a8d')
     version('4.4.2', sha256='843335c7d238493f1b4cb8e07555ccfe99a3fa521bf162e9d8eaa6733aa1f949')
diff --git a/var/spack/repos/builtin/packages/cubew/package.py b/var/spack/repos/builtin/packages/cubew/package.py
index d761f102f3b..c21310601b9 100644
--- a/var/spack/repos/builtin/packages/cubew/package.py
+++ b/var/spack/repos/builtin/packages/cubew/package.py
@@ -12,6 +12,7 @@ class Cubew(AutotoolsPackage):
     homepage = "http://www.scalasca.org/software/cube-4.x/download.html"
     url = "http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/cubew-4.4.tar.gz"
 
+    version('4.5', sha256='16bd8fd864197a74ca65f7325761ad75d73d555072326e95e1338cff39f28a5c')
     version('4.4.3', sha256='93fff6cc1e8b0780f0171ef5302a2e1a257f99b6383fbfc1b9b82f925ceff501')
     version('4.4.2', sha256='31a71e9a05e6523de2b86b4026821bbb75fb411eb5b18ae38b27c1f44158014a')
     version('4.4.1', sha256='c09e3f5a3533ebedee2cc7dfaacd7bac4680c14c3fa540669466583a23f04b67')

From 24ff34335bc0051abb9e843d53bc68872267301e Mon Sep 17 00:00:00 2001
From: Matthias Diener <mdiener@illinois.edu>
Date: Mon, 15 Jun 2020 15:50:56 -0500
Subject: [PATCH 710/802] dateutils: add version 0.4.7 (#17106)

---
 var/spack/repos/builtin/packages/dateutils/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/dateutils/package.py b/var/spack/repos/builtin/packages/dateutils/package.py
index 39e616876b7..89277319424 100644
--- a/var/spack/repos/builtin/packages/dateutils/package.py
+++ b/var/spack/repos/builtin/packages/dateutils/package.py
@@ -13,6 +13,7 @@ class Dateutils(AutotoolsPackage):
     homepage = "http://www.fresse.org/dateutils/"
     url      = "https://github.com/hroptatyr/dateutils/releases/download/v0.4.6/dateutils-0.4.6.tar.xz"
 
+    version('0.4.7', sha256='49725457f5bef45ea424baade8999a6e54496e357f64280474ff7134a54f599a')
     version('0.4.6', sha256='26a071317ae5710f226a3e6ba9a54d3764cd9efe3965aecc18e75372088757cd')
     version('0.4.5', sha256='16d6a0fe7b7d49ddbb303f33538dd7304a0d4af5a0369bcbf275db6a5060cbde')
 

From e5066664ab6f89464a90efbf85121663dbcd2132 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 15 Jun 2020 17:10:49 -0700
Subject: [PATCH 711/802] README: Update LLNL release number to Apache-2.0/MIT
 version (#17109)

The release number in the README had not been updated since we did the
relicense to Apache-2.0 OR MIT in v0.12.0. LLNL-CODE-811652 is Spack's
new LLNL release number.
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index a55828808d5..a2d704e6c24 100644
--- a/README.md
+++ b/README.md
@@ -122,4 +122,4 @@ See [LICENSE-MIT](https://github.com/spack/spack/blob/develop/LICENSE-MIT),
 
 SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-LLNL-CODE-647188
+LLNL-CODE-811652

From 01d9063bb1f411b9d57b528119e0b080b3a6e6b2 Mon Sep 17 00:00:00 2001
From: h-denpo <57649496+h-denpo@users.noreply.github.com>
Date: Tue, 16 Jun 2020 12:29:35 +0900
Subject: [PATCH 712/802] ffb: prevent the architecture to be always "x86_64"
 (#17093)

---
 var/spack/repos/builtin/packages/ffb/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/ffb/package.py b/var/spack/repos/builtin/packages/ffb/package.py
index e7c1272a134..d9de2b9862c 100644
--- a/var/spack/repos/builtin/packages/ffb/package.py
+++ b/var/spack/repos/builtin/packages/ffb/package.py
@@ -107,6 +107,10 @@ def edit(self, spec, prefix):
                 m.filter(r'-lmpi_f77', '')
         os.chmod(makeall, 0o755)
 
+        editfile = join_path('lib', 'src', 'Makeall')
+        m = FileFilter(editfile)
+        m.filter(r'x86_64-linux', '{0}-linux'.format(spec.target.family))
+
         editfile = join_path('lib', 'src', 'REVOCAP_Refiner-0.4.3', 'OPTIONS')
         m = FileFilter(editfile)
         m.filter(r'ARCH\s*=.*$', 'ARCH= $(shell arch)-linux')

From cb028aaf12df15127339fa752108fc860a5c3dbf Mon Sep 17 00:00:00 2001
From: David Beckingsale <davidbeckingsale@gmail.com>
Date: Mon, 15 Jun 2020 20:35:23 -0700
Subject: [PATCH 713/802] Update master to main for RAJA and Umpire (#17107)

---
 var/spack/repos/builtin/packages/raja/package.py   | 2 +-
 var/spack/repos/builtin/packages/umpire/package.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/raja/package.py b/var/spack/repos/builtin/packages/raja/package.py
index de9652dbc1e..b7a62180568 100644
--- a/var/spack/repos/builtin/packages/raja/package.py
+++ b/var/spack/repos/builtin/packages/raja/package.py
@@ -13,7 +13,7 @@ class Raja(CMakePackage, CudaPackage):
     git      = "https://github.com/LLNL/RAJA.git"
 
     version('develop', branch='develop', submodules='True')
-    version('master',  branch='master',  submodules='True')
+    version('main',  branch='main',  submodules='True')
     version('0.11.0', tag='v0.11.0', submodules="True")
     version('0.10.1', tag='v0.10.1', submodules="True")
     version('0.10.0', tag='v0.10.0', submodules="True")
diff --git a/var/spack/repos/builtin/packages/umpire/package.py b/var/spack/repos/builtin/packages/umpire/package.py
index fb6b779d1b3..928d8aa80cb 100644
--- a/var/spack/repos/builtin/packages/umpire/package.py
+++ b/var/spack/repos/builtin/packages/umpire/package.py
@@ -15,7 +15,7 @@ class Umpire(CMakePackage, CudaPackage):
     git      = 'https://github.com/LLNL/Umpire.git'
 
     version('develop', branch='develop', submodules='True')
-    version('master', branch='master', submodules='True')
+    version('main', branch='main', submodules='True')
     version('2.1.0', tag='v2.1.0', submodules='True')
     version('2.0.0', tag='v2.0.0', submodules='True')
     version('1.1.0', tag='v1.1.0', submodules='True')

From 32558525f6324b75f30cdc415ef0b996b47bed76 Mon Sep 17 00:00:00 2001
From: Miroslav Stoyanov <30537612+mkstoyanov@users.noreply.github.com>
Date: Mon, 15 Jun 2020 23:44:47 -0400
Subject: [PATCH 714/802] heffte: added v1.0 (#17102)

---
 .../repos/builtin/packages/heffte/package.py  | 42 ++++++++++++++-----
 .../builtin/packages/heffte/threads10.patch   | 13 ++++++
 2 files changed, 44 insertions(+), 11 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/heffte/threads10.patch

diff --git a/var/spack/repos/builtin/packages/heffte/package.py b/var/spack/repos/builtin/packages/heffte/package.py
index 4a3fec0f339..45f9b1ee8c7 100644
--- a/var/spack/repos/builtin/packages/heffte/package.py
+++ b/var/spack/repos/builtin/packages/heffte/package.py
@@ -10,23 +10,43 @@ class Heffte(CMakePackage):
     """Highly Efficient FFT for Exascale"""
 
     homepage = "https://bitbucket.org/icl/heffte"
-    url      = "https://bitbucket.org/icl/heffte/get/v0.1.tar.gz"
+    url      = "https://bitbucket.org/icl/heffte/get/v1.0.tar.gz"
     git      = "https://bitbucket.org/icl/heffte.git"
 
-    version('master', branch='master')
+    maintainers = ['mkstoyanov']
+
+    version('develop', branch='master')
+    version('1.0', sha256='0902479fb5b1bad01438ca0a72efd577a3529c3d8bad0028f3c18d3a4935ca74')
     version('0.2', sha256='4e76ae60982b316c2e873b2e5735669b22620fefa1fc82f325cdb6989bec78d1')
     version('0.1', sha256='d279a03298d2dc76574b1ae1031acb4ea964348cf359273d1afa4668b5bfe748')
 
+    patch('threads10.patch', when='@1.0')
+
+    variant('shared', default=True, description='Builds with shared libraries')
+    variant('fftw', default=False, description='Builds with support for FFTW backend')
+    variant('mkl',  default=False, description='Builds with support for MKL backend')
     variant('cuda', default=False, description='Builds with support for GPUs via CUDA')
 
-    depends_on('fftw')
-    depends_on('mpi')
-    depends_on('cuda', when="+cuda")
+    conflicts('~fftw', when='~mkl~cuda')  # requires at least one backend
+    conflicts('+fftw', when='+mkl')  # old API supports at most one CPU backend
+    conflicts('openmpi~cuda', when='+cuda')  # +cuda requires CUDA enabled OpenMPI
+
+    depends_on('mpi', type=('build', 'run'))
+
+    depends_on('fftw@3.3.8:', when="+fftw", type=('build', 'run'))
+    depends_on('intel@16.0:', when="+mkl", type=('build', 'run'))
+    depends_on('cuda@8.0:', when="+cuda", type=('build', 'run'))
 
     def cmake_args(self):
-        args = ['-DBUILD_SHARED=ON']
-        if '+cuda' in self.spec:
-            args.append('-DBUILD_GPU=ON')
-        else:
-            args.append('-DBUILD_GPU=OFF')
-        return args
+        return [
+            '-DBUILD_SHARED_LIBS={0:1s}'.format(
+                'ON' if '+shared' in self.spec else 'OFF'),
+            '-DBUILD_GPU={0:1s}'.format(
+                'ON' if ('+cuda' in self.spec and
+                         '+fftw' in self.spec) else 'OFF'),
+            '-DHeffte_ENABLE_CUDA={0:1s}'.format(
+                'ON' if '+cuda' in self.spec else 'OFF'),
+            '-DHeffte_ENABLE_FFTW={0:1s}'.format(
+                'ON' if '+fftw' in self.spec else 'OFF'),
+            '-DHeffte_ENABLE_MKL={0:1s}'.format(
+                'ON' if '+mkl' in self.spec else 'OFF'), ]
diff --git a/var/spack/repos/builtin/packages/heffte/threads10.patch b/var/spack/repos/builtin/packages/heffte/threads10.patch
new file mode 100644
index 00000000000..41d55d9bb80
--- /dev/null
+++ b/var/spack/repos/builtin/packages/heffte/threads10.patch
@@ -0,0 +1,13 @@
+diff --git a/cmake/HeffteConfig.cmake b/cmake/HeffteConfig.cmake
+index bd67de9..ca06086 100644
+--- a/cmake/HeffteConfig.cmake
++++ b/cmake/HeffteConfig.cmake
+@@ -19,6 +19,8 @@ if (NOT TARGET MPI::MPI_CXX)
+     find_package(MPI REQUIRED)
+ endif()
+ 
++find_package(Threads)
++
+ if ("@BUILD_SHARED_LIBS@")
+     set(Heffte_SHARED_FOUND "ON")
+ else()

From 70be1038fdc70c36ee0b92e8580d0768eb9e177e Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 16 Jun 2020 11:59:31 +0800
Subject: [PATCH 715/802] memtester: added new package at v4.3.0 (#17097)

---
 .../builtin/packages/memtester/package.py     | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/memtester/package.py

diff --git a/var/spack/repos/builtin/packages/memtester/package.py b/var/spack/repos/builtin/packages/memtester/package.py
new file mode 100644
index 00000000000..7821d1b15df
--- /dev/null
+++ b/var/spack/repos/builtin/packages/memtester/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Memtester(MakefilePackage):
+    """A userspace utility for testing the memory subsystem for faults."""
+
+    homepage = "http://pyropus.ca/software/memtester/"
+    url      = "http://pyropus.ca/software/memtester/old-versions/memtester-4.3.0.tar.gz"
+
+    version('4.3.0', sha256='f9dfe2fd737c38fad6535bbab327da9a21f7ce4ea6f18c7b3339adef6bf5fd88')
+    version('4.2.2', sha256='a494569d58d642c796332a1b7f3b4b86845b52da66c15c96fbeecd74e48dae8e')
+    version('4.2.1', sha256='3433e1c757e56457610f5a97bf1a2d612c609290eba5183dd273e070134a21d2')
+    version('4.2.0', sha256='cb9d5437a0c429d18500bddef93084bb2fead0d5ccfedfd00ee28ff118e52695')
+    version('4.1.3', sha256='ac56f0b6d6d6e58bcf2a3fa7f2c9b29894f5177871f21115a1906c535106acf6')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter("Makefile")
+        makefile.filter("INSTALLPATH\t= /usr/local",
+                        "INSTALLPATH\t= {0}".format(self.prefix))

From d1aa54115c2af1e86cecc558806ae4a3127122e3 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 16 Jun 2020 12:00:53 +0800
Subject: [PATCH 716/802] cyrus-sasl: added new package at 2.1.27 (#17096)

---
 .../builtin/packages/cyrus-sasl/package.py    | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/cyrus-sasl/package.py

diff --git a/var/spack/repos/builtin/packages/cyrus-sasl/package.py b/var/spack/repos/builtin/packages/cyrus-sasl/package.py
new file mode 100644
index 00000000000..98848ccff98
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cyrus-sasl/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class CyrusSasl(AutotoolsPackage):
+    """This is the Cyrus SASL API implementation. It can be used on the
+    client or server side to provide authentication and authorization
+    services."""
+
+    homepage = "https://github.com/cyrusimap/cyrus-sasl"
+    url      = "https://github.com/cyrusimap/cyrus-sasl/archive/cyrus-sasl-2.1.27.tar.gz"
+
+    version('2.1.27', sha256='b564d773803dc4cff42d2bdc04c80f2b105897a724c247817d4e4a99dd6b9976')
+    version('2.1.26', sha256='7c14d1b5bd1434adf2dd79f70538617e6aa2a7bde447454b90b84ac5c4d034ba')
+    version('2.1.25', sha256='8bfd4fa4def54c760e5061f2a74c278384c3b9807f02c4b07dab68b5894cc7c1')
+    version('2.1.24', sha256='1df15c492f7ecb90be49531a347b3df21b041c2e0325dcc4fc5a6e98384c40dd')
+    version('2.1.23', sha256='b1ec43f62d68446a6a5879925c63d94e26089c5a46cd83e061dd685d014c7d1f')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')

From 6f07f8ae3efe28bb62376a0cf8f51b7effc56c98 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 16 Jun 2020 12:08:45 +0800
Subject: [PATCH 717/802] netdata: added new package at v1.22.1 (#17094)

---
 .../repos/builtin/packages/netdata/package.py | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/netdata/package.py

diff --git a/var/spack/repos/builtin/packages/netdata/package.py b/var/spack/repos/builtin/packages/netdata/package.py
new file mode 100644
index 00000000000..830e2334522
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netdata/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Netdata(AutotoolsPackage):
+    """Real-time performance monitoring, done right!"""
+
+    homepage = "https://www.netdata.cloud/"
+    url      = "https://github.com/netdata/netdata/archive/v1.22.1.tar.gz"
+
+    version('1.22.1', sha256='6efd785eab82f98892b4b4017cadfa4ce1688985915499bc75f2f888765a3446')
+
+    depends_on('m4',       type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('libuv')
+    depends_on('libuuid')

From 06c06a5665334ee9038ecd8cab03d75ec70a6d71 Mon Sep 17 00:00:00 2001
From: Sinan <sbulutw@gmail.com>
Date: Mon, 15 Jun 2020 21:15:50 -0700
Subject: [PATCH 718/802] arrayfire: added new package at v3.7.0 (#15598)

Co-authored-by: Sinan81 <Sinan81@github>
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
---
 .../builtin/packages/arrayfire/package.py     | 46 +++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/arrayfire/package.py

diff --git a/var/spack/repos/builtin/packages/arrayfire/package.py b/var/spack/repos/builtin/packages/arrayfire/package.py
new file mode 100644
index 00000000000..983bd7e775e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/arrayfire/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Arrayfire(CMakePackage, CudaPackage):
+    """ArrayFire is a high performance software library for parallel computing
+    with an easy-to-use API. Its array based function set makes parallel
+    programming more accessible."""
+
+    homepage = "http://arrayfire.org/docs/index.htm"
+    git      = "https://github.com/arrayfire/arrayfire.git"
+
+    version('master', submodules=True)
+    version('3.7.0', submodules=True, tag='v3.7.0')
+
+    variant('cuda',   default=False, description='Enable Cuda backend')
+    variant('forge',   default=False, description='Enable graphics library')
+    variant('opencl', default=False, description='Enable OpenCL backend')
+
+    depends_on('boost@1.65:')
+    depends_on('fftw')
+    depends_on('blas')
+    depends_on('cuda@7.5:', when='+cuda')
+    depends_on('opencl +icd', when='+opencl')
+    # TODO add more opencl backends:
+    # currently only Cuda backend is enabled
+    # https://github.com/arrayfire/arrayfire/wiki/Build-Instructions-for-Linux#opencl-backend-dependencies
+
+    depends_on('fontconfig', when='+forge')
+    depends_on('glfw@3.1.4:', when='+forge')
+
+    def cmake_args(self):
+        args = []
+        args.extend([
+            '-DAF_BUILD_CUDA={0}'.format(
+                'ON' if '+cuda' in self.spec else 'OFF'),
+            '-DAF_BUILD_FORGE={0}'.format(
+                'ON' if '+forge' in self.spec else 'OFF'),
+            '-DAF_BUILD_OPENCL={0}'.format(
+                'ON' if '+opencl' in self.spec else 'OFF'),
+        ])
+        return args

From e8fc7871da15ee8050950d5cf436e0cca338b7a6 Mon Sep 17 00:00:00 2001
From: Kai Torben Ohlhus <k.ohlhus@gmail.com>
Date: Tue, 16 Jun 2020 13:22:48 +0900
Subject: [PATCH 719/802] openblas: added v0.3.10. (#17086)

[OpenBLAS 0.3.10](https://github.com/xianyi/OpenBLAS/releases/tag/v0.3.10) was released.
---
 var/spack/repos/builtin/packages/openblas/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index da2b461d396..46cca3afe3c 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -18,6 +18,7 @@ class Openblas(MakefilePackage):
     git      = 'https://github.com/xianyi/OpenBLAS.git'
 
     version('develop', branch='develop')
+    version('0.3.10', sha256='0484d275f87e9b8641ff2eecaa9df2830cbe276ac79ad80494822721de6e1693')
     version('0.3.9', sha256='17d4677264dfbc4433e97076220adc79b050e4f8a083ea3f853a53af253bc380')
     version('0.3.8', sha256='8f86ade36f0dbed9ac90eb62575137388359d97d8f93093b38abe166ad7ef3a8')
     version('0.3.7', sha256='bde136122cef3dd6efe2de1c6f65c10955bbb0cc01a520c2342f5287c28f9379')

From f54c9ae305aa1e3627ee9af1b75e763d284aa1ae Mon Sep 17 00:00:00 2001
From: "Jose E. Roman" <jroman@dsic.upv.es>
Date: Tue, 16 Jun 2020 06:25:30 +0200
Subject: [PATCH 720/802] SLEPc: added v3.13.3 (#17085)

---
 var/spack/repos/builtin/packages/slepc/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py
index 13b88188407..869cceaa59d 100644
--- a/var/spack/repos/builtin/packages/slepc/package.py
+++ b/var/spack/repos/builtin/packages/slepc/package.py
@@ -18,6 +18,7 @@ class Slepc(Package):
     maintainers = ['joseeroman', 'balay']
 
     version('master', branch='master')
+    version('3.13.3', sha256='23d179c22b4b2f22d29fa0ac0a62f5355a964d3bc245a667e9332347c5aa8f81')
     version('3.13.2', sha256='04cb8306cb5d4d990509710d7f8ae949bdc2c7eb850930b8d0b0b5ca99f6c70d')
     version('3.13.1', sha256='f4a5ede4ebdee5e15153ce31c1421209c7b794bd94be1430018615fb0838b879')
     version('3.13.0', sha256='f1f3c2d13a1a6914e7bf4746d38761e107ea866f50927b639e4ad5918dd1e53b')

From 0111f2932f88ddf27fb1eb5584f73d21f5a36fba Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Tue, 16 Jun 2020 07:44:04 +0200
Subject: [PATCH 721/802] pcre2: add version 10.35; JIT support (#17037)

---
 var/spack/repos/builtin/packages/pcre2/package.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/var/spack/repos/builtin/packages/pcre2/package.py b/var/spack/repos/builtin/packages/pcre2/package.py
index eaa5928ae27..2b19f9cb7b9 100644
--- a/var/spack/repos/builtin/packages/pcre2/package.py
+++ b/var/spack/repos/builtin/packages/pcre2/package.py
@@ -14,11 +14,14 @@ class Pcre2(AutotoolsPackage):
     homepage = "http://www.pcre.org"""
     url      = "https://ftp.pcre.org/pub/pcre/pcre2-10.31.tar.bz2"
 
+    version('10.35', sha256='9ccba8e02b0ce78046cdfb52e5c177f0f445e421059e43becca4359c669d4613')
     version('10.31', sha256='e07d538704aa65e477b6a392b32ff9fc5edf75ab9a40ddfc876186c4ff4d68ac')
     version('10.20', sha256='332e287101c9e9567d1ed55391b338b32f1f72c5b5ee7cc81ef2274a53ad487a')
 
     variant('multibyte', default=True,
             description='Enable support for 16 and 32 bit characters.')
+    variant('jit', default=False,
+            description='enable Just-In-Time compiling support')
 
     def configure_args(self):
         args = []
@@ -27,6 +30,9 @@ def configure_args(self):
             args.append('--enable-pcre2-16')
             args.append('--enable-pcre2-32')
 
+        if '+jit' in self.spec:
+            args.append('--enable-jit')
+
         return args
 
     @property

From d4f0a8f70b9ccfbf4ea20d08e34261e52a773e6f Mon Sep 17 00:00:00 2001
From: Jen Herting <jen@herting.cc>
Date: Tue, 16 Jun 2020 01:46:35 -0400
Subject: [PATCH 722/802] [py-torchvision] added dependency of ffmpeg (#17032)

* [py-torchvision] added dependency of ffmpeg

* [py-torchvision] needs ffmpeg >= 3.1. See: https://github.com/pytorch/vision/issues/1597

* [py-torchvision] ffmpeg dependency is only for py-torchvision versions >= 0.4.2.
---
 var/spack/repos/builtin/packages/py-torchvision/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-torchvision/package.py b/var/spack/repos/builtin/packages/py-torchvision/package.py
index 9d4c3a0efaf..2105ec19880 100644
--- a/var/spack/repos/builtin/packages/py-torchvision/package.py
+++ b/var/spack/repos/builtin/packages/py-torchvision/package.py
@@ -42,3 +42,5 @@ class PyTorchvision(PythonPackage):
     # Many of the datasets require additional dependencies to use.
     # These can be installed after the fact.
     depends_on('py-scipy', type='test')
+
+    depends_on('ffmpeg@3.1:', when='@0.4.2:')

From 7e322b31845b2e56358abe5fd241526b20ae534c Mon Sep 17 00:00:00 2001
From: Andrew W Elble <aweits@rit.edu>
Date: Tue, 16 Jun 2020 01:57:00 -0400
Subject: [PATCH 723/802] CUDA: remove preexisting log file before install
 (#17018)

cuda: 10.1 and onward, installers will crash if /tmp/cuda-installer.log
exists

Try to help if user owns the file, otherwise try to provide useful
info. Clean up the file post-install to try to avoid the whole issue.
---
 var/spack/repos/builtin/packages/cuda/package.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py
index 13675fb7744..ce1fdf69b9b 100644
--- a/var/spack/repos/builtin/packages/cuda/package.py
+++ b/var/spack/repos/builtin/packages/cuda/package.py
@@ -8,6 +8,7 @@
 from llnl.util.filesystem import LibraryList
 import os
 import platform
+import llnl.util.tty as tty
 
 # FIXME Remove hack for polymorphic versions
 # This package uses a ugly hack to be able to dispatch, given the same
@@ -85,6 +86,14 @@ def setup_run_environment(self, env):
         env.set('CUDA_HOME', self.prefix)
 
     def install(self, spec, prefix):
+        if os.path.exists('/tmp/cuda-installer.log'):
+            try:
+                os.remove('/tmp/cuda-installer.log')
+            except OSError:
+                if spec.satisfies('@10.1:'):
+                    tty.die("The cuda installer will segfault due to the "
+                            "presence of /tmp/cuda-installer.log "
+                            "please remove the file and try again ")
         runfile = glob(join_path(self.stage.source_path, 'cuda*_linux*'))[0]
         chmod = which('chmod')
         chmod('+x', runfile)
@@ -110,6 +119,10 @@ def install(self, spec, prefix):
             arguments.append('--toolkitpath=%s' % prefix)   # Where to install
 
         runfile(*arguments)
+        try:
+            os.remove('/tmp/cuda-installer.log')
+        except OSError:
+            pass
 
     @property
     def libs(self):

From a492187973fe55600d0c18159b3f374a079a23db Mon Sep 17 00:00:00 2001
From: Sergey Kosukhin <sergey.kosukhin@mpimet.mpg.de>
Date: Tue, 16 Jun 2020 08:05:46 +0200
Subject: [PATCH 724/802] hdf5: fix libtool files (#17009)

---
 .../repos/builtin/packages/hdf5/package.py    | 14 ++++++++++-
 .../repos/builtin/packages/libaec/package.py  | 23 +++++++++++++++++++
 .../repos/builtin/packages/libszip/package.py | 16 +++++++++++++
 3 files changed, 52 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index 57032141498..c81ffb74dcd 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -243,7 +243,19 @@ def configure_args(self):
             extra_args.append('--with-default-api-version=' + api)
 
         if '+szip' in self.spec:
-            extra_args.append('--with-szlib=%s' % self.spec['szip'].prefix)
+            szip_spec = self.spec['szip']
+            # The configure script of HDF5 accepts a comma-separated tuple of
+            # two paths: the first one points to the directory with include
+            # files, the second one points to the directory with library files.
+            # If the second path is not specified, the configure script assumes
+            # that it equals to prefix/lib. However, the correct directory
+            # might be prefix/lib64. It is not a problem when the building is
+            # done with Spack's compiler wrapper but it makes the Libtool
+            # files (*.la) invalid, which makes it problematic to use the
+            # installed library outside of Spack environment.
+            extra_args.append('--with-szlib=%s,%s' %
+                              (szip_spec.headers.directories[0],
+                               szip_spec.libs.directories[0]))
         else:
             extra_args.append('--without-szlib')
 
diff --git a/var/spack/repos/builtin/packages/libaec/package.py b/var/spack/repos/builtin/packages/libaec/package.py
index 5f12c653f1a..3ea9833b62c 100644
--- a/var/spack/repos/builtin/packages/libaec/package.py
+++ b/var/spack/repos/builtin/packages/libaec/package.py
@@ -22,3 +22,26 @@ class Libaec(CMakePackage):
     version('1.0.2', sha256='b9e5bbbc8bf9cbfd3b9b4ce38b3311f2c88d3d99f476edb35590eb0006aa1fc5')
     version('1.0.1', sha256='3668eb4ed36724441e488a7aadc197426afef4b1e8bd139af6d3e36023906459')
     version('1.0.0', sha256='849f08b08ddaaffe543d06d0ced5e4ee3e526b13a67c5f422d126b1c9cf1b546')
+
+    @property
+    def libs(self):
+        query = self.spec.last_query
+
+        libraries = ['libaec']
+
+        if 'szip' == query.name or 'szip' in query.extra_parameters:
+            libraries.insert(0, 'libsz')
+
+        shared = 'static' not in query.extra_parameters
+
+        libs = find_libraries(
+            libraries, root=self.prefix, shared=shared, recursive=True
+        )
+
+        if not libs:
+            msg = 'Unable to recursively locate {0} {1} libraries in {2}'
+            raise spack.error.NoLibrariesError(
+                msg.format('shared' if shared else 'static',
+                           self.spec.name,
+                           self.spec.prefix))
+        return libs
diff --git a/var/spack/repos/builtin/packages/libszip/package.py b/var/spack/repos/builtin/packages/libszip/package.py
index 00a2b9b5bcb..b72e2ba2765 100644
--- a/var/spack/repos/builtin/packages/libszip/package.py
+++ b/var/spack/repos/builtin/packages/libszip/package.py
@@ -24,6 +24,22 @@ class Libszip(AutotoolsPackage):
     version('2.1.1', sha256='21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412')
     version('2.1',   sha256='a816d95d5662e8279625abdbea7d0e62157d7d1f028020b1075500bf483ed5ef')
 
+    @property
+    def libs(self):
+        shared = 'static' not in self.spec.last_query.extra_parameters
+
+        libs = find_libraries(
+            'libsz', root=self.prefix, shared=shared, recursive=True
+        )
+
+        if not libs:
+            msg = 'Unable to recursively locate {0} {1} libraries in {2}'
+            raise spack.error.NoLibrariesError(
+                msg.format('shared' if shared else 'static',
+                           self.spec.name,
+                           self.spec.prefix))
+        return libs
+
     def configure_args(self):
         return [
             '--enable-production',

From 8882dc0d96fe589ef7e20bc21a67f77c9bc8e595 Mon Sep 17 00:00:00 2001
From: John Jolly <john.jolly@gmail.com>
Date: Sat, 6 Jun 2020 00:20:58 -0600
Subject: [PATCH 725/802] chill: Update dependency versions

Specified Python to be v2.7 only, as Python3 support is not currently
implemented in chill.

Update chill dependency versions for the following libraries to the
specific versions:

* rose:  v0.9.13.0
* bison: v3.4.2

Both rose and iegenlib are build time dependencies, but are also run
time dependencies. Added 'run' to the build type for both dependencies.
---
 var/spack/repos/builtin/packages/chill/package.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/chill/package.py b/var/spack/repos/builtin/packages/chill/package.py
index d33ab4a9591..96afa55379b 100644
--- a/var/spack/repos/builtin/packages/chill/package.py
+++ b/var/spack/repos/builtin/packages/chill/package.py
@@ -19,15 +19,16 @@ class Chill(AutotoolsPackage):
     version('0.3', sha256='574b622368a6bfaadbe9c1fa02fabefdc6c006069246f67d299f943b7e1d8aa3')
 
     depends_on('boost@1.66.0 cxxstd=11', type='build')
-    depends_on('rose@0.9.10.0 +cxx11', type='build')
+    depends_on('rose@0.9.13.0: +cxx11', type=('build', 'run'))
     depends_on('autoconf', type='build')
     depends_on('automake@1.14:',  type='build')
     depends_on('libtool', type='build')
     depends_on('m4', type='build')
-    depends_on('iegenlib', type='build')
-    depends_on('bison@3.4', type='build')
+    depends_on('iegenlib', type=('build', 'run'))
+    depends_on('bison@3.4.2:', type='build')
     depends_on('flex', type='build')
-    depends_on('python')
+    # Does not currrently work with Python3
+    depends_on('python@2.7:2.8')
 
     build_directory = 'spack-build'
 

From 9f73e60ba9d3775ef4dda9c815412f28ed80b518 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 16 Jun 2020 14:28:44 +0800
Subject: [PATCH 726/802] Add new package: lzop (#17098)

---
 .../repos/builtin/packages/lzop/package.py    | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/lzop/package.py

diff --git a/var/spack/repos/builtin/packages/lzop/package.py b/var/spack/repos/builtin/packages/lzop/package.py
new file mode 100644
index 00000000000..9a7096e01bb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lzop/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Lzop(CMakePackage):
+    """lzop is a file compressor which is very similar to gzip. lzop uses
+    the LZO data compression library for compression services, and its main
+    advantages over gzip are much higher compression and decompression speed
+    (at the cost of some compression ratio)."""
+
+    homepage = "https://www.lzop.org"
+    url      = "https://www.lzop.org/download/lzop-1.03.tar.gz"
+
+    version('1.04',    sha256='7e72b62a8a60aff5200a047eea0773a8fb205caf7acbe1774d95147f305a2f41')
+    version('1.03',    sha256='c1425b8c77d49f5a679d5a126c90ea6ad99585a55e335a613cae59e909dbb2c9')
+    version('1.01',    sha256='28acd94d933befbc3af986abcfe833173fb7563b66533fdb4ac592f38bb944c7')
+
+    depends_on('pkgconfig', type='build')
+    depends_on('lzo')

From e28561241bb63b1661105b76e4ab91bc8d62027d Mon Sep 17 00:00:00 2001
From: vvolkl <valentin.volkl@cern.ch>
Date: Tue, 16 Jun 2020 08:31:41 +0200
Subject: [PATCH 727/802] ROOT: set LD_LIBRARY_PATH when ~rpath (#16899)

Allow Spack to build with ROOT as an external dependency by setting
LD_LIBRARY_PATH: given that the external package was not built by
Spack, dependents would not be able to locate libraries using RPATHs
when running ROOT binaries.
---
 var/spack/repos/builtin/packages/root/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/root/package.py b/var/spack/repos/builtin/packages/root/package.py
index b1591f455e3..0e590e30ae5 100644
--- a/var/spack/repos/builtin/packages/root/package.py
+++ b/var/spack/repos/builtin/packages/root/package.py
@@ -492,12 +492,16 @@ def setup_dependent_build_environment(self, env, dependent_spec):
         env.prepend_path('PATH', self.prefix.bin)
         env.append_path('CMAKE_MODULE_PATH', '{0}/cmake'
                         .format(self.prefix))
+        if "+rpath" not in self.spec:
+            env.prepend_path('LD_LIBRARY_PATH', self.prefix.lib)
 
     def setup_dependent_run_environment(self, env, dependent_spec):
         env.set('ROOTSYS', self.prefix)
         env.set('ROOT_VERSION', 'v{0}'.format(self.version.up_to(1)))
         env.prepend_path('PYTHONPATH', self.prefix.lib)
         env.prepend_path('PATH', self.prefix.bin)
+        if "+rpath" not in self.spec:
+            env.prepend_path('LD_LIBRARY_PATH', self.prefix.lib)
 
     def _process_opts(self, *opt_lists):
         """Process all provided boolean option lists into CMake arguments.

From 0f484380f5ceb86913ed671e1e380df260c82fab Mon Sep 17 00:00:00 2001
From: victorusu <victorusu@users.noreply.github.com>
Date: Tue, 16 Jun 2020 13:49:47 +0200
Subject: [PATCH 728/802] reframe: fix package bugs with v3.0 (#17104)

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---
 var/spack/repos/builtin/packages/reframe/package.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/reframe/package.py b/var/spack/repos/builtin/packages/reframe/package.py
index ff7581f4c08..00e200d3ec2 100644
--- a/var/spack/repos/builtin/packages/reframe/package.py
+++ b/var/spack/repos/builtin/packages/reframe/package.py
@@ -23,7 +23,7 @@ class Reframe(Package):
     maintainers = ['victorusu', 'vkarak']
 
     version('master',   branch='master')
-    version('3.0',       sha256='c4fe84a92d961546e4d0e33ca3476ba0d4cebc908eb4e33897f646bd1fd5205b')
+    version('3.0',       sha256='fb76b4513c03b84f5b3bbbc988f7747e5b58f04c983b3935bab1f2e81adccb82')
     version('2.21',      sha256='f35d4fda2f9672c87d3ef664d9a2d6eb0c01c88218a31772a6645c32c8934c4d')
     version('2.20',      sha256='310c18d705858bbe6bd9a2dc4d382b254c1f093b0671d72363f2111e8c162ba4')
     version('2.17.3',    sha256='dc8dfb2ccb9a966303879b7cdcd188c47063e9b7999cbd5d6255223b066bf357')
@@ -57,6 +57,6 @@ def install(self, spec, prefix):
         install_tree(self.stage.source_path, self.prefix)
 
     def setup_run_environment(self, env):
-        if spec.version >= Version('3.0'):
-            if "+docs" in spec:
+        if self.spec.version >= Version('3.0'):
+            if "+docs" in self.spec:
                 env.prepend_path('MANPATH',  self.prefix.docs.man)

From 4b48f70393a20ef65f5e1394226d3829997431c5 Mon Sep 17 00:00:00 2001
From: "Tomoki, Karatsu" <49965247+t-karatsu@users.noreply.github.com>
Date: Tue, 16 Jun 2020 21:51:29 +0900
Subject: [PATCH 729/802] gobject-introspection: build sequentially when using
 the Fujitsu compiler. (#17092)

---
 .../repos/builtin/packages/gobject-introspection/package.py   | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/gobject-introspection/package.py b/var/spack/repos/builtin/packages/gobject-introspection/package.py
index 294d1ba46e7..20823fd77fe 100644
--- a/var/spack/repos/builtin/packages/gobject-introspection/package.py
+++ b/var/spack/repos/builtin/packages/gobject-introspection/package.py
@@ -73,3 +73,7 @@ def install(self, spec, prefix):
 
     def setup_build_environment(self, env):
         env.set('SPACK_SBANG', "%s/bin/sbang" % spack_root)
+
+    @property
+    def parallel(self):
+        return not self.spec.satisfies('%fj')

From 0095c4c25c459b5d7d25ce0462eed753b4036166 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 16 Jun 2020 10:45:36 -0700
Subject: [PATCH 730/802] python: fix distutils for python modules (e.g.
 matplotlib) with  C and C++ source files (#16856)

* python: adding a distutils fix to improve build compatibility for C++ extension modules (e.g. py-matplotlib)

* python: added C/C++ distutils patches for python@3.6:3.8
---
 .../repos/builtin/packages/python/package.py  |  14 +
 .../python/python-2.7-distutils-C++.patch     | 260 ++++++++++++++++++
 .../python/python-3.6-distutils-C++.patch     | 241 ++++++++++++++++
 .../python/python-3.7+-distutils-C++.patch    | 257 +++++++++++++++++
 4 files changed, 772 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/python/python-2.7-distutils-C++.patch
 create mode 100644 var/spack/repos/builtin/packages/python/python-3.6-distutils-C++.patch
 create mode 100644 var/spack/repos/builtin/packages/python/python-3.7+-distutils-C++.patch

diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 2311f6ad39a..7a143695a38 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -157,6 +157,20 @@ class Python(AutotoolsPackage):
         # a Mac.
         depends_on('libuuid', when='+uuid')
 
+    # Python needs to be patched to build extensions w/ mixed C/C++ code:
+    # https://github.com/NixOS/nixpkgs/pull/19585/files
+    # https://bugs.python.org/issue1222585
+    #
+    # NOTE: This patch puts Spack's default Python installation out of
+    # sync with standard Python installs. If you're using such an
+    # installation as an external and encountering build issues with mixed
+    # C/C++ modules, consider installing a Spack-managed Python with
+    # this patch instead. For more information, see:
+    # https://github.com/spack/spack/pull/16856
+    patch('python-2.7-distutils-C++.patch', when='@2.7')
+    patch('python-3.6-distutils-C++.patch', when='@3.6')
+    patch('python-3.7+-distutils-C++.patch', when='@3.7:3.8')
+
     patch('tkinter.patch', when='@:2.8,3.3:3.7 platform=darwin')
 
     # Ensure that distutils chooses correct compiler option for RPATH on cray:
diff --git a/var/spack/repos/builtin/packages/python/python-2.7-distutils-C++.patch b/var/spack/repos/builtin/packages/python/python-2.7-distutils-C++.patch
new file mode 100644
index 00000000000..d6710066d53
--- /dev/null
+++ b/var/spack/repos/builtin/packages/python/python-2.7-distutils-C++.patch
@@ -0,0 +1,260 @@
+--- a/Lib/distutils/cygwinccompiler.py
++++ b/Lib/distutils/cygwinccompiler.py
+@@ -117,8 +117,10 @@
+         # dllwrap 2.10.90 is buggy
+         if self.ld_version >= "2.10.90":
+             self.linker_dll = "gcc"
++            self.linker_dll_cxx = "g++"
+         else:
+             self.linker_dll = "dllwrap"
++            self.linker_dll_cxx = "dllwrap"
+ 
+         # ld_version >= "2.13" support -shared so use it instead of
+         # -mdll -static
+@@ -132,9 +134,13 @@
+         self.set_executables(compiler='gcc -mcygwin -O -Wall',
+                              compiler_so='gcc -mcygwin -mdll -O -Wall',
+                              compiler_cxx='g++ -mcygwin -O -Wall',
++                             compiler_so_cxx='g++ -mcygwin -mdll -O -Wall',
+                              linker_exe='gcc -mcygwin',
+                              linker_so=('%s -mcygwin %s' %
+-                                        (self.linker_dll, shared_option)))
++                                        (self.linker_dll, shared_option)),
++                             linker_exe_cxx='g++ -mcygwin',
++                             linker_so_cxx=('%s -mcygwin %s' %
++                                            (self.linker_dll_cxx, shared_option)))
+ 
+         # cygwin and mingw32 need different sets of libraries
+         if self.gcc_version == "2.91.57":
+@@ -160,8 +166,12 @@
+                 raise CompileError, msg
+         else: # for other files use the C-compiler
+             try:
+-                self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
+-                           extra_postargs)
++                if self.detect_language(src) == 'c++':
++                    self.spawn(self.compiler_so_cxx + cc_args + [src, '-o', obj] +
++                               extra_postargs)
++                else:
++                    self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
++                               extra_postargs)
+             except DistutilsExecError, msg:
+                 raise CompileError, msg
+ 
+@@ -327,9 +337,14 @@
+         self.set_executables(compiler='gcc%s -O -Wall' % no_cygwin,
+                              compiler_so='gcc%s -mdll -O -Wall' % no_cygwin,
+                              compiler_cxx='g++%s -O -Wall' % no_cygwin,
++                             compiler_so_cxx='g++%s -mdll -O -Wall' % no_cygwin,
+                              linker_exe='gcc%s' % no_cygwin,
+                              linker_so='%s%s %s %s'
+                                     % (self.linker_dll, no_cygwin,
++                                       shared_option, entry_point),
++                             linker_exe_cxx='g++%s' % no_cygwin,
++                             linker_so_cxx='%s%s %s %s'
++                                    % (self.linker_dll_cxx, no_cygwin,
+                                        shared_option, entry_point))
+         # Maybe we should also append -mthreads, but then the finished
+         # dlls need another dll (mingwm10.dll see Mingw32 docs)
+--- a/Lib/distutils/emxccompiler.py
++++ b/Lib/distutils/emxccompiler.py
+@@ -65,8 +65,12 @@
+         # XXX optimization, warnings etc. should be customizable.
+         self.set_executables(compiler='gcc -Zomf -Zmt -O3 -fomit-frame-pointer -mprobe -Wall',
+                              compiler_so='gcc -Zomf -Zmt -O3 -fomit-frame-pointer -mprobe -Wall',
++                             compiler_cxx='g++ -Zomf -Zmt -O3 -fomit-frame-pointer -mprobe -Wall',
++                             compiler_so_cxx='g++ -Zomf -Zmt -O3 -fomit-frame-pointer -mprobe -Wall',
+                              linker_exe='gcc -Zomf -Zmt -Zcrtdll',
+-                             linker_so='gcc -Zomf -Zmt -Zcrtdll -Zdll')
++                             linker_so='gcc -Zomf -Zmt -Zcrtdll -Zdll',
++                             linker_exe_cxx='g++ -Zomf -Zmt -Zcrtdll',
++                             linker_so_cxx='g++ -Zomf -Zmt -Zcrtdll -Zdll')
+ 
+         # want the gcc library statically linked (so that we don't have
+         # to distribute a version dependent on the compiler we have)
+@@ -83,8 +87,12 @@
+                 raise CompileError, msg
+         else: # for other files use the C-compiler
+             try:
+-                self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
+-                           extra_postargs)
++                if self.detect_language(src) == 'c++':
++                    self.spawn(self.compiler_so_cxx + cc_args + [src, '-o', obj] +
++                               extra_postargs)
++                else:
++                    self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
++                               extra_postargs)
+             except DistutilsExecError, msg:
+                 raise CompileError, msg
+ 
+--- a/Lib/distutils/sysconfig.py
++++ b/Lib/distutils/sysconfig.py
+@@ -170,10 +170,12 @@
+                 _osx_support.customize_compiler(_config_vars)
+                 _config_vars['CUSTOMIZED_OSX_COMPILER'] = 'True'
+ 
+-        (cc, cxx, opt, cflags, ccshared, ldshared, so_ext, ar, ar_flags) = \
+-            get_config_vars('CC', 'CXX', 'OPT', 'CFLAGS',
+-                            'CCSHARED', 'LDSHARED', 'SO', 'AR',
+-                            'ARFLAGS')
++        (cc, cxx, ccshared, ldshared, ldcxxshared, so_ext, ar, ar_flags) = \
++            get_config_vars('CC', 'CXX', 'CCSHARED', 'LDSHARED', 'LDCXXSHARED',
++                            'SO', 'AR', 'ARFLAGS')
++
++        cflags = ''
++        cxxflags = ''
+ 
+         if 'CC' in os.environ:
+             newcc = os.environ['CC']
+@@ -188,19 +190,27 @@
+             cxx = os.environ['CXX']
+         if 'LDSHARED' in os.environ:
+             ldshared = os.environ['LDSHARED']
++        if 'LDCXXSHARED' in os.environ:
++            ldcxxshared = os.environ['LDCXXSHARED']
+         if 'CPP' in os.environ:
+             cpp = os.environ['CPP']
+         else:
+             cpp = cc + " -E"           # not always
+         if 'LDFLAGS' in os.environ:
+             ldshared = ldshared + ' ' + os.environ['LDFLAGS']
++            ldcxxshared = ldcxxshared + ' ' + os.environ['LDFLAGS']
+         if 'CFLAGS' in os.environ:
+-            cflags = opt + ' ' + os.environ['CFLAGS']
++            cflags = os.environ['CFLAGS']
+             ldshared = ldshared + ' ' + os.environ['CFLAGS']
++        if 'CXXFLAGS' in os.environ:
++            cxxflags = os.environ['CXXFLAGS']
++            ldcxxshared = ldcxxshared + ' ' + os.environ['CXXFLAGS']
+         if 'CPPFLAGS' in os.environ:
+             cpp = cpp + ' ' + os.environ['CPPFLAGS']
+             cflags = cflags + ' ' + os.environ['CPPFLAGS']
++            cxxflags = cxxflags + ' ' + os.environ['CPPFLAGS']
+             ldshared = ldshared + ' ' + os.environ['CPPFLAGS']
++            ldcxxshared = ldcxxshared + ' ' + os.environ['CPPFLAGS']
+         if 'AR' in os.environ:
+             ar = os.environ['AR']
+         if 'ARFLAGS' in os.environ:
+@@ -209,13 +219,17 @@
+             archiver = ar + ' ' + ar_flags
+ 
+         cc_cmd = cc + ' ' + cflags
++        cxx_cmd = cxx + ' ' + cxxflags
+         compiler.set_executables(
+             preprocessor=cpp,
+             compiler=cc_cmd,
+             compiler_so=cc_cmd + ' ' + ccshared,
+-            compiler_cxx=cxx,
++            compiler_cxx=cxx_cmd,
++            compiler_so_cxx=cxx_cmd + ' ' + ccshared,
+             linker_so=ldshared,
+             linker_exe=cc,
++            linker_so_cxx=ldcxxshared,
++            linker_exe_cxx=cxx,
+             archiver=archiver)
+ 
+         compiler.shared_lib_extension = so_ext
+--- a/Lib/distutils/unixccompiler.py
++++ b/Lib/distutils/unixccompiler.py
+@@ -55,14 +55,17 @@
+     # are pretty generic; they will probably have to be set by an outsider
+     # (eg. using information discovered by the sysconfig about building
+     # Python extensions).
+-    executables = {'preprocessor' : None,
+-                   'compiler'     : ["cc"],
+-                   'compiler_so'  : ["cc"],
+-                   'compiler_cxx' : ["cc"],
+-                   'linker_so'    : ["cc", "-shared"],
+-                   'linker_exe'   : ["cc"],
+-                   'archiver'     : ["ar", "-cr"],
+-                   'ranlib'       : None,
++    executables = {'preprocessor'    : None,
++                   'compiler'        : ["cc"],
++                   'compiler_so'     : ["cc"],
++                   'compiler_cxx'    : ["c++"],
++                   'compiler_so_cxx' : ["c++"],
++                   'linker_so'       : ["cc", "-shared"],
++                   'linker_exe'      : ["cc"],
++                   'linker_so_cxx'   : ["c++", "-shared"],
++                   'linker_exe_cxx'  : ["c++"],
++                   'archiver'        : ["ar", "-cr"],
++                   'ranlib'          : None,
+                   }
+ 
+     if sys.platform[:6] == "darwin":
+@@ -112,12 +115,19 @@
+ 
+     def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts):
+         compiler_so = self.compiler_so
++        compiler_so_cxx = self.compiler_so_cxx
+         if sys.platform == 'darwin':
+             compiler_so = _osx_support.compiler_fixup(compiler_so,
+                                                     cc_args + extra_postargs)
++            compiler_so_cxx = _osx_support.compiler_fixup(compiler_so_cxx,
++                                                    cc_args + extra_postargs)
+         try:
+-            self.spawn(compiler_so + cc_args + [src, '-o', obj] +
+-                       extra_postargs)
++            if self.detect_language(src) == 'c++':
++                self.spawn(compiler_so_cxx + cc_args + [src, '-o', obj] +
++                           extra_postargs)
++            else:
++                self.spawn(compiler_so + cc_args + [src, '-o', obj] +
++                           extra_postargs)
+         except DistutilsExecError, msg:
+             raise CompileError, msg
+ 
+@@ -174,23 +184,16 @@
+                 ld_args.extend(extra_postargs)
+             self.mkpath(os.path.dirname(output_filename))
+             try:
+-                if target_desc == CCompiler.EXECUTABLE:
+-                    linker = self.linker_exe[:]
++                if target_lang == "c++":
++                    if target_desc == CCompiler.EXECUTABLE:
++                        linker = self.linker_exe_cxx[:]
++                    else:
++                        linker = self.linker_so_cxx[:]
+                 else:
+-                    linker = self.linker_so[:]
+-                if target_lang == "c++" and self.compiler_cxx:
+-                    # skip over environment variable settings if /usr/bin/env
+-                    # is used to set up the linker's environment.
+-                    # This is needed on OSX. Note: this assumes that the
+-                    # normal and C++ compiler have the same environment
+-                    # settings.
+-                    i = 0
+-                    if os.path.basename(linker[0]) == "env":
+-                        i = 1
+-                        while '=' in linker[i]:
+-                            i = i + 1
+-
+-                    linker[i] = self.compiler_cxx[i]
++                    if target_desc == CCompiler.EXECUTABLE:
++                        linker = self.linker_exe[:]
++                    else:
++                        linker = self.linker_so[:]
+ 
+                 if sys.platform == 'darwin':
+                     linker = _osx_support.compiler_fixup(linker, ld_args)
+--- a/Lib/_osx_support.py
++++ b/Lib/_osx_support.py
+@@ -14,13 +14,13 @@
+ # configuration variables that may contain universal build flags,
+ # like "-arch" or "-isdkroot", that may need customization for
+ # the user environment
+-_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'LDFLAGS', 'CPPFLAGS', 'BASECFLAGS',
+-                            'BLDSHARED', 'LDSHARED', 'CC', 'CXX',
+-                            'PY_CFLAGS', 'PY_LDFLAGS', 'PY_CPPFLAGS',
+-                            'PY_CORE_CFLAGS')
++_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'CXXFLAGS', 'LDFLAGS', 'CPPFLAGS',
++                          'BASECFLAGS', 'BLDSHARED', 'LDSHARED', 'LDCXXSHARED',
++                          'CC', 'CXX', 'PY_CFLAGS', 'PY_LDFLAGS',
++                          'PY_CPPFLAGS', 'PY_CORE_CFLAGS')
+ 
+ # configuration variables that may contain compiler calls
+-_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'CC', 'CXX')
++_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'LDCXXSHARED', 'CC', 'CXX')
+ 
+ # prefix added to original configuration variable names
+ _INITPRE = '_OSX_SUPPORT_INITIAL_'
diff --git a/var/spack/repos/builtin/packages/python/python-3.6-distutils-C++.patch b/var/spack/repos/builtin/packages/python/python-3.6-distutils-C++.patch
new file mode 100644
index 00000000000..5728fad6f77
--- /dev/null
+++ b/var/spack/repos/builtin/packages/python/python-3.6-distutils-C++.patch
@@ -0,0 +1,241 @@
+--- a/Lib/_osx_support.py
++++ b/Lib/_osx_support.py
+@@ -14,13 +14,13 @@ __all__ = [
+ # configuration variables that may contain universal build flags,
+ # like "-arch" or "-isdkroot", that may need customization for
+ # the user environment
+-_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'LDFLAGS', 'CPPFLAGS', 'BASECFLAGS',
+-                            'BLDSHARED', 'LDSHARED', 'CC', 'CXX',
+-                            'PY_CFLAGS', 'PY_LDFLAGS', 'PY_CPPFLAGS',
+-                            'PY_CORE_CFLAGS', 'PY_CORE_LDFLAGS')
++_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'CXXFLAGS', 'LDFLAGS', 'CPPFLAGS',
++                          'BASECFLAGS', 'BLDSHARED', 'LDSHARED', 'LDCXXSHARED',
++                          'CC', 'CXX', 'PY_CFLAGS', 'PY_LDFLAGS',
++                          'PY_CPPFLAGS', 'PY_CORE_LDFLAGS', 'PY_CORE_CFLAGS')
+ 
+ # configuration variables that may contain compiler calls
+-_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'CC', 'CXX')
++_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'LDCXXSHARED', 'CC', 'CXX')
+ 
+ # prefix added to original configuration variable names
+ _INITPRE = '_OSX_SUPPORT_INITIAL_'
+--- a/Lib/distutils/cygwinccompiler.py
++++ b/Lib/distutils/cygwinccompiler.py
+@@ -125,8 +125,10 @@ class CygwinCCompiler(UnixCCompiler):
+         # dllwrap 2.10.90 is buggy
+         if self.ld_version >= "2.10.90":
+             self.linker_dll = "gcc"
++            self.linker_dll_cxx = "g++"
+         else:
+             self.linker_dll = "dllwrap"
++            self.linker_dll_cxx = "dllwrap"
+ 
+         # ld_version >= "2.13" support -shared so use it instead of
+         # -mdll -static
+@@ -140,9 +142,13 @@ class CygwinCCompiler(UnixCCompiler):
+         self.set_executables(compiler='gcc -mcygwin -O -Wall',
+                              compiler_so='gcc -mcygwin -mdll -O -Wall',
+                              compiler_cxx='g++ -mcygwin -O -Wall',
++                             compiler_so_cxx='g++ -mcygwin -mdll -O -Wall',
+                              linker_exe='gcc -mcygwin',
+                              linker_so=('%s -mcygwin %s' %
+-                                        (self.linker_dll, shared_option)))
++                                        (self.linker_dll, shared_option)),
++                             linker_exe_cxx='g++ -mcygwin',
++                             linker_so_cxx=('%s -mcygwin %s' %
++                                            (self.linker_dll_cxx, shared_option)))
+ 
+         # cygwin and mingw32 need different sets of libraries
+         if self.gcc_version == "2.91.57":
+@@ -166,8 +172,12 @@ class CygwinCCompiler(UnixCCompiler):
+                 raise CompileError(msg)
+         else: # for other files use the C-compiler
+             try:
+-                self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
+-                           extra_postargs)
++                if self.detect_language(src) == 'c++':
++                    self.spawn(self.compiler_so_cxx + cc_args + [src, '-o', obj] +
++                               extra_postargs)
++                else:
++                    self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
++                               extra_postargs)
+             except DistutilsExecError as msg:
+                 raise CompileError(msg)
+ 
+@@ -302,9 +312,14 @@ class Mingw32CCompiler(CygwinCCompiler):
+         self.set_executables(compiler='gcc -O -Wall',
+                              compiler_so='gcc -mdll -O -Wall',
+                              compiler_cxx='g++ -O -Wall',
++                             compiler_so_cxx='g++ -mdll -O -Wall',
+                              linker_exe='gcc',
+                              linker_so='%s %s %s'
+                                         % (self.linker_dll, shared_option,
++                                           entry_point),
++                             linker_exe_cxx='g++',
++                             linker_so_cxx='%s %s %s'
++                                        % (self.linker_dll_cxx, shared_option,
+                                            entry_point))
+         # Maybe we should also append -mthreads, but then the finished
+         # dlls need another dll (mingwm10.dll see Mingw32 docs)
+--- a/Lib/distutils/sysconfig.py
++++ b/Lib/distutils/sysconfig.py
+@@ -170,9 +170,11 @@ def customize_compiler(compiler):
+                 _osx_support.customize_compiler(_config_vars)
+                 _config_vars['CUSTOMIZED_OSX_COMPILER'] = 'True'
+ 
+-        (cc, cxx, opt, cflags, ccshared, ldshared, shlib_suffix, ar, ar_flags) = \
+-            get_config_vars('CC', 'CXX', 'OPT', 'CFLAGS',
+-                            'CCSHARED', 'LDSHARED', 'SHLIB_SUFFIX', 'AR', 'ARFLAGS')
++        (cc, cxx, cflags, ccshared, ldshared, ldcxxshared, shlib_suffix, ar, ar_flags) = \
++            get_config_vars('CC', 'CXX', 'CFLAGS', 'CCSHARED', 'LDSHARED', 'LDCXXSHARED',
++                            'SHLIB_SUFFIX', 'AR', 'ARFLAGS')
++
++        cxxflags = cflags
+ 
+         if 'CC' in os.environ:
+             newcc = os.environ['CC']
+@@ -187,19 +189,27 @@ def customize_compiler(compiler):
+             cxx = os.environ['CXX']
+         if 'LDSHARED' in os.environ:
+             ldshared = os.environ['LDSHARED']
++        if 'LDCXXSHARED' in os.environ:
++            ldcxxshared = os.environ['LDCXXSHARED']
+         if 'CPP' in os.environ:
+             cpp = os.environ['CPP']
+         else:
+             cpp = cc + " -E"           # not always
+         if 'LDFLAGS' in os.environ:
+             ldshared = ldshared + ' ' + os.environ['LDFLAGS']
++            ldcxxshared = ldcxxshared + ' ' + os.environ['LDFLAGS']
+         if 'CFLAGS' in os.environ:
+-            cflags = opt + ' ' + os.environ['CFLAGS']
++            cflags = os.environ['CFLAGS']
+             ldshared = ldshared + ' ' + os.environ['CFLAGS']
++        if 'CXXFLAGS' in os.environ:
++            cxxflags = os.environ['CXXFLAGS']
++            ldcxxshared = ldcxxshared + ' ' + os.environ['CXXFLAGS']
+         if 'CPPFLAGS' in os.environ:
+             cpp = cpp + ' ' + os.environ['CPPFLAGS']
+             cflags = cflags + ' ' + os.environ['CPPFLAGS']
++            cxxflags = cxxflags + ' ' + os.environ['CPPFLAGS']
+             ldshared = ldshared + ' ' + os.environ['CPPFLAGS']
++            ldcxxshared = ldcxxshared + ' ' + os.environ['CPPFLAGS']
+         if 'AR' in os.environ:
+             ar = os.environ['AR']
+         if 'ARFLAGS' in os.environ:
+@@ -208,13 +218,17 @@ def customize_compiler(compiler):
+             archiver = ar + ' ' + ar_flags
+ 
+         cc_cmd = cc + ' ' + cflags
++        cxx_cmd = cxx + ' ' + cxxflags
+         compiler.set_executables(
+             preprocessor=cpp,
+             compiler=cc_cmd,
+             compiler_so=cc_cmd + ' ' + ccshared,
+-            compiler_cxx=cxx,
++            compiler_cxx=cxx_cmd,
++            compiler_so_cxx=cxx_cmd + ' ' + ccshared,
+             linker_so=ldshared,
+             linker_exe=cc,
++            linker_so_cxx=ldcxxshared,
++            linker_exe_cxx=cxx,
+             archiver=archiver)
+ 
+         compiler.shared_lib_extension = shlib_suffix
+--- a/Lib/distutils/unixccompiler.py
++++ b/Lib/distutils/unixccompiler.py
+@@ -52,14 +52,17 @@ class UnixCCompiler(CCompiler):
+     # are pretty generic; they will probably have to be set by an outsider
+     # (eg. using information discovered by the sysconfig about building
+     # Python extensions).
+-    executables = {'preprocessor' : None,
+-                   'compiler'     : ["cc"],
+-                   'compiler_so'  : ["cc"],
+-                   'compiler_cxx' : ["cc"],
+-                   'linker_so'    : ["cc", "-shared"],
+-                   'linker_exe'   : ["cc"],
+-                   'archiver'     : ["ar", "-cr"],
+-                   'ranlib'       : None,
++    executables = {'preprocessor'    : None,
++                   'compiler'        : ["cc"],
++                   'compiler_so'     : ["cc"],
++                   'compiler_cxx'    : ["c++"],
++                   'compiler_so_cxx' : ["c++"],
++                   'linker_so'       : ["cc", "-shared"],
++                   'linker_exe'      : ["cc"],
++                   'linker_so_cxx'   : ["c++", "-shared"],
++                   'linker_exe_cxx'  : ["c++"],
++                   'archiver'        : ["ar", "-cr"],
++                   'ranlib'          : None,
+                   }
+ 
+     if sys.platform[:6] == "darwin":
+@@ -110,12 +113,19 @@ class UnixCCompiler(CCompiler):
+ 
+     def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts):
+         compiler_so = self.compiler_so
++        compiler_so_cxx = self.compiler_so_cxx
+         if sys.platform == 'darwin':
+             compiler_so = _osx_support.compiler_fixup(compiler_so,
+                                                     cc_args + extra_postargs)
++            compiler_so_cxx = _osx_support.compiler_fixup(compiler_so_cxx,
++                                                    cc_args + extra_postargs)
+         try:
+-            self.spawn(compiler_so + cc_args + [src, '-o', obj] +
+-                       extra_postargs)
++            if self.detect_language(src) == 'c++':
++                self.spawn(compiler_so_cxx + cc_args + [src, '-o', obj] +
++                           extra_postargs)
++            else:
++                self.spawn(compiler_so + cc_args + [src, '-o', obj] +
++                           extra_postargs)
+         except DistutilsExecError as msg:
+             raise CompileError(msg)
+ 
+@@ -173,22 +183,16 @@ class UnixCCompiler(CCompiler):
+                 ld_args.extend(extra_postargs)
+             self.mkpath(os.path.dirname(output_filename))
+             try:
+-                if target_desc == CCompiler.EXECUTABLE:
+-                    linker = self.linker_exe[:]
++                if target_lang == "c++":
++                    if target_desc == CCompiler.EXECUTABLE:
++                        linker = self.linker_exe_cxx[:]
++                    else:
++                        linker = self.linker_so_cxx[:]
+                 else:
+-                    linker = self.linker_so[:]
+-                if target_lang == "c++" and self.compiler_cxx:
+-                    # skip over environment variable settings if /usr/bin/env
+-                    # is used to set up the linker's environment.
+-                    # This is needed on OSX. Note: this assumes that the
+-                    # normal and C++ compiler have the same environment
+-                    # settings.
+-                    i = 0
+-                    if os.path.basename(linker[0]) == "env":
+-                        i = 1
+-                        while '=' in linker[i]:
+-                            i += 1
+-                    linker[i] = self.compiler_cxx[i]
++                    if target_desc == CCompiler.EXECUTABLE:
++                        linker = self.linker_exe[:]
++                    else:
++                        linker = self.linker_so[:]
+ 
+                 if sys.platform == 'darwin':
+                     linker = _osx_support.compiler_fixup(linker, ld_args)
+--- a/Makefile.pre.in
++++ b/Makefile.pre.in
+@@ -584,10 +584,10 @@ sharedmods: $(BUILDPYTHON) pybuilddir.txt Modules/_math.o
+ 	    *\ -s*|s*) quiet="-q";; \
+ 	    *) quiet="";; \
+ 	esac; \
+-	echo "$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' OPT='$(OPT)' \
++	echo "$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' CFLAGS='$(PY_CFLAGS)' \
+ 		_TCLTK_INCLUDES='$(TCLTK_INCLUDES)' _TCLTK_LIBS='$(TCLTK_LIBS)' \
+ 		$(PYTHON_FOR_BUILD) $(srcdir)/setup.py $$quiet build"; \
+-	$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' OPT='$(OPT)' \
++	$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' CFLAGS='$(PY_CFLAGS)' \
+ 		_TCLTK_INCLUDES='$(TCLTK_INCLUDES)' _TCLTK_LIBS='$(TCLTK_LIBS)' \
+ 		$(PYTHON_FOR_BUILD) $(srcdir)/setup.py $$quiet build
+ 
diff --git a/var/spack/repos/builtin/packages/python/python-3.7+-distutils-C++.patch b/var/spack/repos/builtin/packages/python/python-3.7+-distutils-C++.patch
new file mode 100644
index 00000000000..02daf0a11bf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/python/python-3.7+-distutils-C++.patch
@@ -0,0 +1,257 @@
+diff --git a/Lib/_osx_support.py b/Lib/_osx_support.py
+index db6674e..ccbe09a 100644
+--- a/Lib/_osx_support.py
++++ b/Lib/_osx_support.py
+@@ -14,13 +14,13 @@ __all__ = [
+ # configuration variables that may contain universal build flags,
+ # like "-arch" or "-isdkroot", that may need customization for
+ # the user environment
+-_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'LDFLAGS', 'CPPFLAGS', 'BASECFLAGS',
+-                            'BLDSHARED', 'LDSHARED', 'CC', 'CXX',
+-                            'PY_CFLAGS', 'PY_LDFLAGS', 'PY_CPPFLAGS',
+-                            'PY_CORE_CFLAGS', 'PY_CORE_LDFLAGS')
++_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'CXXFLAGS', 'LDFLAGS', 'CPPFLAGS',
++                          'BASECFLAGS', 'BLDSHARED', 'LDSHARED', 'LDCXXSHARED',
++                          'CC', 'CXX', 'PY_CFLAGS', 'PY_LDFLAGS',
++                          'PY_CPPFLAGS', 'PY_CORE_LDFLAGS', 'PY_CORE_CFLAGS')
+ 
+ # configuration variables that may contain compiler calls
+-_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'CC', 'CXX')
++_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'LDCXXSHARED', 'CC', 'CXX')
+ 
+ # prefix added to original configuration variable names
+ _INITPRE = '_OSX_SUPPORT_INITIAL_'
+diff --git a/Lib/distutils/cygwinccompiler.py b/Lib/distutils/cygwinccompiler.py
+index 6c5d777..640fa2d 100644
+--- a/Lib/distutils/cygwinccompiler.py
++++ b/Lib/distutils/cygwinccompiler.py
+@@ -125,8 +125,10 @@ class CygwinCCompiler(UnixCCompiler):
+         # dllwrap 2.10.90 is buggy
+         if self.ld_version >= "2.10.90":
+             self.linker_dll = "gcc"
++            self.linker_dll_cxx = "g++"
+         else:
+             self.linker_dll = "dllwrap"
++            self.linker_dll_cxx = "dllwrap"
+ 
+         # ld_version >= "2.13" support -shared so use it instead of
+         # -mdll -static
+@@ -140,9 +142,13 @@ class CygwinCCompiler(UnixCCompiler):
+         self.set_executables(compiler='gcc -mcygwin -O -Wall',
+                              compiler_so='gcc -mcygwin -mdll -O -Wall',
+                              compiler_cxx='g++ -mcygwin -O -Wall',
++                             compiler_so_cxx='g++ -mcygwin -mdll -O -Wall',
+                              linker_exe='gcc -mcygwin',
+                              linker_so=('%s -mcygwin %s' %
+-                                        (self.linker_dll, shared_option)))
++                                        (self.linker_dll, shared_option)),
++                             linker_exe_cxx='g++ -mcygwin',
++                             linker_so_cxx=('%s -mcygwin %s' %
++                                            (self.linker_dll_cxx, shared_option)))
+ 
+         # cygwin and mingw32 need different sets of libraries
+         if self.gcc_version == "2.91.57":
+@@ -166,8 +172,12 @@ class CygwinCCompiler(UnixCCompiler):
+                 raise CompileError(msg)
+         else: # for other files use the C-compiler
+             try:
+-                self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
+-                           extra_postargs)
++                if self.detect_language(src) == 'c++':
++                    self.spawn(self.compiler_so_cxx + cc_args + [src, '-o', obj] +
++                               extra_postargs)
++                else:
++                    self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
++                               extra_postargs)
+             except DistutilsExecError as msg:
+                 raise CompileError(msg)
+ 
+@@ -302,9 +312,14 @@ class Mingw32CCompiler(CygwinCCompiler):
+         self.set_executables(compiler='gcc -O -Wall',
+                              compiler_so='gcc -mdll -O -Wall',
+                              compiler_cxx='g++ -O -Wall',
++                             compiler_so_cxx='g++ -mdll -O -Wall',
+                              linker_exe='gcc',
+                              linker_so='%s %s %s'
+                                         % (self.linker_dll, shared_option,
++                                           entry_point),
++                             linker_exe_cxx='g++',
++                             linker_so_cxx='%s %s %s'
++                                        % (self.linker_dll_cxx, shared_option,
+                                            entry_point))
+         # Maybe we should also append -mthreads, but then the finished
+         # dlls need another dll (mingwm10.dll see Mingw32 docs)
+diff --git a/Lib/distutils/sysconfig.py b/Lib/distutils/sysconfig.py
+index 0a034ee..ecf4759 100644
+--- a/Lib/distutils/sysconfig.py
++++ b/Lib/distutils/sysconfig.py
+@@ -188,9 +188,11 @@ def customize_compiler(compiler):
+                 _osx_support.customize_compiler(_config_vars)
+                 _config_vars['CUSTOMIZED_OSX_COMPILER'] = 'True'
+ 
+-        (cc, cxx, cflags, ccshared, ldshared, shlib_suffix, ar, ar_flags) = \
+-            get_config_vars('CC', 'CXX', 'CFLAGS',
+-                            'CCSHARED', 'LDSHARED', 'SHLIB_SUFFIX', 'AR', 'ARFLAGS')
++        (cc, cxx, cflags, ccshared, ldshared, ldcxxshared, shlib_suffix, ar, ar_flags) = \
++            get_config_vars('CC', 'CXX', 'CFLAGS', 'CCSHARED', 'LDSHARED', 'LDCXXSHARED',
++                            'SHLIB_SUFFIX', 'AR', 'ARFLAGS')
++
++        cxxflags = cflags
+ 
+         if 'CC' in os.environ:
+             newcc = os.environ['CC']
+@@ -205,19 +207,27 @@ def customize_compiler(compiler):
+             cxx = os.environ['CXX']
+         if 'LDSHARED' in os.environ:
+             ldshared = os.environ['LDSHARED']
++        if 'LDCXXSHARED' in os.environ:
++            ldcxxshared = os.environ['LDCXXSHARED']
+         if 'CPP' in os.environ:
+             cpp = os.environ['CPP']
+         else:
+             cpp = cc + " -E"           # not always
+         if 'LDFLAGS' in os.environ:
+             ldshared = ldshared + ' ' + os.environ['LDFLAGS']
++            ldcxxshared = ldcxxshared + ' ' + os.environ['LDFLAGS']
+         if 'CFLAGS' in os.environ:
+             cflags = cflags + ' ' + os.environ['CFLAGS']
+             ldshared = ldshared + ' ' + os.environ['CFLAGS']
++        if 'CXXFLAGS' in os.environ:
++            cxxflags = cxxflags + ' ' + os.environ['CXXFLAGS']
++            ldcxxshared = ldcxxshared + ' ' + os.environ['CXXFLAGS']
+         if 'CPPFLAGS' in os.environ:
+             cpp = cpp + ' ' + os.environ['CPPFLAGS']
+             cflags = cflags + ' ' + os.environ['CPPFLAGS']
++            cxxflags = cxxflags + ' ' + os.environ['CPPFLAGS']
+             ldshared = ldshared + ' ' + os.environ['CPPFLAGS']
++            ldcxxshared = ldcxxshared + ' ' + os.environ['CPPFLAGS']
+         if 'AR' in os.environ:
+             ar = os.environ['AR']
+         if 'ARFLAGS' in os.environ:
+@@ -226,13 +236,17 @@ def customize_compiler(compiler):
+             archiver = ar + ' ' + ar_flags
+ 
+         cc_cmd = cc + ' ' + cflags
++        cxx_cmd = cxx + ' ' + cxxflags
+         compiler.set_executables(
+             preprocessor=cpp,
+             compiler=cc_cmd,
+             compiler_so=cc_cmd + ' ' + ccshared,
+-            compiler_cxx=cxx,
++            compiler_cxx=cxx_cmd,
++            compiler_so_cxx=cxx_cmd + ' ' + ccshared,
+             linker_so=ldshared,
+             linker_exe=cc,
++            linker_so_cxx=ldcxxshared,
++            linker_exe_cxx=cxx,
+             archiver=archiver)
+ 
+         compiler.shared_lib_extension = shlib_suffix
+diff --git a/Lib/distutils/unixccompiler.py b/Lib/distutils/unixccompiler.py
+index d10a78d..7e88781 100644
+--- a/Lib/distutils/unixccompiler.py
++++ b/Lib/distutils/unixccompiler.py
+@@ -52,14 +52,17 @@ class UnixCCompiler(CCompiler):
+     # are pretty generic; they will probably have to be set by an outsider
+     # (eg. using information discovered by the sysconfig about building
+     # Python extensions).
+-    executables = {'preprocessor' : None,
+-                   'compiler'     : ["cc"],
+-                   'compiler_so'  : ["cc"],
+-                   'compiler_cxx' : ["cc"],
+-                   'linker_so'    : ["cc", "-shared"],
+-                   'linker_exe'   : ["cc"],
+-                   'archiver'     : ["ar", "-cr"],
+-                   'ranlib'       : None,
++    executables = {'preprocessor'    : None,
++                   'compiler'        : ["cc"],
++                   'compiler_so'     : ["cc"],
++                   'compiler_cxx'    : ["c++"],
++                   'compiler_so_cxx' : ["c++"],
++                   'linker_so'       : ["cc", "-shared"],
++                   'linker_exe'      : ["cc"],
++                   'linker_so_cxx'   : ["c++", "-shared"],
++                   'linker_exe_cxx'  : ["c++"],
++                   'archiver'        : ["ar", "-cr"],
++                   'ranlib'          : None,
+                   }
+ 
+     if sys.platform[:6] == "darwin":
+@@ -110,12 +113,19 @@ class UnixCCompiler(CCompiler):
+ 
+     def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts):
+         compiler_so = self.compiler_so
++        compiler_so_cxx = self.compiler_so_cxx
+         if sys.platform == 'darwin':
+             compiler_so = _osx_support.compiler_fixup(compiler_so,
+                                                     cc_args + extra_postargs)
++            compiler_so_cxx = _osx_support.compiler_fixup(compiler_so_cxx,
++                                                    cc_args + extra_postargs)
+         try:
+-            self.spawn(compiler_so + cc_args + [src, '-o', obj] +
+-                       extra_postargs)
++            if self.detect_language(src) == 'c++':
++                self.spawn(compiler_so_cxx + cc_args + [src, '-o', obj] +
++                           extra_postargs)
++            else:
++                self.spawn(compiler_so + cc_args + [src, '-o', obj] +
++                           extra_postargs)
+         except DistutilsExecError as msg:
+             raise CompileError(msg)
+ 
+@@ -173,30 +183,16 @@ class UnixCCompiler(CCompiler):
+                 ld_args.extend(extra_postargs)
+             self.mkpath(os.path.dirname(output_filename))
+             try:
+-                if target_desc == CCompiler.EXECUTABLE:
+-                    linker = self.linker_exe[:]
++                if target_lang == "c++":
++                    if target_desc == CCompiler.EXECUTABLE:
++                        linker = self.linker_exe_cxx[:]
++                    else:
++                        linker = self.linker_so_cxx[:]
+                 else:
+-                    linker = self.linker_so[:]
+-                if target_lang == "c++" and self.compiler_cxx:
+-                    # skip over environment variable settings if /usr/bin/env
+-                    # is used to set up the linker's environment.
+-                    # This is needed on OSX. Note: this assumes that the
+-                    # normal and C++ compiler have the same environment
+-                    # settings.
+-                    i = 0
+-                    if os.path.basename(linker[0]) == "env":
+-                        i = 1
+-                        while '=' in linker[i]:
+-                            i += 1
+-
+-                    if os.path.basename(linker[i]) == 'ld_so_aix':
+-                        # AIX platforms prefix the compiler with the ld_so_aix
+-                        # script, so we need to adjust our linker index
+-                        offset = 1
++                    if target_desc == CCompiler.EXECUTABLE:
++                        linker = self.linker_exe[:]
+                     else:
+-                        offset = 0
+-
+-                    linker[i+offset] = self.compiler_cxx[i]
++                        linker = self.linker_so[:]
+ 
+                 if sys.platform == 'darwin':
+                     linker = _osx_support.compiler_fixup(linker, ld_args)
+diff --git a/Makefile.pre.in b/Makefile.pre.in
+index 35ca1a8..cfa79df 100644
+--- a/Makefile.pre.in
++++ b/Makefile.pre.in
+@@ -618,10 +618,10 @@ sharedmods: $(BUILDPYTHON) pybuilddir.txt Modules/_math.o
+ 	    *\ -s*|s*) quiet="-q";; \
+ 	    *) quiet="";; \
+ 	esac; \
+-	echo "$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' OPT='$(OPT)' \
++	echo "$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' CFLAGS='$(PY_CFLAGS)' \
+ 		_TCLTK_INCLUDES='$(TCLTK_INCLUDES)' _TCLTK_LIBS='$(TCLTK_LIBS)' \
+ 		$(PYTHON_FOR_BUILD) $(srcdir)/setup.py $$quiet build"; \
+-	$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' OPT='$(OPT)' \
++	$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' CFLAGS='$(PY_CFLAGS)' \
+ 		_TCLTK_INCLUDES='$(TCLTK_INCLUDES)' _TCLTK_LIBS='$(TCLTK_LIBS)' \
+ 		$(PYTHON_FOR_BUILD) $(srcdir)/setup.py $$quiet build
+ 

From e816b66c94410103e3f208f50b63d674599e27c2 Mon Sep 17 00:00:00 2001
From: Omar Padron <omar.padron@kitware.com>
Date: Tue, 16 Jun 2020 14:11:13 -0400
Subject: [PATCH 731/802] fix docker image entrypoints (#17105)

Also removes extraneous prompt and ssh handling logic.
---
 share/spack/docker/centos-6.dockerfile    |  74 +++++----
 share/spack/docker/centos-7.dockerfile    |  74 +++++----
 share/spack/docker/entrypoint.bash        | 172 ++++++++++++++++-----
 share/spack/docker/handle-prompt.sh       | 173 ----------------------
 share/spack/docker/handle-ssh.sh          |  50 -------
 share/spack/docker/ubuntu-1604.dockerfile |  87 +++++------
 share/spack/docker/ubuntu-1804.dockerfile |  87 +++++------
 7 files changed, 275 insertions(+), 442 deletions(-)
 delete mode 100644 share/spack/docker/handle-prompt.sh
 delete mode 100644 share/spack/docker/handle-ssh.sh

diff --git a/share/spack/docker/centos-6.dockerfile b/share/spack/docker/centos-6.dockerfile
index 72aa934f99a..fe919f3c885 100644
--- a/share/spack/docker/centos-6.dockerfile
+++ b/share/spack/docker/centos-6.dockerfile
@@ -16,46 +16,42 @@ COPY share $SPACK_ROOT/share
 COPY var   $SPACK_ROOT/var
 RUN mkdir -p $SPACK_ROOT/opt/spack
 
-RUN yum update -y                                             \
- && yum install -y epel-release                               \
- && yum update -y                                             \
+RUN ln -s $SPACK_ROOT/share/spack/docker/entrypoint.bash \
+          /usr/local/bin/docker-shell \
+ && ln -s $SPACK_ROOT/share/spack/docker/entrypoint.bash \
+          /usr/local/bin/interactive-shell \
+ && ln -s $SPACK_ROOT/share/spack/docker/entrypoint.bash \
+          /usr/local/bin/spack-env
+
+RUN yum update -y \
+ && yum install -y epel-release \
+ && yum update -y \
  && yum --enablerepo epel groupinstall -y "Development Tools" \
- && yum --enablerepo epel install -y                          \
-        curl           findutils gcc-c++    gcc               \
-        gcc-gfortran   git       gnupg2     hostname          \
-        iproute        Lmod      make       patch             \
-        openssh-server python    python-pip tcl               \
-        unzip          which                                  \
- && pip install boto3                                         \
- && rm -rf /var/cache/yum                                     \
+ && yum --enablerepo epel install -y \
+        curl \
+        findutils \
+        gcc-c++ \
+        gcc \
+        gcc-gfortran \
+        git \
+        gnupg2 \
+        hostname \
+        iproute \
+        Lmod \
+        make \
+        patch \
+        python \
+        python-pip \
+        tcl \
+        unzip \
+        which \
+ && pip install boto3 \
+ && rm -rf /var/cache/yum \
  && yum clean all
 
-RUN ( echo ". /usr/share/lmod/lmod/init/bash"                       \
- &&   echo ". \$SPACK_ROOT/share/spack/setup-env.sh"                \
- &&   echo "if [ \"\$CURRENTLY_BUILDING_DOCKER_IMAGE\" '!=' '1' ]"  \
- &&   echo "then"                                                   \
- &&   echo "  . \$SPACK_ROOT/share/spack/spack-completion.bash"     \
- &&   echo "fi"                                                   ) \
-       >> /etc/profile.d/spack.sh                                   \
- && ( echo "f=\"\$SPACK_ROOT/share/spack/docker/handle-ssh.sh\""    \
- &&   echo "if [ -f \"\$f\" ]"                                      \
- &&   echo "then"                                                   \
- &&   echo "  .  \"\$f\""                                           \
- &&   echo "else"                                                   \
- &&   cat  $SPACK_ROOT/share/spack/docker/handle-ssh.sh             \
- &&   echo "fi"                                                   ) \
-       >> /etc/profile.d/handle-ssh.sh                              \
- && ( echo "f=\"\$SPACK_ROOT/share/spack/docker/handle-prompt.sh\"" \
- &&   echo "if [ -f \"\$f\" ]"                                      \
- &&   echo "then"                                                   \
- &&   echo "  .  \"\$f\""                                           \
- &&   echo "else"                                                   \
- &&   cat  $SPACK_ROOT/share/spack/docker/handle-prompt.sh          \
- &&   echo "fi"                                                   ) \
-       >> /etc/profile.d/handle-prompt.sh                           \
- && mkdir -p /root/.spack                                           \
- && cp $SPACK_ROOT/share/spack/docker/modules.yaml                  \
-        /root/.spack/modules.yaml                                   \
+RUN mkdir -p /root/.spack \
+ && cp $SPACK_ROOT/share/spack/docker/modules.yaml \
+        /root/.spack/modules.yaml \
  && rm -rf /root/*.* /run/nologin $SPACK_ROOT/.git
 
 # [WORKAROUND]
@@ -66,10 +62,10 @@ RUN [ -f ~/.profile ]                                               \
  || true
 
 WORKDIR /root
-SHELL ["/bin/bash", "-l", "-c"]
+SHELL ["docker-shell"]
 
 # TODO: add a command to Spack that (re)creates the package cache
 RUN spack spec hdf5+mpi
 
 ENTRYPOINT ["/bin/bash", "/opt/spack/share/spack/docker/entrypoint.bash"]
-CMD ["docker-shell"]
+CMD ["interactive-shell"]
diff --git a/share/spack/docker/centos-7.dockerfile b/share/spack/docker/centos-7.dockerfile
index 6aa969fef82..67affa1af9f 100644
--- a/share/spack/docker/centos-7.dockerfile
+++ b/share/spack/docker/centos-7.dockerfile
@@ -16,46 +16,42 @@ COPY share $SPACK_ROOT/share
 COPY var   $SPACK_ROOT/var
 RUN mkdir -p $SPACK_ROOT/opt/spack
 
-RUN yum update -y                                             \
- && yum install -y epel-release                               \
- && yum update -y                                             \
+RUN ln -s $SPACK_ROOT/share/spack/docker/entrypoint.bash \
+          /usr/local/bin/docker-shell \
+ && ln -s $SPACK_ROOT/share/spack/docker/entrypoint.bash \
+          /usr/local/bin/interactive-shell \
+ && ln -s $SPACK_ROOT/share/spack/docker/entrypoint.bash \
+          /usr/local/bin/spack-env
+
+RUN yum update -y \
+ && yum install -y epel-release \
+ && yum update -y \
  && yum --enablerepo epel groupinstall -y "Development Tools" \
- && yum --enablerepo epel install -y                          \
-        curl           findutils gcc-c++    gcc               \
-        gcc-gfortran   git       gnupg2     hostname          \
-        iproute        Lmod      make       patch             \
-        openssh-server python    python-pip tcl               \
-        unzip          which                                  \
- && pip install boto3                                         \
- && rm -rf /var/cache/yum                                     \
+ && yum --enablerepo epel install -y \
+        curl \
+        findutils \
+        gcc-c++ \
+        gcc \
+        gcc-gfortran \
+        git \
+        gnupg2 \
+        hostname \
+        iproute \
+        Lmod \
+        make \
+        patch \
+        python \
+        python-pip \
+        tcl \
+        unzip \
+        which \
+ && pip install boto3 \
+ && rm -rf /var/cache/yum \
  && yum clean all
 
-RUN ( echo ". /usr/share/lmod/lmod/init/bash"                       \
- &&   echo ". \$SPACK_ROOT/share/spack/setup-env.sh"                \
- &&   echo "if [ \"\$CURRENTLY_BUILDING_DOCKER_IMAGE\" '!=' '1' ]"  \
- &&   echo "then"                                                   \
- &&   echo "  . \$SPACK_ROOT/share/spack/spack-completion.bash"     \
- &&   echo "fi"                                                   ) \
-       >> /etc/profile.d/spack.sh                                   \
- && ( echo "f=\"\$SPACK_ROOT/share/spack/docker/handle-ssh.sh\""    \
- &&   echo "if [ -f \"\$f\" ]"                                      \
- &&   echo "then"                                                   \
- &&   echo "  .  \"\$f\""                                           \
- &&   echo "else"                                                   \
- &&   cat  $SPACK_ROOT/share/spack/docker/handle-ssh.sh             \
- &&   echo "fi"                                                   ) \
-       >> /etc/profile.d/handle-ssh.sh                              \
- && ( echo "f=\"\$SPACK_ROOT/share/spack/docker/handle-prompt.sh\"" \
- &&   echo "if [ -f \"\$f\" ]"                                      \
- &&   echo "then"                                                   \
- &&   echo "  .  \"\$f\""                                           \
- &&   echo "else"                                                   \
- &&   cat  $SPACK_ROOT/share/spack/docker/handle-prompt.sh          \
- &&   echo "fi"                                                   ) \
-       >> /etc/profile.d/handle-prompt.sh                           \
- && mkdir -p /root/.spack                                           \
- && cp $SPACK_ROOT/share/spack/docker/modules.yaml                  \
-        /root/.spack/modules.yaml                                   \
+RUN mkdir -p /root/.spack \
+ && cp $SPACK_ROOT/share/spack/docker/modules.yaml \
+        /root/.spack/modules.yaml \
  && rm -rf /root/*.* /run/nologin $SPACK_ROOT/.git
 
 # [WORKAROUND]
@@ -66,10 +62,10 @@ RUN [ -f ~/.profile ]                                               \
  || true
 
 WORKDIR /root
-SHELL ["/bin/bash", "-l", "-c"]
+SHELL ["docker-shell"]
 
 # TODO: add a command to Spack that (re)creates the package cache
 RUN spack spec hdf5+mpi
 
 ENTRYPOINT ["/bin/bash", "/opt/spack/share/spack/docker/entrypoint.bash"]
-CMD ["docker-shell"]
+CMD ["interactive-shell"]
diff --git a/share/spack/docker/entrypoint.bash b/share/spack/docker/entrypoint.bash
index 775747d904d..fbd7baf2bcd 100755
--- a/share/spack/docker/entrypoint.bash
+++ b/share/spack/docker/entrypoint.bash
@@ -1,45 +1,143 @@
-#! /usr/bin/env bash -e
+#! /usr/bin/env bash
 #
 # Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-unset CURRENTLY_BUILDING_DOCKER_IMAGE
+mode=oneshot
 
-if [ "$1" '=' 'docker-shell' ] ; then
-    if [ -t 0 ] ; then
-        exec bash -il
-    else
-        (
-            echo -n "It looks like you're trying to run an intractive shell"
-            echo -n " session, but either no psuedo-TTY is allocateed for this"
-            echo -n " container's STDIN, or it is closed."
-            echo
-
-            echo -n "Make sure you run docker with the --interactive and --tty"
-            echo -n " options."
-            echo
-        ) >&2
-
-        exit 1
-    fi
-else
-    exec 3>&1
-    exec 4>&2
-
-    exec 1>&-
-    exec 2>&-
-
-    source /etc/profile.d/spack.sh
-    source /etc/profile.d/handle-ssh.sh
-
-    exec 1>&3
-    exec 2>&4
-
-    exec 3>&-
-    exec 4>&-
-
-    spack "$@"
-    exit $?
+if [ "$( basename "$0" )" '=' 'spack-env' ] ; then
+    mode=spackenv
+elif [ "$( basename "$0" )" '=' 'docker-shell' ] ; then
+    mode=dockershell
+elif [ "$( basename "$0" )" '=' 'interactive-shell' ] ; then
+    mode=interactiveshell
+elif [ "$1" '=' 'docker-shell' ] ; then
+    mode=dockershell
+    shift
+elif [ "$1" '=' 'interactive-shell' ] ; then
+    mode=interactiveshell
+    shift
 fi
+
+case "$mode" in
+    "spackenv")
+        # Scenario 1: Run as if the image had no ENTRYPOINT
+        #
+        # Necessary for use cases where the command to run and all
+        # arguments must be accepted in the CMD portion. (e.g.: Gitlab CI
+        # Runners)
+        #
+        # Roughly equivalent to
+        #   docker run ... --entrypoint spack-env ... sh -c "..."
+        #
+        # The shell script runs with spack pre-loaded and ready to use.
+        . $SPACK_ROOT/share/spack/setup-env.sh
+        unset CURRENTLY_BUILDING_DOCKER_IMAGE
+        exec "$@"
+        ;;
+
+    "dockershell")
+        # Scenario 2: Accept shell code from a RUN command in a
+        # Dockerfile
+        #
+        # For new Docker images that start FROM this image as its base.
+        # Prepared so that subsequent RUN commands can take advantage of
+        # Spack without having to manually (re)initialize.
+        #
+        # Example:
+        #   FROM spack/centos7
+        #   COPY spack.yaml .
+        #   RUN spack install  # <- Spack is loaded and ready to use.
+        #                      # No manual initialization necessary.
+        . $SPACK_ROOT/share/spack/setup-env.sh
+        exec bash -c "$*"
+        ;;
+
+    "interactiveshell")
+        # Scenario 3: Run an interactive shell session with Spack
+        # preloaded.
+        #
+        # Create a container meant for an interactive shell session.
+        # Additional checks are performed to ensure that stdin is a tty
+        # and additional shell completion files are sourced.  The user is
+        # presented with a shell prompt from which they may issue Spack
+        # commands.
+        #
+        # This is the default behavior when running with no CMD or
+        # ENTRYPOINT overrides:
+        #   docker run -it spack/centos7
+        if [ -t 0 ] ; then
+            . $SPACK_ROOT/share/spack/setup-env.sh
+            . $SPACK_ROOT/share/spack/spack-completion.bash
+            unset CURRENTLY_BUILDING_DOCKER_IMAGE
+            exec bash -i
+        else
+            (
+                echo -n "It looks like you're trying to run an"
+                echo -n " intractive shell session, but either no"
+                echo -n " psuedo-TTY is allocated for this container's"
+                echo    " STDIN, or it is closed."
+                echo
+
+                echo -n "Make sure you run docker with the --interactive"
+                echo -n " and --tty options."
+                echo
+            ) >&2
+
+            exit 1
+        fi
+        ;;
+
+    "oneshot")
+        # Scenario 4: Run a one-shot Spack command from the host command
+        # line.
+        #
+        # Triggered by providing arguments to `docker run`.  Arguments
+        # are passed along to the container's underlying spack
+        # installation, allowing users to use the image as if it were
+        # spack, itself.  Pass volume mount information to `docker run`
+        # to persist the effects of running in this mode.
+        #
+        # This is the default behavior when running with a CMD override.
+        #
+        # Examples:
+        #   # concretize the same spec on different OSes
+        #   docker run --rm spack/ubuntu-xenial spec zlib
+        #   docker run --rm spack/centos7 spec zlib
+        #
+        #   # a "wetter" dry-run;
+        #   # install a package and then throw away the results.
+        #   docker run --rm spack/centos7 install libiconv
+        #   docker run --rm spack/centos7 find libiconv
+        #     ==> No package matches the query: libiconv
+        #
+        #   # use docker volumes to persist changes
+        #   docker run --rm -v ...:/spack spack/centos7 install ...
+        #   docker run --rm -v ...:/spack spack/centos7 install ...
+        #   docker run --rm -v ...:/spack spack/centos7 install ...
+        exec 3>&1
+        exec 4>&2
+
+        exec 1>&-
+        exec 2>&-
+
+        . $SPACK_ROOT/share/spack/setup-env.sh
+        unset CURRENTLY_BUILDING_DOCKER_IMAGE
+
+        exec 1>&3
+        exec 2>&4
+
+        exec 3>&-
+        exec 4>&-
+
+        spack "$@"
+        exit $?
+        ;;
+
+    *)
+        echo "INTERNAL ERROR - UNRECOGNIZED MODE: $mode" >&2
+        exit 1
+        ;;
+esac
diff --git a/share/spack/docker/handle-prompt.sh b/share/spack/docker/handle-prompt.sh
deleted file mode 100644
index a01047463e2..00000000000
--- a/share/spack/docker/handle-prompt.sh
+++ /dev/null
@@ -1,173 +0,0 @@
-# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-if [ "$CURRENTLY_BUILDING_DOCKER_IMAGE" '!=' '1' ] ; then
-
-if [ x$SPACK_PROMPT '!=' x0 ] ; then
-
-__tmp="`mktemp -d`"
-
-__trylock() {
-    local dir
-    dir="$__tmp/$1.lock"
-    mkdir "$dir" &>/dev/null
-    return $?
-}
-
-__queue_init() {
-    local r
-    local w
-
-    mkdir "$__tmp/$1.read.lock" ; r=$?
-    mkdir "$__tmp/$1.write.lock" ; w=$?
-
-    if [ "$r" '=' '0' -a "$w" '=' '0' ] ; then
-        return 0
-    else
-        return 1
-    fi
-}
-
-__queue_try_read() {
-    __trylock "$1.read"
-    return $?
-}
-
-__queue_try_write() {
-    __trylock "$1.write"
-    return $?
-}
-
-__queue_make_readable() {
-    rm -r "$__tmp/$1.read.lock" &>/dev/null
-    return $?
-}
-
-__queue_make_writable() {
-    rm -r "$__tmp/$1.write.lock" &>/dev/null
-    return $?
-}
-
-__read() {
-    cat "$__tmp/$1" 2> /dev/null
-    return $?
-}
-
-__write() {
-    cat > "$__tmp/$1" 2> /dev/null
-    return $?
-}
-
-__revparse_head() {
-    head="`git -C "$SPACK_ROOT" rev-parse $@ HEAD 2>/dev/null`"
-    result="$?"
-    if [ "$result" '!=' '0' ] ; then
-        head="`git --git-dir="$SPACK_ROOT"/.git \\
-              --work-tree="$SPACK_ROOT" rev-parse $@ HEAD 2>/dev/null`"
-        result="$?"
-    fi
-
-    echo "$head"
-    return $result
-}
-
-__git_head() {
-    head="`__revparse_head --abbrev-ref`"
-    if [ "$?" '=' '0' ] ; then
-        if [ "$head" '=' 'HEAD' ] ; then
-            head="`__revparse_head | cut -c1-8`..."
-        fi
-
-        echo "$head"
-    fi
-}
-
-__update_prompt() {
-    local prompt
-    prompt=''
-    linux_distro="$DOCKERFILE_DISTRO"
-    if [ -n "$linux_distro" ] ; then
-        linux_distro='\[\e[1;34m\][\[\e[0;34m\]'"$linux_distro"'\[\e[1;34m\]]'
-        if [ -n "$prompt" ] ; then
-            prompt="$prompt "
-        fi
-        prompt="$prompt$linux_distro"
-    fi
-
-    git_head="`__git_head`"
-
-    if [ -n "$git_head" ] ; then
-        git_head='\[\e[1;32m\](\[\e[0;32m\]'"$git_head"'\[\e[1;32m\])'
-        if [ -n "$prompt" ] ; then
-            prompt="$prompt "
-        fi
-        prompt="$prompt$git_head"
-    fi
-
-    if [ -n "$prompt" ] ; then
-        prompt="$prompt "
-    fi
-    prompt="$prompt"'\[\e[0;m\]\W: '
-    echo "$prompt" | __write prompt
-}
-
-set -m
-(
-    __queue_init query
-    __queue_init prompt
-
-    __update_prompt
-    __queue_make_readable prompt
-
-    __queue_make_writable query
-
-    while sleep 0.010 ; do
-        last_q_time=''
-
-        while sleep 0.010 ; do
-            q_time="`date +%s%N`"
-            if __queue_try_read query ; then
-                last_q_time="$q_time"
-                __queue_make_writable query
-            fi
-
-            if [ -n "$last_q_time" -a \
-                "$(( (q_time - last_q_time)/10000000 > 100 ))" '=' '1' ] ; then
-                break
-            fi
-        done
-
-        __update_prompt
-        __queue_make_readable prompt
-    done
-) &>/dev/null &
-set +m
-
-__update_prompt_main_first_call=1
-__update_prompt_main() {
-    if [ "$__update_prompt_main_first_call" '=' '1' ] ; then
-        while sleep 0.001 ; do
-            if __queue_try_read prompt ; then
-                PS1="`__read prompt`"
-                break
-            fi
-        done
-        __update_prompt_main_first_call=0
-    else
-        if __queue_try_read prompt ; then
-            PS1="`__read prompt`"
-        fi
-    fi
-
-    if __queue_try_write query ; then
-        __queue_make_readable query
-    fi
-}
-
-PROMPT_COMMAND=__update_prompt_main
-
-fi # [ x$SPACK_PROMPT '!=' x0 ]
-
-fi # [ "$CURRENTLY_BUILDING_DOCKER_IMAGE" '!=' '1' ]
diff --git a/share/spack/docker/handle-ssh.sh b/share/spack/docker/handle-ssh.sh
deleted file mode 100644
index 18e5ae259d8..00000000000
--- a/share/spack/docker/handle-ssh.sh
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-if [ "$CURRENTLY_BUILDING_DOCKER_IMAGE" '!=' '1' ] ; then
-
-uid="`id -u`"
-if [ "$uid" '=' '0' ] ; then
-    key_types="dsa ecdsa rsa"
-    if [ "$DOCKERFILE_BASE" '!=' 'centos:6' ] ; then
-        key_types="${key_types} ed25519"
-    fi
-
-    for key_type in $key_types ; do
-        private_key_file="/etc/ssh/ssh_host_${key_type}_key"
-        public_key_file="$private_key_file.pub"
-
-        if [ '!' -f "$private_key_file" ] ; then
-            ssh-keygen \
-                -q -t "$key_type" -N "" -f "$private_key_file"
-            chmod 600 "$private_key_file"
-            chmod 644 "$public_key_file"
-        fi
-    done
-
-    mkdir -p /var/run/sshd
-
-    pgrep -u 0 -U 0 sshd &> /dev/null
-    if [ '!' "$?" '=' '0' ] ; then
-        nohup /usr/sbin/sshd -f /etc/ssh/sshd_config < /dev/null &> /dev/null
-    fi
-fi
-
-if [ '!' -f "$HOME/.ssh/id_rsa" ] ; then
-    ssh-keygen \
-        -t rsa -C "spack.developer@docker.host" -N "" -f "$HOME/.ssh/id_rsa"
-    cat "$HOME/.ssh/id_rsa.pub" >> "$HOME/.ssh/authorized_keys"
-    chmod 600 "$HOME/.ssh/authorized_keys"
-
-    docker_ip="`ip address show dev eth0 |
-                grep inet |
-                cut -d' ' -f 6 |
-                cut -d/ -f 1`"
-
-    ssh-keyscan -t rsa 127.0.0.1 localhost "$docker_ip" "`hostname`" \
-        > "$HOME/.ssh/known_hosts" 2> /dev/null
-fi
-
-fi # [ "$CURRENTLY_BUILDING_DOCKER_IMAGE" '!=' '1' ]
diff --git a/share/spack/docker/ubuntu-1604.dockerfile b/share/spack/docker/ubuntu-1604.dockerfile
index e7a6783d24c..7891c5a2614 100644
--- a/share/spack/docker/ubuntu-1604.dockerfile
+++ b/share/spack/docker/ubuntu-1604.dockerfile
@@ -16,29 +16,35 @@ COPY share $SPACK_ROOT/share
 COPY var   $SPACK_ROOT/var
 RUN mkdir -p $SPACK_ROOT/opt/spack
 
-RUN apt-get -yqq update                           \
- && apt-get -yqq install --no-install-recommends  \
-        build-essential                           \
-        ca-certificates                           \
-        curl                                      \
-        file                                      \
-        g++                                       \
-        gcc                                       \
-        gfortran                                  \
-        git                                       \
-        gnupg2                                    \
-        iproute2                                  \
-        lmod                                      \
-        locales                                   \
-        lua-posix                                 \
-        make                                      \
-        openssh-server                            \
-        python3                                   \
-        python3-pip                               \
-        tcl                                       \
-        unzip                                     \
- && locale-gen en_US.UTF-8                        \
- && pip3 install boto3                            \
+RUN ln -s $SPACK_ROOT/share/spack/docker/entrypoint.bash \
+          /usr/local/bin/docker-shell \
+ && ln -s $SPACK_ROOT/share/spack/docker/entrypoint.bash \
+          /usr/local/bin/interactive-shell \
+ && ln -s $SPACK_ROOT/share/spack/docker/entrypoint.bash \
+          /usr/local/bin/spack-env
+
+RUN apt-get -yqq update \
+ && apt-get -yqq install --no-install-recommends \
+        build-essential \
+        ca-certificates \
+        curl \
+        file \
+        g++ \
+        gcc \
+        gfortran \
+        git \
+        gnupg2 \
+        iproute2 \
+        lmod \
+        locales \
+        lua-posix \
+        make \
+        python3 \
+        python3-pip \
+        tcl \
+        unzip \
+ && locale-gen en_US.UTF-8 \
+ && pip3 install boto3 \
  && rm -rf /var/lib/apt/lists/*
 
 # Add LANG default to en_US.UTF-8
@@ -46,33 +52,10 @@ ENV LANGUAGE en_US.UTF-8
 ENV LANG en_US.UTF-8
 ENV LC_ALL en_US.UTF-8
 
-RUN ( echo ". /usr/share/lmod/lmod/init/bash"                       \
- &&   echo ". \$SPACK_ROOT/share/spack/setup-env.sh"                \
- &&   echo "if [ \"\$CURRENTLY_BUILDING_DOCKER_IMAGE\" '!=' '1' ]"  \
- &&   echo "then"                                                   \
- &&   echo "  . \$SPACK_ROOT/share/spack/spack-completion.bash"     \
- &&   echo "fi"                                                   ) \
-       >> /etc/profile.d/spack.sh                                   \
- && ( echo "f=\"\$SPACK_ROOT/share/spack/docker/handle-ssh.sh\""    \
- &&   echo "if [ -f \"\$f\" ]"                                      \
- &&   echo "then"                                                   \
- &&   echo "  .  \"\$f\""                                           \
- &&   echo "else"                                                   \
- &&   cat  $SPACK_ROOT/share/spack/docker/handle-ssh.sh             \
- &&   echo "fi"                                                   ) \
-       >> /etc/profile.d/handle-ssh.sh                              \
- && ( echo "f=\"\$SPACK_ROOT/share/spack/docker/handle-prompt.sh\"" \
- &&   echo "if [ -f \"\$f\" ]"                                      \
- &&   echo "then"                                                   \
- &&   echo "  .  \"\$f\""                                           \
- &&   echo "else"                                                   \
- &&   cat  $SPACK_ROOT/share/spack/docker/handle-prompt.sh          \
- &&   echo "fi"                                                   ) \
-       >> /etc/profile.d/handle-prompt.sh                           \
- && mkdir -p /root/.spack                                           \
- && cp $SPACK_ROOT/share/spack/docker/modules.yaml                  \
-        /root/.spack/modules.yaml                                   \
- && rm -rf /root/*.* $SPACK_ROOT/.git
+RUN mkdir -p /root/.spack \
+ && cp $SPACK_ROOT/share/spack/docker/modules.yaml \
+        /root/.spack/modules.yaml \
+ && rm -rf /root/*.* /run/nologin $SPACK_ROOT/.git
 
 # [WORKAROUND]
 # https://superuser.com/questions/1241548/
@@ -82,10 +65,10 @@ RUN [ -f ~/.profile ]                                               \
  || true
 
 WORKDIR /root
-SHELL ["/bin/bash", "-l", "-c"]
+SHELL ["docker-shell"]
 
 # TODO: add a command to Spack that (re)creates the package cache
 RUN spack spec hdf5+mpi
 
 ENTRYPOINT ["/bin/bash", "/opt/spack/share/spack/docker/entrypoint.bash"]
-CMD ["docker-shell"]
+CMD ["interactive-shell"]
diff --git a/share/spack/docker/ubuntu-1804.dockerfile b/share/spack/docker/ubuntu-1804.dockerfile
index 5950908e1ee..c0793314760 100644
--- a/share/spack/docker/ubuntu-1804.dockerfile
+++ b/share/spack/docker/ubuntu-1804.dockerfile
@@ -16,29 +16,35 @@ COPY share $SPACK_ROOT/share
 COPY var   $SPACK_ROOT/var
 RUN mkdir -p $SPACK_ROOT/opt/spack
 
-RUN apt-get -yqq update                           \
- && apt-get -yqq install --no-install-recommends  \
-        build-essential                           \
-        ca-certificates                           \
-        curl                                      \
-        file                                      \
-        g++                                       \
-        gcc                                       \
-        gfortran                                  \
-        git                                       \
-        gnupg2                                    \
-        iproute2                                  \
-        lmod                                      \
-        locales                                   \
-        lua-posix                                 \
-        make                                      \
-        openssh-server                            \
-        python3                                   \
-        python3-pip                               \
-        tcl                                       \
-        unzip                                     \
- && locale-gen en_US.UTF-8                        \
- && pip3 install boto3                            \
+RUN ln -s $SPACK_ROOT/share/spack/docker/entrypoint.bash \
+          /usr/local/bin/docker-shell \
+ && ln -s $SPACK_ROOT/share/spack/docker/entrypoint.bash \
+          /usr/local/bin/interactive-shell \
+ && ln -s $SPACK_ROOT/share/spack/docker/entrypoint.bash \
+          /usr/local/bin/spack-env
+
+RUN apt-get -yqq update \
+ && apt-get -yqq install --no-install-recommends \
+        build-essential \
+        ca-certificates \
+        curl \
+        file \
+        g++ \
+        gcc \
+        gfortran \
+        git \
+        gnupg2 \
+        iproute2 \
+        lmod \
+        locales \
+        lua-posix \
+        make \
+        python3 \
+        python3-pip \
+        tcl \
+        unzip \
+ && locale-gen en_US.UTF-8 \
+ && pip3 install boto3 \
  && rm -rf /var/lib/apt/lists/*
 
 # Add LANG default to en_US.UTF-8
@@ -46,33 +52,10 @@ ENV LANGUAGE en_US.UTF-8
 ENV LANG en_US.UTF-8
 ENV LC_ALL en_US.UTF-8
 
-RUN ( echo ". /usr/share/lmod/lmod/init/bash"                       \
- &&   echo ". \$SPACK_ROOT/share/spack/setup-env.sh"                \
- &&   echo "if [ \"\$CURRENTLY_BUILDING_DOCKER_IMAGE\" '!=' '1' ]"  \
- &&   echo "then"                                                   \
- &&   echo "  . \$SPACK_ROOT/share/spack/spack-completion.bash"     \
- &&   echo "fi"                                                   ) \
-       >> /etc/profile.d/spack.sh                                   \
- && ( echo "f=\"\$SPACK_ROOT/share/spack/docker/handle-ssh.sh\""    \
- &&   echo "if [ -f \"\$f\" ]"                                      \
- &&   echo "then"                                                   \
- &&   echo "  .  \"\$f\""                                           \
- &&   echo "else"                                                   \
- &&   cat  $SPACK_ROOT/share/spack/docker/handle-ssh.sh             \
- &&   echo "fi"                                                   ) \
-       >> /etc/profile.d/handle-ssh.sh                              \
- && ( echo "f=\"\$SPACK_ROOT/share/spack/docker/handle-prompt.sh\"" \
- &&   echo "if [ -f \"\$f\" ]"                                      \
- &&   echo "then"                                                   \
- &&   echo "  .  \"\$f\""                                           \
- &&   echo "else"                                                   \
- &&   cat  $SPACK_ROOT/share/spack/docker/handle-prompt.sh          \
- &&   echo "fi"                                                   ) \
-       >> /etc/profile.d/handle-prompt.sh                           \
- && mkdir -p /root/.spack                                           \
- && cp $SPACK_ROOT/share/spack/docker/modules.yaml                  \
-        /root/.spack/modules.yaml                                   \
- && rm -rf /root/*.* $SPACK_ROOT/.git
+RUN mkdir -p /root/.spack \
+ && cp $SPACK_ROOT/share/spack/docker/modules.yaml \
+        /root/.spack/modules.yaml \
+ && rm -rf /root/*.* /run/nologin $SPACK_ROOT/.git
 
 # [WORKAROUND]
 # https://superuser.com/questions/1241548/
@@ -86,10 +69,10 @@ RUN [ -f ~/.profile ]                                               \
 RUN ln -s posix_c.so /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so
 
 WORKDIR /root
-SHELL ["/bin/bash", "-l", "-c"]
+SHELL ["docker-shell"]
 
 # TODO: add a command to Spack that (re)creates the package cache
 RUN spack spec hdf5+mpi
 
 ENTRYPOINT ["/bin/bash", "/opt/spack/share/spack/docker/entrypoint.bash"]
-CMD ["docker-shell"]
+CMD ["interactive-shell"]

From dc31afe67d5b684ce7ab7d49088d895f28c78410 Mon Sep 17 00:00:00 2001
From: psakievich <psakiev@sandia.gov>
Date: Tue, 16 Jun 2020 12:27:33 -0600
Subject: [PATCH 732/802] Yaml spec parsing corner case (#17101)

* Catch yaml filename corner case in spec parser

* improved regex and remove redundant error checking

Co-authored-by: Gregory Becker <becker33@llnl.gov>
---
 lib/spack/spack/spec.py             |  9 ++-------
 lib/spack/spack/test/spec_syntax.py | 26 ++++++++++++++++++++++++++
 2 files changed, 28 insertions(+), 7 deletions(-)

diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 03f334597a7..b09d72003e6 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -3945,7 +3945,8 @@ def __init__(self):
 
             # Filenames match before identifiers, so no initial filename
             # component is parsed as a spec (e.g., in subdir/spec.yaml)
-            (r'[/\w.-]+\.yaml[^\b]*', lambda scanner, v: self.token(FILE, v)),
+            (r'[/\w.-]*/[/\w/-]+\.yaml[^\b]*',
+             lambda scanner, v: self.token(FILE, v)),
 
             # Hash match after filename. No valid filename can be a hash
             # (files end w/.yaml), but a hash can match a filename prefix.
@@ -4096,11 +4097,6 @@ def spec_from_file(self):
         """
         path = self.token.value
 
-        # don't treat builtin.yaml, builtin.yaml-cpp, etc. as filenames
-        if re.match(spec_id_re + '$', path):
-            self.push_tokens([spack.parse.Token(ID, self.token.value)])
-            return None
-
         # Special case where someone omits a space after a filename. Consider:
         #
         #     libdwarf^/some/path/to/libelf.yamllibdwarf ^../../libelf.yaml
@@ -4112,7 +4108,6 @@ def spec_from_file(self):
             raise SpecFilenameError(
                 "Spec filename must end in .yaml: '{0}'".format(path))
 
-        # if we get here, we're *finally* interpreting path as a filename
         if not os.path.exists(path):
             raise NoSuchSpecFileError("No such spec file: '{0}'".format(path))
 
diff --git a/lib/spack/spack/test/spec_syntax.py b/lib/spack/spack/test/spec_syntax.py
index 688c89022cb..c9a2100b09e 100644
--- a/lib/spack/spack/test/spec_syntax.py
+++ b/lib/spack/spack/test/spec_syntax.py
@@ -188,6 +188,32 @@ def test_full_specs(self):
             " ^_openmpi@1.2:1.4,1.6%intel@12.1~qt_4 debug=2"
             " ^stackwalker@8.1_1e arch=test-redhat6-x86")
 
+    def test_yaml_specs(self):
+        self.check_parse(
+            "yaml-cpp@0.1.8%intel@12.1"
+            " ^boost@3.1.4")
+        tempspec = r"builtin.yaml-cpp%gcc"
+        self.check_parse(
+            tempspec.strip("builtin."),
+            spec=tempspec)
+        tempspec = r"testrepo.yaml-cpp%gcc"
+        self.check_parse(
+            tempspec.strip("testrepo."),
+            spec=tempspec)
+        tempspec = r"builtin.yaml-cpp@0.1.8%gcc"
+        self.check_parse(
+            tempspec.strip("builtin."),
+            spec=tempspec)
+        tempspec = r"builtin.yaml-cpp@0.1.8%gcc@7.2.0"
+        self.check_parse(
+            tempspec.strip("builtin."),
+            spec=tempspec)
+        tempspec = r"builtin.yaml-cpp@0.1.8%gcc@7.2.0" \
+            r" ^boost@3.1.4"
+        self.check_parse(
+            tempspec.strip("builtin."),
+            spec=tempspec)
+
     def test_canonicalize(self):
         self.check_parse(
             "mvapich_foo"

From 4a948060cfd4db3df4be44748d13d5736bf83f05 Mon Sep 17 00:00:00 2001
From: Tom Payerle <payerle@umd.edu>
Date: Tue, 16 Jun 2020 14:33:35 -0400
Subject: [PATCH 733/802] VTK: add version 9.0.0; update Python dependency
 constraints (#17019)

In Python 3.8, the reserved "tp_print" slot was changed from a function
pointer to a number, which broke the Python wrapping code in vtk@8
(causing "cannot convert 'std::nullptr_t' to 'Py_ssize_t'" errors in
various places).  This is fixed in vtk@9.0.0.

This patch:

1) adds vtk@9.0.0
2) updates depends_on constraints to only use python@3.8: for vtk@9:
   vtk@:8 depends on python@2, and vtk@8.0.1:8.9.9 depends on python@:3.7
3) Adds CMake flag VTK_PYTHON_VERSION=3 when using python@3 with vtk@9
---
 .../repos/builtin/packages/vtk/package.py     | 20 ++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py
index 87fce79af29..e99f779fede 100644
--- a/var/spack/repos/builtin/packages/vtk/package.py
+++ b/var/spack/repos/builtin/packages/vtk/package.py
@@ -15,11 +15,12 @@ class Vtk(CMakePackage):
     processing and visualization. """
 
     homepage = "http://www.vtk.org"
-    url      = "http://www.vtk.org/files/release/8.0/VTK-8.0.1.tar.gz"
+    url      = "https://www.vtk.org/files/release/9.0/VTK-9.0.0.tar.gz"
     list_url = "http://www.vtk.org/download/"
 
     maintainers = ['chuckatkins', 'danlipsa']
 
+    version('9.0.0', sha256='15def4e6f84d72f82386617fe595ec124dda3cbd13ea19a0dcd91583197d8715')
     version('8.2.0', sha256='34c3dc775261be5e45a8049155f7228b6bd668106c72a3c435d95730d17d57bb')
     version('8.1.2', sha256='0995fb36857dd76ccfb8bb07350c214d9f9099e80b1e66b4a8909311f24ff0db')
     version('8.1.1', sha256='71a09b4340f0a9c58559fe946dc745ab68a866cf20636a41d97b6046cb736324')
@@ -44,11 +45,18 @@ class Vtk(CMakePackage):
     # At the moment, we cannot build with both osmesa and qt, but as of
     # VTK 8.1, that should change
     conflicts('+osmesa', when='+qt')
-    conflicts('^python@3:', when='@:8.0')
 
     extends('python', when='+python')
 
-    depends_on('python@2.7:', when='+python', type=('build', 'run'))
+    # Acceptable python versions depend on vtk version
+    # We need vtk at least 8.0.1 for python@3,
+    # and at least 9.0 for python@3.8
+    depends_on('python@2.7:2.9', when='@:8.0 +python', type=('build', 'run'))
+    depends_on('python@2.7:3.7.9', when='@8.0.1:8.9 +python',
+               type=('build', 'run'))
+    depends_on('python@2.7:', when='@9.0: +python', type=('build', 'run'))
+
+    # We need mpi4py if buidling python wrappers and using MPI
     depends_on('py-mpi4py', when='+python+mpi', type='run')
 
     # python3.7 compatibility patch backported from upstream
@@ -164,6 +172,8 @@ def cmake_args(self):
             ])
             if '+mpi' in spec:
                 cmake_args.append('-DVTK_USE_SYSTEM_MPI4PY:BOOL=ON')
+            if spec.satisfies('@9.0.0: ^python@3:'):
+                cmake_args.append('-DVTK_PYTHON_VERSION=3')
         else:
             cmake_args.append('-DVTK_WRAP_PYTHON=OFF')
 
@@ -273,8 +283,8 @@ def cmake_args(self):
             # in March 2014 (see
             # https://public.kitware.com/pipermail/vtkusers/2014-March/083368.html)
             if (self.spec.satisfies('%clang') and
-                self.compiler.is_apple and
-                self.compiler.version >= Version('5.1.0')):
+                    self.compiler.is_apple and
+                    self.compiler.version >= Version('5.1.0')):
                 cmake_args.extend(['-DVTK_REQUIRED_OBJCXX_FLAGS='])
 
             # A bug in tao pegtl causes build failures with intel compilers

From ff816f76b3fe765fd1f1d86ef2e9b1772fdfb7a4 Mon Sep 17 00:00:00 2001
From: Andrew W Elble <aweits@rit.edu>
Date: Tue, 16 Jun 2020 15:35:49 -0400
Subject: [PATCH 734/802] ruby: add version 2.7.1 (#17112)

---
 var/spack/repos/builtin/packages/ruby/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index c4f2a7dcc9b..0a67b9baa7a 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -15,6 +15,7 @@ class Ruby(AutotoolsPackage):
     list_url = "http://cache.ruby-lang.org/pub/ruby/"
     list_depth = 1
 
+    version('2.7.1', sha256='d418483bdd0000576c1370571121a6eb24582116db0b7bb2005e90e250eae418')
     version('2.6.2', sha256='a0405d2bf2c2d2f332033b70dff354d224a864ab0edd462b7a413420453b49ab')
     version('2.5.3', sha256='9828d03852c37c20fa333a0264f2490f07338576734d910ee3fd538c9520846c')
     version('2.2.0', sha256='7671e394abfb5d262fbcd3b27a71bf78737c7e9347fa21c39e58b0bb9c4840fc')

From 4652b217cfc2edc4a39833ea61790b7cd5ba6b05 Mon Sep 17 00:00:00 2001
From: Geoffrey Oxberry <goxberry@gmail.com>
Date: Tue, 16 Jun 2020 15:34:18 -0700
Subject: [PATCH 735/802] pango: add libffi, glib, and other dependencies
 (#12384)

---
 var/spack/repos/builtin/packages/pango/package.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/pango/package.py b/var/spack/repos/builtin/packages/pango/package.py
index 52874160fc4..7d7ef787cec 100644
--- a/var/spack/repos/builtin/packages/pango/package.py
+++ b/var/spack/repos/builtin/packages/pango/package.py
@@ -23,7 +23,7 @@ class Pango(AutotoolsPackage):
 
     variant('X', default=False, description="Enable an X toolkit")
 
-    depends_on("pkgconfig", type="build")
+    depends_on("pkgconfig@0.9.0:", type="build")
     depends_on("harfbuzz")
     depends_on("cairo+ft+fc")
     depends_on("cairo~X", when='~X')
@@ -31,6 +31,14 @@ class Pango(AutotoolsPackage):
     depends_on("libxft", when='+X')
     depends_on("glib")
     depends_on('gobject-introspection')
+    depends_on('fontconfig')
+    depends_on('freetype@2:')
+    depends_on('libffi')
+
+    depends_on('harfbuzz@1.2.3:', when='@1.41.0')
+    depends_on('libxft@2.0.0:', when='@1.41.0 +X')
+    depends_on('glib@2.33.12:', when='@1.41.0')
+    depends_on('fontconfig@2.11.91:', when='@1.41.0')
 
     def url_for_version(self, version):
         url = "http://ftp.gnome.org/pub/GNOME/sources/pango/{0}/pango-{1}.tar.xz"

From 896a14af820bd9ebde8488d7fa89d6032a40e3eb Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Tue, 16 Jun 2020 15:53:34 -0700
Subject: [PATCH 736/802] Doc: E4S Build Cache Link (#16986)

Link to the E4S build cache in the according section of the docs.
---
 lib/spack/docs/binary_caches.rst | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/lib/spack/docs/binary_caches.rst b/lib/spack/docs/binary_caches.rst
index 614ad2864c8..6e8c91c9431 100644
--- a/lib/spack/docs/binary_caches.rst
+++ b/lib/spack/docs/binary_caches.rst
@@ -57,6 +57,12 @@ Build caches are installed via:
 
    $ spack buildcache install
 
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+List of popular build caches
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+* `Extreme-scale Scientific Software Stack (E4S) <https://e4s-project.github.io/>`_: `build cache <https://oaciss.uoregon.edu/e4s/inventory.html>`_
+
 
 ----------
 Relocation

From 84e117b4976c58c713ba8525e701c628043722d0 Mon Sep 17 00:00:00 2001
From: takanori-ihara <62980219+takanori-ihara@users.noreply.github.com>
Date: Wed, 17 Jun 2020 11:59:20 +0900
Subject: [PATCH 737/802] Add compiler option to use with Fujitsu compiler
 (#17067)

* Add compiler option to use with Fujitsu compiler

* Fix flake8 error

* remove 1-1_fcc_tf_patch.patch

* fix flake8 error
---
 var/spack/repos/builtin/packages/linsys-v/package.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/linsys-v/package.py b/var/spack/repos/builtin/packages/linsys-v/package.py
index cc8e94c26bb..545a2a8bec9 100644
--- a/var/spack/repos/builtin/packages/linsys-v/package.py
+++ b/var/spack/repos/builtin/packages/linsys-v/package.py
@@ -50,7 +50,9 @@ def patch(self):
             )
             makefile.filter(
                 r"^CFLAGS\s+=\s-Kfast,openmp",
-                "CFLAGS=-Ofast {0}".format(self.compiler.openmp_flag),
+                "CFLAGS=-Ofast -fstrict-aliasing {0}".format(
+                    self.compiler.openmp_flag
+                ),
             )
             makefile.filter(
                 r"^LIBS\s+=\s-SCALAPACK\s-SSL2BLAMP",

From b0c73c3325ac26fdc7aae4cd17e74260eee1087d Mon Sep 17 00:00:00 2001
From: takanori-ihara <62980219+takanori-ihara@users.noreply.github.com>
Date: Wed, 17 Jun 2020 12:18:04 +0900
Subject: [PATCH 738/802] bazel: Update for use with Fujitsu compiler (#16860)

* bazel: Update for use with Fujitsu compiler

* bazel: Fix for use with Fujitsu compiler

* bazel: Fix flake8 error

* bazel: add conflicts setting for use with Fujitsu compiler

* fix flake8 error

* fix flake8 error
---
 .../repos/builtin/packages/bazel/package.py   | 14 +++++++
 .../packages/bazel/patch_for_fcc.patch        | 37 +++++++++++++++++++
 .../packages/bazel/patch_for_fcc2.patch       | 11 ++++++
 3 files changed, 62 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/bazel/patch_for_fcc.patch
 create mode 100644 var/spack/repos/builtin/packages/bazel/patch_for_fcc2.patch

diff --git a/var/spack/repos/builtin/packages/bazel/package.py b/var/spack/repos/builtin/packages/bazel/package.py
index a3bd59a8b1b..27f2da0597d 100644
--- a/var/spack/repos/builtin/packages/bazel/package.py
+++ b/var/spack/repos/builtin/packages/bazel/package.py
@@ -130,6 +130,16 @@ class Bazel(Package):
     patch('compile-0.4.patch',  when='@0.4:0.5')
     patch('compile-0.3.patch',  when='@:0.3')
 
+    # for fcc
+    patch('patch_for_fcc.patch', when='@0.29.1:%fj')
+    patch('patch_for_fcc2.patch', when='@0.25:%fj')
+    conflicts(
+        '%fj',
+        when='@:0.24.1',
+        msg='Fujitsu Compiler cannot build 0.24.1 or less, '
+        'please use a newer release.'
+    )
+
     patch('disabledepcheck.patch', when='@0.3.2:+nodepfail')
     patch('disabledepcheck_old.patch', when='@0.3.0:0.3.1+nodepfail')
 
@@ -201,3 +211,7 @@ def test(self):
 
     def setup_dependent_package(self, module, dependent_spec):
         module.bazel = Executable('bazel')
+
+    @property
+    def parallel(self):
+        return not self.spec.satisfies('%fj')
diff --git a/var/spack/repos/builtin/packages/bazel/patch_for_fcc.patch b/var/spack/repos/builtin/packages/bazel/patch_for_fcc.patch
new file mode 100644
index 00000000000..d90448b0bae
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/patch_for_fcc.patch
@@ -0,0 +1,37 @@
+diff --git a/src/main/cpp/blaze_util_posix.cc b/src/main/cpp/blaze_util_posix.cc
+index 87ba899180..1c967ee818 100644
+--- a/src/main/cpp/blaze_util_posix.cc
++++ b/src/main/cpp/blaze_util_posix.cc
+@@ -565,7 +565,8 @@ static int setlk(int fd, struct flock *lock) {
+   // Prefer OFD locks if available.  POSIX locks can be lost "accidentally"
+   // due to any close() on the lock file, and are not reliably preserved
+   // across execve() on Linux, which we need for --batch mode.
+-  if (fcntl(fd, F_OFD_SETLK, lock) == 0) return 0;
++  //if (fcntl(fd, F_OFD_SETLK, lock) == 0) return 0;
++  if (fcntl(fd, F_SETLK, lock) == 0) return 0;
+   if (errno != EINVAL) {
+     if (errno != EACCES && errno != EAGAIN) {
+       BAZEL_DIE(blaze_exit_code::LOCAL_ENVIRONMENTAL_ERROR)
+diff --git a/tools/cpp/unix_cc_configure.bzl b/tools/cpp/unix_cc_configure.bzl
+index ccb18a431a..0c5c8fd6f0 100644
+--- a/tools/cpp/unix_cc_configure.bzl
++++ b/tools/cpp/unix_cc_configure.bzl
+@@ -379,7 +379,8 @@ def configure_unix_toolchain(repository_ctx, cpu_value, overriden_tools):
+         "",
+         False,
+     ), ":")
+-    gold_linker_path = _find_gold_linker_path(repository_ctx, cc)
++    #gold_linker_path = _find_gold_linker_path(repository_ctx, cc)
++    gold_linker_path = None
+     cc_path = repository_ctx.path(cc)
+     if not str(cc_path).startswith(str(repository_ctx.path(".")) + "/"):
+         # cc is outside the repository, set -B
+@@ -468,7 +469,7 @@ def configure_unix_toolchain(repository_ctx, cpu_value, overriden_tools):
+                     # Security hardening requires optimization.
+                     # We need to undef it as some distributions now have it enabled by default.
+                     "-U_FORTIFY_SOURCE",
+-                    "-fstack-protector",
++                    #"-fstack-protector",
+                     # All warnings are enabled. Maybe enable -Werror as well?
+                     "-Wall",
+                     # Enable a few more warnings that aren't part of -Wall.
diff --git a/var/spack/repos/builtin/packages/bazel/patch_for_fcc2.patch b/var/spack/repos/builtin/packages/bazel/patch_for_fcc2.patch
new file mode 100644
index 00000000000..709e5ee0202
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/patch_for_fcc2.patch
@@ -0,0 +1,11 @@
+--- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java
++++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java
+@@ -185,7 +185,7 @@ public class BazelRuleClassProvider {
+ 
+         Map<String, String> spackEnv = System.getenv();
+         for (String envName : spackEnv.keySet()) {
+-          if (envName.startsWith("SPACK_")) {
++          if ((envName.startsWith("SPACK_")) || (envName.equals("fcc_ENV")) || (envName.equals("FCC_ENV"))) {
+             env.put(envName, spackEnv.get(envName));
+           }
+         }

From 6e467d13a4992791ccab196b02873778f5f46a51 Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Wed, 17 Jun 2020 12:24:38 +0900
Subject: [PATCH 739/802] mxnet: avoid GNU parallel shuffle without openmp.
 (#17095)

---
 var/spack/repos/builtin/packages/mxnet/package.py   |  1 +
 .../builtin/packages/mxnet/parallell_shuffle.patch  | 13 +++++++++++++
 2 files changed, 14 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/mxnet/parallell_shuffle.patch

diff --git a/var/spack/repos/builtin/packages/mxnet/package.py b/var/spack/repos/builtin/packages/mxnet/package.py
index 2ff65265a7b..8ef5035c077 100644
--- a/var/spack/repos/builtin/packages/mxnet/package.py
+++ b/var/spack/repos/builtin/packages/mxnet/package.py
@@ -46,6 +46,7 @@ class Mxnet(MakefilePackage):
 
     patch('makefile.patch', when='@0.10:0.11')
     patch('makefile.opencv.patch', when='@1.6.0')
+    patch('parallell_shuffle.patch', when='@1.6.0')
 
     def build(self, spec, prefix):
         # copy template configuration file
diff --git a/var/spack/repos/builtin/packages/mxnet/parallell_shuffle.patch b/var/spack/repos/builtin/packages/mxnet/parallell_shuffle.patch
new file mode 100644
index 00000000000..eb286cde57a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mxnet/parallell_shuffle.patch
@@ -0,0 +1,13 @@
+--- a/src/operator/random/shuffle_op.cc	2020-01-31 08:45:22.000000000 +0900
++++ b/src/operator/random/shuffle_op.cc	2020-06-15 11:34:32.000000000 +0900
+@@ -22,8 +22,8 @@
+  * \file shuffle_op.cc
+  * \brief Operator to shuffle elements of an NDArray
+  */
+-#if !defined (__ANDROID__) && ((__GNUC__ > 4 &&\
+-    !defined(__clang__major__)) || (__clang_major__ > 4 && __linux__))
++#if ((__GNUC__ > 4 && !defined(__clang__major__)) || (__clang_major__ > 4 && __linux__)) && \
++  defined(_OPENMP) && !defined(__ANDROID__)
+         #define USE_GNU_PARALLEL_SHUFFLE
+ #endif
+ 

From 8e6f0c353cc40970051326ea9540beabb388baca Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Tue, 16 Jun 2020 22:35:03 -0500
Subject: [PATCH 740/802] Add patch for older versions of py-tensorflow
 (#17122)

Versions of py-tensorflow between versions 1.1 and 1.14 need a patch to
avoid an import error on the cloud package even if built without support
for the cloud package.
---
 .../packages/py-tensorflow/contrib_cloud_1.1.patch | 14 ++++++++++++++
 .../py-tensorflow/contrib_cloud_1.10.patch         | 14 ++++++++++++++
 .../packages/py-tensorflow/contrib_cloud_1.4.patch | 14 ++++++++++++++
 .../packages/py-tensorflow/contrib_cloud_1.9.patch | 14 ++++++++++++++
 .../builtin/packages/py-tensorflow/package.py      |  8 ++++++++
 5 files changed, 64 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.1.patch
 create mode 100644 var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.10.patch
 create mode 100644 var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.4.patch
 create mode 100644 var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.9.patch

diff --git a/var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.1.patch b/var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.1.patch
new file mode 100644
index 00000000000..8813edf3659
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.1.patch
@@ -0,0 +1,14 @@
+--- a/tensorflow/contrib/__init__.py	2020-05-05 17:52:57.716350118 -0500
++++ b/tensorflow/contrib/__init__.py	2020-05-05 17:56:55.665192882 -0500
+@@ -20,7 +20,10 @@
+ 
+ # Add projects here, they will show up under tf.contrib.
+ from tensorflow.contrib import bayesflow
+-from tensorflow.contrib import cloud
++try:
++    from tensorflow.contrib import cloud
++except ImportError:
++    pass
+ from tensorflow.contrib import compiler
+ from tensorflow.contrib import copy_graph
+ from tensorflow.contrib import crf
diff --git a/var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.10.patch b/var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.10.patch
new file mode 100644
index 00000000000..e76defff499
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.10.patch
@@ -0,0 +1,14 @@
+--- a/tensorflow/contrib/__init__.py	2020-05-05 18:14:30.701463150 -0500
++++ b/tensorflow/contrib/__init__.py	2020-05-05 18:15:12.392435370 -0500
+@@ -26,7 +26,10 @@
+ from tensorflow.contrib import bayesflow
+ from tensorflow.contrib import checkpoint
+ if os.name != "nt":
+-  from tensorflow.contrib import cloud
++    try:
++        from tensorflow.contrib import cloud
++    except ImportError:
++        pass
+ from tensorflow.contrib import cluster_resolver
+ from tensorflow.contrib import coder
+ from tensorflow.contrib import compiler
diff --git a/var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.4.patch b/var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.4.patch
new file mode 100644
index 00000000000..a65417233ed
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.4.patch
@@ -0,0 +1,14 @@
+--- a/tensorflow/contrib/__init__.py	2020-05-05 18:08:09.361724827 -0500
++++ b/tensorflow/contrib/__init__.py	2020-05-05 18:08:46.345699058 -0500
+@@ -20,7 +20,10 @@
+ 
+ # Add projects here, they will show up under tf.contrib.
+ from tensorflow.contrib import bayesflow
+-from tensorflow.contrib import cloud
++try:
++    from tensorflow.contrib import cloud
++except ImportError:
++    pass
+ from tensorflow.contrib import cluster_resolver
+ from tensorflow.contrib import compiler
+ from tensorflow.contrib import copy_graph
diff --git a/var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.9.patch b/var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.9.patch
new file mode 100644
index 00000000000..2a0ac1f7137
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-tensorflow/contrib_cloud_1.9.patch
@@ -0,0 +1,14 @@
+--- a/tensorflow/contrib/__init__.py	2020-05-05 18:11:33.660582455 -0500
++++ b/tensorflow/contrib/__init__.py	2020-05-05 18:12:32.570541708 -0500
+@@ -25,7 +25,10 @@
+ from tensorflow.contrib import batching
+ from tensorflow.contrib import bayesflow
+ from tensorflow.contrib import checkpoint
+-from tensorflow.contrib import cloud
++try:
++    from tensorflow.contrib import cloud
++except ImportError:
++    pass
+ from tensorflow.contrib import cluster_resolver
+ from tensorflow.contrib import coder
+ from tensorflow.contrib import compiler
diff --git a/var/spack/repos/builtin/packages/py-tensorflow/package.py b/var/spack/repos/builtin/packages/py-tensorflow/package.py
index 6bdc7e69be3..3b2c0ac0621 100644
--- a/var/spack/repos/builtin/packages/py-tensorflow/package.py
+++ b/var/spack/repos/builtin/packages/py-tensorflow/package.py
@@ -255,6 +255,14 @@ class PyTensorflow(Package, CudaPackage):
     # Allows 2.0.* releases to build with '--config=nogcp'
     patch('0001-Remove-contrib-cloud-bigtable-and-storage-ops-kernel.patch',
           when='@2.0.0:2.0.1')
+    # do not import contrib.cloud if not available
+    patch('https://github.com/tensorflow/tensorflow/commit/ed62ac8203999513dfae03498e871ea35eb60cc4.patch',
+          sha256='c37d14622a86b164e2411ea45a04f756ac61b2044d251f19ab17733c508e5305', when='@1.14.0')
+    # import_contrib_cloud patch for older versions
+    patch('contrib_cloud_1.10.patch', when='@1.10:1.13')
+    patch('contrib_cloud_1.9.patch', when='@1.9')
+    patch('contrib_cloud_1.4.patch', when='@1.4:1.8')
+    patch('contrib_cloud_1.1.patch', when='@1.1:1.3')
 
     phases = ['configure', 'build', 'install']
 

From fd8971feecbb03ff076e20c47372866533612ea0 Mon Sep 17 00:00:00 2001
From: h-denpo <57649496+h-denpo@users.noreply.github.com>
Date: Wed, 17 Jun 2020 12:36:08 +0900
Subject: [PATCH 741/802] Modified for Fujitsu compiler. (#17124)

---
 .../builtin/packages/ffb/fj_compiler.patch    | 10 +++++
 .../repos/builtin/packages/ffb/package.py     | 13 +++++++
 .../packages/ffb/revocap_refiner.patch        | 38 +++++++++++++------
 3 files changed, 49 insertions(+), 12 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/ffb/fj_compiler.patch

diff --git a/var/spack/repos/builtin/packages/ffb/fj_compiler.patch b/var/spack/repos/builtin/packages/ffb/fj_compiler.patch
new file mode 100644
index 00000000000..2f733ced38f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ffb/fj_compiler.patch
@@ -0,0 +1,10 @@
+--- FFB8.org/util/xvx2gf/XVX.h	2013-03-26 10:09:49.000000000 +0900
++++ FFB8.new/util/xvx2gf/XVX.h	2020-06-16 16:00:06.408500236 +0900
+@@ -5,6 +5,7 @@
+ #include <algorithm>
+ #include <cassert>
+ #include <vector>
++#include <stdint.h>
+ 
+ #define MAX_LEVEL	32
+ 
diff --git a/var/spack/repos/builtin/packages/ffb/package.py b/var/spack/repos/builtin/packages/ffb/package.py
index d9de2b9862c..c7d10955832 100644
--- a/var/spack/repos/builtin/packages/ffb/package.py
+++ b/var/spack/repos/builtin/packages/ffb/package.py
@@ -15,6 +15,7 @@ class Ffb(MakefilePackage):
     version('8.1', sha256='1ad008c909152b6c27668bafbad820da3e6ec3309c7e858ddb785f0a3d6e43ae')
 
     patch('revocap_refiner.patch')
+    patch('fj_compiler.patch', when='%fj')
 
     depends_on('mpi')
     depends_on('blas')
@@ -52,6 +53,7 @@ def edit(self, spec, prefix):
             r'#LES3DHOME   =', 'LES3DHOME= {0}\n'.format(workdir))
         make = join_path('make', 'OPTION')
         m = FileFilter(make)
+        m.filter(r'CPP\s*=.*$', 'CPP = /usr/bin/cpp')
         m.filter(r'CCOM\s*=.*$', 'CCOM = {0}'.format(spack_cc))
         m.filter(r'COPT\s*=.*$', 'COPT = {0}'.format(cflags))
         m.filter(r'FCOM\s*=.*$', 'FCOM = {0}\n'.format(spack_fc))
@@ -141,6 +143,17 @@ def edit(self, spec, prefix):
         m.filter(r'LIBS = -lfort -lgf2 -ldd_mpi -lmpi_f77',
                  'LIBS = -lfort -lgf2  -ldd_mpi')
 
+        if spec.satisfies('%gcc'):
+            editfile = join_path('util', 'xvx2gf', 'FILES')
+            m = FileFilter(editfile)
+            m.filter(r'LIBS = -lgf2 -lz -lifcore -limf -ldl',
+                     'LIBS = -lgf2 -lz -ldl')
+        elif spec.satisfies('%fj'):
+            editfile = join_path('util', 'xvx2gf', 'FILES')
+            m = FileFilter(editfile)
+            m.filter(r'LIBS = -lgf2 -lz -lifcore -limf -ldl',
+                     'LIBS = -lgf2 -lz -ldl -linkfortran')
+
     def build(self, spec, prefix):
         for m in [join_path('make',  'Makeall'),
                   join_path('lib', 'src', 'dd_mpi', 'Makeall'),
diff --git a/var/spack/repos/builtin/packages/ffb/revocap_refiner.patch b/var/spack/repos/builtin/packages/ffb/revocap_refiner.patch
index 20886120cbd..13d34bacd3a 100644
--- a/var/spack/repos/builtin/packages/ffb/revocap_refiner.patch
+++ b/var/spack/repos/builtin/packages/ffb/revocap_refiner.patch
@@ -1,6 +1,6 @@
 diff -uprN FFB8.org/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Bucket.h FFB8.new/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Bucket.h
 --- FFB8.org/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Bucket.h	2013-03-26 10:09:31.000000000 +0900
-+++ FFB8.new/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Bucket.h	2020-05-29 16:35:09.690918296 +0900
++++ FFB8.new/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Bucket.h	2020-06-16 11:33:05.765408337 +0900
 @@ -64,7 +64,7 @@ public:
  		numY = this->ynum;
  		numZ = this->znum;
@@ -10,15 +10,29 @@ diff -uprN FFB8.org/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Bucket.h FFB8.new
  		return this->xnum * this->ynum * this->znum;
  	};
  
-diff -uprN FFB8.org/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Common.h FFB8.new/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Common.h
---- FFB8.org/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Common.h	2013-03-26 10:09:31.000000000 +0900
-+++ FFB8.new/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Common.h	2020-05-29 16:35:48.756606155 +0900
-@@ -13,7 +13,7 @@
- #                                                                      #
- ----------------------------------------------------------------------*/
- #pragma once
+@@ -81,12 +81,6 @@ public:
+ 
+ 		int getIndex() const{ return it->first; };
+ 
+-		void getIndices(int &i,int &j,int &k) const{
+-			i = it->first / (ynum*znum);
+-			j = (it->first - i*ynum*znum) / znum;
+-			k = it->first - i*ynum*znum - j*znum;
+-		};
 -
-+#include <cstdlib>
- #ifndef PI
-  #define PI 3.1415926535897932384626
- #endif
+ 		iterator& operator++(void){ ++it; return *this; };
+ 
+ 		iterator  operator++(int n){
+@@ -124,12 +118,6 @@ public:
+ 
+ 		int getIndex() const{ return it->first; };
+ 
+-		void getIndices(int &i,int &j,int &k) const{
+-			i = it->first / (ynum*znum);
+-			j = (it->first - i*ynum*znum) / znum;
+-			k = it->first - i*ynum*znum - j*znum;
+-		};
+-
+ 		const_iterator& operator++(void){ ++it; return *this; };
+ 
+ 		const_iterator operator++(int n){

From 93fcca900fa5b63e1afbaf9e220060aaa442ecf9 Mon Sep 17 00:00:00 2001
From: "Seth R. Johnson" <johnsonsr@ornl.gov>
Date: Wed, 17 Jun 2020 01:42:56 -0400
Subject: [PATCH 742/802] vecgeom: add version 1.1.7 (#17120)

---
 var/spack/repos/builtin/packages/vecgeom/package.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/var/spack/repos/builtin/packages/vecgeom/package.py b/var/spack/repos/builtin/packages/vecgeom/package.py
index 20352f77123..1df60770f5c 100644
--- a/var/spack/repos/builtin/packages/vecgeom/package.py
+++ b/var/spack/repos/builtin/packages/vecgeom/package.py
@@ -18,6 +18,7 @@ class Vecgeom(CMakePackage, CudaPackage):
     maintainers = ['drbenmorgan', 'sethrj']
 
     version('master', branch='master')
+    version('1.1.7', sha256='cc79a0baa783b21ecc399c4e7cca925ca340e6aeb96e3b2cad45c141557519bf')
     version('1.1.6', sha256='c4806a6b67d01b40074b8cc6865d78574a6a1c573be51696f2ecdf98b9cb954a')
     version('1.1.5', sha256='da674f3bbc75c30f56c1a2d251fa8930c899f27fa64b03a36569924030d87b95')
     version('1.1.3', sha256='ada09e8b6b2fa6c058290302b2cb5a6c2e644192aab1623c31d18c6a2f4c01c8')
@@ -45,6 +46,11 @@ class Vecgeom(CMakePackage, CudaPackage):
 
     conflicts('+cuda', when='@:1.1.5')
 
+    # Fix missing CMAKE_CUDA_STANDARD
+    patch('https://gitlab.cern.ch/VecGeom/VecGeom/-/commit/7094dd180ef694f2abb7463cafcedfb8b8ed30a1.diff',
+          sha256='34f1a6899616e40bce33d80a38a9b409f819cbaab07b2e3be7f4ec4bedb52b29',
+          when='@1.1.7 +cuda')
+
     for std in _cxxstd_values:
         depends_on('geant4 cxxstd=' + std, when='+geant4 cxxstd=' + std)
         depends_on('root cxxstd=' + std, when='+root cxxstd=' + std)

From 0c28d8932f2a437ca18b1731126fdcba82c84b1a Mon Sep 17 00:00:00 2001
From: Ryan Mast <mast9@llnl.gov>
Date: Tue, 16 Jun 2020 07:37:12 -0700
Subject: [PATCH 743/802] helics: Add version 2.5.2

---
 var/spack/repos/builtin/packages/helics/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/helics/package.py b/var/spack/repos/builtin/packages/helics/package.py
index f2bb52dec6a..50bfe67fa81 100644
--- a/var/spack/repos/builtin/packages/helics/package.py
+++ b/var/spack/repos/builtin/packages/helics/package.py
@@ -19,6 +19,7 @@ class Helics(CMakePackage):
 
     version('develop', branch='develop', submodules=True)
     version('master', branch='master', submodules=True)
+    version('2.5.2', sha256='81928f7e30233a07ae2bfe6c5489fdd958364c0549b2a3e6fdc6163d4b390311')
     version('2.5.1', sha256='3fc3507f7c074ff8b6a17fe54676334158fb2ff7cc8e7f4df011938f28fdbbca')
     version('2.5.0', sha256='6f4f9308ebb59d82d71cf068e0d9d66b6edfa7792d61d54f0a61bf20dd2a7428')
     version('2.4.2', sha256='957856f06ed6d622f05dfe53df7768bba8fe2336d841252f5fac8345070fa5cb')

From 494a523636e8e9e48c909908c5a536e8ef20fbdf Mon Sep 17 00:00:00 2001
From: Fabian Brandt <fabian.brandt-tumescheit@informatik.hu-berlin.de>
Date: Wed, 17 Jun 2020 07:44:43 +0200
Subject: [PATCH 744/802] libnetworkit: add version 7.0 (#17111)

---
 var/spack/repos/builtin/packages/libnetworkit/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/libnetworkit/package.py b/var/spack/repos/builtin/packages/libnetworkit/package.py
index 5d7f58eb906..04ea7b4e9d8 100644
--- a/var/spack/repos/builtin/packages/libnetworkit/package.py
+++ b/var/spack/repos/builtin/packages/libnetworkit/package.py
@@ -22,6 +22,7 @@ class Libnetworkit(CMakePackage):
 
     maintainers = ['fabratu']
 
+    version('7.0', sha256='4faf16c5fae3e14d3c1b6f30e25c6e093dcf6a3dbf021235f3161ac2a527f682')
     version('6.1', sha256='22c953ea1054c356663b31c77114c2f0c8fec17e0e707aeec23026241beab9b2')
 
     variant('static', default=False, description='Enables the build of shared libraries')

From d2b745b3d6daf3ccd8e0517161d169cb5c3ce712 Mon Sep 17 00:00:00 2001
From: Muhammad Haseeb <mhase003@fiu.edu>
Date: Wed, 17 Jun 2020 01:55:46 -0400
Subject: [PATCH 745/802] lua: requires -ltermcap when building (#17108)

---
 var/spack/repos/builtin/packages/lua/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py
index 1c6b152aa34..e00e499abcf 100644
--- a/var/spack/repos/builtin/packages/lua/package.py
+++ b/var/spack/repos/builtin/packages/lua/package.py
@@ -54,7 +54,7 @@ def install(self, spec, prefix):
              'MYLDFLAGS=-L%s -L%s' % (
                  spec['readline'].prefix.lib,
                  spec['ncurses'].prefix.lib),
-             'MYLIBS=-lncursesw',
+             'MYLIBS=-lncursesw -ltermcap',
              'CC=%s -std=gnu99 %s' % (spack_cc,
                                       self.compiler.cc_pic_flag),
              target)

From dc0dfe9220ecd16b207dea9695a64fb845666f6c Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Wed, 17 Jun 2020 14:04:00 +0800
Subject: [PATCH 746/802] New package: lynx (#17099)

---
 .../repos/builtin/packages/lynx/package.py    | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/lynx/package.py

diff --git a/var/spack/repos/builtin/packages/lynx/package.py b/var/spack/repos/builtin/packages/lynx/package.py
new file mode 100644
index 00000000000..66c6f5408e9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lynx/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Lynx(AutotoolsPackage):
+    """Lynx is the text web browser."""
+
+    homepage = "https://lynx.invisible-island.net/"
+    url      = "https://invisible-mirror.net/archives/lynx/tarballs/lynx2.8.9rel.1.tar.gz"
+
+    version('2.8.9.1', sha256='a46e4167b8f02c066d2fe2eafcc5603367be0e3fe2e59e9fc4eb016f306afc8e')
+
+    depends_on('ncurses')
+
+    def url_for_version(self, version):
+        version_str = version.string
+        index = version_str.rfind('.')
+        tmp = list(version_str)
+        if index >= 0:
+            tmp.insert(index, 'rel')
+            version_str = ''.join(tmp)
+        else:
+            version_str = version
+        url = "https://invisible-mirror.net/archives/lynx/tarballs/lynx{0}.tar.gz".format(version_str)
+        return url

From eb5f1886b78a2b79c9fb5748addaad69c1a56591 Mon Sep 17 00:00:00 2001
From: takanori-ihara <62980219+takanori-ihara@users.noreply.github.com>
Date: Wed, 17 Jun 2020 22:00:36 +0900
Subject: [PATCH 747/802] py-tensorflow: Update for use with Fujitsu compiler
 (#17088)

* py-tensorflow: Update for use with Fujitsu compiler

* py-tensorflow: remove -march option

* fix flake8 error
---
 .../packages/py-tensorflow/1-1_fcc_tf_patch.patch    | 12 ++++++++++++
 .../repos/builtin/packages/py-tensorflow/package.py  |  9 +++++++++
 2 files changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-tensorflow/1-1_fcc_tf_patch.patch

diff --git a/var/spack/repos/builtin/packages/py-tensorflow/1-1_fcc_tf_patch.patch b/var/spack/repos/builtin/packages/py-tensorflow/1-1_fcc_tf_patch.patch
new file mode 100644
index 00000000000..281cd63b143
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-tensorflow/1-1_fcc_tf_patch.patch
@@ -0,0 +1,12 @@
+diff --git a/tensorflow/tensorflow.bzl b/tensorflow/tensorflow.bzl
+index 740f24ec4a..7b8300f678 100644
+--- a/tensorflow/tensorflow.bzl
++++ b/tensorflow/tensorflow.bzl
+@@ -1604,6 +1604,7 @@ def _py_wrap_cc_impl(ctx):
+         outputs = outputs,
+         mnemonic = "PythonSwig",
+         progress_message = "SWIGing " + src.path,
++        use_default_shell_env = True,
+     )
+     return struct(files = depset(outputs))
+ 
diff --git a/var/spack/repos/builtin/packages/py-tensorflow/package.py b/var/spack/repos/builtin/packages/py-tensorflow/package.py
index 3b2c0ac0621..5c8a10a4a92 100644
--- a/var/spack/repos/builtin/packages/py-tensorflow/package.py
+++ b/var/spack/repos/builtin/packages/py-tensorflow/package.py
@@ -255,6 +255,10 @@ class PyTensorflow(Package, CudaPackage):
     # Allows 2.0.* releases to build with '--config=nogcp'
     patch('0001-Remove-contrib-cloud-bigtable-and-storage-ops-kernel.patch',
           when='@2.0.0:2.0.1')
+
+    # for fcc
+    patch('1-1_fcc_tf_patch.patch', when='@2.1.0:2.1.99%fj')
+
     # do not import contrib.cloud if not available
     patch('https://github.com/tensorflow/tensorflow/commit/ed62ac8203999513dfae03498e871ea35eb60cc4.patch',
           sha256='c37d14622a86b164e2411ea45a04f756ac61b2044d251f19ab17733c508e5305', when='@1.14.0')
@@ -635,6 +639,11 @@ def post_configure_fixes(self):
                         'build --action_env LD_LIBRARY_PATH="' + slibs + '"',
                         '.tf_configure.bazelrc')
 
+        filter_file('build:opt --copt=-march=native', '',
+                    '.tf_configure.bazelrc')
+        filter_file('build:opt --host_copt=-march=native', '',
+                    '.tf_configure.bazelrc')
+
     def build(self, spec, prefix):
         tmp_path = env['TEST_TMPDIR']
 

From e90c229dab42760f9fcf6f72267b35d054dbf606 Mon Sep 17 00:00:00 2001
From: "Seth R. Johnson" <johnsonsr@ornl.gov>
Date: Wed, 17 Jun 2020 10:34:53 -0400
Subject: [PATCH 748/802] Fix/clarify some trilinos variants/dependencies
 (#17006)

- Parallel HDF5 isn't required -- the comment seems to be about a
  transitive dependency with pnetcdf.
- Boost usage should respect the variant, not automatically be reenabled
  when choosing DTK.
---
 var/spack/repos/builtin/packages/trilinos/package.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 5e8a96a16aa..16f916849c3 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -288,6 +288,7 @@ class Trilinos(CMakePackage):
     conflicts('+zoltan2', when='~xpetra')
     conflicts('+zoltan2', when='~zoltan')
 
+    conflicts('+dtk', when='~boost')
     conflicts('+dtk', when='~intrepid2')
     conflicts('+dtk', when='~kokkos')
     conflicts('+dtk', when='~teuchos')
@@ -330,9 +331,9 @@ class Trilinos(CMakePackage):
     depends_on('blas')
     depends_on('lapack')
     depends_on('boost', when='+boost')
-    depends_on('boost', when='+dtk')
-    depends_on('matio', when='+matio')
     depends_on('glm', when='+glm')
+    depends_on('hdf5+hl', when='+hdf5')
+    depends_on('matio', when='+matio')
     depends_on('metis@5:', when='+metis')
     depends_on('suite-sparse', when='+suite-sparse')
     depends_on('zlib', when="+zlib")
@@ -364,14 +365,12 @@ class Trilinos(CMakePackage):
     depends_on('hypre~internal-superlu~int64', when='+hypre')
     depends_on('hypre@xsdk-0.2.0~internal-superlu', when='@xsdk-0.2.0+hypre')
     depends_on('hypre@develop~internal-superlu', when='@develop+hypre')
-    # We need hdf5+hl to match with netcdf during concretization
-    depends_on('hdf5+hl+mpi', when='+hdf5+mpi')
     depends_on('python', when='+python')
     depends_on('py-numpy', when='+python', type=('build', 'run'))
     depends_on('swig', when='+python')
 
     # Dependencies/conflicts when MPI is disabled
-    depends_on('hdf5+hl~mpi', when='+hdf5~mpi')
+    depends_on('hdf5~mpi', when='+hdf5~mpi')
     conflicts('+parmetis', when='~mpi')
     conflicts('+pnetcdf', when='~mpi')
 

From eca08c77e383692d0c00c964f1c129b0996f5bc1 Mon Sep 17 00:00:00 2001
From: Sergey Kosukhin <sergey.kosukhin@mpimet.mpg.de>
Date: Wed, 17 Jun 2020 17:32:08 +0200
Subject: [PATCH 749/802] openmpi: fixes for NAG compiler (#17073)

* openmpi: fixes for NAG compiler

* openmpi: more fixes
---
 .../1.10.4_1.10.999.patch}                    |   0
 .../2.0.0_2.1.1.patch}                        |   0
 .../2.1.2_2.1.3_3.0.0.patch}                  |   0
 .../2.1.4_2.1.999_3.0.1_4.patch}              |   0
 .../repos/builtin/packages/openmpi/package.py | 115 +++-
 .../openmpi/use_mpi_tkr_sizeof/step_1.patch   | 584 ++++++++++++++++++
 .../openmpi/use_mpi_tkr_sizeof/step_2.patch   |  22 +
 7 files changed, 700 insertions(+), 21 deletions(-)
 rename var/spack/repos/builtin/packages/openmpi/{nag_ltmain_4.patch => nag_pthread/1.10.4_1.10.999.patch} (100%)
 rename var/spack/repos/builtin/packages/openmpi/{nag_ltmain_3.patch => nag_pthread/2.0.0_2.1.1.patch} (100%)
 rename var/spack/repos/builtin/packages/openmpi/{nag_ltmain_2.patch => nag_pthread/2.1.2_2.1.3_3.0.0.patch} (100%)
 rename var/spack/repos/builtin/packages/openmpi/{nag_ltmain_1.patch => nag_pthread/2.1.4_2.1.999_3.0.1_4.patch} (100%)
 create mode 100644 var/spack/repos/builtin/packages/openmpi/use_mpi_tkr_sizeof/step_1.patch
 create mode 100644 var/spack/repos/builtin/packages/openmpi/use_mpi_tkr_sizeof/step_2.patch

diff --git a/var/spack/repos/builtin/packages/openmpi/nag_ltmain_4.patch b/var/spack/repos/builtin/packages/openmpi/nag_pthread/1.10.4_1.10.999.patch
similarity index 100%
rename from var/spack/repos/builtin/packages/openmpi/nag_ltmain_4.patch
rename to var/spack/repos/builtin/packages/openmpi/nag_pthread/1.10.4_1.10.999.patch
diff --git a/var/spack/repos/builtin/packages/openmpi/nag_ltmain_3.patch b/var/spack/repos/builtin/packages/openmpi/nag_pthread/2.0.0_2.1.1.patch
similarity index 100%
rename from var/spack/repos/builtin/packages/openmpi/nag_ltmain_3.patch
rename to var/spack/repos/builtin/packages/openmpi/nag_pthread/2.0.0_2.1.1.patch
diff --git a/var/spack/repos/builtin/packages/openmpi/nag_ltmain_2.patch b/var/spack/repos/builtin/packages/openmpi/nag_pthread/2.1.2_2.1.3_3.0.0.patch
similarity index 100%
rename from var/spack/repos/builtin/packages/openmpi/nag_ltmain_2.patch
rename to var/spack/repos/builtin/packages/openmpi/nag_pthread/2.1.2_2.1.3_3.0.0.patch
diff --git a/var/spack/repos/builtin/packages/openmpi/nag_ltmain_1.patch b/var/spack/repos/builtin/packages/openmpi/nag_pthread/2.1.4_2.1.999_3.0.1_4.patch
similarity index 100%
rename from var/spack/repos/builtin/packages/openmpi/nag_ltmain_1.patch
rename to var/spack/repos/builtin/packages/openmpi/nag_pthread/2.1.4_2.1.999_3.0.1_4.patch
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index b3dcac253e2..ee2f76ea19e 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -4,6 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 
+import itertools
 import os
 import sys
 import llnl.util.tty as tty
@@ -157,12 +158,26 @@ class Openmpi(AutotoolsPackage):
     patch('btl_vader.patch', when='@3.0.1:3.0.2')
     patch('btl_vader.patch', when='@3.1.0:3.1.2')
 
-    # Reported upstream: https://github.com/open-mpi/ompi/pull/6378
+    # Make NAG compiler pass the -pthread option to the linker:
+    # https://github.com/open-mpi/ompi/pull/6378
     # We support only versions based on Libtool 2.4.6.
-    patch('nag_ltmain_1.patch', when='@2.1.4:2.1.999,3.0.1:4%nag')
-    patch('nag_ltmain_2.patch', when='@2.1.2:2.1.3,3.0.0%nag')
-    patch('nag_ltmain_3.patch', when='@2.0.0:2.1.1%nag')
-    patch('nag_ltmain_4.patch', when='@1.10.4:1.10.999%nag')
+    patch('nag_pthread/2.1.4_2.1.999_3.0.1_4.patch', when='@2.1.4:2.1.999,3.0.1:4%nag')
+    patch('nag_pthread/2.1.2_2.1.3_3.0.0.patch', when='@2.1.2:2.1.3,3.0.0%nag')
+    patch('nag_pthread/2.0.0_2.1.1.patch', when='@2.0.0:2.1.1%nag')
+    patch('nag_pthread/1.10.4_1.10.999.patch', when='@1.10.4:1.10.999%nag')
+
+    # Fix MPI_Sizeof() in the "mpi" Fortran module for compilers that do not
+    # support "IGNORE TKR" functionality (e.g. NAG).
+    # The issue has been resolved upstream in two steps:
+    #   1) https://github.com/open-mpi/ompi/pull/2294
+    #   2) https://github.com/open-mpi/ompi/pull/5099
+    # The first one was applied starting version v3.0.0 and backported to
+    # v1.10. A subset with relevant modifications is applicable starting
+    # version 1.8.4.
+    patch('use_mpi_tkr_sizeof/step_1.patch', when='@1.8.4:1.10.6,2:2.999')
+    # The second patch was applied starting version v4.0.0 and backported to
+    # v2.x, v3.0.x, and v3.1.x.
+    patch('use_mpi_tkr_sizeof/step_2.patch', when='@1.8.4:2.1.3,3:3.0.1')
 
     variant(
         'fabrics',
@@ -192,7 +207,8 @@ class Openmpi(AutotoolsPackage):
             description='Enable MPI_THREAD_MULTIPLE support')
     variant('cuda', default=False, description='Enable CUDA support')
     variant('pmi', default=False, description='Enable PMI support')
-    variant('runpath', default=True, description='Enable wrapper runpath')
+    variant('wrapper-rpath', default=True,
+            description='Enable rpath support in the wrappers')
     variant('cxx', default=False, description='Enable C++ MPI bindings')
     variant('cxx_exceptions', default=False, description='Enable C++ Exception support')
     variant('gpfs', default=True, description='Enable GPFS support (if present)')
@@ -274,6 +290,9 @@ class Openmpi(AutotoolsPackage):
     conflicts('fabrics=libfabric', when='@:1.8')  # libfabric support was added in 1.10.0
     # It may be worth considering making libfabric an exclusive fabrics choice
 
+    # RPATH support in the wrappers was added in 1.7.4
+    conflicts('+wrapper-rpath', when='@:1.7.3')
+
     def url_for_version(self, version):
         url = "http://www.open-mpi.org/software/ompi/v{0}/downloads/openmpi-{1}.tar.bz2"
         return url.format(version.up_to(2), version)
@@ -369,12 +388,10 @@ def configure_args(self):
             '--disable-silent-rules'
         ]
 
-        # Add extra_rpaths dirs from compilers.yaml into link wrapper
-        rpaths = [self.compiler.cc_rpath_arg + path
-                  for path in self.compiler.extra_rpaths]
-        config_args.extend([
-            '--with-wrapper-ldflags={0}'.format(' '.join(rpaths))
-        ])
+        # All rpath flags should be appended with self.compiler.cc_rpath_arg.
+        # Later, we might need to update share/openmpi/mpic++-wrapper-data.txt
+        # and mpifort-wrapper-data.txt (see filter_rpaths()).
+        wrapper_ldflags = []
 
         if '+atomics' in spec:
             config_args.append('--enable-builtin-atomics')
@@ -418,12 +435,6 @@ def configure_args(self):
         if 'fabrics=auto' not in spec:
             config_args.extend(self.with_or_without('fabrics',
                                                     activation_value='prefix'))
-        # The wrappers fail to automatically link libfabric. This will cause
-        # undefined references unless we add the appropriate flags.
-        if 'fabrics=libfabric' in spec:
-            config_args.append('--with-wrapper-ldflags=-L{0} -Wl,-rpath={0}'
-                               .format(spec['libfabric'].prefix.lib))
-            config_args.append('--with-wrapper-libs=-lfabric')
 
         # Schedulers
         if 'schedulers=auto' not in spec:
@@ -499,12 +510,24 @@ def configure_args(self):
             else:
                 config_args.append('--without-cuda')
 
-        if '+runpath' in spec:
+        if '+wrapper-rpath' in spec:
             config_args.append('--enable-wrapper-rpath')
-            config_args.append('--enable-wrapper-runpath')
+
+            # Disable new dynamic tags in the wrapper (--disable-new-dtags)
+            # In the newer versions this can be done with a configure option
+            # (for older versions, we rely on filter_compiler_wrappers() and
+            # filter_pc_files()):
+            if spec.satisfies('@3.0.5:'):
+                config_args.append('--disable-wrapper-runpath')
+
+            # Add extra_rpaths and implicit_rpaths into the wrappers.
+            wrapper_ldflags.extend([
+                self.compiler.cc_rpath_arg + path
+                for path in itertools.chain(
+                    self.compiler.extra_rpaths,
+                    self.compiler.implicit_rpaths())])
         else:
             config_args.append('--disable-wrapper-rpath')
-            config_args.append('--disable-wrapper-runpath')
 
         if spec.satisfies('@:4'):
             if '+cxx' in spec:
@@ -517,8 +540,58 @@ def configure_args(self):
             else:
                 config_args.append('--disable-cxx-exceptions')
 
+        if wrapper_ldflags:
+            config_args.append(
+                '--with-wrapper-ldflags={0}'.format(' '.join(wrapper_ldflags)))
+
         return config_args
 
+    @when('+wrapper-rpath')
+    @run_after('install')
+    def filter_rpaths(self):
+
+        def filter_lang_rpaths(lang_tokens, rpath_arg):
+            if self.compiler.cc_rpath_arg == rpath_arg:
+                return
+
+            files = find(self.spec.prefix.share.openmpi,
+                         ['*{0}-wrapper-data*'.format(t) for t in lang_tokens])
+            files.extend(find(self.spec.prefix.lib.pkgconfig,
+                              ['ompi-{0}.pc'.format(t) for t in lang_tokens]))
+
+            x = FileFilter(*[f for f in files if not os.path.islink(f)])
+
+            # Replace self.compiler.cc_rpath_arg, which have been added as
+            # '--with-wrapper-ldflags', with rpath_arg in the respective
+            # language-specific wrappers and pkg-config files.
+            x.filter(self.compiler.cc_rpath_arg, rpath_arg,
+                     string=True, backup=False)
+
+            if self.spec.satisfies('@:1.10.3,2:2.1.1'):
+                # Replace Libtool-style RPATH prefixes '-Wl,-rpath -Wl,' with
+                # rpath_arg for old version of OpenMPI, which assumed that CXX
+                # and FC had the same prefixes as CC.
+                x.filter('-Wl,-rpath -Wl,', rpath_arg,
+                         string=True, backup=False)
+
+        filter_lang_rpaths(['c++', 'CC', 'cxx'], self.compiler.cxx_rpath_arg)
+        filter_lang_rpaths(['fort', 'f77', 'f90'], self.compiler.fc_rpath_arg)
+
+    @when('@:3.0.4+wrapper-rpath')
+    @run_after('install')
+    def filter_pc_files(self):
+        files = find(self.spec.prefix.lib.pkgconfig, '*.pc')
+        x = FileFilter(*[f for f in files if not os.path.islink(f)])
+
+        # Remove this linking flag if present (it turns RPATH into RUNPATH)
+        x.filter('{0}--enable-new-dtags'.format(self.compiler.linker_arg), '',
+                 string=True, backup=False)
+
+        # NAG compiler is usually mixed with GCC, which has a different
+        # prefix for linker arguments.
+        if self.compiler.name == 'nag':
+            x.filter('-Wl,--enable-new-dtags', '', string=True, backup=False)
+
     @run_after('install')
     def delete_mpirun_mpiexec(self):
         # The preferred way to run an application when Slurm is the
diff --git a/var/spack/repos/builtin/packages/openmpi/use_mpi_tkr_sizeof/step_1.patch b/var/spack/repos/builtin/packages/openmpi/use_mpi_tkr_sizeof/step_1.patch
new file mode 100644
index 00000000000..53d9e0018db
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openmpi/use_mpi_tkr_sizeof/step_1.patch
@@ -0,0 +1,584 @@
+--- a/ompi/mpi/fortran/use-mpi-tkr/mpi-f90-interfaces.h
++++ b/ompi/mpi/fortran/use-mpi-tkr/mpi-f90-interfaces.h
+@@ -1650,570 +1650,6 @@ end subroutine MPI_Request_get_status
+ end interface
+ 
+ 
+-interface MPI_Sizeof
+-
+-subroutine MPI_Sizeof0DCH(x, size, ierror)
+-  character, intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof0DCH
+-
+-
+-subroutine MPI_Sizeof0DL(x, size, ierror)
+-  logical, intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof0DL
+-
+-
+-subroutine MPI_Sizeof0DI1(x, size, ierror)
+-  integer*1, intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof0DI1
+-
+-
+-subroutine MPI_Sizeof0DI2(x, size, ierror)
+-  integer*2, intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof0DI2
+-
+-
+-subroutine MPI_Sizeof0DI4(x, size, ierror)
+-  integer*4, intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof0DI4
+-
+-
+-subroutine MPI_Sizeof0DI8(x, size, ierror)
+-  integer*8, intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof0DI8
+-
+-
+-subroutine MPI_Sizeof0DR4(x, size, ierror)
+-  real*4, intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof0DR4
+-
+-
+-subroutine MPI_Sizeof0DR8(x, size, ierror)
+-  real*8, intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof0DR8
+-
+-
+-subroutine MPI_Sizeof0DC8(x, size, ierror)
+-  complex*8, intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof0DC8
+-
+-
+-subroutine MPI_Sizeof0DC16(x, size, ierror)
+-  complex*16, intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof0DC16
+-
+-
+-subroutine MPI_Sizeof1DCH(x, size, ierror)
+-  character, dimension(*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof1DCH
+-
+-
+-subroutine MPI_Sizeof1DL(x, size, ierror)
+-  logical, dimension(*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof1DL
+-
+-
+-subroutine MPI_Sizeof1DI1(x, size, ierror)
+-  integer*1, dimension(*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof1DI1
+-
+-
+-subroutine MPI_Sizeof1DI2(x, size, ierror)
+-  integer*2, dimension(*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof1DI2
+-
+-
+-subroutine MPI_Sizeof1DI4(x, size, ierror)
+-  integer*4, dimension(*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof1DI4
+-
+-
+-subroutine MPI_Sizeof1DI8(x, size, ierror)
+-  integer*8, dimension(*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof1DI8
+-
+-
+-subroutine MPI_Sizeof1DR4(x, size, ierror)
+-  real*4, dimension(*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof1DR4
+-
+-
+-subroutine MPI_Sizeof1DR8(x, size, ierror)
+-  real*8, dimension(*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof1DR8
+-
+-
+-subroutine MPI_Sizeof1DC8(x, size, ierror)
+-  complex*8, dimension(*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof1DC8
+-
+-
+-subroutine MPI_Sizeof1DC16(x, size, ierror)
+-  complex*16, dimension(*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof1DC16
+-
+-
+-subroutine MPI_Sizeof2DCH(x, size, ierror)
+-  character, dimension(1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof2DCH
+-
+-
+-subroutine MPI_Sizeof2DL(x, size, ierror)
+-  logical, dimension(1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof2DL
+-
+-
+-subroutine MPI_Sizeof2DI1(x, size, ierror)
+-  integer*1, dimension(1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof2DI1
+-
+-
+-subroutine MPI_Sizeof2DI2(x, size, ierror)
+-  integer*2, dimension(1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof2DI2
+-
+-
+-subroutine MPI_Sizeof2DI4(x, size, ierror)
+-  integer*4, dimension(1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof2DI4
+-
+-
+-subroutine MPI_Sizeof2DI8(x, size, ierror)
+-  integer*8, dimension(1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof2DI8
+-
+-
+-subroutine MPI_Sizeof2DR4(x, size, ierror)
+-  real*4, dimension(1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof2DR4
+-
+-
+-subroutine MPI_Sizeof2DR8(x, size, ierror)
+-  real*8, dimension(1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof2DR8
+-
+-
+-subroutine MPI_Sizeof2DC8(x, size, ierror)
+-  complex*8, dimension(1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof2DC8
+-
+-
+-subroutine MPI_Sizeof2DC16(x, size, ierror)
+-  complex*16, dimension(1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof2DC16
+-
+-
+-subroutine MPI_Sizeof3DCH(x, size, ierror)
+-  character, dimension(1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof3DCH
+-
+-
+-subroutine MPI_Sizeof3DL(x, size, ierror)
+-  logical, dimension(1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof3DL
+-
+-
+-subroutine MPI_Sizeof3DI1(x, size, ierror)
+-  integer*1, dimension(1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof3DI1
+-
+-
+-subroutine MPI_Sizeof3DI2(x, size, ierror)
+-  integer*2, dimension(1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof3DI2
+-
+-
+-subroutine MPI_Sizeof3DI4(x, size, ierror)
+-  integer*4, dimension(1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof3DI4
+-
+-
+-subroutine MPI_Sizeof3DI8(x, size, ierror)
+-  integer*8, dimension(1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof3DI8
+-
+-
+-subroutine MPI_Sizeof3DR4(x, size, ierror)
+-  real*4, dimension(1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof3DR4
+-
+-
+-subroutine MPI_Sizeof3DR8(x, size, ierror)
+-  real*8, dimension(1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof3DR8
+-
+-
+-subroutine MPI_Sizeof3DC8(x, size, ierror)
+-  complex*8, dimension(1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof3DC8
+-
+-
+-subroutine MPI_Sizeof3DC16(x, size, ierror)
+-  complex*16, dimension(1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof3DC16
+-
+-
+-subroutine MPI_Sizeof4DCH(x, size, ierror)
+-  character, dimension(1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof4DCH
+-
+-
+-subroutine MPI_Sizeof4DL(x, size, ierror)
+-  logical, dimension(1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof4DL
+-
+-
+-subroutine MPI_Sizeof4DI1(x, size, ierror)
+-  integer*1, dimension(1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof4DI1
+-
+-
+-subroutine MPI_Sizeof4DI2(x, size, ierror)
+-  integer*2, dimension(1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof4DI2
+-
+-
+-subroutine MPI_Sizeof4DI4(x, size, ierror)
+-  integer*4, dimension(1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof4DI4
+-
+-
+-subroutine MPI_Sizeof4DI8(x, size, ierror)
+-  integer*8, dimension(1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof4DI8
+-
+-
+-subroutine MPI_Sizeof4DR4(x, size, ierror)
+-  real*4, dimension(1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof4DR4
+-
+-
+-subroutine MPI_Sizeof4DR8(x, size, ierror)
+-  real*8, dimension(1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof4DR8
+-
+-
+-subroutine MPI_Sizeof4DC8(x, size, ierror)
+-  complex*8, dimension(1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof4DC8
+-
+-
+-subroutine MPI_Sizeof4DC16(x, size, ierror)
+-  complex*16, dimension(1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof4DC16
+-
+-
+-subroutine MPI_Sizeof5DCH(x, size, ierror)
+-  character, dimension(1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof5DCH
+-
+-
+-subroutine MPI_Sizeof5DL(x, size, ierror)
+-  logical, dimension(1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof5DL
+-
+-
+-subroutine MPI_Sizeof5DI1(x, size, ierror)
+-  integer*1, dimension(1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof5DI1
+-
+-
+-subroutine MPI_Sizeof5DI2(x, size, ierror)
+-  integer*2, dimension(1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof5DI2
+-
+-
+-subroutine MPI_Sizeof5DI4(x, size, ierror)
+-  integer*4, dimension(1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof5DI4
+-
+-
+-subroutine MPI_Sizeof5DI8(x, size, ierror)
+-  integer*8, dimension(1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof5DI8
+-
+-
+-subroutine MPI_Sizeof5DR4(x, size, ierror)
+-  real*4, dimension(1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof5DR4
+-
+-
+-subroutine MPI_Sizeof5DR8(x, size, ierror)
+-  real*8, dimension(1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof5DR8
+-
+-
+-subroutine MPI_Sizeof5DC8(x, size, ierror)
+-  complex*8, dimension(1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof5DC8
+-
+-
+-subroutine MPI_Sizeof5DC16(x, size, ierror)
+-  complex*16, dimension(1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof5DC16
+-
+-
+-subroutine MPI_Sizeof6DCH(x, size, ierror)
+-  character, dimension(1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof6DCH
+-
+-
+-subroutine MPI_Sizeof6DL(x, size, ierror)
+-  logical, dimension(1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof6DL
+-
+-
+-subroutine MPI_Sizeof6DI1(x, size, ierror)
+-  integer*1, dimension(1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof6DI1
+-
+-
+-subroutine MPI_Sizeof6DI2(x, size, ierror)
+-  integer*2, dimension(1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof6DI2
+-
+-
+-subroutine MPI_Sizeof6DI4(x, size, ierror)
+-  integer*4, dimension(1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof6DI4
+-
+-
+-subroutine MPI_Sizeof6DI8(x, size, ierror)
+-  integer*8, dimension(1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof6DI8
+-
+-
+-subroutine MPI_Sizeof6DR4(x, size, ierror)
+-  real*4, dimension(1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof6DR4
+-
+-
+-subroutine MPI_Sizeof6DR8(x, size, ierror)
+-  real*8, dimension(1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof6DR8
+-
+-
+-subroutine MPI_Sizeof6DC8(x, size, ierror)
+-  complex*8, dimension(1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof6DC8
+-
+-
+-subroutine MPI_Sizeof6DC16(x, size, ierror)
+-  complex*16, dimension(1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof6DC16
+-
+-
+-subroutine MPI_Sizeof7DCH(x, size, ierror)
+-  character, dimension(1,1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof7DCH
+-
+-
+-subroutine MPI_Sizeof7DL(x, size, ierror)
+-  logical, dimension(1,1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof7DL
+-
+-
+-subroutine MPI_Sizeof7DI1(x, size, ierror)
+-  integer*1, dimension(1,1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof7DI1
+-
+-
+-subroutine MPI_Sizeof7DI2(x, size, ierror)
+-  integer*2, dimension(1,1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof7DI2
+-
+-
+-subroutine MPI_Sizeof7DI4(x, size, ierror)
+-  integer*4, dimension(1,1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof7DI4
+-
+-
+-subroutine MPI_Sizeof7DI8(x, size, ierror)
+-  integer*8, dimension(1,1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof7DI8
+-
+-
+-subroutine MPI_Sizeof7DR4(x, size, ierror)
+-  real*4, dimension(1,1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof7DR4
+-
+-
+-subroutine MPI_Sizeof7DR8(x, size, ierror)
+-  real*8, dimension(1,1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof7DR8
+-
+-
+-subroutine MPI_Sizeof7DC8(x, size, ierror)
+-  complex*8, dimension(1,1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof7DC8
+-
+-
+-subroutine MPI_Sizeof7DC16(x, size, ierror)
+-  complex*16, dimension(1,1,1,1,1,1,*), intent(in) :: x
+-  integer, intent(out) :: size
+-  integer, intent(out) :: ierror
+-end subroutine MPI_Sizeof7DC16
+-
+-end interface
+-
+-
+ interface MPI_Start
+ 
+ subroutine MPI_Start(request, ierror)
+--- a/ompi/mpi/fortran/use-mpi-tkr/mpi.F90
++++ b/ompi/mpi/fortran/use-mpi-tkr/mpi.F90
+@@ -50,4 +50,8 @@ module mpi
+ 
+   include "mpi-f90-interfaces.h"
+ 
++#if OMPI_FORTRAN_BUILD_SIZEOF
++  include "mpi-tkr-sizeof.h"
++#endif
++
+ end module mpi
diff --git a/var/spack/repos/builtin/packages/openmpi/use_mpi_tkr_sizeof/step_2.patch b/var/spack/repos/builtin/packages/openmpi/use_mpi_tkr_sizeof/step_2.patch
new file mode 100644
index 00000000000..6ca5051a596
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openmpi/use_mpi_tkr_sizeof/step_2.patch
@@ -0,0 +1,22 @@
+--- a/ompi/mpi/fortran/configure-fortran-output.h.in
++++ b/ompi/mpi/fortran/configure-fortran-output.h.in
+@@ -47,6 +47,8 @@
+ ! Line 2 of the ignore TKR syntax
+ #define OMPI_FORTRAN_IGNORE_TKR_TYPE @OMPI_FORTRAN_IGNORE_TKR_TYPE@
+ 
++
++#define OMPI_FORTRAN_BUILD_SIZEOF @OMPI_FORTRAN_BUILD_SIZEOF@
+ ! Integers
+ 
+ #define OMPI_HAVE_FORTRAN_INTEGER1 @OMPI_HAVE_FORTRAN_INTEGER1@
+--- a/ompi/mpi/fortran/use-mpi-tkr/Makefile.in
++++ b/ompi/mpi/fortran/use-mpi-tkr/Makefile.in
+@@ -2023,6 +2023,8 @@ uninstall-am: uninstall-libLTLIBRARIES uninstall-local
+ @OMPI_BUILD_FORTRAN_USEMPI_TKR_BINDINGS_TRUE@mpi.lo: $(top_builddir)/ompi/mpi/fortran/configure-fortran-output.h
+ @OMPI_BUILD_FORTRAN_USEMPI_TKR_BINDINGS_TRUE@mpi.lo: mpi-f90-cptr-interfaces.F90
+ 
++@BUILD_FORTRAN_SIZEOF_TRUE@@OMPI_BUILD_FORTRAN_USEMPI_TKR_BINDINGS_TRUE@mpi.lo: mpi-tkr-sizeof.h
++
+ @OMPI_BUILD_FORTRAN_USEMPI_TKR_BINDINGS_TRUE@mpi-tkr-sizeof.h: $(top_builddir)/config.status
+ @OMPI_BUILD_FORTRAN_USEMPI_TKR_BINDINGS_TRUE@mpi-tkr-sizeof.h: $(sizeof_pl)
+ @OMPI_BUILD_FORTRAN_USEMPI_TKR_BINDINGS_TRUE@mpi-tkr-sizeof.h:

From ad18933ef400ecbb879feebb32368ab7cc898493 Mon Sep 17 00:00:00 2001
From: Michio Ogawa <michioga@users.noreply.github.com>
Date: Thu, 18 Jun 2020 00:45:51 +0900
Subject: [PATCH 750/802] FrontISTR: various updates to the package (#17089)

* Added maintainers
* Refined dependencies
* Changed git url
---
 .../builtin/packages/frontistr/package.py     | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/frontistr/package.py b/var/spack/repos/builtin/packages/frontistr/package.py
index 0a0cf7d6283..ebdfa0a3e31 100644
--- a/var/spack/repos/builtin/packages/frontistr/package.py
+++ b/var/spack/repos/builtin/packages/frontistr/package.py
@@ -11,18 +11,25 @@ class Frontistr(CMakePackage):
     """Open-Source Large-Scale Parallel FEM Program for
         Nonlinear Structural Analysis"""
 
-    homepage = "https://github.com/FrontISTR/FrontISTR"
-    git      = "https://github.com/FrontISTR/FrontISTR.git"
+    homepage = "https://www.frontistr.com/"
+    git      = "https://gitlab.com/FrontISTR-Commons/FrontISTR.git"
+    maintainers = ['hiroshi.okuda', 'kgoto', 'morita', 'inagaki', 'michioga']
 
     version('5.0', tag='v5.0')
+    version('master', tag='master')
+
+    variant('build_type', default='RELEASE',
+            description='CMake build type',
+            values=('DEBUG', 'RELEASE'))
 
     depends_on('mpi')
-    depends_on('revocap-refiner')
-    depends_on('revocap-coupler')
     depends_on('blas')
-    depends_on('metis')
+    depends_on('lapack')
     depends_on('scalapack')
-    depends_on('mumps +mpi')
+    depends_on('revocap-refiner')
+    # depends_on('revocap-coupler')
+    depends_on('metis')
+    depends_on('mumps')
     depends_on('trilinos')
 
     def cmake_args(self):

From 03880f54139ff97e144833378842034c0f2d2a3b Mon Sep 17 00:00:00 2001
From: vvolkl <valentin.volkl@cern.ch>
Date: Wed, 17 Jun 2020 19:13:27 +0200
Subject: [PATCH 751/802] Split hepmc Into hepmc and hepmc3 (#16892)

---
 .../repos/builtin/packages/acts/package.py    |  2 +-
 .../repos/builtin/packages/hepmc/package.py   | 46 +--------------
 .../repos/builtin/packages/hepmc3/package.py  | 57 +++++++++++++++++++
 3 files changed, 59 insertions(+), 46 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/hepmc3/package.py

diff --git a/var/spack/repos/builtin/packages/acts/package.py b/var/spack/repos/builtin/packages/acts/package.py
index 09113f2cd82..849c326b18a 100644
--- a/var/spack/repos/builtin/packages/acts/package.py
+++ b/var/spack/repos/builtin/packages/acts/package.py
@@ -96,7 +96,7 @@ class Acts(CMakePackage):
     depends_on('dd4hep @1.10: +geant4 +xercesc', when='+dd4hep +geant4')
     depends_on('eigen @3.2.9:', type='build')
     depends_on('geant4', when='+geant4')
-    depends_on('hepmc@3.1:', when='+hepmc3')
+    depends_on('hepmc3@3.1:', when='+hepmc3')
     depends_on('heppdt', when='+hepmc3')
     depends_on('intel-tbb', when='+examples')
     depends_on('nlohmann-json @3.2.0:', when='@0.14: +json')
diff --git a/var/spack/repos/builtin/packages/hepmc/package.py b/var/spack/repos/builtin/packages/hepmc/package.py
index d208e7ecde3..6581615a2be 100644
--- a/var/spack/repos/builtin/packages/hepmc/package.py
+++ b/var/spack/repos/builtin/packages/hepmc/package.py
@@ -14,11 +14,6 @@ class Hepmc(CMakePackage):
     homepage = "http://hepmc.web.cern.ch/hepmc/"
     url      = "http://hepmc.web.cern.ch/hepmc/releases/hepmc2.06.09.tgz"
 
-    version('3.2.0', sha256='f132387763d170f25a7cc9f0bd586b83373c09acf0c3daa5504063ba460f89fc')
-    version('3.1.2', sha256='4133074b3928252877982f3d4b4c6c750bb7a324eb6c7bb2afc6fa256da3ecc7')
-    version('3.1.1', sha256='2fcbc9964d6f9f7776289d65f9c73033f85c15bf5f0df00c429a6a1d8b8248bb')
-    version('3.1.0', sha256='cd37eed619d58369041018b8627274ad790020a4714b54ac05ad1ebc1a6e7f8a')
-    version('3.0.0',   sha256='7ac3c939a857a5ad67bea1e77e3eb16e80d38cfdf825252ac57160634c26d9ec')
     version('2.06.10', sha256='5adedd9e3f7447e1e5fc01b72f745ab87da2c1611df89208bb3d7c6ea94c11a4')
     version('2.06.09', sha256='e0f8fddd38472c5615210894444686ac5d72df3be682f7d151b562b236d9b422')
     version('2.06.08', sha256='8be6c1793e0a045f07ddb88bb64b46de7e66a52e75fb72b3f82f9a3e3ba8a8ce')
@@ -26,52 +21,13 @@ class Hepmc(CMakePackage):
     version('2.06.06', sha256='8cdff26c10783ed4248220a84a43b7e1f9b59cc2c9a29bd634d024ca469db125')
     version('2.06.05', sha256='4c411077cc97522c03b74f973264b8d9fd2b6ccec0efc7ceced2645371c73618')
 
-    variant('python', default=False, description='Enable Python bindings')
-    variant('rootio', default=False, description='Enable ROOT I/O')
-    variant('interfaces', default=False, description='Install interfaces for some Monte-Carlo Event Gens')
-
     depends_on('cmake@2.8.9:', type='build')
-    depends_on('python', when='+python')
-    depends_on('root', when='+rootio')
 
-    conflicts('+python', when='@:3.1')
-    conflicts('+rootio', when='@:2')
-    conflicts('+interfaces', when='@:2')
-
-    @when('@:2')
     def cmake_args(self):
         return ['-Dmomentum:STRING=GEV', '-Dlength:STRING=MM']
 
-    @when('@3:')
-    def cmake_args(self):
-        spec = self.spec
-        args = [
-            '-Dmomentum:STRING=GEV',
-            '-Dlength:STRING=MM',
-            '-DHEPMC3_ENABLE_PYTHON={0}'.format(spec.satisfies('+python')),
-            '-DHEPMC3_ENABLE_ROOTIO={0}'.format(spec.satisfies('+rootio')),
-            '-DHEPMC3_INSTALL_INTERFACES={0}'.format(
-                spec.satisfies('+interfaces')),
-        ]
-
-        if self.spec.satisfies('+python'):
-            py_ver = spec['python'].version.up_to(2)
-            py_sitepkg = join_path(self.prefix, site_packages_dir)
-            args.extend([
-                '-DHEPMC3_PYTHON_VERSIONS={0}'.format(py_ver),
-                '-DHEPMC3_Python_SITEARCH{0}={1}'.format(
-                    py_ver.joined, py_sitepkg)
-            ])
-
-        if self.spec.satisfies('+rootio'):
-            args.append('-DROOT_DIR={0}'.format(self.spec['root'].prefix))
-
-        return args
-
     def url_for_version(self, version):
-        if version > Version("3.0.0"):
-            url = "http://hepmc.web.cern.ch/hepmc/releases/HepMC3-{0}.tar.gz"
-        elif version <= Version("2.06.08"):
+        if version <= Version("2.06.08"):
             url = "http://lcgapp.cern.ch/project/simu/HepMC/download/HepMC-{0}.tar.gz"
         else:
             url = "http://hepmc.web.cern.ch/hepmc/releases/hepmc{0}.tgz"
diff --git a/var/spack/repos/builtin/packages/hepmc3/package.py b/var/spack/repos/builtin/packages/hepmc3/package.py
new file mode 100644
index 00000000000..95cc4014570
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hepmc3/package.py
@@ -0,0 +1,57 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Hepmc3(CMakePackage):
+    """The HepMC package is an object oriented, C++ event record for
+       High Energy Physics Monte Carlo generators and simulation."""
+
+    homepage = "https://cern.ch/hepmc"
+    url      = "https://gitlab.cern.ch/hepmc/HepMC3/-/archive/3.2.1/HepMC3-3.2.1.tar.gz"
+    git      = "https://gitlab.cern.ch/hepmc/HepMC3.git"
+
+    maintainers = ['vvolkl']
+
+    version('3.2.1', sha256='6e4e4bb5708af105d4bf74efc2745e6efe704e942d46a8042f7dcae37a4739fe')
+    version('3.2.0', sha256='f132387763d170f25a7cc9f0bd586b83373c09acf0c3daa5504063ba460f89fc')
+    version('3.1.2', sha256='4133074b3928252877982f3d4b4c6c750bb7a324eb6c7bb2afc6fa256da3ecc7')
+    version('3.1.1', sha256='2fcbc9964d6f9f7776289d65f9c73033f85c15bf5f0df00c429a6a1d8b8248bb')
+    version('3.1.0', sha256='cd37eed619d58369041018b8627274ad790020a4714b54ac05ad1ebc1a6e7f8a')
+    # note that version 3.0.0 is not supported
+    # conflicts with cmake configuration
+
+    variant('python', default=False, description='Enable Python bindings')
+    variant('rootio', default=False, description='Enable ROOT I/O')
+    variant('interfaces', default=False, description='Install interfaces for some Monte-Carlo Event Gens')
+
+    depends_on('cmake@2.8.9:', type='build')
+    depends_on('root', when='+rootio')
+    depends_on('python', when="+python")
+
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            '-Dmomentum:STRING=GEV',
+            '-Dlength:STRING=MM',
+            '-DHEPMC3_ENABLE_PYTHON={0}'.format(spec.satisfies('+python')),
+            '-DHEPMC3_ENABLE_ROOTIO={0}'.format(spec.satisfies('+rootio')),
+            '-DHEPMC3_INSTALL_INTERFACES={0}'.format(
+                spec.satisfies('+interfaces')),
+        ]
+
+        if self.spec.satisfies('+python'):
+            py_ver = spec['python'].version.up_to(2)
+            py_sitepkg = join_path(self.prefix, site_packages_dir)
+            args.extend([
+                '-DHEPMC3_PYTHON_VERSIONS={0}'.format(py_ver),
+                '-DHEPMC3_Python_SITEARCH{0}={1}'.format(
+                    py_ver.joined, py_sitepkg)
+            ])
+
+        if self.spec.satisfies('+rootio'):
+            args.append('-DROOT_DIR={0}'.format(self.spec['root'].prefix))
+        return args

From 506f31b7a7fa1ebabdb4ce5d1764b0a197e62989 Mon Sep 17 00:00:00 2001
From: Chris White <white238@llnl.gov>
Date: Wed, 17 Jun 2020 10:43:47 -0700
Subject: [PATCH 752/802] axom conduit mfem build fixes (#17121)

* honor global compiler flags

* Honor debug variant when using global compiler flags

* Add cppflags to c/cxx flags, clarify flag handling
---
 .../repos/builtin/packages/axom/package.py    | 58 +++++++++++++------
 .../repos/builtin/packages/conduit/package.py | 36 +++++++++++-
 .../repos/builtin/packages/mfem/package.py    | 15 +++++
 3 files changed, 91 insertions(+), 18 deletions(-)

diff --git a/var/spack/repos/builtin/packages/axom/package.py b/var/spack/repos/builtin/packages/axom/package.py
index 46b411b4e7a..2eb3ae226c9 100644
--- a/var/spack/repos/builtin/packages/axom/package.py
+++ b/var/spack/repos/builtin/packages/axom/package.py
@@ -65,10 +65,10 @@ class Axom(CMakePackage, CudaPackage):
     # -----------------------------------------------------------------------
     # Variants
     # -----------------------------------------------------------------------
-    variant('debug', default=False,
+    variant('debug',    default=False,
             description='Build debug instead of optimized version')
 
-    variant('fortran', default=True, description="Build with Fortran support")
+    variant('fortran',  default=True, description="Build with Fortran support")
 
     variant("python",   default=False, description="Build python support")
 
@@ -77,16 +77,16 @@ class Axom(CMakePackage, CudaPackage):
 
     variant("mfem",     default=False, description="Build with mfem")
     variant("hdf5",     default=True, description="Build with hdf5")
-    variant("lua",      default=False, description="Build with Lua")
+    variant("lua",      default=True, description="Build with Lua")
     variant("scr",      default=False, description="Build with SCR")
     variant("umpire",   default=True, description="Build with umpire")
 
     variant("raja",     default=True, description="Build with raja")
-    variant("cub",     default=True,
+    variant("cub",      default=True,
             description="Build with RAJA's internal CUB support")
 
     varmsg = "Build development tools (such as Sphinx, Uncrustify, etc...)"
-    variant("devtools",  default=False, description=varmsg)
+    variant("devtools", default=False, description=varmsg)
 
     # -----------------------------------------------------------------------
     # Dependencies
@@ -124,7 +124,7 @@ class Axom(CMakePackage, CudaPackage):
         depends_on('umpire cuda_arch={0}'.format(sm_),
                    when='+umpire cuda_arch={0}'.format(sm_))
 
-    depends_on("mfem~mpi~hypre~metis~gzstream", when="+mfem")
+    depends_on("mfem~mpi~hypre~metis~zlib", when="+mfem")
 
     depends_on("python", when="+python")
 
@@ -137,6 +137,12 @@ class Axom(CMakePackage, CudaPackage):
     depends_on("py-shroud", when="+devtools")
     depends_on("uncrustify@0.61", when="+devtools")
 
+    def flag_handler(self, name, flags):
+        if name in ('cflags', 'cxxflags', 'fflags'):
+            # the package manages these flags in another way
+            return (None, None, None)
+        return (flags, None, None)
+
     def _get_sys_type(self, spec):
         sys_type = spec.architecture
         # if on llnl systems, we can use the SYS_TYPE
@@ -210,6 +216,33 @@ def hostconfig(self, spec, prefix):
         else:
             cfg.write(cmake_cache_option("ENABLE_FORTRAN", False))
 
+        # use global spack compiler flags
+        cppflags = ' '.join(spec.compiler_flags['cppflags'])
+        if cppflags:
+            # avoid always ending up with ' ' with no flags defined
+            cppflags += ' '
+        cflags = cppflags + ' '.join(spec.compiler_flags['cflags'])
+        if cflags:
+            cfg.write(cmake_cache_entry("CMAKE_C_FLAGS", cflags))
+        cxxflags = cppflags + ' '.join(spec.compiler_flags['cxxflags'])
+        if cxxflags:
+            cfg.write(cmake_cache_entry("CMAKE_CXX_FLAGS", cxxflags))
+        fflags = ' '.join(spec.compiler_flags['fflags'])
+        if fflags:
+            cfg.write(cmake_cache_entry("CMAKE_Fortran_FLAGS", fflags))
+
+        if ("gfortran" in f_compiler) and ("clang" in cpp_compiler):
+            libdir = pjoin(os.path.dirname(
+                           os.path.dirname(cpp_compiler)), "lib")
+            flags = ""
+            for _libpath in [libdir, libdir + "64"]:
+                if os.path.exists(_libpath):
+                    flags += " -Wl,-rpath,{0}".format(_libpath)
+            description = ("Adds a missing libstdc++ rpath")
+            if flags:
+                cfg.write(cmake_cache_entry("BLT_EXE_LINKER_FLAGS", flags,
+                                            description))
+
         # TPL locations
         cfg.write("#------------------{0}\n".format("-" * 60))
         cfg.write("# TPLs\n")
@@ -433,9 +466,9 @@ def hostconfig(self, spec, prefix):
                                       os.path.dirname(f_compiler)), "lib")
                 description = ("Adds a missing rpath for libraries "
                                "associated with the fortran compiler")
+                linker_flags = "${BLT_EXE_LINKER_FLAGS} -Wl,-rpath," + libdir
                 cfg.write(cmake_cache_entry("BLT_EXE_LINKER_FLAGS",
-                                            "-Wl,-rpath," + libdir,
-                                            description))
+                                            linker_flags, description))
 
             if "+cuda" in spec:
                 cfg.write("#------------------{0}\n".format("-" * 60))
@@ -485,15 +518,6 @@ def hostconfig(self, spec, prefix):
                 cfg.write("# nvcc does not like gtest's 'pthreads' flag\n")
                 cfg.write(cmake_cache_option("gtest_disable_pthreads", True))
 
-        if ("gfortran" in f_compiler) and ("clang" in cpp_compiler):
-            clanglibdir = pjoin(os.path.dirname(
-                                os.path.dirname(cpp_compiler)), "lib")
-            flags = "-Wl,-rpath,{0}".format(clanglibdir)
-            description = ("Adds a missing rpath for libraries "
-                           "associated with the fortran compiler")
-            cfg.write(cmake_cache_entry("BLT_EXE_LINKER_FLAGS", flags,
-                                        description))
-
         cfg.write("\n")
         cfg.close()
         tty.info("Spack generated Axom host-config file: " + host_config_path)
diff --git a/var/spack/repos/builtin/packages/conduit/package.py b/var/spack/repos/builtin/packages/conduit/package.py
index 2e6ec094091..9928884e924 100644
--- a/var/spack/repos/builtin/packages/conduit/package.py
+++ b/var/spack/repos/builtin/packages/conduit/package.py
@@ -147,6 +147,12 @@ class Conduit(Package):
     # build phases used by this package
     phases = ["configure", "build", "install"]
 
+    def flag_handler(self, name, flags):
+        if name in ('cflags', 'cxxflags', 'fflags'):
+            # the package manages these flags in another way
+            return (None, None, None)
+        return (flags, None, None)
+
     def setup_build_environment(self, env):
         env.set('CTEST_OUTPUT_ON_FAILURE', '1')
 
@@ -350,6 +356,33 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
         else:
             cfg.write(cmake_cache_entry("BUILD_SHARED_LIBS", "OFF"))
 
+        # use global spack compiler flags
+        cppflags = ' '.join(spec.compiler_flags['cppflags'])
+        if cppflags:
+            # avoid always ending up with ' ' with no flags defined
+            cppflags += ' '
+        cflags = cppflags + ' '.join(spec.compiler_flags['cflags'])
+        if cflags:
+            cfg.write(cmake_cache_entry("CMAKE_C_FLAGS", cflags))
+        cxxflags = cppflags + ' '.join(spec.compiler_flags['cxxflags'])
+        if cxxflags:
+            cfg.write(cmake_cache_entry("CMAKE_CXX_FLAGS", cxxflags))
+        fflags = ' '.join(spec.compiler_flags['fflags'])
+        if fflags:
+            cfg.write(cmake_cache_entry("CMAKE_Fortran_FLAGS", fflags))
+
+        if ("gfortran" in f_compiler) and ("clang" in cpp_compiler):
+            libdir = os.path.join(os.path.dirname(
+                                  os.path.dirname(f_compiler)), "lib")
+            flags = ""
+            for _libpath in [libdir, libdir + "64"]:
+                if os.path.exists(_libpath):
+                    flags += " -Wl,-rpath,{0}".format(_libpath)
+            description = ("Adds a missing libstdc++ rpath")
+            if flags:
+                cfg.write(cmake_cache_entry("BLT_EXE_LINKER_FLAGS", flags,
+                                            description))
+
         #######################
         # Unit Tests
         #######################
@@ -380,7 +413,8 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
                     # Grab lib directory for the current fortran compiler
                     libdir = os.path.join(os.path.dirname(
                                           os.path.dirname(f_compiler)), "lib")
-                    flags = "-lstdc++ -Wl,-rpath," + libdir
+                    flags  = "${BLT_EXE_LINKER_FLAGS} -lstdc++ "
+                    flags += "-Wl,-rpath,{0} -Wl,-rpath,{0}64".format(libdir)
                     cfg.write(cmake_cache_entry("BLT_EXE_LINKER_FLAGS",
                                                 flags))
 
diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py
index 5f6d8b5c0a2..3a4abab49bf 100644
--- a/var/spack/repos/builtin/packages/mfem/package.py
+++ b/var/spack/repos/builtin/packages/mfem/package.py
@@ -366,6 +366,21 @@ def find_optional_library(name, prefix):
         cxxflags = spec.compiler_flags['cxxflags']
 
         if cxxflags:
+            # Add opt/debug flags if they are not present in global cxx flags
+            opt_flag_found = any(f in self.compiler.opt_flags
+                                 for f in cxxflags)
+            debug_flag_found = any(f in self.compiler.debug_flags
+                                   for f in cxxflags)
+
+            if '+debug' in spec:
+                if not debug_flag_found:
+                    cxxflags.append('-g')
+                if not opt_flag_found:
+                    cxxflags.append('-O0')
+            else:
+                if not opt_flag_found:
+                    cxxflags.append('-O2')
+
             cxxflags = [(xcompiler + flag) for flag in cxxflags]
             if '+cuda' in spec:
                 cxxflags += [

From 01b277ad0fe15e6f42f9f403126da5de68994737 Mon Sep 17 00:00:00 2001
From: Sergey Kosukhin <sergey.kosukhin@mpimet.mpg.de>
Date: Wed, 17 Jun 2020 21:41:24 +0200
Subject: [PATCH 753/802] openmpi: options for local transport (#16831)

---
 .../repos/builtin/packages/fca/package.py     |  31 ++++
 .../repos/builtin/packages/hcoll/package.py   |  31 ++++
 .../repos/builtin/packages/knem/package.py    |  46 ++++++
 .../repos/builtin/packages/openmpi/package.py | 142 ++++++++++++++----
 .../repos/builtin/packages/xpmem/package.py   |  91 +++++++++++
 5 files changed, 310 insertions(+), 31 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/fca/package.py
 create mode 100644 var/spack/repos/builtin/packages/hcoll/package.py
 create mode 100644 var/spack/repos/builtin/packages/knem/package.py
 create mode 100644 var/spack/repos/builtin/packages/xpmem/package.py

diff --git a/var/spack/repos/builtin/packages/fca/package.py b/var/spack/repos/builtin/packages/fca/package.py
new file mode 100644
index 00000000000..ca91a43b4ec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fca/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fca(Package):
+    """Legacy interface for Mellanox Fabric Collective Accelerator (FCA). FCA
+    is a MPI-integrated software package that utilizes CORE-Direct technology
+    for implementing the MPI collective communications."""
+
+    homepage = 'https://www.mellanox.com/products/fca'
+    has_code = False
+
+    version('2.5.2431')
+
+    # FCA needs to be added as an external package to SPACK. For this, the
+    # config file packages.yaml needs to be adjusted:
+    #
+    # fca:
+    #   version: [2.5.2431]
+    #   paths:
+    #     fca@2.5.2431: /opt/mellanox/fca (path to your FCA installation)
+    #   buildable: False
+
+    def install(self, spec, prefix):
+        raise InstallError(
+            self.spec.format('{name} is not installable, you need to specify '
+                             'it as an external package in packages.yaml'))
diff --git a/var/spack/repos/builtin/packages/hcoll/package.py b/var/spack/repos/builtin/packages/hcoll/package.py
new file mode 100644
index 00000000000..f39e2e75960
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hcoll/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Hcoll(Package):
+    """Modern interface for Mellanox Fabric Collective Accelerator (FCA). FCA
+    is a MPI-integrated software package that utilizes CORE-Direct technology
+    for implementing the MPI collective communications."""
+
+    homepage = 'https://www.mellanox.com/products/fca'
+    has_code = False
+
+    version('3.9.1927')
+
+    # HCOLL needs to be added as an external package to SPACK. For this, the
+    # config file packages.yaml needs to be adjusted:
+    #
+    # hcoll:
+    #   version: [3.9.1927]
+    #   paths:
+    #     hcoll@3.9.1927: /opt/mellanox/hcoll (path to your HCOLL installation)
+    #   buildable: False
+
+    def install(self, spec, prefix):
+        raise InstallError(
+            self.spec.format('{name} is not installable, you need to specify '
+                             'it as an external package in packages.yaml'))
diff --git a/var/spack/repos/builtin/packages/knem/package.py b/var/spack/repos/builtin/packages/knem/package.py
new file mode 100644
index 00000000000..473a1783193
--- /dev/null
+++ b/var/spack/repos/builtin/packages/knem/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Knem(AutotoolsPackage):
+    """KNEM is a Linux kernel module enabling high-performance intra-node MPI
+    communication for large messages."""
+
+    homepage = "http://knem.gforge.inria.fr"
+    url = "http://gforge.inria.fr/frs/download.php/37186/knem-1.1.3.tar.gz"
+    list_url = "http://knem.gforge.inria.fr/download"
+
+    maintainers = ['skosukhin']
+
+    version('1.1.3', sha256='50d3c4a20c140108b8ce47aaafd0ade0927d6f507e1b5cc690dd6bddeef30f60')
+
+    variant('hwloc', default=True,
+            description='Enable hwloc in the user-space tools')
+
+    depends_on('hwloc', when='+hwloc')
+    depends_on('pkgconfig', type='build', when='+hwloc')
+
+    # The support for hwloc was added in 0.9.1:
+    conflicts('+hwloc', when='@:0.9.0')
+
+    # Ideally, we should list all non-Linux-based platforms here:
+    conflicts('platform=darwin')
+
+    # All compilers except for gcc are in conflict:
+    for __compiler in spack.compilers.supported_compilers():
+        if __compiler != 'gcc':
+            conflicts('%{0}'.format(__compiler),
+                      msg='Linux kernel module must be compiled with gcc')
+
+    @run_before('build')
+    def override_kernel_compiler(self):
+        # Override the compiler for kernel module source files. We need
+        # this additional argument for all installation phases.
+        make.add_default_arg('CC={0}'.format(spack_cc))
+
+    def configure_args(self):
+        return self.enable_or_disable('hwloc')
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index ee2f76ea19e..4065e85a591 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -182,19 +182,25 @@ class Openmpi(AutotoolsPackage):
     variant(
         'fabrics',
         values=disjoint_sets(
-            ('auto',), ('psm', 'psm2', 'verbs', 'mxm', 'ucx', 'libfabric')
+            ('auto',),
+            ('psm', 'psm2', 'verbs',
+             'mxm', 'ucx', 'ofi',
+             'fca', 'hcoll',
+             'xpmem', 'cma', 'knem')  # shared memory transports
         ).with_non_feature_values('auto', 'none'),
         description="List of fabrics that are enabled; "
-        "'auto' lets openmpi determine",
+                    "'auto' lets openmpi determine",
     )
 
     variant(
         'schedulers',
         values=disjoint_sets(
-            ('auto',), ('alps', 'lsf', 'tm', 'slurm', 'sge', 'loadleveler')
+            ('auto',),
+            ('alps', 'lsf', 'tm',
+             'slurm', 'sge', 'loadleveler')
         ).with_non_feature_values('auto', 'none'),
         description="List of schedulers for which support is enabled; "
-        "'auto' lets openmpi determine",
+                    "'auto' lets openmpi determine",
     )
 
     # Additional support options
@@ -259,39 +265,59 @@ class Openmpi(AutotoolsPackage):
     depends_on('zlib', when='@3.0.0:')
     depends_on('valgrind~mpi', when='+memchecker')
 
+    depends_on('opa-psm2', when='fabrics=psm2')
+    depends_on('rdma-core', when='fabrics=verbs')
+    depends_on('mxm', when='fabrics=mxm')
+    depends_on('binutils+libiberty', when='fabrics=mxm')
     depends_on('ucx', when='fabrics=ucx')
     depends_on('ucx +thread_multiple', when='fabrics=ucx +thread_multiple')
     depends_on('ucx +thread_multiple', when='@3.0.0: fabrics=ucx')
-    depends_on('libfabric', when='fabrics=libfabric')
-    depends_on('opa-psm2', when='fabrics=psm2')
-    depends_on('mxm', when='fabrics=mxm')
-    depends_on('binutils+libiberty', when='fabrics=mxm')
-    depends_on('rdma-core', when='fabrics=verbs')
+    depends_on('libfabric', when='fabrics=ofi')
+    depends_on('fca', when='fabrics=fca')
+    depends_on('hcoll', when='fabrics=hcoll')
+    depends_on('xpmem', when='fabrics=xpmem')
+    depends_on('knem', when='fabrics=knem')
 
-    depends_on('slurm', when='schedulers=slurm')
     depends_on('lsf', when='schedulers=lsf')
     depends_on('openpbs', when='schedulers=tm')
+    depends_on('slurm', when='schedulers=slurm')
+
+    # CUDA support was added in 1.7
+    conflicts('+cuda', when='@:1.6')
+    # PMI support was added in 1.5.5
+    conflicts('+pmi', when='@:1.5.4')
+    # RPATH support in the wrappers was added in 1.7.4
+    conflicts('+wrapper-rpath', when='@:1.7.3')
 
-    conflicts('+cuda', when='@:1.6')  # CUDA support was added in 1.7
-    conflicts('fabrics=psm2', when='@:1.8')  # PSM2 support was added in 1.10.0
-    conflicts('fabrics=mxm', when='@:1.5.3')  # MXM support was added in 1.5.4
-    conflicts('+pmi', when='@:1.5.4')  # PMI support was added in 1.5.5
-    conflicts('schedulers=slurm ~pmi', when='@1.5.4:',
-              msg='+pmi is required for openmpi(>=1.5.5) to work with SLURM.')
-    conflicts('schedulers=loadleveler', when='@3.0.0:',
-              msg='The loadleveler scheduler is not supported with '
-              'openmpi(>=3.0.0).')
     conflicts('+cxx', when='@5:',
               msg='C++ MPI bindings are removed in 5.0.X release')
     conflicts('+cxx_exceptions', when='@5:',
               msg='C++ exceptions are removed in 5.0.X release')
 
-    filter_compiler_wrappers('openmpi/*-wrapper-data*', relative_root='share')
-    conflicts('fabrics=libfabric', when='@:1.8')  # libfabric support was added in 1.10.0
-    # It may be worth considering making libfabric an exclusive fabrics choice
+    # PSM2 support was added in 1.10.0
+    conflicts('fabrics=psm2', when='@:1.8')
+    # MXM support was added in 1.5.4
+    conflicts('fabrics=mxm', when='@:1.5.3')
+    # libfabric (OFI) support was added in 1.10.0
+    conflicts('fabrics=ofi', when='@:1.8')
+    # fca support was added in 1.5.0 and removed in 5.0.0
+    conflicts('fabrics=fca', when='@:1.4,5:')
+    # hcoll support was added in 1.7.3:
+    conflicts('fabrics=hcoll', when='@:1.7.2')
+    # xpmem support was added in 1.7
+    conflicts('fabrics=xpmem', when='@:1.6')
+    # cma support was added in 1.7
+    conflicts('fabrics=cma', when='@:1.6')
+    # knem support was added in 1.5
+    conflicts('fabrics=knem', when='@:1.4')
 
-    # RPATH support in the wrappers was added in 1.7.4
-    conflicts('+wrapper-rpath', when='@:1.7.3')
+    conflicts('schedulers=slurm ~pmi', when='@1.5.4:',
+              msg='+pmi is required for openmpi(>=1.5.5) to work with SLURM.')
+    conflicts('schedulers=loadleveler', when='@3.0.0:',
+              msg='The loadleveler scheduler is not supported with '
+              'openmpi(>=3.0.0).')
+
+    filter_compiler_wrappers('openmpi/*-wrapper-data*', relative_root='share')
 
     def url_for_version(self, version):
         url = "http://www.open-mpi.org/software/ompi/v{0}/downloads/openmpi-{1}.tar.bz2"
@@ -343,6 +369,17 @@ def setup_dependent_package(self, module, dependent_spec):
             join_path(self.prefix.lib, 'libmpi.{0}'.format(dso_suffix))
         ]
 
+    # Most of the following with_or_without methods might seem redundant
+    # because Spack compiler wrapper adds the required -I and -L flags, which
+    # is enough for the configure script to find them. However, we also need
+    # the flags in Libtool (lib/*.la) and pkg-config (lib/pkgconfig/*.pc).
+    # Therefore, we pass the prefixes explicitly.
+
+    def with_or_without_psm2(self, activated):
+        if not activated:
+            return '--without-psm2'
+        return '--with-psm2={0}'.format(self.spec['opa-psm2'].prefix)
+
     def with_or_without_verbs(self, activated):
         # Up through version 1.6, this option was named --with-openib.
         # In version 1.7, it was renamed to be --with-verbs.
@@ -351,16 +388,54 @@ def with_or_without_verbs(self, activated):
             return '--without-{0}'.format(opt)
         return '--with-{0}={1}'.format(opt, self.spec['rdma-core'].prefix)
 
+    def with_or_without_mxm(self, activated):
+        if not activated:
+            return '--without-mxm'
+        return '--with-mxm={0}'.format(self.spec['mxm'].prefix)
+
+    def with_or_without_ucx(self, activated):
+        if not activated:
+            return '--without-ucx'
+        return '--with-ucx={0}'.format(self.spec['ucx'].prefix)
+
+    def with_or_without_ofi(self, activated):
+        # Up through version 3.0.3 this option was name --with-libfabric.
+        # In version 3.0.4, the old name was deprecated in favor of --with-ofi.
+        opt = 'ofi' if self.spec.satisfies('@3.0.4:') else 'libfabric'
+        if not activated:
+            return '--without-{0}'.format(opt)
+        return '--with-{0}={1}'.format(opt, self.spec['libfabric'].prefix)
+
+    def with_or_without_fca(self, activated):
+        if not activated:
+            return '--without-fca'
+        return '--with-fca={0}'.format(self.spec['fca'].prefix)
+
+    def with_or_without_hcoll(self, activated):
+        if not activated:
+            return '--without-hcoll'
+        return '--with-hcoll={0}'.format(self.spec['hcoll'].prefix)
+
+    def with_or_without_xpmem(self, activated):
+        if not activated:
+            return '--without-xpmem'
+        return '--with-xpmem={0}'.format(self.spec['xpmem'].prefix)
+
+    def with_or_without_knem(self, activated):
+        if not activated:
+            return '--without-knem'
+        return '--with-knem={0}'.format(self.spec['knem'].prefix)
+
+    def with_or_without_lsf(self, activated):
+        if not activated:
+            return '--without-lsf'
+        return '--with-lsf={0}'.format(self.spec['lsf'].prefix)
+
     def with_or_without_tm(self, activated):
         if not activated:
             return '--without-tm'
         return '--with-tm={0}'.format(self.spec['openpbs'].prefix)
 
-    def with_or_without_psm2(self, activated):
-        if not activated:
-            return '--without-psm2'
-        return '--with-psm2={0}'.format(self.spec['opa-psm2'].prefix)
-
     @run_before('autoreconf')
     def die_without_fortran(self):
         # Until we can pass variants such as +fortran through virtual
@@ -433,8 +508,13 @@ def configure_args(self):
 
         # Fabrics
         if 'fabrics=auto' not in spec:
-            config_args.extend(self.with_or_without('fabrics',
-                                                    activation_value='prefix'))
+            config_args.extend(self.with_or_without('fabrics'))
+
+        if spec.satisfies('@2.0.0'):
+            if 'fabrics=xpmem' in spec and 'platform=cray' in spec:
+                config_args.append('--with-cray-xpmem')
+            else:
+                config_args.append('--without-cray-xpmem')
 
         # Schedulers
         if 'schedulers=auto' not in spec:
diff --git a/var/spack/repos/builtin/packages/xpmem/package.py b/var/spack/repos/builtin/packages/xpmem/package.py
new file mode 100644
index 00000000000..90fa58df063
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xpmem/package.py
@@ -0,0 +1,91 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Xpmem(AutotoolsPackage):
+    """XPMEM is a Linux kernel module that enables a process to map the memory
+    of another process into its virtual address space."""
+
+    # The README file of the repository says that the development was
+    # transferred to a new repository on GitLab: http://gitlab.com/hjelmn/xpmem
+    # However, it looks like that the repository on GitHub has a more recent
+    # version of the codebase.
+    homepage = "https://github.com/hjelmn/xpmem"
+    url = "https://github.com/hjelmn/xpmem/archive/v2.6.3.tar.gz"
+    git = "https://github.com/hjelmn/xpmem.git"
+
+    maintainers = ['skosukhin']
+
+    version('master', branch='master')
+
+    # Versions starting 2.6.4 are neither tagged nor released in the repo
+    # (the choice of commits is based on the commit history of
+    # 'kernel/xpmem_private.h'):
+    version('2.6.5', commit='4efeed9cbaabe971f3766d67cb108e2c3316d4b8')
+    version('2.6.4', commit='522054850e4d1479d69f50f7190d1548bf9749fd')
+
+    # Released versions:
+    version('2.6.3', sha256='ee239a32269f33234cdbdb94db29c12287862934c0784328d34aff82a9fa8b54')
+    version('2.6.2', sha256='2c1a93b4cb20ed73c2093435a7afec513e0e797aa1e49d4d964cc6bdae89d65b')
+
+    variant('kernel-module', default=True,
+            description='Enable building the kernel module')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+
+    # It will become possible to disable the kernel module only starting 2.6.6:
+    # https://github.com/hjelmn/xpmem/pull/24
+    conflicts('~kernel-module', when='@:2.6.5')
+
+    # Ideally, we should list all non-Linux-based platforms here:
+    conflicts('+kernel-module', when='platform=darwin')
+
+    # All compilers except for gcc are in conflict with +kernel-module:
+    for __compiler in spack.compilers.supported_compilers():
+        if __compiler != 'gcc':
+            conflicts('+kernel-module',
+                      when='%{0}'.format(__compiler),
+                      msg='Linux kernel module must be compiled with gcc')
+
+    def autoreconf(self, spec, prefix):
+        Executable('./autogen.sh')()
+
+    @run_before('build')
+    def override_kernel_compiler(self):
+        # Override the compiler for kernel module source files. We need
+        # this additional argument for all installation phases.
+        if '+kernel-module' in self.spec:
+            make.add_default_arg('CC={0}'.format(spack_cc))
+
+    def configure_args(self):
+        args = []
+
+        if '~kernel-module' in self.spec:
+            # The kernel module is enabled by default. An attempt of explicit
+            # enabling with '--enable-kernel-module' disables the module.
+            args.extend('--disable-kernel-module')
+
+        if self.spec.satisfies('@:2.6.5'):
+            fmt = self.spec.format
+            # The following arguments will not be needed starting 2.6.6:
+            # https://github.com/hjelmn/xpmem/pull/18
+            args.extend([
+                fmt('--with-default-prefix={prefix}'),
+                fmt('--with-module={prefix.share}/Modules/{name}/{version}')])
+
+        return args
+
+    @when('@:2.6.5')
+    def install(self, spec, prefix):
+        with working_dir(self.build_directory):
+            # Override the hardcoded prefix for 'cray-xpmem.conf'
+            make('ldsoconfdir={0}'.format(
+                self.spec.prefix.etc.join('ld.so.conf.d')),
+                *self.install_targets)

From f7008f37d482deb2adc42c91a09b4987528e9c60 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Tue, 16 Jun 2020 15:30:56 +0200
Subject: [PATCH 754/802] slurm: Fix build with gcc@10:

gcc@10: defaults to -fno-common, which breaks slurm up to version
20-02-1. For more details, see https://gcc.gnu.org/gcc-10/porting_to.html
---
 var/spack/repos/builtin/packages/slurm/package.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/var/spack/repos/builtin/packages/slurm/package.py b/var/spack/repos/builtin/packages/slurm/package.py
index c0d4cc01a91..ed69d08a774 100644
--- a/var/spack/repos/builtin/packages/slurm/package.py
+++ b/var/spack/repos/builtin/packages/slurm/package.py
@@ -63,6 +63,15 @@ class Slurm(AutotoolsPackage):
     depends_on('mariadb', when='+mariadb')
     depends_on('pmix', when='+pmix')
 
+    def flag_handler(self, name, flags):
+        wrapper_flags = None
+
+        if name == 'cflags':
+            if self.spec.satisfies('@:20-02-1 %gcc@10:'):
+                wrapper_flags = ['-fcommon']
+
+        return (wrapper_flags, None, flags)
+
     def configure_args(self):
 
         spec = self.spec

From c0cdc004091ffe5bf310ca69e7b9f3b1f1c008d0 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 17 Jun 2020 16:01:46 -0500
Subject: [PATCH 755/802] oneDNN: add v1.5.0 (#17137)

---
 var/spack/repos/builtin/packages/onednn/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/onednn/package.py b/var/spack/repos/builtin/packages/onednn/package.py
index 995cf40942a..b723fabd9c9 100644
--- a/var/spack/repos/builtin/packages/onednn/package.py
+++ b/var/spack/repos/builtin/packages/onednn/package.py
@@ -12,10 +12,11 @@ class Onednn(CMakePackage):
     Formerly known as Intel MKL-DNN and DNNL."""
 
     homepage = "https://01.org/dnnl"
-    url      = "https://github.com/oneapi-src/oneDNN/archive/v1.4.tar.gz"
+    url      = "https://github.com/oneapi-src/oneDNN/archive/v1.5.tar.gz"
 
     maintainers = ['adamjstewart']
 
+    version('1.5',    sha256='2aacc00129418185e0bc1269d3ef82f93f08de2c336932989c0c360279129edb')
     version('1.4',    sha256='54737bcb4dc1961d32ee75da3ecc529fa48198f8b2ca863a079e19a9c4adb70f')
     version('1.3',    sha256='b87c23b40a93ef5e479c81028db71c4847225b1a170f82af5e79f1cda826d3bf')
     version('1.2.2',  sha256='251dd17643cff285f38b020fc4ac9245d8d596f3e2140b98982ffc32eae3943c')

From 5b59e883c1bb30b5893bb6bd3d6ea6be2e3c294e Mon Sep 17 00:00:00 2001
From: Greg Becker <becker33@llnl.gov>
Date: Wed, 17 Jun 2020 17:53:30 -0500
Subject: [PATCH 756/802] cray module do not work without CRAY_LD_LIBRARY_PATH
 (#17031)

Co-authored-by: Gregory Becker <becker33.llnl.gov>
---
 lib/spack/spack/build_environment.py | 12 ++++++++----
 lib/spack/spack/util/module_cmd.py   |  2 +-
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 435de8594ec..f997110b4c9 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -32,6 +32,7 @@
 Skimming this module is a nice way to get acquainted with the types of
 calls you can make from within the install() function.
 """
+import re
 import inspect
 import multiprocessing
 import os
@@ -148,11 +149,14 @@ def clean_environment():
     env.unset('DYLD_LIBRARY_PATH')
     env.unset('DYLD_FALLBACK_LIBRARY_PATH')
 
-    # On Cray systems newer than CNL5, unset CRAY_LD_LIBRARY_PATH to avoid
-    # interference with Spack dependencies. CNL5 (e.g. Blue Waters) requires
-    # these variables to be set.
+    # On Cray "cluster" systems, unset CRAY_LD_LIBRARY_PATH to avoid
+    # interference with Spack dependencies.
+    # CNL requires these variables to be set (or at least some of them,
+    # depending on the CNL version).
     hostarch = arch.Arch(arch.platform(), 'default_os', 'default_target')
-    if str(hostarch.platform) == 'cray' and str(hostarch.os) != 'cnl5':
+    on_cray = str(hostarch.platform) == 'cray'
+    using_cnl = re.match(r'cnl\d+', str(hostarch.os))
+    if on_cray and not using_cnl:
         env.unset('CRAY_LD_LIBRARY_PATH')
         for varname in os.environ.keys():
             if 'PKGCONF' in varname:
diff --git a/lib/spack/spack/util/module_cmd.py b/lib/spack/spack/util/module_cmd.py
index a5ebe73c847..7017b2ecb6d 100644
--- a/lib/spack/spack/util/module_cmd.py
+++ b/lib/spack/spack/util/module_cmd.py
@@ -127,7 +127,7 @@ def get_path_args_from_module_line(line):
         # OPERATION VAR_NAME PATH_ARG
         words = line.split()
         if len(words) > 2:
-            path_arg = line.split()[2]
+            path_arg = words[2]
         else:
             return []
 

From c8199ece656aa49796d80bf99aa8d43492ebfd1f Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Wed, 17 Jun 2020 21:30:41 -0700
Subject: [PATCH 757/802] python: fix patch issue for 2.7.X, 3.7.X (#17140)

* python: fixing patch issue for 2.7.X, 3.7.X versions (#17128)

* python: fixing the C/C++ 'distutils' patching for @3.7.0:3.7.1
---
 .../repos/builtin/packages/python/package.py  |  17 +-
 .../python/python-2.7.17+-distutils-C++.patch | 269 ++++++++++++++++++
 ...patch => python-2.7.8-distutils-C++.patch} |   0
 ...patch => python-3.6.8-distutils-C++.patch} |   0
 .../python/python-3.7.3-distutils-C++.patch   | 256 +++++++++++++++++
 ...atch => python-3.7.4+-distutils-C++.patch} |   0
 6 files changed, 539 insertions(+), 3 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/python/python-2.7.17+-distutils-C++.patch
 rename var/spack/repos/builtin/packages/python/{python-2.7-distutils-C++.patch => python-2.7.8-distutils-C++.patch} (100%)
 rename var/spack/repos/builtin/packages/python/{python-3.6-distutils-C++.patch => python-3.6.8-distutils-C++.patch} (100%)
 create mode 100644 var/spack/repos/builtin/packages/python/python-3.7.3-distutils-C++.patch
 rename var/spack/repos/builtin/packages/python/{python-3.7+-distutils-C++.patch => python-3.7.4+-distutils-C++.patch} (100%)

diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 7a143695a38..bca6162c64a 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -167,9 +167,11 @@ class Python(AutotoolsPackage):
     # C/C++ modules, consider installing a Spack-managed Python with
     # this patch instead. For more information, see:
     # https://github.com/spack/spack/pull/16856
-    patch('python-2.7-distutils-C++.patch', when='@2.7')
-    patch('python-3.6-distutils-C++.patch', when='@3.6')
-    patch('python-3.7+-distutils-C++.patch', when='@3.7:3.8')
+    patch('python-2.7.8-distutils-C++.patch', when='@2.7.8:2.7.16')
+    patch('python-2.7.17+-distutils-C++.patch', when='@2.7.17:2.7.18')
+    patch('python-3.6.8-distutils-C++.patch', when='@3.6.8,3.7.2')
+    patch('python-3.7.3-distutils-C++.patch', when='@3.7.3')
+    patch('python-3.7.4+-distutils-C++.patch', when='@3.7.4:3.8')
 
     patch('tkinter.patch', when='@:2.8,3.3:3.7 platform=darwin')
 
@@ -267,6 +269,15 @@ def setup_build_environment(self, env):
             tty.warn(('Python v{0} may not install properly if Python '
                       'user configurations are present.').format(self.version))
 
+        # TODO: Python has incomplete support for Python modules with mixed
+        # C/C++ source, and patches are required to enable building for these
+        # modules. All Python versions without a viable patch are installed
+        # with a warning message about this potentially erroneous behavior.
+        if not spec.satisfies('@2.7.8:2.7.18,3.6.8,3.7.2:3.8.3'):
+            tty.warn(('Python v{0} does not have the C++ "distutils" patch; '
+                      'errors may occur when installing Python modules w/ '
+                      'mixed C/C++ source files.').format(self.version))
+
         # Need this to allow python build to find the Python installation.
         env.set('MACOSX_DEPLOYMENT_TARGET', platform.mac_ver()[0])
 
diff --git a/var/spack/repos/builtin/packages/python/python-2.7.17+-distutils-C++.patch b/var/spack/repos/builtin/packages/python/python-2.7.17+-distutils-C++.patch
new file mode 100644
index 00000000000..1d2249fcfc0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/python/python-2.7.17+-distutils-C++.patch
@@ -0,0 +1,269 @@
+diff --git a/Lib/_osx_support.py b/Lib/_osx_support.py
+index d2aaae7..8bcdb05 100644
+--- a/Lib/_osx_support.py
++++ b/Lib/_osx_support.py
+@@ -14,13 +14,13 @@ __all__ = [
+ # configuration variables that may contain universal build flags,
+ # like "-arch" or "-isdkroot", that may need customization for
+ # the user environment
+-_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'LDFLAGS', 'CPPFLAGS', 'BASECFLAGS',
+-                            'BLDSHARED', 'LDSHARED', 'CC', 'CXX',
+-                            'PY_CFLAGS', 'PY_LDFLAGS', 'PY_CPPFLAGS',
+-                            'PY_CORE_CFLAGS')
++_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'CXXFLAGS', 'LDFLAGS', 'CPPFLAGS',
++                          'BASECFLAGS', 'BLDSHARED', 'LDSHARED', 'LDCXXSHARED',
++                          'CC', 'CXX', 'PY_CFLAGS', 'PY_LDFLAGS',
++                          'PY_CPPFLAGS', 'PY_CORE_CFLAGS')
+ 
+ # configuration variables that may contain compiler calls
+-_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'CC', 'CXX')
++_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'LDCXXSHARED', 'CC', 'CXX')
+ 
+ # prefix added to original configuration variable names
+ _INITPRE = '_OSX_SUPPORT_INITIAL_'
+diff --git a/Lib/distutils/cygwinccompiler.py b/Lib/distutils/cygwinccompiler.py
+index 258e138..13b7d0c 100644
+--- a/Lib/distutils/cygwinccompiler.py
++++ b/Lib/distutils/cygwinccompiler.py
+@@ -117,8 +117,10 @@ class CygwinCCompiler (UnixCCompiler):
+         # dllwrap 2.10.90 is buggy
+         if self.ld_version >= "2.10.90":
+             self.linker_dll = "gcc"
++            self.linker_dll_cxx = "g++"
+         else:
+             self.linker_dll = "dllwrap"
++            self.linker_dll_cxx = "dllwrap"
+ 
+         # ld_version >= "2.13" support -shared so use it instead of
+         # -mdll -static
+@@ -132,9 +134,13 @@ class CygwinCCompiler (UnixCCompiler):
+         self.set_executables(compiler='gcc -mcygwin -O -Wall',
+                              compiler_so='gcc -mcygwin -mdll -O -Wall',
+                              compiler_cxx='g++ -mcygwin -O -Wall',
++                             compiler_so_cxx='g++ -mcygwin -mdll -O -Wall',
+                              linker_exe='gcc -mcygwin',
+                              linker_so=('%s -mcygwin %s' %
+-                                        (self.linker_dll, shared_option)))
++                                        (self.linker_dll, shared_option)),
++                             linker_exe_cxx='g++ -mcygwin',
++                             linker_so_cxx=('%s -mcygwin %s' %
++                                            (self.linker_dll_cxx, shared_option)))
+ 
+         # cygwin and mingw32 need different sets of libraries
+         if self.gcc_version == "2.91.57":
+@@ -160,8 +166,12 @@ class CygwinCCompiler (UnixCCompiler):
+                 raise CompileError, msg
+         else: # for other files use the C-compiler
+             try:
+-                self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
+-                           extra_postargs)
++                if self.detect_language(src) == 'c++':
++                    self.spawn(self.compiler_so_cxx + cc_args + [src, '-o', obj] +
++                               extra_postargs)
++                else:
++                    self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
++                               extra_postargs)
+             except DistutilsExecError, msg:
+                 raise CompileError, msg
+ 
+@@ -327,9 +337,14 @@ class Mingw32CCompiler (CygwinCCompiler):
+         self.set_executables(compiler='gcc%s -O -Wall' % no_cygwin,
+                              compiler_so='gcc%s -mdll -O -Wall' % no_cygwin,
+                              compiler_cxx='g++%s -O -Wall' % no_cygwin,
++                             compiler_so_cxx='g++%s -mdll -O -Wall' % no_cygwin,
+                              linker_exe='gcc%s' % no_cygwin,
+                              linker_so='%s%s %s %s'
+                                     % (self.linker_dll, no_cygwin,
++                                       shared_option, entry_point),
++                             linker_exe_cxx='g++%s' % no_cygwin,
++                             linker_so_cxx='%s%s %s %s'
++                                    % (self.linker_dll_cxx, no_cygwin,
+                                        shared_option, entry_point))
+         # Maybe we should also append -mthreads, but then the finished
+         # dlls need another dll (mingwm10.dll see Mingw32 docs)
+diff --git a/Lib/distutils/emxccompiler.py b/Lib/distutils/emxccompiler.py
+index a017205..bdc532c 100644
+--- a/Lib/distutils/emxccompiler.py
++++ b/Lib/distutils/emxccompiler.py
+@@ -65,8 +65,12 @@ class EMXCCompiler (UnixCCompiler):
+         # XXX optimization, warnings etc. should be customizable.
+         self.set_executables(compiler='gcc -Zomf -Zmt -O3 -fomit-frame-pointer -mprobe -Wall',
+                              compiler_so='gcc -Zomf -Zmt -O3 -fomit-frame-pointer -mprobe -Wall',
++                             compiler_cxx='g++ -Zomf -Zmt -O3 -fomit-frame-pointer -mprobe -Wall',
++                             compiler_so_cxx='g++ -Zomf -Zmt -O3 -fomit-frame-pointer -mprobe -Wall',
+                              linker_exe='gcc -Zomf -Zmt -Zcrtdll',
+-                             linker_so='gcc -Zomf -Zmt -Zcrtdll -Zdll')
++                             linker_so='gcc -Zomf -Zmt -Zcrtdll -Zdll',
++                             linker_exe_cxx='g++ -Zomf -Zmt -Zcrtdll',
++                             linker_so_cxx='g++ -Zomf -Zmt -Zcrtdll -Zdll')
+ 
+         # want the gcc library statically linked (so that we don't have
+         # to distribute a version dependent on the compiler we have)
+@@ -83,8 +87,12 @@ class EMXCCompiler (UnixCCompiler):
+                 raise CompileError, msg
+         else: # for other files use the C-compiler
+             try:
+-                self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
+-                           extra_postargs)
++                if self.detect_language(src) == 'c++':
++                    self.spawn(self.compiler_so_cxx + cc_args + [src, '-o', obj] +
++                               extra_postargs)
++                else:
++                    self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
++                               extra_postargs)
+             except DistutilsExecError, msg:
+                 raise CompileError, msg
+ 
+diff --git a/Lib/distutils/sysconfig.py b/Lib/distutils/sysconfig.py
+index 1a4b792..9d724b2 100644
+--- a/Lib/distutils/sysconfig.py
++++ b/Lib/distutils/sysconfig.py
+@@ -181,10 +181,12 @@ def customize_compiler(compiler):
+                 _osx_support.customize_compiler(_config_vars)
+                 _config_vars['CUSTOMIZED_OSX_COMPILER'] = 'True'
+ 
+-        (cc, cxx, cflags, ccshared, ldshared, so_ext, ar, ar_flags) = \
+-            get_config_vars('CC', 'CXX', 'CFLAGS',
+-                            'CCSHARED', 'LDSHARED', 'SO', 'AR',
+-                            'ARFLAGS')
++        (cc, cxx, ccshared, ldshared, ldcxxshared, so_ext, ar, ar_flags) = \
++            get_config_vars('CC', 'CXX', 'CCSHARED', 'LDSHARED', 'LDCXXSHARED',
++                            'SO', 'AR', 'ARFLAGS')
++
++        cflags = ''
++        cxxflags = ''
+ 
+         if 'CC' in os.environ:
+             newcc = os.environ['CC']
+@@ -199,19 +201,27 @@ def customize_compiler(compiler):
+             cxx = os.environ['CXX']
+         if 'LDSHARED' in os.environ:
+             ldshared = os.environ['LDSHARED']
++        if 'LDCXXSHARED' in os.environ:
++            ldcxxshared = os.environ['LDCXXSHARED']
+         if 'CPP' in os.environ:
+             cpp = os.environ['CPP']
+         else:
+             cpp = cc + " -E"           # not always
+         if 'LDFLAGS' in os.environ:
+             ldshared = ldshared + ' ' + os.environ['LDFLAGS']
++            ldcxxshared = ldcxxshared + ' ' + os.environ['LDFLAGS']
+         if 'CFLAGS' in os.environ:
+             cflags = cflags + ' ' + os.environ['CFLAGS']
+             ldshared = ldshared + ' ' + os.environ['CFLAGS']
++        if 'CXXFLAGS' in os.environ:
++            cxxflags = cxxflags + ' ' + os.environ['CXXFLAGS']
++            ldcxxshared = ldcxxshared + ' ' + os.environ['CXXFLAGS']
+         if 'CPPFLAGS' in os.environ:
+             cpp = cpp + ' ' + os.environ['CPPFLAGS']
+             cflags = cflags + ' ' + os.environ['CPPFLAGS']
++            cxxflags = cxxflags + ' ' + os.environ['CPPFLAGS']
+             ldshared = ldshared + ' ' + os.environ['CPPFLAGS']
++            ldcxxshared = ldcxxshared + ' ' + os.environ['CPPFLAGS']
+         if 'AR' in os.environ:
+             ar = os.environ['AR']
+         if 'ARFLAGS' in os.environ:
+@@ -220,13 +230,17 @@ def customize_compiler(compiler):
+             archiver = ar + ' ' + ar_flags
+ 
+         cc_cmd = cc + ' ' + cflags
++        cxx_cmd = cxx + ' ' + cxxflags
+         compiler.set_executables(
+             preprocessor=cpp,
+             compiler=cc_cmd,
+             compiler_so=cc_cmd + ' ' + ccshared,
+-            compiler_cxx=cxx,
++            compiler_cxx=cxx_cmd,
++            compiler_so_cxx=cxx_cmd + ' ' + ccshared,
+             linker_so=ldshared,
+             linker_exe=cc,
++            linker_so_cxx=ldcxxshared,
++            linker_exe_cxx=cxx,
+             archiver=archiver)
+ 
+         compiler.shared_lib_extension = so_ext
+diff --git a/Lib/distutils/unixccompiler.py b/Lib/distutils/unixccompiler.py
+index 3af540e..f8f7efe 100644
+--- a/Lib/distutils/unixccompiler.py
++++ b/Lib/distutils/unixccompiler.py
+@@ -55,14 +55,17 @@ class UnixCCompiler(CCompiler):
+     # are pretty generic; they will probably have to be set by an outsider
+     # (eg. using information discovered by the sysconfig about building
+     # Python extensions).
+-    executables = {'preprocessor' : None,
+-                   'compiler'     : ["cc"],
+-                   'compiler_so'  : ["cc"],
+-                   'compiler_cxx' : ["cc"],
+-                   'linker_so'    : ["cc", "-shared"],
+-                   'linker_exe'   : ["cc"],
+-                   'archiver'     : ["ar", "-cr"],
+-                   'ranlib'       : None,
++    executables = {'preprocessor'    : None,
++                   'compiler'        : ["cc"],
++                   'compiler_so'     : ["cc"],
++                   'compiler_cxx'    : ["c++"],
++                   'compiler_so_cxx' : ["c++"],
++                   'linker_so'       : ["cc", "-shared"],
++                   'linker_exe'      : ["cc"],
++                   'linker_so_cxx'   : ["c++", "-shared"],
++                   'linker_exe_cxx'  : ["c++"],
++                   'archiver'        : ["ar", "-cr"],
++                   'ranlib'          : None,
+                   }
+ 
+     if sys.platform[:6] == "darwin":
+@@ -114,12 +117,19 @@ class UnixCCompiler(CCompiler):
+ 
+     def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts):
+         compiler_so = self.compiler_so
++        compiler_so_cxx = self.compiler_so_cxx
+         if sys.platform == 'darwin':
+             compiler_so = _osx_support.compiler_fixup(compiler_so,
+                                                     cc_args + extra_postargs)
++            compiler_so_cxx = _osx_support.compiler_fixup(compiler_so_cxx,
++                                                    cc_args + extra_postargs)
+         try:
+-            self.spawn(compiler_so + cc_args + [src, '-o', obj] +
+-                       extra_postargs)
++            if self.detect_language(src) == 'c++':
++                self.spawn(compiler_so_cxx + cc_args + [src, '-o', obj] +
++                           extra_postargs)
++            else:
++                self.spawn(compiler_so + cc_args + [src, '-o', obj] +
++                           extra_postargs)
+         except DistutilsExecError, msg:
+             raise CompileError, msg
+ 
+@@ -176,23 +186,16 @@ class UnixCCompiler(CCompiler):
+                 ld_args.extend(extra_postargs)
+             self.mkpath(os.path.dirname(output_filename))
+             try:
+-                if target_desc == CCompiler.EXECUTABLE:
+-                    linker = self.linker_exe[:]
++                if target_lang == "c++":
++                    if target_desc == CCompiler.EXECUTABLE:
++                        linker = self.linker_exe_cxx[:]
++                    else:
++                        linker = self.linker_so_cxx[:]
+                 else:
+-                    linker = self.linker_so[:]
+-                if target_lang == "c++" and self.compiler_cxx:
+-                    # skip over environment variable settings if /usr/bin/env
+-                    # is used to set up the linker's environment.
+-                    # This is needed on OSX. Note: this assumes that the
+-                    # normal and C++ compiler have the same environment
+-                    # settings.
+-                    i = 0
+-                    if os.path.basename(linker[0]) == "env":
+-                        i = 1
+-                        while '=' in linker[i]:
+-                            i = i + 1
+-
+-                    linker[i] = self.compiler_cxx[i]
++                    if target_desc == CCompiler.EXECUTABLE:
++                        linker = self.linker_exe[:]
++                    else:
++                        linker = self.linker_so[:]
+ 
+                 if sys.platform == 'darwin':
+                     linker = _osx_support.compiler_fixup(linker, ld_args)
diff --git a/var/spack/repos/builtin/packages/python/python-2.7-distutils-C++.patch b/var/spack/repos/builtin/packages/python/python-2.7.8-distutils-C++.patch
similarity index 100%
rename from var/spack/repos/builtin/packages/python/python-2.7-distutils-C++.patch
rename to var/spack/repos/builtin/packages/python/python-2.7.8-distutils-C++.patch
diff --git a/var/spack/repos/builtin/packages/python/python-3.6-distutils-C++.patch b/var/spack/repos/builtin/packages/python/python-3.6.8-distutils-C++.patch
similarity index 100%
rename from var/spack/repos/builtin/packages/python/python-3.6-distutils-C++.patch
rename to var/spack/repos/builtin/packages/python/python-3.6.8-distutils-C++.patch
diff --git a/var/spack/repos/builtin/packages/python/python-3.7.3-distutils-C++.patch b/var/spack/repos/builtin/packages/python/python-3.7.3-distutils-C++.patch
new file mode 100644
index 00000000000..e29323bf0b5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/python/python-3.7.3-distutils-C++.patch
@@ -0,0 +1,256 @@
+diff --git a/Lib/_osx_support.py b/Lib/_osx_support.py
+index db6674e..ccbe09a 100644
+--- a/Lib/_osx_support.py
++++ b/Lib/_osx_support.py
+@@ -14,13 +14,13 @@ __all__ = [
+ # configuration variables that may contain universal build flags,
+ # like "-arch" or "-isdkroot", that may need customization for
+ # the user environment
+-_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'LDFLAGS', 'CPPFLAGS', 'BASECFLAGS',
+-                            'BLDSHARED', 'LDSHARED', 'CC', 'CXX',
+-                            'PY_CFLAGS', 'PY_LDFLAGS', 'PY_CPPFLAGS',
+-                            'PY_CORE_CFLAGS', 'PY_CORE_LDFLAGS')
++_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'CXXFLAGS', 'LDFLAGS', 'CPPFLAGS',
++                          'BASECFLAGS', 'BLDSHARED', 'LDSHARED', 'LDCXXSHARED',
++                          'CC', 'CXX', 'PY_CFLAGS', 'PY_LDFLAGS',
++                          'PY_CPPFLAGS', 'PY_CORE_LDFLAGS', 'PY_CORE_CFLAGS')
+ 
+ # configuration variables that may contain compiler calls
+-_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'CC', 'CXX')
++_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'LDCXXSHARED', 'CC', 'CXX')
+ 
+ # prefix added to original configuration variable names
+ _INITPRE = '_OSX_SUPPORT_INITIAL_'
+diff --git a/Lib/distutils/cygwinccompiler.py b/Lib/distutils/cygwinccompiler.py
+index 6c5d777..640fa2d 100644
+--- a/Lib/distutils/cygwinccompiler.py
++++ b/Lib/distutils/cygwinccompiler.py
+@@ -125,8 +125,10 @@ class CygwinCCompiler(UnixCCompiler):
+         # dllwrap 2.10.90 is buggy
+         if self.ld_version >= "2.10.90":
+             self.linker_dll = "gcc"
++            self.linker_dll_cxx = "g++"
+         else:
+             self.linker_dll = "dllwrap"
++            self.linker_dll_cxx = "dllwrap"
+ 
+         # ld_version >= "2.13" support -shared so use it instead of
+         # -mdll -static
+@@ -140,9 +142,13 @@ class CygwinCCompiler(UnixCCompiler):
+         self.set_executables(compiler='gcc -mcygwin -O -Wall',
+                              compiler_so='gcc -mcygwin -mdll -O -Wall',
+                              compiler_cxx='g++ -mcygwin -O -Wall',
++                             compiler_so_cxx='g++ -mcygwin -mdll -O -Wall',
+                              linker_exe='gcc -mcygwin',
+                              linker_so=('%s -mcygwin %s' %
+-                                        (self.linker_dll, shared_option)))
++                                        (self.linker_dll, shared_option)),
++                             linker_exe_cxx='g++ -mcygwin',
++                             linker_so_cxx=('%s -mcygwin %s' %
++                                            (self.linker_dll_cxx, shared_option)))
+ 
+         # cygwin and mingw32 need different sets of libraries
+         if self.gcc_version == "2.91.57":
+@@ -166,8 +172,12 @@ class CygwinCCompiler(UnixCCompiler):
+                 raise CompileError(msg)
+         else: # for other files use the C-compiler
+             try:
+-                self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
+-                           extra_postargs)
++                if self.detect_language(src) == 'c++':
++                    self.spawn(self.compiler_so_cxx + cc_args + [src, '-o', obj] +
++                               extra_postargs)
++                else:
++                    self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
++                               extra_postargs)
+             except DistutilsExecError as msg:
+                 raise CompileError(msg)
+ 
+@@ -302,9 +312,14 @@ class Mingw32CCompiler(CygwinCCompiler):
+         self.set_executables(compiler='gcc -O -Wall',
+                              compiler_so='gcc -mdll -O -Wall',
+                              compiler_cxx='g++ -O -Wall',
++                             compiler_so_cxx='g++ -mdll -O -Wall',
+                              linker_exe='gcc',
+                              linker_so='%s %s %s'
+                                         % (self.linker_dll, shared_option,
++                                           entry_point),
++                             linker_exe_cxx='g++',
++                             linker_so_cxx='%s %s %s'
++                                        % (self.linker_dll_cxx, shared_option,
+                                            entry_point))
+         # Maybe we should also append -mthreads, but then the finished
+         # dlls need another dll (mingwm10.dll see Mingw32 docs)
+diff --git a/Lib/distutils/sysconfig.py b/Lib/distutils/sysconfig.py
+index 83160f8..b735369 100644
+--- a/Lib/distutils/sysconfig.py
++++ b/Lib/distutils/sysconfig.py
+@@ -183,9 +183,11 @@ def customize_compiler(compiler):
+                 _osx_support.customize_compiler(_config_vars)
+                 _config_vars['CUSTOMIZED_OSX_COMPILER'] = 'True'
+ 
+-        (cc, cxx, opt, cflags, ccshared, ldshared, shlib_suffix, ar, ar_flags) = \
++        (cc, cxx, opt, cflags, ccshared, ldshared, ldcxxshared, shlib_suffix, ar, ar_flags) = \
+             get_config_vars('CC', 'CXX', 'OPT', 'CFLAGS',
+-                            'CCSHARED', 'LDSHARED', 'SHLIB_SUFFIX', 'AR', 'ARFLAGS')
++                            'CCSHARED', 'LDSHARED', 'LDCXXSHARED', 'SHLIB_SUFFIX', 'AR', 'ARFLAGS')
++
++        cxxflags = cflags
+ 
+         if 'CC' in os.environ:
+             newcc = os.environ['CC']
+@@ -200,19 +202,27 @@ def customize_compiler(compiler):
+             cxx = os.environ['CXX']
+         if 'LDSHARED' in os.environ:
+             ldshared = os.environ['LDSHARED']
++        if 'LDCXXSHARED' in os.environ:
++            ldcxxshared = os.environ['LDCXXSHARED']
+         if 'CPP' in os.environ:
+             cpp = os.environ['CPP']
+         else:
+             cpp = cc + " -E"           # not always
+         if 'LDFLAGS' in os.environ:
+             ldshared = ldshared + ' ' + os.environ['LDFLAGS']
++            ldcxxshared = ldcxxshared + ' ' + os.environ['LDFLAGS']
+         if 'CFLAGS' in os.environ:
+             cflags = opt + ' ' + os.environ['CFLAGS']
+             ldshared = ldshared + ' ' + os.environ['CFLAGS']
++        if 'CXXFLAGS' in os.environ:
++            cxxflags = opt + ' ' + os.environ['CXXFLAGS']
++            ldcxxshared = ldcxxshared + ' ' + os.environ['CXXFLAGS']
+         if 'CPPFLAGS' in os.environ:
+             cpp = cpp + ' ' + os.environ['CPPFLAGS']
++            cxxflags = cxxflags + ' ' + os.environ['CPPFLAGS']
+             cflags = cflags + ' ' + os.environ['CPPFLAGS']
+             ldshared = ldshared + ' ' + os.environ['CPPFLAGS']
++            ldcxxshared = ldcxxshared + ' ' + os.environ['CPPFLAGS']
+         if 'AR' in os.environ:
+             ar = os.environ['AR']
+         if 'ARFLAGS' in os.environ:
+@@ -221,13 +231,17 @@ def customize_compiler(compiler):
+             archiver = ar + ' ' + ar_flags
+ 
+         cc_cmd = cc + ' ' + cflags
++        cxx_cmd = cxx + ' ' + cxxflags
+         compiler.set_executables(
+             preprocessor=cpp,
+             compiler=cc_cmd,
+             compiler_so=cc_cmd + ' ' + ccshared,
+-            compiler_cxx=cxx,
++            compiler_cxx=cxx_cmd,
++            compiler_so_cxx=cxx_cmd + ' ' + ccshared,
+             linker_so=ldshared,
+             linker_exe=cc,
++            linker_so_cxx=ldcxxshared,
++            linker_exe_cxx=cxx,
+             archiver=archiver)
+ 
+         compiler.shared_lib_extension = shlib_suffix
+diff --git a/Lib/distutils/unixccompiler.py b/Lib/distutils/unixccompiler.py
+index d10a78d..7e88781 100644
+--- a/Lib/distutils/unixccompiler.py
++++ b/Lib/distutils/unixccompiler.py
+@@ -52,14 +52,17 @@ class UnixCCompiler(CCompiler):
+     # are pretty generic; they will probably have to be set by an outsider
+     # (eg. using information discovered by the sysconfig about building
+     # Python extensions).
+-    executables = {'preprocessor' : None,
+-                   'compiler'     : ["cc"],
+-                   'compiler_so'  : ["cc"],
+-                   'compiler_cxx' : ["cc"],
+-                   'linker_so'    : ["cc", "-shared"],
+-                   'linker_exe'   : ["cc"],
+-                   'archiver'     : ["ar", "-cr"],
+-                   'ranlib'       : None,
++    executables = {'preprocessor'    : None,
++                   'compiler'        : ["cc"],
++                   'compiler_so'     : ["cc"],
++                   'compiler_cxx'    : ["c++"],
++                   'compiler_so_cxx' : ["c++"],
++                   'linker_so'       : ["cc", "-shared"],
++                   'linker_exe'      : ["cc"],
++                   'linker_so_cxx'   : ["c++", "-shared"],
++                   'linker_exe_cxx'  : ["c++"],
++                   'archiver'        : ["ar", "-cr"],
++                   'ranlib'          : None,
+                   }
+ 
+     if sys.platform[:6] == "darwin":
+@@ -110,12 +113,19 @@ class UnixCCompiler(CCompiler):
+ 
+     def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts):
+         compiler_so = self.compiler_so
++        compiler_so_cxx = self.compiler_so_cxx
+         if sys.platform == 'darwin':
+             compiler_so = _osx_support.compiler_fixup(compiler_so,
+                                                     cc_args + extra_postargs)
++            compiler_so_cxx = _osx_support.compiler_fixup(compiler_so_cxx,
++                                                    cc_args + extra_postargs)
+         try:
+-            self.spawn(compiler_so + cc_args + [src, '-o', obj] +
+-                       extra_postargs)
++            if self.detect_language(src) == 'c++':
++                self.spawn(compiler_so_cxx + cc_args + [src, '-o', obj] +
++                           extra_postargs)
++            else:
++                self.spawn(compiler_so + cc_args + [src, '-o', obj] +
++                           extra_postargs)
+         except DistutilsExecError as msg:
+             raise CompileError(msg)
+ 
+@@ -173,30 +183,16 @@ class UnixCCompiler(CCompiler):
+                 ld_args.extend(extra_postargs)
+             self.mkpath(os.path.dirname(output_filename))
+             try:
+-                if target_desc == CCompiler.EXECUTABLE:
+-                    linker = self.linker_exe[:]
++                if target_lang == "c++":
++                    if target_desc == CCompiler.EXECUTABLE:
++                        linker = self.linker_exe_cxx[:]
++                    else:
++                        linker = self.linker_so_cxx[:]
+                 else:
+-                    linker = self.linker_so[:]
+-                if target_lang == "c++" and self.compiler_cxx:
+-                    # skip over environment variable settings if /usr/bin/env
+-                    # is used to set up the linker's environment.
+-                    # This is needed on OSX. Note: this assumes that the
+-                    # normal and C++ compiler have the same environment
+-                    # settings.
+-                    i = 0
+-                    if os.path.basename(linker[0]) == "env":
+-                        i = 1
+-                        while '=' in linker[i]:
+-                            i += 1
+-
+-                    if os.path.basename(linker[i]) == 'ld_so_aix':
+-                        # AIX platforms prefix the compiler with the ld_so_aix
+-                        # script, so we need to adjust our linker index
+-                        offset = 1
++                    if target_desc == CCompiler.EXECUTABLE:
++                        linker = self.linker_exe[:]
+                     else:
+-                        offset = 0
+-
+-                    linker[i+offset] = self.compiler_cxx[i]
++                        linker = self.linker_so[:]
+ 
+                 if sys.platform == 'darwin':
+                     linker = _osx_support.compiler_fixup(linker, ld_args)
+diff --git a/Makefile.pre.in b/Makefile.pre.in
+index 2d2e11f..8456e3f 100644
+--- a/Makefile.pre.in
++++ b/Makefile.pre.in
+@@ -615,10 +615,10 @@ sharedmods: $(BUILDPYTHON) pybuilddir.txt Modules/_math.o
+ 	    *\ -s*|s*) quiet="-q";; \
+ 	    *) quiet="";; \
+ 	esac; \
+-	echo "$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' OPT='$(OPT)' \
++	echo "$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' CFLAGS='$(PY_CFLAGS)' \
+ 		_TCLTK_INCLUDES='$(TCLTK_INCLUDES)' _TCLTK_LIBS='$(TCLTK_LIBS)' \
+ 		$(PYTHON_FOR_BUILD) $(srcdir)/setup.py $$quiet build"; \
+-	$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' OPT='$(OPT)' \
++	$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' CFLAGS='$(PY_CFLAGS)' \
+ 		_TCLTK_INCLUDES='$(TCLTK_INCLUDES)' _TCLTK_LIBS='$(TCLTK_LIBS)' \
+ 		$(PYTHON_FOR_BUILD) $(srcdir)/setup.py $$quiet build
+ 
diff --git a/var/spack/repos/builtin/packages/python/python-3.7+-distutils-C++.patch b/var/spack/repos/builtin/packages/python/python-3.7.4+-distutils-C++.patch
similarity index 100%
rename from var/spack/repos/builtin/packages/python/python-3.7+-distutils-C++.patch
rename to var/spack/repos/builtin/packages/python/python-3.7.4+-distutils-C++.patch

From 1bb94f2913b8657ce098230f33a08be38e1ba05a Mon Sep 17 00:00:00 2001
From: "Seth R. Johnson" <johnsonsr@ornl.gov>
Date: Thu, 18 Jun 2020 00:32:25 -0400
Subject: [PATCH 758/802] glib: fix 2.56 build with python@2 (#17144)

* glib: fix 2.56 build with python@2

* flake8
---
 var/spack/repos/builtin/packages/glib/package.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py
index 4d648ddb3a4..6426286b355 100644
--- a/var/spack/repos/builtin/packages/glib/package.py
+++ b/var/spack/repos/builtin/packages/glib/package.py
@@ -141,10 +141,18 @@ def configure_args(self):
             args.append('--with-libiconv=maybe')
         else:
             args.append('--with-libiconv=gnu')
-        if 'tracing=dtrace' in self.spec or 'tracing=systemtap' in self.spec:
-            args.append('--enable-tracing')
+        if self.spec.satisfies('@2.56:'):
+            for value in ('dtrace', 'systemtap'):
+                if ('tracing=' + value) in self.spec:
+                    args.append('--enable-' + value)
+                else:
+                    args.append('--disable-' + value)
         else:
-            args.append('--disable-tracing')
+            if ('tracing=dtrace' in self.spec
+                    or 'tracing=systemtap' in self.spec):
+                args.append('--enable-tracing')
+            else:
+                args.append('--disable-tracing')
         # SELinux is not available in Spack, so glib should not use it.
         args.append('--disable-selinux')
         # glib should not use the globally installed gtk-doc. Otherwise,

From 58e20430b1d33aa4edcad46e9b1c70332eb55066 Mon Sep 17 00:00:00 2001
From: Toyohisa Kameyama <kameyama@riken.jp>
Date: Thu, 18 Jun 2020 16:43:06 +0900
Subject: [PATCH 759/802] minimap2: fix a typo in the recipe (#17148)

---
 var/spack/repos/builtin/packages/minimap2/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/minimap2/package.py b/var/spack/repos/builtin/packages/minimap2/package.py
index 16f7f7aec12..4c8e2a1c4c3 100644
--- a/var/spack/repos/builtin/packages/minimap2/package.py
+++ b/var/spack/repos/builtin/packages/minimap2/package.py
@@ -28,7 +28,7 @@ def install_minimap2(self):
         if self.spec.target.family == 'aarch64':
             make_arg.extend([
                 'arm_neon=1',
-                'aarch64~1'
+                'aarch64=1'
             ])
         make(*make_arg)
         mkdirp(prefix.bin)

From 1f85d6ecebd555ae219637cdc9e1ec475f962f48 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 18 Jun 2020 02:44:03 -0500
Subject: [PATCH 760/802] Docs: fix rst link to spack ci (#17147)

---
 lib/spack/docs/pipelines.rst | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/spack/docs/pipelines.rst b/lib/spack/docs/pipelines.rst
index d1128163b1f..ee3b4e8ad62 100644
--- a/lib/spack/docs/pipelines.rst
+++ b/lib/spack/docs/pipelines.rst
@@ -103,7 +103,7 @@ needed for pipeline operation that should not be visible in a spack environment
 file.  These environment variables are described in more detail
 :ref:`ci_environment_variables`.
 
-.. _cmd_spack_ci:
+.. _cmd-spack-ci:
 
 ^^^^^^^^^^^^^^^^^^
 ``spack ci``
@@ -112,7 +112,7 @@ file.  These environment variables are described in more detail
 Super-command for functionality related to generating pipelines and executing
 pipeline jobs.
 
-.. _cmd_spack_ci_generate:
+.. _cmd-spack-ci-generate:
 
 ^^^^^^^^^^^^^^^^^^^^^
 ``spack ci generate``
@@ -121,7 +121,7 @@ pipeline jobs.
 Concretizes the specs in the active environment, stages them (as described in
 :ref:`staging_algorithm`), and writes the resulting ``.gitlab-ci.yml`` to disk.
 
-.. _cmd_spack_ci_rebuild:
+.. _cmd-spack-ci-rebuild:
 
 ^^^^^^^^^^^^^^^^^^^^
 ``spack ci rebuild``

From 2fd3ab3c9c93110e71018681f9759eb166a639c9 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Thu, 18 Jun 2020 01:37:32 -0700
Subject: [PATCH 761/802] Fetching from urls: Error Message (#16434)

* Fetching from urls: Error Message

Fix the error message when fetching from consecutive `urls` of a
package version. Each fail should show the currently failing URL,
not the first url.

Example multi-problem run that occured in real life:
```
==> 5821: Installing util-macros
curl: (28) Connection timed out after 10000 milliseconds
curl: (16) Error in the HTTP2 framing layer
curl: (22) The requested URL returned error: 403 Forbidden
==> Fetching https://www.x.org/archive/individual/util/util-macros-1.19.1.tar.bz2
==> Failed to fetch file from URL: https://www.x.org/archive/individual/util/util-macros-1.19.1.tar.bz2
    Curl failed with error 28
==> Fetching https://mirrors.ircam.fr/pub/x.org/individual/util/util-macros-1.19.1.tar.bz2
==> Failed to fetch file from URL: https://www.x.org/archive/individual/util/util-macros-1.19.1.tar.bz2
    Curl failed with error 16
==> Fetching http://xorg.mirrors.pair.com/individual/util/util-macros-1.19.1.tar.bz2
==> Failed to fetch file from URL: https://www.x.org/archive/individual/util/util-macros-1.19.1.tar.bz2
    URL https://www.x.org/archive/individual/util/util-macros-1.19.1.tar.bz2 was not found!
==> Fetching from https://www.x.org/archive/individual/util/util-macros-1.19.1.tar.bz2 failed.
==> Error: FetchError: All fetchers failed for spack-stage-util-macros-1.19.1-se2a2e74oyusj2r4esgcb7pr3qhh45ef
```

- `urls[0]`: HTTP2 layer error
- `urls[1]`: timeout
- `urls[2]`: missing file on mirror

* x.org: two more mirrors

x.org mirrors are a bit tricky, since many are out-of-sync or off.
A good package to test with is `util-macros`, which had a "recent"
release.
---
 lib/spack/spack/build_systems/xorg.py | 5 +++++
 lib/spack/spack/fetch_strategy.py     | 9 +++++----
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/lib/spack/spack/build_systems/xorg.py b/lib/spack/spack/build_systems/xorg.py
index 815bb7c26b5..ae28b30929b 100644
--- a/lib/spack/spack/build_systems/xorg.py
+++ b/lib/spack/spack/build_systems/xorg.py
@@ -14,9 +14,14 @@ class XorgPackage(spack.package.PackageBase):
     xorg_mirror_path = None
 
     #: List of x.org mirrors used by Spack
+    #  Note: x.org mirrors are a bit tricky, since many are out-of-sync or off.
+    #        A good package to test with is `util-macros`, which had a "recent"
+    #        release.
     base_mirrors = [
         'https://www.x.org/archive/individual/',
         'https://mirrors.ircam.fr/pub/x.org/individual/',
+        'https://mirror.transip.net/xorg/individual/',
+        'ftp://ftp.freedesktop.org/pub/xorg/individual/',
         'http://xorg.mirrors.pair.com/individual/'
     ]
 
diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index c6200565e5b..5f0cc4db5d7 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -292,6 +292,7 @@ def fetch(self):
             tty.msg("Already downloaded %s" % self.archive_file)
             return
 
+        url = None
         for url in self.candidate_urls:
             try:
                 partial_file, save_file = self._fetch_from_url(url)
@@ -303,7 +304,7 @@ def fetch(self):
                 pass
 
         if not self.archive_file:
-            raise FailedDownloadError(self.url)
+            raise FailedDownloadError(url)
 
     def _fetch_from_url(self, url):
         save_file = None
@@ -369,12 +370,12 @@ def _fetch_from_url(self, url):
             if curl.returncode == 22:
                 # This is a 404.  Curl will print the error.
                 raise FailedDownloadError(
-                    self.url, "URL %s was not found!" % self.url)
+                    url, "URL %s was not found!" % url)
 
             elif curl.returncode == 60:
                 # This is a certificate error.  Suggest spack -k
                 raise FailedDownloadError(
-                    self.url,
+                    url,
                     "Curl was unable to fetch due to invalid certificate. "
                     "This is either an attack, or your cluster's SSL "
                     "configuration is bad.  If you believe your SSL "
@@ -386,7 +387,7 @@ def _fetch_from_url(self, url):
                 # This is some other curl error.  Curl will print the
                 # error, but print a spack message too
                 raise FailedDownloadError(
-                    self.url,
+                    url,
                     "Curl failed with error %d" % curl.returncode)
 
         # Check if we somehow got an HTML file rather than the archive we

From 4fe78bceaa9d4390f3ed0641a4223033aaf87b67 Mon Sep 17 00:00:00 2001
From: Itaru Kitayama <ikitayama@users.noreply.github.com>
Date: Thu, 18 Jun 2020 17:40:54 +0900
Subject: [PATCH 762/802] cube and libjpeg-turbo: added cube v4.5 and
 libjpeg-turbo v2.0.4 (#17132)

---
 var/spack/repos/builtin/packages/cube/package.py          | 1 +
 var/spack/repos/builtin/packages/libjpeg-turbo/package.py | 1 +
 2 files changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/cube/package.py b/var/spack/repos/builtin/packages/cube/package.py
index d3bdd366173..d2eeb203c00 100644
--- a/var/spack/repos/builtin/packages/cube/package.py
+++ b/var/spack/repos/builtin/packages/cube/package.py
@@ -17,6 +17,7 @@ class Cube(AutotoolsPackage):
     homepage = "http://www.scalasca.org/software/cube-4.x/download.html"
     url      = "http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/cubegui-4.4.2.tar.gz"
 
+    version('4.5', sha256='ffe84108adce0adf06dca80820d941b1a60a5580a8bacc8f7c1b6989c8ab1bfa')
     version('4.4.4', sha256='9b7b96d5a64b558a9017cc3599bba93a42095534e018e3de9b1f80ab6d04cc34')
     version('4.4.3', sha256='bf4b0f2ff68507ff82ba24eb4895aed961710dae16d783c222a12f152440cf36')
     version('4.4.2', sha256='29b6479616a524f8325f5031a883963bf965fb92569de33271a020f08650ec7b')
diff --git a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py
index 10bddc37e03..a78c4af66cd 100644
--- a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py
+++ b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py
@@ -15,6 +15,7 @@ class LibjpegTurbo(Package):
     homepage = "https://libjpeg-turbo.org/"
     url      = "https://github.com/libjpeg-turbo/libjpeg-turbo/archive/2.0.3.tar.gz"
 
+    version('2.0.4', sha256='33dd8547efd5543639e890efbf2ef52d5a21df81faf41bb940657af916a23406')
     version('2.0.3', sha256='a69598bf079463b34d45ca7268462a18b6507fdaa62bb1dfd212f02041499b5d')
     version('2.0.2', sha256='b45255bd476c19c7c6b198c07c0487e8b8536373b82f2b38346b32b4fa7bb942')
     version('1.5.90', sha256='cb948ade92561d8626fd7866a4a7ba3b952f9759ea3dd642927bc687470f60b7')

From 910d25870616f7407f5b28649c6134e75b7dacbf Mon Sep 17 00:00:00 2001
From: Shintaro Iwasaki <siwasaki@anl.gov>
Date: Thu, 18 Jun 2020 04:11:59 -0500
Subject: [PATCH 763/802] argobots, bolt: updates to package.py (#17117)

---
 .../repos/builtin/packages/argobots/package.py  | 17 ++++++-----------
 .../repos/builtin/packages/bolt/package.py      |  2 +-
 2 files changed, 7 insertions(+), 12 deletions(-)

diff --git a/var/spack/repos/builtin/packages/argobots/package.py b/var/spack/repos/builtin/packages/argobots/package.py
index 3db9014afbe..2dc8212eb7f 100644
--- a/var/spack/repos/builtin/packages/argobots/package.py
+++ b/var/spack/repos/builtin/packages/argobots/package.py
@@ -20,21 +20,16 @@ class Argobots(AutotoolsPackage):
     git      = "https://github.com/pmodels/argobots.git"
     maintainers = ['shintaro-iwasaki']
 
-    version("master", branch="master")
-    version("1.0", sha256="36a0815f7bf99900a9c9c1eef61ef9b3b76aa2cfc4594a304f6c8c3296da8def",
-            preferred=True)
-    version("1.0rc2", sha256="7496b8bd39930a548b01aa3b1fe8f8b582c272600ef6a05ddc4398cf21dc12a2")
-    version("1.0rc1", sha256="2dc4487556dce602655a6535f501136f0edc3575708029c80b1af6dccd069ce7")
-    version("1.0b1", sha256="480b85b0e8db288400088a57c2dc5639f556843b06b0492841920c38348a2a3e")
-    version("1.0a1", sha256="bef93e06026ddeba8809474923176803e64d08e1425672cd7c5b424c797d5d9d")
+    version("main", branch="main")
+    version("1.0", sha256="36a0815f7bf99900a9c9c1eef61ef9b3b76aa2cfc4594a304f6c8c3296da8def")
 
     variant("valgrind", default=False, description="Enable Valgrind")
     variant("debug", default=False, description="Compiled with debugging symbols")
 
-    depends_on("m4", type=("build"), when="@master")
-    depends_on("autoconf", type=("build"), when="@master")
-    depends_on("automake", type=("build"), when="@master")
-    depends_on("libtool", type=("build"), when="@master")
+    depends_on("m4", type=("build"), when="@main")
+    depends_on("autoconf", type=("build"), when="@main")
+    depends_on("automake", type=("build"), when="@main")
+    depends_on("libtool", type=("build"), when="@main")
     depends_on("valgrind", when="+valgrind")
 
     def configure_args(self):
diff --git a/var/spack/repos/builtin/packages/bolt/package.py b/var/spack/repos/builtin/packages/bolt/package.py
index 0b131b4d7a7..b4e4cf95ce9 100644
--- a/var/spack/repos/builtin/packages/bolt/package.py
+++ b/var/spack/repos/builtin/packages/bolt/package.py
@@ -22,7 +22,7 @@ class Bolt(CMakePackage):
     git      = "https://github.com/pmodels/bolt.git"
     maintainers = ['shintaro-iwasaki']
 
-    version("master", branch="master")
+    version("main", branch="main")
     version("1.0", sha256="1c0d2f75597485ca36335d313a73736594e75c8a36123c5a6f54d01b5ba5c384")
 
     depends_on('argobots')

From 82eb71cb953db0d95d15caed0d3b73232736e638 Mon Sep 17 00:00:00 2001
From: Omar Padron <omar.padron@kitware.com>
Date: Thu, 18 Jun 2020 05:16:24 -0400
Subject: [PATCH 764/802] Explicitly install setuptools in docker images
 (#17143)

---
 share/spack/docker/centos-6.dockerfile    | 1 +
 share/spack/docker/centos-7.dockerfile    | 1 +
 share/spack/docker/ubuntu-1604.dockerfile | 1 +
 share/spack/docker/ubuntu-1804.dockerfile | 1 +
 4 files changed, 4 insertions(+)

diff --git a/share/spack/docker/centos-6.dockerfile b/share/spack/docker/centos-6.dockerfile
index fe919f3c885..8c971124a53 100644
--- a/share/spack/docker/centos-6.dockerfile
+++ b/share/spack/docker/centos-6.dockerfile
@@ -42,6 +42,7 @@ RUN yum update -y \
         patch \
         python \
         python-pip \
+        python-setuptools \
         tcl \
         unzip \
         which \
diff --git a/share/spack/docker/centos-7.dockerfile b/share/spack/docker/centos-7.dockerfile
index 67affa1af9f..292663d9222 100644
--- a/share/spack/docker/centos-7.dockerfile
+++ b/share/spack/docker/centos-7.dockerfile
@@ -42,6 +42,7 @@ RUN yum update -y \
         patch \
         python \
         python-pip \
+        python-setuptools \
         tcl \
         unzip \
         which \
diff --git a/share/spack/docker/ubuntu-1604.dockerfile b/share/spack/docker/ubuntu-1604.dockerfile
index 7891c5a2614..1f7db8bea9c 100644
--- a/share/spack/docker/ubuntu-1604.dockerfile
+++ b/share/spack/docker/ubuntu-1604.dockerfile
@@ -41,6 +41,7 @@ RUN apt-get -yqq update \
         make \
         python3 \
         python3-pip \
+        python3-setuptools \
         tcl \
         unzip \
  && locale-gen en_US.UTF-8 \
diff --git a/share/spack/docker/ubuntu-1804.dockerfile b/share/spack/docker/ubuntu-1804.dockerfile
index c0793314760..a8d9577b664 100644
--- a/share/spack/docker/ubuntu-1804.dockerfile
+++ b/share/spack/docker/ubuntu-1804.dockerfile
@@ -41,6 +41,7 @@ RUN apt-get -yqq update \
         make \
         python3 \
         python3-pip \
+        python3-setuptools \
         tcl \
         unzip \
  && locale-gen en_US.UTF-8 \

From 1de20f00b6d72a6c51f1f8e151081c7d34427fe3 Mon Sep 17 00:00:00 2001
From: Sinan <sbulutw@gmail.com>
Date: Thu, 18 Jun 2020 02:20:17 -0700
Subject: [PATCH 765/802] arrayfire: added cudnn as a dependency when +cuda
 (#17146)

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
---
 var/spack/repos/builtin/packages/arrayfire/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/arrayfire/package.py b/var/spack/repos/builtin/packages/arrayfire/package.py
index 983bd7e775e..d3a7b65e2c1 100644
--- a/var/spack/repos/builtin/packages/arrayfire/package.py
+++ b/var/spack/repos/builtin/packages/arrayfire/package.py
@@ -25,6 +25,7 @@ class Arrayfire(CMakePackage, CudaPackage):
     depends_on('fftw')
     depends_on('blas')
     depends_on('cuda@7.5:', when='+cuda')
+    depends_on('cudnn', when='+cuda')
     depends_on('opencl +icd', when='+opencl')
     # TODO add more opencl backends:
     # currently only Cuda backend is enabled

From 2a13bad8eb6a8045228359afda8451c7a6dd3b60 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Thu, 18 Jun 2020 20:42:52 +0800
Subject: [PATCH 766/802] atop: fix ld error (#17150)

---
 var/spack/repos/builtin/packages/atop/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/atop/package.py b/var/spack/repos/builtin/packages/atop/package.py
index c06d27cbd7b..3c0772fc4e4 100644
--- a/var/spack/repos/builtin/packages/atop/package.py
+++ b/var/spack/repos/builtin/packages/atop/package.py
@@ -20,6 +20,9 @@ class Atop(Package):
     depends_on('zlib')
     depends_on('ncurses')
 
+    def setup_build_environment(self, env):
+        env.append_flags('LDFLAGS', '-ltinfo')
+
     def install(self, spec, prefix):
         make()
         mkdirp(prefix.bin)

From 68c13d76f9b12dcd777a915426aa2a552944fb45 Mon Sep 17 00:00:00 2001
From: lorddavidiii <githuh@qi0.de>
Date: Thu, 18 Jun 2020 14:43:52 +0200
Subject: [PATCH 767/802] arpack-ng: fix build with gcc@10: (#17131)

---
 var/spack/repos/builtin/packages/arpack-ng/package.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
index 35a263541f3..1698a0e4bd1 100644
--- a/var/spack/repos/builtin/packages/arpack-ng/package.py
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -85,6 +85,12 @@ def libs(self):
             libraries, root=self.prefix, shared=True, recursive=True
         )
 
+    @when('@:3.7.0 %gcc@10:')
+    def setup_build_environment(self, env):
+        # version up to and including 3.7.0 are not ported to gcc 10
+        # https://github.com/opencollab/arpack-ng/issues/242
+        env.set('FFLAGS', '-fallow-argument-mismatch')
+
     @when('@3.4.0:')
     def install(self, spec, prefix):
 

From 6d9f0262de6269b895673315a1c36c4f6888419e Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Thu, 18 Jun 2020 14:44:32 +0200
Subject: [PATCH 768/802] libjpeg-turbo: fixed sha256 (#17154)

---
 .../repos/builtin/packages/libjpeg-turbo/package.py  | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py
index a78c4af66cd..4b81a01ef6c 100644
--- a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py
+++ b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py
@@ -8,14 +8,16 @@
 
 class LibjpegTurbo(Package):
     """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to
-       accelerate baseline JPEG compression and decompression. libjpeg is a
-       library that implements JPEG image encoding, decoding and
-       transcoding."""
+    accelerate baseline JPEG compression and decompression.
+
+    libjpeg is a library that implements JPEG image encoding, decoding and
+    transcoding.
+    """
     # https://github.com/libjpeg-turbo/libjpeg-turbo/blob/master/BUILDING.md
     homepage = "https://libjpeg-turbo.org/"
-    url      = "https://github.com/libjpeg-turbo/libjpeg-turbo/archive/2.0.3.tar.gz"
+    url = "https://github.com/libjpeg-turbo/libjpeg-turbo/archive/2.0.3.tar.gz"
 
-    version('2.0.4', sha256='33dd8547efd5543639e890efbf2ef52d5a21df81faf41bb940657af916a23406')
+    version('2.0.4', sha256='7777c3c19762940cff42b3ba4d7cd5c52d1671b39a79532050c85efb99079064')
     version('2.0.3', sha256='a69598bf079463b34d45ca7268462a18b6507fdaa62bb1dfd212f02041499b5d')
     version('2.0.2', sha256='b45255bd476c19c7c6b198c07c0487e8b8536373b82f2b38346b32b4fa7bb942')
     version('1.5.90', sha256='cb948ade92561d8626fd7866a4a7ba3b952f9759ea3dd642927bc687470f60b7')

From 33e6d0f378aa2bd325a15de275844cc68bc491f6 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 18 Jun 2020 17:24:14 -0500
Subject: [PATCH 769/802] py-matplotlib: add v3.2.2 (#17160)

---
 var/spack/repos/builtin/packages/py-matplotlib/package.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py
index 9b9b77f00a2..a1b4c94e409 100644
--- a/var/spack/repos/builtin/packages/py-matplotlib/package.py
+++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py
@@ -13,7 +13,7 @@ class PyMatplotlib(PythonPackage):
     and interactive visualizations in Python."""
 
     homepage = "https://matplotlib.org/"
-    url      = "https://pypi.io/packages/source/m/matplotlib/matplotlib-3.2.1.tar.gz"
+    url      = "https://pypi.io/packages/source/m/matplotlib/matplotlib-3.2.2.tar.gz"
 
     maintainers = ['adamjstewart']
 
@@ -27,6 +27,7 @@ class PyMatplotlib(PythonPackage):
         'matplotlib.testing.jpl_units'
     ]
 
+    version('3.2.2', sha256='3d77a6630d093d74cbbfebaa0571d00790966be1ed204e4a8239f5cbd6835c5d')
     version('3.2.1', sha256='ffe2f9cdcea1086fc414e82f42271ecf1976700b8edd16ca9d376189c6d93aee')
     version('3.2.0', sha256='651d76daf9168250370d4befb09f79875daa2224a9096d97dfc3ed764c842be4')
     version('3.1.3', sha256='db3121f12fb9b99f105d1413aebaeb3d943f269f3d262b45586d12765866f0c6')
@@ -127,7 +128,10 @@ class PyMatplotlib(PythonPackage):
     depends_on('pkgconfig', type='build')
 
     # Testing dependencies
-    depends_on('py-pytest', type='test')
+    # https://matplotlib.org/devel/testing.html#requirements
+    depends_on('py-pytest@3.6:', type='test')
+    depends_on('ghostscript@9.0:', type='test')
+    # depends_on('inkscape@:0.999', type='test')
 
     msg = 'MacOSX backend requires the Cocoa headers included with XCode'
     conflicts('platform=linux', when='backend=macosx', msg=msg)

From 5a0c5de50b168e34278a876942cda93ddd440c84 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 18 Jun 2020 17:24:27 -0500
Subject: [PATCH 770/802] py-pandas: add v1.0.5 (#17161)

---
 var/spack/repos/builtin/packages/py-pandas/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py
index 152f3a0d4c2..3fba468a270 100644
--- a/var/spack/repos/builtin/packages/py-pandas/package.py
+++ b/var/spack/repos/builtin/packages/py-pandas/package.py
@@ -12,7 +12,7 @@ class PyPandas(PythonPackage):
     programming language."""
 
     homepage = "https://pandas.pydata.org/"
-    url = "https://pypi.io/packages/source/p/pandas/pandas-1.0.4.tar.gz"
+    url = "https://pypi.io/packages/source/p/pandas/pandas-1.0.5.tar.gz"
 
     maintainers = ['adamjstewart']
     import_modules = [
@@ -29,6 +29,7 @@ class PyPandas(PythonPackage):
         'pandas.api.extensions'
     ]
 
+    version('1.0.5',  sha256='69c5d920a0b2a9838e677f78f4dde506b95ea8e4d30da25859db6469ded84fa8')
     version('1.0.4',  sha256='b35d625282baa7b51e82e52622c300a1ca9f786711b2af7cbe64f1e6831f4126')
     version('1.0.3',  sha256='32f42e322fb903d0e189a4c10b75ba70d90958cc4f66a1781ed027f1a1d14586')
     version('1.0.2',  sha256='76334ba36aa42f93b6b47b79cbc32187d3a178a4ab1c3a478c8f4198bcd93a73')

From b80d5e74e52542ae8961acda16b57951d36c1925 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 18 Jun 2020 17:24:38 -0500
Subject: [PATCH 771/802] PyTorch: add v1.5.1 (#17167)

---
 var/spack/repos/builtin/packages/py-torch/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py
index 4878c343762..c240144f11d 100644
--- a/var/spack/repos/builtin/packages/py-torch/package.py
+++ b/var/spack/repos/builtin/packages/py-torch/package.py
@@ -50,6 +50,7 @@ class PyTorch(PythonPackage, CudaPackage):
     ]
 
     version('master', branch='master', submodules=True)
+    version('1.5.1', tag='v1.5.1', submodules=True)
     version('1.5.0', tag='v1.5.0', submodules=True)
     version('1.4.1', tag='v1.4.1', submodules=True)
     version('1.4.0', tag='v1.4.0', submodules=True,
@@ -170,7 +171,7 @@ class PyTorch(PythonPackage, CudaPackage):
     # https://github.com/pytorch/pytorch/pull/35607
     # https://github.com/pytorch/pytorch/pull/37865
     # Fixes CMake configuration error when XNNPACK is disabled
-    patch('xnnpack.patch', when='@1.5.0')
+    patch('xnnpack.patch', when='@1.5.0:1.5.999')
 
     # https://github.com/pytorch/pytorch/pull/37086
     # Fixes compilation with Clang 9.0.0 and Apple Clang 11.0.3

From b73536b4ad15fbbac3a99908fb6db40a68642066 Mon Sep 17 00:00:00 2001
From: Alexander Knieps <alexanderrobom@web.de>
Date: Fri, 19 Jun 2020 18:03:25 +0200
Subject: [PATCH 772/802] Update to swipl package (#17173)

* Added version 8.2.0, added dependency for documentation build, added variants for documentations

* Renamed variant '+man' to '+html'

Co-authored-by: Alexander Knieps <a.knieps@fz-juelich.de>
---
 var/spack/repos/builtin/packages/swipl/package.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/var/spack/repos/builtin/packages/swipl/package.py b/var/spack/repos/builtin/packages/swipl/package.py
index 6cba487a7d2..da3e161c2c6 100644
--- a/var/spack/repos/builtin/packages/swipl/package.py
+++ b/var/spack/repos/builtin/packages/swipl/package.py
@@ -24,6 +24,7 @@ class Swipl(CMakePackage):
 
     maintainers = ['alexrobomind']
 
+    version('8.2.0', sha256='d8c9f3adb9cd997a5fed7b5f5dbfe971d2defda969b9066ada158e4202c09c3c')
     version('8.0.3', sha256='cee59c0a477c8166d722703f6e52f962028f3ac43a5f41240ecb45dbdbe2d6ae')
 
     variant('gmp', default=True, description='bignum and rational number support')
@@ -32,10 +33,14 @@ class Swipl(CMakePackage):
     variant('zlib', default=True, description='Compressed streams support')
     variant('odbc', default=True, description='ODBC database access')
     variant('unwind', default=True, description='Build with stack traces in crash reports')
+    variant('html', default=True, description='Install the HTML documentation')
+    variant('pdfdoc', default=False, description='Build the PDF documentation')
 
     depends_on('uuid')
     depends_on('readline')
 
+    depends_on('libarchive', when='+html')
+
     depends_on('gmp', when='+gmp')
     depends_on('unwind', when='+unwind')
     depends_on('unixodbc', when='+odbc')
@@ -65,6 +70,8 @@ def append_switch(variant, cmake_flag):
         append_switch('+gmp', 'USE_GMP')
         append_switch('+xpce', 'SWIPL_PACKAGES_X')
         append_switch('+odbc', 'SWIPL_PACKAGES_ODBC')
+        append_switch('+html', 'INSTALL_DOCUMENTATION')
+        append_switch('+pdfdoc', 'BUILD_PDF_DOCUMENTATION')
 
         # The variants ssl and zlib are implicitly set up by CMake
 

From 844312f2135169b9e329710e178177df0553e412 Mon Sep 17 00:00:00 2001
From: G-Ragghianti <33492707+G-Ragghianti@users.noreply.github.com>
Date: Fri, 19 Jun 2020 12:10:03 -0400
Subject: [PATCH 773/802] Updated slate package to use new git repo.  Added
 maintainer. (#17165)

* Updated slate package to use new git repo.  Added maintainer.
---
 var/spack/repos/builtin/packages/slate/package.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/slate/package.py b/var/spack/repos/builtin/packages/slate/package.py
index 67264d3bc92..cae0a0e8df5 100644
--- a/var/spack/repos/builtin/packages/slate/package.py
+++ b/var/spack/repos/builtin/packages/slate/package.py
@@ -16,10 +16,10 @@ class Slate(Package):
     solvers."""
 
     homepage = "https://icl.utk.edu/slate/"
-    hg      = "https://bitbucket.org/icl/slate"
-    maintainers = ['G-Ragghianti']
+    git      = "https://bitbucket.org/icl/slate"
+    maintainers = ['G-Ragghianti', 'mgates3']
 
-    version('develop', hg=hg)
+    version('develop', submodules=True)
 
     variant('cuda',   default=True, description='Build with CUDA support.')
     variant('mpi',    default=True, description='Build with MPI support.')
@@ -27,7 +27,6 @@ class Slate(Package):
 
     depends_on('cuda@9:', when='+cuda')
     depends_on('intel-mkl')
-    depends_on('mercurial', type='build')
     depends_on('mpi', when='+mpi')
 
     conflicts('%gcc@:5')

From a20ba315f57bcbbb73838d1b67a15a9e14d580cd Mon Sep 17 00:00:00 2001
From: Chris White <white238@llnl.gov>
Date: Fri, 19 Jun 2020 12:31:09 -0700
Subject: [PATCH 774/802] Axom/Conduit: Fix error when fortran is not defined
 (#17171)

* Fix error when fortran is not defined

* Guard more ~fortran cases
---
 var/spack/repos/builtin/packages/axom/package.py    | 8 +++++---
 var/spack/repos/builtin/packages/conduit/package.py | 4 +++-
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/axom/package.py b/var/spack/repos/builtin/packages/axom/package.py
index 2eb3ae226c9..add0619a3e8 100644
--- a/var/spack/repos/builtin/packages/axom/package.py
+++ b/var/spack/repos/builtin/packages/axom/package.py
@@ -231,7 +231,9 @@ def hostconfig(self, spec, prefix):
         if fflags:
             cfg.write(cmake_cache_entry("CMAKE_Fortran_FLAGS", fflags))
 
-        if ("gfortran" in f_compiler) and ("clang" in cpp_compiler):
+        if ((f_compiler is not None)
+           and ("gfortran" in f_compiler)
+           and ("clang" in cpp_compiler)):
             libdir = pjoin(os.path.dirname(
                            os.path.dirname(cpp_compiler)), "lib")
             flags = ""
@@ -444,7 +446,7 @@ def hostconfig(self, spec, prefix):
 
         # Override XL compiler family
         familymsg = ("Override to proper compiler family for XL")
-        if "xlf" in f_compiler:
+        if (f_compiler is not None) and ("xlf" in f_compiler):
             cfg.write(cmake_cache_entry("CMAKE_Fortran_COMPILER_ID", "XL",
                                         familymsg))
         if "xlc" in c_compiler:
@@ -455,7 +457,7 @@ def hostconfig(self, spec, prefix):
                                         familymsg))
 
         if spec.satisfies('target=ppc64le:'):
-            if "xlf" in f_compiler:
+            if (f_compiler is not None) and ("xlf" in f_compiler):
                 description = ("Converts C-style comments to Fortran style "
                                "in preprocessed files")
                 cfg.write(cmake_cache_entry("BLT_FORTRAN_FLAGS",
diff --git a/var/spack/repos/builtin/packages/conduit/package.py b/var/spack/repos/builtin/packages/conduit/package.py
index 9928884e924..b8b23bccbee 100644
--- a/var/spack/repos/builtin/packages/conduit/package.py
+++ b/var/spack/repos/builtin/packages/conduit/package.py
@@ -371,7 +371,9 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
         if fflags:
             cfg.write(cmake_cache_entry("CMAKE_Fortran_FLAGS", fflags))
 
-        if ("gfortran" in f_compiler) and ("clang" in cpp_compiler):
+        if ((f_compiler is not None)
+           and ("gfortran" in f_compiler)
+           and ("clang" in cpp_compiler)):
             libdir = os.path.join(os.path.dirname(
                                   os.path.dirname(f_compiler)), "lib")
             flags = ""

From c7f6608f5ecdb165e21622b56ab9163c8d8d238a Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sat, 20 Jun 2020 17:46:10 -0500
Subject: [PATCH 775/802] NumPy: add v1.19.0 (#17183)

---
 var/spack/repos/builtin/packages/py-numpy/package.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index 4659a449ebf..f437b43063c 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -16,7 +16,7 @@ class PyNumpy(PythonPackage):
     number capabilities"""
 
     homepage = "https://numpy.org/"
-    url      = "https://pypi.io/packages/source/n/numpy/numpy-1.18.5.zip"
+    url      = "https://pypi.io/packages/source/n/numpy/numpy-1.19.0.zip"
     git      = "https://github.com/numpy/numpy.git"
 
     maintainers = ['adamjstewart']
@@ -30,6 +30,7 @@ class PyNumpy(PythonPackage):
     ]
 
     version('master', branch='master')
+    version('1.19.0', sha256='76766cc80d6128750075378d3bb7812cf146415bd29b588616f72c943c00d598')
     version('1.18.5', sha256='34e96e9dae65c4839bd80012023aadd6ee2ccb73ce7fdf3074c62f301e63120b')
     version('1.18.4', sha256='bbcc85aaf4cd84ba057decaead058f43191cc0e30d6bc5d44fe336dc3d3f4509')
     version('1.18.3', sha256='e46e2384209c91996d5ec16744234d1c906ab79a701ce1a26155c9ec890b8dc8')
@@ -82,6 +83,7 @@ class PyNumpy(PythonPackage):
     depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
     depends_on('python@2.7:2.8,3.5:', type=('build', 'run'), when='@1.16:')
     depends_on('python@3.5:', type=('build', 'run'), when='@1.17:')
+    depends_on('python@3.6:', type=('build', 'run'), when='@1.19:')
     depends_on('py-setuptools', type='build')
     # Check pyproject.toml for updates to the required cython version
     depends_on('py-cython@0.29.13:', when='@1.18.0:', type='build')
@@ -91,6 +93,7 @@ class PyNumpy(PythonPackage):
 
     depends_on('py-nose@1.0.0:', when='@:1.14', type='test')
     depends_on('py-pytest', when='@1.15:', type='test')
+    depends_on('py-hypothesis', when='@1.19:', type='test')
 
     # Allows you to specify order of BLAS/LAPACK preference
     # https://github.com/numpy/numpy/pull/13132

From 4bfa844de08e1b786ed3d09fb403fb4b645c6fef Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Mon, 22 Jun 2020 01:20:04 -0500
Subject: [PATCH 776/802] SciPy: add v1.5.0 (#17189)

---
 var/spack/repos/builtin/packages/py-scipy/package.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py
index 7baf0bbb38a..6775d533fa8 100644
--- a/var/spack/repos/builtin/packages/py-scipy/package.py
+++ b/var/spack/repos/builtin/packages/py-scipy/package.py
@@ -12,7 +12,7 @@ class PyScipy(PythonPackage):
     as routines for numerical integration and optimization."""
 
     homepage = "https://www.scipy.org/"
-    url      = "https://pypi.io/packages/source/s/scipy/scipy-1.4.1.tar.gz"
+    url      = "https://pypi.io/packages/source/s/scipy/scipy-1.5.0.tar.gz"
 
     maintainers = ['adamjstewart']
     install_time_test_callbacks = ['install_test', 'import_module_test']
@@ -30,6 +30,7 @@ class PyScipy(PythonPackage):
         'scipy.sparse.linalg.eigen.lobpcg', 'scipy.special._precompute'
     ]
 
+    version('1.5.0',  sha256='4ff72877d19b295ee7f7727615ea8238f2d59159df0bdd98f91754be4a2767f0')
     version('1.4.1',  sha256='dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59')
     version('1.4.0',  sha256='31f7cfa93b01507c935c12b535e24812594002a02a56803d7cd063e9920d25e8')
     version('1.3.3',  sha256='64bf4e8ae0db2d42b58477817f648d81e77f0b381d0ea4427385bba3f959380a')
@@ -50,14 +51,17 @@ class PyScipy(PythonPackage):
     depends_on('python@2.6:2.8,3.2:', type=('build', 'run'))
     depends_on('python@2.7:2.8,3.4:', when='@0.18:', type=('build', 'run'))
     depends_on('python@3.5:', when='@1.3:', type=('build', 'run'))
+    depends_on('python@3.6:', when='@1.5:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
-    depends_on('py-pybind11@2.4.0:', when='@1.4.1:', type='build')
     depends_on('py-pybind11@2.2.4:', when='@1.4.0:', type='build')
+    depends_on('py-pybind11@2.4.0:', when='@1.4.1:', type='build')
+    depends_on('py-pybind11@2.4.3:', when='@1.5.0:', type='build')
     depends_on('py-numpy@1.5.1:+blas+lapack', type=('build', 'run'))
     depends_on('py-numpy@1.6.2:+blas+lapack', when='@0.16:', type=('build', 'run'))
     depends_on('py-numpy@1.7.1:+blas+lapack', when='@0.18:', type=('build', 'run'))
     depends_on('py-numpy@1.8.2:+blas+lapack', when='@0.19:', type=('build', 'run'))
     depends_on('py-numpy@1.13.3:+blas+lapack', when='@1.3:', type=('build', 'run'))
+    depends_on('py-numpy@1.14.5:+blas+lapack', when='@1.5:', type=('build', 'run'))
     depends_on('py-pytest', type='test')
 
     # NOTE: scipy picks up Blas/Lapack from numpy, see

From 0cddfb9d8a203f6d319480869f95f3e06f88dd07 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Mon, 22 Jun 2020 08:30:17 +0200
Subject: [PATCH 777/802] meson: added v0.54.3 (#17190)

---
 var/spack/repos/builtin/packages/meson/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/meson/package.py b/var/spack/repos/builtin/packages/meson/package.py
index 39971c7076c..8ff3ddf32e0 100644
--- a/var/spack/repos/builtin/packages/meson/package.py
+++ b/var/spack/repos/builtin/packages/meson/package.py
@@ -16,6 +16,7 @@ class Meson(PythonPackage):
 
     maintainers = ['michaelkuhn']
 
+    version('0.54.3', sha256='c25caff342b5368bfe33fab6108f454fcf12e2f2cef70817205872ddef669e8b')
     version('0.54.2', sha256='85cafdc70ae7d1d9d506e7356b917c649c4df2077bd6a0382db37648aa4ecbdb')
     version('0.54.1', sha256='854e8b94ab36e5aece813d2b2aee8a639bd52201dfea50890722ac9128e2f59e')
     version('0.54.0', sha256='95efdbaa7cb3e915ab9a7b26b1412475398fdc3e834842a780f1646c7764f2d9')

From e91d7988e5ef9b582fd7dcf37eed2eb9f9d1e11a Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Mon, 22 Jun 2020 00:36:01 -0600
Subject: [PATCH 778/802] votca-*: added v1.6.1 (#17186)

---
 .../repos/builtin/packages/votca-csg-tutorials/package.py     | 4 +++-
 var/spack/repos/builtin/packages/votca-csg/package.py         | 4 +++-
 var/spack/repos/builtin/packages/votca-csgapps/package.py     | 4 +++-
 var/spack/repos/builtin/packages/votca-tools/package.py       | 1 +
 var/spack/repos/builtin/packages/votca-xtp/package.py         | 4 +++-
 5 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/votca-csg-tutorials/package.py b/var/spack/repos/builtin/packages/votca-csg-tutorials/package.py
index b20c767fce7..4b54e4b9aa5 100644
--- a/var/spack/repos/builtin/packages/votca-csg-tutorials/package.py
+++ b/var/spack/repos/builtin/packages/votca-csg-tutorials/package.py
@@ -22,12 +22,14 @@ class VotcaCsgTutorials(CMakePackage):
 
     version('master', branch='master')
     version('stable', branch='stable')
+    version('1.6.1', sha256='d8428c4a03ce42d88317045ec555af3defa022fd9a61f05e07b57c5577288c8c')
     version('1.6', sha256='54946c647724f1beb95942d47ec7f4cf7a95a59ec7268522693d5ec723585daf')
     version('1.5.1',   sha256='e35cea92df0e7d05ca7b449c1b5d84d887a3a23c7796abe3b84e4d6feec7faca')
     version('1.5',     sha256='03b841fb94129cf59781a7a5e3b71936c414aa9dfa17a50d7bc856d46274580c')
     version('1.4.1',   sha256='623724192c3a7d76b603a74a3326f181045f10f38b9f56dce754a90f1a74556e')
     version('1.4',     sha256='27d50acd68a9d8557fef18ec2b0c62841ae91c22275ab9afbd65c35e4dd5f719')
 
-    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "master", "stable"]:
+    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "1.6.1", "master",
+              "stable"]:
         depends_on('votca-csg@%s' % v, when="@%s:%s.0" % (v, v))
     depends_on("boost")
diff --git a/var/spack/repos/builtin/packages/votca-csg/package.py b/var/spack/repos/builtin/packages/votca-csg/package.py
index deffd257397..f6b43266e56 100644
--- a/var/spack/repos/builtin/packages/votca-csg/package.py
+++ b/var/spack/repos/builtin/packages/votca-csg/package.py
@@ -22,6 +22,7 @@ class VotcaCsg(CMakePackage):
 
     version('master', branch='master')
     version('stable', branch='stable')
+    version('1.6.1', sha256='ed12bcb1ccdf71f54e21cdcc9803add4b8ebdc6b8263cb5b0034f5db01e31dbb')
     version('1.6', sha256='8cf6a4ac3ef7347c720a44d8a676f8cbd1462e162f6113de39f27b89354465ea')
     version('1.5.1', sha256='7fca1261bd267bf38d2edd26259730fed3126c0c3fd91fb81940dbe17bb568fd')
     version('1.5', sha256='160387cdc51f87dd20ff2e2eed97086beee415d48f3c92f4199f6109068c8ff4')
@@ -29,7 +30,8 @@ class VotcaCsg(CMakePackage):
     version('1.4', sha256='c13e7febd792de8c3d426203f089bd4d33b8067f9db5e8840e4579c88b61146e')
 
     depends_on("cmake@2.8:", type='build')
-    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "master", "stable"]:
+    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "1.6.1", "master",
+              "stable"]:
         depends_on('votca-tools@%s' % v, when="@%s:%s.0" % (v, v))
     depends_on("boost")
     depends_on("gromacs~mpi@5.1:2019.9999")
diff --git a/var/spack/repos/builtin/packages/votca-csgapps/package.py b/var/spack/repos/builtin/packages/votca-csgapps/package.py
index dcca20339c5..ad12a83b2a4 100644
--- a/var/spack/repos/builtin/packages/votca-csgapps/package.py
+++ b/var/spack/repos/builtin/packages/votca-csgapps/package.py
@@ -22,12 +22,14 @@ class VotcaCsgapps(CMakePackage):
 
     version('master', branch='master')
     version('stable', branch='stable')
+    version('1.6.1', sha256='03c7cef2a76e73cf953b2b5ea2cdca765ec1a2627d0a9d8869d46166e63d197c')
     version('1.6', sha256='084bbc5b179bb7eb8f6671d2d5fa13e69e68946570c9120a7e4b10aff1866e2e')
     version('1.5.1',   sha256='b4946711e88a1745688b6cce5aad872e6e2ea200fededf38d77a864883e3750e')
     version('1.5',     sha256='18b40ce6222509bc70aa9d56b8c538cd5903edf7294d6f95530668e555206d5b')
     version('1.4.1',   sha256='095d9ee4cd49d2fd79c10e0e84e6890b755e54dec6a5cd580a2b4241ba230a2b')
     version('1.4',     sha256='4ea8348c2f7de3cc488f48fbd8652e69b52515441952766c06ff67ed1aaf69a0')
 
-    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "master", "stable"]:
+    for v in ["1.4", "1.4.1", "1.5", "1.5.1", "1.6", "1.6.1", "master",
+              "stable"]:
         depends_on('votca-csg@%s' % v, when="@%s:%s.0" % (v, v))
     depends_on("boost")
diff --git a/var/spack/repos/builtin/packages/votca-tools/package.py b/var/spack/repos/builtin/packages/votca-tools/package.py
index 09f8e5aab69..f676fb633b6 100644
--- a/var/spack/repos/builtin/packages/votca-tools/package.py
+++ b/var/spack/repos/builtin/packages/votca-tools/package.py
@@ -22,6 +22,7 @@ class VotcaTools(CMakePackage):
 
     version('master', branch='master')
     version('stable', branch='stable')
+    version('1.6.1', sha256='3e8f51d484cb3fdfbeb851aab387807ba4c40aecef8317c90182da68ad282dcc')
     version('1.6', sha256='cfd0fedc80fecd009f743b5df47777508d76bf3ef294a508a9f11fbb42efe9a5')
     version('1.5.1', sha256='4be4fe25a2910e24e1720cd9022d214001d38196033ade8f9d6e618b4f47d5c4')
     version('1.5', sha256='a82a6596c24ff06e79eab17ca02f4405745ceeeb66369693a59023ad0b62cf22')
diff --git a/var/spack/repos/builtin/packages/votca-xtp/package.py b/var/spack/repos/builtin/packages/votca-xtp/package.py
index 21cfdf4edb1..98c546c069b 100644
--- a/var/spack/repos/builtin/packages/votca-xtp/package.py
+++ b/var/spack/repos/builtin/packages/votca-xtp/package.py
@@ -22,13 +22,15 @@ class VotcaXtp(CMakePackage):
 
     version('master', branch='master')
     version('stable', branch='stable')
+    version('1.6.1', sha256='886af50bc12457bbafb06dc927b7fd4cadc3db1b4615b24a08953f6b358debef')
     version('1.6', sha256='695c2d9d3f924103481529f992e3723bdce10b8edfc294421a849cdf51dbbb6e')
     version('1.5.1', sha256='17a7722e5a32d236e4f1f6f88b680da4ba5f52bcf65bca3687c6a1c731d10881')
     version('1.5', sha256='b40b6d19e13f0650e84b8beebe86ce5c09071624f18d66df826f9d8584b4d3c8')
     version('1.4.1', sha256='4b53d371d6cf648c9e9e9bd1f104d349cafeaf10a02866e3f1d05c574b595a21')
 
     depends_on("cmake@2.8:", type='build')
-    for v in ["1.4.1", "1.5", "1.5.1", "1.6", "master", "stable"]:
+    for v in ["1.4.1", "1.5", "1.5.1", "1.6", "1.6.1", "master",
+              "stable"]:
         depends_on('votca-tools@%s' % v, when="@%s:%s.0" % (v, v))
         depends_on('votca-csg@%s' % v, when="@%s:%s.0" % (v, v))
     depends_on("libxc", when='@stable,1.5:')

From 73b3bbbd22592e47720b0e5f5580a4e3671067e7 Mon Sep 17 00:00:00 2001
From: Hans Pabst <hfp@users.noreply.github.com>
Date: Mon, 22 Jun 2020 08:36:46 +0200
Subject: [PATCH 779/802] libxsmm: added v1.16 (#17185)

---
 var/spack/repos/builtin/packages/libxsmm/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/libxsmm/package.py b/var/spack/repos/builtin/packages/libxsmm/package.py
index 12cfc32dfd2..caf6681e47b 100644
--- a/var/spack/repos/builtin/packages/libxsmm/package.py
+++ b/var/spack/repos/builtin/packages/libxsmm/package.py
@@ -14,10 +14,11 @@ class Libxsmm(MakefilePackage):
     and deep learning primitives."""
 
     homepage = 'https://github.com/hfp/libxsmm'
-    url      = 'https://github.com/hfp/libxsmm/archive/1.15.tar.gz'
+    url      = 'https://github.com/hfp/libxsmm/archive/1.16.tar.gz'
     git      = 'https://github.com/hfp/libxsmm.git'
 
     version('master', branch='master')
+    version('1.16',   sha256='4f4f2ad97815413af80821d2e306eb6f00541941ad412662da05c02361a20e07')
     version('1.15',   sha256='499e5adfbf90cd3673309243c2b56b237d54f86db2437e1ac06c8746b55ab91c')
     version('1.14',   sha256='9c0af4509ea341d1ee2c6c19fc6f19289318c3bd4b17844efeb9e7f9691abf76')
     version('1.13',   sha256='47c034e169820a9633770eece0e0fdd8d4a744e09b81da2af8c2608a4625811e')

From 0b74285a14eb84e897906b8948bea4dddbfba2e9 Mon Sep 17 00:00:00 2001
From: iarspider <iarspider@gmail.com>
Date: Mon, 22 Jun 2020 08:52:19 +0200
Subject: [PATCH 780/802] py-pyheadtail: added new package at v1.14.1 (#17159)

Co-authored-by: iarspider <iarpsider@gmail.com>
---
 .../builtin/packages/py-pyheadtail/package.py | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-pyheadtail/package.py

diff --git a/var/spack/repos/builtin/packages/py-pyheadtail/package.py b/var/spack/repos/builtin/packages/py-pyheadtail/package.py
new file mode 100644
index 00000000000..811bf63b4b0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyheadtail/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyheadtail(PythonPackage):
+    """CERN PyHEADTAIL numerical n-body simulation code for simulating
+    macro-particle beam dynamics with collective effects."""
+
+    homepage = "https://github.com/PyCOMPLETE/PyHEADTAIL"
+    url      = "https://pypi.io/packages/source/P/PyHEADTAIL/PyHEADTAIL-1.14.1.tar.gz"
+
+    version('1.14.1', sha256='bf90ac7e8764176c55e82c363cad7ab43543863b6ef482760ced23b78e917bb4')
+    version('1.13.1', sha256='29c742573a918126b5a9c21806ee0ec6a34ec642a0e6ad200f6d4551bf1bb310')
+
+    depends_on('python', type=('build', 'run'))
+    depends_on('python@3:', when='@1.13.5:', type=('build', 'run'))
+    depends_on('py-cython', type='build')
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-h5py', type=('build', 'run'))

From 3fc963b1f919baa46f5f6f15bb1ca19f2404f600 Mon Sep 17 00:00:00 2001
From: Wouter Deconinck <wdconinc@gmail.com>
Date: Mon, 22 Jun 2020 02:31:57 -0500
Subject: [PATCH 781/802] delphes: better specify the dependency on root
 (#17175)

Compiling delphes with default root cxxstd=11 fails, see e.g. https://sft.its.cern.ch/jira/si/jira.issueviews:issue-html/ROOT-9492/ROOT-9492.html
---
 var/spack/repos/builtin/packages/delphes/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/delphes/package.py b/var/spack/repos/builtin/packages/delphes/package.py
index 723182f616f..b3b511a00fa 100644
--- a/var/spack/repos/builtin/packages/delphes/package.py
+++ b/var/spack/repos/builtin/packages/delphes/package.py
@@ -39,7 +39,8 @@ class Delphes(CMakePackage):
     version('3.0.5', sha256='ab64ec6d2476fbfa40562e7edb510a8ab4c4fe5be77a4353ebf315c2af181a80')
 
     depends_on('cmake', type='build')
-    depends_on('root')
+    depends_on('root cxxstd=14', when='cxxstd=14')
+    depends_on('root cxxstd=17', when='cxxstd=17')
 
     variant('build_type', default='Release',
             description='The build type to build',

From 0d08e18df5106a276543e1eb058d42e7f7dff88d Mon Sep 17 00:00:00 2001
From: Brian Van Essen <vanessen1@llnl.gov>
Date: Mon, 22 Jun 2020 00:32:55 -0700
Subject: [PATCH 782/802] Minor cleanup for conduit and hydrogen (#17136)

* Fix how the Conduit detects that the MPI compiler is the same as the
CC compiler and is more careful when it sets the MPI compilers to be
the Cray PE system compilers.

* Remove unnecessary push of the MPI compilers to the C compilers for Hydrogen.
---
 var/spack/repos/builtin/packages/conduit/package.py  | 2 +-
 var/spack/repos/builtin/packages/hydrogen/package.py | 3 ---
 2 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/conduit/package.py b/var/spack/repos/builtin/packages/conduit/package.py
index b8b23bccbee..8481ddce82f 100644
--- a/var/spack/repos/builtin/packages/conduit/package.py
+++ b/var/spack/repos/builtin/packages/conduit/package.py
@@ -469,7 +469,7 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
             # use those for mpi wrappers, b/c  spec['mpi'].mpicxx
             # etc make return the spack compiler wrappers
             # which can trip up mpi detection in CMake 3.14
-            if cpp_compiler == "CC":
+            if spec['mpi'].mpicc == spack_cc:
                 mpicc_path = "cc"
                 mpicxx_path = "CC"
                 mpifc_path = "ftn"
diff --git a/var/spack/repos/builtin/packages/hydrogen/package.py b/var/spack/repos/builtin/packages/hydrogen/package.py
index c28d0872d90..449fe046dc5 100644
--- a/var/spack/repos/builtin/packages/hydrogen/package.py
+++ b/var/spack/repos/builtin/packages/hydrogen/package.py
@@ -117,9 +117,6 @@ def cmake_args(self):
 
         args = [
             '-DCMAKE_INSTALL_MESSAGE:STRING=LAZY',
-            '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
-            '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
-            '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
             '-DBUILD_SHARED_LIBS:BOOL=%s'      % ('+shared' in spec),
             '-DHydrogen_ENABLE_OPENMP:BOOL=%s'       % ('+hybrid' in spec),
             '-DHydrogen_ENABLE_QUADMATH:BOOL=%s'     % ('+quad' in spec),

From a76545b813d2c7f0e7c174cf1f78755b137e0f60 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Mon, 22 Jun 2020 19:37:26 +0800
Subject: [PATCH 783/802] dos2unix: add build dependency on gettext (#17191)

---
 var/spack/repos/builtin/packages/dos2unix/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/dos2unix/package.py b/var/spack/repos/builtin/packages/dos2unix/package.py
index 926bc5f65f5..8630b8369aa 100644
--- a/var/spack/repos/builtin/packages/dos2unix/package.py
+++ b/var/spack/repos/builtin/packages/dos2unix/package.py
@@ -14,5 +14,7 @@ class Dos2unix(MakefilePackage):
 
     version('7.3.4', sha256='8ccda7bbc5a2f903dafd95900abb5bf5e77a769b572ef25150fde4056c5f30c5')
 
+    depends_on('gettext', type='build')
+
     def install(self, spec, prefix):
         make('prefix={0}'.format(prefix), 'install')

From 54cfec025f084632be28f2a9166df0028069dc82 Mon Sep 17 00:00:00 2001
From: G-Ragghianti <33492707+G-Ragghianti@users.noreply.github.com>
Date: Mon, 22 Jun 2020 08:21:46 -0400
Subject: [PATCH 784/802] blaspp: moved to new git repo (#17184)

Extended the list of maintainers
---
 var/spack/repos/builtin/packages/blaspp/package.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/blaspp/package.py b/var/spack/repos/builtin/packages/blaspp/package.py
index 702c33a51fc..bcc5e80292a 100644
--- a/var/spack/repos/builtin/packages/blaspp/package.py
+++ b/var/spack/repos/builtin/packages/blaspp/package.py
@@ -7,14 +7,15 @@
 
 
 class Blaspp(CMakePackage):
-    """BLAS++: C++ API for the Basic Linear Algebra Subroutines (University of
-    Texas)."""
+    """C++ API for the Basic Linear Algebra Subroutines. Developed by the
+       Innovative Computing Laboratory at the University of Tennessee,
+       Knoxville."""
 
     homepage = "https://bitbucket.org/icl/blaspp"
-    hg       = "https://bitbucket.org/icl/blaspp"
-    maintainers = ['teonnik', 'Sely85']
+    git      = "https://bitbucket.org/icl/blaspp"
+    maintainers = ['teonnik', 'Sely85', 'G-Ragghianti', 'mgates3']
 
-    version('develop', hg=hg, revision="5191c9d")
+    version('develop', commit='6293d96')
 
     variant('gfort',
             default=False,

From 4e9a98997aea9365fc46c4503d813947cbead088 Mon Sep 17 00:00:00 2001
From: Brian Van Essen <vanessen1@llnl.gov>
Date: Mon, 22 Jun 2020 06:22:14 -0700
Subject: [PATCH 785/802] Added 8.0 RC to the versions (#17176)

---
 var/spack/repos/builtin/packages/cudnn/package.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/var/spack/repos/builtin/packages/cudnn/package.py b/var/spack/repos/builtin/packages/cudnn/package.py
index 74f5133d901..f0e8904e346 100644
--- a/var/spack/repos/builtin/packages/cudnn/package.py
+++ b/var/spack/repos/builtin/packages/cudnn/package.py
@@ -22,6 +22,16 @@ class Cudnn(Package):
 
     maintainers = ['adamjstewart']
 
+    # cuDNN 8.0
+    version('8.0.0.180-11.0-linux-x64',
+            sha256='9e75ea70280a77de815e0bdc85d08b67e081bc99a708b574092142344d2ba07e')
+    version('8.0.0.180-11.0-linux-ppc64le',
+            sha256='1229e94731bbca63ee7f5a239f4e1838a51a301d896f3097fbf7377d74704060')
+    version('8.0.0.180-10.2-linux-x64',
+            sha256='0c87c12358ee2b99d57c2a8c7560e3bb93e54bb929f5f8bec4964a72a2bb261d')
+    version('8.0.0.180-10.2-linux-ppc64le',
+            sha256='59e4ad6db15fcc374976e8052fe39e3f30f34079710fb3c7751a64c853d9243f')
+
     # cuDNN 7.6.5
     version('7.6.5.32-10.2-linux-x64',
             sha256='600267f2caaed2fd58eb214ba669d8ea35f396a7d19b94822e6b36f9f7088c20',

From 42f2c168d2374a041d9bbe7b2246a8cae56bb369 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Mon, 22 Jun 2020 08:44:29 -0700
Subject: [PATCH 786/802] swig: fix older builds on newer platforms by updating
 config files (#16854)

* swig: revise 'autotools' automated 'config.*' update mechanism to support 'config.sub' and adapt 'swig' accordingly
---
 lib/spack/spack/build_systems/autotools.py    | 137 ++++++++++--------
 .../repos/builtin/packages/swig/package.py    |   3 +
 2 files changed, 82 insertions(+), 58 deletions(-)

diff --git a/lib/spack/spack/build_systems/autotools.py b/lib/spack/spack/build_systems/autotools.py
index bb17cce46ce..72a2c0afbb0 100644
--- a/lib/spack/spack/build_systems/autotools.py
+++ b/lib/spack/spack/build_systems/autotools.py
@@ -57,8 +57,9 @@ class AutotoolsPackage(PackageBase):
     #: This attribute is used in UI queries that need to know the build
     #: system base class
     build_system_class = 'AutotoolsPackage'
-    #: Whether or not to update ``config.guess`` on old architectures
-    patch_config_guess = True
+    #: Whether or not to update ``config.guess`` and ``config.sub`` on old
+    #: architectures
+    patch_config_files = True
     #: Whether or not to update ``libtool``
     #: (currently only for Arm/Clang/Fujitsu compilers)
     patch_libtool = True
@@ -87,72 +88,92 @@ def archive_files(self):
         return [os.path.join(self.build_directory, 'config.log')]
 
     @run_after('autoreconf')
-    def _do_patch_config_guess(self):
-        """Some packages ship with an older config.guess and need to have
-        this updated when installed on a newer architecture. In particular,
-        config.guess fails for PPC64LE for version prior to a 2013-06-10
-        build date (automake 1.13.4) and for ARM (aarch64)."""
+    def _do_patch_config_files(self):
+        """Some packages ship with older config.guess/config.sub files and
+        need to have these updated when installed on a newer architecture.
+        In particular, config.guess fails for PPC64LE for version prior
+        to a 2013-06-10 build date (automake 1.13.4) and for ARM (aarch64)."""
 
-        if not self.patch_config_guess or (
+        if not self.patch_config_files or (
                 not self.spec.satisfies('target=ppc64le:') and
                 not self.spec.satisfies('target=aarch64:')
         ):
             return
-        my_config_guess = None
-        config_guess = None
-        if os.path.exists('config.guess'):
-            # First search the top-level source directory
-            my_config_guess = 'config.guess'
+
+        # TODO: Expand this to select the 'config.sub'-compatible architecture
+        # for each platform (e.g. 'config.sub' doesn't accept 'power9le', but
+        # does accept 'ppc64le').
+        if self.spec.satisfies('target=ppc64le:'):
+            config_arch = 'ppc64le'
+        elif self.spec.satisfies('target=aarch64:'):
+            config_arch = 'aarch64'
         else:
-            # Then search in all sub directories.
-            # We would like to use AC_CONFIG_AUX_DIR, but not all packages
-            # ship with their configure.in or configure.ac.
-            d = '.'
-            dirs = [os.path.join(d, o) for o in os.listdir(d)
-                    if os.path.isdir(os.path.join(d, o))]
-            for dirname in dirs:
-                path = os.path.join(dirname, 'config.guess')
+            config_arch = 'local'
+
+        my_config_files = {'guess': None, 'sub': None}
+        config_files = {'guess': None, 'sub': None}
+        config_args = {'guess': [], 'sub': [config_arch]}
+
+        for config_name in config_files.keys():
+            config_file = 'config.{0}'.format(config_name)
+            if os.path.exists(config_file):
+                # First search the top-level source directory
+                my_config_files[config_name] = config_file
+            else:
+                # Then search in all sub directories recursively.
+                # We would like to use AC_CONFIG_AUX_DIR, but not all packages
+                # ship with their configure.in or configure.ac.
+                config_path = next((os.path.join(r, f)
+                                    for r, ds, fs in os.walk('.') for f in fs
+                                    if f == config_file), None)
+                my_config_files[config_name] = config_path
+
+            if my_config_files[config_name] is not None:
+                try:
+                    config_path = my_config_files[config_name]
+                    check_call([config_path] + config_args[config_name],
+                               stdout=PIPE, stderr=PIPE)
+                    # The package's config file already runs OK, so just use it
+                    continue
+                except Exception as e:
+                    tty.debug(e)
+            else:
+                continue
+
+            # Look for a spack-installed automake package
+            if 'automake' in self.spec:
+                automake_dir = 'automake-' + str(self.spec['automake'].version)
+                automake_path = os.path.join(self.spec['automake'].prefix,
+                                             'share', automake_dir)
+                path = os.path.join(automake_path, config_file)
                 if os.path.exists(path):
-                    my_config_guess = path
+                    config_files[config_name] = path
+            # Look for the system's config.guess
+            if (config_files[config_name] is None and
+                    os.path.exists('/usr/share')):
+                automake_dir = [s for s in os.listdir('/usr/share') if
+                                "automake" in s]
+                if automake_dir:
+                    automake_path = os.path.join('/usr/share', automake_dir[0])
+                    path = os.path.join(automake_path, config_file)
+                    if os.path.exists(path):
+                        config_files[config_name] = path
+            if config_files[config_name] is not None:
+                try:
+                    config_path = config_files[config_name]
+                    my_config_path = my_config_files[config_name]
 
-        if my_config_guess is not None:
-            try:
-                check_call([my_config_guess], stdout=PIPE, stderr=PIPE)
-                # The package's config.guess already runs OK, so just use it
-                return
-            except Exception as e:
-                tty.debug(e)
-        else:
-            return
+                    check_call([config_path] + config_args[config_name],
+                               stdout=PIPE, stderr=PIPE)
 
-        # Look for a spack-installed automake package
-        if 'automake' in self.spec:
-            automake_path = os.path.join(self.spec['automake'].prefix, 'share',
-                                         'automake-' +
-                                         str(self.spec['automake'].version))
-            path = os.path.join(automake_path, 'config.guess')
-            if os.path.exists(path):
-                config_guess = path
-        # Look for the system's config.guess
-        if config_guess is None and os.path.exists('/usr/share'):
-            automake_dir = [s for s in os.listdir('/usr/share') if
-                            "automake" in s]
-            if automake_dir:
-                automake_path = os.path.join('/usr/share', automake_dir[0])
-                path = os.path.join(automake_path, 'config.guess')
-                if os.path.exists(path):
-                    config_guess = path
-        if config_guess is not None:
-            try:
-                check_call([config_guess], stdout=PIPE, stderr=PIPE)
-                mod = os.stat(my_config_guess).st_mode & 0o777 | stat.S_IWUSR
-                os.chmod(my_config_guess, mod)
-                shutil.copyfile(config_guess, my_config_guess)
-                return
-            except Exception as e:
-                tty.debug(e)
+                    m = os.stat(my_config_path).st_mode & 0o777 | stat.S_IWUSR
+                    os.chmod(my_config_path, m)
+                    shutil.copyfile(config_path, my_config_path)
+                    continue
+                except Exception as e:
+                    tty.debug(e)
 
-        raise RuntimeError('Failed to find suitable config.guess')
+            raise RuntimeError('Failed to find suitable ' + config_file)
 
     @run_before('configure')
     def _set_autotools_environment_variables(self):
diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py
index c6c9824a63a..59a535fb745 100644
--- a/var/spack/repos/builtin/packages/swig/package.py
+++ b/var/spack/repos/builtin/packages/swig/package.py
@@ -43,6 +43,9 @@ class Swig(AutotoolsPackage, SourceforgePackage):
         depends_on('autoconf', type='build', when=_version)
         depends_on('automake', type='build', when=_version)
         depends_on('libtool', type='build', when=_version)
+    # Need newer 'automake' to support newer platforms
+    for _target in ['ppc64le', 'aarch64']:
+        depends_on('automake@1.15:', type='build', when='target={0}:'.format(_target))
     depends_on('pkgconfig', type='build')
 
     build_directory = 'spack-build'

From 224dc951597253f426f16132eab43701a9f1c53e Mon Sep 17 00:00:00 2001
From: Omar Padron <omar.padron@kitware.com>
Date: Mon, 22 Jun 2020 13:19:47 -0400
Subject: [PATCH 787/802] Pre ci optimization (#16372)

* add initial optimization script

* integrate optimization in spack ci

* make optimization opt-in

* fix import error

* flake8 fixes

* update command completion

* work around vermin errors

* fix sphynx errors
---
 lib/spack/spack/ci.py              |   8 +-
 lib/spack/spack/ci_optimization.py | 377 +++++++++++++++++++++++++++++
 lib/spack/spack/cmd/ci.py          |   9 +-
 share/spack/spack-completion.bash  |   2 +-
 4 files changed, 393 insertions(+), 3 deletions(-)
 create mode 100644 lib/spack/spack/ci_optimization.py

diff --git a/lib/spack/spack/ci.py b/lib/spack/spack/ci.py
index 9ba7f39e455..ce74abf29cc 100644
--- a/lib/spack/spack/ci.py
+++ b/lib/spack/spack/ci.py
@@ -449,7 +449,8 @@ def format_job_needs(phase_name, strip_compilers, dep_jobs,
 
 
 def generate_gitlab_ci_yaml(env, print_summary, output_file,
-                            custom_spack_repo=None, custom_spack_ref=None):
+                            custom_spack_repo=None, custom_spack_ref=None,
+                            run_optimizer=False):
     # FIXME: What's the difference between one that opens with 'spack'
     # and one that opens with 'env'?  This will only handle the former.
     with spack.concretize.disable_compiler_existence_check():
@@ -788,6 +789,11 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
     for output_key, output_value in sorted(output_object.items()):
         sorted_output[output_key] = output_value
 
+    # TODO(opadron): remove this or refactor
+    if run_optimizer:
+        import spack.ci_optimization as ci_opt
+        sorted_output = ci_opt.optimizer(sorted_output)
+
     with open(output_file, 'w') as outf:
         outf.write(syaml.dump_config(sorted_output, default_flow_style=True))
 
diff --git a/lib/spack/spack/ci_optimization.py b/lib/spack/spack/ci_optimization.py
new file mode 100644
index 00000000000..693802d06d5
--- /dev/null
+++ b/lib/spack/spack/ci_optimization.py
@@ -0,0 +1,377 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import collections
+
+try:
+    # dynamically import to keep vermin from complaining
+    collections_abc = __import__('collections.abc')
+except ImportError:
+    collections_abc = collections
+
+import copy
+import hashlib
+
+import spack.util.spack_yaml as syaml
+
+
+def matches(obj, proto):
+    """Returns True if the test object "obj" matches the prototype object
+    "proto".
+
+    If obj and proto are mappings, obj matches proto if (key in obj) and
+    (obj[key] matches proto[key]) for every key in proto.
+
+    If obj and proto are sequences, obj matches proto if they are of the same
+    length and (a matches b) for every (a,b) in zip(obj, proto).
+
+    Otherwise, obj matches proto if obj == proto.
+
+    Precondition: proto must not have any reference cycles
+    """
+    if isinstance(obj, collections_abc.Mapping):
+        if not isinstance(proto, collections_abc.Mapping):
+            return False
+
+        return all(
+            (key in obj and matches(obj[key], val))
+            for key, val in proto.items()
+        )
+
+    if (isinstance(obj, collections_abc.Sequence) and
+            not isinstance(obj, str)):
+
+        if not (isinstance(proto, collections_abc.Sequence) and
+                not isinstance(proto, str)):
+            return False
+
+        if len(obj) != len(proto):
+            return False
+
+        return all(
+            matches(obj[index], val)
+            for index, val in enumerate(proto)
+        )
+
+    return obj == proto
+
+
+def subkeys(obj, proto):
+    """Returns the test mapping "obj" after factoring out the items it has in
+    common with the prototype mapping "proto".
+
+    Consider a recursive merge operation, merge(a, b) on mappings a and b, that
+    returns a mapping, m, whose keys are the union of the keys of a and b, and
+    for every such key, "k", its corresponding value is:
+
+      - merge(a[key], b[key])  if a[key] and b[key] are mappings, or
+      - b[key]                 if (key in b) and not matches(a[key], b[key]),
+                               or
+      - a[key]                 otherwise
+
+
+    If obj and proto are mappings, the returned object is the smallest object,
+    "a", such that merge(a, proto) matches obj.
+
+    Otherwise, obj is returned.
+    """
+    if not (isinstance(obj, collections_abc.Mapping) and
+            isinstance(proto, collections_abc.Mapping)):
+        return obj
+
+    new_obj = {}
+    for key, value in obj.items():
+        if key not in proto:
+            new_obj[key] = value
+            continue
+
+        if (matches(value, proto[key]) and
+            matches(proto[key], value)):
+            continue
+
+        if isinstance(value, collections_abc.Mapping):
+            new_obj[key] = subkeys(value, proto[key])
+            continue
+
+        new_obj[key] = value
+
+    return new_obj
+
+
+def add_extends(yaml, key):
+    """Modifies the given object "yaml" so that it includes an "extends" key
+    whose value features "key".
+
+    If "extends" is not in yaml, then yaml is modified such that
+    yaml["extends"] == key.
+
+    If yaml["extends"] is a str, then yaml is modified such that
+    yaml["extends"] == [yaml["extends"], key]
+
+    If yaml["extends"] is a list that does not include key, then key is
+    appended to the list.
+
+    Otherwise, yaml is left unchanged.
+    """
+
+    has_key = ('extends' in yaml)
+    extends = yaml.get('extends')
+
+    if has_key and not isinstance(extends, (str, collections_abc.Sequence)):
+        return
+
+    if extends is None:
+        yaml['extends'] = key
+        return
+
+    if isinstance(extends, str):
+        if extends != key:
+            yaml['extends'] = [extends, key]
+        return
+
+    if key not in extends:
+        extends.append(key)
+
+
+def common_subobject(yaml, sub):
+    """Factor prototype object "sub" out of the values of mapping "yaml".
+
+    Consider a modified copy of yaml, "new", where for each key, "key" in yaml:
+
+      - If yaml[key] matches sub, then new[key] = subkeys(yaml[key], sub).
+      - Otherwise, new[key] = yaml[key].
+
+    If the above match criteria is not satisfied for any such key, then (yaml,
+    None) is returned. The yaml object is returned unchanged.
+
+    Otherwise, each matching value in new is modified as in
+    add_extends(new[key], common_key), and then new[common_key] is set to sub.
+    The common_key value is chosen such that it does not match any preexisting
+    key in new. In this case, (new, common_key) is returned.
+    """
+    match_list = set(k for k, v in yaml.items() if matches(v, sub))
+
+    if not match_list:
+        return yaml, None
+
+    common_prefix = '.c'
+    common_index = 0
+
+    while True:
+        common_key = ''.join((common_prefix, str(common_index)))
+        if common_key not in yaml:
+            break
+        common_index += 1
+
+    new_yaml = {}
+
+    for key, val in yaml.items():
+        new_yaml[key] = copy.deepcopy(val)
+
+        if not matches(val, sub):
+            continue
+
+        new_yaml[key] = subkeys(new_yaml[key], sub)
+        add_extends(new_yaml[key], common_key)
+
+    new_yaml[common_key] = sub
+
+    return new_yaml, common_key
+
+
+def print_delta(name, old, new, applied=None):
+    delta = new - old
+    reldelta = (1000 * delta) // old
+    reldelta = (reldelta // 10, reldelta % 10)
+
+    if applied is None:
+        applied = (new <= old)
+
+    print('\n'.join((
+        '{} {}:',
+        '  before: {: 10d}',
+        '  after : {: 10d}',
+        '  delta : {:+10d} ({:=+3d}.{}%)',
+    )).format(
+        name,
+        ('+' if applied else 'x'),
+        old,
+        new,
+        delta,
+        reldelta[0],
+        reldelta[1]
+    ))
+
+
+def try_optimization_pass(name, yaml, optimization_pass, *args, **kwargs):
+    """Try applying an optimization pass and return information about the
+    result
+
+    "name" is a string describing the nature of the pass. If it is a non-empty
+    string, summary statistics are also printed to stdout.
+
+    "yaml" is the object to apply the pass to.
+
+    "optimization_pass" is the function implementing the pass to be applied.
+
+    "args" and "kwargs" are the additional arguments to pass to optimization
+    pass. The pass is applied as
+
+    >>> (new_yaml, *other_results) = optimization_pass(yaml, *args, **kwargs)
+
+    The pass's results are greedily rejected if it does not modify the original
+    yaml document, or if it produces a yaml document that serializes to a
+    larger string.
+
+    Returns (new_yaml, yaml, applied, other_results) if applied, or
+    (yaml, new_yaml, applied, other_results) otherwise.
+    """
+    result = optimization_pass(yaml, *args, **kwargs)
+    new_yaml, other_results = result[0], result[1:]
+
+    if new_yaml is yaml:
+        # pass was not applied
+        return (yaml, new_yaml, False, other_results)
+
+    pre_size = len(syaml.dump_config(yaml, default_flow_style=True))
+    post_size = len(syaml.dump_config(new_yaml, default_flow_style=True))
+
+    # pass makes the size worse: not applying
+    applied = (post_size <= pre_size)
+    if applied:
+        yaml, new_yaml = new_yaml, yaml
+
+    if name:
+        print_delta(name, pre_size, post_size, applied)
+
+    return (yaml, new_yaml, applied, other_results)
+
+
+def build_histogram(iterator, key):
+    """Builds a histogram of values given an iterable of mappings and a key.
+
+    For each mapping "m" with key "key" in iterator, the value m[key] is
+    considered.
+
+    Returns a list of tuples (hash, count, proportion, value), where
+
+      - "hash" is a sha1sum hash of the value.
+      - "count" is the number of occurences of values that hash to "hash".
+      - "proportion" is the proportion of all values considered above that
+        hash to "hash".
+      - "value" is one of the values considered above that hash to "hash".
+        Which value is chosen when multiple values hash to the same "hash" is
+        undefined.
+
+    The list is sorted in descending order by count, yielding the most
+    frequently occuring hashes first.
+    """
+    buckets = collections.defaultdict(int)
+    values = {}
+
+    num_objects = 0
+    for obj in iterator:
+        num_objects += 1
+
+        try:
+            val = obj[key]
+        except (KeyError, TypeError):
+            continue
+
+        value_hash = hashlib.sha1()
+        value_hash.update(syaml.dump_config(val).encode())
+        value_hash = value_hash.hexdigest()
+
+        buckets[value_hash] += 1
+        values[value_hash] = val
+
+    return [(h, buckets[h], float(buckets[h]) / num_objects, values[h])
+            for h in sorted(buckets.keys(), key=lambda k: -buckets[k])]
+
+
+def optimizer(yaml):
+    original_size = len(syaml.dump_config(yaml, default_flow_style=True))
+
+    # try factoring out commonly repeated portions
+    common_job = {
+        'variables': {
+            'SPACK_COMPILER_ACTION': 'NONE',
+            'SPACK_RELATED_BUILDS_CDASH': ''
+        },
+
+        'after_script': ['rm -rf "./spack"'],
+
+        'artifacts': {
+            'paths': ['jobs_scratch_dir', 'cdash_report'],
+            'when': 'always'
+        },
+    }
+
+    # look for a list of tags that appear frequently
+    _, count, proportion, tags = next(iter(
+        build_histogram(yaml.values(), 'tags')),
+        (None,) * 4)
+
+    # If a list of tags is found, and there are more than one job that uses it,
+    # *and* the jobs that do use it represent at least 70% of all jobs, then
+    # add the list to the prototype object.
+    if tags and count > 1 and proportion >= 0.70:
+        common_job['tags'] = tags
+
+    # apply common object factorization
+    yaml, other, applied, rest = try_optimization_pass(
+        'general common object factorization',
+        yaml, common_subobject, common_job)
+
+    # look for a common script, and try factoring that out
+    _, count, proportion, script = next(iter(
+        build_histogram(yaml.values(), 'script')),
+        (None,) * 4)
+
+    if script and count > 1 and proportion >= 0.70:
+        yaml, other, applied, rest = try_optimization_pass(
+            'script factorization',
+            yaml, common_subobject, {'script': script})
+
+    # look for a common before_script, and try factoring that out
+    _, count, proportion, script = next(iter(
+        build_histogram(yaml.values(), 'before_script')),
+        (None,) * 4)
+
+    if script and count > 1 and proportion >= 0.70:
+        yaml, other, applied, rest = try_optimization_pass(
+            'before_script factorization',
+            yaml, common_subobject, {'before_script': script})
+
+    # Look specifically for the SPACK_ROOT_SPEC environment variables.
+    # Try to factor them out.
+    h = build_histogram((
+        getattr(val, 'get', lambda *args: {})('variables')
+        for val in yaml.values()), 'SPACK_ROOT_SPEC')
+
+    # In this case, we try to factor out *all* instances of the SPACK_ROOT_SPEC
+    # environment variable; not just the one that appears with the greatest
+    # frequency. We only require that more than 1 job uses a given instance's
+    # value, because we expect the value to be very large, and so expect even
+    # few-to-one factorizations to yield large space savings.
+    counter = 0
+    for _, count, proportion, spec in h:
+        if count <= 1:
+            continue
+
+        counter += 1
+
+        yaml, other, applied, rest = try_optimization_pass(
+            'SPACK_ROOT_SPEC factorization ({count})'.format(count=counter),
+            yaml,
+            common_subobject,
+            {'variables': {'SPACK_ROOT_SPEC': spec}})
+
+    new_size = len(syaml.dump_config(yaml, default_flow_style=True))
+
+    print('\n')
+    print_delta('overall summary', original_size, new_size)
+    print('\n')
+    return yaml
diff --git a/lib/spack/spack/cmd/ci.py b/lib/spack/spack/cmd/ci.py
index 35891edb131..3e57c6656af 100644
--- a/lib/spack/spack/cmd/ci.py
+++ b/lib/spack/spack/cmd/ci.py
@@ -54,6 +54,11 @@ def setup_parser(subparser):
         help="Provide a git branch or tag if a custom spack branch " +
              "should be checked out as a step in each generated job.  " +
              "This argument is ignored if no --spack-repo is provided.")
+    generate.add_argument(
+        '--optimize', action='store_true',
+        help="(Experimental) run the generated document through a series of "
+             "optimization passes designed to reduce the size of the "
+             "generated file.")
     generate.set_defaults(func=ci_generate)
 
     # Check a spec against mirror. Rebuild, create buildcache and push to
@@ -75,6 +80,7 @@ def ci_generate(args):
     copy_yaml_to = args.copy_to
     spack_repo = args.spack_repo
     spack_ref = args.spack_ref
+    run_optimizer = args.optimize
 
     if not output_file:
         gen_ci_dir = os.getcwd()
@@ -86,7 +92,8 @@ def ci_generate(args):
 
     # Generate the jobs
     spack_ci.generate_gitlab_ci_yaml(
-        env, True, output_file, spack_repo, spack_ref)
+        env, True, output_file, spack_repo, spack_ref,
+        run_optimizer=run_optimizer)
 
     if copy_yaml_to:
         copy_to_dir = os.path.dirname(copy_yaml_to)
diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash
index 0a74d144883..ed42ad4eddb 100755
--- a/share/spack/spack-completion.bash
+++ b/share/spack/spack-completion.bash
@@ -474,7 +474,7 @@ _spack_ci() {
 }
 
 _spack_ci_generate() {
-    SPACK_COMPREPLY="-h --help --output-file --copy-to --spack-repo --spack-ref"
+    SPACK_COMPREPLY="-h --help --output-file --copy-to --spack-repo --spack-ref --optimize"
 }
 
 _spack_ci_rebuild() {

From 985c5c7792d9e1f582974490e61f947b43a43b75 Mon Sep 17 00:00:00 2001
From: Jen Herting <jen@herting.cc>
Date: Mon, 22 Jun 2020 14:15:46 -0400
Subject: [PATCH 788/802] [py-macs2] new version and dependency (#16817)

* [py-macs2] Combined commit

- Added version 2.1.3.3
- added dependency py-cython

Author: Jen Herting <jen@herting.cc>
Date:   Tue May 26 16:41:28 2020 -0400

[py-macs2] added sha256=

Author: Andrew Elble <aweits@rit.edu>
Date:   Tue Oct 29 10:34:33 2019 -0400

migrated repos

* [py-macs2] fixed copyright

* [py-macs2] py-cython is build dependency
---
 var/spack/repos/builtin/packages/py-macs2/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-macs2/package.py b/var/spack/repos/builtin/packages/py-macs2/package.py
index c20463b6e94..b9703842b58 100644
--- a/var/spack/repos/builtin/packages/py-macs2/package.py
+++ b/var/spack/repos/builtin/packages/py-macs2/package.py
@@ -15,10 +15,12 @@ class PyMacs2(PythonPackage):
 
     version('2.2.4',          sha256='b131aadc8f5fd94bec35308b821e1f7585def788d2e7c756fc8cac402ffee25b')
     version('2.1.4',          sha256='e4966d001914320829ab859c7bc8e92c6410aa7bdbddfd00b7625e9a0fb15c97')
+    version('2.1.3.3',        sha256='00959e523f45ed92b8429f55944eca6984623ac008d7cdb488c3ffe59c21984a')
     version('2.1.1.20160309', sha256='2008ba838f83f34f8e0fddefe2a3a0159f4a740707c68058f815b31ddad53d26')
 
     depends_on('python@3.5:',    when='@2.2:', type=('build', 'run'))
     depends_on('python@2.7:2.8', when='@:2.1', type=('build', 'run'))
+    depends_on('py-cython', type='build')
 
     # Most Python packages only require py-setuptools as a build dependency.
     # However, py-macs2 requires py-setuptools during runtime as well.

From 735416dbf490252d53f5503cb44dd6a9e028034e Mon Sep 17 00:00:00 2001
From: vvolkl <valentin.volkl@cern.ch>
Date: Mon, 22 Jun 2020 20:16:06 +0200
Subject: [PATCH 789/802] HEP generator update: evtgen, tauola, photos,
 pythia8, lhapdf, whizard (#16880)

* add package evtgen

fix formatting

add evtgen dependencies and update pythia8

fix formatting

* [evtgen] update versions

* [pythia8] add 'without-PACKAGE' args

* fix formatting

* Add LHAPDF

Co-authored-by: iarspider

* Add package whizard

fix formatting

* [pyhtia8, evtgen] add conflict msg re: circular dependencies

* [pyhtia8, evtgen] fix conflicts

* [pyhtia8, evtgen] fix msg string

* Set pythia8 default to ~evtgen
---
 .../repos/builtin/packages/evtgen/g2c.patch   | 22 +++++
 .../repos/builtin/packages/evtgen/package.py  | 55 +++++++++++++
 .../repos/builtin/packages/lhapdf/package.py  | 35 ++++++++
 .../repos/builtin/packages/photos/package.py  | 27 +++++++
 .../repos/builtin/packages/pythia8/package.py | 33 ++++++++
 .../repos/builtin/packages/tauola/package.py  | 26 ++++++
 .../repos/builtin/packages/whizard/package.py | 81 +++++++++++++++++++
 7 files changed, 279 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/evtgen/g2c.patch
 create mode 100644 var/spack/repos/builtin/packages/evtgen/package.py
 create mode 100644 var/spack/repos/builtin/packages/lhapdf/package.py
 create mode 100644 var/spack/repos/builtin/packages/photos/package.py
 create mode 100644 var/spack/repos/builtin/packages/tauola/package.py
 create mode 100644 var/spack/repos/builtin/packages/whizard/package.py

diff --git a/var/spack/repos/builtin/packages/evtgen/g2c.patch b/var/spack/repos/builtin/packages/evtgen/g2c.patch
new file mode 100644
index 00000000000..0cce1d54014
--- /dev/null
+++ b/var/spack/repos/builtin/packages/evtgen/g2c.patch
@@ -0,0 +1,22 @@
+diff --git a/configure b/configure
+index 375e3b7..e47deac 100755
+--- a/configure
++++ b/configure
+@@ -196,7 +196,7 @@ echo "Platform is $ARCH"
+ FFLAGS="${FFLAGS_OPT}"
+ CFLAGS="${CFLAGS_OPT}"
+ CXXFLAGS="${CXXFLAGS_OPT}"
+-FLIBS="-lfrtbegin -lg2c"
++#FLIBS="-lfrtbegin -lg2c"
+ SOFLAGS="-soname"
+ 
+ if [ ${COMPMODE} = OPT ]; then
+@@ -213,7 +213,7 @@ if [ $ARCH = Linux ]; then
+   FFLAGS="${FFLAGS_OPT} -Wno-globals"
+   CFLAGS="${CFLAGS_OPT}"
+   CXXFLAGS="${CXXFLAGS_OPT}"
+-  FLIBS="-lfrtbegin -lg2c"
++  #FLIBS="-lfrtbegin -lg2c"
+   if [ ${COMPMODE} = OPT ]; then
+     FFLAGS="${FFLAGS_OPT}"
+     CFLAGS="${CFLAGS_OPT}"
diff --git a/var/spack/repos/builtin/packages/evtgen/package.py b/var/spack/repos/builtin/packages/evtgen/package.py
new file mode 100644
index 00000000000..514fe026265
--- /dev/null
+++ b/var/spack/repos/builtin/packages/evtgen/package.py
@@ -0,0 +1,55 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Evtgen(AutotoolsPackage):
+    """ EvtGen is a Monte Carlo event generator that simulates
+        the decays of heavy flavour particles, primarily B and D mesons. """
+
+    homepage = "https://evtgen.hepforge.org/"
+    url      = "http://lcgpackages.web.cern.ch/lcgpackages/tarFiles/sources/MCGeneratorsTarFiles/evtgen-R01-07-00.tar.gz"
+
+    maintainers = ['vvolkl']
+
+    version('02-00-00', sha256='02372308e1261b8369d10538a3aa65fe60728ab343fcb64b224dac7313deb719')
+    version('01-07-00', sha256='2648f1e2be5f11568d589d2079f22f589c283a2960390bbdb8d9d7f71bc9c014', preferred=True)
+
+    variant('pythia8', default=True, description='Build with pythia8')
+    variant('tauola', default=False, description='Build with tauola')
+    variant('photos', default=False, description='Build with photos')
+
+    patch("g2c.patch")
+
+    depends_on('hepmc@:2.99.99')
+    depends_on("pythia8", when="+pythia8")
+    depends_on("tauola", when="+tauola")
+    depends_on("photos", when="+photos")
+
+    conflicts("^pythia8+evtgen", when="+pythia8",
+              msg="Building pythia with evtgen bindings and "
+              "evtgen with pythia bindings results in a circular dependency "
+              "that cannot be resolved at the moment! "
+              "Use evtgen+pythia8^pythia8~evtgen.")
+
+    def configure_args(self):
+        args = []
+
+        args.append('--hepmcdir=%s' % self.spec["hepmc"].prefix)
+        if '+pythia8' in self.spec:
+            args.append('--pythiadir=%s' % self.spec['pythia8'].prefix)
+        if '+photos' in self.spec:
+            args.append('--photosdir=%s' % self.spec['photos'].prefix)
+        if '+tauola' in self.spec:
+            args.append('--tauoladir=%s' % self.spec['tauola'].prefix)
+
+        return args
+
+    def build(self, spec, prefix):
+        # avoid parallel compilation errors
+        # due to libext_shared depending on lib_shared
+        make('lib_shared')
+        make('all')
diff --git a/var/spack/repos/builtin/packages/lhapdf/package.py b/var/spack/repos/builtin/packages/lhapdf/package.py
new file mode 100644
index 00000000000..10a69aba755
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lhapdf/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Lhapdf(AutotoolsPackage):
+    """LHAPDF is a general purpose C++ interpolator,
+       used for evaluating PDFs from discretised data files. """
+
+    homepage = "https://lhapdf.hepforge.org/"
+    url      = "https://lhapdf.hepforge.org/downloads/?f=LHAPDF-6.2.3.tar.gz"
+
+    version('6.2.3', sha256='d6e63addc56c57b6286dc43ffc56d901516f4779a93a0f1547e14b32cfd82dd1')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+
+    depends_on('python',        type=('build', 'run'))
+    depends_on('py-cython',     type='build')
+    depends_on('py-setuptools', type='build')
+    depends_on('boost',         type='build')
+    depends_on('yaml-cpp',      type='build', when='@:6.1.5')
+
+    def configure_args(self):
+        args = ['--with-boost=' + self.spec['boost'].prefix,
+                'FCFLAGS=-O3', 'CFLAGS=-O3', 'CXXFLAGS=-O3']
+
+        if self.spec.satisfies('@:6.1.5'):
+            args.append('--with-yaml-cpp=' + self.spec['yaml-cpp'].prefix)
+        return args
diff --git a/var/spack/repos/builtin/packages/photos/package.py b/var/spack/repos/builtin/packages/photos/package.py
new file mode 100644
index 00000000000..6304e194aad
--- /dev/null
+++ b/var/spack/repos/builtin/packages/photos/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Photos(AutotoolsPackage):
+    """ Photos is a Monte Carlo program for bremsstrahlung in the decay
+         of particles and resonances."""
+
+    homepage = "http://photospp.web.cern.ch/photospp/"
+    url      = "http://photospp.web.cern.ch/photospp/resources/PHOTOS.3.61/PHOTOS.3.61-LHC.tar.gz"
+
+    version('3.61', sha256='acd3bcb769ba2a3e263de399e9b89fd6296405c9cbc5045b83baba3e60db4b26')
+
+    maintainers = ['vvolkl']
+
+    depends_on('hepmc@:2.99.99')
+
+    def configure_args(self):
+        args = []
+
+        args.append('--with-hepmc=%s' % self.spec["hepmc"].prefix)
+        args.append('--without-hepmc3')
+        return args
diff --git a/var/spack/repos/builtin/packages/pythia8/package.py b/var/spack/repos/builtin/packages/pythia8/package.py
index 8f2ec41b545..572d65922be 100644
--- a/var/spack/repos/builtin/packages/pythia8/package.py
+++ b/var/spack/repos/builtin/packages/pythia8/package.py
@@ -23,13 +23,46 @@ class Pythia8(AutotoolsPackage):
     version('8212', sha256='f8fb4341c7e8a8be3347eb26b00329a388ccf925313cfbdba655a08d7fd5a70e')
 
     variant('shared', default=True, description='Build shared library')
+    variant('hepmc', default=True, description='Build HepMC2 extensions')
+    variant('evtgen', default=False, description='Build EvtGen extensions')
+    variant('root', default=False, description='Build ROOT extensions')
+    variant('fastjet', default=False, description='Build fastjet extensions')
 
     depends_on('rsync', type='build')
+    depends_on('hepmc@:2.99.99', when="+hepmc")
+    depends_on('root', when="+root")
+    depends_on('evtgen', when="+evtgen")
+    depends_on("fastjet@3.0.0:", when="+fastjet")
+
+    conflicts("^evtgen+pythia8", when="+evtgen",
+              msg="Building pythia with evtgen bindings and "
+              "evtgen with pythia bindings results in a circular dependency "
+              "that cannot be resolved at the moment! "
+              "Use pythia8+evtgen^evtgen~pythia8")
 
     def configure_args(self):
         args = []
 
         if '+shared' in self.spec:
             args.append('--enable-shared')
+        if '+hepmc' in self.spec:
+            args.append('--with-hepmc=%s' % self.spec["hepmc"].prefix)
+        else:
+            args.append('--without-hepmc')
+        if '+fastjet' in self.spec:
+            args.append('--with-fastjet3=%s' % self.spec["fastjet"].prefix)
+        else:
+            args.append('--without-fastjet')
+        if '+evtgen' in self.spec:
+            args.append('--with-evtgen=%s' % self.spec["evtgen"].prefix)
+        else:
+            args.append('--without-evtgen')
+        if '+root' in self.spec:
+            args.append('--with-root=%s' % self.spec["root"].prefix)
+        else:
+            args.append('--without-evtgen')
 
         return args
+
+    def setup_dependent_run_environment(self, env, dependent_spec):
+        env.set('PYTHIA8DATA', self.prefix.share.Pythia8.xmldoc)
diff --git a/var/spack/repos/builtin/packages/tauola/package.py b/var/spack/repos/builtin/packages/tauola/package.py
new file mode 100644
index 00000000000..e850ce4dcc6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tauola/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Tauola(AutotoolsPackage):
+    """ Tauola is a event generator for tau decays."""
+
+    homepage = "https://tauolapp.web.cern.ch/tauolapp/"
+    url      = "https://tauolapp.web.cern.ch/tauolapp/resources/TAUOLA.1.1.8/TAUOLA.1.1.8-LHC.tar.gz"
+
+    version('1.1.8', sha256='3f734e8a967682869cca2c1ffebd3e055562613c40853cc81820d8b666805ed5')
+
+    maintainers = ['vvolkl']
+
+    depends_on('hepmc@:2.99.99')
+
+    def configure_args(self):
+        args = []
+
+        args.append('--with-hepmc=%s' % self.spec["hepmc"].prefix)
+        args.append('--without-hepmc3')
+        return args
diff --git a/var/spack/repos/builtin/packages/whizard/package.py b/var/spack/repos/builtin/packages/whizard/package.py
new file mode 100644
index 00000000000..b6d4ea0921a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/whizard/package.py
@@ -0,0 +1,81 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Whizard(AutotoolsPackage):
+    """WHIZARD is a program system designed for the efficient calculation
+      of multi-particle scattering cross sections
+      and simulated event samples."""
+
+    homepage = "whizard.hepforge.org"
+    url      = "https://whizard.hepforge.org/downloads/?f=whizard-2.8.2.tar.gz"
+
+    maintainers = ['vvolkl']
+
+    version('3.0.0_alpha', sha256='4636e5a10350bb67ccc98cd105bc891ea04f3393c2420f81be3d21240be20009')
+    version('2.8.2', sha256='32c9be342d01b3fc6f947fddce74bf2d81ece37fb39bca1f37778fb0c07e2568', prefered=True)
+    version('2.8.1', sha256='0c759ce0598e25f38e04659f745c5963d238c4b5c12209f16449b6c0bc6dc64e')
+    version('2.8.0', sha256='3b5175eafa879d1baca20237d18fb2b18bee89631e73ada499de9c082d009696')
+
+    variant('hepmc', default=True,
+            description="builds with hepmc")
+
+    variant('pythia8', default=True,
+            description="builds with pythia8")
+
+    variant('fastjet', default=False,
+            description="builds with fastjet")
+
+    variant('lcio', default=False,
+            description="builds with lcio")
+
+    variant('lhapdf', default=False,
+            description="builds with fastjet")
+
+    variant('openmp', default=False,
+            description="builds with openmp")
+
+    variant('latex', default=False,
+            description="data visualization with latex")
+
+    depends_on('ocaml', type='build', when="@3:")
+    depends_on('ocaml@:4.8.2', type='build', when="@:2.99.99")
+    depends_on('hepmc', when="+hepmc")
+    depends_on('pythia8', when="+pythia8")
+    depends_on('lhapdf', when="+lhapdf")
+    depends_on('fastjet', when="+fastjet")
+    depends_on('texlive', when="+latex")
+
+    def configure_args(self):
+        spec = self.spec
+        args = [
+            '--enable-hepmc=%s' % ("yes" if "+hepmc" in spec else "no"),
+            '--enable-fastjet=%s' % ("yes" if "+fastjet" in spec else "no"),
+            '--enable-pythia8=%s' % ("yes" if "+pythia8" in spec else "no"),
+            '--enable-lcio=%s' % ("yes" if "+lcio" in spec else "no"),
+            '--enable-lhapdf=%s' % ("yes" if "+lhapdf" in spec else "no"),
+            # todo: openloops
+            # todo: hoppet
+            # todo: recola
+            # todo: looptools
+            # todo: gosam
+            # todo: pythia6
+        ]
+        if "+openmp" not in spec:
+            args.append('--disable-openmp')
+
+        return args
+
+    def url_for_version(self, version):
+        major = str(version[0])
+        minor = str(version[1])
+        patch = str(version[2])
+        if len(version) == 4:
+            url = "https://whizard.hepforge.org/downloads/?f=whizard-%s.%s.%s_%s.tar.gz" % (major, minor, patch, version[3])
+        else:
+            url = "https://whizard.hepforge.org/downloads/?f=whizard-%s.%s.%s.tar.gz" % (major, minor, patch)
+        return url

From 55f26b0ccb6f53d2a554730c343c6d24a340cc29 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Tue, 23 Jun 2020 08:30:45 +0200
Subject: [PATCH 790/802] lua: fix linking to ncurses (#17206)

PR #17108 broke the build. Spack's ncurses package does not provide a
libtermcap, so we need to use libtinfow.
---
 var/spack/repos/builtin/packages/lua/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py
index e00e499abcf..28554dae5b2 100644
--- a/var/spack/repos/builtin/packages/lua/package.py
+++ b/var/spack/repos/builtin/packages/lua/package.py
@@ -54,7 +54,7 @@ def install(self, spec, prefix):
              'MYLDFLAGS=-L%s -L%s' % (
                  spec['readline'].prefix.lib,
                  spec['ncurses'].prefix.lib),
-             'MYLIBS=-lncursesw -ltermcap',
+             'MYLIBS=-lncursesw -ltinfow',
              'CC=%s -std=gnu99 %s' % (spack_cc,
                                       self.compiler.cc_pic_flag),
              target)

From 1d10c6c73091c6130b3af696d4a9309497dcdd54 Mon Sep 17 00:00:00 2001
From: "Tomoki, Karatsu" <49965247+t-karatsu@users.noreply.github.com>
Date: Tue, 23 Jun 2020 15:54:54 +0900
Subject: [PATCH 791/802] caffe: use MPI compiler when using hdf5+mpi (#17125)

---
 var/spack/repos/builtin/packages/caffe/package.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/var/spack/repos/builtin/packages/caffe/package.py b/var/spack/repos/builtin/packages/caffe/package.py
index 7df83b1d537..187bdc5764e 100644
--- a/var/spack/repos/builtin/packages/caffe/package.py
+++ b/var/spack/repos/builtin/packages/caffe/package.py
@@ -81,4 +81,10 @@ def cmake_args(self):
             version = spec['python'].version.up_to(1)
             args.append('-Dpython_version=%s' % version)
 
+        if spec['hdf5'].satisfies('+mpi'):
+            args.extend([
+                '-DCMAKE_C_COMPILER={0}'.format(self.spec['mpi'].mpicc),
+                '-DCMAKE_CXX_COMPILER={0}'.format(self.spec['mpi'].mpicxx)
+            ])
+
         return args

From 36e603c7d6189c63caffc4e4b011f1491d543473 Mon Sep 17 00:00:00 2001
From: vvolkl <valentin.volkl@cern.ch>
Date: Tue, 23 Jun 2020 08:56:23 +0200
Subject: [PATCH 792/802] whizard: added zlib as a dependency (#17205)

---
 var/spack/repos/builtin/packages/whizard/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/whizard/package.py b/var/spack/repos/builtin/packages/whizard/package.py
index b6d4ea0921a..32271f2df44 100644
--- a/var/spack/repos/builtin/packages/whizard/package.py
+++ b/var/spack/repos/builtin/packages/whizard/package.py
@@ -49,6 +49,7 @@ class Whizard(AutotoolsPackage):
     depends_on('lhapdf', when="+lhapdf")
     depends_on('fastjet', when="+fastjet")
     depends_on('texlive', when="+latex")
+    depends_on('zlib')
 
     def configure_args(self):
         spec = self.spec

From 0ffbd79bd007d7adfd97900bdd99ebc6cbdec6aa Mon Sep 17 00:00:00 2001
From: Wouter Deconinck <wdconinc@gmail.com>
Date: Tue, 23 Jun 2020 02:44:44 -0500
Subject: [PATCH 793/802] [hepmc3] gcc@9.3.0 patch for @3.1.2:3.2.1, conflicts
 for earlier @:3.1.1 (#17182)

See https://gitlab.cern.ch/hepmc/HepMC3/-/commit/ba38f14d8f56c16cc4105d98f6d4540c928c6150, which is included in master and released as of hepmc3@3.2.2
---
 .../ba38f14d8f56c16cc4105d98f6d4540c928c6150.patch   | 12 ++++++++++++
 var/spack/repos/builtin/packages/hepmc3/package.py   |  4 ++++
 2 files changed, 16 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/hepmc3/ba38f14d8f56c16cc4105d98f6d4540c928c6150.patch

diff --git a/var/spack/repos/builtin/packages/hepmc3/ba38f14d8f56c16cc4105d98f6d4540c928c6150.patch b/var/spack/repos/builtin/packages/hepmc3/ba38f14d8f56c16cc4105d98f6d4540c928c6150.patch
new file mode 100644
index 00000000000..b09058104fe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hepmc3/ba38f14d8f56c16cc4105d98f6d4540c928c6150.patch
@@ -0,0 +1,12 @@
+diff --git a/search/include/HepMC3/Feature.h b/search/include/HepMC3/Feature.h
+index 0bd4f92b059d315c4a17ab03d49ba5b20af75d8e..e7717516a99c5c3d2553be2aca21378fb1ae7977 100644
+--- a/search/include/HepMC3/Feature.h
++++ b/search/include/HepMC3/Feature.h
+@@ -293,7 +293,7 @@ public:
+         EvaluatorPtr functor = m_internal;
+         return [value, functor](ConstGenParticlePtr input)->bool{
+             Feature_type local = (*functor)(input);
+-            return fabs(local - value) <= ((fabs(local) < fabs(value))? fabs(value) : fabs(local)) * std::numeric_limits<Feature_type>::epsilon();
++            return std::less_equal<Feature_type>{}(fabs(local - value) ,  std::numeric_limits<Feature_type>::epsilon());
+         };
+     } 
diff --git a/var/spack/repos/builtin/packages/hepmc3/package.py b/var/spack/repos/builtin/packages/hepmc3/package.py
index 95cc4014570..361d3826f5c 100644
--- a/var/spack/repos/builtin/packages/hepmc3/package.py
+++ b/var/spack/repos/builtin/packages/hepmc3/package.py
@@ -16,6 +16,7 @@ class Hepmc3(CMakePackage):
 
     maintainers = ['vvolkl']
 
+    version('3.2.2', sha256='0e8cb4f78f804e38f7d29875db66f65e4c77896749d723548cc70fb7965e2d41')
     version('3.2.1', sha256='6e4e4bb5708af105d4bf74efc2745e6efe704e942d46a8042f7dcae37a4739fe')
     version('3.2.0', sha256='f132387763d170f25a7cc9f0bd586b83373c09acf0c3daa5504063ba460f89fc')
     version('3.1.2', sha256='4133074b3928252877982f3d4b4c6c750bb7a324eb6c7bb2afc6fa256da3ecc7')
@@ -32,6 +33,9 @@ class Hepmc3(CMakePackage):
     depends_on('root', when='+rootio')
     depends_on('python', when="+python")
 
+    conflicts('%gcc@9.3.0', when="@:3.1.1")
+    patch('ba38f14d8f56c16cc4105d98f6d4540c928c6150.patch', when="@3.1.2:3.2.1 %gcc@9.3.0")
+
     def cmake_args(self):
         spec = self.spec
         args = [

From f8e3e8289dca4f2ba73462ef245fb9486e8c3be8 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 23 Jun 2020 02:45:36 -0500
Subject: [PATCH 794/802] py-torchvision: added v0.6.1 (#17203)

---
 var/spack/repos/builtin/packages/py-torchvision/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-torchvision/package.py b/var/spack/repos/builtin/packages/py-torchvision/package.py
index 2105ec19880..4e40117c8d4 100644
--- a/var/spack/repos/builtin/packages/py-torchvision/package.py
+++ b/var/spack/repos/builtin/packages/py-torchvision/package.py
@@ -11,7 +11,7 @@ class PyTorchvision(PythonPackage):
     architectures, and common image transformations for computer vision."""
 
     homepage = "https://github.com/pytorch/vision"
-    url      = "https://github.com/pytorch/vision/archive/v0.6.0.tar.gz"
+    url      = "https://github.com/pytorch/vision/archive/v0.6.1.tar.gz"
 
     maintainers = ['adamjstewart']
     import_modules = [
@@ -21,6 +21,7 @@ class PyTorchvision(PythonPackage):
         'torchvision.models.detection'
     ]
 
+    version('0.6.1', sha256='8173680a976c833640ecbd0d7e6f0a11047bf8833433e2147180efc905e48656')
     version('0.6.0', sha256='02de11b3abe6882de4032ce86dab9c7794cbc84369b44d04e667486580f0f1f7')
     version('0.5.0', sha256='eb9afc93df3d174d975ee0914057a9522f5272310b4d56c150b955c287a4d74d')
     version('0.4.2', sha256='1184a27eab85c9e784bacc6f9d6fec99e168ab4eda6047ef9f709e7fdb22d8f9')

From 07b6834ec5e9b428400de1748e07139324a2b92c Mon Sep 17 00:00:00 2001
From: Howard Pritchard <howardp@lanl.gov>
Date: Tue, 23 Jun 2020 01:46:50 -0600
Subject: [PATCH 795/802] OpenMPI: added v4.0.4 (#17202)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Bug fix release:

4.0.4 -- June, 2020
-----------------------
- Fix a memory patcher issue intercepting shmat and shmdt.  This was
  observed on RHEL 8.x ppc64le (see README for more info).
- Fix an illegal access issue caught using gcc's address sanitizer.
  Thanks to  Georg Geiser for reporting.
- Add checks to avoid conflicts with a libevent library shipped with LSF.
- Switch to linking against libevent_core rather than libevent, if present.
- Add improved support for UCX 1.9 and later.
- Fix an ABI compatibility issue with the Fortran 2008 bindings.
  Thanks to Alastair McKinstry for reporting.
- Fix an issue with rpath of /usr/lib64 when building OMPI on
  systems with Lustre.  Thanks to David Shrader for reporting.
- Fix a memory leak occurring with certain MPI RMA operations.
- Fix an issue with ORTE's mapping of MPI processes to resources.
  Thanks to Alex Margolin for reporting and providing a fix.
- Correct a problem with incorrect error codes being returned
  by OMPI MPI_T functions.
- Fix an issue with debugger tools not being able to attach
  to mpirun more than once.  Thanks to Gregory Lee for reporting.
- Fix an issue with the Fortran compiler wrappers when using
  NAG compilers.  Thanks to Peter Brady for reporting.
- Fix an issue with the ORTE ssh based process launcher at scale.
  Thanks to Benjamín Hernández for reporting.
- Address an issue when using shared MPI I/O operations.  OMPIO will
  now successfully return from the file open statement but will
  raise an error if the file system does not supported shared I/O
  operations.  Thanks to Romain Hild for reporting.
- Fix an issue with MPI_WIN_DETACH.  Thanks to Thomas Naughton for reporting.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
---
 var/spack/repos/builtin/packages/openmpi/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 4065e85a591..4184e64f021 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -33,9 +33,10 @@ class Openmpi(AutotoolsPackage):
     version('master', branch='master')
 
     # Current
-    version('4.0.3', sha256='1402feced8c3847b3ab8252165b90f7d1fa28c23b6b2ca4632b6e4971267fd03')  # libmpi.so.40.20.3
+    version('4.0.4', sha256='47e24eb2223fe5d24438658958a313b6b7a55bb281563542e1afc9dec4a31ac4')  # libmpi.so.40.20.4
 
     # Still supported
+    version('4.0.3', sha256='1402feced8c3847b3ab8252165b90f7d1fa28c23b6b2ca4632b6e4971267fd03')  # libmpi.so.40.20.3
     version('4.0.2', sha256='900bf751be72eccf06de9d186f7b1c4b5c2fa9fa66458e53b77778dffdfe4057')  # libmpi.so.40.20.2
     version('4.0.1', sha256='cce7b6d20522849301727f81282201d609553103ac0b09162cf28d102efb9709')  # libmpi.so.40.20.1
     version('4.0.0', sha256='2f0b8a36cfeb7354b45dda3c5425ef8393c9b04115570b615213faaa3f97366b')  # libmpi.so.40.20.0

From 6fdf5913abac23bf5e15457f4c1337f4d2323981 Mon Sep 17 00:00:00 2001
From: Jen Herting <jen@herting.cc>
Date: Tue, 23 Jun 2020 03:49:05 -0400
Subject: [PATCH 796/802] py-gsd: new package at v1.9.3 (#17200)

Co-authored-by: Andrew Elble <aweits@rit.edu>
---
 .../repos/builtin/packages/py-gsd/package.py  | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-gsd/package.py

diff --git a/var/spack/repos/builtin/packages/py-gsd/package.py b/var/spack/repos/builtin/packages/py-gsd/package.py
new file mode 100644
index 00000000000..f130265d824
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-gsd/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyGsd(PythonPackage):
+    """The GSD file format is the native file format for HOOMD-blue. GSD files
+    store trajectories of the HOOMD-blue system state in a binary file with
+    efficient random access to frames. GSD allows all particle and topology
+    properties to vary from one frame to the next. Use the GSD Python API to
+    specify the initial condition for a HOOMD-blue simulation or analyze
+    trajectory output with a script. Read a GSD trajectory with a visualization
+    tool to explore the behavior of the simulation."""
+
+    homepage = "https://gsd.readthedocs.io/en/stable/#"
+    url      = "https://pypi.io/packages/source/g/gsd/gsd-1.9.3.tar.gz"
+
+    version('1.9.3', sha256='c6b37344e69020f69fda2b8d97f894cb41fd720840abeda682edd680d1cff838')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cython', type='build')
+    depends_on('py-numpy@1.9.3:1.999999', type=('build', 'run'))

From 561f6d6c210f9c7848c9b14f6d9b021217d91fb3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mos=C3=A8=20Giordano?= <giordano@users.noreply.github.com>
Date: Tue, 23 Jun 2020 09:17:32 +0100
Subject: [PATCH 797/802] swfft: Add patch to make it build (#17196)

---
 .../builtin/packages/swfft/include-stdio_h.patch      | 11 +++++++++++
 var/spack/repos/builtin/packages/swfft/package.py     |  4 ++++
 2 files changed, 15 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/swfft/include-stdio_h.patch

diff --git a/var/spack/repos/builtin/packages/swfft/include-stdio_h.patch b/var/spack/repos/builtin/packages/swfft/include-stdio_h.patch
new file mode 100644
index 00000000000..86c9390cae1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/swfft/include-stdio_h.patch
@@ -0,0 +1,11 @@
+--- a/TimingStats.h
++++ b/TimingStats.h
+@@ -56,7 +56,7 @@
+ #define HACC_TIMINGSTATS_H
+ 
+ #include <math.h>
+-
++#include <stdio.h>
+ #include <mpi.h>
+ 
+ // lightweight timing statistics from MPI_Wtime() calls
diff --git a/var/spack/repos/builtin/packages/swfft/package.py b/var/spack/repos/builtin/packages/swfft/package.py
index f6bfae90ec6..3d4766f77b0 100644
--- a/var/spack/repos/builtin/packages/swfft/package.py
+++ b/var/spack/repos/builtin/packages/swfft/package.py
@@ -21,6 +21,10 @@ class Swfft(MakefilePackage):
     depends_on('mpi')
     depends_on('fftw')
 
+    # fix error
+    #     TimingStats.h:94:35: error: 'printf' was not declared in this scope
+    patch('include-stdio_h.patch')
+
     tags = ['proxy-app', 'ecp-proxy-app']
 
     @property

From c41f13ef976e2ade652ccb2afbf4624473386f7e Mon Sep 17 00:00:00 2001
From: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
Date: Tue, 23 Jun 2020 10:18:27 +0200
Subject: [PATCH 798/802] parallel-netcdf: add missing perl dependency (#17156)

parallel-netcdf's buildiface script needs perl during build.
---
 var/spack/repos/builtin/packages/parallel-netcdf/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
index 722efab16e4..e34b766ec81 100644
--- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py
+++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
@@ -50,6 +50,8 @@ def url_for_version(self, version):
     depends_on('automake', when='@master', type='build')
     depends_on('libtool', when='@master', type='build')
 
+    depends_on('perl', type='build')
+
     conflicts('+shared', when='@:1.9%nag+fortran')
     conflicts('+shared', when='@:1.8')
 

From cfc390b41f28817e7ae99061f4364806844a94ef Mon Sep 17 00:00:00 2001
From: Amjad Kotobi <amjadkotbi@gmail.com>
Date: Tue, 23 Jun 2020 10:19:00 +0200
Subject: [PATCH 799/802] r-spatialEco: added v1.3-2 (#17194)

---
 var/spack/repos/builtin/packages/r-spatialeco/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/r-spatialeco/package.py b/var/spack/repos/builtin/packages/r-spatialeco/package.py
index bf93b15a204..f028ebd8d5d 100644
--- a/var/spack/repos/builtin/packages/r-spatialeco/package.py
+++ b/var/spack/repos/builtin/packages/r-spatialeco/package.py
@@ -15,6 +15,7 @@ class RSpatialeco(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/spatialEco_1.3-1.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/spatialEco"
 
+    version('1.3-2', sha256='9dfa427ee8b112446b582f6739a1c40a6e3ad3d050f522082a28ce47c675e57a')
     version('1.3-1', sha256='ff12e26cc1bbf7934fbf712c99765d96ce6817e8055faa15a26d9ebade4bbf1c')
     version('1.3-0', sha256='cfa09673cb3bbed30b243082fc2d63ac09f48b9f072a18d32b95c2c29979d1d0')
 

From 91693ef32e32fac0740bec1987d992bcfd251523 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Tue, 23 Jun 2020 16:20:28 +0800
Subject: [PATCH 800/802] strace: added v5.3 to v5.7 (#17193)

---
 var/spack/repos/builtin/packages/strace/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/repos/builtin/packages/strace/package.py b/var/spack/repos/builtin/packages/strace/package.py
index f1b282e5305..a46a98b2bc5 100644
--- a/var/spack/repos/builtin/packages/strace/package.py
+++ b/var/spack/repos/builtin/packages/strace/package.py
@@ -17,6 +17,11 @@ class Strace(AutotoolsPackage):
 
     conflicts('platform=darwin', msg='strace runs only on Linux.')
 
+    version('5.7', sha256='b284b59f9bcd95b9728cea5bd5c0edc5ebe360af73dc76fbf6334f11c777ccd8')
+    version('5.6', sha256='189968eeae06ed9e20166ec55a830943c84374676a457c9fe010edc7541f1b01')
+    version('5.5', sha256='9f58958c8e59ea62293d907d10572e352b582bd7948ed21aa28ebb47e5bf30ff')
+    version('5.4', sha256='f7d00514d51290b6db78ad7a9de709baf93caa5981498924cbc9a744cfd2a741')
+    version('5.3', sha256='6c131198749656401fe3efd6b4b16a07ea867e8f530867ceae8930bbc937a047')
     version('5.2', sha256='d513bc085609a9afd64faf2ce71deb95b96faf46cd7bc86048bc655e4e4c24d2')
     version('5.1', sha256='f5a341b97d7da88ee3760626872a4899bf23cf8dee56901f114be5b1837a9a8b')
     version('5.0', sha256='3b7ad77eb2b81dc6078046a9cc56eed5242b67b63748e7fc28f7c2daf4e647da')

From 404ff9eb326566b98d836af92acf4e91ac419392 Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Tue, 23 Jun 2020 03:34:47 -0500
Subject: [PATCH 801/802] dock: new package at 6.9 (#17138)

---
 .../repos/builtin/packages/dock/package.py    | 59 +++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/dock/package.py

diff --git a/var/spack/repos/builtin/packages/dock/package.py b/var/spack/repos/builtin/packages/dock/package.py
new file mode 100644
index 00000000000..2493be97f1c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dock/package.py
@@ -0,0 +1,59 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Dock(Package):
+    """DOCK is a molecular docking program used in drug discovery.
+
+       This program, given a protein binding site and a small molecule, tries
+       to predict the correct binding mode of the small molecule in the binding
+       site, and the associated binding energy."""
+
+    homepage = "http://dock.compbio.ucsf.edu/DOCK_6/index.htm"
+    url      = "file://{0}/dock.6.9_source.tar.gz".format(os.getcwd())
+
+    version('6.9', sha256='c2caef9b4bb47bb0cb437f6dc21f4c605fd3d0d9cc817fa13748c050dc87a5a8')
+
+    variant('mpi', default=True, description='Enable mpi')
+
+    depends_on('bison', type='build')
+    depends_on('mpi', when='+mpi')
+
+    def setup_build_environment(self, env):
+        if '+mpi' in self.spec:
+            env.set('MPICH_HOME', self.spec['mpi'].prefix)
+
+    def install(self, spec, prefix):
+        compiler_targets = {
+            'gcc': 'gnu',
+            'intel': 'intel',
+            'pgi': 'pgi',
+            'sgi': 'sgi',
+        }
+
+        if self.compiler.name not in compiler_targets:
+            template = 'Unsupported compiler {0}! Supported compilers: {1}'
+            err = template.format(self.compiler.name,
+                                  ', '.join(list(compiler_targets.keys())))
+
+            raise InstallError(err)
+
+        if self.compiler.name == 'pgi' and '+mpi' in spec:
+            raise InstallError('Parallel output is not supported with pgi.')
+
+        with working_dir('install'):
+            sh_args = ['./configure', compiler_targets[self.compiler.name]]
+
+            if '+mpi' in spec:
+                sh_args.append('parallel')
+
+            which('sh')(*sh_args)
+            which('make')('YACC=bison -o y.tab.c')
+
+        mkdirp(prefix.bin)
+        install_tree('bin', prefix.bin)

From 239b709f97028d3595f615e914fc4662ae48925f Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Tue, 23 Jun 2020 15:24:02 +0200
Subject: [PATCH 802/802] Added unit tests to Github Actions (#16610)

* Added unit tests to Github Actions

* Set user e-mail and name for git tests to succeed

* Simplify setup.sh logic

* Replicate Travis script on Github Actions

* Update flags since '.' is not allowed

* Added badge, simplified workflow

* Remove pinning of coverage

* Remove unit tests run on Github Actions from Travis
---
 .github/workflows/linux_unit_tests.yaml | 61 +++++++++++++++++++++++++
 .travis.yml                             | 21 ---------
 README.md                               |  5 +-
 share/spack/qa/setup.sh                 | 15 ++----
 4 files changed, 67 insertions(+), 35 deletions(-)
 create mode 100644 .github/workflows/linux_unit_tests.yaml

diff --git a/.github/workflows/linux_unit_tests.yaml b/.github/workflows/linux_unit_tests.yaml
new file mode 100644
index 00000000000..0fe20200ad3
--- /dev/null
+++ b/.github/workflows/linux_unit_tests.yaml
@@ -0,0 +1,61 @@
+name: linux tests
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+  pull_request:
+    branches:
+      - master
+      - develop
+jobs:
+  unittests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [2.7, 3.5, 3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install System packages
+      run: |
+          sudo apt-get -y update
+          sudo apt-get install -y coreutils gfortran graphviz gnupg2 mercurial ninja-build patchelf
+          # Needed for kcov
+          sudo apt-get -y install cmake binutils-dev libcurl4-openssl-dev zlib1g-dev libdw-dev libiberty-dev
+    - name: Install Python packages
+      run: |
+          pip install --upgrade pip six setuptools codecov coverage
+    - name: Setup git configuration
+      run: |
+          # Need this for the git tests to succeed.
+          git --version
+          git config --global user.email "spack@example.com"
+          git config --global user.name "Test User"
+          git fetch -u origin develop:develop
+    - name: Install kcov for bash script coverage
+      env:
+          KCOV_VERSION: 34
+      run: |
+          KCOV_ROOT=$(mktemp -d)
+          wget --output-document=${KCOV_ROOT}/${KCOV_VERSION}.tar.gz https://github.com/SimonKagstrom/kcov/archive/v${KCOV_VERSION}.tar.gz
+          tar -C ${KCOV_ROOT} -xzvf ${KCOV_ROOT}/${KCOV_VERSION}.tar.gz
+          mkdir -p ${KCOV_ROOT}/build
+          cd ${KCOV_ROOT}/build && cmake -Wno-dev ${KCOV_ROOT}/kcov-${KCOV_VERSION} && cd -
+          make -C ${KCOV_ROOT}/build && sudo  make -C ${KCOV_ROOT}/build install
+    - name: Run unit tests
+      env:
+          COVERAGE: true
+      run: |
+          share/spack/qa/run-unit-tests
+          coverage combine
+          coverage xml
+    - name: Upload to codecov.io
+      uses: codecov/codecov-action@v1
+      with:
+        flags: unittests,linux
diff --git a/.travis.yml b/.travis.yml
index 8107ad876d8..b59d1666d8b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -41,27 +41,6 @@ jobs:
             - realpath
             - zsh
       env: [ TEST_SUITE=unit, COVERAGE=true ]
-    - python: '2.7'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=unit, COVERAGE=true, KCOV_VERSION=34 ]
-    - python: '3.5'
-      os: linux
-      dist: xenial
-      language: python
-      env: TEST_SUITE=unit
-    - python: '3.6'
-      os: linux
-      language: python
-      env: TEST_SUITE=unit
-    - python: '3.7'
-      os: linux
-      language: python
-      env: TEST_SUITE=unit
-    - python: '3.8'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=unit, COVERAGE=true, KCOV_VERSION=34 ]
     - python: '3.8'
       os: linux
       language: python
diff --git a/README.md b/README.md
index a2d704e6c24..d278378ce7a 100644
--- a/README.md
+++ b/README.md
@@ -1,9 +1,10 @@
 # <img src="https://cdn.rawgit.com/spack/spack/develop/share/spack/logo/spack-logo.svg" width="64" valign="middle" alt="Spack"/> Spack
 
-[![](https://github.com/spack/spack/workflows/macos%20tests/badge.svg)](https://github.com/spack/spack/actions)
-[![Build Status](https://travis-ci.com/spack/spack.svg?branch=develop)](https://travis-ci.com/spack/spack)
+[![MacOS Tests](https://github.com/spack/spack/workflows/macos%20tests/badge.svg)](https://github.com/spack/spack/actions)
+[![Linux Tests](https://github.com/spack/spack/workflows/linux%20tests/badge.svg)](https://github.com/spack/spack/actions)
 [![Linux Builds](https://github.com/spack/spack/workflows/linux%20builds/badge.svg)](https://github.com/spack/spack/actions)
 [![macOS Builds (nightly)](https://github.com/spack/spack/workflows/macOS%20builds%20nightly/badge.svg?branch=develop)](https://github.com/spack/spack/actions?query=workflow%3A%22macOS+builds+nightly%22)
+[![Build Status](https://travis-ci.com/spack/spack.svg?branch=develop)](https://travis-ci.com/spack/spack)
 [![codecov](https://codecov.io/gh/spack/spack/branch/develop/graph/badge.svg)](https://codecov.io/gh/spack/spack)
 [![Read the Docs](https://readthedocs.org/projects/spack/badge/?version=latest)](https://spack.readthedocs.io)
 [![Slack](https://spackpm.herokuapp.com/badge.svg)](https://spackpm.herokuapp.com)
diff --git a/share/spack/qa/setup.sh b/share/spack/qa/setup.sh
index 61fb2a7706c..65364790154 100755
--- a/share/spack/qa/setup.sh
+++ b/share/spack/qa/setup.sh
@@ -20,24 +20,15 @@ export SPACK_ROOT=$(realpath "$QA_DIR/../../..")
 coverage=""
 coverage_run=""
 
-# bash coverage depends on some other factors -- there are issues with
-# kcov for Python 2.6, unit tests, and build tests.
-if [[ $TEST_SUITE == unit &&   # kcov segfaults for the MPICH build test
-      $TRAVIS_OS_NAME == linux &&
-      $TRAVIS_PYTHON_VERSION != 2.6 ]];
-then
-    BASH_COVERAGE="true"
-else
-    BASH_COVERAGE="false"
-fi
-
 # Set up some variables for running coverage tests.
 if [[ "$COVERAGE" == "true" ]]; then
     # these set up coverage for Python
     coverage=coverage
     coverage_run="coverage run"
 
-    if [ "$BASH_COVERAGE" = true ]; then
+    # bash coverage depends on some other factors -- there are issues with
+    # kcov for Python 2.6, unit tests, and build tests.
+    if [[ $TRAVIS_PYTHON_VERSION != 2.6 ]]; then
         mkdir -p coverage
         cc_script="$SPACK_ROOT/lib/spack/env/cc"
         bashcov=$(realpath ${QA_DIR}/bashcov)