From cd511791d19929dbd5ce4916e72e194f9b9f131f Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Thu, 12 Jan 2017 18:11:48 +0100
Subject: [PATCH 01/25] configure and build command: fix the stop iteration
 semantics

- broke somewhere between bdf48322696290d4e3d00ed12b7c7fe6ca213478 (#2810) and 17b13b161b3ddcd691ea7ed90165cfab6dec3950
---
 lib/spack/spack/build_environment.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 67b00c67494..7046c81c2fb 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -553,6 +553,11 @@ def child_execution(child_connection, input_stream):
             setup_package(pkg, dirty=dirty)
             function(input_stream)
             child_connection.send(None)
+        except StopIteration as e:
+            # StopIteration is used to stop installations
+            # before the final stage, mainly for debug purposes
+            tty.msg(e.message)
+            child_connection.send(None)
         except:
             # catch ANYTHING that goes wrong in the child process
             exc_type, exc, tb = sys.exc_info()

From 1128922b444d3390538b2da65937263d9c8a0b50 Mon Sep 17 00:00:00 2001
From: Andrey Prokopenko <aprokop@users.noreply.github.com>
Date: Fri, 13 Jan 2017 11:43:50 -0500
Subject: [PATCH 02/25] boost: fixing boost-1.55.0 for gcc-5 (#2822)

boost-1.55.0 requires patching when compiling with gcc-5. See these
threads:

https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197594
https://svn.boost.org/trac/boost/ticket/10125

Fixes #2821.
---
 .../builtin/packages/boost/boost_10125.patch  | 51 +++++++++++++++++++
 .../repos/builtin/packages/boost/package.py   |  3 ++
 2 files changed, 54 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/boost/boost_10125.patch

diff --git a/var/spack/repos/builtin/packages/boost/boost_10125.patch b/var/spack/repos/builtin/packages/boost/boost_10125.patch
new file mode 100644
index 00000000000..71cfaa871e8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/boost/boost_10125.patch
@@ -0,0 +1,51 @@
+--- a/boost/thread/pthread/once.hpp
++++ b/boost/thread/pthread/once.hpp
+@@ -42,7 +42,7 @@ namespace boost
+   }
+ 
+ #ifdef BOOST_THREAD_PROVIDES_ONCE_CXX11
+-#ifndef BOOST_NO_CXX11_VARIADIC_TEMPLATES
++#if !defined(BOOST_NO_CXX11_VARIADIC_TEMPLATES) && !defined(BOOST_NO_CXX11_RVALUE_REFERENCES)
+     template<typename Function, class ...ArgTypes>
+     inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args);
+ #else
+@@ -65,7 +65,7 @@ namespace boost
+   private:
+       volatile thread_detail::uintmax_atomic_t epoch;
+ 
+-#ifndef BOOST_NO_CXX11_VARIADIC_TEMPLATES
++#if !defined(BOOST_NO_CXX11_VARIADIC_TEMPLATES) && !defined(BOOST_NO_CXX11_RVALUE_REFERENCES)
+       template<typename Function, class ...ArgTypes>
+       friend void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args);
+ #else
+@@ -118,7 +118,7 @@ namespace boost
+     // http://www.open-std.org/jtc1/sc22/wg21/docs/papers/2007/n2444.html
+ 
+ 
+-#ifndef BOOST_NO_CXX11_VARIADIC_TEMPLATES
++#if !defined(BOOST_NO_CXX11_VARIADIC_TEMPLATES) && !defined(BOOST_NO_CXX11_RVALUE_REFERENCES)
+ 
+ 
+   template<typename Function, class ...ArgTypes>
+--- a/boost/thread/pthread/once_atomic.hpp
++++ b/boost/thread/pthread/once_atomic.hpp
+@@ -115,7 +115,7 @@ namespace boost
+ #endif
+ 
+ 
+-#ifndef BOOST_NO_CXX11_VARIADIC_TEMPLATES
++#if !defined(BOOST_NO_CXX11_VARIADIC_TEMPLATES) && !defined(BOOST_NO_CXX11_RVALUE_REFERENCES)
+ 
+   template<typename Function, class ...ArgTypes>
+   inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args)
+--- a/boost/thread/win32/once.hpp
++++ b/boost/thread/win32/once.hpp
+@@ -227,7 +227,7 @@ namespace boost
+         }
+     }
+ 
+-#ifndef BOOST_NO_CXX11_VARIADIC_TEMPLATES
++#if !defined BOOST_NO_CXX11_VARIADIC_TEMPLATES && !defined(BOOST_NO_CXX11_RVALUE_REFERENCES)
+ //#if defined(BOOST_THREAD_RVALUE_REFERENCES_DONT_MATCH_FUNTION_PTR)
+     inline void call_once(once_flag& flag, void (*f)())
+     {
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index fa3f66d8f48..c31e5fc9df0 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -130,6 +130,9 @@ class Boost(Package):
     # Patch fix from https://svn.boost.org/trac/boost/ticket/11856
     patch('boost_11856.patch', when='@1.60.0%gcc@4.4.7')
 
+    # Patch fix from https://svn.boost.org/trac/boost/ticket/10125
+    patch('boost_10125.patch', when='@1.55.0%gcc@5.0:5.9')
+
     def url_for_version(self, version):
         """
         Handle Boost's weird URLs,

From 28ea72d5b2788a9cc69d9ae7b0e801727b1b8d46 Mon Sep 17 00:00:00 2001
From: Matthew Scott Krafczyk <krafczyk.matthew@gmail.com>
Date: Sun, 15 Jan 2017 05:27:17 -0500
Subject: [PATCH 03/25] Add the package py-sphinx-bootstrap-theme (#2825)

---
 .../py-sphinx-bootstrap-theme/package.py      | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py

diff --git a/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py b/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py
new file mode 100644
index 00000000000..38f127dfc44
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class PySphinxBootstrapTheme(Package):
+    """Sphinx Bootstrap Theme."""
+
+    homepage = "https://pypi.python.org/pypi/sphinx-bootstrap-theme/"
+    url      = "https://pypi.io/packages/source/s/sphinx-bootstrap-theme/sphinx-bootstrap-theme-0.4.13.tar.gz"
+
+    version('0.4.13', '32e513a9c8ffbb8c1e4b036e8f74fb51')
+
+    extends('python')
+
+    depends_on('py-setuptools', type='build')
+
+    def install(self, spec, prefix):
+        setup_py('install', '--prefix={0}'.format(prefix))

From 1f4ca71e21a2a5f66759951de2c9754ddecd537c Mon Sep 17 00:00:00 2001
From: Stephen McDowell <svenevs@users.noreply.github.com>
Date: Sun, 15 Jan 2017 05:29:29 -0500
Subject: [PATCH 04/25] Adding the py-ipdb package for more stable debugging
 with iPython. (#2824)

* Adding the py-ipdb package for more stable debugging with iPython.

* Removing deprecated python support, adding missing dependencies.

* Adding version checks for (i)python
---
 .../repos/builtin/packages/py-ipdb/package.py | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-ipdb/package.py

diff --git a/var/spack/repos/builtin/packages/py-ipdb/package.py b/var/spack/repos/builtin/packages/py-ipdb/package.py
new file mode 100644
index 00000000000..ab7982a76a3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-ipdb/package.py
@@ -0,0 +1,58 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class PyIpdb(Package):
+    """ipdb is the iPython debugger and has many additional features, including
+    a better interactive debugging experience via colorized output."""
+
+    homepage = "https://pypi.python.org/pypi/ipdb"
+    url      = "https://pypi.io/packages/source/i/ipdb/ipdb-0.10.1.tar.gz"
+
+    version('0.10.1', '4aeab65f633ddc98ebdb5eebf08dc713')
+
+    # :TODO:
+    # There might be potential to add variants here, but at the time of writing
+    # this the original packager does not know what they are. See the 3rd party
+    # section on ipdb's GitHub:
+    #     https://github.com/gotcha/ipdb#third-party-support
+    extends('python')
+    depends_on('python@2.6:2.7,3.2:')
+
+    # Dependencies gathered from:
+    #     https://github.com/gotcha/ipdb/blob/master/setup.py
+    # However additional dependencies added below were found via testing.
+    depends_on('py-setuptools',      type='build')
+    # ipdb needs iPython and others available at runtime
+    depends_on('py-ipython@0.10.2:', type=('build', 'link'))
+    depends_on('py-traitlets',       type=('build', 'link'))
+    depends_on('py-six',             type=('build', 'link'))
+    depends_on('py-pexpect',         type=('build', 'link'))
+    depends_on('py-prompt-toolkit',  type=('build', 'link'))
+
+    def install(self, spec, prefix):
+        # Installation is uncomplicated, this should suffice.
+        setup_py('install', '--prefix={0}'.format(prefix))

From c6c6773c03098f2eb22619ddde90ce3ebfcbc99b Mon Sep 17 00:00:00 2001
From: Gregory Lee <lee218@llnl.gov>
Date: Sun, 15 Jan 2017 02:30:12 -0800
Subject: [PATCH 05/25] added psutil python package (#2812)

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

diff --git a/var/spack/repos/builtin/packages/py-psutil/package.py b/var/spack/repos/builtin/packages/py-psutil/package.py
new file mode 100644
index 00000000000..7aa776d2a12
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-psutil/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class PyPsutil(Package):
+    """psutil is a cross-platform library for retrieving information on
+    running processes and system utilization (CPU, memory, disks, network)
+    in Python."""
+
+    homepage = "https://pypi.python.org/pypi/psutil"
+    url      = "https://pypi.python.org/packages/d9/c8/8c7a2ab8ec108ba9ab9a4762c5a0d67c283d41b13b5ce46be81fdcae3656/psutil-5.0.1.tar.gz"
+
+    version('5.0.1', '153dc8be94badc4072016ceeac7808dc')
+
+    extends('python')
+    depends_on('python@2.6:')
+    depends_on('py-setuptools', type='build')
+
+    def install(self, spec, prefix):
+        setup_py('install', '--prefix=%s' % prefix)

From 957cb968c619e32fc764babb8dc8ed977b42c789 Mon Sep 17 00:00:00 2001
From: danielsjensen1 <danielsjensen1@gmail.com>
Date: Sun, 15 Jan 2017 03:30:47 -0700
Subject: [PATCH 06/25] Features/octopus 6.0 (#2819)

* Added support for Octopus 6.0 and the optional libraries: metis, parmetis, netcdf, arpack-ng, and scalapack.

* Fix PEP 8 line too long error.

* Changed format syntax {} to {0} to support Python 2.6.
---
 .../repos/builtin/packages/octopus/package.py | 61 ++++++++++++++++---
 1 file changed, 53 insertions(+), 8 deletions(-)

diff --git a/var/spack/repos/builtin/packages/octopus/package.py b/var/spack/repos/builtin/packages/octopus/package.py
index a100f7896a2..b74befbe350 100644
--- a/var/spack/repos/builtin/packages/octopus/package.py
+++ b/var/spack/repos/builtin/packages/octopus/package.py
@@ -30,22 +30,47 @@ class Octopus(Package):
     theory code."""
 
     homepage = "http://www.tddft.org/programs/octopus/"
-    url      = "http://www.tddft.org/programs/octopus/down.php?file=5.0.1/octopus-5.0.1.tar.gz"
+    base_url = "http://www.tddft.org/programs/octopus/down.php?file="
 
+    version('6.0', '5d1168c2a8d7fd9cb9492eaebaa7182e')
     version('5.0.1', '2b6392ab67b843f9d4ca7413fc07e822')
 
+    # Sample url is:
+    # "http://www.tddft.org/programs/octopus/down.php?file=5.0.1/octopus-5.0.1.tar.gz"
+    def url_for_version(self, version):
+        return '{0}/{1}/octopus-{1}.tar.gz'.format(Octopus.base_url, 
+                                                   version.dotted)
+
+    variant('scalapack', default=False,
+            description='Compile with Scalapack')
+    variant('metis', default=True,
+            description='Compile with METIS')
+    variant('parmetis', default=False,
+            description='Compile with ParMETIS')
+    variant('netcdf', default=False,
+            description='Compile with Netcdf')
+    variant('arpack-ng', default=False,
+            description='Compile with ARPACK-ng')
+
     depends_on('blas')
     depends_on('gsl')
     depends_on('lapack')
     depends_on('libxc')
     depends_on('mpi')
     depends_on('fftw+mpi')
+    depends_on('metis@5:', when='+metis')
+    depends_on('parmetis', when='+parmetis')
+    depends_on('scalapack', when='+scalapack')
+    depends_on('netcdf-fortran', when='+netcdf')
+    depends_on('arpack-ng', when='+arpack-ng')
 
     # optional dependencies:
-    # TODO: scalapack, metis, parmetis, netcdf, etsf-io, sparskit, arpack,
+    # TODO: parmetis, etsf-io, sparskit,
     # feast, libfm, pfft, isf, pnfft
 
     def install(self, spec, prefix):
+        arpack = find_libraries(['libarpack'], root=spec[
+                                'arpack-ng'].prefix.lib, shared=True)
         lapack = spec['lapack'].lapack_libs
         blas = spec['blas'].blas_libs
         args = []
@@ -58,17 +83,37 @@ def install(self, spec, prefix):
             'CC=%s' % spec['mpi'].mpicc,
             'FC=%s' % spec['mpi'].mpifc,
             '--enable-mpi',
-            '--with-fft-lib=-L%s -lfftw3' % spec['fftw'].prefix.lib
-            # --with-blacs=${prefix}/lib/libscalapack.dylib
-            # --with-netcdf-prefix=netcdf-fortran
+            '--with-fft-lib=-L%s -lfftw3' % spec['fftw'].prefix.lib,
+        ])
+        if '+metis' in spec:
+            args.extend([
+                '--with-metis-prefix=%s' % spec['metis'].prefix,
+            ])
+        if '+parmetis' in spec:
+            args.extend([
+                '--with-parmetis-prefix=%s' % spec['parmetis'].prefix,
+            ])
+        if '+netcdf' in spec:
+            args.extend([
+                '--with-netcdf-prefix=%s' % spec['netcdf-fortran'].prefix,
+                '--with-netcdf-include=%s' % 
+                spec['netcdf-fortran'].prefix.include,
+            ])
+        if '+arpack-ng' in spec:
+            args.extend([
+                '--with-arpack={0}'.format(arpack.joined()), 
+            ])
+        if '+scalapack' in spec:
+            args.extend([
+                '--with-blacs=%s' % spec['scalapack'].scalapack_libs,
+                '--with-scalapack=%s' % spec['scalapack'].scalapack_libs,
+            ])
             # --with-etsf-io-prefix=
             # --with-sparskit=${prefix}/lib/libskit.a
             # --with-pfft-prefix=${prefix} --with-mpifftw-prefix=${prefix}
-            # --with-arpack=${prefix}/lib/libarpack.dylib
             # --with-parpack=${prefix}/lib/libparpack.dylib
-            # --with-metis-prefix=${prefix} --with-parmetis-prefix=${prefix}
+            # --with-parmetis-prefix=${prefix}
             # --with-berkeleygw-prefix=${prefix}
-        ])
 
         # When preprocessor expands macros (i.e. CFLAGS) defined as quoted
         # strings the result may be > 132 chars and is terminated.

From 436f6a4ab65943645c68f82691c9ccd234c43d51 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Sun, 15 Jan 2017 11:34:15 +0100
Subject: [PATCH 07/25] get_std_cmake_args delegates to CMakePackage._std_args
 fixes #2665 (#2805)

---
 lib/spack/spack/build_environment.py          | 18 ++++----
 lib/spack/spack/test/build_systems.py         | 42 +++++++++++++++++++
 .../packages/cmake-client/package.py          |  9 ++--
 3 files changed, 55 insertions(+), 14 deletions(-)
 create mode 100644 lib/spack/spack/test/build_systems.py

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 7046c81c2fb..3e6dc12b35a 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -432,19 +432,15 @@ def get_rpaths(pkg):
     return rpaths
 
 
-def get_std_cmake_args(cmake_pkg):
-    # standard CMake arguments
-    ret = ['-DCMAKE_INSTALL_PREFIX=%s' % cmake_pkg.prefix,
-           '-DCMAKE_BUILD_TYPE=RelWithDebInfo',
-           '-DCMAKE_VERBOSE_MAKEFILE=ON']
-    if platform.mac_ver()[0]:
-        ret.append('-DCMAKE_FIND_FRAMEWORK=LAST')
+def get_std_cmake_args(pkg):
+    """Returns the list of standard arguments that would be used if this
+    package was a CMakePackage instance.
 
-    # Set up CMake rpath
-    ret.append('-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE')
-    ret.append('-DCMAKE_INSTALL_RPATH=%s' % ":".join(get_rpaths(cmake_pkg)))
+    :param pkg: pkg under consideration
 
-    return ret
+    :return: list of arguments for cmake
+    """
+    return spack.CMakePackage._std_args(pkg)
 
 
 def parent_class_modules(cls):
diff --git a/lib/spack/spack/test/build_systems.py b/lib/spack/spack/test/build_systems.py
new file mode 100644
index 00000000000..2cafba0333c
--- /dev/null
+++ b/lib/spack/spack/test/build_systems.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+import spack
+from spack.build_environment import get_std_cmake_args
+from spack.spec import Spec
+
+
+def test_cmake_std_args(config, builtin_mock):
+    # Call the function on a CMakePackage instance
+    s = Spec('cmake-client')
+    s.concretize()
+    pkg = spack.repo.get(s)
+    assert pkg.std_cmake_args == get_std_cmake_args(pkg)
+
+    # Call it on another kind of package
+    s = Spec('mpich')
+    s.concretize()
+    pkg = spack.repo.get(s)
+    assert get_std_cmake_args(pkg)
diff --git a/var/spack/repos/builtin.mock/packages/cmake-client/package.py b/var/spack/repos/builtin.mock/packages/cmake-client/package.py
index 0c78f0bf688..51704e3f4b6 100644
--- a/var/spack/repos/builtin.mock/packages/cmake-client/package.py
+++ b/var/spack/repos/builtin.mock/packages/cmake-client/package.py
@@ -32,15 +32,13 @@ def check(condition, msg):
         raise InstallError(msg)
 
 
-class CmakeClient(Package):
+class CmakeClient(CMakePackage):
     """A dumy package that uses cmake."""
     homepage  = 'https://www.example.com'
     url       = 'https://www.example.com/cmake-client-1.0.tar.gz'
 
     version('1.0', '4cb3ff35b2472aae70f542116d616e63')
 
-    depends_on('cmake', type='build')
-
     def setup_environment(self, spack_env, run_env):
         spack_cc    # Ensure spack module-scope variable is avaiabl
         check(from_cmake == "from_cmake",
@@ -68,6 +66,11 @@ def setup_dependent_package(self, module, dspec):
               "link arg on dependency spec not readable from "
               "setup_dependent_package.")
 
+    def cmake(self, spec, prefix):
+        pass
+
+    build = cmake
+
     def install(self, spec, prefix):
         # check that cmake is in the global scope.
         global cmake

From 12edc4e3699929eee37321ec0608b7c220a583db Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sun, 15 Jan 2017 04:34:48 -0600
Subject: [PATCH 08/25] Add latest version of PETSc (#2783)

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

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 7d51bbad487..ee062e92f6f 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -41,6 +41,7 @@ class Petsc(Package):
     version('for-pflotran-0.1.0', git='https://bitbucket.org/petsc/petsc.git',
             commit='7943f4e1472fff9cf1fc630a1100136616e4970f')
 
+    version('3.7.5', 'f00f6e6a3bac39052350dd47194b58a3')
     version('3.7.4', 'aaf94fa54ef83022c14091f10866eedf')
     version('3.7.2', '50da49867ce7a49e7a0c1b37f4ec7b34')
     version('3.6.4', '7632da2375a3df35b8891c9526dbdde7')

From 367f46eee2f8e4165216ab65cfc374aaf6f8c10a Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sun, 15 Jan 2017 04:35:27 -0600
Subject: [PATCH 09/25] Add old version of PGI (#2784)

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

diff --git a/var/spack/repos/builtin/packages/pgi/package.py b/var/spack/repos/builtin/packages/pgi/package.py
index 6fa8457dc9f..e8a2f53497b 100644
--- a/var/spack/repos/builtin/packages/pgi/package.py
+++ b/var/spack/repos/builtin/packages/pgi/package.py
@@ -39,10 +39,10 @@ class Pgi(Package):
     set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html"""
 
     homepage = "http://www.pgroup.com/"
-    url = "file://%s/pgi-16.3.tar.gz" % os.getcwd()
 
     version('16.5', 'a40e8852071b5d600cb42f31631b3de1')
     version('16.3', '618cb7ddbc57d4e4ed1f21a0ab25f427')
+    version('15.7', '84a689217b17cdaf78c39270c70bea5d')
 
     variant('network', default=True,
             description="Perform a network install")
@@ -64,6 +64,10 @@ class Pgi(Package):
     license_vars = ['PGROUPD_LICENSE_FILE', 'LM_LICENSE_FILE']
     license_url = 'http://www.pgroup.com/doc/pgiinstall.pdf'
 
+    def url_for_version(self, version):
+        return "file://{0}/pgilinux-20{1}-{2}-x86_64.tar.gz".format(
+            os.getcwd(), version.up_to(1), version.joined)
+
     def install(self, spec, prefix):
         # Enable the silent installation feature
         os.environ['PGI_SILENT'] = "true"

From 5c4d2627ff4e348969ca710d2a9d69b10db48096 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Sun, 15 Jan 2017 11:35:53 +0100
Subject: [PATCH 10/25] Packages: Add CUDA8 (#2823)

Adds the latest CUDA release, 8.0.44.
---
 var/spack/repos/builtin/packages/cuda/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py
index 36cf3058d73..ed8518f98fe 100644
--- a/var/spack/repos/builtin/packages/cuda/package.py
+++ b/var/spack/repos/builtin/packages/cuda/package.py
@@ -50,6 +50,8 @@ class Cuda(Package):
 
     homepage = "http://www.nvidia.com/object/cuda_home_new.html"
 
+    version('8.0.44', '6dca912f9b7e2b7569b0074a41713640', expand=False,
+            url="file://%s/cuda_8.0.44_linux.run"    % os.getcwd())
     version('7.5.18', '4b3bcecf0dfc35928a0898793cf3e4c6', expand=False,
             url="file://%s/cuda_7.5.18_linux.run"    % os.getcwd())
     version('6.5.14', '90b1b8f77313600cc294d9271741f4da', expand=False,

From 677623962ef70e405ecb6c6d8a01fd105dcfe2c5 Mon Sep 17 00:00:00 2001
From: becker33 <becker33@llnl.gov>
Date: Sun, 15 Jan 2017 02:36:36 -0800
Subject: [PATCH 11/25] Fixed find -lp command (coloring was broken) (#2820)

---
 lib/spack/spack/cmd/__init__.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py
index bcc4524b4f5..3e83dbb789f 100644
--- a/lib/spack/spack/cmd/__init__.py
+++ b/lib/spack/spack/cmd/__init__.py
@@ -219,9 +219,8 @@ def display_specs(specs, **kwargs):
             format = "    %%-%ds%%s" % width
 
             for abbrv, spec in zip(abbreviated, specs):
-                if hashes:
-                    print(gray_hash(spec, hlen), )
-                print(format % (abbrv, spec.prefix))
+                prefix = gray_hash(spec, hlen) if hashes else ''
+                print prefix + (format % (abbrv, spec.prefix))
 
         elif mode == 'deps':
             for spec in specs:

From 0d367bbd203eab4cdde78cfe6b81a8a5e61a1572 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 15 Jan 2017 02:37:20 -0800
Subject: [PATCH 12/25] Add a test to exercise non-buildable external packages.
 (#2833)

---
 .../spack/test/concretize_preferences.py      | 32 +++++++++++++++++--
 1 file changed, 30 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/test/concretize_preferences.py b/lib/spack/spack/test/concretize_preferences.py
index b95fc83010b..54df4e15631 100644
--- a/lib/spack/spack/test/concretize_preferences.py
+++ b/lib/spack/spack/test/concretize_preferences.py
@@ -43,6 +43,9 @@ def concretize_scope(config, tmpdir):
     spack.config.config_scopes.pop('concretize')
     spack.package_prefs._pkgsort = PreferredPackages()
 
+    # reset provider index each time, too
+    spack.repo._provider_index = None
+
 
 def concretize(abstract_spec):
     return Spec(abstract_spec).concretized()
@@ -123,7 +126,8 @@ def test_no_virtuals_in_packages_yaml(self):
         # set up a packages.yaml file with a vdep as a key.  We use
         # syaml.load here to make sure source lines in the config are
         # attached to parsed strings, as the error message uses them.
-        conf = syaml.load("""mpi:
+        conf = syaml.load("""\
+mpi:
     paths:
       mpi-with-lapack@2.1: /path/to/lapack
 """)
@@ -135,7 +139,8 @@ def test_no_virtuals_in_packages_yaml(self):
 
     def test_all_is_not_a_virtual(self):
         """Verify that `all` is allowed in packages.yaml."""
-        conf = syaml.load("""all:
+        conf = syaml.load("""\
+all:
         variants: [+mpi]
 """)
         spack.config.update_config('packages', conf, 'concretize')
@@ -143,3 +148,26 @@ def test_all_is_not_a_virtual(self):
         # should be no error for 'all':
         spack.package_prefs._pkgsort = PreferredPackages()
         spack.package_prefs.get_packages_config()
+
+    def test_external_mpi(self):
+        # make sure this doesn't give us an external first.
+        spec = Spec('mpi')
+        spec.concretize()
+        assert not spec['mpi'].external
+
+        # load config
+        conf = syaml.load("""\
+all:
+    providers:
+        mpi: [mpich]
+mpich:
+    buildable: false
+    paths:
+        mpich@3.0.4: /dummy/path
+""")
+        spack.config.update_config('packages', conf, 'concretize')
+
+        # ensure that once config is in place, external is used
+        spec = Spec('mpi')
+        spec.concretize()
+        assert spec['mpich'].external == '/dummy/path'

From 3f7b4ab7aa7a31b421b6b392701435020c6fd6eb Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Sun, 15 Jan 2017 11:38:14 +0100
Subject: [PATCH 13/25] Clang & Boost: No PCH (#2827)

Although it hurts a little, officially pre-compiled headers in
boost are only supported for gcc & msvc and the latest clang
releases still fail to build boost with it.

Therefore, I disabled building those to get boost build with
clang 3.9.0 on an Ubuntu 14.04 (x86).

Links to documentation and boost bug reports are inline, so
people can later on check if they still apply. Seems just to
be a bug in `Boost.Build` that tries to set `-o` with multiple
output files.
---
 var/spack/repos/builtin/packages/boost/package.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index c31e5fc9df0..738e8a0e35a 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -254,6 +254,13 @@ def determine_b2_options(self, spec, options):
                 'toolset=%s' % self.determine_toolset(spec)
             ])
 
+        # clang is not officially supported for pre-compiled headers
+        # 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'):
+            options.extend(['pch=off'])
+
         return threadingOpts
 
     def add_buildopt_symlinks(self, prefix):

From 7fce4c5083bf218cc53049915f6853152f37f7bc Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sun, 15 Jan 2017 05:16:41 -0600
Subject: [PATCH 14/25] Add list_url to cmake (#2714)

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

diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index d2f1e27a0b2..60c95b91842 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -28,8 +28,10 @@
 class Cmake(Package):
     """A cross-platform, open-source build system. CMake is a family of
        tools designed to build, test and package software."""
-    homepage  = 'https://www.cmake.org'
-    url       = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
+    homepage = 'https://www.cmake.org'
+    url      = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
+    list_url = 'https://cmake.org/files/'
+    list_depth = 2
 
     version('3.7.1',    'd031d5a06e9f1c5367cdfc56fbd2a1c8')
     version('3.6.1',    'd6dd661380adacdb12f41b926ec99545')

From f2d4c15395b04ff4ca181ca7b1ddfe2bb7a3bee5 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sun, 15 Jan 2017 05:18:52 -0600
Subject: [PATCH 15/25] Remove cmake build dep from CMakePackages (#2684)

---
 lib/spack/spack/cmd/create.py                                 | 4 ----
 .../repos/builtin/packages/everytrace-example/package.py      | 1 -
 var/spack/repos/builtin/packages/everytrace/package.py        | 1 -
 var/spack/repos/builtin/packages/ibmisc/package.py            | 1 -
 var/spack/repos/builtin/packages/icet/package.py              | 1 -
 var/spack/repos/builtin/packages/jansson/package.py           | 2 --
 var/spack/repos/builtin/packages/libspatialindex/package.py   | 2 --
 var/spack/repos/builtin/packages/libwebsockets/package.py     | 1 -
 var/spack/repos/builtin/packages/trilinos/package.py          | 2 --
 var/spack/repos/builtin/packages/xsdktrilinos/package.py      | 4 +---
 10 files changed, 1 insertion(+), 18 deletions(-)

diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py
index 2d25e8c8a9a..cac67f22af2 100644
--- a/lib/spack/spack/cmd/create.py
+++ b/lib/spack/spack/cmd/create.py
@@ -155,10 +155,6 @@ class CMakeGuess(DefaultGuess):
     """Provides appropriate overrides for cmake-based packages"""
     base_class_name = 'CMakePackage'
 
-    dependencies = """\
-    # FIXME: Add additional dependencies if required.
-    depends_on('cmake', type='build')"""
-
     body = """\
     def cmake_args(self):
         # FIXME: Add arguments other than
diff --git a/var/spack/repos/builtin/packages/everytrace-example/package.py b/var/spack/repos/builtin/packages/everytrace-example/package.py
index 8c49e04634a..76b437a38a0 100644
--- a/var/spack/repos/builtin/packages/everytrace-example/package.py
+++ b/var/spack/repos/builtin/packages/everytrace-example/package.py
@@ -33,7 +33,6 @@ class EverytraceExample(CMakePackage):
             git='https://github.com/citibeth/everytrace-example.git',
             branch='develop')
 
-    depends_on('cmake', type='build')
     depends_on('everytrace+mpi+fortran')
 
     # Currently the only MPI this everytrace works with.
diff --git a/var/spack/repos/builtin/packages/everytrace/package.py b/var/spack/repos/builtin/packages/everytrace/package.py
index a3f3e2cfcee..d884c7b165b 100644
--- a/var/spack/repos/builtin/packages/everytrace/package.py
+++ b/var/spack/repos/builtin/packages/everytrace/package.py
@@ -39,7 +39,6 @@ class Everytrace(CMakePackage):
     variant('fortran', default=True,
             description='Enable use with Fortran programs')
 
-    depends_on('cmake', type='build')
     depends_on('mpi', when='+mpi')
 
     def cmake_args(self):
diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py
index 7365eac46aa..f3252055078 100644
--- a/var/spack/repos/builtin/packages/ibmisc/package.py
+++ b/var/spack/repos/builtin/packages/ibmisc/package.py
@@ -64,7 +64,6 @@ class Ibmisc(CMakePackage):
     depends_on('boost', when='+boost')
 
     # Build dependencies
-    depends_on('cmake', type='build')
     depends_on('doxygen', type='build')
 
     def cmake_args(self):
diff --git a/var/spack/repos/builtin/packages/icet/package.py b/var/spack/repos/builtin/packages/icet/package.py
index cdace1481f6..f8260f19519 100644
--- a/var/spack/repos/builtin/packages/icet/package.py
+++ b/var/spack/repos/builtin/packages/icet/package.py
@@ -36,7 +36,6 @@ class Icet(CMakePackage):
             git='https://gitlab.kitware.com/icet/icet.git')
     version('2.1.1', '4f971c51105a64937460d482adca2a6c')
 
-    depends_on('cmake', type='build')
     depends_on('mpi')
 
     def url_for_version(self, version):
diff --git a/var/spack/repos/builtin/packages/jansson/package.py b/var/spack/repos/builtin/packages/jansson/package.py
index 8ba7829bbc7..e6100607aaf 100644
--- a/var/spack/repos/builtin/packages/jansson/package.py
+++ b/var/spack/repos/builtin/packages/jansson/package.py
@@ -33,5 +33,3 @@ class Jansson(CMakePackage):
     url      = "https://github.com/akheron/jansson/archive/v2.9.tar.gz"
 
     version('2.9', 'd2db25c437b359fc5a065ed938962237')
-
-    depends_on('cmake', type='build')
diff --git a/var/spack/repos/builtin/packages/libspatialindex/package.py b/var/spack/repos/builtin/packages/libspatialindex/package.py
index 731e47a9914..5dd839a7c37 100644
--- a/var/spack/repos/builtin/packages/libspatialindex/package.py
+++ b/var/spack/repos/builtin/packages/libspatialindex/package.py
@@ -30,5 +30,3 @@ class Libspatialindex(CMakePackage):
     url      = "https://github.com/libspatialindex/libspatialindex/tarball/1.8.5"
 
     version('1.8.5', 'a95d8159714dbda9a274792cd273d298')
-
-    depends_on("cmake", type='build')
diff --git a/var/spack/repos/builtin/packages/libwebsockets/package.py b/var/spack/repos/builtin/packages/libwebsockets/package.py
index 904ad887ecb..3ce58a4c369 100644
--- a/var/spack/repos/builtin/packages/libwebsockets/package.py
+++ b/var/spack/repos/builtin/packages/libwebsockets/package.py
@@ -35,6 +35,5 @@ class Libwebsockets(CMakePackage):
     version('2.0.3', 'a025156d606d90579e65d53ccd062a94')
     version('1.7.9', '7b3692ead5ae00fd0e1d56c080170f07')
 
-    depends_on('cmake', type='build')
     depends_on('zlib')
     depends_on('openssl')
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 7558430953c..4b3412ce7af 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -90,8 +90,6 @@ def url_for_version(self, version):
             description='Builds a debug version of the libraries')
     variant('boost',        default=True, description='Compile with Boost')
 
-    depends_on('cmake', type='build')
-
     # Everything should be compiled with -fpic
     depends_on('blas')
     depends_on('lapack')
diff --git a/var/spack/repos/builtin/packages/xsdktrilinos/package.py b/var/spack/repos/builtin/packages/xsdktrilinos/package.py
index 7aea15ed9cd..ea490544354 100644
--- a/var/spack/repos/builtin/packages/xsdktrilinos/package.py
+++ b/var/spack/repos/builtin/packages/xsdktrilinos/package.py
@@ -28,7 +28,7 @@
 
 class Xsdktrilinos(CMakePackage):
     """xSDKTrilinos contains the portions of Trilinos that depend on PETSc
-    because they would cause a circular dependency if built as part of 
+    because they would cause a circular dependency if built as part of
     Trilinos.
     """
     homepage = "https://trilinos.org/"
@@ -51,8 +51,6 @@ def url_for_version(self, version):
     variant('debug',        default=False,
             description='Builds a debug version of the libraries')
 
-    depends_on('cmake', type='build')
-
     # MPI related dependencies
     depends_on('mpi')
     depends_on('hypre~internal-superlu', when='+hypre')

From 4b7b595e3cac6207e2f1a19fe5d250faf74ca495 Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret <jppelteret@gmail.com>
Date: Mon, 16 Jan 2017 01:20:26 +0100
Subject: [PATCH 16/25] New package: CppAD (#2832)

---
 .../repos/builtin/packages/cppad/package.py   | 48 +++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/cppad/package.py

diff --git a/var/spack/repos/builtin/packages/cppad/package.py b/var/spack/repos/builtin/packages/cppad/package.py
new file mode 100644
index 00000000000..1ec31bbeefa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cppad/package.py
@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Cppad(CMakePackage):
+    """A Package for Differentiation of C++ Algorithms."""
+
+    homepage = "https://www.coin-or.org/CppAD/"
+
+    version('20170114', '565a534dc813fa1289764222cd8c11ea')
+    version('develop', git='https://github.com/coin-or/CppAD.git')
+
+    depends_on('cmake', type='build')
+
+    def url_for_version(self, version):
+        """Handle version-based custom URLs."""
+        return "http://www.coin-or.org/download/source/CppAD/cppad-%s.gpl.tgz" % (version)
+
+    def cmake_args(self):
+        # This package does not obey CMAKE_INSTALL_PREFIX
+        args = [
+            "-Dcppad_prefix=%s" % (self.prefix),
+            "-Dcmake_install_docdir=share/cppad/doc"
+        ]
+        return args

From f480e3449eeb047e055af5bbfdf41eefd8de8d1a Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sun, 15 Jan 2017 18:23:16 -0600
Subject: [PATCH 17/25] Added customization for make targets in 'build' and
 'install' phases for CMakePackage (#2742)

* Added customization for make targets in 'build' and 'install' phases for CMakePackage

* Use rst in build system docs so that Sphinx generates nice API docs

* Allow AutotoolsPackages to be built in a different directory

* Flake8

* Fix missing import

* Allow configure to be located in different directory

* Update espressopp to use build targets

* Flake8

* Sphinx fix, lists must be a new paragraph

* Back out change that allowed a configure script in a different directory than build_directory

* Add missing deps, build in parallel

* Missing space for rst list
---
 lib/spack/spack/build_systems/autotools.py    | 52 ++++++++++++-------
 lib/spack/spack/build_systems/cmake.py        | 40 ++++++++------
 lib/spack/spack/build_systems/makefile.py     | 11 ++--
 lib/spack/spack/build_systems/r.py            |  1 +
 .../builtin/packages/espressopp/package.py    | 21 ++++----
 .../repos/builtin/packages/tcl/package.py     | 14 ++---
 .../repos/builtin/packages/tk/package.py      | 20 +++----
 .../repos/builtin/packages/zlib/package.py    | 13 ++---
 8 files changed, 95 insertions(+), 77 deletions(-)

diff --git a/lib/spack/spack/build_systems/autotools.py b/lib/spack/spack/build_systems/autotools.py
index dea4ae002f0..78a4df5e117 100644
--- a/lib/spack/spack/build_systems/autotools.py
+++ b/lib/spack/spack/build_systems/autotools.py
@@ -31,6 +31,7 @@
 from subprocess import check_call
 
 import llnl.util.tty as tty
+from llnl.util.filesystem import working_dir
 from spack.package import PackageBase
 
 
@@ -38,16 +39,17 @@ class AutotoolsPackage(PackageBase):
     """Specialized class for packages that are built using GNU Autotools
 
     This class provides four phases that can be overridden:
-    - autoreconf
-    - configure
-    - build
-    - install
+
+    * autoreconf
+    * configure
+    * build
+    * install
 
     They all have sensible defaults and for many packages the only thing
-    necessary will be to override `configure_args`
+    necessary will be to override ``configure_args``
 
     Additionally, you may specify make targets for build and install
-    phases by overriding `build_targets` and `install_targets`
+    phases by overriding ``build_targets`` and ``install_targets``
     """
     phases = ['autoreconf', 'configure', 'build', 'install']
     # To be used in UI queries that require to know which
@@ -124,6 +126,10 @@ def do_patch_config_guess(self):
 
         return False
 
+    def build_directory(self):
+        """Override to provide another place to build the package"""
+        return self.stage.source_path
+
     def patch(self):
         """Perform any required patches."""
 
@@ -138,39 +144,44 @@ def autoreconf(self, spec, prefix):
 
     @PackageBase.sanity_check('autoreconf')
     def is_configure_or_die(self):
-        """Checks the presence of a `configure` file after the
+        """Checks the presence of a ``configure`` file after the
         autoreconf phase"""
-        if not os.path.exists('configure'):
-            raise RuntimeError(
-                'configure script not found in {0}'.format(os.getcwd()))
+        with working_dir(self.build_directory()):
+            if not os.path.exists('configure'):
+                raise RuntimeError(
+                    'configure script not found in {0}'.format(os.getcwd()))
 
     def configure_args(self):
         """Method to be overridden. Should return an iterable containing
-        all the arguments that must be passed to configure, except --prefix
+        all the arguments that must be passed to configure, except ``--prefix``
         """
         return []
 
     def configure(self, spec, prefix):
-        """Runs configure with the arguments specified in `configure_args`
+        """Runs configure with the arguments specified in ``configure_args``
         and an appropriately set prefix
         """
         options = ['--prefix={0}'.format(prefix)] + self.configure_args()
-        inspect.getmodule(self).configure(*options)
+
+        with working_dir(self.build_directory()):
+            inspect.getmodule(self).configure(*options)
 
     def build(self, spec, prefix):
         """Make the build targets"""
-        inspect.getmodule(self).make(*self.build_targets)
+        with working_dir(self.build_directory()):
+            inspect.getmodule(self).make(*self.build_targets)
 
     def install(self, spec, prefix):
         """Make the install targets"""
-        inspect.getmodule(self).make(*self.install_targets)
+        with working_dir(self.build_directory()):
+            inspect.getmodule(self).make(*self.install_targets)
 
     @PackageBase.sanity_check('build')
     @PackageBase.on_package_attributes(run_tests=True)
     def _run_default_function(self):
-        """This function is run after build if self.run_tests == True
+        """This function is run after build if ``self.run_tests == True``
 
-        It will search for a method named `check` and run it. A sensible
+        It will search for a method named ``check`` and run it. A sensible
         default is provided in the base class.
         """
         try:
@@ -181,11 +192,12 @@ def _run_default_function(self):
             tty.msg('Skipping default sanity checks [method `check` not implemented]')  # NOQA: ignore=E501
 
     def check(self):
-        """Default test : search the Makefile for targets `test` and `check`
+        """Default test: search the Makefile for targets ``test`` and ``check``
         and run them if found.
         """
-        self._if_make_target_execute('test')
-        self._if_make_target_execute('check')
+        with working_dir(self.build_directory()):
+            self._if_make_target_execute('test')
+            self._if_make_target_execute('check')
 
     # Check that self.prefix is there after installation
     PackageBase.sanity_check('install')(PackageBase.sanity_check_prefix)
diff --git a/lib/spack/spack/build_systems/cmake.py b/lib/spack/spack/build_systems/cmake.py
index e097f7e44f1..61d45784e8f 100644
--- a/lib/spack/spack/build_systems/cmake.py
+++ b/lib/spack/spack/build_systems/cmake.py
@@ -24,7 +24,6 @@
 ##############################################################################
 
 import inspect
-import os
 import platform
 
 import llnl.util.tty as tty
@@ -35,21 +34,28 @@
 
 
 class CMakePackage(PackageBase):
-    """Specialized class for packages that are built using cmake
+    """Specialized class for packages that are built using CMake
 
     This class provides three phases that can be overridden:
-    - cmake
-    - build
-    - install
+
+    * cmake
+    * build
+    * install
 
     They all have sensible defaults and for many packages the only thing
-    necessary will be to override `cmake_args`
+    necessary will be to override ``cmake_args``
+
+    Additionally, you may specify make targets for build and install
+    phases by overriding ``build_targets`` and ``install_targets``
     """
     phases = ['cmake', 'build', 'install']
     # To be used in UI queries that require to know which
     # build-system class we are using
     build_system_class = 'CMakePackage'
 
+    build_targets = []
+    install_targets = ['install']
+
     depends_on('cmake', type='build')
 
     def build_type(self):
@@ -97,8 +103,9 @@ def build_directory(self):
     def cmake_args(self):
         """Method to be overridden. Should return an iterable containing
         all the arguments that must be passed to configure, except:
-        - CMAKE_INSTALL_PREFIX
-        - CMAKE_BUILD_TYPE
+
+        * CMAKE_INSTALL_PREFIX
+        * CMAKE_BUILD_TYPE
         """
         return []
 
@@ -106,26 +113,25 @@ def cmake(self, spec, prefix):
         """Run cmake in the build directory"""
         options = [self.root_cmakelists_dir()] + self.std_cmake_args + \
             self.cmake_args()
-        create = not os.path.exists(self.build_directory())
-        with working_dir(self.build_directory(), create=create):
+        with working_dir(self.build_directory(), create=True):
             inspect.getmodule(self).cmake(*options)
 
     def build(self, spec, prefix):
-        """The usual `make` after cmake"""
+        """Make the build targets"""
         with working_dir(self.build_directory()):
-            inspect.getmodule(self).make()
+            inspect.getmodule(self).make(*self.build_targets)
 
     def install(self, spec, prefix):
-        """...and the final `make install` after cmake"""
+        """Make the install targets"""
         with working_dir(self.build_directory()):
-            inspect.getmodule(self).make('install')
+            inspect.getmodule(self).make(*self.install_targets)
 
     @PackageBase.sanity_check('build')
     @PackageBase.on_package_attributes(run_tests=True)
     def _run_default_function(self):
-        """This function is run after build if self.run_tests == True
+        """This function is run after build if ``self.run_tests == True``
 
-        It will search for a method named `check` and run it. A sensible
+        It will search for a method named ``check`` and run it. A sensible
         default is provided in the base class.
         """
         try:
@@ -136,7 +142,7 @@ def _run_default_function(self):
             tty.msg('Skipping default build sanity checks [method `check` not implemented]')  # NOQA: ignore=E501
 
     def check(self):
-        """Default test : search the Makefile for the target `test`
+        """Default test: search the Makefile for the target ``test``
         and run them if found.
         """
         with working_dir(self.build_directory()):
diff --git a/lib/spack/spack/build_systems/makefile.py b/lib/spack/spack/build_systems/makefile.py
index fcc7ed2c995..a56f316109a 100644
--- a/lib/spack/spack/build_systems/makefile.py
+++ b/lib/spack/spack/build_systems/makefile.py
@@ -34,9 +34,10 @@ class MakefilePackage(PackageBase):
     """Specialized class for packages that are built using editable Makefiles
 
     This class provides three phases that can be overridden:
-    - edit
-    - build
-    - install
+
+    * edit
+    * build
+    * install
 
     It is necessary to override the 'edit' phase, while 'build' and 'install'
     have sensible defaults.
@@ -58,12 +59,12 @@ def edit(self, spec, prefix):
         tty.msg('Using default implementation: skipping edit phase.')
 
     def build(self, spec, prefix):
-        """Default build phase : call make passing build_args"""
+        """Make the build targets"""
         with working_dir(self.build_directory()):
             inspect.getmodule(self).make(*self.build_targets)
 
     def install(self, spec, prefix):
-        """Default install phase : call make passing install_args"""
+        """Make the install targets"""
         with working_dir(self.build_directory()):
             inspect.getmodule(self).make(*self.install_targets)
 
diff --git a/lib/spack/spack/build_systems/r.py b/lib/spack/spack/build_systems/r.py
index 52b3d82c601..f642f2dfd82 100644
--- a/lib/spack/spack/build_systems/r.py
+++ b/lib/spack/spack/build_systems/r.py
@@ -33,6 +33,7 @@ class RPackage(PackageBase):
     """Specialized class for packages that are built using R
 
     This class provides a single phase that can be overridden:
+
     * install
 
     It has sensible defaults and for many packages the only thing
diff --git a/var/spack/repos/builtin/packages/espressopp/package.py b/var/spack/repos/builtin/packages/espressopp/package.py
index 21e1cc13178..2903a02f7de 100644
--- a/var/spack/repos/builtin/packages/espressopp/package.py
+++ b/var/spack/repos/builtin/packages/espressopp/package.py
@@ -36,7 +36,7 @@ class Espressopp(CMakePackage):
     url      = "https://github.com/espressopp/espressopp/tarball/v1.9.4.1"
 
     version('develop', git='https://github.com/espressopp/espressopp.git', branch='master')
-    version('1.9.4.1', '0da74a6d4e1bfa6a2a24fca354245a4f') 
+    version('1.9.4.1', '0da74a6d4e1bfa6a2a24fca354245a4f')
     version('1.9.4', 'f2a27993a83547ad014335006eea74ea')
 
     variant('debug', default=False, description='Build debug version')
@@ -54,20 +54,23 @@ class Espressopp(CMakePackage):
     depends_on("fftw")
     depends_on("py-sphinx", when="+ug", type='build')
     depends_on("py-sphinx", when="+pdf", type='build')
+    depends_on('py-numpy', when="+ug", type='build')
+    depends_on('py-numpy', when="+pdf", type='build')
+    depends_on('py-matplotlib', when="+ug", type='build')
+    depends_on('py-matplotlib', when="+pdf", type='build')
     depends_on("texlive", when="+pdf", type='build')
     depends_on("doxygen", when="+dg", type='build')
 
-    def cmake_args(self):
+    def build_type(self):
         spec = self.spec
-        options = []
-        options.extend(['-DEXTERNAL_MPI4PY=ON', '-DEXTERNAL_BOOST=ON'])
         if '+debug' in spec:
-            options.extend(['-DCMAKE_BUILD_TYPE:STRING=Debug'])
+            return 'Debug'
         else:
-            options.extend(['-DCMAKE_BUILD_TYPE:STRING=Release'])
-        
-        return options 
-   
+            return 'Release'
+
+    def cmake_args(self):
+        return ['-DEXTERNAL_MPI4PY=ON', '-DEXTERNAL_BOOST=ON']
+
     def build(self, spec, prefix):
         with working_dir(self.build_directory()):
             make()
diff --git a/var/spack/repos/builtin/packages/tcl/package.py b/var/spack/repos/builtin/packages/tcl/package.py
index 16d896acc6c..d9b535305db 100644
--- a/var/spack/repos/builtin/packages/tcl/package.py
+++ b/var/spack/repos/builtin/packages/tcl/package.py
@@ -25,7 +25,7 @@
 from spack import *
 
 
-class Tcl(Package):
+class Tcl(AutotoolsPackage):
     """Tcl (Tool Command Language) is a very powerful but easy to
        learn dynamic programming language, suitable for a very wide
        range of uses, including web and desktop applications,
@@ -52,10 +52,10 @@ def setup_environment(self, spack_env, env):
         env.set('TCL_LIBRARY', join_path(self.prefix.lib, 'tcl{0}'.format(
                 self.spec.version.up_to(2))))
 
-    def install(self, spec, prefix):
-        with working_dir('unix'):
-            configure("--prefix={0}".format(prefix))
-            make()
-            make("install")
-        with working_dir(prefix.bin):
+    def build_directory(self):
+        return 'unix'
+
+    @AutotoolsPackage.sanity_check('install')
+    def symlink_tclsh(self):
+        with working_dir(self.prefix.bin):
             symlink('tclsh{0}'.format(self.version.up_to(2)), 'tclsh')
diff --git a/var/spack/repos/builtin/packages/tk/package.py b/var/spack/repos/builtin/packages/tk/package.py
index 1abcd26a240..071db04e635 100644
--- a/var/spack/repos/builtin/packages/tk/package.py
+++ b/var/spack/repos/builtin/packages/tk/package.py
@@ -25,7 +25,7 @@
 from spack import *
 
 
-class Tk(Package):
+class Tk(AutotoolsPackage):
     """Tk is a graphical user interface toolkit that takes developing
        desktop applications to a higher level than conventional
        approaches. Tk is the standard GUI not only for Tcl, but for
@@ -46,15 +46,15 @@ def url_for_version(self, version):
         base_url = "http://prdownloads.sourceforge.net/tcl"
         return "{0}/tk{1}-src.tar.gz".format(base_url, version)
 
-    def setup_environment(self, spack_env, env):
+    def setup_environment(self, spack_env, run_env):
         # When using Tkinter from within spack provided python+tk, python
         # will not be able to find Tcl/Tk unless TK_LIBRARY is set.
-        env.set('TK_LIBRARY', join_path(self.prefix.lib, 'tk{0}'.format(
-                self.spec.version.up_to(2))))
+        run_env.set('TK_LIBRARY', join_path(self.prefix.lib, 'tk{0}'.format(
+            self.spec.version.up_to(2))))
 
-    def install(self, spec, prefix):
-        with working_dir('unix'):
-            configure("--prefix={0}".format(prefix),
-                      "--with-tcl={0}".format(spec['tcl'].prefix.lib))
-            make()
-            make("install")
+    def build_directory(self):
+        return 'unix'
+
+    def configure_args(self):
+        spec = self.spec
+        return ['--with-tcl={0}'.format(spec['tcl'].prefix.lib)]
diff --git a/var/spack/repos/builtin/packages/zlib/package.py b/var/spack/repos/builtin/packages/zlib/package.py
index a20f6ff802b..ea758e01889 100644
--- a/var/spack/repos/builtin/packages/zlib/package.py
+++ b/var/spack/repos/builtin/packages/zlib/package.py
@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-from os import environ
 
 
 class Zlib(AutotoolsPackage):
@@ -35,17 +34,13 @@ class Zlib(AutotoolsPackage):
 
     version('1.2.10', 'd9794246f853d15ce0fcbf79b9a3cf13')
     # author had this to say about 1.2.9....
-    # Due to the bug fixes, any installations of 1.2.9 should be immediately 
+    # Due to the bug fixes, any installations of 1.2.9 should be immediately
     # replaced with 1.2.10.
     version('1.2.8', '44d667c142d7cda120332623eab69f40')
 
     variant('pic', default=True,
             description='Produce position-independent code (for shared libs)')
 
-    def configure(self, spec, prefix):
-
-        if '+pic' in spec:
-            environ['CFLAGS'] = self.compiler.pic_flag
-
-        config_args = ['--prefix', prefix]
-        configure(*config_args)
+    def setup_environment(self, spack_env, run_env):
+        if '+pic' in self.spec:
+            spack_env.set('CFLAGS', self.compiler.pic_flag)

From e3a631c90ee5538cba419e15b8071f5fd123d629 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sun, 15 Jan 2017 18:23:52 -0600
Subject: [PATCH 18/25] Add Astra package (#2800)

---
 .../repos/builtin/packages/astra/package.py   | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/astra/package.py

diff --git a/var/spack/repos/builtin/packages/astra/package.py b/var/spack/repos/builtin/packages/astra/package.py
new file mode 100644
index 00000000000..e32e70cada2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/astra/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Astra(Package):
+    """A Space Charge Tracking Algorithm."""
+
+    homepage = "http://www.desy.de/~mpyflo/"
+
+    version('2016-11-30', '17135b7a4adbacc1843a50a6a2ae2c25', expand=False,
+            url='http://www.desy.de/~mpyflo/Astra_for_64_Bit_Linux/Astra')
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('Astra', prefix.bin)
+
+        chmod = which('chmod')
+        chmod('+x', join_path(prefix.bin, 'Astra'))

From b2f29b855b2af712890584287cf9d61b5b136aba Mon Sep 17 00:00:00 2001
From: Jon Rood <jon.rood@nrel.gov>
Date: Sun, 15 Jan 2017 18:07:44 -0700
Subject: [PATCH 19/25] Updating BoxLib with the ability to build again.
 (#2813)

* Updating BoxLib with the ability to build again.

* Using Spack MPI compilers directly.

* Fixing typo.

* Using tarball from github archive for boxlib.
---
 .../repos/builtin/packages/boxlib/package.py  | 30 ++++++++++---------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/var/spack/repos/builtin/packages/boxlib/package.py b/var/spack/repos/builtin/packages/boxlib/package.py
index 4f41aba6c6a..8d46014d3b2 100644
--- a/var/spack/repos/builtin/packages/boxlib/package.py
+++ b/var/spack/repos/builtin/packages/boxlib/package.py
@@ -25,26 +25,28 @@
 from spack import *
 
 
-class Boxlib(Package):
+class Boxlib(CMakePackage):
     """BoxLib, a software framework for massively parallel
        block-structured adaptive mesh refinement (AMR) codes."""
 
     homepage = "https://ccse.lbl.gov/BoxLib/"
-    url = "https://ccse.lbl.gov/pub/Downloads/BoxLib.git"
+    url = "https://github.com/BoxLib-Codes/BoxLib/archive/16.12.2.tar.gz"
 
-    # TODO: figure out how best to version this.  No tags in the repo!
-    version('master', git='https://ccse.lbl.gov/pub/Downloads/BoxLib.git')
+    version('16.12.2', 'a28d92a5ff3fbbdbbd0a776a59f18526')
 
     depends_on('mpi')
-    depends_on('cmake', type='build')
 
-    def install(self, spec, prefix):
-        args = std_cmake_args
-        args += ['-DCCSE_ENABLE_MPI=1',
-                 '-DCMAKE_C_COMPILER=%s' % which('mpicc'),
-                 '-DCMAKE_CXX_COMPILER=%s' % which('mpicxx'),
-                 '-DCMAKE_Fortran_COMPILER=%s' % which('mpif90')]
+    def cmake_args(self):
+        spec = self.spec
+        options = []
 
-        cmake('.', *args)
-        make()
-        make("install")
+        options.extend([
+            # '-DBL_SPACEDIM=3',
+            '-DENABLE_POSITION_INDEPENDENT_CODE=ON',
+            '-DENABLE_FBASELIB=ON',
+            '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
+            '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
+            '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc
+        ])
+
+        return options

From a091eeceab650609ca3f88473bb3b6dc2c722573 Mon Sep 17 00:00:00 2001
From: becker33 <becker33@llnl.gov>
Date: Sun, 15 Jan 2017 19:17:54 -0800
Subject: [PATCH 20/25] Parser fix (#2769)

* Fixed parser to eliminate need for escape quotes. TODO: Fix double call to shlex, fix spaces in spec __str__

* Fixed double shlex

* cleanup

* rebased on develop

* Fixed parsing for multiple specs; broken since #360

* Revoked elimination of the `-` sigil in the syntax, and added it back into tests

* flake8

* more flake8

* Cleaned up dead code and added comments to parsing code

* bugfix for spaces in arguments; new bug found in testing

* Added unit tests for kv pairs in parsing/lexing

* Even more flake8

* ... yet another flake8

* Allow multiple specs in install

* unfathomable levels of flake8

* Updated documentation to match parser fix
---
 lib/spack/docs/basic_usage.rst                |  17 +--
 lib/spack/docs/features.rst                   |   2 +-
 lib/spack/docs/getting_started.rst            |   2 +-
 lib/spack/docs/tutorial_sc16_spack_basics.rst |  20 ++--
 lib/spack/spack/cmd/__init__.py               |   3 -
 lib/spack/spack/cmd/install.py                |  60 +++++-----
 lib/spack/spack/parse.py                      |  56 +++++++--
 lib/spack/spack/spec.py                       |  80 +++++++------
 lib/spack/spack/test/spec_syntax.py           | 109 ++++++++++++++++--
 9 files changed, 243 insertions(+), 106 deletions(-)

diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst
index 7ec61334db1..f25247579b1 100644
--- a/lib/spack/docs/basic_usage.rst
+++ b/lib/spack/docs/basic_usage.rst
@@ -647,8 +647,8 @@ avoid ambiguity.
 
 When spack normalizes specs, it prints them out with no spaces boolean
 variants using the backwards compatibility syntax and uses only ``~``
-for disabled boolean variants.  We allow ``-`` and spaces on the command
-line is provided for convenience and legibility.
+for disabled boolean variants.  The ``-`` and spaces on the command
+line are provided for convenience and legibility.
 
 ^^^^^^^^^^^^^^
 Compiler Flags
@@ -658,14 +658,17 @@ Compiler flags are specified using the same syntax as non-boolean variants,
 but fulfill a different purpose. While the function of a variant is set by
 the package, compiler flags are used by the compiler wrappers to inject
 flags into the compile line of the build. Additionally, compiler flags are
-inherited by dependencies. ``spack install libdwarf cppflags=\"-g\"`` will
+inherited by dependencies. ``spack install libdwarf cppflags="-g"`` will
 install both libdwarf and libelf with the ``-g`` flag injected into their
 compile line.
 
-Notice that the value of the compiler flags must be escape quoted on the
-command line. From within python files, the same spec would be specified
-``libdwarf cppflags="-g"``. This is necessary because of how the shell
-handles the quote symbols.
+Notice that the value of the compiler flags must be quoted if it
+contains any spaces. Any of ``cppflags=-O3``, ``cppflags="-O3"``,
+``cppflags='-O3'``, and ``cppflags="-O3 -fPIC"`` are acceptable, but
+``cppflags=-O3 -fPIC`` is not. Additionally, if they value of the
+compiler flags is not the last thing on the line, it must be followed
+by a space. The commmand ``spack install libelf cppflags="-O3"%intel``
+will be interpreted as an attempt to set `cppflags="-O3%intel"``.
 
 The six compiler flags are injected in the order of implicit make commands
 in GNU Autotools. If all flags are set, the order is
diff --git a/lib/spack/docs/features.rst b/lib/spack/docs/features.rst
index 2df1d182d6d..8d7c1ec0cdf 100644
--- a/lib/spack/docs/features.rst
+++ b/lib/spack/docs/features.rst
@@ -41,7 +41,7 @@ platform, all on the command line.
    $ spack install mpileaks@1.1.2 %gcc@4.7.3 +debug
 
    # Add compiler flags using the conventional names
-   $ spack install mpileaks@1.1.2 %gcc@4.7.3 cppflags=\"-O3 -floop-block\"
+   $ spack install mpileaks@1.1.2 %gcc@4.7.3 cppflags="-O3 -floop-block"
 
    # Cross-compile for a different architecture with arch=
    $ spack install mpileaks@1.1.2 arch=bgqos_0
diff --git a/lib/spack/docs/getting_started.rst b/lib/spack/docs/getting_started.rst
index 8e5ee7f3790..efc1965ce97 100644
--- a/lib/spack/docs/getting_started.rst
+++ b/lib/spack/docs/getting_started.rst
@@ -632,7 +632,7 @@ the command line:
 
 .. code-block:: console
 
-   $ spack install openmpi fflags=\"-mismatch\"
+   $ spack install openmpi fflags="-mismatch"
 
 Or it can be set permanently in your ``compilers.yaml``:
 
diff --git a/lib/spack/docs/tutorial_sc16_spack_basics.rst b/lib/spack/docs/tutorial_sc16_spack_basics.rst
index 532410058dd..9511907cebb 100644
--- a/lib/spack/docs/tutorial_sc16_spack_basics.rst
+++ b/lib/spack/docs/tutorial_sc16_spack_basics.rst
@@ -184,15 +184,15 @@ compilers.
   [+] ~/spack/opt/spack/linux-redhat6-x86_64/intel-15.0.4/libelf-0.8.13-w33hrejdyqu2j2gggdswitls2zv6kdsi
 
 
-The spec syntax also includes compiler flags. Spack accepts ``cppflags``,
-``cflags``, ``cxxflags``, ``fflags``, ``ldflags``, and ``ldlibs``
-parameters.  The values of these fields must be escape-quoted with ``\"``
-on the command line. These values are injected into the compile line
-automatically by the Spack compiler wrappers.
+The spec syntax also includes compiler flags. Spack accepts
+``cppflags``, ``cflags``, ``cxxflags``, ``fflags``, ``ldflags``, and
+``ldlibs`` parameters.  The values of these fields must be quoted on
+the command line if they include spaces. These values are injected
+into the compile line automatically by the Spack compiler wrappers.
 
 .. code-block:: console
 
-  $ spack install libelf @0.8.12 cppflags=\"-O3\"
+  $ spack install libelf @0.8.12 cppflags="-O3"
   ==> Installing libelf
   ==> Trying to fetch from ~/spack/var/spack/cache/libelf/libelf-0.8.12.tar.gz
   ################################################################################################################################################################################# 100.0%
@@ -309,7 +309,7 @@ top-level package, we can also specify about a dependency using ``^``.
 
 Packages can also be referred to from the command line by their package
 hash. Using the ``spack find -lf`` command earlier we saw that the hash
-of our optimized installation of libelf (``cppflags=\"-O3\"``) began with
+of our optimized installation of libelf (``cppflags="-O3"``) began with
 ``vrv2ttb``. We can now explicitly build with that package without typing
 the entire spec, by using the ``/`` sigil to refer to it by hash. As with
 other tools like git, you do not need to specify an *entire* hash on the
@@ -1103,8 +1103,8 @@ already covered in the :ref:`basics-tutorial-install` and
 The ``spack find`` command can accept what we call "anonymous specs."
 These are expressions in spec syntax that do not contain a package
 name. For example, `spack find %intel` will return every package built
-with the intel compiler, and ``spack find cppflags=\\"-O3\\"`` will
-return every package which was built with ``cppflags=\\"-O3\\"``.
+with the intel compiler, and ``spack find cppflags="-O3"`` will
+return every package which was built with ``cppflags="-O3"``.
 
 .. code-block:: console
 
@@ -1115,7 +1115,7 @@ return every package which was built with ``cppflags=\\"-O3\\"``.
 
 
 
-  $ spack find cppflags=\"-O3\"
+  $ spack find cppflags="-O3"
   ==> 1 installed packages.
   -- linux-redhat6-x86_64 / gcc@4.4.7 -----------------------------
   libelf@0.8.12
diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py
index 3e83dbb789f..6fa08830144 100644
--- a/lib/spack/spack/cmd/__init__.py
+++ b/lib/spack/spack/cmd/__init__.py
@@ -108,9 +108,6 @@ def parse_specs(args, **kwargs):
     concretize = kwargs.get('concretize', False)
     normalize = kwargs.get('normalize', False)
 
-    if isinstance(args, (python_list, tuple)):
-        args = " ".join(args)
-
     try:
         specs = spack.spec.parse(args)
         for spec in specs:
diff --git a/lib/spack/spack/cmd/install.py b/lib/spack/spack/cmd/install.py
index 38994790ae3..3731fe3c81a 100644
--- a/lib/spack/spack/cmd/install.py
+++ b/lib/spack/spack/cmd/install.py
@@ -315,36 +315,36 @@ def install(parser, args, **kwargs):
 
     # Spec from cli
     specs = spack.cmd.parse_specs(args.package, concretize=True)
-    if len(specs) != 1:
-        tty.error('only one spec can be installed at a time.')
-    spec = specs.pop()
+    if len(specs) == 0:
+        tty.error('The `spack install` command requires a spec to install.')
 
-    # Check if we were asked to produce some log for dashboards
-    if args.log_format is not None:
-        # Compute the filename for logging
-        log_filename = args.log_file
-        if not log_filename:
-            log_filename = default_log_file(spec)
-        # Create the test suite in which to log results
-        test_suite = TestSuite(spec)
-        # Decorate PackageBase.do_install to get installation status
-        PackageBase.do_install = junit_output(
-            spec, test_suite
-        )(PackageBase.do_install)
+    for spec in specs:
+        # Check if we were asked to produce some log for dashboards
+        if args.log_format is not None:
+            # Compute the filename for logging
+            log_filename = args.log_file
+            if not log_filename:
+                log_filename = default_log_file(spec)
+            # Create the test suite in which to log results
+            test_suite = TestSuite(spec)
+            # Decorate PackageBase.do_install to get installation status
+            PackageBase.do_install = junit_output(
+                spec, test_suite
+            )(PackageBase.do_install)
 
-    # Do the actual installation
-    if args.things_to_install == 'dependencies':
-        # Install dependencies as-if they were installed
-        # for root (explicit=False in the DB)
-        kwargs['explicit'] = False
-        for s in spec.dependencies():
-            p = spack.repo.get(s)
-            p.do_install(**kwargs)
-    else:
-        package = spack.repo.get(spec)
-        kwargs['explicit'] = True
-        package.do_install(**kwargs)
+        # Do the actual installation
+        if args.things_to_install == 'dependencies':
+            # Install dependencies as-if they were installed
+            # for root (explicit=False in the DB)
+            kwargs['explicit'] = False
+            for s in spec.dependencies():
+                p = spack.repo.get(s)
+                p.do_install(**kwargs)
+        else:
+            package = spack.repo.get(spec)
+            kwargs['explicit'] = True
+            package.do_install(**kwargs)
 
-    # Dump log file if asked to
-    if args.log_format is not None:
-        test_suite.dump(log_filename)
+        # Dump log file if asked to
+        if args.log_format is not None:
+            test_suite.dump(log_filename)
diff --git a/lib/spack/spack/parse.py b/lib/spack/spack/parse.py
index 1b88db2d7c5..e116175823b 100644
--- a/lib/spack/spack/parse.py
+++ b/lib/spack/spack/parse.py
@@ -23,6 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import re
+import shlex
 import itertools
 import spack.error
 
@@ -53,18 +54,55 @@ def __cmp__(self, other):
 class Lexer(object):
     """Base class for Lexers that keep track of line numbers."""
 
-    def __init__(self, lexicon):
-        self.scanner = re.Scanner(lexicon)
+    def __init__(self, lexicon0, mode_switches_01=[],
+                 lexicon1=[], mode_switches_10=[]):
+        self.scanner0 = re.Scanner(lexicon0)
+        self.mode_switches_01 = mode_switches_01
+        self.scanner1 = re.Scanner(lexicon1)
+        self.mode_switches_10 = mode_switches_10
+        self.mode = 0
 
     def token(self, type, value=''):
-        return Token(type, value,
-                     self.scanner.match.start(0), self.scanner.match.end(0))
+        if self.mode == 0:
+            return Token(type, value,
+                         self.scanner0.match.start(0),
+                         self.scanner0.match.end(0))
+        else:
+            return Token(type, value,
+                         self.scanner1.match.start(0),
+                         self.scanner1.match.end(0))
+
+    def lex_word(self, word):
+        scanner = self.scanner0
+        mode_switches = self.mode_switches_01
+        if self.mode == 1:
+            scanner = self.scanner1
+            mode_switches = self.mode_switches_10
+
+        tokens, remainder = scanner.scan(word)
+        remainder_used = 0
+
+        for i, t in enumerate(tokens):
+            if t.type in mode_switches:
+                # Combine post-switch tokens with remainder and
+                # scan in other mode
+                self.mode = 1 - self.mode  # swap 0/1
+                remainder_used = 1
+                tokens = tokens[:i + 1] + self.lex_word(
+                    word[word.index(t.value) + len(t.value):])
+                break
+
+        if remainder and not remainder_used:
+            raise LexError("Invalid character", word, word.index(remainder))
+
+        return tokens
 
     def lex(self, text):
-        tokens, remainder = self.scanner.scan(text)
-        if remainder:
-            raise LexError("Invalid character", text, text.index(remainder))
-        return tokens
+        lexed = []
+        for word in text:
+            tokens = self.lex_word(word)
+            lexed.extend(tokens)
+        return lexed
 
 
 class Parser(object):
@@ -121,6 +159,8 @@ def expect(self, id):
             sys.exit(1)
 
     def setup(self, text):
+        if isinstance(text, basestring):
+            text = shlex.split(text)
         self.text = text
         self.push_tokens(self.lexer.lex(text))
 
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 8c6dd36c845..e34f2b799d3 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -614,7 +614,7 @@ def __str__(self):
         if type(self.value) == bool:
             return '{0}{1}'.format('+' if self.value else '~', self.name)
         else:
-            return ' {0}={1}'.format(self.name, self.value)
+            return ' {0}={1} '.format(self.name, self.value)
 
 
 class VariantMap(HashableMap):
@@ -731,7 +731,8 @@ def __str__(self):
         cond_symbol = ' ' if len(sorted_keys) > 0 else ''
         return cond_symbol + ' '.join(
             str(key) + '=\"' + ' '.join(
-                str(f) for f in self[key]) + '\"' for key in sorted_keys)
+                str(f) for f in self[key]) + '\"'
+            for key in sorted_keys) + cond_symbol
 
 
 class DependencyMap(HashableMap):
@@ -2447,7 +2448,8 @@ def write(s, c):
                         write(fmt % str(self.variants), c)
                 elif c == '=':
                     if self.architecture and str(self.architecture):
-                        write(fmt % (' arch' + c + str(self.architecture)), c)
+                        a_str = ' arch' + c + str(self.architecture) + ' '
+                        write(fmt % (a_str), c)
                 elif c == '#':
                     out.write('-' + fmt % (self.dag_hash(7)))
                 elif c == '$':
@@ -2506,7 +2508,7 @@ def write(s, c):
                         write(fmt % str(self.variants), '+')
                 elif named_str == 'ARCHITECTURE':
                     if self.architecture and str(self.architecture):
-                        write(fmt % str(self.architecture), ' arch=')
+                        write(fmt % str(self.architecture) + ' ', ' arch=')
                 elif named_str == 'SHA1':
                     if self.dependencies:
                         out.write(fmt % str(self.dag_hash(7)))
@@ -2576,7 +2578,8 @@ def __cmp__(self, other):
         return 0
 
     def __str__(self):
-        return self.format() + self.dep_string()
+        ret = self.format() + self.dep_string()
+        return ret.strip()
 
     def _install_status(self):
         """Helper for tree to print DB install status."""
@@ -2650,7 +2653,7 @@ def __repr__(self):
 #
 # These are possible token types in the spec grammar.
 #
-HASH, DEP, AT, COLON, COMMA, ON, OFF, PCT, EQ, QT, ID = range(11)
+HASH, DEP, AT, COLON, COMMA, ON, OFF, PCT, EQ, ID, VAL = range(11)
 
 
 class SpecLexer(spack.parse.Lexer):
@@ -2671,10 +2674,12 @@ def __init__(self):
             (r'\=', lambda scanner, val: self.token(EQ,    val)),
             # This is more liberal than identifier_re (see above).
             # Checked by check_identifier() for better error messages.
-            (r'([\"\'])(?:(?=(\\?))\2.)*?\1',
-             lambda scanner, val: self.token(QT, val)),
             (r'\w[\w.-]*', lambda scanner, val: self.token(ID,    val)),
-            (r'\s+', lambda scanner, val: None)])
+            (r'\s+', lambda scanner, val: None)],
+            [EQ],
+            [(r'[\S].*', lambda scanner, val: self.token(VAL,    val)),
+             (r'\s+', lambda scanner, val: None)],
+            [VAL])
 
 
 # Lexer is always the same for every parser.
@@ -2689,36 +2694,49 @@ def __init__(self):
 
     def do_parse(self):
         specs = []
+
         try:
-            while self.next:
+            while self.next or self.previous:
                 # TODO: clean this parsing up a bit
                 if self.previous:
+                    # We picked up the name of this spec while finishing the
+                    # previous spec
                     specs.append(self.spec(self.previous.value))
-                if self.accept(ID):
+                    self.previous = None
+                elif self.accept(ID):
                     self.previous = self.token
                     if self.accept(EQ):
+                        # We're either parsing an anonymous spec beginning
+                        # with a key-value pair or adding a key-value pair
+                        # to the last spec
                         if not specs:
                             specs.append(self.spec(None))
-                        if self.accept(QT):
-                            self.token.value = self.token.value[1:-1]
-                        else:
-                            self.expect(ID)
+                        self.expect(VAL)
                         specs[-1]._add_flag(
                             self.previous.value, self.token.value)
+                        self.previous = None
                     else:
-                        specs.append(self.spec(self.previous.value))
-                    self.previous = None
+                        # We're parsing a new spec by name
+                        value = self.previous.value
+                        self.previous = None
+                        specs.append(self.spec(value))
                 elif self.accept(HASH):
+                    # We're finding a spec by hash
                     specs.append(self.spec_by_hash())
 
                 elif self.accept(DEP):
                     if not specs:
+                        # We're parsing an anonymous spec beginning with a
+                        # dependency
                         self.previous = self.token
                         specs.append(self.spec(None))
                         self.previous = None
                     if self.accept(HASH):
+                        # We're finding a dependency by hash for an anonymous
+                        # spec
                         dep = self.spec_by_hash()
                     else:
+                        # We're adding a dependency to the last spec
                         self.expect(ID)
                         dep = self.spec(self.token.value)
 
@@ -2727,11 +2745,12 @@ def do_parse(self):
                     specs[-1]._add_dependency(dep, ())
 
                 else:
-                    # Attempt to construct an anonymous spec, but check that
-                    # the first token is valid
-                    # TODO: Is this check even necessary, or will it all be Lex
-                    # errors now?
-                    specs.append(self.spec(None, True))
+                    # If the next token can be part of a valid anonymous spec,
+                    # create the anonymous spec
+                    if self.next.type in (AT, ON, OFF, PCT):
+                        specs.append(self.spec(None))
+                    else:
+                        self.unexpected_token()
 
         except spack.parse.ParseError as e:
             raise SpecParseError(e)
@@ -2768,7 +2787,7 @@ def spec_by_hash(self):
 
         return matches[0]
 
-    def spec(self, name, check_valid_token=False):
+    def spec(self, name):
         """Parse a spec out of the input.  If a spec is supplied, then initialize
            and return it instead of creating a new one."""
         if name:
@@ -2819,35 +2838,28 @@ def spec(self, name, check_valid_token=False):
                 for version in vlist:
                     spec._add_version(version)
                 added_version = True
-                check_valid_token = False
 
             elif self.accept(ON):
                 spec._add_variant(self.variant(), True)
-                check_valid_token = False
 
             elif self.accept(OFF):
                 spec._add_variant(self.variant(), False)
-                check_valid_token = False
 
             elif self.accept(PCT):
                 spec._set_compiler(self.compiler())
-                check_valid_token = False
 
             elif self.accept(ID):
                 self.previous = self.token
                 if self.accept(EQ):
-                    if self.accept(QT):
-                        self.token.value = self.token.value[1:-1]
-                    else:
-                        self.expect(ID)
+                    # We're adding a key-value pair to the spec
+                    self.expect(VAL)
                     spec._add_flag(self.previous.value, self.token.value)
                     self.previous = None
                 else:
-                    return spec
+                    # We've found the start of a new spec. Go back to do_parse
+                    break
 
             else:
-                if check_valid_token:
-                    self.unexpected_token()
                 break
 
         # If there was no version in the spec, consier it an open range
diff --git a/lib/spack/spack/test/spec_syntax.py b/lib/spack/spack/test/spec_syntax.py
index 3cf094f25ae..043d9b176fb 100644
--- a/lib/spack/spack/test/spec_syntax.py
+++ b/lib/spack/spack/test/spec_syntax.py
@@ -23,6 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import pytest
+import shlex
 
 import spack.spec as sp
 from spack.parse import Token
@@ -53,6 +54,34 @@
                Token(sp.AT),
                Token(sp.ID, '8.1_1e')]
 
+# Another sample lexer output with a kv pair.
+kv_lex = [Token(sp.ID, 'mvapich_foo'),
+          Token(sp.ID, 'debug'),
+          Token(sp.EQ),
+          Token(sp.VAL, '4'),
+          Token(sp.DEP),
+          Token(sp.ID, '_openmpi'),
+          Token(sp.AT),
+          Token(sp.ID, '1.2'),
+          Token(sp.COLON),
+          Token(sp.ID, '1.4'),
+          Token(sp.COMMA),
+          Token(sp.ID, '1.6'),
+          Token(sp.PCT),
+          Token(sp.ID, 'intel'),
+          Token(sp.AT),
+          Token(sp.ID, '12.1'),
+          Token(sp.COLON),
+          Token(sp.ID, '12.6'),
+          Token(sp.ON),
+          Token(sp.ID, 'debug'),
+          Token(sp.OFF),
+          Token(sp.ID, 'qt_4'),
+          Token(sp.DEP),
+          Token(sp.ID, 'stackwalker'),
+          Token(sp.AT),
+          Token(sp.ID, '8.1_1e')]
+
 
 class TestSpecSyntax(object):
     # ========================================================================
@@ -81,9 +110,10 @@ def check_parse(self, expected, spec=None, remove_arch=True):
 
     def check_lex(self, tokens, spec):
         """Check that the provided spec parses to the provided token list."""
+        spec = shlex.split(spec)
         lex_output = sp.SpecLexer().lex(spec)
         for tok, spec_tok in zip(tokens, lex_output):
-            if tok.type == sp.ID:
+            if tok.type == sp.ID or tok.type == sp.VAL:
                 assert tok == spec_tok
             else:
                 # Only check the type for non-identifiers.
@@ -112,10 +142,19 @@ def test_dependencies_with_versions(self):
         self.check_parse("openmpi^hwloc@:1.4b7-rc3")
         self.check_parse("openmpi^hwloc@1.2e6:1.4b7-rc3")
 
-    @pytest.mark.xfail
     def test_multiple_specs(self):
         self.check_parse("mvapich emacs")
 
+    def test_multiple_specs_after_kv(self):
+        self.check_parse('mvapich cppflags="-O3 -fPIC" emacs')
+        self.check_parse('mvapich cflags="-O3" emacs',
+                         'mvapich cflags=-O3 emacs')
+
+    def test_multiple_specs_long_second(self):
+        self.check_parse('mvapich emacs@1.1.1%intel cflags="-O3"',
+                         'mvapich emacs @1.1.1 %intel cflags=-O3')
+        self.check_parse('mvapich cflags="-O3 -fPIC" emacs^ncurses%intel')
+
     def test_full_specs(self):
         self.check_parse(
             "mvapich_foo"
@@ -123,15 +162,15 @@ 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 debug=2 ~qt_4"
             "^stackwalker@8.1_1e")
         self.check_parse(
             'mvapich_foo'
-            '^_openmpi@1.2:1.4,1.6%intel@12.1 cppflags="-O3"+debug~qt_4'
+            '^_openmpi@1.2:1.4,1.6%intel@12.1 cppflags="-O3" +debug~qt_4'
             '^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 debug=2 ~qt_4"
             "^stackwalker@8.1_1e arch=test-redhat6-x86_32")
 
     def test_canonicalize(self):
@@ -158,19 +197,19 @@ def test_canonicalize(self):
             "x ^y~f+e~d+c~b+a@4,2:3,1%intel@4,3,2,1")
 
         self.check_parse(
-            "x arch=test-redhat6-None"
-            "^y arch=test-None-x86_64"
+            "x arch=test-redhat6-None "
+            "^y arch=test-None-x86_64 "
             "^z arch=linux-None-None",
 
-            "x os=fe"
-            "^y target=be"
+            "x os=fe "
+            "^y target=be "
             "^z platform=linux")
 
         self.check_parse(
-            "x arch=test-debian6-x86_64"
+            "x arch=test-debian6-x86_64 "
             "^y arch=test-debian6-x86_64",
 
-            "x os=default_os target=default_target"
+            "x os=default_os target=default_target "
             "^y os=default_os target=default_target")
 
         self.check_parse("x^y", "x@: ^y@:")
@@ -184,7 +223,7 @@ def test_duplicate_variant(self):
             'x@1.2+debug+debug',
             'x ^y@1.2+debug debug=true',
             'x ^y@1.2 debug=false debug=true',
-            'x ^y@1.2 debug=false~debug'
+            'x ^y@1.2 debug=false ~debug'
         ]
         self._check_raises(DuplicateVariantError, duplicates)
 
@@ -277,3 +316,49 @@ def test_way_too_many_spaces(self):
             "mvapich_foo "
             "^ _openmpi @1.2 : 1.4 , 1.6 % intel @ 12.1 : 12.6 + debug - qt_4 "
             "^ stackwalker @ 8.1_1e")
+        self.check_lex(
+            complex_lex,
+            "mvapich_foo "
+            "^ _openmpi @1.2 : 1.4 , 1.6 % intel @ 12.1 : 12.6 + debug ~ qt_4 "
+            "^ stackwalker @ 8.1_1e")
+
+    def test_kv_with_quotes(self):
+        self.check_lex(
+            kv_lex,
+            "mvapich_foo debug='4' "
+            "^ _openmpi @1.2 : 1.4 , 1.6 % intel @ 12.1 : 12.6 + debug - qt_4 "
+            "^ stackwalker @ 8.1_1e")
+        self.check_lex(
+            kv_lex,
+            'mvapich_foo debug="4" '
+            "^ _openmpi @1.2 : 1.4 , 1.6 % intel @ 12.1 : 12.6 + debug - qt_4 "
+            "^ stackwalker @ 8.1_1e")
+        self.check_lex(
+            kv_lex,
+            "mvapich_foo 'debug = 4' "
+            "^ _openmpi @1.2 : 1.4 , 1.6 % intel @ 12.1 : 12.6 + debug - qt_4 "
+            "^ stackwalker @ 8.1_1e")
+
+    def test_kv_without_quotes(self):
+        self.check_lex(
+            kv_lex,
+            "mvapich_foo debug=4 "
+            "^ _openmpi @1.2 : 1.4 , 1.6 % intel @ 12.1 : 12.6 + debug - qt_4 "
+            "^ stackwalker @ 8.1_1e")
+
+    def test_kv_with_spaces(self):
+        self.check_lex(
+            kv_lex,
+            "mvapich_foo debug = 4 "
+            "^ _openmpi @1.2 : 1.4 , 1.6 % intel @ 12.1 : 12.6 + debug - qt_4 "
+            "^ stackwalker @ 8.1_1e")
+        self.check_lex(
+            kv_lex,
+            "mvapich_foo debug =4 "
+            "^ _openmpi @1.2 : 1.4 , 1.6 % intel @ 12.1 : 12.6 + debug - qt_4 "
+            "^ stackwalker @ 8.1_1e")
+        self.check_lex(
+            kv_lex,
+            "mvapich_foo debug= 4 "
+            "^ _openmpi @1.2 : 1.4 , 1.6 % intel @ 12.1 : 12.6 + debug - qt_4 "
+            "^ stackwalker @ 8.1_1e")

From e2697e4a37185a5493580e0399067ecaff6d86c7 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Mon, 16 Jan 2017 10:17:35 +0100
Subject: [PATCH 21/25] isl: add latest version (#2834)

added latest version of isl. Needed to get llvm/clang in the latest
trunk to build via spack, but there are more versions available.
what is the policy regarding those? Add what we need for now?
---
 var/spack/repos/builtin/packages/isl/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/isl/package.py b/var/spack/repos/builtin/packages/isl/package.py
index 259f4881f5a..f6188e6b3e0 100644
--- a/var/spack/repos/builtin/packages/isl/package.py
+++ b/var/spack/repos/builtin/packages/isl/package.py
@@ -31,6 +31,7 @@ class Isl(Package):
     homepage = "http://isl.gforge.inria.fr"
     url      = "http://isl.gforge.inria.fr/isl-0.14.tar.bz2"
 
+    version('0.18', '11436d6b205e516635b666090b94ab32')
     version('0.14', 'acd347243fca5609e3df37dba47fd0bb')
 
     depends_on("gmp")

From 8365dbd959f0c8346017c64298fa1cac06122609 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 16 Jan 2017 11:23:07 +0100
Subject: [PATCH 22/25] petsc: add 64bit variant (#2655)

* petsc: add 64bit variant

* hypre: add int64 variant

* superlu-dist: add int64 variant

* petsc: add int64 variant

* metis: rename idx64 to int64 to make it consistent with other packages

* mumps: rename idx64 to int64 to make it consistent with other packages

* dealii: rename 64bit to int64 to make it consistent with other packages
---
 .../repos/builtin/packages/dealii/package.py  | 12 ++++----
 .../repos/builtin/packages/hypre/package.py   |  5 ++++
 .../repos/builtin/packages/metis/package.py   |  8 ++---
 .../repos/builtin/packages/mumps/package.py   |  4 +--
 .../repos/builtin/packages/petsc/package.py   | 29 +++++++++++++------
 .../builtin/packages/superlu-dist/package.py  |  9 ++++--
 6 files changed, 44 insertions(+), 23 deletions(-)

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 8c31b90f519..66267b2d9a7 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -66,7 +66,7 @@ class Dealii(CMakePackage):
             description='Compile with Trilinos (only with MPI)')
     variant('python',   default=True,
             description='Compile with Python bindings')
-    variant('64bit',    default=False,
+    variant('int64',    default=False,
             description='Compile with 64 bit indices support')
 
     # required dependencies, light version
@@ -108,11 +108,11 @@ class Dealii(CMakePackage):
     depends_on("netcdf-cxx",       when='+netcdf+mpi')
     depends_on("oce",              when='+oce')
     depends_on("p4est",            when='+p4est+mpi')
-    depends_on("petsc+mpi",        when='@8.4.2:+petsc+mpi~64bit')
+    depends_on("petsc+mpi",        when='@8.4.2:+petsc+mpi~int64')
     depends_on('python',           when='@8.5.0:+python')
-    depends_on("slepc",            when='@8.4.2:+slepc+petsc+mpi~64bit')
-    depends_on("petsc@:3.6.4+mpi", when='@:8.4.1+petsc+mpi~64bit')
-    depends_on("slepc@:3.6.3",     when='@:8.4.1+slepc+petsc+mpi~64bit')
+    depends_on("slepc",            when='@8.4.2:+slepc+petsc+mpi~int64')
+    depends_on("petsc@:3.6.4+mpi", when='@:8.4.1+petsc+mpi~int64')
+    depends_on("slepc@:3.6.3",     when='@:8.4.1+slepc+petsc+mpi~int64')
     depends_on("trilinos",         when='+trilinos+mpi')
 
     def build_type(self):
@@ -244,7 +244,7 @@ def cmake_args(self):
 
         # 64 bit indices
         options.extend([
-            '-DDEAL_II_WITH_64BIT_INDICES=%s' % ('+64bit' in spec)
+            '-DDEAL_II_WITH_64BIT_INDICES=%s' % ('+int64' in spec)
         ])
 
         return options
diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index 82a6b06b1f1..ed0f665462f 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -46,6 +46,8 @@ class Hypre(Package):
     # SuperluDist have conflicting headers with those in Hypre
     variant('internal-superlu', default=True,
             description="Use internal Superlu routines")
+    variant('int64', default=False,
+            description="Use 64bit integers")
 
     depends_on("mpi")
     depends_on("blas")
@@ -68,6 +70,9 @@ def install(self, spec, prefix):
             '--with-blas-lib-dirs=%s' % ' '.join(blas.directories)
         ]
 
+        if '+int64' in self.spec:
+            configure_args.append('--enable-bigint')
+
         if '+shared' in self.spec:
             configure_args.append("--enable-shared")
 
diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index ca48a47817a..b66677288c1 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -47,7 +47,7 @@ class Metis(Package):
     variant('debug', default=False, description='Builds the library in debug mode.')
     variant('gdb', default=False, description='Enables gdb support.')
 
-    variant('idx64', default=False, description='Sets the bit width of METIS\'s index type to 64.')
+    variant('int64', default=False, description='Sets the bit width of METIS\'s index type to 64.')
     variant('real64', default=False, description='Sets the bit width of METIS\'s real type to 64.')
 
     depends_on('cmake@2.8:', when='@5:', type='build')
@@ -69,7 +69,7 @@ def patch(self):
 
         metis_header.filter(
             r'(\b)(IDXTYPEWIDTH )(\d+)(\b)',
-            r'\1\2{0}\4'.format('64' if '+idx64' in self.spec else '32'),
+            r'\1\2{0}\4'.format('64' if '+int64' in self.spec else '32'),
         )
         metis_header.filter(
             r'(\b)(REALTYPEWIDTH )(\d+)(\b)',
@@ -87,9 +87,9 @@ def patch(self):
     @when('@:4')
     def install(self, spec, prefix):
         # Process library spec and options
-        if any('+{0}'.format(v) in spec for v in ['gdb', 'idx64', 'real64']):
+        if any('+{0}'.format(v) in spec for v in ['gdb', 'int64', 'real64']):
             raise InstallError('METIS@:4 does not support the following '
-                               'variants: gdb, idx64, real64.')
+                               'variants: gdb, int64, real64.')
 
         options = ['COPTIONS=-fPIC']
         if '+debug' in spec:
diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index fcb6549d297..82d0c606b68 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -55,7 +55,7 @@ class Mumps(Package):
             description='Activate the compilation of smumps')
     variant('complex', default=True,
             description='Activate the compilation of cmumps and/or zmumps')
-    variant('idx64', default=False,
+    variant('int64', default=False,
             description='Use int64_t/integer*8 as default index type')
     variant('shared', default=True, description='Build shared libraries')
 
@@ -125,7 +125,7 @@ def write_makefile_inc(self):
         fpic = '-fPIC' if '+shared' in self.spec else ''
         # TODO: test this part, it needs a full blas, scalapack and
         # partitionning environment with 64bit integers
-        if '+idx64' in self.spec:
+        if '+int64' in self.spec:
             makefile_conf.extend(
                 # the fortran compilation flags most probably are
                 # working only for intel and gnu compilers this is
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index ee062e92f6f..a9d4ff60655 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -67,14 +67,19 @@ class Petsc(Package):
     variant('hypre',   default=True,
             description='Activates support for Hypre (only parallel)')
     variant('mumps',   default=True,
-            description='Activates support for MUMPS (only parallel)')
+            description='Activates support for MUMPS (only parallel'
+            ' and 32bit indices)')
     variant('superlu-dist', default=True,
             description='Activates support for SuperluDist (only parallel)')
+    variant('int64', default=False,
+            description='Compile with 64bit indices')
 
     # Virtual dependencies
     # Git repository needs sowing to build Fortran interface
     depends_on('sowing', when='@develop')
 
+    # PETSc, hypre, superlu_dist when built with int64 use 32 bit integers
+    # with BLAS/LAPACK
     depends_on('blas')
     depends_on('lapack')
     depends_on('mpi', when='+mpi')
@@ -84,7 +89,8 @@ class Petsc(Package):
 
     # Other dependencies
     depends_on('boost', when='@:3.5+boost')
-    depends_on('metis@5:', when='+metis')
+    depends_on('metis@5:~int64', when='+metis~int64')
+    depends_on('metis@5:+int64', when='+metis+int64')
 
     depends_on('hdf5+mpi', when='+hdf5+mpi')
     depends_on('parmetis', when='+metis+mpi')
@@ -92,12 +98,16 @@ class Petsc(Package):
     # Also PETSc prefer to build it without internal superlu, likely due to
     # conflict in headers see
     # https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py
-    depends_on('hypre~internal-superlu', when='+hypre+mpi~complex')
-    depends_on('superlu-dist@:4.3', when='@3.4.4:3.6.4+superlu-dist+mpi')
-    depends_on('superlu-dist@5.0.0:', when='@3.7:+superlu-dist+mpi')
-    depends_on('superlu-dist@5.0.0:', when='@for-pflotran-0.1.0+superlu-dist+mpi')
-    depends_on('mumps+mpi', when='+mumps+mpi')
-    depends_on('scalapack', when='+mumps+mpi')
+    depends_on('hypre~internal-superlu~int64', when='+hypre+mpi~complex~int64')
+    depends_on('hypre~internal-superlu+int64', when='+hypre+mpi~complex+int64')
+    depends_on('superlu-dist@:4.3~int64', when='@3.4.4:3.6.4+superlu-dist+mpi~int64')
+    depends_on('superlu-dist@:4.3+int64', when='@3.4.4:3.6.4+superlu-dist+mpi+int64')
+    depends_on('superlu-dist@5.0.0:~int64', when='@3.7:+superlu-dist+mpi~int64')
+    depends_on('superlu-dist@5.0.0:+int64', when='@3.7:+superlu-dist+mpi+int64')
+    depends_on('superlu-dist@5.0.0:~int64', when='@for-pflotran-0.1.0+superlu-dist+mpi~int64')
+    depends_on('superlu-dist@5.0.0:+int64', when='@for-pflotran-0.1.0+superlu-dist+mpi+int64')
+    depends_on('mumps+mpi', when='+mumps+mpi~int64')
+    depends_on('scalapack', when='+mumps+mpi~int64')
 
     def mpi_dependent_options(self):
         if '~mpi' in self.spec:
@@ -146,7 +156,8 @@ def install(self, spec, prefix):
             '--with-scalar-type=%s' % (
                 'complex' if '+complex' in spec else 'real'),
             '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'),
-            '--with-debugging=%s' % ('1' if '+debug' in spec else '0')
+            '--with-debugging=%s' % ('1' if '+debug' in spec else '0'),
+            '--with-64-bit-indices=%s' % ('1' if '+int64' in spec else '0')
         ])
         # Make sure we use exactly the same Blas/Lapack libraries
         # across the DAG. To that end list them explicitly
diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index 7d04673182b..f076358e90e 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -43,6 +43,9 @@ class SuperluDist(Package):
     version('4.0', 'c0b98b611df227ae050bc1635c6940e0')
     version('3.3', 'f4805659157d93a962500902c219046b')
 
+    variant('int64', default=False,
+            description="Use 64bit integers")
+
     depends_on('mpi')
     depends_on('blas')
     depends_on('lapack')
@@ -66,8 +69,10 @@ def install(self, spec, prefix):
             'ARCHFLAGS    = cr',
             'RANLIB       = true',
             'CC           = {0}'.format(self.spec['mpi'].mpicc),
-            'CFLAGS       = -fPIC -std=c99 -O2 -I%s -I%s' % (
-                spec['parmetis'].prefix.include, spec['metis'].prefix.include),
+            'CFLAGS       = -fPIC -std=c99 -O2 -I%s -I%s %s' % (
+                spec['parmetis'].prefix.include,
+                spec['metis'].prefix.include,
+                '-D_LONGINT' if '+int64' in spec else ''),
             'NOOPTS       = -fPIC -std=c99',
             'FORTRAN      = {0}'.format(self.spec['mpi'].mpif77),
             'F90FLAGS     = -O2',

From de7be6694f8e65a0e7b5589148cfcbf162217ab9 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 16 Jan 2017 03:03:52 -0800
Subject: [PATCH 23/25] Fix issue with Mac OS version detection in m4 package.
 (#2835)

---
 var/spack/repos/builtin/packages/m4/package.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py
index 15dbf4793ba..ebfbc28612e 100644
--- a/var/spack/repos/builtin/packages/m4/package.py
+++ b/var/spack/repos/builtin/packages/m4/package.py
@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import sys
 
 
 class M4(AutotoolsPackage):
@@ -52,8 +51,9 @@ def configure_args(self):
             args.append('--without-libsigsegv-prefix')
 
         # http://lists.gnu.org/archive/html/bug-m4/2016-09/msg00002.html
-        if (sys.platform == 'darwin') and (spec.satisfies('%gcc')) and \
-           (spec.architecture.platform_os.version == '10.12'):
+        arch = spec.architecture
+        if (arch.platform == 'darwin' and arch.platform_os == 'sierra' and
+            '%gcc' in spec):
             args.append('ac_cv_type_struct_sched_param=yes')
 
         return args

From 6e8058ad41930017c1a95cdb1620145144cf00ff Mon Sep 17 00:00:00 2001
From: Jon Rood <jon.rood@nrel.gov>
Date: Mon, 16 Jan 2017 04:21:52 -0700
Subject: [PATCH 24/25] Specify Python location in VisIt in a more uniform
 fashion. (#2803)

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

diff --git a/var/spack/repos/builtin/packages/visit/package.py b/var/spack/repos/builtin/packages/visit/package.py
index ba1224daee1..48a3762a2a7 100644
--- a/var/spack/repos/builtin/packages/visit/package.py
+++ b/var/spack/repos/builtin/packages/visit/package.py
@@ -44,7 +44,6 @@ class Visit(Package):
 
     def install(self, spec, prefix):
         qt_bin = spec['qt'].prefix.bin
-        python_bin = spec['python'].prefix.bin
 
         with working_dir('spack-build', create=True):
             cmake_args = std_cmake_args[:]
@@ -53,7 +52,7 @@ def install(self, spec, prefix):
                 '-DVTK_MINOR_VERSION=1',
                 '-DVISIT_USE_GLEW=OFF',
                 '-DVISIT_LOC_QMAKE_EXE:FILEPATH={0}/qmake-qt4'.format(qt_bin),
-                '-DPYTHON_EXECUTABLE:FILEPATH={0}/python'.format(python_bin),
+                '-DPYTHON_DIR:PATH={0}'.format(spec['python'].prefix),
                 '-DVISIT_SILO_DIR:PATH={0}'.format(spec['silo'].prefix),
                 '-DVISIT_HDF5_DIR:PATH={0}'.format(spec['hdf5'].prefix),
                 '-DVISIT_VTK_DIR:PATH={0}'.format(spec['vtk'].prefix),

From aa3cc0ea817ffee8ebf292c8f15eb8eb0fc26866 Mon Sep 17 00:00:00 2001
From: George Hartzell <hartzell@alerce.com>
Date: Mon, 16 Jan 2017 03:25:39 -0800
Subject: [PATCH 25/25] Add lmod support for `spack module loads` (#2758)

The `spack module loads` command only supported tcl and dotkit.
This adds support for lmod.
---
 lib/spack/spack/cmd/module.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py
index 5887cbf495b..b4ee5613397 100644
--- a/lib/spack/spack/cmd/module.py
+++ b/lib/spack/spack/cmd/module.py
@@ -132,6 +132,7 @@ def loads(mtype, specs, args):
 
     module_commands = {
         'tcl': 'module load ',
+        'lmod': 'module load ',
         'dotkit': 'dotkit use '
     }