WarpX: Patch no-MPI & Lib Install (#34913)

Fixes WarpX issues:
- https://github.com/ECP-WarpX/WarpX/pull/3134
- https://github.com/ECP-WarpX/WarpX/pull/3141

and uses GitHub patch URLs directly instead of storing
patch copies.

lib/spack/llnl/util/lang.py

@@ -11,7 +11,9 @@
 import os
 import re
 import sys
+import traceback
 from datetime import datetime, timedelta
+from typing import List, Tuple
 
 import six
 from six import string_types
@@ -1009,3 +1011,64 @@ def __repr__(self):
 
     def __str__(self):
         return str(self.data)
+
+
+class GroupedExceptionHandler(object):
+    """A generic mechanism to coalesce multiple exceptions and preserve tracebacks."""
+
+    def __init__(self):
+        self.exceptions = []    # type: List[Tuple[str, Exception, List[str]]]
+
+    def __bool__(self):
+        """Whether any exceptions were handled."""
+        return bool(self.exceptions)
+
+    def forward(self, context):
+        # type: (str) -> GroupedExceptionForwarder
+        """Return a contextmanager which extracts tracebacks and prefixes a message."""
+        return GroupedExceptionForwarder(context, self)
+
+    def _receive_forwarded(self, context, exc, tb):
+        # type: (str, Exception, List[str]) -> None
+        self.exceptions.append((context, exc, tb))
+
+    def grouped_message(self, with_tracebacks=True):
+        # type: (bool) -> str
+        """Print out an error message coalescing all the forwarded errors."""
+        each_exception_message = [
+            '{0} raised {1}: {2}{3}'.format(
+                context,
+                exc.__class__.__name__,
+                exc,
+                '\n{0}'.format(''.join(tb)) if with_tracebacks else '',
+            )
+            for context, exc, tb in self.exceptions
+        ]
+        return 'due to the following failures:\n{0}'.format(
+            '\n'.join(each_exception_message)
+        )
+
+
+class GroupedExceptionForwarder(object):
+    """A contextmanager to capture exceptions and forward them to a
+    GroupedExceptionHandler."""
+
+    def __init__(self, context, handler):
+        # type: (str, GroupedExceptionHandler) -> None
+        self._context = context
+        self._handler = handler
+
+    def __enter__(self):
+        return None
+
+    def __exit__(self, exc_type, exc_value, tb):
+        if exc_value is not None:
+            self._handler._receive_forwarded(
+                self._context,
+                exc_value,
+                traceback.format_tb(tb),
+            )
+
+        # Suppress any exception from being re-raised:
+        # https://docs.python.org/3/reference/datamodel.html#object.__exit__.
+        return True

lib/spack/spack/bootstrap.py

@@ -21,6 +21,7 @@
 
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
+from llnl.util.lang import GroupedExceptionHandler
 
 import spack.binary_distribution
 import spack.config
@@ -417,11 +418,10 @@ def _make_bootstrapper(conf):
     return _bootstrap_methods[btype](conf)
 
 
-def _source_is_trusted(conf):
+def _validate_source_is_trusted(conf):
     trusted, name = spack.config.get('bootstrap:trusted'), conf['name']
     if name not in trusted:
-        return False
-    return trusted[name]
+        raise ValueError('source is not trusted')
 
 
 def spec_for_current_python():
@@ -488,34 +488,25 @@ def ensure_module_importable_or_raise(module, abstract_spec=None):
     abstract_spec = abstract_spec or module
     source_configs = spack.config.get('bootstrap:sources', [])
 
-    errors = {}
+    h = GroupedExceptionHandler()
 
     for current_config in source_configs:
-        if not _source_is_trusted(current_config):
-            msg = ('[BOOTSTRAP MODULE {0}] Skipping source "{1}" since it is '
-                   'not trusted').format(module, current_config['name'])
-            tty.debug(msg)
-            continue
+        with h.forward(current_config['name']):
+            _validate_source_is_trusted(current_config)
 
-        b = _make_bootstrapper(current_config)
-        try:
+            b = _make_bootstrapper(current_config)
             if b.try_import(module, abstract_spec):
                 return
-        except Exception as e:
-            msg = '[BOOTSTRAP MODULE {0}] Unexpected error "{1}"'
-            tty.debug(msg.format(module, str(e)))
-            errors[current_config['name']] = e
 
-    # We couldn't import in any way, so raise an import error
-    msg = 'cannot bootstrap the "{0}" Python module'.format(module)
+    assert h, 'expected at least one exception to have been raised at this point: while bootstrapping {0}'.format(module)  # noqa: E501
+    msg = 'cannot bootstrap the "{0}" Python module '.format(module)
     if abstract_spec:
-        msg += ' from spec "{0}"'.format(abstract_spec)
-    msg += ' due to the following failures:\n'
-    for method in errors:
-        err = errors[method]
-        msg += "    '{0}' raised {1}: {2}\n".format(
-            method, err.__class__.__name__, str(err))
-    msg += '    Please run `spack -d spec zlib` for more verbose error messages'
+        msg += 'from spec "{0}" '.format(abstract_spec)
+    if tty.is_debug():
+        msg += h.grouped_message(with_tracebacks=True)
+    else:
+        msg += h.grouped_message(with_tracebacks=False)
+        msg += '\nRun `spack --debug ...` for more detailed errors'
     raise ImportError(msg)
 
 
@@ -539,15 +530,14 @@ def ensure_executables_in_path_or_raise(executables, abstract_spec):
 
     executables_str = ', '.join(executables)
     source_configs = spack.config.get('bootstrap:sources', [])
-    for current_config in source_configs:
-        if not _source_is_trusted(current_config):
-            msg = ('[BOOTSTRAP EXECUTABLES {0}] Skipping source "{1}" since it is '
-                   'not trusted').format(executables_str, current_config['name'])
-            tty.debug(msg)
-            continue
 
-        b = _make_bootstrapper(current_config)
-        try:
+    h = GroupedExceptionHandler()
+
+    for current_config in source_configs:
+        with h.forward(current_config['name']):
+            _validate_source_is_trusted(current_config)
+
+            b = _make_bootstrapper(current_config)
             if b.try_search_path(executables, abstract_spec):
                 # Additional environment variables needed
                 concrete_spec, cmd = b.last_search['spec'], b.last_search['command']
@@ -562,14 +552,16 @@ def ensure_executables_in_path_or_raise(executables, abstract_spec):
                     )
                 cmd.add_default_envmod(env_mods)
                 return cmd
-        except Exception as e:
-            msg = '[BOOTSTRAP EXECUTABLES {0}] Unexpected error "{1}"'
-            tty.debug(msg.format(executables_str, str(e)))
 
-    # We couldn't import in any way, so raise an import error
-    msg = 'cannot bootstrap any of the {0} executables'.format(executables_str)
+    assert h, 'expected at least one exception to have been raised at this point: while bootstrapping {0}'.format(executables_str)  # noqa: E501
+    msg = 'cannot bootstrap any of the {0} executables '.format(executables_str)
     if abstract_spec:
-        msg += ' from spec "{0}"'.format(abstract_spec)
+        msg += 'from spec "{0}" '.format(abstract_spec)
+    if tty.is_debug():
+        msg += h.grouped_message(with_tracebacks=True)
+    else:
+        msg += h.grouped_message(with_tracebacks=False)
+        msg += '\nRun `spack --debug ...` for more detailed errors'
     raise RuntimeError(msg)
 
 

lib/spack/spack/cmd/stage.py

@@ -27,12 +27,6 @@ def setup_parser(subparser):
 
 
 def stage(parser, args):
-    # We temporarily modify the working directory when setting up a stage, so we need to
-    # convert this to an absolute path here in order for it to remain valid later.
-    custom_path = os.path.abspath(args.path) if args.path else None
-    if custom_path:
-        spack.stage.create_stage_root(custom_path)
-
     if not args.specs:
         env = ev.active_environment()
         if env:
@@ -54,6 +48,10 @@ def stage(parser, args):
 
     specs = spack.cmd.parse_specs(args.specs, concretize=False)
 
+    # We temporarily modify the working directory when setting up a stage, so we need to
+    # convert this to an absolute path here in order for it to remain valid later.
+    custom_path = os.path.abspath(args.path) if args.path else None
+
     # prevent multiple specs from extracting in the same folder
     if len(specs) > 1 and custom_path:
         tty.die("`--path` requires a single spec, but multiple were provided")

lib/spack/spack/cmd/uninstall.py

@@ -235,7 +235,7 @@ def is_ready(dag_hash):
 
         # If this spec is only used as a build dependency, we can uninstall
         return all(
-            dspec.deptypes == ("build",)
+            dspec.deptypes == ("build",) or not dspec.parent.installed
             for dspec in record.spec.edges_from_dependents()
         )
 

lib/spack/spack/test/bootstrap.py

@@ -62,6 +62,22 @@ def test_raising_exception_if_bootstrap_disabled(mutable_config):
         spack.bootstrap.store_path()
 
 
+def test_raising_exception_module_importable():
+    with pytest.raises(
+        ImportError,
+        match='cannot bootstrap the "asdf" Python module',
+    ):
+        spack.bootstrap.ensure_module_importable_or_raise("asdf")
+
+
+def test_raising_exception_executables_in_path():
+    with pytest.raises(
+        RuntimeError,
+        match="cannot bootstrap any of the asdf, fdsa executables",
+    ):
+        spack.bootstrap.ensure_executables_in_path_or_raise(["asdf", "fdsa"], "python")
+
+
 @pytest.mark.regression('25603')
 def test_bootstrap_deactivates_environments(active_mock_environment):
     assert spack.environment.active_environment() == active_mock_environment

lib/spack/spack/test/cmd/stage.py

@@ -41,7 +41,6 @@ def check_stage_path(monkeypatch, tmpdir):
 
     def fake_stage(pkg, mirror_only=False):
         assert pkg.path == expected_path
-        assert os.path.isdir(expected_path), expected_path
 
     monkeypatch.setattr(spack.package.PackageBase, 'do_stage', fake_stage)
 

lib/spack/spack/test/llnl/util/lang.py

@@ -6,6 +6,7 @@
 import os.path
 import sys
 from datetime import datetime, timedelta
+from textwrap import dedent
 
 import pytest
 
@@ -270,3 +271,37 @@ def f(*args, **kwargs):
 def test_dedupe():
     assert [x for x in dedupe([1, 2, 1, 3, 2])] == [1, 2, 3]
     assert [x for x in dedupe([1, -2, 1, 3, 2], key=abs)] == [1, -2, 3]
+
+
+def test_grouped_exception():
+    h = llnl.util.lang.GroupedExceptionHandler()
+
+    def inner():
+        raise ValueError('wow!')
+
+    with h.forward('inner method'):
+        inner()
+
+    with h.forward('top-level'):
+        raise TypeError('ok')
+
+    assert h.grouped_message(with_tracebacks=False) == dedent("""\
+    due to the following failures:
+    inner method raised ValueError: wow!
+    top-level raised TypeError: ok""")
+
+    assert h.grouped_message(with_tracebacks=True) == dedent("""\
+    due to the following failures:
+    inner method raised ValueError: wow!
+      File "{0}", \
+line 283, in test_grouped_exception
+        inner()
+      File "{0}", \
+line 280, in inner
+        raise ValueError('wow!')
+
+    top-level raised TypeError: ok
+      File "{0}", \
+line 286, in test_grouped_exception
+        raise TypeError('ok')
+    """).format(__file__)

lib/spack/spack/util/compression.py

@@ -5,6 +5,7 @@
 
 import os
 import re
+import sys
 from itertools import product
 
 from spack.util.executable import which
@@ -18,6 +19,8 @@
 ALLOWED_ARCHIVE_TYPES = [".".join(ext) for ext in product(
     PRE_EXTS, EXTS)] + PRE_EXTS + EXTS + NOTAR_EXTS
 
+is_windows = sys.platform == 'win32'
+
 
 def allowed_archive(path):
     return any(path.endswith(t) for t in ALLOWED_ARCHIVE_TYPES)
@@ -48,15 +51,14 @@ def _unzip(archive_file):
     Args:
         archive_file (str): absolute path of the file to be decompressed
     """
-    try:
-        from zipfile import ZipFile
-        destination_abspath = os.getcwd()
-        with ZipFile(archive_file, 'r') as zf:
-            zf.extractall(destination_abspath)
-    except ImportError:
-        unzip = which('unzip', required=True)
-        unzip.add_default_arg('-q')
-        return unzip
+    exe = 'unzip'
+    arg = '-q'
+    if is_windows:
+        exe = 'tar'
+        arg = '-xf'
+    unzip = which(exe, required=True)
+    unzip.add_default_arg(arg)
+    unzip(archive_file)
 
 
 def decompressor_for(path, extension=None):

share/spack/gitlab/cloud_pipelines/.gitlab-ci.yml

@@ -60,8 +60,8 @@ default:
 .develop-build:
   extends: [ ".develop", ".build" ]
   variables:
-    AWS_ACCESS_KEY_ID: ${MIRRORS_AWS_ACCESS_KEY_ID}
-    AWS_SECRET_ACCESS_KEY: ${MIRRORS_AWS_SECRET_ACCESS_KEY}
+    AWS_ACCESS_KEY_ID: ${PROTECTED_MIRRORS_AWS_ACCESS_KEY_ID}
+    AWS_SECRET_ACCESS_KEY: ${PROTECTED_MIRRORS_AWS_SECRET_ACCESS_KEY}
     SPACK_SIGNING_KEY: ${PACKAGE_SIGNING_KEY}
 
 ########################################

var/spack/repos/builtin/packages/ascent/ascent-find-adios2-pr922.patch

@@ -0,0 +1,99 @@
+diff --git a/src/cmake/thirdparty/SetupADIOS.cmake b/src/cmake/thirdparty/SetupADIOS.cmake
+index 7a7f038d..4b56b7e0 100644
+--- a/src/cmake/thirdparty/SetupADIOS.cmake
++++ b/src/cmake/thirdparty/SetupADIOS.cmake
+@@ -10,32 +10,32 @@
+ #
+ ###############################################################################
+ 
+-# first Check for ADIOS_DIR
++# first Check for ADIOS_ROOT
+ 
+-if(NOT ADIOS_DIR)
+-    MESSAGE(FATAL_ERROR "ADIOS support needs explicit ADIOS_DIR")
++if(NOT ADIOS_ROOT)
++    MESSAGE(FATAL_ERROR "ADIOS support needs explicit ADIOS_ROOT")
+ endif()
+ 
+-MESSAGE(STATUS "Looking for ADIOS using ADIOS_DIR = ${ADIOS_DIR}")
++MESSAGE(STATUS "Looking for ADIOS using ADIOS_ROOT = ${ADIOS_ROOT}")
+ 
+ # CMake's FindADIOS module uses the ADIOS_ROOT env var
+-set(ADIOS_ROOT ${ADIOS_DIR})
++set(ADIOS_ROOT ${ADIOS_ROOT})
+ set(ENV{ADIOS_ROOT} ${ADIOS_ROOT})
+ 
+ # Use CMake's FindADIOS module, which uses hdf5's compiler wrappers to extract
+ # all the info about the hdf5 install
+-include(${ADIOS_DIR}/etc/FindADIOS.cmake)
++include(${ADIOS_ROOT}/etc/FindADIOS.cmake)
+ 
+-# FindADIOS sets ADIOS_DIR to it's installed CMake info if it exists
+-# we want to keep ADIOS_DIR as the root dir of the install to be
++# FindADIOS sets ADIOS_ROOT to it's installed CMake info if it exists
++# we want to keep ADIOS_ROOT as the root dir of the install to be
+ # consistent with other packages
+ 
+-set(ADIOS_DIR ${ADIOS_ROOT} CACHE PATH "" FORCE)
++set(ADIOS_ROOT ${ADIOS_ROOT} CACHE PATH "" FORCE)
+ # not sure why we need to set this, but we do
+ #set(ADIOS_FOUND TRUE CACHE PATH "" FORCE)
+ 
+ if(NOT ADIOS_FOUND)
+-    message(FATAL_ERROR "ADIOS_DIR is not a path to a valid ADIOS install")
++    message(FATAL_ERROR "ADIOS_ROOT is not a path to a valid ADIOS install")
+ endif()
+ 
+ blt_register_library(NAME adios
+diff --git a/src/cmake/thirdparty/SetupADIOS2.cmake b/src/cmake/thirdparty/SetupADIOS2.cmake
+index d93c3e5b..3133c72c 100644
+--- a/src/cmake/thirdparty/SetupADIOS2.cmake
++++ b/src/cmake/thirdparty/SetupADIOS2.cmake
+@@ -10,21 +10,39 @@
+ #
+ ###############################################################################
+ 
+-# first Check for ADIOS_DIR
+-if(NOT ADIOS2_DIR)
+-    MESSAGE(FATAL_ERROR "ADIOS2 support needs explicit ADIOS2_DIR")
++# Handle legacy usage of ADIOS2_DIR
++if (ADIOS2_DIR AND NOT ADIOS2_ROOT)
++  # If find_package(ADIOS2) has already been called this will fail
++  if (NOT EXISTS ${ADIOS2_DIR}/include)
++    get_filename_component(tmp "${ADIOS2_DIR}" DIRECTORY)
++    get_filename_component(tmp "${tmp}" DIRECTORY)
++    get_filename_component(tmp "${tmp}" DIRECTORY)
++    if (EXISTS ${tmp}/include)
++      set(ADIOS2_ROOT "${tmp}" CACHE PATH "")
++    else ()
++      message(FATAL_ERROR "Could not determine ADIOS2_ROOT from ADIOS2_DIR")
++    endif ()
++  else ()
++    set(ADIOS2_ROOT "${ADIOS2_DIR}" CACHE PATH "")
++  endif ()
++endif ()
++
++# Check for ADIOS_ROOT
++if(NOT ADIOS2_ROOT)
++    MESSAGE(FATAL_ERROR "ADIOS2 support needs explicit ADIOS2_ROOT")
+ endif()
+ 
+-MESSAGE(STATUS "Looking for ADIOS2 using ADIOS2_DIR = ${ADIOS2_DIR}")
++MESSAGE(STATUS "Looking for ADIOS2 using ADIOS2_ROOT = ${ADIOS2_ROOT}")
+ 
+-set(ADIOS2_DIR_ORIG ${ADIOS2_DIR})
++set(ADIOS2_DIR_ORIG ${ADIOS2_ROOT})
+ 
+ find_package(ADIOS2 REQUIRED
+              NO_DEFAULT_PATH
+-             PATHS ${ADIOS2_DIR}/lib/cmake/adios2)
++             PATHS ${ADIOS2_ROOT})
+ 
++# ADIOS2_DIR is set by find_package
+ message(STATUS "FOUND ADIOS2 at ${ADIOS2_DIR}")
+ 
+ blt_register_library(NAME adios2
+-                     INCLUDES ${ADIOS2_INCLUDE_DIR}
+-                     LIBRARIES ${ADIOS2_LIB_DIRS} ${ADIOS2_LIBRARIES} )
++  INCLUDES ${ADIOS2_INCLUDE_DIR}
++  LIBRARIES ${ADIOS2_LIB_DIRS} ${ADIOS2_LIBRARIES} )

var/spack/repos/builtin/packages/ascent/package.py

@@ -102,6 +102,9 @@ class Ascent(CMakePackage, CudaPackage):
     # patch for allowing +shared+cuda
     # https://github.com/Alpine-DAV/ascent/pull/903
     patch('ascent-shared-cuda-pr903.patch', when='@0.8.0')
+    # patch for finding ADIOS2 more reliably
+    # https://github.com/Alpine-DAV/ascent/pull/922
+    patch('ascent-find-adios2-pr922.patch', when='@0.8.0')
 
     ##########################################################################
     # package dependencies

var/spack/repos/builtin/packages/bricks/package.py

@@ -0,0 +1,88 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bricks(CMakePackage):
+
+    """Bricks is a data layout and code generation framework,
+       enabling performance-portable stencil computations across
+       a multitude of architectures."""
+
+    # url for your package's homepage here.
+    homepage = "https://bricks.run/"
+    git = 'https://github.com/CtopCsUtahEdu/bricklib.git'
+
+    test_requires_compiler = True
+
+    # List of GitHub accounts to notify when the package is updated.
+    maintainers = ['ztuowen', 'drhansj']
+
+    version('r0.1', branch='r0.1')
+
+    variant('cuda', default=False, description='Build bricks with CUDA enabled')
+
+    # Building a variant of cmake without openssl is to match how the
+    # ECP E4S project builds cmake in their e4s-base-cuda Docker image
+    depends_on('cmake', type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('opencl-clhpp', when='+cuda')
+    depends_on('cuda', when='+cuda')
+    depends_on('mpi')
+
+    def cmake_args(self):
+        """CMake arguments for configure stage"""
+        args = []
+
+        return args
+
+    def flag_handler(self, name, flags):
+        """Set build flags as needed"""
+        if name in ['cflags', 'cxxflags', 'cppflags']:
+            # There are many vector instrinsics used in this package. If
+            # the package is built on a native architecture, then it likely
+            # will not run (illegal instruction fault) on a less feature-
+            # rich architecture.
+            # If you intend to use this package in an architecturally-
+            # heterogeneous environment, then the package should be build
+            # with "target=x86_64". This will ensure that all Intel
+            # architectures can use the libraries and tests in this
+            # project by forceing the AVX2 flag in gcc.
+            if name == 'cxxflags' and self.spec.target == 'x86_64':
+                flags.append('-mavx2')
+            return (None, flags, None)
+        return(flags, None, None)
+
+    @run_after('install')
+    def copy_test_sources(self):
+        """Files to copy into test cache"""
+        srcs = [join_path('examples', 'external', 'CMakeLists.txt'),
+                join_path('examples', 'external', 'main.cpp'),
+                join_path('examples', 'external', '7pt.py')]
+        self.cache_extra_test_sources(srcs)
+
+    def test(self):
+        """Test bricklib package"""
+        # Test prebuilt binary
+        source_dir = join_path(self.test_suite.current_test_cache_dir,
+                               'examples', 'external')
+
+        self.run_test(exe='cmake',
+                      options=['.'],
+                      purpose='Configure bricklib example',
+                      work_dir=source_dir)
+
+        self.run_test(exe='cmake',
+                      options=['--build', '.'],
+                      purpose='Build bricklib example',
+                      work_dir=source_dir)
+
+        self.run_test(exe=join_path(source_dir, 'example'),
+                      options=[],
+                      purpose='Execute bricklib example',
+                      work_dir=source_dir)

var/spack/repos/builtin/packages/ceed/package.py

@@ -18,6 +18,7 @@ class Ceed(BundlePackage, CudaPackage, ROCmPackage):
 
     maintainers = ['jedbrown', 'v-dobrev', 'tzanio']
 
+    version('5.0.0')
     version('4.0.0')
     version('3.0.0')
     version('2.0.0')
@@ -32,11 +33,24 @@ class Ceed(BundlePackage, CudaPackage, ROCmPackage):
             description='Build PETSc and HPGMG')
     variant('pumi', default=True,
             description='Build PUMI')
+    variant('omega-h', default=True,
+            description='Build Omega_h')
     variant('quickbuild', default=True,
             description='Speed-up the build by disabling variants in packages')
     # TODO: Add 'int64' variant?
 
     # LibCEED
+    # ceed 5.0
+    with when('@5.0.0'):
+        depends_on('libceed@0.10~occa')
+        depends_on('libceed~cuda', when='~cuda')
+        for arch in CudaPackage.cuda_arch_values:
+            depends_on('libceed+cuda+magma cuda_arch={0}'.format(arch),
+                       when='+cuda cuda_arch={0}'.format(arch))
+        depends_on('libceed~rocm', when='~rocm')
+        for target in ROCmPackage.amdgpu_targets:
+            depends_on('libceed+rocm amdgpu_target={0}'.format(target),
+                       when='+rocm amdgpu_target={0}'.format(target))
     # ceed 4.0
     depends_on('libceed@0.8~cuda', when='@4.0.0~cuda')
     for arch in CudaPackage.cuda_arch_values:
@@ -64,7 +78,15 @@ class Ceed(BundlePackage, CudaPackage, ROCmPackage):
     depends_on('libceed@0.2+occa', when='@1.0.0+occa')
     depends_on('libceed@0.2~occa', when='@1.0.0~occa')
 
+    # FMS
+    # ceed-5.0
+    depends_on('libfms@0.2.0', when='@5.0.0')
+    depends_on('libfms@0.2.0~conduit', when='@5.0.0+quickbuild')
+
     # OCCA
+    # ceed-5.0
+    depends_on('occa@1.1.0~cuda', when='@5.0.0+occa~cuda')
+    depends_on('occa@1.1.0+cuda', when='@5.0.0+occa+cuda')
     # ceed-4.0
     depends_on('occa@1.1.0~cuda', when='@4.0.0+occa~cuda')
     depends_on('occa@1.1.0+cuda', when='@4.0.0+occa+cuda')
@@ -79,22 +101,24 @@ class Ceed(BundlePackage, CudaPackage, ROCmPackage):
     depends_on('occa@1.0.0-alpha.5+cuda', when='@1.0.0+occa+cuda')
 
     # NekRS
-    # ceed-4.0
-    depends_on('nekrs@21.0', when='@4.0.0+nek')
+    # ceed-4.0 and ceed-5.0
+    depends_on('nekrs@21.0%gcc', when='@4.0.0:5+nek')
     for arch in CudaPackage.cuda_arch_values:
         depends_on('nekrs@21.0+cuda cuda_arch={0}'.format(arch),
-                   when='@4.0.0+nek+cuda cuda_arch={0}'.format(arch))
+                   when='@4.0.0:5+nek+cuda cuda_arch={0}'.format(arch))
     for target in ROCmPackage.amdgpu_targets:
         depends_on('nekrs@21.0+rocm amdgpu_target={0}'.format(target),
-                   when='@4.0.0+nek+rocm amdgpu_target={0}'.format(target))
+                   when='@4.0.0:5+nek+rocm amdgpu_target={0}'.format(target))
 
     # Nek5000, GSLIB, Nekbone, and NekCEM
-    # ceed-3.0 and ceed-4.0
-    depends_on('nek5000@19.0', when='@3.0.0:4+nek')
-    depends_on('nektools@19.0%gcc', when='@3.0.0:4+nek')
+    # ceed-5.0 - specific
+    depends_on('gslib@1.0.7', when='@5.0.0+nek')
+    # ceed-3.0, ceed-4.0, and ceed-5.0
+    depends_on('nek5000@19.0', when='@3.0.0:5+nek')
+    depends_on('nektools@19.0%gcc', when='@3.0.0:5+nek')
     depends_on('gslib@1.0.6', when='@3.0.0:4+nek')
-    depends_on('nekbone@17.0', when='@3.0.0:4+nek')
-    depends_on('nekcem@c8db04b', when='@3.0.0:4+nek')
+    depends_on('nekbone@17.0', when='@3.0.0:5+nek')
+    depends_on('nekcem@c8db04b', when='@3.0.0:5+nek')
     # ceed-2.0
     depends_on('nek5000@17.0', when='@2.0.0+nek')
     depends_on('nektools@17.0%gcc', when='@2.0.0+nek')
@@ -109,6 +133,21 @@ class Ceed(BundlePackage, CudaPackage, ROCmPackage):
     depends_on('nekcem@0b8bedd', when='@1.0.0+nek')
 
     # PETSc
+    # ceed 5.0
+    with when('@5.0.0+petsc'):
+        depends_on('petsc@3.17')
+        depends_on('ratel@0.1.2')
+        for arch in CudaPackage.cuda_arch_values:
+            depends_on('petsc+cuda cuda_arch={0}'.format(arch),
+                       when='+cuda cuda_arch={0}'.format(arch))
+            depends_on('ratel+cuda cuda_arch={0}'.format(arch),
+                       when='+cuda cuda_arch={0}'.format(arch))
+        for target in ROCmPackage.amdgpu_targets:
+            depends_on('petsc+rocm amdgpu_target={0}'.format(target),
+                       when='+rocm amdgpu_target={0}'.format(target))
+            depends_on('ratel+rocm amdgpu_target={0}'.format(target),
+                       when='+rocm amdgpu_target={0}'.format(target))
+        depends_on('petsc~hdf5~superlu-dist', when='+quickbuild')
     # ceed 4.0
     depends_on('petsc@3.15.0:3.15', when='@4.0.0:4+petsc')
     for arch in CudaPackage.cuda_arch_values:
@@ -159,6 +198,13 @@ class Ceed(BundlePackage, CudaPackage, ROCmPackage):
     depends_on('hpgmg@a0a5510df23b+fe', when='@1.0.0+petsc')
 
     # MAGMA
+    # ceed 5.0
+    for arch in CudaPackage.cuda_arch_values:
+        depends_on('magma@2.6.2+cuda cuda_arch={0}'.format(arch),
+                   when='@5.0.0+cuda cuda_arch={0}'.format(arch))
+    for target in ROCmPackage.amdgpu_targets:
+        depends_on('magma@2.6.2~cuda+rocm amdgpu_target={0}'.format(target),
+                   when='@5.0.0+rocm amdgpu_target={0}'.format(target))
     # ceed-4.0
     for arch in CudaPackage.cuda_arch_values:
         depends_on('magma@2.5.4 cuda_arch={0}'.format(arch),
@@ -171,6 +217,8 @@ class Ceed(BundlePackage, CudaPackage, ROCmPackage):
     depends_on('magma@2.3.0', when='@1.0.0+cuda')
 
     # PUMI
+    # ceed-5.0
+    depends_on('pumi@2.2.7', when='@5.0.0+pumi')
     # ceed-4.0
     depends_on('pumi@2.2.5', when='@4.0.0+pumi')
     # ceed-3.0
@@ -180,7 +228,28 @@ class Ceed(BundlePackage, CudaPackage, ROCmPackage):
     # ceed-1.0
     depends_on('pumi@2.1.0', when='@1.0.0+pumi')
 
+    # Omega_h
+    # ceed-5.0
+    depends_on('omega-h@scorec.10.1.0', when='@5.0.0+omega-h')
+    depends_on('omega-h~trilinos', when='@5.0.0+omega-h+quickbuild')
+
     # MFEM, Laghos, Remhos
+    # ceed 5.0
+    with when('@5.0.0+mfem'):
+        depends_on('mfem@4.4.0+mpi+examples+miniapps')
+        depends_on('mfem+petsc', when='+petsc')
+        depends_on('mfem+pumi', when='+pumi')
+        depends_on('mfem+gslib', when='+nek')
+        depends_on('mfem+libceed+fms')
+        for arch in CudaPackage.cuda_arch_values:
+            depends_on('mfem+cuda cuda_arch={0}'.format(arch),
+                       when='+cuda cuda_arch={0}'.format(arch))
+        for target in ROCmPackage.amdgpu_targets:
+            depends_on('mfem+rocm amdgpu_target={0}'.format(target),
+                       when='+rocm amdgpu_target={0}'.format(target))
+        depends_on('mfem+occa', when='+occa')
+        depends_on('laghos@3.1')
+        depends_on('remhos@1.0')
     # ceed-4.0
     depends_on('mfem@4.2.0+mpi+examples+miniapps', when='@4.0.0+mfem~petsc')
     depends_on('mfem@4.2.0+mpi+petsc+examples+miniapps',

var/spack/repos/builtin/packages/gslib/package.py

@@ -13,6 +13,7 @@ class Gslib(Package):
     git      = "https://github.com/gslib/gslib.git"
 
     version('develop', branch='master')
+    version('1.0.7', tag='v1.0.7')
     version('1.0.6', tag='v1.0.6')
     version('1.0.5', tag='v1.0.5')
     version('1.0.4', tag='v1.0.4')

var/spack/repos/builtin/packages/laghos/package.py

@@ -34,7 +34,7 @@ class Laghos(MakefilePackage):
     depends_on('mfem+mpi~metis', when='~metis')
 
     depends_on('mfem@develop', when='@develop')
-    depends_on('mfem@4.2.0', when='@3.1')
+    depends_on('mfem@4.2.0:', when='@3.1')
     depends_on('mfem@4.1.0:4.1', when='@3.0')
     # Recommended mfem version for laghos v2.0 is: ^mfem@3.4.1-laghos-v2.0
     depends_on('mfem@3.4.0:', when='@2.0')

var/spack/repos/builtin/packages/libceed/package.py

@@ -12,7 +12,7 @@ class Libceed(MakefilePackage, CudaPackage, ROCmPackage):
     homepage = "https://github.com/CEED/libCEED"
     git = "https://github.com/CEED/libCEED.git"
 
-    maintainers = ['jedbrown', 'v-dobrev', 'tzanio']
+    maintainers = ['jedbrown', 'v-dobrev', 'tzanio', 'jeremylt']
 
     version('develop', branch='main')
     version('0.10.1', tag='v0.10.1')
@@ -107,6 +107,8 @@ def common_make_opts(self):
 
             if '+cuda' in spec:
                 makeopts += ['CUDA_DIR=%s' % spec['cuda'].prefix]
+                makeopts += ['CUDA_ARCH=sm_%s' %
+                             spec.variants['cuda_arch'].value]
                 if spec.satisfies('@:0.4'):
                     nvccflags = ['-ccbin %s -Xcompiler "%s" -Xcompiler %s' %
                                  (compiler.cxx, opt, compiler.cc_pic_flag)]
@@ -118,6 +120,8 @@ def common_make_opts(self):
 
             if '+rocm' in spec:
                 makeopts += ['HIP_DIR=%s' % spec['hip'].prefix]
+                amdgpu_target = ','.join(spec.variants['amdgpu_target'].value)
+                makeopts += ['HIP_ARCH=%s' % amdgpu_target]
                 if spec.satisfies('@0.8'):
                     makeopts += ['HIPBLAS_DIR=%s' % spec['hipblas'].prefix]
 
@@ -138,7 +142,8 @@ def build_targets(self):
 
     @property
     def install_targets(self):
-        return ['prefix={0}'.format(self.prefix)] + self.common_make_opts
+        return ['install', 'prefix={0}'.format(self.prefix)] + \
+            self.common_make_opts
 
     def check(self):
         make('prove', *self.common_make_opts, parallel=False)

var/spack/repos/builtin/packages/libfms/package.py

@@ -0,0 +1,59 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libfms(CMakePackage):
+    """Field and Mesh Specification (FMS) library"""
+
+    homepage = "https://github.com/CEED/FMS"
+    git = "https://github.com/CEED/FMS.git"
+
+    tags = ['FEM', 'Meshes', 'Fields', 'High-order', 'I/O', 'Data-exchange']
+
+    maintainers = ['v-dobrev', 'tzanio', 'cwsmith']
+
+    version('develop', branch='master')
+    version('0.2.0', tag='v0.2')
+
+    variant('conduit', default=True,
+            description='Build with Conduit I/O support')
+    variant('shared', default=True,
+            description='Build shared libraries')
+
+    depends_on('cmake@3.1:', type='build')
+    depends_on('conduit@0.7.1:', when='+conduit')
+
+    def cmake_args(self):
+        args = []
+        args.extend([
+            self.define_from_variant('BUILD_SHARED_LIBS', 'shared'),
+        ])
+        if '+conduit' in self.spec:
+            args.extend([
+                self.define('CONDUIT_DIR', self.spec['conduit'].prefix)
+            ])
+
+        return args
+
+    @property
+    def headers(self):
+        """Export the FMS headers.
+           Sample usage: spec['libfms'].headers.cpp_flags
+        """
+        fms_h_names = ['fms', 'fmsio']
+        hdrs = find_headers(fms_h_names, self.prefix.include, recursive=False)
+        return hdrs or None  # Raise an error if no headers are found
+
+    @property
+    def libs(self):
+        """Export the FMS library.
+           Sample usage: spec['libfms'].libs.ld_flags
+        """
+        is_shared = '+shared' in self.spec
+        libs = find_libraries('libfms', root=self.prefix, shared=is_shared,
+                              recursive=True)
+        return libs or None  # Raise an error if no libs are found

var/spack/repos/builtin/packages/mfem/package.py

@@ -102,10 +102,10 @@ class Mfem(Package, CudaPackage, ROCmPackage):
             description='Build static library')
     variant('shared', default=False,
             description='Build shared library')
-    variant('mpi', default=True,
+    variant('mpi', default=True, sticky=True,
             description='Enable MPI parallelism')
     # Can we make the default value for 'metis' to depend on the 'mpi' value?
-    variant('metis', default=True,
+    variant('metis', default=True, sticky=True,
             description='Enable METIS support')
     variant('openmp', default=False,
             description='Enable OpenMP parallelism')
@@ -153,6 +153,8 @@ class Mfem(Package, CudaPackage, ROCmPackage):
             description='Enable secure sockets using GnuTLS')
     variant('libunwind', default=False,
             description='Enable backtrace on error support using Libunwind')
+    variant('fms', default=False, when='@4.3.0:',
+            description='Enable FMS I/O support')
     # TODO: SIMD, Ginkgo, ADIOS2, HiOp, MKL CPardiso, Axom/Sidre
     variant('timer', default='auto',
             values=('auto', 'std', 'posix', 'mac', 'mpi'),
@@ -287,6 +289,7 @@ class Mfem(Package, CudaPackage, ROCmPackage):
     depends_on('gnutls', when='+gnutls')
     depends_on('conduit@0.3.1:,master:', when='+conduit')
     depends_on('conduit+mpi', when='+conduit+mpi')
+    depends_on('libfms@0.2.0:', when='+fms')
 
     # The MFEM 4.0.0 SuperLU interface fails when using hypre@2.16.0 and
     # superlu-dist@6.1.1. See https://github.com/mfem/mfem/issues/983.
@@ -486,6 +489,7 @@ def find_optional_library(name, prefix):
             'MFEM_USE_AMGX=%s' % yes_no('+amgx'),
             'MFEM_USE_CEED=%s' % yes_no('+libceed'),
             'MFEM_USE_UMPIRE=%s' % yes_no('+umpire'),
+            'MFEM_USE_FMS=%s' % yes_no('+fms'),
             'MFEM_MPIEXEC=%s' % mfem_mpiexec,
             'MFEM_MPIEXEC_NP=%s' % mfem_mpiexec_np]
 
@@ -830,6 +834,12 @@ def find_optional_library(name, prefix):
                 'CONDUIT_OPT=%s' % conduit_opt_flags,
                 'CONDUIT_LIB=%s' % ld_flags_from_library_list(libs)]
 
+        if '+fms' in spec:
+            libfms = spec['libfms']
+            options += [
+                'FMS_OPT=%s' % libfms.headers.cpp_flags,
+                'FMS_LIB=%s' % ld_flags_from_library_list(libfms.libs)]
+
         make('config', *options, parallel=False)
         make('info', parallel=False)
 

var/spack/repos/builtin/packages/omega-h/package.py

@@ -4,7 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 
-class OmegaH(CMakePackage):
+class OmegaH(CMakePackage, CudaPackage):
     """Omega_h is a C++11 library providing data structures and algorithms
     for adaptive discretizations. Its specialty is anisotropic triangle and
     tetrahedral mesh adaptation. It runs efficiently on most modern HPC
@@ -45,6 +45,12 @@ class OmegaH(CMakePackage):
     depends_on('mpi', when='+mpi')
     depends_on('trilinos +kokkos', when='+trilinos')
     depends_on('zlib', when='+zlib')
+    # Note: '+cuda' and 'cuda_arch' variants are added by the CudaPackage
+    depends_on('cuda', when='+cuda')
+    conflicts('cuda@11.2:', when='@scorec.10.1.0:', msg='Thrust is broken in CUDA >= 11.2.* see https://github.com/sandialabs/omega_h/issues/366')
+    # the sandia repo has a fix for cuda > 11.2 support
+    #  see github.com/sandialabs/omega_h/pull/373
+    conflicts('cuda@11.2:', when='@:9.34.4', msg='Thrust is broken in CUDA >= 11.2.* see https://github.com/sandialabs/omega_h/issues/366')
 
     # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=86610
     conflicts('%gcc@8:8.2', when='@:9.22.1')
@@ -66,10 +72,21 @@ def cmake_args(self):
             args.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
         if '+mpi' in self.spec:
             args.append('-DOmega_h_USE_MPI:BOOL=ON')
-            args.append('-DCMAKE_CXX_COMPILER:FILEPATH={0}'.format(
-                self.spec['mpi'].mpicxx))
+            ver = self.spec.version
+            # old versions don't call find_package(MPI)
+            if ver < Version('9.33.2') and 'scorec' not in str(ver):
+                args.append('-DCMAKE_CXX_COMPILER:FILEPATH={0}'.format(
+                    self.spec['mpi'].mpicxx))
         else:
             args.append('-DOmega_h_USE_MPI:BOOL=OFF')
+        if '+cuda' in self.spec:
+            args.append('-DOmega_h_USE_CUDA:BOOL=ON')
+            cuda_arch_list = self.spec.variants['cuda_arch'].value
+            cuda_arch = cuda_arch_list[0]
+            if cuda_arch != 'none':
+                args.append('-DOmega_h_CUDA_ARCH={0}'.format(cuda_arch))
+        else:
+            args.append('-DOmega_h_USE_CUDA:BOOL=OFF')
         if '+trilinos' in self.spec:
             args.append('-DOmega_h_USE_Trilinos:BOOL=ON')
         if '+zlib' in self.spec:

var/spack/repos/builtin/packages/py-pyworld/package.py

@@ -0,0 +1,22 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyworld(PythonPackage):
+    """PyWorld wrappers WORLD, which is a free software for high-quality speech
+    analysis, manipulation and synthesis. It can estimate fundamental frequency
+    (F0), aperiodicity and spectral envelope and also generate the speech like
+    input speech with only estimated parameters.i"""
+
+    homepage = "https://github.com/JeremyCCHsu/Python-Wrapper-for-World-Vocoder"
+    pypi     = "pyworld/pyworld-0.3.0.tar.gz"
+
+    version('0.3.0', sha256='e19b5d8445e0c4fc45ded71863aeaaf2680064b4626b0e7c90f72e9ace9f6b5b')
+
+    depends_on('py-setuptools',     type='build')
+    depends_on('py-numpy@:1.19',    type=('build', 'run'))
+    depends_on('py-cython@0.24.0:', type='build')

var/spack/repos/builtin/packages/qt/package.py

@@ -30,6 +30,7 @@ class Qt(Package):
 
     phases = ['configure', 'build', 'install']
 
+    version('5.15.4', sha256='615ff68d7af8eef3167de1fd15eac1b150e1fd69d1e2f4239e54447e7797253b')
     version('5.15.3', sha256='b7412734698a87f4a0ae20751bab32b1b07fdc351476ad8e35328dbe10efdedb')
     version('5.15.2', sha256='3a530d1b243b5dec00bc54937455471aaa3e56849d2593edb8ded07228202240')
     version('5.14.2', sha256='c6fcd53c744df89e7d3223c02838a33309bd1c291fcb6f9341505fe99f7f19fa')

var/spack/repos/builtin/packages/ratel/package.py

@@ -64,7 +64,8 @@ def build_targets(self):
 
     @property
     def install_targets(self):
-        return ['prefix={0}'.format(self.prefix)] + self.common_make_opts
+        return ['install', 'prefix={0}'.format(self.prefix)] + \
+            self.common_make_opts
 
     def check(self):
         make('prove', *self.common_make_opts, parallel=False)

var/spack/repos/builtin/packages/tau/package.py

@@ -28,6 +28,7 @@ class Tau(Package):
     tags = ['e4s']
 
     version('master', branch='master')
+    version('2.31.1', sha256='bf445b9d4fe40a5672a7b175044d2133791c4dfb36a214c1a55a931aebc06b9d')
     version('2.31', sha256='27e73c395dd2a42b91591ce4a76b88b1f67663ef13aa19ef4297c68f45d946c2')
     version('2.30.2', sha256='43f84a15b71a226f8a64d966f0cb46022bcfbaefb341295ecc6fa80bb82bbfb4')
     version('2.30.1', sha256='9c20ca1b4f4e80d885f24491cee598068871f0e9dd67906a5e47e4b4147d08fc')

var/spack/repos/builtin/packages/warpx/2626.patch

@@ -1,34 +0,0 @@
-From 9785e706229622626133c4b03c7abd004f62023f Mon Sep 17 00:00:00 2001
-From: Axel Huebl <axel.huebl@plasma.ninja>
-Date: Sat, 4 Dec 2021 15:28:13 -0800
-Subject: [PATCH] Fix: Installed Symlink LIB
-
-The latest patch to these routines broke our library alias in installs.
-
-By default, this variable is relative and needs the prefix appended.
-In some cases, e.g., if externally set, it can already be absolute. In that
-case, we skip adding the prefix.
----
- CMakeLists.txt | 7 ++++++-
- 1 file changed, 6 insertions(+), 1 deletion(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 04092ba962..a549546ab9 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -343,9 +343,14 @@ if(WarpX_LIB)
-     else()
-         set(mod_ext "so")
-     endif()
-+    if(IS_ABSOLUTE ${CMAKE_INSTALL_LIBDIR})
-+        set(ABS_INSTALL_LIB_DIR ${CMAKE_INSTALL_LIBDIR})
-+    else()
-+        set(ABS_INSTALL_LIB_DIR ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR})
-+    endif()
-     install(CODE "file(CREATE_LINK
-         $<TARGET_FILE_NAME:shared>
--        ${CMAKE_INSTALL_LIBDIR}/libwarpx.${lib_suffix}.${mod_ext}
-+        ${ABS_INSTALL_LIB_DIR}/libwarpx.${lib_suffix}.${mod_ext}
-         COPY_ON_ERROR SYMBOLIC)")
- endif()
- 

var/spack/repos/builtin/packages/warpx/package.py

@@ -132,7 +132,22 @@ class Warpx(CMakePackage):
     # The symbolic aliases for our +lib target were missing in the install
     # location
     # https://github.com/ECP-WarpX/WarpX/pull/2626
-    patch('2626.patch', when='@21.12')
+    patch('https://github.com/ECP-WarpX/WarpX/pull/2626.patch?full_index=1',
+          sha256='a431d4664049d6dcb6454166d6a948d8069322a111816ca5ce01553800607544',
+          when='@21.12')
+
+    # Workaround for AMReX<=22.06 no-MPI Gather
+    # https://github.com/ECP-WarpX/WarpX/pull/3134
+    # https://github.com/AMReX-Codes/amrex/pull/2793
+    patch('https://github.com/ECP-WarpX/WarpX/pull/3134.patch?full_index=1',
+          sha256='b786ce64a3c2c2b96ff2e635f0ee48532e4ae7ad9637dbf03f11c0768c290690',
+          when='@22.02:22.05')
+
+    # Forgot to install ABLASTR library
+    # https://github.com/ECP-WarpX/WarpX/pull/3141
+    patch('https://github.com/ECP-WarpX/WarpX/pull/3141.patch?full_index=1',
+          sha256='dab6fb44556ee1fd466a4cb0e20f89bde1ce445c9a51a2c0f59d1740863b5e7d',
+          when='@22.04,22.05')
 
     def cmake_args(self):
         spec = self.spec
@@ -168,10 +183,15 @@ def cmake_args(self):
     def libs(self):
         libsuffix = {'1': '1d', '2': '2d', '3': '3d', 'rz': 'rz'}
         dims = self.spec.variants['dims'].value
-        return find_libraries(
+        libs = find_libraries(
             ['libwarpx.' + libsuffix[dims]], root=self.prefix, recursive=True,
             shared=True
         )
+        libs += find_libraries(
+            ['libablastr'], root=self.prefix, recursive=True,
+            shared=self.spec.variants['shared']
+        )
+        return libs
 
     # WarpX has many examples to serve as a suitable smoke check. One
     # that is typical was chosen here