Merge branch 'develop' into features/shared

bin/sbang

@@ -103,10 +103,10 @@ interpreter_f="${interpreter_v[0]}"
 
 # Invoke any interpreter found, or raise an error if none was found.
 if [[ -n "$interpreter_f" ]]; then
-    if [[ "${interpreter_f##*/}" = "perl" ]]; then
+    if [[ "${interpreter_f##*/}" = "perl"* ]]; then
-        exec $interpreter_v -x "$@"
+        exec $interpreter -x "$@"
     else
-        exec $interpreter_v "$@"
+        exec $interpreter "$@"
     fi
 else
     echo "error: sbang found no interpreter in $script"

lib/spack/docs/basic_usage.rst

@@ -929,11 +929,13 @@ in GNU Autotools. If all flags are set, the order is
 Compiler environment variables and additional RPATHs
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-In the exceptional case a compiler requires setting special environment
+Sometimes compilers require setting special environment variables to
-variables, like an explicit library load path. These can bet set in an
+operate correctly. Spack handles these cases by allowing custom environment
-extra section in the compiler configuration (the supported environment
+modifications in the ``environment`` attribute of the compiler configuration
-modification commands are: ``set``, ``unset``, ``append-path``, and
+section. See also the :ref:`configuration_environment_variables` section
-``prepend-path``). The user can also specify additional ``RPATHs`` that the
+of the configuration files docs for more information.
+
+It is also possible to specify additional ``RPATHs`` that the
 compiler will add to all executables generated by that compiler.  This is
 useful for forcing certain compilers to RPATH their own runtime libraries, so
 that executables will run without the need to set ``LD_LIBRARY_PATH``.
@@ -950,28 +952,19 @@ that executables will run without the need to set ``LD_LIBRARY_PATH``.
           fc: /opt/gcc/bin/gfortran
         environment:
           unset:
-            BAD_VARIABLE: # The colon is required but the value must be empty
+            - BAD_VARIABLE
           set:
             GOOD_VARIABLE_NUM: 1
             GOOD_VARIABLE_STR: good
-          prepend-path:
+          prepend_path:
             PATH: /path/to/binutils
-          append-path:
+          append_path:
             LD_LIBRARY_PATH: /opt/gcc/lib
         extra_rpaths:
         - /path/to/some/compiler/runtime/directory
         - /path/to/some/other/compiler/runtime/directory
 
 
-.. note::
-
-   The section `environment` is interpreted as an ordered dictionary, which
-   means two things. First, environment modification are applied in the order
-   they are specified in the configuration file. Second, you cannot express
-   environment modifications that require mixing different commands, i.e. you
-   cannot `set` one variable, than `prepend-path` to another one, and than
-   again `set` a third one.
-
 ^^^^^^^^^^^^^^^^^^^^^^^
 Architecture specifiers
 ^^^^^^^^^^^^^^^^^^^^^^^

lib/spack/docs/configuration.rst

@@ -427,6 +427,33 @@ home directory, and ``~user`` will expand to a specified user's home
 directory. The ``~`` must appear at the beginning of the path, or Spack
 will not expand it.
 
+.. _configuration_environment_variables:
+
+-------------------------
+Environment Modifications
+-------------------------
+
+Spack allows to prescribe custom environment modifications in a few places
+within its configuration files. Every time these modifications are allowed
+they are specified as a dictionary, like in the following example:
+
+.. code-block:: yaml
+
+   environment:
+     set:
+       LICENSE_FILE: '/path/to/license'
+     unset:
+     - CPATH
+     - LIBRARY_PATH
+     append_path:
+       PATH: '/new/bin/dir'
+
+The possible actions that are permitted are ``set``, ``unset``, ``append_path``,
+``prepend_path`` and finally ``remove_path``. They all require a dictionary
+of variable names mapped to the values used for the modification.
+The only exception is ``unset`` that requires just a list of variable names.
+No particular order is ensured on the execution of each of these modifications.
+
 ----------------------------
 Seeing Spack's Configuration
 ----------------------------

lib/spack/spack/binary_distribution.py

@@ -663,7 +663,7 @@ def extract_tarball(spec, filename, allow_root=False, unsigned=False,
 _cached_specs = None
 
 
-def get_specs(force=False):
+def get_specs(force=False, use_arch=False):
     """
     Get spec.yaml's for build caches available on mirror
     """
@@ -690,7 +690,13 @@ def get_specs(force=False):
                 for file in files:
                     if re.search('spec.yaml', file):
                         link = url_util.join(fetch_url_build_cache, file)
-                        urls.add(link)
+                        if use_arch and re.search('%s-%s' %
+                                                  (spack.architecture.platform,
+                                                   spack.architecture.os),
+                                                  file):
+                            urls.add(link)
+                        else:
+                            urls.add(link)
         else:
             tty.msg("Finding buildcaches at %s" %
                     url_util.format(fetch_url_build_cache))
@@ -698,7 +704,13 @@ def get_specs(force=False):
                 url_util.join(fetch_url_build_cache, 'index.html'))
             for link in links:
                 if re.search("spec.yaml", link):
-                    urls.add(link)
+                    if use_arch and re.search('%s-%s' %
+                                              (spack.architecture.platform,
+                                               spack.architecture.os),
+                                              link):
+                        urls.add(link)
+                    else:
+                        urls.add(link)
 
     _cached_specs = []
     for link in urls:

lib/spack/spack/build_environment.py

@@ -39,7 +39,6 @@
 import sys
 import traceback
 import types
-from six import iteritems
 from six import StringIO
 
 import llnl.util.tty as tty
@@ -52,6 +51,7 @@
 import spack.config
 import spack.main
 import spack.paths
+import spack.schema.environment
 import spack.store
 from spack.util.string import plural
 from spack.util.environment import (
@@ -342,21 +342,7 @@ def set_build_environment_variables(pkg, env, dirty):
     # Set environment variables if specified for
     # the given compiler
     compiler = pkg.compiler
-    environment = compiler.environment
+    env.extend(spack.schema.environment.parse(compiler.environment))
-
-    for command, variable in iteritems(environment):
-        if command == 'set':
-            for name, value in iteritems(variable):
-                env.set(name, value)
-        elif command == 'unset':
-            for name, _ in iteritems(variable):
-                env.unset(name)
-        elif command == 'prepend-path':
-            for name, value in iteritems(variable):
-                env.prepend_path(name, value)
-        elif command == 'append-path':
-            for name, value in iteritems(variable):
-                env.append_path(name, value)
 
     if compiler.extra_rpaths:
         extra_rpaths = ':'.join(compiler.extra_rpaths)

lib/spack/spack/cmd/config.py

@@ -56,6 +56,8 @@ def setup_parser(subparser):
         '--print-file', action='store_true',
         help="print the file name that would be edited")
 
+    sp.add_parser('list', help='list configuration sections')
+
 
 def _get_scope_and_section(args):
     """Extract config scope and section from arguments."""
@@ -83,7 +85,6 @@ def config_get(args):
 
     With no arguments and an active environment, print the contents of
     the environment's manifest file (spack.yaml).
-
     """
     scope, section = _get_scope_and_section(args)
 
@@ -113,7 +114,6 @@ def config_edit(args):
 
     With no arguments and an active environment, edit the spack.yaml for
     the active environment.
-
     """
     scope, section = _get_scope_and_section(args)
     if not scope and not section:
@@ -127,8 +127,19 @@ def config_edit(args):
         editor(config_file)
 
 
+def config_list(args):
+    """List the possible configuration sections.
+
+    Used primarily for shell tab completion scripts.
+    """
+    print(' '.join(list(spack.config.section_schemas)))
+
+
 def config(parser, args):
-    action = {'get': config_get,
+    action = {
-              'blame': config_blame,
+        'get': config_get,
-              'edit': config_edit}
+        'blame': config_blame,
+        'edit': config_edit,
+        'list': config_list,
+    }
     action[args.config_command](args)

lib/spack/spack/cmd/list.py

@@ -23,7 +23,7 @@
 from spack.version import VersionList
 
 if sys.version_info > (3, 1):
-    from html import escape
+    from html import escape  # novm
 else:
     from cgi import escape
 

lib/spack/spack/modules/common.py

@@ -28,26 +28,24 @@
 Each of the four classes needs to be sub-classed when implementing a new
 module type.
 """
+import collections
 import copy
 import datetime
 import inspect
 import os.path
 import re
-import collections
 
-import six
 import llnl.util.filesystem
 import llnl.util.tty as tty
-
-import spack.paths
 import spack.build_environment as build_environment
-import spack.util.environment
-import spack.tengine as tengine
-import spack.util.path
-import spack.util.environment
 import spack.error
-import spack.util.spack_yaml as syaml
+import spack.paths
+import spack.schema.environment
+import spack.tengine as tengine
+import spack.util.environment
 import spack.util.file_permissions as fp
+import spack.util.path
+import spack.util.spack_yaml as syaml
 
 
 #: config section for this file
@@ -417,22 +415,7 @@ def env(self):
         """List of environment modifications that should be done in the
         module.
         """
-        env_mods = spack.util.environment.EnvironmentModifications()
+        return spack.schema.environment.parse(self.conf.get('environment', {}))
-        actions = self.conf.get('environment', {})
-
-        def process_arglist(arglist):
-            if method == 'unset':
-                for x in arglist:
-                    yield (x,)
-            else:
-                for x in six.iteritems(arglist):
-                    yield x
-
-        for method, arglist in actions.items():
-            for args in process_arglist(arglist):
-                getattr(env_mods, method)(*args)
-
-        return env_mods
 
     @property
     def suffixes(self):

lib/spack/spack/package.py

@@ -1507,7 +1507,7 @@ def _update_explicit_entry_in_db(self, rec, explicit):
 
     def try_install_from_binary_cache(self, explicit):
         tty.msg('Searching for binary cache of %s' % self.name)
-        specs = binary_distribution.get_specs()
+        specs = binary_distribution.get_specs(use_arch=True)
         binary_spec = spack.spec.Spec.from_dict(self.spec.to_dict())
         binary_spec._mark_concrete()
         if binary_spec not in specs:

lib/spack/spack/schema/compilers.py

@@ -8,7 +8,7 @@
 .. literalinclude:: _spack_root/lib/spack/spack/schema/compilers.py
    :lines: 13-
 """
-
+import spack.schema.environment
 
 #: Properties for inclusion in other schemas
 properties = {
@@ -68,50 +68,7 @@
                                 {'type': 'boolean'}
                             ]
                         },
-                        'environment': {
+                        'environment': spack.schema.environment.definition,
-                            'type': 'object',
-                            'default': {},
-                            'additionalProperties': False,
-                            'properties': {
-                                'set': {
-                                    'type': 'object',
-                                    'patternProperties': {
-                                        # Variable name
-                                        r'\w[\w-]*': {
-                                            'anyOf': [{'type': 'string'},
-                                                      {'type': 'number'}]
-                                        }
-                                    }
-                                },
-                                'unset': {
-                                    'type': 'object',
-                                    'patternProperties': {
-                                        # Variable name
-                                        r'\w[\w-]*': {'type': 'null'}
-                                    }
-                                },
-                                'prepend-path': {
-                                    'type': 'object',
-                                    'patternProperties': {
-                                        # Variable name
-                                        r'\w[\w-]*': {
-                                            'anyOf': [{'type': 'string'},
-                                                      {'type': 'number'}]
-                                        }
-                                    }
-                                },
-                                'append-path': {
-                                    'type': 'object',
-                                    'patternProperties': {
-                                        # Variable name
-                                        r'\w[\w-]*': {
-                                            'anyOf': [{'type': 'string'},
-                                                      {'type': 'number'}]
-                                        }
-                                    }
-                                }
-                            }
-                        },
                         'extra_rpaths': {
                             'type': 'array',
                             'default': [],

lib/spack/spack/schema/environment.py

@@ -0,0 +1,58 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+"""Schema for environment modifications. Meant for inclusion in other
+schemas.
+"""
+
+array_of_strings_or_num = {
+    'type': 'array', 'default': [], 'items':
+        {'anyOf': [{'type': 'string'}, {'type': 'number'}]}
+}
+
+dictionary_of_strings_or_num = {
+    'type': 'object', 'patternProperties':
+        {r'\w[\w-]*': {'anyOf': [{'type': 'string'}, {'type': 'number'}]}}
+}
+
+definition = {
+    'type': 'object',
+    'default': {},
+    'additionalProperties': False,
+    'properties': {
+        'set': dictionary_of_strings_or_num,
+        'unset': array_of_strings_or_num,
+        'prepend_path': dictionary_of_strings_or_num,
+        'append_path': dictionary_of_strings_or_num,
+        'remove_path': dictionary_of_strings_or_num
+    }
+}
+
+
+def parse(config_obj):
+    """Returns an EnvironmentModifications object containing the modifications
+    parsed from input.
+
+    Args:
+        config_obj: a configuration dictionary conforming to the
+            schema definition for environment modifications
+    """
+    import spack.util.environment as ev
+    try:
+        from collections import Sequence  # novm
+    except ImportError:
+        from collections.abc import Sequence  # novm
+
+    env = ev.EnvironmentModifications()
+    for command, variable in config_obj.items():
+        # Distinguish between commands that take only a name as argument
+        # (e.g. unset) and commands that take a name and a value.
+        if isinstance(variable, Sequence):
+            for name in variable:
+                getattr(env, command)(name)
+        else:
+            for name, value in variable.items():
+                getattr(env, command)(name, value)
+
+    return env

lib/spack/spack/schema/modules.py

@@ -8,6 +8,8 @@
 .. literalinclude:: _spack_root/lib/spack/spack/schema/modules.py
    :lines: 13-
 """
+import spack.schema.environment
+
 
 #: Matches a spec or a multi-valued variant but not another
 #: valid keyword.
@@ -66,17 +68,7 @@
                 }
             }
         },
-        'environment': {
+        'environment': spack.schema.environment.definition
-            'type': 'object',
-            'default': {},
-            'additionalProperties': False,
-            'properties': {
-                'set': dictionary_of_strings,
-                'unset': array_of_strings,
-                'prepend_path': dictionary_of_strings,
-                'append_path': dictionary_of_strings
-            }
-        }
     }
 }
 

lib/spack/spack/test/build_environment.py

@@ -14,7 +14,6 @@
 from spack.paths import build_env_path
 from spack.build_environment import dso_suffix, _static_to_shared_library
 from spack.util.executable import Executable
-from spack.util.spack_yaml import syaml_dict, syaml_str
 from spack.util.environment import EnvironmentModifications
 
 from llnl.util.filesystem import LibraryList, HeaderList
@@ -65,6 +64,18 @@ def build_environment(working_env):
         del os.environ[name]
 
 
+@pytest.fixture
+def ensure_env_variables(config, mock_packages, monkeypatch, working_env):
+    """Returns a function that takes a dictionary and updates os.environ
+    for the test lifetime accordingly. Plugs-in mock config and repo.
+    """
+    def _ensure(env_mods):
+        for name, value in env_mods.items():
+            monkeypatch.setenv(name, value)
+
+    return _ensure
+
+
 def test_static_to_shared_library(build_environment):
     os.environ['SPACK_TEST_COMMAND'] = 'dump-args'
 
@@ -119,79 +130,58 @@ def _set_wrong_cc(x):
     assert os.environ['ANOTHER_VAR'] == 'THIS_IS_SET'
 
 
-@pytest.mark.usefixtures('config', 'mock_packages')
+@pytest.mark.parametrize('initial,modifications,expected', [
-def test_compiler_config_modifications(monkeypatch, working_env):
+    # Set and unset variables
-    s = spack.spec.Spec('cmake')
+    ({'SOME_VAR_STR': '', 'SOME_VAR_NUM': '0'},
-    s.concretize()
+     {'set': {'SOME_VAR_STR': 'SOME_STR', 'SOME_VAR_NUM': 1}},
-    pkg = s.package
+     {'SOME_VAR_STR': 'SOME_STR', 'SOME_VAR_NUM': '1'}),
+    ({'SOME_VAR_STR': ''},
+     {'unset': ['SOME_VAR_STR']},
+     {'SOME_VAR_STR': None}),
+    ({},  # Set a variable that was not defined already
+     {'set': {'SOME_VAR_STR': 'SOME_STR'}},
+     {'SOME_VAR_STR': 'SOME_STR'}),
+    # Append and prepend to the same variable
+    ({'EMPTY_PATH_LIST': '/path/middle'},
+     {'prepend_path': {'EMPTY_PATH_LIST': '/path/first'},
+      'append_path': {'EMPTY_PATH_LIST': '/path/last'}},
+     {'EMPTY_PATH_LIST': '/path/first:/path/middle:/path/last'}),
+    # Append and prepend from empty variables
+    ({'EMPTY_PATH_LIST': '', 'SOME_VAR_STR': ''},
+     {'prepend_path': {'EMPTY_PATH_LIST': '/path/first'},
+      'append_path': {'SOME_VAR_STR': '/path/last'}},
+     {'EMPTY_PATH_LIST': '/path/first', 'SOME_VAR_STR': '/path/last'}),
+    ({},  # Same as before but on variables that were not defined
+     {'prepend_path': {'EMPTY_PATH_LIST': '/path/first'},
+      'append_path': {'SOME_VAR_STR': '/path/last'}},
+     {'EMPTY_PATH_LIST': '/path/first', 'SOME_VAR_STR': '/path/last'}),
+    # Remove a path from a list
+    ({'EMPTY_PATH_LIST': '/path/first:/path/middle:/path/last'},
+     {'remove_path': {'EMPTY_PATH_LIST': '/path/middle'}},
+     {'EMPTY_PATH_LIST': '/path/first:/path/last'}),
+    ({'EMPTY_PATH_LIST': '/only/path'},
+     {'remove_path': {'EMPTY_PATH_LIST': '/only/path'}},
+     {'EMPTY_PATH_LIST': ''}),
+])
+def test_compiler_config_modifications(
+        initial, modifications, expected, ensure_env_variables, monkeypatch
+):
+    # Set the environment as per prerequisites
+    ensure_env_variables(initial)
 
-    os.environ['SOME_VAR_STR'] = ''
+    # Monkeypatch a pkg.compiler.environment with the required modifications
-    os.environ['SOME_VAR_NUM'] = '0'
+    pkg = spack.spec.Spec('cmake').concretized().package
-    os.environ['PATH_LIST'] = '/path/third:/path/forth'
+    monkeypatch.setattr(pkg.compiler, 'environment', modifications)
-    os.environ['EMPTY_PATH_LIST'] = ''
-    os.environ.pop('NEW_PATH_LIST', None)
 
-    env_mod = syaml_dict()
+    # Trigger the modifications
-    set_cmd = syaml_dict()
-    env_mod[syaml_str('set')] = set_cmd
-
-    set_cmd[syaml_str('SOME_VAR_STR')] = syaml_str('SOME_STR')
-    set_cmd[syaml_str('SOME_VAR_NUM')] = 1
-
-    monkeypatch.setattr(pkg.compiler, 'environment', env_mod)
     spack.build_environment.setup_package(pkg, False)
-    assert os.environ['SOME_VAR_STR'] == 'SOME_STR'
-    assert os.environ['SOME_VAR_NUM'] == str(1)
 
-    env_mod = syaml_dict()
+    # Check they were applied
-    unset_cmd = syaml_dict()
+    for name, value in expected.items():
-    env_mod[syaml_str('unset')] = unset_cmd
+        if value is not None:
-
+            assert os.environ[name] == value
-    unset_cmd[syaml_str('SOME_VAR_STR')] = None
+            continue
-
+        assert name not in os.environ
-    monkeypatch.setattr(pkg.compiler, 'environment', env_mod)
-    assert 'SOME_VAR_STR' in os.environ
-    spack.build_environment.setup_package(pkg, False)
-    assert 'SOME_VAR_STR' not in os.environ
-
-    env_mod = syaml_dict()
-    set_cmd = syaml_dict()
-    env_mod[syaml_str('set')] = set_cmd
-    append_cmd = syaml_dict()
-    env_mod[syaml_str('append-path')] = append_cmd
-    unset_cmd = syaml_dict()
-    env_mod[syaml_str('unset')] = unset_cmd
-    prepend_cmd = syaml_dict()
-    env_mod[syaml_str('prepend-path')] = prepend_cmd
-
-    set_cmd[syaml_str('EMPTY_PATH_LIST')] = syaml_str('/path/middle')
-
-    append_cmd[syaml_str('PATH_LIST')] = syaml_str('/path/last')
-    append_cmd[syaml_str('EMPTY_PATH_LIST')] = syaml_str('/path/last')
-    append_cmd[syaml_str('NEW_PATH_LIST')] = syaml_str('/path/last')
-
-    unset_cmd[syaml_str('SOME_VAR_NUM')] = None
-
-    prepend_cmd[syaml_str('PATH_LIST')] = syaml_str('/path/first:/path/second')
-    prepend_cmd[syaml_str('EMPTY_PATH_LIST')] = syaml_str('/path/first')
-    prepend_cmd[syaml_str('NEW_PATH_LIST')] = syaml_str('/path/first')
-    prepend_cmd[syaml_str('SOME_VAR_NUM')] = syaml_str('/8')
-
-    assert 'SOME_VAR_NUM' in os.environ
-    monkeypatch.setattr(pkg.compiler, 'environment', env_mod)
-    spack.build_environment.setup_package(pkg, False)
-    # Check that the order of modifications is respected and the
-    # variable was unset before it was prepended.
-    assert os.environ['SOME_VAR_NUM'] == '/8'
-
-    expected = '/path/first:/path/second:/path/third:/path/forth:/path/last'
-    assert os.environ['PATH_LIST'] == expected
-
-    expected = '/path/first:/path/middle:/path/last'
-    assert os.environ['EMPTY_PATH_LIST'] == expected
-
-    expected = '/path/first:/path/last'
-    assert os.environ['NEW_PATH_LIST'] == expected
 
 
 @pytest.mark.regression('9107')

lib/spack/spack/test/cmd/config.py

@@ -91,3 +91,9 @@ def test_config_edit_fails_correctly_with_no_env(mutable_mock_env_path):
 def test_config_get_fails_correctly_with_no_env(mutable_mock_env_path):
     output = config('get', fail_on_error=False)
     assert "requires a section argument or an active environment" in output
+
+
+def test_config_list():
+    output = config('list')
+    assert 'compilers' in output
+    assert 'packages' in output

lib/spack/spack/test/data/config/config.yaml

@@ -12,3 +12,6 @@ config:
   verify_ssl: true
   checksum: true
   dirty: false
+  module_roots:
+    tcl:    $spack/share/spack/modules
+    lmod:   $spack/share/spack/lmod

lib/spack/spack/util/environment.py

@@ -17,7 +17,6 @@
 
 import llnl.util.tty as tty
 import spack.util.executable as executable
-from spack.util.module_cmd import py_cmd
 
 from llnl.util.lang import dedupe
 
@@ -919,8 +918,14 @@ def _source_single_file(file_and_args, environment):
         source_file.extend(x for x in file_and_args)
         source_file = ' '.join(source_file)
 
-        dump_environment = 'PYTHONHOME="{0}" "{1}" -c "{2}"'.format(
+        # If the environment contains 'python' use it, if not
-            sys.prefix, sys.executable, py_cmd)
+        # go with sys.executable. Below we just need a working
+        # Python interpreter, not necessarily sys.executable.
+        python_cmd = executable.which('python3', 'python', 'python2')
+        python_cmd = python_cmd.name if python_cmd else sys.executable
+
+        dump_cmd = 'import os, json; print(json.dumps(dict(os.environ)))'
+        dump_environment = python_cmd + ' -c "{0}"'.format(dump_cmd)
 
         # Try to source the file
         source_file_arguments = ' '.join([

lib/spack/spack/util/module_cmd.py

@@ -18,7 +18,7 @@
 # This list is not exhaustive. Currently we only use load and unload
 # If we need another option that changes the environment, add it here.
 module_change_commands = ['load', 'swap', 'unload', 'purge', 'use', 'unuse']
-py_cmd = 'import os; import json; print(json.dumps(dict(os.environ)))'
+py_cmd = "'import os;import json;print(json.dumps(dict(os.environ)))'"
 
 # This is just to enable testing. I hate it but we can't find a better way
 _test_mode = False
@@ -32,8 +32,7 @@ def module(*args):
     if args[0] in module_change_commands:
         # Do the module manipulation, then output the environment in JSON
         # and read the JSON back in the parent process to update os.environ
-        module_cmd += ' > /dev/null; PYTHONHOME="{0}" "{1}" -c "{2}"'.format(
+        module_cmd += ' >/dev/null;' + sys.executable + ' -c %s' % py_cmd
-            sys.prefix, sys.executable, py_cmd)
         module_p  = subprocess.Popen(module_cmd,
                                      stdout=subprocess.PIPE,
                                      stderr=subprocess.STDOUT,

lib/spack/spack/util/web.py

@@ -21,7 +21,7 @@
 
 try:
     # Python 2 had these in the HTMLParser package.
-    from HTMLParser import HTMLParser, HTMLParseError
+    from HTMLParser import HTMLParser, HTMLParseError  # novm
 except ImportError:
     # In Python 3, things moved to html.parser
     from html.parser import HTMLParser
@@ -80,7 +80,7 @@ class NonDaemonPool(multiprocessing.pool.Pool):
         Process = NonDaemonProcess
 else:
 
-    class NonDaemonContext(type(multiprocessing.get_context())):
+    class NonDaemonContext(type(multiprocessing.get_context())):  # novm
         Process = NonDaemonProcess
 
     class NonDaemonPool(multiprocessing.pool.Pool):
@@ -128,7 +128,7 @@ def read_from_url(url, accept_content_type=None):
                 warn_no_ssl_cert_checking()
             else:
                 # User wants SSL verification, and it *can* be provided.
-                context = ssl.create_default_context()
+                context = ssl.create_default_context()  # novm
         else:
             # User has explicitly indicated that they do not want SSL
             # verification.

share/spack/bash/spack-completion.in

@@ -218,7 +218,7 @@ _keys() {
 _config_sections() {
     if [[ -z "${SPACK_CONFIG_SECTIONS:-}" ]]
     then
-        SPACK_CONFIG_SECTIONS="compilers mirrors repos packages modules config upstreams"
+        SPACK_CONFIG_SECTIONS="$(spack config list)"
     fi
     SPACK_COMPREPLY="$SPACK_CONFIG_SECTIONS"
 }

share/spack/spack-completion.bash

@@ -218,7 +218,7 @@ _keys() {
 _config_sections() {
     if [[ -z "${SPACK_CONFIG_SECTIONS:-}" ]]
     then
-        SPACK_CONFIG_SECTIONS="compilers mirrors repos packages modules config upstreams"
+        SPACK_CONFIG_SECTIONS="$(spack config list)"
     fi
     SPACK_COMPREPLY="$SPACK_CONFIG_SECTIONS"
 }
@@ -584,7 +584,7 @@ _spack_config() {
     then
         SPACK_COMPREPLY="-h --help --scope"
     else
-        SPACK_COMPREPLY="get blame edit"
+        SPACK_COMPREPLY="get blame edit list"
     fi
 }
 
@@ -615,6 +615,10 @@ _spack_config_edit() {
     fi
 }
 
+_spack_config_list() {
+    SPACK_COMPREPLY="-h --help"
+}
+
 _spack_configure() {
     if $list_options
     then

var/spack/repos/builtin/packages/acts-core/package.py

@@ -34,6 +34,8 @@ class ActsCore(CMakePackage):
     maintainers = ['HadrienG2']
 
     version('develop', branch='master')
+    version('0.15.0', commit='267c28f69c561e64369661a6235b03b5a610d6da')
+    version('0.14.0', commit='38d678fcb205b77d60326eae913fbb1b054acea1')
     version('0.13.0', commit='b33f7270ddbbb33050b7ec60b4fa255dc2bfdc88')
     version('0.12.1', commit='a8b3d36e7c6cb86487637589e0eff7bbe626054a')
     version('0.12.0', commit='f9cda77299606d78c889fb1db2576c1971a271c4')
@@ -68,10 +70,11 @@ class ActsCore(CMakePackage):
     variant('json', default=False, description='Build the Json plugin')
     variant('tgeo', default=False, description='Build the TGeo plugin')
 
-    depends_on('cmake @3.9:', type='build')
+    depends_on('cmake @3.11:', type='build')
     depends_on('boost @1.62:1.69.99 +program_options +test', when='@:0.10.3')
     depends_on('boost @1.62: +program_options +test', when='@0.10.4:')
     depends_on('eigen @3.2.9:', type='build')
+    depends_on('nlohmann-json @3.2.0:', when='@0.14.0: +json')
     depends_on('root @6.10: cxxstd=14', when='+tgeo @:0.8.0')
     depends_on('root @6.10:', when='+tgeo @0.8.1:')
     depends_on('dd4hep @1.2:', when='+dd4hep')
@@ -99,4 +102,7 @@ def cmake_variant(cmake_label, spack_variant):
             cxxstd = spec['root'].variants['cxxstd'].value
             args.append("-DCMAKE_CXX_STANDARD={0}".format(cxxstd))
 
+        if spec.satisfies('@0.14.0: +json'):
+            args.append("-DACTS_USE_BUNDLED_NLOHMANN_JSON=OFF")
+
         return args

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

@@ -12,11 +12,13 @@ class Amrex(CMakePackage):
     mesh refinement (AMR) applications."""
 
     homepage = "https://amrex-codes.github.io/amrex/"
+    url      = "https://github.com/AMReX-Codes/amrex/archive/20.01.tar.gz"
     git      = "https://github.com/AMReX-Codes/amrex.git"
 
     maintainers = ['mic84', 'asalmgren']
 
     version('develop', branch='development')
+    version('20.01', sha256='f7026d267ca5de79ec7e740264d54230f419776d40feae705e939be0b1d8e0d3')
     version('19.10', commit='52844b32b7da11e9733b9a7f4a782e51de7f5e1e')  # tag:19.10
     version('19.08', commit='bdd1146139e8727a513d451075f900c172eb81fd')  # tag:19.08
     version('18.10.1', commit='260b53169badaa760b91dfc60ea6b2ea3d9ccf06')  # tag:18.10.1

var/spack/repos/builtin/packages/asdf-cxx/package.py

@@ -0,0 +1,47 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class AsdfCxx(CMakePackage):
+    """ASDF - Advanced Scientific Data Format, a C++ implementation"""
+
+    homepage = "https://github.com/eschnett/asdf-cxx"
+    url      = "https://github.com/eschnett/asdf-cxx/archive/version/1.0.0.tar.gz"
+
+    maintainers = ['eschnett']
+
+    version('7.2.1', sha256='40864f4f27d3ce8acb5169b57211ce6ac3805f0a6de9c1dfd5f994f4a5beccda')
+    version('7.2.0', sha256='faded85d44288afb83f13634d2139adee07e06f7ea60960c6f2ef8d898c0aa09')
+    version('7.1.0', sha256='81fd8c7f91f8daf0f85a1486480ae9e736b9712e82ccb858271f7ee2c2b425f7')
+    version('7.0.0', sha256='a50718dfa68b86b0c3e280e6a9d0a4edb03d500ba70244bd38fa86bac1433979')
+    version('6.3.0', sha256='44a24cc490cf776106edcfded6006d63d28889dfe985cce3bd565d5151add9c8')
+    version('6.0.0', sha256='76ab0a893191a33a88a753d09a20135470f809c66173794fa3e37a2437ea3cde')
+    version('5.0.0', sha256='876c83bcc7514f2584dbf5462bd5b7de89b41301ec127451342079e703cd6a67')
+    version('4.0.1', sha256='c4597b8353b0e181d97c6702dae0cb69a558ae5b553945298757433615bb199b')
+    version('3.1.0', sha256='15de5156460ed581e1e755955e6a1b557758a6497d083c4873d143c05e720078')
+    version('3.0.0', sha256='a6d42f7d875eff2f1ff6af836a44e7a44fcc6be3409605d45f236e07d70c65db')
+    version('2.6.1', sha256='631426bd2784c2175b5a5035c12e91b0b0d36691f9972df427b41080ace43fc3')
+    version('2.5.1', sha256='d3c1f690716bd0883c4d429c9fa895ce41e6223bafa87624f9f1530c0d2e654c')
+    version('2.5.0', sha256='916e9021063c41eb7922ed69c958ea87757cdfcb7263d0d3fda31f0233dbbaaf')
+    version('2.4.1', sha256='a300bf11d4fd9923eb109c5f8e1067f2ef96f284ea43fafd871b469118d42597')
+    version('2.4.0', sha256='965360858bcacb6df4602fdff55924f7b9daf0750b27ac3f31781e23b54e8f93')
+    version('2.3.1', sha256='7c3ecf4fdafff5da57edb8b0c75b2e1f9c6bf42097c483025ff49f0a65094e22')
+    version('2.2.1', sha256='a34679d8690ff118bedd20652caebdb9c3fb5f628aca7ed2f535a026b28b3853')
+    version('2.1.1', sha256='f1a801b82facb2c0913ca3dce9c62970651e58fae8bc232f5079a1c4773ec6fa')
+    version('2.1.0', sha256='066c2c1033be41e10b874ceec1e87267fd792c40d46cbc768b05ba94cca234a1')
+    version('1.1.0', sha256='3e23b9cd16254f5adbf878145e320f56b4d3ad75de23d2c761eb7f04150926c5')
+    version('1.0.0', sha256='0b63594a1dec27cc85d25adbf900b6e936b5015f579b9b892b983151bec96775')
+
+    variant('python', default=True, description="Enable Python support")
+
+    depends_on('bzip2')
+    depends_on('openssl')
+    depends_on('py-numpy', type=('build', 'run'), when='+python')
+    depends_on('python', type=('build', 'run'), when='+python')
+    depends_on('swig', type='build', when='+python')
+    depends_on('yaml-cpp')
+    depends_on('zlib')

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

@@ -6,7 +6,7 @@
 from spack import *
 
 
-class Charliecloud(MakefilePackage):
+class Charliecloud(AutotoolsPackage):
     """Lightweight user-defined software stacks for HPC."""
 
     homepage = "https://hpc.github.io/charliecloud"
@@ -14,19 +14,7 @@ class Charliecloud(MakefilePackage):
     git      = "https://github.com/hpc/charliecloud.git"
 
     version('master', branch='master')
-    version('0.12',   sha256='8a90f33406905cee935b5673a1159232b0b71845f4b6a26d28ca88f5d3f55891')
+    version('0.13',   sha256='5740bff6e410ca99484c1bdf3dbe834c0f753c846d55c19d6162967a3e2718e0')
-    version('0.11',   sha256='942d3c7a74c978fd7420cb2b255e618f4f0acaafb6025160bc3a4deeb687ef3c')
-    version('0.10',   sha256='5cf00b170e7568750ca0b828c43c0857c39674860b480d757057450d69f1a21e')
-    version('0.9.10', sha256='44e821b62f9c447749d3ed0d2b2e44d374153058814704a5543e83f42db2a45a')
-    version('0.9.9',  sha256='2624c5a0b19a01c9bca0acf873ceeaec401b9185a23e9108fadbcee0b9d74736')
-    version('0.9.8',  sha256='903bcce05b19501b5524ef57a929d2f4c6ddeacb0e8443fcb2fe6963e2f29229')
-    version('0.9.7',  sha256='ec80a4b9bef3a2161a783e11d99cc58e09a32dfbc8a6234c8f7ce7fa76e2f62d')
-    version('0.9.6',  sha256='50e20d5e2a3710cd06e7c999db22495b07ef0fb15ffbc0af3bccac5387f0fddb')
-    version('0.9.3',  sha256='f1bf032377b8845bc9a93b8a4fad6386161e35900223c0acc61d1f3aa3a87bc7')
-    version('0.9.2',  sha256='8d0e4804d412beef720a66f886a0a78bce42f3269e880ebf11f602581f8047d4')
-    version('0.9.1',  sha256='8e69150a271285da71ece7a09b48251ef6593f72207c5126741d9976aa737d95')
-    version('0.9.0',  sha256='7e74cb16e31fd9d502198f7509bab14d1049ec68ba90b15e277e76f805db9458')
-    version('0.2.4',  sha256='b9a8ff54b9d296e30b2cf5d64a7e732ad09e14b989645aaa5eee8a1dc7ee34e5')
 
     depends_on('python@3.4:', type=('build', 'run'))
 
@@ -45,13 +33,14 @@ class Charliecloud(MakefilePackage):
     # bash automated testing harness (bats)
     depends_on('bats@0.4.0', type='test')
 
-    def url_for_version(self, version):
+    def configure_args(self):
-        if version >= Version('0.9.8'):
-            url = "https://github.com/hpc/charliecloud/releases/download/v{0}/charliecloud-{0}.tar.gz"
-        else:
-            url = "https://github.com/hpc/charliecloud/archive/v{0}.tar.gz"
-        return url.format(version)
 
-    @property
+        args = []
-    def install_targets(self):
+
-        return ['install', 'PREFIX=%s' % self.prefix]
+        if '+docs' not in self.spec:
+            args.append('--disable-html')
+
+        if '+builder' not in self.spec:
+            args.append('--disable-ch-grow')
+
+        return args

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

@@ -15,6 +15,7 @@ class Curl(AutotoolsPackage):
     # URL must remain http:// so Spack can bootstrap curl
     url      = "http://curl.haxx.se/download/curl-7.60.0.tar.bz2"
 
+    version('7.68.0', sha256='207f54917dd6a2dc733065ccf18d61bb5bebeaceb5df49cd9445483e8623eeb9')
     version('7.63.0', sha256='9bab7ed4ecff77020a312d84cc5fb7eb02d58419d218f267477a724a17fd8dd8')
     version('7.60.0', sha256='897dfb2204bd99be328279f88f55b7c61592216b0542fcbe995c60aa92871e9b')
     version('7.59.0', sha256='b5920ffd6a8c95585fb95070e0ced38322790cb335c39d0dab852d12e157b5a0')

var/spack/repos/builtin/packages/h5cpp/package.py

@@ -7,15 +7,16 @@
 
 
 class H5cpp(CMakePackage):
-    """Easy to use HDF5 C++ templates for Serial and Paralell HDF5"""
+    """Easy to use HDF5 C++ templates for Serial and Parallel HDF5"""
 
     homepage = "http://h5cpp.org"
-    # url      = "https://github.com/steven-varga/h5cpp"
+    url      = "https://github.com/steven-varga/h5cpp/archive/v1.10.4-5.tar.gz"
     git      = "https://github.com/steven-varga/h5cpp.git"
 
     maintainers = ['eschnett']
 
-    version('master',  branch='master')
+    version('master', branch='master')
+    version('1.10.4-5', sha256='42d0ca1aaff1ead8998a26d892a51c12b1b89023382f191dc438bd0fa4513455')
 
     variant('mpi', default=True, description='Include MPI support')
 

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

@@ -27,6 +27,9 @@ class Harfbuzz(AutotoolsPackage):
     depends_on("zlib")
     depends_on("graphite2", when='+graphite2')
 
+    conflicts('%intel', when='@2.3.1:',
+              msg='harfbuzz-2.3.1 does not build with the Intel compiler')
+
     def configure_args(self):
         args = []
         # disable building of gtk-doc files following #9771

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

@@ -28,6 +28,7 @@ class Hwloc(AutotoolsPackage):
     git = 'https://github.com/open-mpi/hwloc.git'
 
     version('master', branch='master')
+    version('2.1.0',  sha256='1fb8cc1438de548e16ec3bb9e4b2abb9f7ce5656f71c0906583819fcfa8c2031')
     version('2.0.2',  sha256='27dcfe42e3fb3422b72ce48b48bf601c0a3e46e850ee72d9bdd17b5863b6e42c')
     version('2.0.1',  sha256='f1156df22fc2365a31a3dc5f752c53aad49e34a5e22d75ed231cd97eaa437f9d')
     version('2.0.0',  sha256='a0d425a0fc7c7e3f2c92a272ffaffbd913005556b4443e1887d2e1718d902887')

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

@@ -19,6 +19,7 @@ class Hydrogen(CMakePackage):
     maintainers = ['bvanessen']
 
     version('develop', branch='hydrogen')
+    version('1.3.3', sha256='140112066b84d33ca4b75c8e520fb15748fa648c4d2b934c1eb5510173ede5f5')
     version('1.3.2', sha256='50bc5e87955f8130003d04dfd9dcad63107e92b82704f8107baf95b0ccf98ed6')
     version('1.3.1', sha256='a8b8521458e9e747f2b24af87c4c2749a06e500019c383e0cefb33e5df6aaa1d')
     version('1.3.0', sha256='0f3006aa1d8235ecdd621e7344c99f56651c6836c2e1bc0cf006331b70126b36')
@@ -58,6 +59,8 @@ class Hydrogen(CMakePackage):
             description='Builds with Aluminum communication library')
     variant('omp_taskloops', default=False,
             description='Use OpenMP taskloops instead of parallel for loops.')
+    variant('half', default=True,
+            description='Builds with support for FP16 precision data types')
 
     # Note that #1712 forces us to enumerate the different blas variants
     depends_on('openblas', when='blas=openblas ~openmp_blas ~int64_blas')
@@ -94,6 +97,7 @@ class Hydrogen(CMakePackage):
 
     depends_on('cuda', when='+cuda')
     depends_on('cub', when='+cuda')
+    depends_on('half', when='+half')
 
     conflicts('@0:0.98', msg="Hydrogen did not exist before v0.99. " +
               "Did you mean to use Elemental instead?")
@@ -127,6 +131,7 @@ def cmake_args(self):
             '-DHydrogen_ENABLE_CUB=%s' % ('+cuda' in spec),
             '-DHydrogen_ENABLE_CUDA=%s' % ('+cuda' in spec),
             '-DHydrogen_ENABLE_TESTING=%s' % ('+test' in spec),
+            '-DHydrogen_ENABLE_HALF=%s' % ('+half' in spec),
         ]
 
         # Add support for OS X to find OpenMP

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

@@ -11,9 +11,10 @@ class Ior(AutotoolsPackage):
     using POSIX, MPI-IO, or HDF5 interfaces."""
 
     homepage = "https://github.com/hpc/ior"
-    url      = "https://github.com/hpc/ior/archive/3.2.0.tar.gz"
+    url      = "https://github.com/hpc/ior/archive/3.2.1.tar.gz"
 
-    version('3.2.0',    sha256='91a766fb9c34b5780705d0997b71b236a1120da46652763ba11d9a8c44251852')
+    version('3.2.1', sha256='ebcf2495aecb357370a91a2d5852cfd83bba72765e586bcfaf15fb79ca46d00e')
+    version('3.2.0', sha256='91a766fb9c34b5780705d0997b71b236a1120da46652763ba11d9a8c44251852')
     version('3.0.1', sha256='0cbefbcdb02fb13ba364e102f9e7cc2dcf761698533dac25de446a3a3e81390d')
 
     variant('hdf5',  default=False, description='support IO with HDF5 backend')

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

@@ -48,6 +48,7 @@ class Lbann(CMakePackage):
             '(note that for v0.99 conduit is required)')
     variant('vtune', default=False, description='Builds with support for Intel VTune')
     variant('docs', default=False, description='Builds with support for building documentation')
+    variant('extras', default=False, description='Add python modules for LBANN related tools')
 
     conflicts('@:0.90,0.99:', when='~conduit')
 
@@ -96,7 +97,6 @@ class Lbann(CMakePackage):
                '~pthreads_pf ~python ~qt ~stitching ~superres ~ts ~video'
                '~videostab ~videoio ~vtk', when='+opencv')
 
-    depends_on('protobuf@3.6.1: build_type=Release')
     depends_on('cnpy')
     depends_on('nccl', when='@0.94:0.98.2 +gpu +nccl')
 
@@ -107,20 +107,22 @@ class Lbann(CMakePackage):
     extends("python")
     depends_on('py-setuptools', type='build')
     depends_on('py-argparse', type='run', when='@:0.90,0.99: ^python@:2.6')
-    depends_on('py-configparser', type='run', when='@:0.90,0.99:')
+    depends_on('py-configparser', type='run', when='@:0.90,0.99: +extras')
-    depends_on('py-graphviz@0.10.1:', type='run', when='@:0.90,0.99:')
+    depends_on('py-graphviz@0.10.1:', type='run', when='@:0.90,0.99: +extras')
-    depends_on('py-matplotlib@3.0.0:', type='run', when='@:0.90,0.99:')
+    depends_on('py-matplotlib@3.0.0:', type='run', when='@:0.90,0.99: +extras')
-    depends_on('py-numpy@1.16.0:', type=('build', 'run'), when='@:0.90,0.99:')
+    depends_on('py-numpy@1.16.0:', type=('build', 'run'), when='@:0.90,0.99: +extras')
-    depends_on('py-onnx@1.3.0:', type='run', when='@:0.90,0.99:')
+    depends_on('py-onnx@1.3.0:', type='run', when='@:0.90,0.99: +extras')
-    depends_on('py-pandas@0.24.1:', type='run', when='@:0.90,0.99:')
+    depends_on('py-pandas@0.24.1:', type='run', when='@:0.90,0.99: +extras')
-    depends_on('py-texttable@1.4.0:', type='run', when='@:0.90,0.99:')
+    depends_on('py-texttable@1.4.0:', type='run', when='@:0.90,0.99: +extras')
     depends_on('py-pytest', type='test', when='@:0.90,0.99:')
-    depends_on('py-protobuf+cpp', type='run', when='@:0.90,0.99:')
+    depends_on('py-protobuf+cpp@3.6.1:', type=('build', 'run'), when='@:0.90,0.99:')
 
     depends_on('py-breathe', type='build', when='+docs')
     depends_on('py-m2r', type='build', when='+docs')
 
     depends_on('cereal')
+    depends_on('catch2', type='test')
+    depends_on('clara')
 
     generator = 'Ninja'
     depends_on('ninja', type='build')

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

@@ -15,6 +15,7 @@ class Libcircle(AutotoolsPackage):
     url      = "https://github.com/hpc/libcircle/releases/download/0.2.1-rc.1/libcircle-0.2.1-rc.1.tar.gz"
 
     version('master', branch='master')
+    version('0.3.0',      sha256='5ce38eb5b3c2b394bca1316310758f276c893dd3f4c15d7bc14ea05d3110ce58', url='https://github.com/hpc/libcircle/releases/download/v0.3/libcircle-0.3.0.tar.gz')
     version('0.2.1-rc.1', sha256='5747f91cf4417023304dcc92fd07e3617ac712ca1eeb698880979bbca3f54865')
 
     depends_on('mpi')

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

@@ -49,10 +49,6 @@ class Libhio(AutotoolsPackage):
     patch('0001-hdf5-make-docs-optional.patch', when="@1.4.1.0")
     patch('0001-spack-fix-for-spack-to-work-on-non-cray-systems.patch', when="@1.4.1.2")
 
-    def autoreconf(self, spec, prefix):
-        autoreconf = which('autoreconf')
-        autoreconf('-ifv')
-
     def configure_args(self):
         spec = self.spec
         args = []

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

@@ -87,20 +87,16 @@ class Llvm(CMakePackage):
     variant('omp_tsan', default=False,
             description="Build with OpenMP capable thread sanitizer")
     variant('python', default=False, description="Install python bindings")
-    variant('flang', default=False,
-            description='Build flang branch version instead')
 
     extends('python', when='+python')
 
     # Build dependency
     depends_on('cmake@3.4.3:', type='build')
     depends_on('python@2.7:2.8', when='@:4.999 ~python', type='build')
-    depends_on('python@2.7:2.8', when='@5: ~python +flang', type='build')
     depends_on('python', when='@5: ~python', type='build')
 
     # Universal dependency
     depends_on('python@2.7:2.8', when='@:4.999+python')
-    depends_on('python@2.7:2.8', when='@5:+python+flang')
     depends_on('python', when='@5:+python')
 
     # openmp dependencies
@@ -119,59 +115,6 @@ class Llvm(CMakePackage):
     depends_on('gmp', when='@:3.6.999 +polly')
     depends_on('isl', when='@:3.6.999 +polly')
 
-    resource(name='flang-llvm',
-             git='https://github.com/flang-compiler/llvm.git',
-             branch='release_60',
-             placement='llvm-flang',
-             when='llvm@develop+flang')
-
-    resource(name='flang-llvm',
-             git='https://github.com/flang-compiler/llvm.git',
-             commit='d8b30082648dc869eba68f9e539605f437d7760c',
-             placement='llvm-flang',
-             when='@7.0.1+flang')
-
-    resource(name='flang-llvm',
-             git='https://github.com/flang-compiler/llvm.git',
-             commit='f26a3ece4ccd68a52f5aa970ec42837ee0743296',
-             placement='llvm-flang',
-             when='@6.0.0+flang')
-
-    resource(name='flang-driver',
-             git='https://github.com/flang-compiler/flang-driver.git',
-             branch='release_60',
-             destination='llvm-flang/tools',
-             placement='clang',
-             when='llvm@develop+flang')
-
-    resource(name='flang-driver',
-             git='https://github.com/flang-compiler/flang-driver.git',
-             commit='dd7587310ae498c22514a33e1a2546b86af9cf25',
-             destination='llvm-flang/tools',
-             placement='clang',
-             when='@7.0.1+flang')
-
-    resource(name='flang-driver',
-             git='https://github.com/flang-compiler/flang-driver.git',
-             commit='e079fa68cb35a53c88c41a1939f90b94d539e984',
-             destination='llvm-flang/tools',
-             placement='clang',
-             when='@6.0.0+flang')
-
-    resource(name='openmp',
-             git='https://github.com/llvm-mirror/openmp.git',
-             branch='release_60',
-             destination='llvm-flang/projects',
-             placement='openmp',
-             when='@develop+flang')
-
-    resource(name='openmp',
-             git='https://github.com/llvm-mirror/openmp.git',
-             commit='d5aa29cb3bcf51289d326b4e565613db8aff65ef',
-             destination='llvm-flang/projects',
-             placement='openmp',
-             when='@6:7.0.1+flang')
-
     conflicts('+clang_extra', when='~clang')
     conflicts('+lldb',        when='~clang')
 
@@ -182,15 +125,6 @@ class Llvm(CMakePackage):
     # OMP TSAN exists in > 5.x
     conflicts('+omp_tsan', when='@:5.99')
 
-    # +flang conflicts other variants
-    conflicts('+gold', when='+flang')
-    conflicts('+lldb', when='+flang')
-    conflicts('+lld', when='+flang')
-    conflicts('+copiler-rt', when='+flang')
-    conflicts('+libcxx', when='+flang')
-    conflicts('+polly', when='+flang')
-    conflicts('+internal_unwind', when='+flang')
-
     # Github issue #4986
     patch('llvm_gcc7.patch', when='@4.0.0:4.0.1+lldb %gcc@7.0:')
     # Backport from llvm master + additional fix
@@ -235,13 +169,7 @@ def setup_run_environment(self, env):
             env.set('CC', join_path(self.spec.prefix.bin, 'clang'))
             env.set('CXX', join_path(self.spec.prefix.bin, 'clang++'))
 
-    # When building flang we do not use the mono repo
+    root_cmakelists_dir = 'llvm'
-    @property
-    def root_cmakelists_dir(self):
-        if '+flang' in self.spec:
-            return 'llvm-flang'
-        else:
-            return 'llvm'
 
     def cmake_args(self):
         spec = self.spec
@@ -283,7 +211,7 @@ def cmake_args(self):
         if '+libcxx' in spec:
             projects.append('libcxx')
             projects.append('libcxxabi')
-            if spec.satisfies('@3.9.0:') and '+flang' not in spec:
+            if spec.satisfies('@3.9.0:'):
                 cmake_args.append('-DCLANG_DEFAULT_CXX_STDLIB=libc++')
         if '+internal_unwind' in spec:
             projects.append('libunwind')
@@ -300,14 +228,10 @@ def cmake_args(self):
         if '+all_targets' not in spec:  # all is default on cmake
 
             targets = ['NVPTX', 'AMDGPU']
-            if (spec.version < Version('3.9.0')
+            if (spec.version < Version('3.9.0')):
-                and '+flang' not in spec):
                 # Starting in 3.9.0 CppBackend is no longer a target (see
                 # LLVM_ALL_TARGETS in llvm's top-level CMakeLists.txt for
                 # the complete list of targets)
-
-                # This also applies to the version of llvm used by flang
-                # hence the test to see if the version starts with "flang".
                 targets.append('CppBackend')
 
             if spec.target.family == 'x86' or spec.target.family == 'x86_64':
@@ -340,10 +264,9 @@ def cmake_args(self):
                spec.satisfies('platform=linux'):
                 cmake_args.append('-DCMAKE_BUILD_WITH_INSTALL_RPATH=1')
 
-        if '+flang' not in spec:
+        # Semicolon seperated list of projects to enable
-            # Semicolon seperated list of projects to enable
+        cmake_args.append(
-            cmake_args.append(
+            '-DLLVM_ENABLE_PROJECTS:STRING={0}'.format(';'.join(projects)))
-                '-DLLVM_ENABLE_PROJECTS:STRING={0}'.format(';'.join(projects)))
 
         return cmake_args
 

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

@@ -17,6 +17,7 @@ class Magma(CMakePackage):
     url = "http://icl.cs.utk.edu/projectsfiles/magma/downloads/magma-2.2.0.tar.gz"
     maintainers = ['luszczek']
 
+    version('2.5.2', sha256='065feb85558f9dd6f4cc4db36ac633a3f787827fc832d0b578a049a43a195620')
     version('2.5.1', sha256='ce32c199131515336b30c92a907effe0c441ebc5c5bdb255e4b06b2508de109f')
     version('2.5.0', sha256='4fd45c7e46bd9d9124253e7838bbfb9e6003c64c2c67ffcff02e6c36d2bcfa33')
     version('2.4.0', sha256='4eb839b1295405fd29c8a6f5b4ed578476010bf976af46573f80d1169f1f9a4f')

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

@@ -0,0 +1,19 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Mbdyn(AutotoolsPackage):
+    """MBDyn is the first and possibly the only free general purpose
+    multibody dynamics analysis software."""
+
+    homepage = "https://www.mbdyn.org/"
+    url      = "https://www.mbdyn.org/userfiles/downloads/mbdyn-1.7.3.tar.gz"
+
+    version('1.7.3', sha256='3cf05cd1cb14c1af3d987aac119b6ecf0d835bc1aee06bc4cf7cc5a245c1f36d')
+
+    # Failed to build mbdyn with gcc@4.8.5 and gcc@9.2.0
+    conflicts('%gcc@:5.0,9.0:')

var/spack/repos/builtin/packages/p3dfft3/package.py

@@ -0,0 +1,103 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class P3dfft3(AutotoolsPackage):
+    """P3DFFT++ (a.k.a. P3DFFT v. 3) is a new generation of P3DFFT library
+    that aims to provide a comprehensive framework for simulating multiscale
+    phenomena. It takes the essence of P3DFFT further by creating an
+    extensible, modular structure uniquely adaptable to a greater range
+    of use cases."""
+
+    homepage = "https://www.p3dfft.net"
+    url      = "https://github.com/sdsc/p3dfft.3/archive/v3.0.0.tar.gz"
+    git      = "https://github.com/sdsc/p3dfft.3.git"
+
+    version('develop', branch='master')
+    version('3.0.0', sha256='1c549e78097d1545d18552b039be0d11cdb96be46efe99a16b65fd5d546dbfa7')
+
+    variant('fftw', default=True,
+            description='Builds with FFTW library')
+    variant('essl', default=False,
+            description='Builds with ESSL library')
+    variant('mpi', default=True,
+            description="Enable MPI support.")
+    variant('measure', default=False,
+            description="Define if you want to use"
+                        "the measure fftw planner flag")
+    variant('estimate', default=False,
+            description="Define if you want to"
+                        "use the estimate fftw planner flag")
+    variant('patient', default=False,
+            description="Define if you want to"
+                        "use the patient fftw planner flag")
+
+    # TODO: Add more configure options!
+
+    depends_on('mpi', when='+mpi')
+    depends_on('fftw', when='+fftw')
+    depends_on('essl', when='+essl')
+
+    def configure_args(self):
+        args = []
+
+        if '%gcc' in self.spec:
+            args.append('--enable-gnu')
+
+        if '%intel' in self.spec:
+            args.append('--enable-intel')
+
+        if '%xl' in self.spec:
+            args.append('--enable-ibm')
+
+        if '%cce' in self.spec:
+            args.append('--enable-cray')
+
+        if '%pgi' in self.spec:
+            args.append('--enable-pgi')
+
+        if '+mpi' in self.spec:
+            args.append('CC=%s' % self.spec['mpi'].mpicc)
+            args.append('CXX=%s' % self.spec['mpi'].mpicxx)
+            args.append('FC=%s' % self.spec['mpi'].mpifc)
+
+        if '+openmpi' in self.spec:
+            args.append('--enable-openmpi')
+
+        if '+fftw' in self.spec:
+            args.append('--enable-fftw')
+
+            if '@:3.0.0' in self.spec:
+                args.append('--with-fftw-lib=%s' %
+                            self.spec['fftw'].prefix.lib)
+                args.append('--with-fftw-inc=%s' %
+                            self.spec['fftw'].prefix.include)
+            else:
+                args.append('--with-fftw=%s' % self.spec['fftw'].prefix)
+
+            if 'fftw+measure' in self.spec:
+                args.append('--enable-fftwmeasure')
+            if 'fftw+estimate' in self.spec:
+                args.append('--enable-fftwestimate')
+            if 'fftw+patient' in self.spec:
+                args.append('--enable-fftwpatient')
+
+        if '+essl' in self.spec:
+            args.append('--enable-essl')
+            args.append('--with-essl-lib=%s' %
+                        self.spec['essl'].prefix.lib)
+            args.append('--with-essl-inc=%s' %
+                        self.spec['essl'].prefix.include)
+
+        if '+mkl' in self.spec:
+            args.append('--enable-mkl')
+            args.append('--with-mkl-lib=%s' %
+                        self.spec['mkl'].prefix.lib)
+            args.append('--with-mkl-inc=%s' %
+                        self.spec['mkl'].prefix.include)
+
+        return args

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

@@ -43,6 +43,10 @@ def configure(self, spec, prefix):
             options.append('-icpc')
         elif self.compiler.name == 'pgi':
             options.append('-pgCC')
+        elif self.compiler.name == 'gcc':
+            options.append('-GNU')
+        else:
+            raise InstallError('Unknown/unsupported compiler family')
 
         configure(*options)
 

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

@@ -12,10 +12,11 @@ class PyOpppy(PythonPackage):
     output and dump files generated by scientific software packages."""
 
     homepage = "https://github.com/lanl/opppy"
-    url = "https://github.com/lanl/OPPPY/archive/OPPPY-0_1_1.tar.gz"
+    url = "https://github.com/lanl/OPPPY/archive/opppy-0_1_2.tar.gz"
     git = "https://github.com/lanl/opppy.git"
 
     version('master', branch='master')
+    version('0_1_2', sha256='ef3795d3164fa0aa7ea7da7e223d6d0a48d2960aefd03a7d90cdb8b8f480cd4c')
     version('0_1_1', sha256='505c023853e75552abc65de9777a125ecb6a99a1cb4e605a4f702af837e3168b')
 
     depends_on('py-setuptools', type=('build', 'run'))

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

@@ -22,6 +22,8 @@ class PyPygdal(PythonPackage):
 
     version('3.0.1.5', sha256='1222f69fe5e6b632d0d2a42d3acb8fac80fb4577c05e01969d8cd5548192ccaa')
     version('2.4.2.5', sha256='73386683c0b10ab43b6d64257fca2ba812f53ec61b268de8811565fd9ae9bacd')
+    version('2.4.1.6', sha256='5d1af98ad09f59e34e3b332cf20630b532b33c7120295aaaabbccebf58a11aa4')
+    version('2.4.0.6', sha256='728d11f3ecae0cd3493cd27dab599a0b6184f5504cc172d49400d88ea2b24a9c')
     version('1.11.5.3', sha256='746d13b73a284446a1b604772f869789eabfe6e69dee463f537da27845b29fa7')
     version('1.11.4.3', sha256='99d4b0c94d57ae50592924faaa65cc6a0c0892d83764e9f24ef9270c3a4b111a')
 
@@ -29,5 +31,7 @@ class PyPygdal(PythonPackage):
     depends_on('py-numpy@1.0.0:', type=('build', 'run'))
     depends_on('gdal@3.0.1', type=('build', 'link', 'run'), when='@3.0.1.5')
     depends_on('gdal@2.4.2', type=('build', 'link', 'run'), when='@2.4.2.5')
+    depends_on('gdal@2.4.1', type=('build', 'link', 'run'), when='@2.4.1.6')
+    depends_on('gdal@2.4.0', type=('build', 'link', 'run'), when='@2.4.0.6')
     depends_on('gdal@1.11.5', type=('build', 'link', 'run'), when='@1.11.5.3')
     depends_on('gdal@1.11.4', type=('build', 'link', 'run'), when='@1.11.4.3')

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

@@ -19,7 +19,9 @@ class PyTensorflow(Package, CudaPackage):
     import_modules = ['tensorflow']
 
     version('2.1.0',  sha256='638e541a4981f52c69da4a311815f1e7989bf1d67a41d204511966e1daed14f7')
+    version('2.0.1',  sha256='29197d30923b9670992ee4b9c6161f50c7452e9a4158c720746e846080ac245a')
     version('2.0.0',  sha256='49b5f0495cd681cbcb5296a4476853d4aea19a43bdd9f179c928a977308a0617')
+    version('1.15.2', sha256='d95d75d26a298211b5e802842e87fda5b8b14f6ad83719377b391e5fb71b8746')
     version('1.15.1', sha256='19b6e72bc8675937f618cede364d7228a71c2eeaffc42801bcefd98dda7ca056')
     version('1.15.0', sha256='a5d49c00a175a61da7431a9b289747d62339be9cf37600330ad63b611f7f5dc9')
     version('1.14.0', sha256='aa2a6a1daafa3af66807cfe0bc77bfe1144a9a53df9a96bab52e3e575b3047ed')

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

@@ -62,6 +62,7 @@ class PyTorch(PythonPackage, CudaPackage):
     version('0.4.0', tag='v0.4.0', submodules=True)
     version('0.3.1', tag='v0.3.1', submodules=True)
 
+    variant('cuda', default=True, description='Build with CUDA')
     variant('cudnn', default=True, description='Enables the cuDNN build')
     variant('magma', default=False, description='Enables the MAGMA build')
     variant('fbgemm', default=False, description='Enables the FBGEMM build')
@@ -100,6 +101,27 @@ class PyTorch(PythonPackage, CudaPackage):
     conflicts('+zstd', when='@:1.0')
     conflicts('+tbb', when='@:1.1')
 
+    cuda_arch_conflict = ('This version of Torch/Caffe2 only supports compute '
+                          'capabilities ')
+
+    conflicts('cuda_arch=none', when='+cuda+caffe2',
+              msg='Must specify CUDA compute capabilities of your GPU, see '
+              'https://developer.nvidia.com/cuda-gpus')
+    conflicts('cuda_arch=52', when='@1.3.0:+cuda+caffe2',
+              msg=cuda_arch_conflict + '>=5.3')
+    conflicts('cuda_arch=50', when='@1.3.0:+cuda+caffe2',
+              msg=cuda_arch_conflict + '>=5.3')
+    conflicts('cuda_arch=35', when='@1.3.0:+cuda+caffe2',
+              msg=cuda_arch_conflict + '>=5.3')
+    conflicts('cuda_arch=32', when='@1.3.0:+cuda+caffe2',
+              msg=cuda_arch_conflict + '>=5.3')
+    conflicts('cuda_arch=30', when='@1.3.0:+cuda+caffe2',
+              msg=cuda_arch_conflict + '>=5.3')
+    conflicts('cuda_arch=30', when='@1.2.0:+cuda+caffe2',
+              msg=cuda_arch_conflict + '>=3.2')
+    conflicts('cuda_arch=20', when='@1.0.0:+cuda+caffe2',
+              msg=cuda_arch_conflict + '>=3.0')
+
     # Required dependencies
     depends_on('cmake@3.5:', type='build')
     # Use Ninja generator to speed up build times
@@ -128,7 +150,10 @@ class PyTorch(PythonPackage, CudaPackage):
     # depends_on('fbgemm', when='+fbgemm')
     # TODO: add dependency: https://github.com/ROCmSoftwarePlatform/MIOpen
     # depends_on('miopen', when='+miopen')
-    depends_on('intel-mkl-dnn', when='+mkldnn')
+    # TODO: See if there is a way to use an external mkldnn installation.
+    # Currently, only older versions of py-torch use an external mkldnn
+    # library.
+    depends_on('intel-mkl-dnn', when='@0.4:0.4.1+mkldnn')
     # TODO: add dependency: https://github.com/Maratyszcza/NNPACK
     # depends_on('nnpack', when='+nnpack')
     depends_on('qnnpack', when='+qnnpack')
@@ -197,6 +222,10 @@ def enable_or_disable(variant, keyword='USE', var=None, newer=False):
         enable_or_disable('cuda')
         if '+cuda' in self.spec:
             env.set('CUDA_HOME', self.spec['cuda'].prefix)
+            torch_cuda_arch = ';'.join('{0:.1f}'.format(float(i) / 10.0) for i
+                                       in
+                                       self.spec.variants['cuda_arch'].value)
+            env.set('TORCH_CUDA_ARCH_LIST', torch_cuda_arch)
 
         enable_or_disable('cudnn')
         if '+cudnn' in self.spec:
@@ -213,7 +242,7 @@ def enable_or_disable(variant, keyword='USE', var=None, newer=False):
             env.set('MIOPEN_LIBRARY', self.spec['miopen'].libs[0])
 
         enable_or_disable('mkldnn')
-        if '+mkldnn' in self.spec:
+        if '@0.4:0.4.1+mkldnn' in self.spec:
             env.set('MKLDNN_HOME', self.spec['intel-mkl-dnn'].prefix)
 
         enable_or_disable('nnpack')

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

@@ -0,0 +1,23 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyVermin(PythonPackage):
+    """Concurrently detect the minimum Python versions needed to run code."""
+
+    homepage = "https://github.com/netromdk/vermin"
+    url      = "https://github.com/netromdk/vermin/archive/v0.10.0.tar.gz"
+
+    import_modules = ['vermin']
+
+    version('0.10.0', sha256='3458a4d084bba5c95fd7208888aaf0e324a07ee092786ee4e5529f539ab4951f')
+
+    depends_on('python@2.7:', type=('build', 'run'))
+    depends_on('py-setuptools', type=('build', 'run'))
+
+    def test(self):
+        make('test')

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

@@ -23,7 +23,7 @@ class Simulationio(CMakePackage):
     variant('pic', default=True,
             description="Produce position-independent code")
 
-    depends_on('hdf5 +cxx @:1.10.0-patch1')
+    depends_on('hdf5 +cxx @1.10.1:')
     depends_on('julia', when='+julia', type=('build', 'run'))
     depends_on('py-h5py', when='+python', type=('build', 'run'))
     depends_on('py-numpy', when='+python', type=('build', 'run'))

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

@@ -91,6 +91,9 @@ class Vtk(CMakePackage):
     depends_on('libpng')
     depends_on('libtiff')
     depends_on('zlib')
+    depends_on('eigen', when='@8.2.0:')
+    depends_on('double-conversion', when='@8.2.0:')
+    depends_on('sqlite', when='@8.2.0:')
 
     def url_for_version(self, version):
         url = "http://www.vtk.org/files/release/{0}/VTK-{1}.tar.gz"
@@ -117,8 +120,6 @@ def cmake_args(self):
             # However, in a few cases we can't do without them yet
             '-DVTK_USE_SYSTEM_GL2PS:BOOL=OFF',
             '-DVTK_USE_SYSTEM_LIBHARU=OFF',
-            '-DVTK_USE_SYSTEM_LIBPROJ4:BOOL=OFF',
-            '-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=OFF',
 
             '-DNETCDF_DIR={0}'.format(spec['netcdf-c'].prefix),
             '-DNETCDF_C_ROOT={0}'.format(spec['netcdf-c'].prefix),
@@ -132,6 +133,20 @@ def cmake_args(self):
             '-DVTK_WRAP_TCL=OFF',
         ]
 
+        # Some variable names have changed
+        if spec.satisfies('@8.2.0:'):
+            cmake_args.extend([
+                '-DVTK_USE_SYSTEM_OGG:BOOL=OFF',
+                '-DVTK_USE_SYSTEM_THEORA:BOOL=OFF',
+                '-DVTK_USE_SYSTEM_LIBPROJ:BOOL=OFF',
+                '-DVTK_USE_SYSTEM_PUGIXML:BOOL=OFF',
+            ])
+        else:
+            cmake_args.extend([
+                '-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=OFF',
+                '-DVTK_USE_SYSTEM_LIBPROJ4:BOOL=OFF',
+            ])
+
         if '+mpi' in spec:
             cmake_args.extend([
                 '-DVTK_Group_MPI:BOOL=ON',

var/spack/repos/builtin/packages/yaml-cpp/package.py

@@ -17,6 +17,7 @@ class YamlCpp(CMakePackage):
     git      = "https://github.com/jbeder/yaml-cpp.git"
 
     version('develop', branch='master')
+    version('0.6.3', sha256='77ea1b90b3718aa0c324207cb29418f5bced2354c2e483a9523d98c3460af1ed')
     version('0.6.2', sha256='e4d8560e163c3d875fd5d9e5542b5fd5bec810febdcba61481fe5fc4e6b1fd05')
     version('0.5.3', sha256='decc5beabb86e8ed9ebeb04358d5363a5c4f72d458b2c788cb2f3ac9c19467b2')
 

var/spack/repos/builtin/packages/z3/package.py

@@ -22,6 +22,7 @@ class Z3(MakefilePackage):
 
     variant('python', default=False, description='Enable python binding')
     depends_on('python', type=('build', 'run'))
+    extends('python', when='+python')
 
     # Referenced: https://github.com/Z3Prover/z3/issues/1016
     patch('fix_1016_1.patch', when='@:4.4.1')
@@ -31,9 +32,18 @@ class Z3(MakefilePackage):
 
     def configure_args(self):
         spec = self.spec
-        return [
+
-            '--python' if '+python' in spec else ''
+        args = []
-        ]
+
+        if spec.satisfies('+python'):
+            args.append('--python')
+            args.append(
+                '--pypkgdir=%s' % join_path(
+                    prefix.lib,
+                    'python%s' % spec['python'].version.up_to(2),
+                    'site-packages'))
+
+        return args
 
     def bootstrap(self, spec, prefix):
         options = ['--prefix={0}'.format(prefix)] + self.configure_args()