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Merge tag 'v0.15.0' into features/shared

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This commit is contained in:
Carson Woods
2020-06-30 19:24:15 -05:00
parent 1965e1e606 d4bf70d988
commit 4bb26802ed
108 changed files with 3162 additions and 705 deletions
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1
.github/workflows/linux_build_tests.yaml vendored
View File

@@ -5,6 +5,7 @@ on:
branches:
- master
- develop
- releases/**
pull_request:
branches:
- master

1
.github/workflows/linux_unit_tests.yaml vendored
View File

@@ -5,6 +5,7 @@ on:
branches:
- master
- develop
- releases/**
pull_request:
branches:
- master

1
.github/workflows/macos_unit_tests.yaml vendored
View File

@@ -5,6 +5,7 @@ on:
branches:
- master
- develop
- releases/**
pull_request:
branches:
- master

1
.github/workflows/minimum_python_versions.yaml vendored
View File

@@ -5,6 +5,7 @@ on:
branches:
- master
- develop
- releases/**
pull_request:
branches:
- master

2
.travis.yml
View File

@@ -40,6 +40,7 @@ jobs:
- ninja-build
- realpath
- zsh
- fish
env: [ TEST_SUITE=unit, COVERAGE=true ]
- python: '3.8'
os: linux
@@ -73,6 +74,7 @@ addons:
- ninja-build
- patchelf
- zsh
- fish
update: true
# ~/.ccache needs to be cached directly as Travis is not taking care of it

98
CHANGELOG.md
View File

@@ -1,4 +1,98 @@
# v0.14.2 (2019-04-15)
# v0.15.0 (2020-06-28)
`v0.15.0` is a major feature release.
## Major Features in this release
1. **Cray support** Spack will now work properly on Cray "Cluster"
systems (non XC systems) and after a `module purge` command on Cray
systems. See #12989
2. **Virtual package configuration** Virtual packages are allowed in
packages.yaml configuration. This allows users to specify a virtual
package as non-buildable without needing to specify for each
implementation. See #14934
3. **New config subcommands** This release adds `spack config add` and
`spack config remove` commands to add to and remove from yaml
configuration files from the CLI. See #13920
4. **Environment activation** Anonymous environments are **no longer**
automatically activated in the current working directory. To activate
an environment from a `spack.yaml` file in the current directory, use
the `spack env activate .` command. This removes a concern that users
were too easily polluting their anonymous environments with accidental
installations. See #17258
5. **Apple clang compiler** The clang compiler and the apple-clang
compiler are now separate compilers in Spack. This allows Spack to
improve support for the apple-clang compiler. See #17110
6. **Finding external packages** Spack packages can now support an API
for finding external installations. This allows the `spack external
find` command to automatically add installations of those packages to
the user's configuration. See #15158
## Additional new features of note
* support for using Spack with the fish shell (#9279)
* `spack load --first` option to load first match (instead of prompting user) (#15622)
* support the Cray cce compiler both new and classic versions (#17256, #12989)
* `spack dev-build` command:
* supports stopping before a specified phase (#14699)
* supports automatically launching a shell in the build environment (#14887)
* `spack install --fail-fast` allows builds to fail at the first error (rather than best-effort) (#15295)
* environments: SpecList references can be dereferenced as compiler or dependency constraints (#15245)
* `spack view` command: new support for a copy/relocate view type (#16480)
* ci pipelines: see documentation for several improvements
* `spack mirror -a` command now supports excluding packages (#14154)
* `spack buildcache create` is now environment-aware (#16580)
* module generation: more flexible format for specifying naming schemes (#16629)
* lmod module generation: packages can be configured as core specs for lmod hierarchy (#16517)
## Deprecations and Removals
The following commands were deprecated in v0.13.0, and have now been removed:
* `spack configure`
* `spack build`
* `spack diy`
The following commands were deprecated in v0.14.0, and will be removed in the next major release:
* `spack bootstrap`
## Bugfixes
Some of the most notable bugfixes in this release include:
* Spack environments can now contain the string `-h` (#15429)
* The `spack install` gracefully handles being backgrounded (#15723, #14682)
* Spack uses `-isystem` instead of `-I` in cases that the underlying build system does as well (#16077)
* Spack no longer prints any specs that cannot be safely copied into a Spack command (#16462)
* Incomplete Spack environments containing python no longer cause problems (#16473)
* Several improvements to binary package relocation
## Package Improvements
The Spack project is constantly engaged in routine maintenance,
bugfixes, and improvements for the package ecosystem. Of particular
note in this release are the following:
* Spack now contains 4339 packages. There are 430 newly supported packages in v0.15.0
* GCC now builds properly on ARM architectures (#17280)
* Python: patched to support compiling mixed C/C++ python modules through distutils (#16856)
* improvements to pytorch and py-tensorflow packages
* improvements to major MPI implementations: mvapich2, mpich, openmpi, and others
## Spack Project Management:
* Much of the Spack CI infrastructure has moved from Travis to GitHub Actions (#16610, #14220, #16345)
* All merges to the `develop` branch run E4S CI pipeline (#16338)
* New `spack debug report` command makes reporting bugs easier (#15834)
# v0.14.2 (2020-04-15)
This is a minor release on the `0.14` series. It includes performance
improvements and bug fixes:
@@ -13,7 +107,7 @@ improvements and bug fixes:
* Avoid adding spurious `LMOD` env vars to Intel modules (#15778)
* Don't output [+] for mock installs run during tests (#15609)
# v0.14.1 (2019-03-20)
# v0.14.1 (2020-03-20)
This is a bugfix release on top of `v0.14.0`. Specific fixes include:

2
lib/spack/docs/containers.rst
View File

@@ -165,7 +165,7 @@ of environments:
# Extra instructions
extra_instructions:
final: |
RUN echo 'export PS1="\[$(tput bold)\]\[$(tput setaf 1)\][gromacs]\[$(tput setaf 2)\]\u\[$(tput sgr0)\]:\w $ \[$(tput sgr0)\]"' >> ~/.bashrc
RUN echo 'export PS1="\[$(tput bold)\]\[$(tput setaf 1)\][gromacs]\[$(tput setaf 2)\]\u\[$(tput sgr0)\]:\w $ \[$(tput sgr0)\]"' >> ~/.bashrc
# Labels for the image
labels:

9
lib/spack/docs/environments.rst
View File

@@ -167,15 +167,6 @@ Any directory can be treated as an environment if it contains a file
$ spack env activate -d /path/to/directory
Spack commands that are environment sensitive will also act on the
environment any time the current working directory contains a
``spack.yaml`` file. Changing working directory to a directory
containing a ``spack.yaml`` file is equivalent to the command:
.. code-block:: console
$ spack env activate -d /path/to/dir --without-view
Anonymous specs can be created in place using the command:
.. code-block:: console

2
lib/spack/docs/pipelines.rst
View File

@@ -45,6 +45,7 @@ for setting up a build pipeline are as follows:
tags:
- <custom-tag>
script:
- spack env activate .
- spack ci generate
--output-file "${CI_PROJECT_DIR}/jobs_scratch_dir/pipeline.yml"
artifacts:
@@ -384,6 +385,7 @@ a custom spack and make sure the generated rebuild jobs will clone it too:
- git clone ${SPACK_REPO} --branch ${SPACK_REF}
- . ./spack/share/spack/setup-env.sh
script:
- spack env activate .
- spack ci generate
--spack-repo ${SPACK_REPO} --spack-ref ${SPACK_REF}
--output-file "${CI_PROJECT_DIR}/jobs_scratch_dir/pipeline.yml"

2
lib/spack/spack/__init__.py
View File

@@ -5,7 +5,7 @@
#: major, minor, patch version for Spack, in a tuple
spack_version_info = (0, 14, 2)
spack_version_info = (0, 15, 0)
#: String containing Spack version joined with .'s
spack_version = '.'.join(str(v) for v in spack_version_info)

114
lib/spack/spack/binary_distribution.py
View File

@@ -25,6 +25,7 @@
import spack.cmd
import spack.config as config
import spack.database as spack_db
import spack.fetch_strategy as fs
import spack.util.gpg
import spack.relocate as relocate
@@ -32,7 +33,6 @@
import spack.mirror
import spack.util.url as url_util
import spack.util.web as web_util
from spack.spec import Spec
from spack.stage import Stage
from spack.util.gpg import Gpg
@@ -282,31 +282,47 @@ def sign_tarball(key, force, specfile_path):
def generate_package_index(cache_prefix):
"""Create the build cache index page.
Creates (or replaces) the "index.html" page at the location given in
Creates (or replaces) the "index.json" page at the location given in
cache_prefix. This page contains a link for each binary package (*.yaml)
and public key (*.key) under cache_prefix.
"""
tmpdir = tempfile.mkdtemp()
try:
index_html_path = os.path.join(tmpdir, 'index.html')
file_list = (
entry
for entry in web_util.list_url(cache_prefix)
if (entry.endswith('.yaml')
or entry.endswith('.key')))
db_root_dir = os.path.join(tmpdir, 'db_root')
db = spack_db.Database(None, db_dir=db_root_dir,
enable_transaction_locking=False,
record_fields=['spec', 'ref_count'])
with open(index_html_path, 'w') as f:
f.write(BUILD_CACHE_INDEX_TEMPLATE.format(
title='Spack Package Index',
path_list='\n'.join(
BUILD_CACHE_INDEX_ENTRY_TEMPLATE.format(path=path)
for path in file_list)))
file_list = (
entry
for entry in web_util.list_url(cache_prefix)
if entry.endswith('.yaml'))
tty.debug('Retrieving spec.yaml files from {0} to build index'.format(
cache_prefix))
for file_path in file_list:
try:
yaml_url = url_util.join(cache_prefix, file_path)
tty.debug('fetching {0}'.format(yaml_url))
_, _, yaml_file = web_util.read_from_url(yaml_url)
yaml_contents = codecs.getreader('utf-8')(yaml_file).read()
# yaml_obj = syaml.load(yaml_contents)
# s = Spec.from_yaml(yaml_obj)
s = Spec.from_yaml(yaml_contents)
db.add(s, None)
except (URLError, web_util.SpackWebError) as url_err:
tty.error('Error reading spec.yaml: {0}'.format(file_path))
tty.error(url_err)
try:
index_json_path = os.path.join(db_root_dir, 'index.json')
with open(index_json_path, 'w') as f:
db._write_to_file(f)
web_util.push_to_url(
index_html_path,
url_util.join(cache_prefix, 'index.html'),
index_json_path,
url_util.join(cache_prefix, 'index.json'),
keep_original=False,
extra_args={'ContentType': 'text/html'})
extra_args={'ContentType': 'application/json'})
finally:
shutil.rmtree(tmpdir)
@@ -825,49 +841,55 @@ def get_spec(spec=None, force=False):
return try_download_specs(urls=urls, force=force)
def get_specs(force=False, allarch=False):
def get_specs(allarch=False):
"""
Get spec.yaml's for build caches available on mirror
"""
global _cached_specs
arch = architecture.Arch(architecture.platform(),
'default_os', 'default_target')
arch_pattern = ('([^-]*-[^-]*-[^-]*)')
if not allarch:
arch_pattern = '(%s-%s-[^-]*)' % (arch.platform, arch.os)
regex_pattern = '%s(.*)(spec.yaml$)' % (arch_pattern)
arch_re = re.compile(regex_pattern)
if not spack.mirror.MirrorCollection():
tty.debug("No Spack mirrors are currently configured")
return {}
urls = set()
for mirror in spack.mirror.MirrorCollection().values():
fetch_url_build_cache = url_util.join(
mirror.fetch_url, _build_cache_relative_path)
mirror_dir = url_util.local_file_path(fetch_url_build_cache)
if mirror_dir:
tty.msg("Finding buildcaches in %s" % mirror_dir)
if os.path.exists(mirror_dir):
files = os.listdir(mirror_dir)
for file in files:
m = arch_re.search(file)
if m:
link = url_util.join(fetch_url_build_cache, file)
urls.add(link)
else:
tty.msg("Finding buildcaches at %s" %
url_util.format(fetch_url_build_cache))
p, links = web_util.spider(
url_util.join(fetch_url_build_cache, 'index.html'))
for link in links:
m = arch_re.search(link)
if m:
urls.add(link)
tty.msg("Finding buildcaches at %s" %
url_util.format(fetch_url_build_cache))
return try_download_specs(urls=urls, force=force)
index_url = url_util.join(fetch_url_build_cache, 'index.json')
try:
_, _, file_stream = web_util.read_from_url(
index_url, 'application/json')
index_object = codecs.getreader('utf-8')(file_stream).read()
except (URLError, web_util.SpackWebError) as url_err:
tty.error('Failed to read index {0}'.format(index_url))
tty.debug(url_err)
# Just return whatever specs we may already have cached
return _cached_specs
tmpdir = tempfile.mkdtemp()
index_file_path = os.path.join(tmpdir, 'index.json')
with open(index_file_path, 'w') as fd:
fd.write(index_object)
db_root_dir = os.path.join(tmpdir, 'db_root')
db = spack_db.Database(None, db_dir=db_root_dir,
enable_transaction_locking=False)
db._read_from_file(index_file_path)
spec_list = db.query_local(installed=False)
for indexed_spec in spec_list:
spec_arch = architecture.arch_for_spec(indexed_spec.architecture)
if (allarch is True or spec_arch == arch):
_cached_specs.add(indexed_spec)
return _cached_specs
def get_keys(install=False, trust=False, force=False):

3
lib/spack/spack/build_environment.py
View File

@@ -198,6 +198,9 @@ def set_compiler_environment_variables(pkg, env):
compiler = pkg.compiler
spec = pkg.spec
# Make sure the executables for this compiler exist
compiler.verify_executables()
# Set compiler variables used by CMake and autotools
assert all(key in compiler.link_paths for key in (
'cc', 'cxx', 'f77', 'fc'))

6
lib/spack/spack/build_systems/autotools.py
View File

@@ -118,13 +118,15 @@ def _do_patch_config_files(self):
config_file = 'config.{0}'.format(config_name)
if os.path.exists(config_file):
# First search the top-level source directory
my_config_files[config_name] = config_file
my_config_files[config_name] = os.path.join(
self.configure_directory, config_file)
else:
# Then search in all sub directories recursively.
# We would like to use AC_CONFIG_AUX_DIR, but not all packages
# ship with their configure.in or configure.ac.
config_path = next((os.path.join(r, f)
for r, ds, fs in os.walk('.') for f in fs
for r, ds, fs in os.walk(
self.configure_directory) for f in fs
if f == config_file), None)
my_config_files[config_name] = config_path

11
lib/spack/spack/ci.py
View File

@@ -612,7 +612,10 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
if 'enable-debug-messages' in gitlab_ci:
debug_flag = '-d '
job_scripts = ['spack {0}ci rebuild'.format(debug_flag)]
job_scripts = [
'spack env activate .',
'spack {0}ci rebuild'.format(debug_flag),
]
compiler_action = 'NONE'
if len(phases) > 1:
@@ -1025,9 +1028,9 @@ def read_cdashid_from_mirror(spec, mirror_url):
def push_mirror_contents(env, spec, yaml_path, mirror_url, build_id):
if mirror_url:
tty.debug('Creating buildcache')
buildcache._createtarball(env, yaml_path, None, True, False,
mirror_url, None, True, False, False, True,
False)
buildcache._createtarball(env, spec_yaml=yaml_path, add_deps=False,
output_location=mirror_url, force=True,
allow_root=True)
if build_id:
tty.debug('Writing cdashid ({0}) to remote mirror: {1}'.format(
build_id, mirror_url))

27
lib/spack/spack/ci_optimization.py
View File

@@ -17,6 +17,19 @@
import spack.util.spack_yaml as syaml
def sort_yaml_obj(obj):
if isinstance(obj, collections_abc.Mapping):
return syaml.syaml_dict(
(k, sort_yaml_obj(v))
for k, v in
sorted(obj.items(), key=(lambda item: str(item[0]))))
if isinstance(obj, collections_abc.Sequence) and not isinstance(obj, str):
return syaml.syaml_list(sort_yaml_obj(x) for x in obj)
return obj
def matches(obj, proto):
"""Returns True if the test object "obj" matches the prototype object
"proto".
@@ -235,8 +248,10 @@ def try_optimization_pass(name, yaml, optimization_pass, *args, **kwargs):
# pass was not applied
return (yaml, new_yaml, False, other_results)
pre_size = len(syaml.dump_config(yaml, default_flow_style=True))
post_size = len(syaml.dump_config(new_yaml, default_flow_style=True))
pre_size = len(syaml.dump_config(
sort_yaml_obj(yaml), default_flow_style=True))
post_size = len(syaml.dump_config(
sort_yaml_obj(new_yaml), default_flow_style=True))
# pass makes the size worse: not applying
applied = (post_size <= pre_size)
@@ -281,7 +296,7 @@ def build_histogram(iterator, key):
continue
value_hash = hashlib.sha1()
value_hash.update(syaml.dump_config(val).encode())
value_hash.update(syaml.dump_config(sort_yaml_obj(val)).encode())
value_hash = value_hash.hexdigest()
buckets[value_hash] += 1
@@ -292,7 +307,8 @@ def build_histogram(iterator, key):
def optimizer(yaml):
original_size = len(syaml.dump_config(yaml, default_flow_style=True))
original_size = len(syaml.dump_config(
sort_yaml_obj(yaml), default_flow_style=True))
# try factoring out commonly repeated portions
common_job = {
@@ -369,7 +385,8 @@ def optimizer(yaml):
common_subobject,
{'variables': {'SPACK_ROOT_SPEC': spec}})
new_size = len(syaml.dump_config(yaml, default_flow_style=True))
new_size = len(syaml.dump_config(
sort_yaml_obj(yaml), default_flow_style=True))
print('\n')
print_delta('overall summary', original_size, new_size)

45
lib/spack/spack/cmd/build.py
View File

@@ -1,45 +0,0 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import spack.cmd.configure as cfg
import llnl.util.tty as tty
from spack.build_systems.autotools import AutotoolsPackage
from spack.build_systems.cmake import CMakePackage
from spack.build_systems.qmake import QMakePackage
from spack.build_systems.scons import SConsPackage
from spack.build_systems.waf import WafPackage
from spack.build_systems.python import PythonPackage
from spack.build_systems.perl import PerlPackage
from spack.build_systems.meson import MesonPackage
from spack.build_systems.sip import SIPPackage
description = 'DEPRECATED: stops at build stage when installing a package'
section = "build"
level = "long"
build_system_to_phase = {
AutotoolsPackage: 'build',
CMakePackage: 'build',
QMakePackage: 'build',
SConsPackage: 'build',
WafPackage: 'build',
PythonPackage: 'build',
PerlPackage: 'build',
MesonPackage: 'build',
SIPPackage: 'build',
}
def setup_parser(subparser):
cfg.setup_parser(subparser)
def build(parser, args):
tty.warn("This command is deprecated. Use `spack install --until` to"
" select an end phase instead. The `spack build` command will be"
" removed in a future version of Spack")
cfg._stop_at_phase_during_install(args, build, build_system_to_phase)

41
lib/spack/spack/cmd/buildcache.py
View File

@@ -68,9 +68,9 @@ def setup_parser(subparser):
type=str,
help="URL of the mirror where " +
"buildcaches will be written.")
create.add_argument('--no-rebuild-index', action='store_true',
default=False, help="skip rebuilding index after " +
"building package(s)")
create.add_argument('--rebuild-index', action='store_true',
default=False, help="Regenerate buildcache index " +
"after building package(s)")
create.add_argument('-y', '--spec-yaml', default=None,
help='Create buildcache entry for spec from yaml file')
create.add_argument('--only', default='package,dependencies',
@@ -108,8 +108,6 @@ def setup_parser(subparser):
action='store_true',
dest='variants',
help='show variants in output (can be long)')
listcache.add_argument('-f', '--force', action='store_true',
help="force new download of specs")
listcache.add_argument('-a', '--allarch', action='store_true',
help="list specs for all available architectures" +
" instead of default platform and OS")
@@ -291,7 +289,7 @@ def match_downloaded_specs(pkgs, allow_multiple_matches=False, force=False,
specs_from_cli = []
has_errors = False
allarch = other_arch
specs = bindist.get_specs(force, allarch)
specs = bindist.get_specs(allarch)
for pkg in pkgs:
matches = []
tty.msg("buildcache spec(s) matching %s \n" % pkg)
@@ -323,9 +321,10 @@ def match_downloaded_specs(pkgs, allow_multiple_matches=False, force=False,
return specs_from_cli
def _createtarball(env, spec_yaml, packages, add_spec, add_deps,
output_location, key, force, rel, unsigned, allow_root,
no_rebuild_index):
def _createtarball(env, spec_yaml=None, packages=None, add_spec=True,
add_deps=True, output_location=os.getcwd(),
signing_key=None, force=False, make_relative=False,
unsigned=False, allow_root=False, rebuild_index=False):
if spec_yaml:
packages = set()
with open(spec_yaml, 'r') as fd:
@@ -355,10 +354,6 @@ def _createtarball(env, spec_yaml, packages, add_spec, add_deps,
msg = 'Buildcache files will be output to %s/build_cache' % outdir
tty.msg(msg)
signkey = None
if key:
signkey = key
matches = find_matching_specs(pkgs, env=env)
if matches:
@@ -398,9 +393,9 @@ def _createtarball(env, spec_yaml, packages, add_spec, add_deps,
for spec in specs:
tty.debug('creating binary cache file for package %s ' % spec.format())
bindist.build_tarball(spec, outdir, force, rel,
unsigned, allow_root, signkey,
not no_rebuild_index)
bindist.build_tarball(spec, outdir, force, make_relative,
unsigned, allow_root, signing_key,
rebuild_index)
def createtarball(args):
@@ -447,9 +442,12 @@ def createtarball(args):
add_spec = ('package' in args.things_to_install)
add_deps = ('dependencies' in args.things_to_install)
_createtarball(env, args.spec_yaml, args.specs, add_spec, add_deps,
output_location, args.key, args.force, args.rel,
args.unsigned, args.allow_root, args.no_rebuild_index)
_createtarball(env, spec_yaml=args.spec_yaml, packages=args.specs,
add_spec=add_spec, add_deps=add_deps,
output_location=output_location, signing_key=args.key,
force=args.force, make_relative=args.rel,
unsigned=args.unsigned, allow_root=args.allow_root,
rebuild_index=args.rebuild_index)
def installtarball(args):
@@ -458,8 +456,7 @@ def installtarball(args):
tty.die("build cache file installation requires" +
" at least one package spec argument")
pkgs = set(args.specs)
matches = match_downloaded_specs(pkgs, args.multiple, args.force,
args.otherarch)
matches = match_downloaded_specs(pkgs, args.multiple, args.otherarch)
for match in matches:
install_tarball(match, args)
@@ -491,7 +488,7 @@ def install_tarball(spec, args):
def listspecs(args):
"""list binary packages available from mirrors"""
specs = bindist.get_specs(args.force, args.allarch)
specs = bindist.get_specs(args.allarch)
if args.specs:
constraints = set(args.specs)
specs = [s for s in specs if any(s.satisfies(c) for c in constraints)]

8
lib/spack/spack/cmd/ci.py
View File

@@ -38,7 +38,7 @@ def setup_parser(subparser):
generate = subparsers.add_parser('generate', help=ci_generate.__doc__)
generate.add_argument(
'--output-file', default=None,
help="Absolute path to file where generated jobs file should be " +
help="Path to file where generated jobs file should be " +
"written. The default is .gitlab-ci.yml in the root of the " +
"repository.")
generate.add_argument(
@@ -88,10 +88,10 @@ def ci_generate(args):
use_dependencies = args.dependencies
if not output_file:
gen_ci_dir = os.getcwd()
output_file = os.path.join(gen_ci_dir, '.gitlab-ci.yml')
output_file = os.path.abspath(".gitlab-ci.yml")
else:
gen_ci_dir = os.path.dirname(output_file)
output_file_path = os.path.abspath(output_file)
gen_ci_dir = os.path.dirname(output_file_path)
if not os.path.exists(gen_ci_dir):
os.makedirs(gen_ci_dir)

4
lib/spack/spack/cmd/compiler.py
View File

@@ -37,7 +37,7 @@ def setup_parser(subparser):
find_parser.add_argument('add_paths', nargs=argparse.REMAINDER)
find_parser.add_argument(
'--scope', choices=scopes, metavar=scopes_metavar,
default=spack.config.default_modify_scope(),
default=spack.config.default_modify_scope('compilers'),
help="configuration scope to modify")
# Remove
@@ -49,7 +49,7 @@ def setup_parser(subparser):
remove_parser.add_argument('compiler_spec')
remove_parser.add_argument(
'--scope', choices=scopes, metavar=scopes_metavar,
default=spack.config.default_modify_scope(),
default=spack.config.default_modify_scope('compilers'),
help="configuration scope to modify")
# List

85
lib/spack/spack/cmd/configure.py
View File

@@ -1,85 +0,0 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import argparse
import llnl.util.tty as tty
import spack.cmd
import spack.cmd.common.arguments as arguments
import spack.cmd.install as inst
from spack.build_systems.autotools import AutotoolsPackage
from spack.build_systems.cmake import CMakePackage
from spack.build_systems.qmake import QMakePackage
from spack.build_systems.waf import WafPackage
from spack.build_systems.perl import PerlPackage
from spack.build_systems.intel import IntelPackage
from spack.build_systems.meson import MesonPackage
from spack.build_systems.sip import SIPPackage
description = 'DEPRECATED: stage and configure a package but do not install'
section = "build"
level = "long"
build_system_to_phase = {
AutotoolsPackage: 'configure',
CMakePackage: 'cmake',
QMakePackage: 'qmake',
WafPackage: 'configure',
PerlPackage: 'configure',
IntelPackage: 'configure',
MesonPackage: 'meson',
SIPPackage: 'configure',
}
def setup_parser(subparser):
subparser.add_argument(
'-v', '--verbose',
action='store_true',
help="print additional output during builds"
)
arguments.add_common_arguments(subparser, ['spec'])
def _stop_at_phase_during_install(args, calling_fn, phase_mapping):
if not args.package:
tty.die("configure requires at least one package argument")
# TODO: to be refactored with code in install
specs = spack.cmd.parse_specs(args.package, concretize=True)
if len(specs) != 1:
tty.error('only one spec can be installed at a time.')
spec = specs.pop()
pkg = spec.package
try:
key = [cls for cls in phase_mapping if isinstance(pkg, cls)].pop()
phase = phase_mapping[key]
# Install package dependencies if needed
parser = argparse.ArgumentParser()
inst.setup_parser(parser)
tty.msg('Checking dependencies for {0}'.format(args.spec[0]))
cli_args = ['-v'] if args.verbose else []
install_args = parser.parse_args(cli_args + ['--only=dependencies'])
install_args.spec = args.spec
inst.install(parser, install_args)
# Install package and stop at the given phase
cli_args = ['-v'] if args.verbose else []
install_args = parser.parse_args(cli_args + ['--only=package'])
install_args.spec = args.spec
inst.install(parser, install_args, stop_at=phase)
except IndexError:
tty.error(
'Package {0} has no {1} phase, or its {1} phase is not separated from install'.format( # NOQA: ignore=E501
spec.name, calling_fn.__name__)
)
def configure(parser, args):
tty.warn("This command is deprecated. Use `spack install --until` to"
" select an end phase instead. The `spack configure` command will"
" be removed in a future version of Spack.")
_stop_at_phase_during_install(args, configure, build_system_to_phase)

20
lib/spack/spack/cmd/diy.py
View File

@@ -1,20 +0,0 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import spack.cmd.dev_build
import llnl.util.tty as tty
description = "DEPRECATED: do-it-yourself: build from local source directory"
section = "build"
level = "long"
def setup_parser(subparser):
spack.cmd.dev_build.setup_parser(subparser)
def diy(self, args):
tty.warn("`spack diy` has been renamed to `spack dev-build`."
"The `diy` command will be removed in a future version of Spack")
spack.cmd.dev_build.dev_build(self, args)

6
lib/spack/spack/cmd/env.py
View File

@@ -52,6 +52,9 @@ def env_activate_setup_parser(subparser):
shells.add_argument(
'--csh', action='store_const', dest='shell', const='csh',
help="print csh commands to activate the environment")
shells.add_argument(
'--fish', action='store_const', dest='shell', const='fish',
help="print fish commands to activate the environment")
view_options = subparser.add_mutually_exclusive_group()
view_options.add_argument(
@@ -127,6 +130,9 @@ def env_deactivate_setup_parser(subparser):
shells.add_argument(
'--csh', action='store_const', dest='shell', const='csh',
help="print csh commands to deactivate the environment")
shells.add_argument(
'--fish', action='store_const', dest='shell', const='fish',
help="print fish commands to activate the environment")
def env_deactivate(args):

3
lib/spack/spack/cmd/load.py
View File

@@ -32,6 +32,9 @@ def setup_parser(subparser):
shells.add_argument(
'--csh', action='store_const', dest='shell', const='csh',
help="print csh commands to load the package")
shells.add_argument(
'--fish', action='store_const', dest='shell', const='fish',
help="print fish commands to load the package")
subparser.add_argument(
'--first',

11
lib/spack/spack/cmd/setup.py
View File

@@ -39,13 +39,6 @@ def setup_parser(subparser):
arguments.add_common_arguments(cd_group, ['clean', 'dirty'])
def spack_transitive_include_path():
return ';'.join(
os.path.join(dep, 'include')
for dep in os.environ['SPACK_DEPENDENCIES'].split(os.pathsep)
)
def write_spconfig(package, dirty):
# Set-up the environment
spack.build_environment.setup_package(package, dirty)
@@ -57,8 +50,8 @@ def write_spconfig(package, dirty):
paths = os.environ['PATH'].split(':')
paths = [item for item in paths if 'spack/env' not in item]
env['PATH'] = ':'.join(paths)
env['SPACK_TRANSITIVE_INCLUDE_PATH'] = spack_transitive_include_path()
env['CMAKE_PREFIX_PATH'] = os.environ['CMAKE_PREFIX_PATH']
env['SPACK_INCLUDE_DIRS'] = os.environ['SPACK_INCLUDE_DIRS']
env['CC'] = os.environ['SPACK_CC']
env['CXX'] = os.environ['SPACK_CXX']
env['FC'] = os.environ['SPACK_FC']
@@ -84,7 +77,7 @@ def cmdlist(str):
if name.find('PATH') < 0:
fout.write('env[%s] = %s\n' % (repr(name), repr(val)))
else:
if name == 'SPACK_TRANSITIVE_INCLUDE_PATH':
if name == 'SPACK_INCLUDE_DIRS':
sep = ';'
else:
sep = ':'

3
lib/spack/spack/cmd/unload.py
View File

@@ -31,6 +31,9 @@ def setup_parser(subparser):
shells.add_argument(
'--csh', action='store_const', dest='shell', const='csh',
help="print csh commands to activate the environment")
shells.add_argument(
'--fish', action='store_const', dest='shell', const='fish',
help="print fish commands to load the package")
subparser.add_argument('-a', '--all', action='store_true',
help='unload all loaded Spack packages.')

214
lib/spack/spack/cmd/upload_s3.py
View File

@@ -1,214 +0,0 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
# TODO: This will be merged into the buildcache command once
# everything is working.
import os
import re
import sys
try:
import boto3
import botocore
have_boto3_support = True
except ImportError:
have_boto3_support = False
import llnl.util.tty as tty
from spack.error import SpackError
import spack.tengine as template_engine
from spack.spec import Spec
import spack.binary_distribution as bindist
description = "temporary command to upload buildcaches to 's3.spack.io'"
section = "packaging"
level = "long"
def setup_parser(subparser):
setup_parser.parser = subparser
subparsers = subparser.add_subparsers(help='upload-s3 sub-commands')
# sub-command to upload a built spec to s3
spec = subparsers.add_parser('spec', help=upload_spec.__doc__)
spec.add_argument('-s', '--spec', default=None,
help='Spec to upload')
spec.add_argument('-y', '--spec-yaml', default=None,
help='Path to spec yaml file containing spec to upload')
spec.add_argument('-b', '--base-dir', default=None,
help='Path to root of buildcaches')
spec.add_argument('-e', '--endpoint-url',
default='https://s3.spack.io', help='URL of mirror')
spec.set_defaults(func=upload_spec)
# sub-command to update the index of a buildcache on s3
index = subparsers.add_parser('index', help=update_index.__doc__)
index.add_argument('-e', '--endpoint-url',
default='https://s3.spack.io', help='URL of mirror')
index.set_defaults(func=update_index)
def get_s3_session(endpoint_url):
if not have_boto3_support:
raise SpackError('boto3 module not available')
session = boto3.Session()
s3 = session.resource('s3', endpoint_url=endpoint_url)
bucket_names = []
for bucket in s3.buckets.all():
bucket_names.append(bucket.name)
if len(bucket_names) > 1:
raise SpackError('More than one bucket associated with credentials')
bucket_name = bucket_names[0]
return s3, bucket_name
def update_index(args):
"""Update the index of an s3 buildcache"""
s3, bucket_name = get_s3_session(args.endpoint_url)
bucket = s3.Bucket(bucket_name)
exists = True
try:
s3.meta.client.head_bucket(Bucket=bucket_name)
except botocore.exceptions.ClientError as e:
# If a client error is thrown, then check that it was a 404 error.
# If it was a 404 error, then the bucket does not exist.
error_code = e.response['Error']['Code']
if error_code == '404':
exists = False
if not exists:
tty.error('S3 bucket "{0}" does not exist'.format(bucket_name))
sys.exit(1)
build_cache_dir = os.path.join(
'mirror', bindist.build_cache_relative_path())
spec_yaml_regex = re.compile('{0}/(.+\\.spec\\.yaml)$'.format(
build_cache_dir))
spack_regex = re.compile('{0}/([^/]+)/.+\\.spack$'.format(
build_cache_dir))
top_level_keys = set()
for key in bucket.objects.all():
m = spec_yaml_regex.search(key.key)
if m:
top_level_keys.add(m.group(1))
print(m.group(1))
continue
m = spack_regex.search(key.key)
if m:
top_level_keys.add(m.group(1))
print(m.group(1))
continue
index_data = {
'top_level_keys': top_level_keys,
}
env = template_engine.make_environment()
template_dir = 'misc'
index_template = os.path.join(template_dir, 'buildcache_index.html')
t = env.get_template(index_template)
contents = t.render(index_data)
index_key = os.path.join(build_cache_dir, 'index.html')
tty.debug('Generated index:')
tty.debug(contents)
tty.debug('Pushing it to {0} -> {1}'.format(bucket_name, index_key))
s3_obj = s3.Object(bucket_name, index_key)
s3_obj.put(Body=contents, ACL='public-read')
def upload_spec(args):
"""Upload a spec to s3 bucket"""
if not args.spec and not args.spec_yaml:
tty.error('Cannot upload spec without spec arg or path to spec yaml')
sys.exit(1)
if not args.base_dir:
tty.error('No base directory for buildcache specified')
sys.exit(1)
if args.spec:
try:
spec = Spec(args.spec)
spec.concretize()
except Exception as e:
tty.debug(e)
tty.error('Unable to concrectize spec from string {0}'.format(
args.spec))
sys.exit(1)
else:
try:
with open(args.spec_yaml, 'r') as fd:
spec = Spec.from_yaml(fd.read())
except Exception as e:
tty.debug(e)
tty.error('Unable to concrectize spec from yaml {0}'.format(
args.spec_yaml))
sys.exit(1)
s3, bucket_name = get_s3_session(args.endpoint_url)
build_cache_dir = bindist.build_cache_relative_path()
tarball_key = os.path.join(
build_cache_dir, bindist.tarball_path_name(spec, '.spack'))
tarball_path = os.path.join(args.base_dir, tarball_key)
specfile_key = os.path.join(
build_cache_dir, bindist.tarball_name(spec, '.spec.yaml'))
specfile_path = os.path.join(args.base_dir, specfile_key)
cdashidfile_key = os.path.join(
build_cache_dir, bindist.tarball_name(spec, '.cdashid'))
cdashidfile_path = os.path.join(args.base_dir, cdashidfile_key)
tty.msg('Uploading {0}'.format(tarball_key))
s3.meta.client.upload_file(
tarball_path, bucket_name,
os.path.join('mirror', tarball_key),
ExtraArgs={'ACL': 'public-read'})
tty.msg('Uploading {0}'.format(specfile_key))
s3.meta.client.upload_file(
specfile_path, bucket_name,
os.path.join('mirror', specfile_key),
ExtraArgs={'ACL': 'public-read'})
if os.path.exists(cdashidfile_path):
tty.msg('Uploading {0}'.format(cdashidfile_key))
s3.meta.client.upload_file(
cdashidfile_path, bucket_name,
os.path.join('mirror', cdashidfile_key),
ExtraArgs={'ACL': 'public-read'})
def upload_s3(parser, args):
if args.func:
args.func(args)

59
lib/spack/spack/compiler.py
View File

@@ -27,12 +27,6 @@
__all__ = ['Compiler']
def _verify_executables(*paths):
for path in paths:
if not os.path.isfile(path) and os.access(path, os.X_OK):
raise CompilerAccessError(path)
@llnl.util.lang.memoized
def get_compiler_version_output(compiler_path, version_arg, ignore_errors=()):
"""Invokes the compiler at a given path passing a single
@@ -158,6 +152,10 @@ def _parse_non_system_link_dirs(string):
"""
link_dirs = _parse_link_paths(string)
# Remove directories that do not exist. Some versions of the Cray compiler
# report nonexistent directories
link_dirs = [d for d in link_dirs if os.path.isdir(d)]
# Return set of directories containing needed compiler libs, minus
# system paths. Note that 'filter_system_paths' only checks for an
# exact match, while 'in_system_subdirectory' checks if a path contains
@@ -271,20 +269,16 @@ def __init__(self, cspec, operating_system, target,
self.extra_rpaths = extra_rpaths
self.enable_implicit_rpaths = enable_implicit_rpaths
def check(exe):
if exe is None:
return None
_verify_executables(exe)
return exe
self.cc = check(paths[0])
self.cxx = check(paths[1])
self.cc = paths[0]
self.cxx = paths[1]
self.f77 = None
self.fc = None
if len(paths) > 2:
self.f77 = check(paths[2])
self.f77 = paths[2]
if len(paths) == 3:
self.fc = self.f77
else:
self.fc = check(paths[3])
self.fc = paths[3]
self.environment = environment
self.extra_rpaths = extra_rpaths or []
@@ -298,6 +292,31 @@ def check(exe):
if value is not None:
self.flags[flag] = tokenize_flags(value)
def verify_executables(self):
"""Raise an error if any of the compiler executables is not valid.
This method confirms that for all of the compilers (cc, cxx, f77, fc)
that have paths, those paths exist and are executable by the current
user.
Raises a CompilerAccessError if any of the non-null paths for the
compiler are not accessible.
"""
def accessible_exe(exe):
# compilers may contain executable names (on Cray or user edited)
if not os.path.isabs(exe):
exe = spack.util.executable.which_string(exe)
if not exe:
return False
return os.path.isfile(exe) and os.access(exe, os.X_OK)
# setup environment before verifying in case we have executable names
# instead of absolute paths
with self._compiler_environment():
missing = [cmp for cmp in (self.cc, self.cxx, self.f77, self.fc)
if cmp and not accessible_exe(cmp)]
if missing:
raise CompilerAccessError(self, missing)
@property
def version(self):
return self.spec.version
@@ -575,10 +594,10 @@ def _compiler_environment(self):
class CompilerAccessError(spack.error.SpackError):
def __init__(self, path):
super(CompilerAccessError, self).__init__(
"'%s' is not a valid compiler." % path)
def __init__(self, compiler, paths):
msg = "Compiler '%s' has executables that are missing" % compiler.spec
msg += " or are not executable: %s" % paths
super(CompilerAccessError, self).__init__(msg)
class InvalidCompilerError(spack.error.SpackError):

8
lib/spack/spack/compilers/cce.py
View File

@@ -91,16 +91,24 @@ def c11_flag(self):
@property
def cc_pic_flag(self):
if self.is_clang_based:
return "-fPIC"
return "-h PIC"
@property
def cxx_pic_flag(self):
if self.is_clang_based:
return "-fPIC"
return "-h PIC"
@property
def f77_pic_flag(self):
if self.is_clang_based:
return "-fPIC"
return "-h PIC"
@property
def fc_pic_flag(self):
if self.is_clang_based:
return "-fPIC"
return "-h PIC"

14
lib/spack/spack/container/images.json
View File

@@ -11,7 +11,8 @@
"0.14.0": "0.14.0",
"0.14.1": "0.14.1",
"0.14.2": "0.14.2",
"0.14.3": "0.14.3"
"0.15": "0.15",
"0.15.0": "0.15.0"
}
},
"ubuntu:16.04": {
@@ -26,7 +27,8 @@
"0.14.0": "0.14.0",
"0.14.1": "0.14.1",
"0.14.2": "0.14.2",
"0.14.3": "0.14.3"
"0.15": "0.15",
"0.15.0": "0.15.0"
}
},
"centos:7": {
@@ -41,7 +43,8 @@
"0.14.0": "0.14.0",
"0.14.1": "0.14.1",
"0.14.2": "0.14.2",
"0.14.3": "0.14.3"
"0.15": "0.15",
"0.15.0": "0.15.0"
}
},
"centos:6": {
@@ -56,7 +59,8 @@
"0.14.0": "0.14.0",
"0.14.1": "0.14.1",
"0.14.2": "0.14.2",
"0.14.3": "0.14.3"
"0.15": "0.15",
"0.15.0": "0.15.0"
}
}
}
}

72
lib/spack/spack/database.py
View File

@@ -48,6 +48,12 @@
from spack.util.crypto import bit_length
from spack.version import Version
@contextlib.contextmanager
def nullcontext(*args, **kwargs):
yield
# TODO: Provide an API automatically retyring a build after detecting and
# TODO: clearing a failure.
@@ -87,6 +93,17 @@
# Types of dependencies tracked by the database
_tracked_deps = ('link', 'run')
# Default list of fields written for each install record
default_install_record_fields = [
'spec',
'ref_count',
'path',
'installed',
'explicit',
'installation_time',
'deprecated_for',
]
def _now():
"""Returns the time since the epoch"""
@@ -187,17 +204,17 @@ def install_type_matches(self, installed):
else:
return InstallStatuses.MISSING in installed
def to_dict(self):
rec_dict = {
'spec': self.spec.to_node_dict(),
'path': self.path,
'installed': self.installed,
'ref_count': self.ref_count,
'explicit': self.explicit,
'installation_time': self.installation_time,
}
if self.deprecated_for:
rec_dict.update({'deprecated_for': self.deprecated_for})
def to_dict(self, include_fields=default_install_record_fields):
rec_dict = {}
for field_name in include_fields:
if field_name == 'spec':
rec_dict.update({'spec': self.spec.to_node_dict()})
elif field_name == 'deprecated_for' and self.deprecated_for:
rec_dict.update({'deprecated_for': self.deprecated_for})
else:
rec_dict.update({field_name: getattr(self, field_name)})
return rec_dict
@classmethod
@@ -206,9 +223,12 @@ def from_dict(cls, spec, dictionary):
d.pop('spec', None)
# Old databases may have "None" for path for externals
if d['path'] == 'None':
if 'path' not in d or d['path'] == 'None':
d['path'] = None
if 'installed' not in d:
d['installed'] = False
return InstallRecord(spec, **d)
@@ -275,7 +295,8 @@ class Database(object):
_prefix_failures = {}
def __init__(self, root, db_dir=None, upstream_dbs=None,
is_upstream=False):
is_upstream=False, enable_transaction_locking=True,
record_fields=default_install_record_fields):
"""Create a Database for Spack installations under ``root``.
A Database is a cache of Specs data from ``$prefix/spec.yaml``
@@ -293,6 +314,12 @@ def __init__(self, root, db_dir=None, upstream_dbs=None,
Caller may optionally provide a custom ``db_dir`` parameter
where data will be stored. This is intended to be used for
testing the Database class.
This class supports writing buildcache index files, in which case
certain fields are not needed in each install record, and no
transaction locking is required. To use this feature, provide
``enable_transaction_locking=False``, and specify a list of needed
fields in ``record_fields``.
"""
self.root = root
@@ -375,14 +402,23 @@ def __init__(self, root, db_dir=None, upstream_dbs=None,
# message)
self._fail_when_missing_deps = False
if enable_transaction_locking:
self._write_transaction_impl = lk.WriteTransaction
self._read_transaction_impl = lk.ReadTransaction
else:
self._write_transaction_impl = nullcontext
self._read_transaction_impl = nullcontext
self._record_fields = record_fields
def write_transaction(self):
"""Get a write lock context manager for use in a `with` block."""
return lk.WriteTransaction(
return self._write_transaction_impl(
self.lock, acquire=self._read, release=self._write)
def read_transaction(self):
"""Get a read lock context manager for use in a `with` block."""
return lk.ReadTransaction(self.lock, acquire=self._read)
return self._read_transaction_impl(self.lock, acquire=self._read)
def _failed_spec_path(self, spec):
"""Return the path to the spec's failure file, which may not exist."""
@@ -592,7 +628,8 @@ def _write_to_file(self, stream):
This function does not do any locking or transactions.
"""
# map from per-spec hash code to installation record.
installs = dict((k, v.to_dict()) for k, v in self._data.items())
installs = dict((k, v.to_dict(include_fields=self._record_fields))
for k, v in self._data.items())
# database includes installation list and version.
@@ -726,7 +763,8 @@ def check(cond, msg):
self.reindex(spack.store.layout)
installs = dict(
(k, v.to_dict()) for k, v in self._data.items()
(k, v.to_dict(include_fields=self._record_fields))
for k, v in self._data.items()
)
def invalid_record(hash_key, error):

42
lib/spack/spack/environment.py
View File

@@ -115,7 +115,7 @@ def activate(
use_env_repo (bool): use the packages exactly as they appear in the
environment's repository
add_view (bool): generate commands to add view to path variables
shell (string): One of `sh`, `csh`.
shell (string): One of `sh`, `csh`, `fish`.
prompt (string): string to add to the users prompt, or None
Returns:
@@ -141,6 +141,19 @@ def activate(
cmds += 'if (! $?SPACK_OLD_PROMPT ) '
cmds += 'setenv SPACK_OLD_PROMPT "${prompt}";\n'
cmds += 'set prompt="%s ${prompt}";\n' % prompt
elif shell == 'fish':
if os.getenv('TERM') and 'color' in os.getenv('TERM') and prompt:
prompt = colorize('@G{%s} ' % prompt, color=True)
cmds += 'set -gx SPACK_ENV %s;\n' % env.path
cmds += 'function despacktivate;\n'
cmds += ' spack env deactivate;\n'
cmds += 'end;\n'
#
# NOTE: We're not changing the fish_prompt function (which is fish's
# solution to the PS1 variable) here. This is a bit fiddly, and easy to
# screw up => spend time reasearching a solution. Feedback welcome.
#
else:
if os.getenv('TERM') and 'color' in os.getenv('TERM') and prompt:
prompt = colorize('@G{%s} ' % prompt, color=True)
@@ -156,6 +169,12 @@ def activate(
cmds += 'fi;\n'
cmds += 'export PS1="%s ${PS1}";\n' % prompt
#
# NOTE in the fish-shell: Path variables are a special kind of variable
# used to support colon-delimited path lists including PATH, CDPATH,
# MANPATH, PYTHONPATH, etc. All variables that end in PATH (case-sensitive)
# become PATH variables.
#
if add_view and default_view_name in env.views:
with spack.store.db.read_transaction():
cmds += env.add_default_view_to_shell(shell)
@@ -167,7 +186,7 @@ def deactivate(shell='sh'):
"""Undo any configuration or repo settings modified by ``activate()``.
Arguments:
shell (string): One of `sh`, `csh`. Shell style to use.
shell (string): One of `sh`, `csh`, `fish`. Shell style to use.
Returns:
(string): shell commands for `shell` to undo environment variables
@@ -191,6 +210,12 @@ def deactivate(shell='sh'):
cmds += 'set prompt="$SPACK_OLD_PROMPT" && '
cmds += 'unsetenv SPACK_OLD_PROMPT;\n'
cmds += 'unalias despacktivate;\n'
elif shell == 'fish':
cmds += 'set -e SPACK_ENV;\n'
cmds += 'functions -e despacktivate;\n'
#
# NOTE: Not changing fish_prompt (above) => no need to restore it here.
#
else:
cmds += 'if [ ! -z ${SPACK_ENV+x} ]; then\n'
cmds += 'unset SPACK_ENV; export SPACK_ENV;\n'
@@ -247,18 +272,13 @@ def find_environment(args):
# at env_dir (env and env_dir are mutually exclusive)
env = getattr(args, 'env_dir', None)
# if no argument, look for a manifest file
# if no argument, look for the environment variable
if not env:
if os.path.exists(manifest_name):
env = os.getcwd()
env = os.environ.get(spack_env_var)
# if no env, env_dir, or manifest try the environment
# nothing was set; there's no active environment
if not env:
env = os.environ.get(spack_env_var)
# nothing was set; there's no active environment
if not env:
return None
return None
# if we get here, env isn't the name of a spack environment; it has
# to be a path to an environment, or there is something wrong.

3
lib/spack/spack/operating_systems/cray_backend.py
View File

@@ -146,7 +146,8 @@ def detect_version(self, detect_version_args):
compiler_cls.PrgEnv_compiler
)
matches = re.findall(version_regex, output)
version = tuple(version for _, version in matches)
version = tuple(version for _, version in matches
if 'classic' not in version)
compiler_id = detect_version_args.id
value = detect_version_args._replace(
id=compiler_id._replace(version=version)

44
lib/spack/spack/operating_systems/cray_frontend.py
View File

@@ -5,8 +5,11 @@
import contextlib
import os
import re
import llnl.util.filesystem as fs
import llnl.util.lang
import llnl.util.tty as tty
from spack.operating_systems.linux_distro import LinuxDistro
from spack.util.environment import get_path
@@ -60,6 +63,43 @@ def compiler_search_paths(self):
This prevents from detecting Cray compiler wrappers and avoids
possible false detections.
"""
import spack.compilers
with unload_programming_environment():
search_paths = fs.search_paths_for_executables(*get_path('PATH'))
return search_paths
search_paths = get_path('PATH')
extract_path_re = re.compile(r'prepend-path[\s]*PATH[\s]*([/\w\.:-]*)')
for compiler_cls in spack.compilers.all_compiler_types():
# Check if the compiler class is supported on Cray
prg_env = getattr(compiler_cls, 'PrgEnv', None)
compiler_module = getattr(compiler_cls, 'PrgEnv_compiler', None)
if not (prg_env and compiler_module):
continue
# It is supported, check which versions are available
output = module('avail', compiler_cls.PrgEnv_compiler)
version_regex = r'({0})/([\d\.]+[\d]-?[\w]*)'.format(
compiler_cls.PrgEnv_compiler
)
matches = re.findall(version_regex, output)
versions = tuple(version for _, version in matches
if 'classic' not in version)
# Now inspect the modules and add to paths
msg = "[CRAY FE] Detected FE compiler [name={0}, versions={1}]"
tty.debug(msg.format(compiler_module, versions))
for v in versions:
try:
current_module = compiler_module + '/' + v
out = module('show', current_module)
match = extract_path_re.search(out)
search_paths += match.group(1).split(':')
except Exception as e:
msg = ("[CRAY FE] An unexpected error occurred while "
"detecting FE compiler [compiler={0}, "
" version={1}, error={2}]")
tty.debug(msg.format(compiler_cls.name, v, str(e)))
search_paths = list(llnl.util.lang.dedupe(search_paths))
return fs.search_paths_for_executables(*search_paths)

1
lib/spack/spack/operating_systems/mac_os.py
View File

@@ -54,6 +54,7 @@ def __init__(self):
'10.13': 'highsierra',
'10.14': 'mojave',
'10.15': 'catalina',
'11.0': 'bigsur',
}
mac_ver = str(macos_version().up_to(2))

42
lib/spack/spack/schema/buildcache_spec.py Normal file
View File

@@ -0,0 +1,42 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
"""Schema for a buildcache spec.yaml file
.. literalinclude:: _spack_root/lib/spack/spack/schema/buildcache_spec.py
:lines: 14-
"""
import spack.schema.spec
schema = {
'$schema': 'http://json-schema.org/schema#',
'title': 'Spack buildcache spec.yaml schema',
'type': 'object',
# 'additionalProperties': True,
'properties': {
'buildinfo': {
'type': 'object',
'additionalProperties': False,
'required': ['relative_prefix'],
'properties': {
'relative_prefix': {'type': 'string'},
'relative_rpaths': {'type': 'boolean'},
},
},
'full_hash': {'type': 'string'},
'spec': {
'type': 'array',
'items': spack.schema.spec.properties,
},
'binary_cache_checksum': {
'type': 'object',
'properties': {
'hash_algorithm': {'type': 'string'},
'hash': {'type': 'string'},
},
},
},
}

3
lib/spack/spack/schema/container.py
View File

@@ -31,7 +31,8 @@
'type': 'string',
'enum': [
'develop',
'0.14', '0.14.0', '0.14.1', '0.14.2', '0.14.3'
'0.14', '0.14.0', '0.14.1', '0.14.2',
'0.15', '0.15.0',
]
}
},

58
lib/spack/spack/schema/database_index.py Normal file
View File

@@ -0,0 +1,58 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
"""Schema for database index.json file
.. literalinclude:: _spack_root/lib/spack/spack/schema/database_index.py
:lines: 36-
"""
import spack.schema.spec
# spack.schema.spec.properties
#: Full schema with metadata
schema = {
'$schema': 'http://json-schema.org/schema#',
'title': 'Spack spec schema',
'type': 'object',
'required': ['database'],
'additionalProperties': False,
'properties': {
'database': {
'type': 'object',
'required': ['installs', 'version'],
'additionalProperties': False,
'properties': {
'installs': {
'type': 'object',
'patternProperties': {
r'^[\w\d]{32}$': {
'type': 'object',
'properties': {
'spec': spack.schema.spec.properties,
'path': {
'oneOf': [
{'type': 'string'},
{'type': 'null'},
],
},
'installed': {'type': 'boolean'},
'ref_count': {
'type': 'integer',
'minimum': 0,
},
'explicit': {'type': 'boolean'},
'installation_time': {
'type': 'number',
}
},
},
},
},
'version': {'type': 'string'},
}
},
},
}

159
lib/spack/spack/schema/spec.py Normal file
View File

@@ -0,0 +1,159 @@
# 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)
"""Schema for a spec found in spec.yaml or database index.json files
.. literalinclude:: _spack_root/lib/spack/spack/schema/spec.py
:lines: 13-
"""
target = {
'oneOf': [
{
'type': 'string',
}, {
'type': 'object',
'additionalProperties': False,
'required': [
'name',
'vendor',
'features',
'generation',
'parents',
],
'properties': {
'name': {'type': 'string'},
'vendor': {'type': 'string'},
'features': {
'type': 'array',
'items': {'type': 'string'},
},
'generation': {'type': 'integer'},
'parents': {
'type': 'array',
'items': {'type': 'string'},
},
},
},
],
}
arch = {
'type': 'object',
'additionalProperties': False,
'properties': {
'platform': {},
'platform_os': {},
'target': target,
},
}
dependencies = {
'type': 'object',
'patternProperties': {
r'\w[\w-]*': { # package name
'type': 'object',
'properties': {
'hash': {'type': 'string'},
'type': {
'type': 'array',
'items': {'type': 'string'},
},
},
},
},
}
#: Properties for inclusion in other schemas
properties = {
r'\w[\w-]*': { # package name
'type': 'object',
'additionalProperties': False,
'required': [
'version',
'arch',
'compiler',
'namespace',
'parameters',
],
'properties': {
'hash': {'type': 'string'},
'version': {
'oneOf': [
{'type': 'string'},
{'type': 'number'},
],
},
'arch': arch,
'compiler': {
'type': 'object',
'additionalProperties': False,
'properties': {
'name': {'type': 'string'},
'version': {'type': 'string'},
},
},
'namespace': {'type': 'string'},
'parameters': {
'type': 'object',
'required': [
'cflags',
'cppflags',
'cxxflags',
'fflags',
'ldflags',
'ldlibs',
],
'additionalProperties': True,
'properties': {
'patches': {
'type': 'array',
'items': {'type': 'string'},
},
'cflags': {
'type': 'array',
'items': {'type': 'string'},
},
'cppflags': {
'type': 'array',
'items': {'type': 'string'},
},
'cxxflags': {
'type': 'array',
'items': {'type': 'string'},
},
'fflags': {
'type': 'array',
'items': {'type': 'string'},
},
'ldflags': {
'type': 'array',
'items': {'type': 'string'},
},
'ldlib': {
'type': 'array',
'items': {'type': 'string'},
},
},
},
'patches': {
'type': 'array',
'items': {},
},
'dependencies': dependencies,
},
},
}
#: Full schema with metadata
schema = {
'$schema': 'http://json-schema.org/schema#',
'title': 'Spack spec schema',
'type': 'object',
'additionalProperties': False,
'patternProperties': properties,
}

41
lib/spack/spack/test/ci.py
View File

@@ -188,8 +188,6 @@ def test_ci_workarounds():
'SPACK_IS_PR_PIPELINE': 'False',
}
common_script = ['spack ci rebuild']
common_before_script = [
'git clone "https://github.com/spack/spack"',
' && '.join((
@@ -219,14 +217,14 @@ def make_build_job(name, deps, stage, use_artifact_buildcache, optimize,
},
'retry': {'max': 2, 'when': ['always']},
'after_script': ['rm -rf "./spack"'],
'image': {'name': 'spack/centos7', 'entrypoint': ['']},
'script': ['spack ci rebuild'],
'image': {'name': 'spack/centos7', 'entrypoint': ['']}
}
if optimize:
result['extends'] = ['.c0', '.c1', '.c2']
result['extends'] = ['.c0', '.c1']
else:
variables['SPACK_ROOT_SPEC'] = fake_root_spec
result['script'] = common_script
result['before_script'] = common_before_script
result['variables'] = variables
@@ -254,7 +252,7 @@ def make_rebuild_index_job(
}
if optimize:
result['extends'] = '.c1'
result['extends'] = '.c0'
else:
result['before_script'] = common_before_script
@@ -262,11 +260,16 @@ def make_rebuild_index_job(
def make_factored_jobs(optimize):
return {
'.c0': {'script': common_script},
'.c1': {'before_script': common_before_script},
'.c2': {'variables': {'SPACK_ROOT_SPEC': fake_root_spec}}
'.c0': {'before_script': common_before_script},
'.c1': {'variables': {'SPACK_ROOT_SPEC': fake_root_spec}}
} if optimize else {}
def make_stage_list(num_build_stages):
return {
'stages': (
['-'.join(('stage', str(i))) for i in range(num_build_stages)]
+ ['stage-rebuild-index'])}
def make_yaml_obj(use_artifact_buildcache, optimize, use_dependencies):
result = {}
@@ -287,22 +290,10 @@ def make_yaml_obj(use_artifact_buildcache, optimize, use_dependencies):
result.update(make_factored_jobs(optimize))
result.update(make_stage_list(3))
return result
def sort_yaml_obj(obj):
if isinstance(obj, collections_abc.Mapping):
result = syaml.syaml_dict()
for k in sorted(obj.keys(), key=str):
result[k] = sort_yaml_obj(obj[k])
return result
if (isinstance(obj, collections_abc.Sequence) and
not isinstance(obj, str)):
return syaml.syaml_list(sorted(
(sort_yaml_obj(x) for x in obj), key=str))
return obj
# test every combination of:
# use artifact buildcache: true or false
# run optimization pass: true or false
@@ -331,8 +322,8 @@ def sort_yaml_obj(obj):
actual = cinw.needs_to_dependencies(actual)
predicted = syaml.dump_config(
sort_yaml_obj(predicted), default_flow_style=True)
ci_opt.sort_yaml_obj(predicted), default_flow_style=True)
actual = syaml.dump_config(
sort_yaml_obj(actual), default_flow_style=True)
ci_opt.sort_yaml_obj(actual), default_flow_style=True)
assert(predicted == actual)

2
lib/spack/spack/test/cmd/buildcache.py
View File

@@ -24,7 +24,7 @@
def mock_get_specs(database, monkeypatch):
specs = database.query_local()
monkeypatch.setattr(
spack.binary_distribution, 'get_specs', lambda x, y: specs
spack.binary_distribution, 'get_specs', lambda x: specs
)

24
lib/spack/spack/test/cmd/ci.py
View File

@@ -4,8 +4,10 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import filecmp
import json
import os
import pytest
from jsonschema import validate
import spack
import spack.ci as ci
@@ -15,6 +17,8 @@
from spack.main import SpackCommand
import spack.paths as spack_paths
import spack.repo as repo
from spack.schema.buildcache_spec import schema as spec_yaml_schema
from spack.schema.database_index import schema as db_idx_schema
from spack.spec import Spec
from spack.util.mock_package import MockPackageMultiRepo
import spack.util.executable as exe
@@ -717,10 +721,28 @@ def test_push_mirror_contents(tmpdir, mutable_mock_env_path, env_deactivate,
ci.push_mirror_contents(
env, concrete_spec, yaml_path, mirror_url, '42')
buildcache_list_output = buildcache_cmd('list', output=str)
buildcache_path = os.path.join(mirror_dir.strpath, 'build_cache')
# Test generating buildcache index while we have bin mirror
buildcache_cmd('update-index', '--mirror-url', mirror_url)
index_path = os.path.join(buildcache_path, 'index.json')
with open(index_path) as idx_fd:
index_object = json.load(idx_fd)
validate(index_object, db_idx_schema)
# Now that index is regenerated, validate "buildcache list" output
buildcache_list_output = buildcache_cmd('list', output=str)
assert('patchelf' in buildcache_list_output)
# Also test buildcache_spec schema
bc_files_list = os.listdir(buildcache_path)
for file_name in bc_files_list:
if file_name.endswith('.spec.yaml'):
spec_yaml_path = os.path.join(buildcache_path, file_name)
with open(spec_yaml_path) as yaml_fd:
yaml_object = syaml.load(yaml_fd)
validate(yaml_object, spec_yaml_schema)
logs_dir = working_dir.join('logs_dir')
if not os.path.exists(logs_dir.strpath):
os.makedirs(logs_dir.strpath)

44
lib/spack/spack/test/compilers/basics.py
View File

@@ -159,7 +159,13 @@ def __init__(self):
default_compiler_entry['paths']['f77']],
environment={})
_get_compiler_link_paths = Compiler._get_compiler_link_paths
def _get_compiler_link_paths(self, paths):
# Mock os.path.isdir so the link paths don't have to exist
old_isdir = os.path.isdir
os.path.isdir = lambda x: True
ret = super(MockCompiler, self)._get_compiler_link_paths(paths)
os.path.isdir = old_isdir
return ret
@property
def name(self):
@@ -222,6 +228,7 @@ def call_compiler(exe, *args, **kwargs):
('f77', 'fflags'),
('f77', 'cppflags'),
])
@pytest.mark.enable_compiler_link_paths
def test_get_compiler_link_paths(monkeypatch, exe, flagname):
# create fake compiler that emits mock verbose output
compiler = MockCompiler()
@@ -261,6 +268,7 @@ def test_get_compiler_link_paths_no_verbose_flag():
assert dirs == []
@pytest.mark.enable_compiler_link_paths
def test_get_compiler_link_paths_load_env(working_env, monkeypatch, tmpdir):
gcc = str(tmpdir.join('gcc'))
with open(gcc, 'w') as f:
@@ -377,6 +385,10 @@ def test_cce_flags():
supported_flag_test("cxx_pic_flag", "-h PIC", "cce@1.0")
supported_flag_test("f77_pic_flag", "-h PIC", "cce@1.0")
supported_flag_test("fc_pic_flag", "-h PIC", "cce@1.0")
supported_flag_test("cc_pic_flag", "-fPIC", "cce@9.1.0")
supported_flag_test("cxx_pic_flag", "-fPIC", "cce@9.1.0")
supported_flag_test("f77_pic_flag", "-fPIC", "cce@9.1.0")
supported_flag_test("fc_pic_flag", "-fPIC", "cce@9.1.0")
supported_flag_test("debug_flags", ['-g', '-G0', '-G1', '-G2', '-Gfast'],
'cce@1.0')
@@ -823,3 +835,33 @@ class MockPackage(object):
pkg = MockPackage()
with pytest.raises(OSError):
compiler.setup_custom_environment(pkg, env)
@pytest.mark.enable_compiler_verification
def test_compiler_executable_verification_raises(tmpdir):
compiler = MockCompiler()
compiler.cc = '/this/path/does/not/exist'
with pytest.raises(spack.compiler.CompilerAccessError):
compiler.verify_executables()
@pytest.mark.enable_compiler_verification
def test_compiler_executable_verification_success(tmpdir):
def prepare_executable(name):
real = str(tmpdir.join('cc').ensure())
fs.set_executable(real)
setattr(compiler, name, real)
# setup mock compiler with real paths
compiler = MockCompiler()
for name in ('cc', 'cxx', 'f77', 'fc'):
prepare_executable(name)
# testing that this doesn't raise an error because the paths exist and
# are executable
compiler.verify_executables()
# Test that null entries don't fail
compiler.cc = None
compiler.verify_executables()

44
lib/spack/spack/test/compilers/detection.py
View File

@@ -4,6 +4,9 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
"""Test detection of compiler version"""
import pytest
import os
import llnl.util.filesystem as fs
import spack.compilers.arm
import spack.compilers.cce
@@ -16,6 +19,9 @@
import spack.compilers.xl
import spack.compilers.xl_r
from spack.operating_systems.cray_frontend import CrayFrontend
import spack.util.module_cmd
@pytest.mark.parametrize('version_str,expected_version', [
('Arm C/C++/Fortran Compiler version 19.0 (build number 73) (based on LLVM 7.0.2)\n' # NOQA
@@ -189,3 +195,41 @@ def test_xl_version_detection(version_str, expected_version):
version = spack.compilers.xl_r.XlR.extract_version_from_output(version_str)
assert version == expected_version
@pytest.mark.parametrize('compiler,version', [
('gcc', '8.1.0'),
('gcc', '1.0.0-foo'),
('pgi', '19.1'),
('pgi', '19.1a'),
('intel', '9.0.0'),
('intel', '0.0.0-foobar')
])
def test_cray_frontend_compiler_detection(
compiler, version, tmpdir, monkeypatch, working_env
):
"""Test that the Cray frontend properly finds compilers form modules"""
# setup the fake compiler directory
compiler_dir = tmpdir.join(compiler)
compiler_exe = compiler_dir.join('cc').ensure()
fs.set_executable(str(compiler_exe))
# mock modules
def _module(cmd, *args):
module_name = '%s/%s' % (compiler, version)
module_contents = 'prepend-path PATH %s' % compiler_dir
if cmd == 'avail':
return module_name if compiler in args[0] else ''
if cmd == 'show':
return module_contents if module_name in args else ''
monkeypatch.setattr(spack.operating_systems.cray_frontend, 'module',
_module)
# remove PATH variable
os.environ.pop('PATH', None)
# get a CrayFrontend object
cray_fe_os = CrayFrontend()
paths = cray_fe_os.compiler_search_paths
assert paths == [str(compiler_dir)]

49
lib/spack/spack/test/conftest.py
View File

@@ -70,6 +70,25 @@ def clean_user_environment():
ev.activate(active)
#
# Disable checks on compiler executable existence
#
@pytest.fixture(scope='function', autouse=True)
def mock_compiler_executable_verification(request, monkeypatch):
"""Mock the compiler executable verification to allow missing executables.
This fixture can be disabled for tests of the compiler verification
functionality by::
@pytest.mark.enable_compiler_verification
If a test is marked in that way this is a no-op."""
if 'enable_compiler_verification' not in request.keywords:
monkeypatch.setattr(spack.compiler.Compiler,
'verify_executables',
lambda x: None)
# Hooks to add command line options or set other custom behaviors.
# They must be placed here to be found by pytest. See:
#
@@ -600,18 +619,26 @@ def dirs_with_libfiles(tmpdir_factory):
@pytest.fixture(scope='function', autouse=True)
def disable_compiler_execution(monkeypatch):
def noop(*args):
return []
def disable_compiler_execution(monkeypatch, request):
"""
This fixture can be disabled for tests of the compiler link path
functionality by::
# Compiler.determine_implicit_rpaths actually runs the compiler. So this
# replaces that function with a noop that simulates finding no implicit
# RPATHs
monkeypatch.setattr(
spack.compiler.Compiler,
'_get_compiler_link_paths',
noop
)
@pytest.mark.enable_compiler_link_paths
If a test is marked in that way this is a no-op."""
if 'enable_compiler_link_paths' not in request.keywords:
def noop(*args):
return []
# Compiler.determine_implicit_rpaths actually runs the compiler. So
# replace that function with a noop that simulates finding no implicit
# RPATHs
monkeypatch.setattr(
spack.compiler.Compiler,
'_get_compiler_link_paths',
noop
)
@pytest.fixture(scope='function')

9
lib/spack/spack/test/database.py
View File

@@ -21,6 +21,8 @@
_use_uuid = False
pass
from jsonschema import validate
import llnl.util.lock as lk
from llnl.util.tty.colify import colify
@@ -31,6 +33,7 @@
import spack.spec
from spack.util.mock_package import MockPackageMultiRepo
from spack.util.executable import Executable
from spack.schema.database_index import schema
pytestmark = pytest.mark.db
@@ -438,6 +441,10 @@ def test_005_db_exists(database):
assert os.path.exists(str(index_file))
assert os.path.exists(str(lock_file))
with open(index_file) as fd:
index_object = json.load(fd)
validate(index_object, schema)
def test_010_all_install_sanity(database):
"""Ensure that the install layout reflects what we think it does."""
@@ -730,6 +737,8 @@ def test_old_external_entries_prefix(mutable_database):
with open(spack.store.db._index_path, 'r') as f:
db_obj = json.loads(f.read())
validate(db_obj, schema)
s = spack.spec.Spec('externaltool')
s.concretize()

9
lib/spack/spack/test/link_paths.py
View File

@@ -2,7 +2,7 @@
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import pytest
import os
import spack.paths
@@ -13,6 +13,13 @@
'compiler_verbose_output')
@pytest.fixture(autouse=True)
def allow_nonexistent_paths(monkeypatch):
# Allow nonexistent paths to be detected as part of the output
# for testing purposes.
monkeypatch.setattr(os.path, 'isdir', lambda x: True)
def check_link_paths(filename, paths):
with open(os.path.join(datadir, filename)) as file:
output = file.read()

4
lib/spack/spack/test/packaging.py
View File

@@ -108,6 +108,8 @@ def test_buildcache(mock_archive, tmpdir):
else:
create_args.insert(create_args.index('-a'), '-u')
create_args.insert(create_args.index('-a'), '--rebuild-index')
args = parser.parse_args(create_args)
buildcache.buildcache(parser, args)
# trigger overwrite warning
@@ -165,7 +167,7 @@ def test_buildcache(mock_archive, tmpdir):
args = parser.parse_args(['list'])
buildcache.buildcache(parser, args)
args = parser.parse_args(['list', '-f'])
args = parser.parse_args(['list'])
buildcache.buildcache(parser, args)
args = parser.parse_args(['list', 'trivial'])

2
lib/spack/spack/util/environment.py
View File

@@ -32,12 +32,14 @@
_shell_set_strings = {
'sh': 'export {0}={1};\n',
'csh': 'setenv {0} {1};\n',
'fish': 'set -gx {0} {1};\n'
}
_shell_unset_strings = {
'sh': 'unset {0};\n',
'csh': 'unsetenv {0};\n',
'fish': 'set -e {0};\n',
}

6
share/spack/qa/run-shell-tests
View File

@@ -25,6 +25,9 @@ check_dependencies $coverage git hg svn
export PATH="$ORIGINAL_PATH"
unset spack
# Convert QA_DIR to absolute path before changing directory
export QA_DIR=$(realpath $QA_DIR)
# Start in the spack root directory
cd "$SPACK_ROOT"
@@ -41,3 +44,6 @@ fi
# Run the test scripts for their output (these will print nicely)
zsh "$QA_DIR/setup-env-test.sh"
dash "$QA_DIR/setup-env-test.sh"
# Run fish tests
fish "$QA_DIR/setup-env-test.fish"

395
share/spack/qa/setup-env-test.fish Executable file
View File

@@ -0,0 +1,395 @@
#!/usr/bin/env fish
#
# 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)
#
# This script tests that Spack's setup-env.fish init script works.
#
function allocate_testing_global -d "allocate global variables used for testing"
# Colors for output
set -gx __spt_red '\033[1;31m'
set -gx __spt_cyan '\033[1;36m'
set -gx __spt_green '\033[1;32m'
set -gx __spt_reset '\033[0m'
# counts of test successes and failures.
set -gx __spt_success 0
set -gx __spt_errors 0
end
function delete_testing_global -d "deallocate global varialbes used for testing"
set -e __spt_red
set -e __spt_cyan
set -e __spt_green
set -e __spt_reset
set -e __spt_success
set -e __spt_errors
end
# ------------------------------------------------------------------------
# Functions for color output.
# ------------------------------------------------------------------------
function echo_red
printf "$__spt_red$argv$__spt_reset\n"
end
function echo_green
printf "$__spt_green$argv$__spt_reset\n"
end
function echo_msg
printf "$__spt_cyan$argv$__spt_reset\n"
end
# ------------------------------------------------------------------------
# Generic functions for testing fish code.
# ------------------------------------------------------------------------
# Print out a header for a group of tests.
function title
echo
echo_msg "$argv"
echo_msg "---------------------------------"
end
# echo FAIL in red text; increment failures
function fail
echo_red FAIL
set __spt_errors (math $__spt_errors+1)
end
# echo SUCCESS in green; increment successes
function pass
echo_green SUCCESS
set __spt_success (math $__spt_success+1)
end
#
# Run a command and suppress output unless it fails.
# On failure, echo the exit code and output.
#
function spt_succeeds
printf "'$argv' succeeds ... "
set -l output (eval $argv 2>&1)
if test $status -ne 0
fail
echo_red "Command failed with error $status"
if test -n "$output"
echo_msg "Output:"
echo "$output"
else
echo_msg "No output."
end
else
pass
end
end
#
# Run a command and suppress output unless it succeeds.
# If the command succeeds, echo the output.
#
function spt_fails
printf "'$argv' fails ... "
set -l output (eval $argv 2>&1)
if test $status -eq 0
fail
echo_red "Command failed with error $status"
if test -n "$output"
echo_msg "Output:"
echo "$output"
else
echo_msg "No output."
end
else
pass
end
end
#
# Ensure that a string is in the output of a command.
# Suppresses output on success.
# On failure, echo the exit code and output.
#
function spt_contains
set -l target_string $argv[1]
set -l remaining_args $argv[2..-1]
printf "'$remaining_args' output contains '$target_string' ... "
set -l output (eval $remaining_args 2>&1)
if not echo "$output" | string match -q -r ".*$target_string.*"
fail
echo_red "Command exited with error $status"
echo_red "'$target_string' was not in output."
if test -n "$output"
echo_msg "Output:"
echo "$output"
else
echo_msg "No output."
end
else
pass
end
end
#
# Ensure that a variable is set.
#
function is_set
printf "'$argv[1]' is set ... "
if test -z "$$argv[1]"
fail
echo_msg "'$argv[1]' was not set!"
else
pass
end
end
#
# Ensure that a variable is not set.
# Fails and prints the value of the variable if it is set.
#
function is_not_set
printf "'$argv[1]' is not set ... "
if test -n "$$argv[1]"
fail
echo_msg "'$argv[1]' was set!"
echo " $$argv[1]"
else
pass
end
end
# -----------------------------------------------------------------------
# Setup test environment and do some preliminary checks
# -----------------------------------------------------------------------
# Make sure no environment is active
set -e SPACK_ENV
true # ignore failing `set -e`
# Source setup-env.sh before tests
set -gx QA_DIR (dirname (status --current-filename))
source $QA_DIR/../setup-env.fish
# -----------------------------------------------------------------------
# Instead of invoking the module and cd commands, we print the arguments that
# Spack invokes the command with, so we can check that Spack passes the expected
# arguments in the tests below.
#
# We make that happen by defining the fish functions below. NOTE: these overwrite
# existing functions => define them last
# -----------------------------------------------------------------------
function module
echo "module $argv"
end
function cd
echo "cd $argv"
end
allocate_testing_global
# -----------------------------------------------------------------------
# Let the testing begin!
# -----------------------------------------------------------------------
title "Testing setup-env.fish with $_sp_shell"
# spack command is now available
spt_succeeds which spack
# create a fake mock package install and store its location for later
title "Setup"
echo "Creating a mock package installation"
spack -m install --fake a
# create a test environment for testing environment commands
echo "Creating a mock environment"
spack env create spack_test_env
# ensure that we uninstall b on exit
function spt_cleanup
set trapped_error false
if test $status -ne 0
set trapped_error true
end
echo "Removing test environment before exiting."
spack env deactivate 2>&1 > /dev/null
spack env rm -y spack_test_env
title "Cleanup"
echo "Removing test packages before exiting."
spack -m uninstall -yf b a
echo
echo "$__spt_success tests succeeded."
echo "$__spt_errors tests failed."
if test "$trapped_error" = false
echo "Exited due to an error."
end
if test "$__spt_errors" -eq 0
if test "$trapped_error" = false
pass
exit 0
else
fail
exit 1
end
else
fail
exit 1
end
delete_testing_global
end
trap spt_cleanup EXIT
# -----------------------------------------------------------------------
# Test all spack commands with special env support
# -----------------------------------------------------------------------
title 'Testing `spack`'
spt_contains 'usage: spack ' spack
spt_contains "usage: spack " spack -h
spt_contains "usage: spack " spack help
spt_contains "usage: spack " spack -H
spt_contains "usage: spack " spack help --all
title 'Testing `spack cd`'
spt_contains "usage: spack cd " spack cd -h
spt_contains "usage: spack cd " spack cd --help
spt_contains "cd $b_install" spack cd -i b
title 'Testing `spack module`'
spt_contains "usage: spack module " spack -m module -h
spt_contains "usage: spack module " spack -m module --help
spt_contains "usage: spack module " spack -m module
title 'Testing `spack load`'
set _b_loc (spack -m location -i b)
set _b_ld $_b_loc"/lib"
set _a_loc (spack -m location -i a)
set _a_ld $_a_loc"/lib"
spt_contains "set -gx LD_LIBRARY_PATH $_b_ld" spack -m load --only package --fish b
spt_succeeds spack -m load b
# test a variable MacOS clears and one it doesn't for recursive loads
spt_contains "set -gx LD_LIBRARY_PATH $_a_ld:$_b_ld" spack -m load --fish a
spt_contains "set -gx LIBRARY_PATH $_a_ld:$_b_ld" spack -m load --fish a
spt_succeeds spack -m load --only dependencies a
spt_succeeds spack -m load --only package a
spt_fails spack -m load d
spt_contains "usage: spack load " spack -m load -h
spt_contains "usage: spack load " spack -m load -h d
spt_contains "usage: spack load " spack -m load --help
title 'Testing `spack unload`'
spack -m load b a # setup
# spt_contains "module unload $b_module" spack -m unload b
spt_succeeds spack -m unload b
spt_succeeds spack -m unload --all
spack -m unload --all # cleanup
spt_fails spack -m unload -l
# spt_contains "module unload -l --arg $b_module" spack -m unload -l --arg b
spt_fails spack -m unload d
spt_contains "usage: spack unload " spack -m unload -h
spt_contains "usage: spack unload " spack -m unload -h d
spt_contains "usage: spack unload " spack -m unload --help
title 'Testing `spack env`'
spt_contains "usage: spack env " spack env -h
spt_contains "usage: spack env " spack env --help
title 'Testing `spack env list`'
spt_contains " spack env list " spack env list -h
spt_contains " spack env list " spack env list --help
title 'Testing `spack env activate`'
spt_contains "No such environment:" spack env activate no_such_environment
spt_contains "usage: spack env activate " spack env activate
spt_contains "usage: spack env activate " spack env activate -h
spt_contains "usage: spack env activate " spack env activate --help
title 'Testing `spack env deactivate`'
spt_contains "Error: No environment is currently active" spack env deactivate
spt_contains "usage: spack env deactivate " spack env deactivate no_such_environment
spt_contains "usage: spack env deactivate " spack env deactivate -h
spt_contains "usage: spack env deactivate " spack env deactivate --help
title 'Testing activate and deactivate together'
echo "Testing 'spack env activate spack_test_env'"
spack env activate spack_test_env
is_set SPACK_ENV
echo "Testing 'spack env deactivate'"
spack env deactivate
is_not_set SPACK_ENV
echo "Testing 'spack env activate spack_test_env'"
spack env activate spack_test_env
is_set SPACK_ENV
echo "Testing 'despacktivate'"
despacktivate
is_not_set SPACK_ENV
#
# NOTE: `--prompt` on fish does nothing => currently not implemented.
#
# echo "Testing 'spack env activate --prompt spack_test_env'"
# spack env activate --prompt spack_test_env
# is_set SPACK_ENV
# is_set SPACK_OLD_PS1
#
# echo "Testing 'despacktivate'"
# despacktivate
# is_not_set SPACK_ENV
# is_not_set SPACK_OLD_PS1

723
share/spack/setup-env.fish Executable file
View File

@@ -0,0 +1,723 @@
# 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)
#################################################################################
#
# This file is part of Spack and sets up the spack environment for the friendly
# interactive shell (fish). This includes module support, and it also puts spack
# in your path. The script also checks that at least module support exists, and
# provides suggestions if it doesn't. Source it like this:
#
# source /path/to/spack/share/spack/setup-env.fish
#
#################################################################################
# This is a wrapper around the spack command that forwards calls to 'spack load'
# and 'spack unload' to shell functions. This in turn allows them to be used to
# invoke environment modules functions.
#
# 'spack load' is smarter than just 'load' because it converts its arguments into
# a unique spack spec that is then passed to module commands. This allows the
# user to load packages without knowing all their installation details.
#
# e.g., rather than requiring a full spec for libelf, the user can type:
#
# spack load libelf
#
# This will first find the available libelf modules and load a matching one. If
# there are two versions of libelf, the user would need to be more specific,
# e.g.:
#
# spack load libelf@0.8.13
#
# This is very similar to how regular spack commands work and it avoids the need
# to come up with a user-friendly naming scheme for spack dotfiles.
#################################################################################
#
# Test for STDERR-NOCARET feature: if this is off, fish will redirect stderr to
# a file named in the string after `^`
#
if status test-feature stderr-nocaret
else
echo "WARNING: you have not enabled the 'stderr-nocaret' feature."
echo "This means that you have to escape the caret (^) character when defining specs."
echo "Consider enabling stderr-nocaret: https://fishshell.com/docs/current/index.html#featureflags"
end
#
# SPACK wrapper function, preprocessing arguments and flags.
#
function spack -d "wrapper for the `spack` command"
#
# DEFINE SUPPORT FUNCTIONS HERE
#
#
# ALLOCATE_SP_SHARED, and DELETE_SP_SHARED allocate (and delete) temporary
# global variables
#
function allocate_sp_shared -d "allocate shared (global variables)"
set -gx __sp_remaining_args
set -gx __sp_subcommand_args
set -gx __sp_module_args
set -gx __sp_stat
set -gx __sp_stdout
set -gx __sp_stderr
end
function delete_sp_shared -d "deallocate shared (global variables)"
set -e __sp_remaining_args
set -e __sp_subcommand_args
set -e __sp_module_args
set -e __sp_stat
set -e __sp_stdout
set -e __sp_stderr
end
#
# STREAM_ARGS and SHIFT_ARGS: helper functions manipulating the `argv` array:
# -> STREAM_ARGS: echos the `argv` array element-by-element
# -> SHIFT_ARGS: echos the `argv` array element-by-element starting with the
# second element. If `argv` has only one element, echo the
# empty string `""`.
# NOTE: while `stream_args` is not strictly necessary, it adds a nice symmetry
# to `shift_args`
#
function stream_args -d "echos args as a stream"
# return the elements of `$argv` as an array
# -> since we want to be able to call it as part of `set x (shift_args
# $x)`, we return these one-at-a-time using echo... this means that the
# sub-command stream will correctly concatenate the output into an array
for elt in $argv
echo $elt
end
end
function shift_args -d "simulates bash shift"
#
# Returns argv[2..-1] (as an array)
# -> if argv has only 1 element, then returns the empty string. This
# simulates the behavior of bash `shift`
#
if test -z "$argv[2]"
# there are no more element, returning the empty string
echo ""
else
# return the next elements `$argv[2..-1]` as an array
# -> since we want to be able to call it as part of `set x (shift_args
# $x)`, we return these one-at-a-time using echo... this means that
# the sub-command stream will correctly concatenate the output into
# an array
for elt in $argv[2..-1]
echo $elt
end
end
end
#
# CAPTURE_ALL: helper function used to capture stdout, stderr, and status
# -> CAPTURE_ALL: there is a bug in fish, that prevents stderr re-capture
# from nested command substitution:
# https://github.com/fish-shell/fish-shell/issues/6459
#
function capture_all
begin;
begin;
eval $argv[1]
set $argv[2] $status # read sets the `status` flag => capture here
end 2>| read -z __err
end 1>| read -z __out
# output arrays
set $argv[3] (echo $__out | string split \n)
set $argv[4] (echo $__err | string split \n)
return 0
end
#
# GET_SP_FLAGS, and GET_MOD_ARGS: support functions for extracting arguments and
# flags. Note bash's `shift` operation is simulated by the `__sp_remaining_args`
# array which is roughly equivalent to `$@` in bash.
#
function get_sp_flags -d "return leading flags"
#
# Accumulate initial flags for main spack command. NOTE: Sets the external
# array: `__sp_remaining_args` containing all unprocessed arguments.
#
# initialize argument counter
set -l i 1
# iterate over elements (`elt`) in `argv` array
for elt in $argv
# match element `elt` of `argv` array to check if it has a leading dash
if echo $elt | string match -r -q "^-"
# by echoing the current `elt`, the calling stream accumulates list
# of valid flags. NOTE that this can also be done by adding to an
# array, but fish functions can only return integers, so this is the
# most elegant solution.
echo $elt
else
# bash compatibility: stop when the match first fails. Upon failure,
# we pack the remainder of `argv` into a global `__sp_remaining_args`
# array (`i` tracks the index of the next element).
set __sp_remaining_args (stream_args $argv[$i..-1])
return
end
# increment argument counter: used in place of bash's `shift` command
set -l i (math $i+1)
end
# if all elements in `argv` are matched, make sure that `__sp_remaining_args`
# is deleted (this might be overkill...).
set -e __sp_remaining_args
end
#
# CHECK_SP_FLAGS, CONTAINS_HELP_FLAGS, CHECK_ENV_ACTIVATE_FLAGS, and
# CHECK_ENV_DEACTIVATE_FLAGS: support functions for checking arguments and flags.
#
function check_sp_flags -d "check spack flags for h/V flags"
#
# Check if inputs contain h or V flags.
#
# combine argument array into single string (space seperated), to be passed
# to regular expression matching (`string match -r`)
set -l _a "$argv"
# skip if called with blank input. Notes: [1] (cf. EOF)
if test -n "$_a"
if echo $_a | string match -r -q ".*h.*"
return 0
end
if echo $_a | string match -r -q ".*V.*"
return 0
end
end
return 1
end
function check_env_activate_flags -d "check spack env subcommand flags for -h, --sh, --csh, or --fish"
#
# Check if inputs contain -h, --sh, --csh, or --fish
#
# combine argument array into single string (space seperated), to be passed
# to regular expression matching (`string match -r`)
set -l _a "$argv"
# skip if called with blank input. Notes: [1] (cf. EOF)
if test -n "$_a"
# looks for a single `-h` (possibly surrounded by spaces)
if echo $_a | string match -r -q " *-h *"
return 0
end
# looks for a single `--sh` (possibly surrounded by spaces)
if echo $_a | string match -r -q " *--sh *"
return 0
end
# looks for a single `--csh` (possibly surrounded by spaces)
if echo $_a | string match -r -q " *--csh *"
return 0
end
# looks for a single `--fish` (possibly surrounded by spaces)
if echo $_a | string match -r -q " *--fish *"
return 0
end
end
return 1
end
function check_env_deactivate_flags -d "check spack env subcommand flags for --sh, --csh, or --fish"
#
# Check if inputs contain -h, --sh, --csh, or --fish
#
# combine argument array into single string (space seperated), to be passed
# to regular expression matching (`string match -r`)
set -l _a "$argv"
# skip if called with blank input. Notes: [1] (cf. EOF)
if test -n "$_a"
# TODO: should this crash (we're clearly using fish, not bash, here)?
# looks for a single `--sh` (possibly surrounded by spaces)
if echo $_a | string match -r -q " *--sh *"
return 0
end
# TODO: should this crash (we're clearly using fish, not csh, here)?
# looks for a single `--csh` (possibly surrounded by spaces)
if echo $_a | string match -r -q " *--csh *"
return 0
end
# looks for a single `--fish` (possibly surrounded by spaces)
if echo $_a | string match -r -q " *--fish *"
return 0
end
end
return 1
end
#
# SPACK RUNNER function, this does all the work!
#
function spack_runner -d "Runner function for the `spack` wrapper"
#
# Accumulate initial flags for main spack command
#
set __sp_remaining_args # remaining (unparsed) arguments
set -l sp_flags (get_sp_flags $argv) # sets __sp_remaining_args
#
# h and V flags don't require further output parsing.
#
if check_sp_flags $sp_flags
command spack $sp_flags $__sp_remaining_args
return 0
end
#
# Isolate subcommand and subcommand specs. Notes: [1] (cf. EOF)
#
set -l sp_subcommand ""
if test -n "$__sp_remaining_args[1]"
set sp_subcommand $__sp_remaining_args[1]
set __sp_remaining_args (shift_args $__sp_remaining_args) # simulates bash shift
end
set -l sp_spec $__sp_remaining_args
#
# Filter out cd, env, and load and unload. For any other commands, just run
# the spack command as is.
#
switch $sp_subcommand
# CASE: spack subcommand is `cd`: if the sub command arg is `-h`, nothing
# further needs to be done. Otherwise, test the location referring the
# subcommand and cd there (if it exists).
case "cd"
set -l sp_arg ""
# Extract the first subcommand argument. Notes: [1] (cf. EOF)
if test -n "$__sp_remaining_args[1]"
set sp_arg $__sp_remaining_args[1]
set __sp_remaining_args (shift_args $__sp_remaining_args) # simulates bash shift
end
# Notes: [2] (cf. EOF)
if test "x$sp_arg" = "x-h"; or test "x$sp_arg" = "x--help"
# nothing more needs to be done for `-h` or `--help`
command spack cd -h
else
# extract location using the subcommand (fish `(...)`)
set -l LOC (command spack location $sp_arg $__sp_remaining_args)
# test location and cd if exists:
if test -d "$LOC"
cd $LOC
else
return 1
end
end
return 0
# CASE: spack subcommand is `env`. Here we get the spack runtime to
# supply the appropriate shell commands for setting the environment
# varibles. These commands are then run by fish (using the `capture_all`
# function, instead of a command substitution).
case "env"
set -l sp_arg ""
# Extract the first subcommand argument. Notes: [1] (cf. EOF)
if test -n "$__sp_remaining_args[1]"
set sp_arg $__sp_remaining_args[1]
set __sp_remaining_args (shift_args $__sp_remaining_args) # simulates bash shift
end
# Notes: [2] (cf. EOF)
if test "x$sp_arg" = "x-h"; or test "x$sp_arg" = "x--help"
# nothing more needs to be done for `-h` or `--help`
command spack env -h
else
switch $sp_arg
case "activate"
set -l _a (stream_args $__sp_remaining_args)
if check_env_activate_flags $_a
# no args or args contain -h/--help, --sh, or --csh: just execute
command spack env activate $_a
else
# actual call to activate: source the output
set -l sp_env_cmd "command spack $sp_flags env activate --fish $__sp_remaining_args"
capture_all $sp_env_cmd __sp_stat __sp_stdout __sp_stderr
eval $__sp_stdout
if test -n "$__sp_stderr"
echo -s \n$__sp_stderr 1>&2 # current fish bug: handle stderr manually
end
end
case "deactivate"
set -l _a (stream_args $__sp_remaining_args)
if check_env_deactivate_flags $_a
# just execute the command if --sh, --csh, or --fish are provided
command spack env deactivate $_a
# Test of further (unparsed arguments). Any other
# arguments are an error or help, so just run help
# -> TODO: This should throw and error but leave as is
# for compatibility with setup-env.sh
# -> Notes: [1] (cf. EOF).
else if test -n "$__sp_remaining_args"
command spack env deactivate -h
else
# no args: source the output of the command
set -l sp_env_cmd "command spack $sp_flags env deactivate --fish"
capture_all $sp_env_cmd __sp_stat __sp_stdout __sp_stderr
eval $__sp_stdout
if test $__sp_stat -ne 0
if test -n "$__sp_stderr"
echo -s \n$__sp_stderr 1>&2 # current fish bug: handle stderr manually
end
return 1
end
end
case "*"
# if $__sp_remaining_args is empty, then don't include it
# as argument (otherwise it will be confused as a blank
# string input!)
if test -n "$__sp_remaining_args"
command spack env $sp_arg $__sp_remaining_args
else
command spack env $sp_arg
end
end
end
# CASE: spack subcommand is either `load`, or `unload`. These statements
# deal with the technical details of actually using modules. Especially
# to deal with the substituting latest version numbers to the module
# command.
case "load" or "unload"
set -l _a (stream_args $__sp_remaining_args)
if check_env_activate_flags $_a
# no args or args contain -h/--help, --sh, or --csh: just execute
command spack $sp_flags $sp_subcommand $__sp_remaining_args
else
# actual call to activate: source the output
set -l sp_env_cmd "command spack $sp_flags $sp_subcommand --fish $__sp_remaining_args"
capture_all $sp_env_cmd __sp_stat __sp_stdout __sp_stderr
eval $__sp_stdout
if test $__sp_stat -ne 0
if test -n "$__sp_stderr"
echo -s \n$__sp_stderr 1>&2 # current fish bug: handle stderr manually
end
return 1
end
end
# CASE: Catch-all
case "*"
command spack $argv
end
return 0
end
#
# RUN SPACK_RUNNER HERE
#
#
# Allocate temporary global variables used for return extra arguments from
# functions. NOTE: remember to call delete_sp_shared whenever returning from
# this function.
#
allocate_sp_shared
#
# Run spack command using the spack_runner.
#
spack_runner $argv
# Capture state of spack_runner (returned below)
set -l stat $status
#
# Delete temprary global variabels allocated in `allocated_sp_shared`.
#
delete_sp_shared
return $stat
end
#################################################################################
# Prepends directories to path, if they exist.
# pathadd /path/to/dir # add to PATH
# or pathadd OTHERPATH /path/to/dir # add to OTHERPATH
#################################################################################
function spack_pathadd -d "Add path to specified variable (defaults to PATH)"
#
# Adds (existing only) paths to specified (defaults to PATH)
# variable. Does not warn attempting to add non-existing path. This is not a
# bug because the MODULEPATH setup tries add all possible compatible systems
# and therefore sp_multi_pathadd relies on this function failing silently.
#
# If no variable name is supplied, just append to PATH otherwise append to
# that variable.
# -> Notes: [1] (cf. EOF).
if test -n "$argv[2]"
set pa_varname $argv[1]
set pa_new_path $argv[2]
else
true # this is a bit of a strange hack! Notes: [3] (cf EOF).
set pa_varname PATH
set pa_new_path $argv[1]
end
set pa_oldvalue $$pa_varname
# skip path is not existing directory
# -> Notes: [1] (cf. EOF).
if test -d "$pa_new_path"
# combine argument array into single string (space seperated), to be
# passed to regular expression matching (`string match -r`)
set -l _a "$pa_oldvalue"
# skip path if it is already contained in the variable
# note spaces in regular expression: we're matching to a space delimited
# list of paths
if not echo $_a | string match -q -r " *$pa_new_path *"
if test -n "$pa_oldvalue"
set $pa_varname $pa_new_path $pa_oldvalue
else
true # this is a bit of a strange hack! Notes: [3] (cf. EOF)
set $pa_varname $pa_new_path
end
end
end
end
function sp_multi_pathadd -d "Helper for adding module-style paths by incorporating compatible systems into pathadd" --inherit-variable _sp_compatible_sys_types
#
# Calls spack_pathadd in path inputs, adding all compatible system types
# (sourced from $_sp_compatible_sys_types) to input paths.
#
for pth in $argv[2]
for systype in $_sp_compatible_sys_types
spack_pathadd $argv[1] "$pth/$systype"
end
end
end
#
# Figure out where this file is. Below code only needs to work in fish
#
set -l sp_source_file (status -f) # name of current file
#
# Find root directory and add bin to path.
#
set -l sp_share_dir (realpath (dirname $sp_source_file))
set -l sp_prefix (realpath (dirname (dirname $sp_share_dir)))
spack_pathadd PATH "$sp_prefix/bin"
set -xg SPACK_ROOT $sp_prefix
#
# No need to determine which shell is being used (obviously it's fish)
#
set -xg SPACK_SHELL "fish"
set -xg _sp_shell "fish"
#
# Check whether we need environment-variables (module) <= `use` is not available
#
set -l need_module "no"
if not functions -q use; and not functions -q module
set need_module "yes"
end
#
# Make environment-modules available to shell
#
function sp_apply_shell_vars -d "applies expressions of the type `a='b'` as `set a b`"
# convert `a='b' to array variable `a b`
set -l expr_token (string trim -c "'" (string split "=" $argv))
# run set command to takes, converting lists of type `a:b:c` to array
# variables `a b c` by splitting around the `:` character
set -xg $expr_token[1] (string split ":" $expr_token[2])
end
if test "$need_module" = "yes"
set -l sp_shell_vars (command spack --print-shell-vars sh,modules)
for sp_var_expr in $sp_shell_vars
sp_apply_shell_vars $sp_var_expr
end
# _sp_module_prefix is set by spack --print-sh-vars
if test "$_sp_module_prefix" != "not_installed"
set -xg MODULE_PREFIX $_sp_module_prefix
spack_pathadd PATH "$MODULE_PREFIX/bin"
end
else
set -l sp_shell_vars (command spack --print-shell-vars sh)
for sp_var_expr in $sp_shell_vars
sp_apply_shell_vars $sp_var_expr
end
end
if test "$need_module" = "yes"
function module -d "wrapper for the `module` command to point at Spack's modules instance" --inherit-variable MODULE_PREFIX
eval $MODULE_PREFIX/bin/modulecmd $SPACK_SHELL $argv
end
end
#
# set module system roots
#
# Search of MODULESPATHS by trying all possible compatible system types as
# module roots.
if test -z "$MODULEPATH"
set -gx MODULEPATH
end
sp_multi_pathadd MODULEPATH $_sp_tcl_roots
#
# NOTES
#
# [1]: `test -n` requires exactly 1 argument. If `argv` is undefined, or if it
# is an array, `test -n $argv` is unpredictable. Instead, encapsulate
# `argv` in a string, and test the string.
#
# [2]: `test "$a" = "$b$` is dangerous if `a` and `b` contain flags at index 1,
# as `test $a` can be interpreted as `test $a[1] $a[2..-1]`. Solution is to
# prepend a non-flag character, eg: `test "x$a" = "x$b"`.
#
# [3]: When the test in the if statement fails, the `status` flag is set to 1.
# `true` here manuallt resets the value of `status` to 0. Since `set`
# passes `status` along, we thus avoid the function returning 1 by mistake.

58
share/spack/spack-completion.bash
View File

@@ -320,7 +320,7 @@ _spack() {
then
SPACK_COMPREPLY="-h --help -H --all-help --color -C --config-scope -d --debug --timestamp --pdb -e --env -D --env-dir -E --no-env --use-env-repo -k --insecure -l --enable-locks -L --disable-locks -m --mock -p --profile --sorted-profile --lines -v --verbose --stacktrace -V --version --print-shell-vars"
else
SPACK_COMPREPLY="activate add arch blame build build-env buildcache cd checksum ci clean clone commands compiler compilers concretize config configure containerize create deactivate debug dependencies dependents deprecate dev-build diy docs edit env extensions external fetch find flake8 gc gpg graph help info install license list load location log-parse maintainers mirror module patch pkg providers pydoc python reindex remove rm repo resource restage setup spec stage test uninstall unload upload-s3 url verify versions view"
SPACK_COMPREPLY="activate add arch blame build-env buildcache cd checksum ci clean clone commands compiler compilers concretize config containerize create deactivate debug dependencies dependents deprecate dev-build docs edit env extensions external fetch find flake8 gc gpg graph help info install license list load location log-parse maintainers mirror module patch pkg providers pydoc python reindex remove rm repo resource restage setup spec stage test uninstall unload url verify versions view"
fi
}
@@ -355,15 +355,6 @@ _spack_blame() {
fi
}
_spack_build() {
if $list_options
then
SPACK_COMPREPLY="-h --help -v --verbose"
else
_all_packages
fi
}
_spack_build_env() {
if $list_options
then
@@ -385,7 +376,7 @@ _spack_buildcache() {
_spack_buildcache_create() {
if $list_options
then
SPACK_COMPREPLY="-h --help -r --rel -f --force -u --unsigned -a --allow-root -k --key -d --directory -m --mirror-name --mirror-url --no-rebuild-index -y --spec-yaml --only"
SPACK_COMPREPLY="-h --help -r --rel -f --force -u --unsigned -a --allow-root -k --key -d --directory -m --mirror-name --mirror-url --rebuild-index -y --spec-yaml --only"
else
_all_packages
fi
@@ -403,7 +394,7 @@ _spack_buildcache_install() {
_spack_buildcache_list() {
if $list_options
then
SPACK_COMPREPLY="-h --help -l --long -L --very-long -v --variants -f --force -a --allarch"
SPACK_COMPREPLY="-h --help -l --long -L --very-long -v --variants -a --allarch"
else
_all_packages
fi
@@ -641,15 +632,6 @@ _spack_config_rm() {
fi
}
_spack_configure() {
if $list_options
then
SPACK_COMPREPLY="-h --help -v --verbose"
else
_all_packages
fi
}
_spack_containerize() {
SPACK_COMPREPLY="-h --help"
}
@@ -725,15 +707,6 @@ _spack_dev_build() {
fi
}
_spack_diy() {
if $list_options
then
SPACK_COMPREPLY="-h --help -j --jobs -d --source-path -i --ignore-dependencies -n --no-checksum --keep-prefix --skip-patch -q --quiet --drop-in -b --before -u --until --clean --dirty"
else
_all_packages
fi
}
_spack_docs() {
SPACK_COMPREPLY="-h --help"
}
@@ -759,14 +732,14 @@ _spack_env() {
_spack_env_activate() {
if $list_options
then
SPACK_COMPREPLY="-h --help --sh --csh -v --with-view -V --without-view -d --dir -p --prompt"
SPACK_COMPREPLY="-h --help --sh --csh --fish -v --with-view -V --without-view -d --dir -p --prompt"
else
_environments
fi
}
_spack_env_deactivate() {
SPACK_COMPREPLY="-h --help --sh --csh"
SPACK_COMPREPLY="-h --help --sh --csh --fish"
}
_spack_env_create() {
@@ -1024,7 +997,7 @@ _spack_list() {
_spack_load() {
if $list_options
then
SPACK_COMPREPLY="-h --help -r --dependencies --sh --csh --first --only"
SPACK_COMPREPLY="-h --help -r --dependencies --sh --csh --fish --first --only"
else
_installed_packages
fi
@@ -1472,29 +1445,12 @@ _spack_uninstall() {
_spack_unload() {
if $list_options
then
SPACK_COMPREPLY="-h --help --sh --csh -a --all"
SPACK_COMPREPLY="-h --help --sh --csh --fish -a --all"
else
_installed_packages
fi
}
_spack_upload_s3() {
if $list_options
then
SPACK_COMPREPLY="-h --help"
else
SPACK_COMPREPLY="spec index"
fi
}
_spack_upload_s3_spec() {
SPACK_COMPREPLY="-h --help -s --spec -y --spec-yaml -b --base-dir -e --endpoint-url"
}
_spack_upload_s3_index() {
SPACK_COMPREPLY="-h --help -e --endpoint-url"
}
_spack_url() {
if $list_options
then

2
share/spack/templates/container/Dockerfile
View File

@@ -7,7 +7,7 @@ RUN mkdir {{ paths.environment }} \
{{ manifest }} > {{ paths.environment }}/spack.yaml
# Install the software, remove unecessary deps
RUN cd {{ paths.environment }} && spack install && spack gc -y
RUN cd {{ paths.environment }} && spack env activate . && spack install && spack gc -y
{% if strip %}
# Strip all the binaries

4
share/spack/templates/container/singularity.def
View File

@@ -11,8 +11,10 @@ EOF
# Install all the required software
. /opt/spack/share/spack/setup-env.sh
spack env activate .
spack install
spack gc -y
spack env deactivate
spack env activate --sh -d . >> {{ paths.environment }}/environment_modifications.sh
{% if strip %}
@@ -87,4 +89,4 @@ Stage: final
{% for label, value in labels.items() %}
{{ label }} {{ value }}
{% endfor %}
{% endif %}
{% endif %}

8
var/spack/repos/builtin/packages/catch2/package.py
View File

@@ -12,8 +12,14 @@ class Catch2(CMakePackage):
homepage = "https://github.com/catchorg/Catch2"
url = "https://github.com/catchorg/Catch2/archive/v2.9.1.tar.gz"
maintainers = ['ax3l']
git = "https://github.com/catchorg/Catch2.git"
maintainers = ["ax3l", "AndrewGaspar"]
# In-Development
version('master', branch='master')
# Releases
version('2.12.3', sha256='78425e7055cea5bad1ff8db7ea0d6dfc0722ece156be1ccf3597c15e674e6943')
version('2.12.1', sha256='e5635c082282ea518a8dd7ee89796c8026af8ea9068cd7402fb1615deacd91c3')
version('2.12.0', sha256='6606b754363d3a4521bfecf717dc1972c50dca282bd428dfb1370ec8b9c26918')
version('2.11.3', sha256='9a6967138062688f04374698fce4ce65908f907d8c0fe5dfe8dc33126bd46543')

10
var/spack/repos/builtin/packages/cleverleaf/fujitsu_add_link_flags.patch Normal file
View File

@@ -0,0 +1,10 @@
--- spack-src/CMakeLists.txt.org 2020-06-29 14:38:00.737544597 +0900
+++ spack-src/CMakeLists.txt 2020-06-29 14:40:33.758297327 +0900
@@ -24,6 +24,6 @@
add_definitions(-DVERSION="git" -DHOST_NAME="cab")
-set(CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS "")
+set(CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS "--linkfortran")
add_subdirectory (src)

4
var/spack/repos/builtin/packages/cleverleaf/package.py
View File

@@ -24,6 +24,10 @@ class Cleverleaf(CMakePackage):
depends_on('boost')
depends_on('cmake@3.1:', type='build')
# The Fujitsu compiler requires the '--linkfortran'
# option to combine C++ and Fortran programs.
patch('fujitsu_add_link_flags.patch', when='%fj')
def flag_handler(self, name, flags):
if self.spec.satisfies('%intel') and name in ['cppflags', 'cxxflags']:
flags.append(self.compiler.cxx11_flag)

1
var/spack/repos/builtin/packages/cmake/package.py
View File

@@ -18,6 +18,7 @@ class Cmake(Package):
executables = ['cmake']
version('3.17.3', sha256='0bd60d512275dc9f6ef2a2865426a184642ceb3761794e6b65bff233b91d8c40')
version('3.17.1', sha256='3aa9114485da39cbd9665a0bfe986894a282d5f0882b1dea960a739496620727')
version('3.17.0', sha256='b74c05b55115eacc4fa2b77a814981dbda05cdc95a53e279fe16b7b272f00847')
version('3.16.5', sha256='5f760b50b8ecc9c0c37135fae5fbf00a2fef617059aa9d61c1bb91653e5a8bfc')

4
var/spack/repos/builtin/packages/codar-cheetah/package.py
View File

@@ -14,10 +14,12 @@ class CodarCheetah(PythonPackage):
maintainers = ['kshitij-v-mehta']
homepage = "https://github.com/CODARcode/cheetah"
url = "https://github.com/CODARcode/cheetah/archive/v0.1.tar.gz"
url = "https://github.com/CODARcode/cheetah/archive/v1.1.0.tar.gz"
git = "https://github.com/CODARcode/cheetah.git"
version('develop', branch='dev')
version('1.1.0', sha256='519a47e4fc5b124b443839fde10b8b72120ab768398628df43e0b570a266434c')
version('1.0.0', sha256='1f935fbc1475a654f3b6d2140d8b2a6079a65c8701655e544ba1fab3a7c1bc19')
version('0.5', sha256='f37a554741eff4bb8407a68f799dd042dfc4df525e84896cad70fccbd6aca6ee')
depends_on('python@3.5:', type=('build', 'run'))

51
var/spack/repos/builtin/packages/coin3d/package.py Normal file
View File

@@ -0,0 +1,51 @@
# 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 Coin3d(AutotoolsPackage):
"""Coin is an OpenGL-based, 3D graphics library that has its roots in the
Open Inventor 2.1 API, which Coin still is compatible with."""
homepage = "https://github.com/coin3d/coin"
url = "https://github.com/coin3d/coin/archive/Coin-4.0.0.tar.gz"
version('3.1.0', sha256='70dd5ef39406e1d9e05eeadd54a5b51884a143e127530876a97744ca54173dc3')
version('3.0.0', sha256='d5c2eb0ecaa5c83d93daf0e9e275e58a6a8dfadc74c873d51b0c939011f81bfa')
version('2.0.0', sha256='6d26435aa962d085b7accd306a0b478069a7de1bc5ca24e22344971852dd097c')
depends_on('boost@1.45.0:', type='build')
depends_on('doxygen', when='+html', type='build')
depends_on('perl', when='+html', type='build')
depends_on('openglu', type='link')
depends_on('opengl', type='link')
depends_on('libsm', type='link')
depends_on('libxext', type='link')
depends_on('libice', type='link')
depends_on('libuuid', type='link')
depends_on('libxcb', type='link')
depends_on('libxau', type='link')
variant('html', default=False, description='Build and install Coin HTML documentation')
variant('man', default=False, description='Build and install Coin man pages')
variant('framework', default=False, description="Do 'UNIX-style' installation on Mac OS X")
variant('shared', default=True, description='Build shared library (off: build static library)')
variant('debug', default=False, description='Make debug build')
variant('symbols', default=False, description='Enable debug symbols')
def configure_args(self):
args = []
args += self.enable_or_disable('framework')
args += self.enable_or_disable('shared')
args += self.enable_or_disable('html')
args += self.enable_or_disable('man')
args += self.enable_or_disable('symbols')
args += self.enable_or_disable('debug')
args.append("--with-boost=" + self.spec['boost'].prefix)
args.append("--with-boost-libdir=" + self.spec['boost'].prefix.lib)
return args

2
var/spack/repos/builtin/packages/cp2k/package.py
View File

@@ -68,7 +68,7 @@ class Cp2k(MakefilePackage, CudaPackage):
variant('lmax',
description='Maximum supported angular momentum (HFX and others)',
default='5',
values=list(HFX_LMAX_RANGE),
values=map(str, HFX_LMAX_RANGE),
multi=False)
depends_on('python', type='build')

2
var/spack/repos/builtin/packages/cuda/package.py
View File

@@ -77,6 +77,7 @@ class Cuda(Package):
depends_on('libxml2', when='@10.1.243:')
def setup_build_environment(self, env):
env.set('CUDAHOSTCXX', self.compiler.cxx)
if self.spec.satisfies('@10.1.243:'):
libxml2_home = self.spec['libxml2'].prefix
env.set('LIBXML2HOME', libxml2_home)
@@ -84,6 +85,7 @@ def setup_build_environment(self, env):
def setup_run_environment(self, env):
env.set('CUDA_HOME', self.prefix)
env.set('CUDAHOSTCXX', self.compiler.cxx)
def install(self, spec, prefix):
if os.path.exists('/tmp/cuda-installer.log'):

32
var/spack/repos/builtin/packages/dssp/package.py Normal file
View File

@@ -0,0 +1,32 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Dssp(AutotoolsPackage):
"""'mkdssp' utility. (dictionary of protein secondary structure)"""
homepage = "https://github.com/cmbi/dssp"
url = "https://github.com/cmbi/dssp/archive/3.1.4.tar.gz"
version('3.1.4', sha256='496282b4b5defc55d111190ab9f1b615a9574a2f090e7cf5444521c747b272d4')
version('2.3.0', sha256='4c95976d86dc64949cb0807fbd58c7bee5393df0001999405863dc90f05846c6')
depends_on('autoconf', type='build')
depends_on('automake', type='build')
depends_on('libtool', type='build')
depends_on('m4', type='build')
depends_on('boost@1.48:')
def configure_args(self):
args = [
"--with-boost=%s" % self.spec['boost'].prefix]
return args
@run_after('configure')
def edit(self):
makefile = FileFilter(join_path(self.stage.source_path, 'Makefile'))
makefile.filter('.*-Werror .*', ' -Wno-error \\')

10
var/spack/repos/builtin/packages/fastjet/package.py
View File

@@ -47,3 +47,13 @@ class Fastjet(AutotoolsPackage):
version('2.3.1', sha256='16c32b420e1aa7d0b6fecddd980ea0f2b7e3c2c66585e06f0eb3142677ab6ccf')
version('2.3.0', sha256='e452fe4a9716627bcdb726cfb0917f46a7ac31f6006330a6ccc1abc43d9c2d53')
# older version use .tar instead of .tar.gz extension, to be added
variant('shared', default=True, description='Builds a shared version of the library')
variant('auto-ptr', default=False, description='Use auto_ptr')
def configure_args(self):
extra_args = ["--enable-allplugins"]
extra_args += self.enable_or_disable('shared')
extra_args += self.enable_or_disable('auto-ptr')
return extra_args

10
var/spack/repos/builtin/packages/ffb/fj_compiler.patch
View File

@@ -1,10 +0,0 @@
--- FFB8.org/util/xvx2gf/XVX.h 2013-03-26 10:09:49.000000000 +0900
+++ FFB8.new/util/xvx2gf/XVX.h 2020-06-16 16:00:06.408500236 +0900
@@ -5,6 +5,7 @@
#include <algorithm>
#include <cassert>
#include <vector>
+#include <stdint.h>
#define MAX_LEVEL 32

60
var/spack/repos/builtin/packages/ffb/fortran-format.patch Normal file
View File

@@ -0,0 +1,60 @@
diff --git a/util/convert/gfmavs.f b/util/convert/gfmavs.f
index debe3ec..34e6f66 100644
--- a/util/convert/gfmavs.f
+++ b/util/convert/gfmavs.f
@@ -422,7 +422,7 @@ C
C
WRITE(IUT6,*) 'GFMAVS: OUTPUTING GRID COORDINATES...'
DO 1100 IP = 1,NP
- WRITE(IUTAVS,'(I8,P3E13.5)') IP,X(IP),Y(IP),Z(IP)
+ WRITE(IUTAVS,'(I8,1P3E13.5)') IP,X(IP),Y(IP),Z(IP)
1100 CONTINUE
C
WRITE(IUT6,*) 'GFMAVS: OUTPUTING ELEMENT DATA...'
@@ -448,7 +448,7 @@ C
C
WRITE(IUT6,*) 'GFMAVS: OUTPUTING VARIABLES DATA...'
DO 1400 IP = 1,NP
- WRITE(IUTAVS,'(I8,P4E13.5)')
+ WRITE(IUTAVS,'(I8,1P4E13.5)')
* IP,U(IP),V(IP),W(IP),P(IP)
1400 CONTINUE
C
@@ -470,7 +470,7 @@ C
C
DO 2100 JB = 1,NPTMP
IP = LPBOUN(JB,ITYPE)
- WRITE(IUTAVS,'(I8,P3E13.5)')
+ WRITE(IUTAVS,'(I8,1P3E13.5)')
* IP,X(IP),Y(IP),Z(IP)
2100 CONTINUE
C
@@ -498,7 +498,7 @@ C
C
DO 2400 JB = 1,NPTMP
IP = LPBOUN(JB,ITYPE)
- WRITE(IUTAVS,'(I8,P7E13.5)')
+ WRITE(IUTAVS,'(I8,1P7E13.5)')
* IP,U(IP),V(IP),W(IP),P(IP),F(IP),T(IP),VIS(IP)
2400 CONTINUE
C
diff --git a/util/multi/partdx_rcap.f b/util/multi/partdx_rcap.f
index a0962b7..aab1876 100644
--- a/util/multi/partdx_rcap.f
+++ b/util/multi/partdx_rcap.f
@@ -448,11 +448,11 @@ C
C
CLOSE(IUTPT)
C
- 700 FORMAT(A,1X,I)
+ 700 FORMAT(A,1X,I8)
701 FORMAT(A,1X,A)
- 702 FORMAT(A,1X,I)
- 703 FORMAT(I,1X,A,1X,8(I,1X))
- 704 FORMAT(I,3(1X,F))
+ 702 FORMAT(A,1X,I8)
+ 703 FORMAT(I8,1X,A,1X,8(I8,1X))
+ 704 FORMAT(I8,3(1X,F13.5))
CC
CC 700 FORMAT(A,1X,I8)
CC 701 FORMAT(A,1X,A)

33
var/spack/repos/builtin/packages/ffb/gffv3tr.patch Normal file
View File

@@ -0,0 +1,33 @@
--- FFB8.org/util/tetra/gffv3tr.f 2013-03-26 10:10:51.000000000 +0900
+++ FFB8.new/util/tetra/gffv3tr.f 2020-06-23 10:32:13.673071588 +0900
@@ -832,7 +832,7 @@ C
LIST2(3)=LEBUF(5,IS2)
C
IMATCH=0
- CALL MATCH4(LIST1,LIST2,IMATCH)
+ CALL MATCH3(LIST1,LIST2,IMATCH)
IF(IMATCH.EQ.1)THEN
LEBUF(6,IS1)=0
LEBUF(6,IS2)=0
@@ -859,17 +859,17 @@ C
RETURN
END
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- SUBROUTINE MATCH4(LIST1,LIST2,IMATCH)
- INTEGER LIST1(4), LIST2(4)
+ SUBROUTINE MATCH3(LIST1,LIST2,IMATCH)
+ INTEGER LIST1(3), LIST2(3)
INTEGER IMATCH
C [INPUT] LIST1,LIST2 :VECTORS TO BE CHECK
C [OUTPUT] IMATCH :0 NOT MATCH ,1 MATCH
C
IMATCH = 0
C
- DO 100 I=1,4
+ DO 100 I=1,3
IBUF=1
- DO 200 J=1,4
+ DO 200 J=1,3
IBUF=IBUF*(LIST1(I)-LIST2(J))
200 CONTINUE
IF(IBUF.NE.0)RETURN

23
var/spack/repos/builtin/packages/ffb/package.py
View File

@@ -15,7 +15,10 @@ class Ffb(MakefilePackage):
version('8.1', sha256='1ad008c909152b6c27668bafbad820da3e6ec3309c7e858ddb785f0a3d6e43ae')
patch('revocap_refiner.patch')
patch('fj_compiler.patch', when='%fj')
patch('revocap_refiner-size_t.patch')
patch('fortran-format.patch')
patch('xvx.patch')
patch('gffv3tr.patch')
depends_on('mpi')
depends_on('blas')
@@ -79,7 +82,7 @@ def edit(self, spec, prefix):
m.write('#!/bin/csh -f\n')
m.write('setenv LES3DHOME {0}\n'.format(workdir))
m.write('cd {0}\n'.format(dd_mpi_dir))
m.write('make lib\n')
m.write('make lib FCOM={0}\n'.format(spec['mpi'].mpifc))
os.chmod(makeall, 0o755)
makeall = join_path('.', 'Makeall.les')
@@ -143,16 +146,16 @@ def edit(self, spec, prefix):
m.filter(r'LIBS = -lfort -lgf2 -ldd_mpi -lmpi_f77',
'LIBS = -lfort -lgf2 -ldd_mpi')
editfile = join_path('util', 'xvx2gf', 'FILES')
cxx_fortran_flags = []
if spec.satisfies('%gcc'):
editfile = join_path('util', 'xvx2gf', 'FILES')
m = FileFilter(editfile)
m.filter(r'LIBS = -lgf2 -lz -lifcore -limf -ldl',
'LIBS = -lgf2 -lz -ldl')
cxx_fortran_flags.append('-lgfortran')
elif spec.satisfies('%intel'):
cxx_fortran_flags.expand(['-lifcore', '-limf'])
elif spec.satisfies('%fj'):
editfile = join_path('util', 'xvx2gf', 'FILES')
m = FileFilter(editfile)
m.filter(r'LIBS = -lgf2 -lz -lifcore -limf -ldl',
'LIBS = -lgf2 -lz -ldl -linkfortran')
cxx_fortran_flags.append('--linkfortran')
m = FileFilter(editfile)
m.filter('-lifcore -limf', ' '.join(cxx_fortran_flags))
def build(self, spec, prefix):
for m in [join_path('make', 'Makeall'),

225
var/spack/repos/builtin/packages/ffb/revocap_refiner-size_t.patch Normal file
View File

@@ -0,0 +1,225 @@
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainer.h b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainer.h
index b5b8525..3e95332 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainer.h
+++ b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainer.h
@@ -38,6 +38,8 @@
namespace kmb{
+using std::size_t;
+
class Matrix4x4;
class Point3DContainer
diff --git a/spack-src/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Bucket.h b/spack-src/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Bucket.h
index cd1d5df..a2fff46 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Bucket.h
+++ b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Bucket.h
@@ -194,7 +194,7 @@
return itClone;
};
- size_t getCount(int i,int j,int k) const{
+ std::size_t getCount(int i,int j,int k) const{
return regions.count(getIndex(i,j,k));
};
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_BLArray.h b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_BLArray.h
index 4761262..b9a0c8c 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_BLArray.h
+++ b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_BLArray.h
@@ -30,6 +30,8 @@
namespace kmb{
+using std::size_t;
+
class BLArrayIndex;
class BLArrayBase
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Classification.h b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Classification.h
index 81b3b9f..51c06cc 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Classification.h
+++ b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Classification.h
@@ -39,6 +39,8 @@
namespace kmb{
+using std::size_t;
+
typedef int classificationType;
template<typename T>
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point2DContainer.h b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point2DContainer.h
index 0f7e548..39278e6 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point2DContainer.h
+++ b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point2DContainer.h
@@ -38,6 +38,8 @@
namespace kmb{
+using std::size_t;
+
class Point2DContainer
{
protected:
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerArray.h b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerArray.h
index c4c0dc9..8852677 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerArray.h
+++ b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerArray.h
@@ -17,6 +17,8 @@
namespace kmb{
+using std::size_t;
+
class Point3DContainerArray : public Point3DContainer
{
private:
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerMArray.h b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerMArray.h
index 51bb315..8bb557f 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerMArray.h
+++ b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerMArray.h
@@ -19,6 +19,8 @@
namespace kmb{
+using std::size_t;
+
class Point3DContainerMArray : public Point3DContainer
{
private:
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerVect.h b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerVect.h
index 1254a5c..57b1763 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerVect.h
+++ b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerVect.h
@@ -31,6 +31,8 @@
namespace kmb{
+using std::size_t;
+
class Point3DContainerVect : public Point3DContainer
{
private:
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DOctree.h b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DOctree.h
index 778e253..b743069 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DOctree.h
+++ b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DOctree.h
@@ -32,6 +32,8 @@
namespace kmb{
+using std::size_t;
+
class Point3DOctree
{
private:
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DOctree.cpp b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DOctree.cpp
index 6a8bb38..d29e6fa 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DOctree.cpp
+++ b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DOctree.cpp
@@ -85,10 +85,10 @@ kmb::Point3DOctree::getLocalCount(void) const
return count;
}
-size_t
+std::size_t
kmb::Point3DOctree::getCount(void) const
{
- size_t sum = 0;
+ std::size_t sum = 0;
if( children != NULL ){
for(int i=0;i<8;++i){
sum += children[i]->getCount();
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point2DContainerMap.cpp b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point2DContainerMap.cpp
index 6838486..2d4874c 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point2DContainerMap.cpp
+++ b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point2DContainerMap.cpp
@@ -33,6 +33,8 @@
#pragma warning(disable:4100)
#endif
+using std::size_t;
+
const char* kmb::Point2DContainerMap::CONTAINER_TYPE = "stl::map<id,Point2D*>";
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerArray.cpp b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerArray.cpp
index 02362fc..b9bf597 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerArray.cpp
+++ b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerArray.cpp
@@ -19,6 +19,8 @@
#pragma warning(disable:4100)
#endif
+using std::size_t;
+
const char* kmb::Point3DContainerArray::CONTAINER_TYPE = "double_array";
kmb::Point3DContainerArray::Point3DContainerArray(void)
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerMap.cpp b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerMap.cpp
index 9619325..24997b6 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerMap.cpp
+++ b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerMap.cpp
@@ -33,6 +33,7 @@
#pragma warning(disable:4100)
#endif
+using std::size_t;
const char* kmb::Point3DContainerMap::CONTAINER_TYPE = "stl::map<id,Point3D*>";
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerVect.cpp b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerVect.cpp
index 06add56..ec55033 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerVect.cpp
+++ b/lib/src/REVOCAP_Refiner-0.4.3/Geometry/kmb_Point3DContainerVect.cpp
@@ -32,6 +32,8 @@
#pragma warning(disable:4100)
#endif
+using std::size_t;
+
const char* kmb::Point3DContainerVect::CONTAINER_TYPE = "stl::vector<Point3D*>";
kmb::Point3DContainerVect::Point3DContainerVect(void)
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/MeshDB/kmbElementContainerNArray.h b/lib/src/REVOCAP_Refiner-0.4.3/MeshDB/kmbElementContainerNArray.h
index f3335d0..138aa5e 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/MeshDB/kmbElementContainerNArray.h
+++ b/lib/src/REVOCAP_Refiner-0.4.3/MeshDB/kmbElementContainerNArray.h
@@ -27,6 +27,8 @@
namespace kmb{
+using std::size_t;
+
class ElementContainerNArray : public ElementContainer
{
protected:
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/MeshDB/kmbNodeNeighborPtrInfo.h b/lib/src/REVOCAP_Refiner-0.4.3/MeshDB/kmbNodeNeighborPtrInfo.h
index 70cdc5e..6a7a4b7 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/MeshDB/kmbNodeNeighborPtrInfo.h
+++ b/lib/src/REVOCAP_Refiner-0.4.3/MeshDB/kmbNodeNeighborPtrInfo.h
@@ -24,6 +24,8 @@
namespace kmb{
+using std::size_t;
+
class Element;
class ElementContainer;
class MeshData;
diff --git a/lib/src/REVOCAP_Refiner-0.4.3/Shape/kmbFittingToSurface.h b/lib/src/REVOCAP_Refiner-0.4.3/Shape/kmbFittingToSurface.h
index 3a6d7dd..5910b77 100644
--- a/lib/src/REVOCAP_Refiner-0.4.3/Shape/kmbFittingToSurface.h
+++ b/lib/src/REVOCAP_Refiner-0.4.3/Shape/kmbFittingToSurface.h
@@ -19,6 +19,8 @@
namespace kmb{
+using std::size_t;
+
class MeshData;
class Surface3D;
template <typename> class Vector2WithIntBindings;

37
var/spack/repos/builtin/packages/ffb/xvx.patch Normal file
View File

@@ -0,0 +1,37 @@
--- FFB8.org/util/xvx2gf/XVX.h 2013-03-26 10:09:49.000000000 +0900
+++ FFB8.new/util/xvx2gf/XVX.h 2020-06-24 14:27:32.000000000 +0900
@@ -5,6 +5,7 @@
#include <algorithm>
#include <cassert>
#include <vector>
+#include <inttypes.h>
#define MAX_LEVEL 32
@@ -182,25 +183,7 @@ public:
void *_ptr;
unsigned char volptr[3];// <20>Ƃ肠<C682><E882A0><EFBFBD><EFBFBD><EFBFBD>ő<EFBFBD>256^3<>܂<EFBFBD> uint<6E>ɂ<EFBFBD><C982><EFBFBD>bitmask<73><6B><EFBFBD><EFBFBD><EFBFBD><EFBFBD>1024^3
- #if _WIN64 // _WIN32<33>Ə<EFBFBD><C68F>Ԃ<EFBFBD><D482>ς<EFBFBD><CF82><EFBFBD><EFBFBD>Ƃ<EFBFBD><C682><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>Ȃ<EFBFBD><C882>̂Œ<CC82><C592>Ӂi64<36>r<EFBFBD>b<EFBFBD>gWindows<77>‹<EFBFBD><C28B>ł́A_WIN32<33><32>_WIN64<36>̗<EFBFBD><CC97><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>`<60><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>j
- typedef unsigned long long int PtrAsInt;
- #elif _WIN32
- typedef unsigned int PtrAsInt;
- #elif __APPLE__
- #if x86_64
- typedef unsigned long long int PtrAsInt;
- #else
- typedef unsigned int PtrAsInt;
- #endif
- #elif __linux__
- #if __x86_64__
- typedef unsigned long long int PtrAsInt;
- #else
- typedef unsigned int PtrAsInt;
- #endif
- #else
- #error you must typedef 'PtrAsInt'
- #endif
+ typedef size_t PtrAsInt;
}ALIGNMENT;
#ifdef __GNUC__
#pragma pack(pop)

8
var/spack/repos/builtin/packages/filebench/package.py
View File

@@ -30,11 +30,3 @@ class Filebench(AutotoolsPackage):
depends_on('m4', type='build')
depends_on('flex', type='build')
depends_on('bison', type='build')
def autoreconf(self, spec, prefix):
sh = which('sh')
sh('libtoolize')
sh('aclocal')
sh('autoheader')
sh('automake', '--add-missing')
sh('autoconf')

85
var/spack/repos/builtin/packages/fjcontrib/package.py Normal file
View File

@@ -0,0 +1,85 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import inspect
from spack import *
class Fjcontrib(AutotoolsPackage):
"""3rd party extensions of FastJet"""
homepage = "https://fastjet.hepforge.org/contrib/"
url = "http://fastjet.hepforge.org/contrib/downloads/fjcontrib-1.044.tar.gz"
version('1.044', sha256='de3f45c2c1bed6d7567483e4a774575a504de8ddc214678bac7f64e9d2e7e7a7')
version('1.043', sha256='ef0f586b19ffd12f392b7facc890a73d31fc11b9f5bb727cf3743d6eb59e9993')
version('1.042', sha256='5b052e93a371c557557fa4a293cca4b08f88ccfb6c43a4df15b2a9f38c6d8831')
version('1.041', sha256='31e244728de7787a582479cbed606a1c2fe5fcf3ad3ba1b0134742de5107510c')
version('1.040', sha256='8fcd261f4dec41d3fcf2d550545d7b6e8e5f54e1604615489e7a2c0e45888663')
version('1.039', sha256='a3b88de5e43edb13cde37ed5821aaed6562eec23a774092547f397b6e0b3f088')
version('1.038', sha256='e90d079706a0db516cfc1170b4c34aa197320d019d71db1f726764f293561b15')
version('1.037', sha256='9d69a4a91ef60557e9cebe14952db64f35ea75c51c14e57c1d998bbed0ad6342')
version('1.036', sha256='ecb93ae43e76dbd485b50d37c234aa039fe455d26c273247bc3c93b273dc24f2')
version('1.035', sha256='bc33e5c8132258213cf569789cbcfc838dbed1c242bd31decc0be1f099d405b6')
version('1.034', sha256='8aa9ff609b678c363d682afde91765f7f1145cdf203c18c3fa15c3e1a9a5bcfa')
version('1.033', sha256='d964370b3db0703e223b42a793b07eafbb3658db1266956fd86e69ea5abab7ea')
version('1.032', sha256='125bae5ab04384596c4bcde1c84a3189034f1e94fd99b6c1025cfac1c1795831')
version('1.031', sha256='edb692e8e4e4bbe5401d8891ccf81bd6d26fd7c41d1ec47bd40f2c0e39be9545')
version('1.030', sha256='e4c47bf808f2c078d6fe332ccff00716fdec618e10b7adbf9344e44c8364dba9')
version('1.029', sha256='9147f533bf806dbef5c80f38a26f2002f4c8dfe5c2e01ce1c8edfef27ed527ed')
version('1.028', sha256='cbc24d6e28b03f3c198103c7ae449f401f2e3b7c8a58d241e87f6a8edd30effa')
version('1.027', sha256='8d983c1622d4163459a67d7208961061699e52e417893c045357cd0d2d6048c4')
version('1.026', sha256='6bfe538f17fb3fbbf2c0010640ed6eeedfe4317e6b56365e727d44639f76e3d7')
version('1.025', sha256='504ff45770e8160f1d3b842ea5962c84faeb9acd2821195b08c7e21a84402dcc')
version('1.024', sha256='be13d4b6dfc3c6a157c521247576d01abaa90413af07a5f13b1d0e3622225116')
version('1.023', sha256='ca8f5520ab8c934ea4458016f66d4d7b08e25e491f8fdb5393572cd411ddde03')
version('1.022', sha256='f505c60a87283f380f083736ac411bd865750e81e59876583a9d5c4085d927ce')
version('1.021', sha256='f4bcd9ca39399a3b7719358e757462ecc7937f73a6b625cbb164173a26847d33')
version('1.020', sha256='1ec2041cb5e7f050e20823a31111c7e61d24c4d7ee546c9714861b16eca83a04')
version('1.019', sha256='adec9e1d3c48fec8d6786b64d9c4e95e79129a156f0b0ed3df7e98d57882ffb2')
version('1.018', sha256='fe9d9661cefba048b19002abec7e75385ed73a8a3f45a29718e110beab142c2c')
version('1.017', sha256='6f711b8b7f63a9a1bdf83cc1df6f7785bd3394e96dddba12186dfb5de352362c')
version('1.016', sha256='9301027a71098ef75c37742a2f60631b2e39eb4d6b73b18db48d31e6aed830a0')
version('1.015', sha256='4b9d56d2b6ae56a894b64920ac9ef59013b1d0a54454e716dd98e724f9ea82c0')
version('1.014', sha256='c8de7a0cc19be7684dcfbc3101f9cd4c9426daa3009726acd5a5cbe5e699544b')
version('1.013', sha256='c2b4838a41431cd1c28d3a836f10c00bb84eb6eb2e6586a28badab66518107a6')
version('1.012', sha256='9215ee5b6465fa64296a0139e727a2eb61255d50faccafaa5b241e408ae54821')
version('1.011', sha256='7e4e62755d5905e9dc4a6ef29728c03da538cbbff381eed32a35f06934304b1d')
version('1.010', sha256='1ae74ef44e3d8ce96fd7eb61571819e8891ff708fd468a71780e693c2081176c')
version('1.009', sha256='dc12cce6f0468b4fab9ec4d9fbb2c3d76e942b3b6965cf609963f65c69c08d2f')
version('1.008', sha256='8cc98d837b0579b605a4731fb69882084948e1f1d2ee20af5c8adade2434e4ed')
version('1.007', sha256='70b9d57e5c690d9af8b5be96eefeea9f8c4c4d1a7f000fe1dac30e5aae36077f')
version('1.006', sha256='e2b6d2c5a666eb4db6bef89ea176df4bc1cdec316f8d18594ab54eb0ce8dcbb6')
version('1.005', sha256='265e682a05c1f5e5cf1560cc4efa99e07b211cb2add5f3a09b5be4363ab9cc7f')
version('1.004', sha256='b397e6f822a1d539ac1f63dc8c0709a7a00eed25f4c011114be71f0b38f8f514')
version('1.003', sha256='79b2d42b1b7a99686fa2e0d95ad39050fd974fdf5ea5066271185ae308299b72')
version('1.002', sha256='b48d2cc0a9c2fcfe3bb7faee3217a50191be4150a62ed2f6419fd0025d2cec92')
version('1.001', sha256='6030dfee59040d2ada4ee582254e60b9ecf4b62598129e7b0a114672cf267491')
version('1.000', sha256='95fa36ae48f03cb941d632b0a537995fb7148a6bd028c4978fab8b7b04332c3b')
version('0.001', sha256='51f24ad55e28fb1f9d698270602e5077c920fcf58d8ccfd274efbe829d7dd821')
version('0.000', sha256='9486b11201e6b6e181b8a3abecd929403ae9aa67de0eb8b7353fb82ab4b89f41')
depends_on('fastjet')
build_targets = ['all', 'fragile-shared']
install_targets = ['install', 'fragile-shared-install']
def configure_args(self):
args = ['--fastjet-config=' +
self.spec['fastjet'].prefix.bin +
'/fastjet-config',
"CXXFLAGS=-O3 -Wall -g " +
self.compiler.cxx_pic_flag]
return args
def build(self, spec, prefix):
with working_dir(self.build_directory):
for target in self.build_targets:
inspect.getmodule(self).make(target)
def install(self, spec, prefix):
with working_dir(self.build_directory):
for target in self.install_targets:
inspect.getmodule(self).make(target)

19
var/spack/repos/builtin/packages/fujitsu-mpi/package.py
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@@ -4,6 +4,7 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import os
class FujitsuMpi(Package):
@@ -28,6 +29,24 @@ def install(self, spec, prefix):
raise InstallError(
'Fujitsu MPI is not installable; it is vendor supplied')
@property
def headers(self):
hdrs = find_headers('mpi', self.prefix.include, recursive=True)
hdrs.directories = os.path.dirname(hdrs[0])
return hdrs or None
@property
def libs(self):
query_parameters = self.spec.last_query.extra_parameters
libraries = ['libmpi']
if 'cxx' in query_parameters:
libraries = ['libmpi_cxx'] + libraries
return find_libraries(
libraries, root=self.prefix, shared=True, recursive=True
)
def setup_dependent_package(self, module, dependent_spec):
self.spec.mpicc = self.prefix.bin.mpifcc
self.spec.mpicxx = self.prefix.bin.mpiFCC

20
var/spack/repos/builtin/packages/gaudi/package.py
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@@ -16,6 +16,7 @@ class Gaudi(CMakePackage):
version('master', branch='master')
# major cmake config overhaul already in use by some
version('develop', git='https://gitlab.cern.ch/clemenci/Gaudi.git', branch='cmake-modernisation')
version('33.2', sha256='26aaf9c4ff237a60ec79af9bd18ad249fc91c16e297ba77e28e4a256123db6e5')
version('33.1', sha256='7eb6b2af64aeb965228d4b6ea66c7f9f57f832f93d5b8ad55c9105235af5b042')
version('33.0', sha256='76a967c41f579acc432593d498875dd4dc1f8afd5061e692741a355a9cf233c8')
version('32.2', sha256='e9ef3eb57fd9ac7b9d5647e278a84b2e6263f29f0b14dbe1321667d44d969d2e')
@@ -32,17 +33,20 @@ class Gaudi(CMakePackage):
description='Build with Intel VTune profiler support')
# only build subdirectory GaudiExamples when +optional
patch("build_testing.patch", when="@:33.1")
patch("build_testing.patch", when="@:33.2")
# fix for the new cmake config, should be merged in branch
patch('python2.patch', when="@develop")
# fixes for the cmake config which could not find newer boost versions
patch("link_target_fixes.patch", when="@33.0:33.1")
patch("link_target_fixes.patch", when="@33.0:33.2")
patch("link_target_fixes32.patch", when="@:32.2")
# These dependencies are needed for a minimal Gaudi build
depends_on('aida')
depends_on('boost@1.67.0: +python')
depends_on('clhep')
depends_on('cmake', type='build')
depends_on('cppgsl')
depends_on('fmt', when='@33.2:')
depends_on('intel-tbb')
depends_on('libuuid')
# some bugs with python 3.8
@@ -60,8 +64,6 @@ class Gaudi(CMakePackage):
depends_on('py-nose', when="@develop", type=('build', 'run'))
# Adding these dependencies triggers the build of most optional components
depends_on('aida', when='+optional')
depends_on('clhep', when='+optional')
depends_on('cppgsl', when='+optional')
depends_on('cppunit', when='+optional')
depends_on('doxygen +graphviz', when='+docs')
@@ -87,16 +89,6 @@ class Gaudi(CMakePackage):
def cmake_args(self):
args = [
self.define_from_variant("BUILD_TESTING", "optional"),
self.define_from_variant("GAUDI_USE_AIDA", "optional"),
self.define_from_variant("GAUDI_USE_XERCESC", "optional"),
self.define_from_variant("GAUDI_USE_CLHEP", "optional"),
self.define_from_variant("GAUDI_USE_HEPPDT", "optional"),
self.define_from_variant("GAUDI_USE_CPPUNIT", "optional"),
self.define_from_variant("GAUDI_USE_UNWIND", "optional"),
self.define_from_variant("GAUDI_USE_GPERFTOOLS", "optional"),
self.define_from_variant("GAUDI_USE_DOXYGEN", "docs"),
self.define_from_variant("GAUDI_USE_INTELAMPLIFIER", "optional"),
self.define_from_variant("GAUDI_USE_JEMALLOC", "optional"),
# this is not really used in spack builds, but needs to be set
"-DHOST_BINARY_TAG=x86_64-linux-gcc9-opt",
]

14
var/spack/repos/builtin/packages/gcc/package.py
View File

@@ -335,15 +335,9 @@ def configure_args(self):
# Binutils
if spec.satisfies('+binutils'):
stage1_ldflags = str(self.rpath_args)
boot_ldflags = stage1_ldflags + ' -static-libstdc++ -static-libgcc'
if '%gcc' in spec:
stage1_ldflags = boot_ldflags
binutils = spec['binutils'].prefix.bin
options.extend([
'--with-sysroot=/',
'--with-stage1-ldflags=' + stage1_ldflags,
'--with-boot-ldflags=' + boot_ldflags,
'--with-gnu-ld',
'--with-ld=' + binutils.ld,
'--with-gnu-as',
@@ -376,6 +370,14 @@ def configure_args(self):
'--with-libiconv-prefix={0}'.format(spec['iconv'].prefix)
])
# enable appropriate bootstrapping flags
stage1_ldflags = str(self.rpath_args)
boot_ldflags = stage1_ldflags + ' -static-libstdc++ -static-libgcc'
if '%gcc' in spec:
stage1_ldflags = boot_ldflags
options.append('--with-stage1-ldflags=' + stage1_ldflags)
options.append('--with-boot-ldflags=' + boot_ldflags)
return options
# run configure/make/make(install) for the nvptx-none target

3
var/spack/repos/builtin/packages/gdal/package.py
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@@ -18,7 +18,7 @@ class Gdal(AutotoolsPackage):
"""
homepage = "https://www.gdal.org/"
url = "https://download.osgeo.org/gdal/3.0.4/gdal-3.0.4.tar.xz"
url = "https://download.osgeo.org/gdal/3.1.1/gdal-3.1.1.tar.xz"
list_url = "https://download.osgeo.org/gdal/"
list_depth = 1
@@ -29,6 +29,7 @@ class Gdal(AutotoolsPackage):
'osgeo.gdal_array', 'osgeo.gdalconst'
]
version('3.1.1', sha256='97154a606339a6c1d87c80fb354d7456fe49828b2ef9a3bc9ed91771a03d2a04')
version('3.1.0', sha256='e754a22242ccbec731aacdb2333b567d4c95b9b02d3ba1ea12f70508d244fcda')
version('3.0.4', sha256='5569a4daa1abcbba47a9d535172fc335194d9214fdb96cd0f139bb57329ae277')
version('3.0.3', sha256='e20add5802265159366f197a8bb354899e1693eab8dbba2208de14a457566109')

2
var/spack/repos/builtin/packages/geant4/package.py
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@@ -88,7 +88,7 @@ class Geant4(CMakePackage):
depends_on("libx11", when='+x11')
depends_on("libxmu", when='+x11')
depends_on("motif", when='+motif')
depends_on("qt@5:", when="+qt")
depends_on("qt@5: +opengl", when="+qt")
# As released, 10.03.03 has issues with respect to using external
# CLHEP.

42
var/spack/repos/builtin/packages/graphblast/package.py Normal file
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@@ -0,0 +1,42 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Graphblast(MakefilePackage, CudaPackage):
"""High-Performance Linear Algebra-based Graph Primitives on GPUs"""
homepage = "https://github.com/gunrock/graphblast"
git = "https://github.com/gunrock/graphblast.git"
version('master', submodules=True)
version('2020-05-07', submodules=True, commit='1a052558a71f2cd67f5d6fe9db3b274c303ef8f6', preferred=True)
variant('cuda', default=True, description="Build with Cuda support")
depends_on('boost +program_options')
# This package is confirmed to compile with:
# gcc@:5.4.0,7.5.0 , boost@1.58.0:1.60.0 , cuda@9:
# TODO: the package doesn't compile as CMakePackage
# once that is fixed it should be converted to a CMakePackage type.
conflicts('cuda_arch=none', when='+cuda',
msg='Must specify CUDA compute capabilities of your GPU. \
See "spack info graphblast"')
def install(self, spec, prefix):
install_tree(self.build_directory, self.prefix)
def patch(self):
cuda_arch_list = self.spec.variants['cuda_arch'].value
arches = 'ARCH = '
for i in cuda_arch_list:
arches = arches +\
' -gencode arch=compute_{0},code=compute_{0}'.format(i)
makefile = FileFilter('common.mk')
makefile.filter(r'^ARCH =.*', arches)

23
var/spack/repos/builtin/packages/half/f16fix.patch Normal file
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@@ -0,0 +1,23 @@
--- a/include/half.hpp.orig 2020-06-26 07:46:50.861595808 -0400
+++ b/include/half.hpp 2020-06-26 07:47:31.353286730 -0400
@@ -266,9 +266,6 @@
#if HALF_ENABLE_CPP11_HASH
#include <functional>
#endif
-#if HALF_ENABLE_F16C_INTRINSICS
- #include <immintrin.h>
-#endif
#ifndef HALF_ENABLE_F16C_INTRINSICS
@@ -281,6 +278,10 @@
#define HALF_ENABLE_F16C_INTRINSICS __F16C__
#endif
+#if HALF_ENABLE_F16C_INTRINSICS
+ #include <immintrin.h>
+#endif
+
#ifdef HALF_DOXYGEN_ONLY
/// Type for internal floating-point computations.
/// This can be predefined to a built-in floating-point type (`float`, `double` or `long double`) to override the internal

2
var/spack/repos/builtin/packages/half/package.py
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@@ -23,6 +23,8 @@ class Half(Package):
version('2.1.0', sha256='ad1788afe0300fa2b02b0d1df128d857f021f92ccf7c8bddd07812685fa07a25')
patch('f16fix.patch')
def install(self, spec, prefix):
mkdirp(prefix.include)
install_tree('include', prefix.include)

58
var/spack/repos/builtin/packages/hepmcanalysis/lcg.patch Normal file
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@@ -0,0 +1,58 @@
--- spack-src/examples/hepmcreader/reader.cc.orig 2013-10-31 11:11:16.000000000 +0100
+++ spack-src/examples/hepmcreader/reader.cc 2013-10-31 11:11:59.000000000 +0100
@@ -172,7 +172,7 @@
for (vector<baseAnalysis*>::const_iterator i(analysis.begin()); i != analysis.end(); ++i) {
(*i)->Finalize(f);
}
-
+f->Close();
// clean up analysis modules and configuration
for (vector<baseAnalysis*>::const_iterator i(analysis.begin()); i != analysis.end(); ++i) {
delete (*i);
--- spack-src/Makefile.orig 2013-09-03 16:52:14.000000000 +0200
+++ spack-src/Makefile 2013-09-03 16:54:04.000000000 +0200
@@ -28,7 +28,7 @@
@mkdir -p $(LIBDIR)
$(CXX) $(CXXFLAGS) $(INCLUDES) \
-shared -o $(LIBDIR)/libHepMCAnalysis.so $(OBJECTS) \
- $(HepMClib) $(HepPDTlib) $(FastJetlib) \
+ $(HepMClib) $(HepPDTlib) $(FastJetlib) $(CLHEPlib) \
$(ROOTGLIBS) $(LINK_LIBS)
--- spack-src/src/baseAnalysis.cc 2013-03-04 19:19:55.000000000 +0100
+++ spack-src/src/baseAnalysis.cc 2014-10-03 07:36:47.000000000 +0200
@@ -281,8 +281,8 @@
double pe = (*p)->momentum().e();
// remove garbage
- if ( isnan( px ) || isnan( py ) || isnan( pz ) || isnan( pe ) ||
- isinf( px ) || isinf( py ) || isinf( pz ) || isinf( pe ) ) {
+ if ( std::isnan( px ) || std::isnan( py ) || std::isnan( pz ) || std::isnan( pe ) ||
+ std::isinf( px ) || std::isinf( py ) || std::isinf( pz ) || std::isinf( pe ) ) {
cout << "baseAnalysis: NaN (Not A Number) found in the event record! Particle will be skipped." << endl;
++m_NanNum;
continue;
--- spack-src/config.mk.orig 2020-06-25 17:05:30.142357100 +0200
+++ spack-src/config.mk 2020-06-25 17:06:24.219319861 +0200
@@ -10,16 +10,16 @@
# -I$(HepPDTdir)/include -I$(ROOTSYS)/include
INCLUDES = $(INCLUDEH) $(INCLUDEF)
-ROOTGLIBS = `root-config --glibs`
-ROOTCFLAGS = `root-config --cflags` -Wno-long-long
+ROOTGLIBS = `$(ROOTSYS)/bin/root-config --glibs`
+ROOTCFLAGS = `$(ROOTSYS)/bin/root-config --cflags` -Wno-long-long
#CLHEP = -L$(CLHEPdir)/lib -lCLHEP # causes problems in HepMCAnalysis_i interface!
-CLHEPlib =
+CLHEPlib = -L$(CLHEPdir)/lib -lCLHEP
# common libraries
HepPDTlib =
#HepPDTlib = -L$(HepPDTdir)/lib -lHepPDT -lHepPID
-HepMClib = $(HepMCdir)/lib/libHepMC.so $(HepMCdir)/lib/libHepMCfio.a
+HepMClib = -L$(HepMCdir)/lib -lHepMC
#FastJetlib = -L$(FastJetdir)/lib -lfastjet -lSISConePlugin -lCDFConesPlugin -lsiscone -lsiscone_spherical
FastJetlib = -L$(FastJetdir)/lib -lfastjet -lfastjetplugins -lsiscone -lsiscone_spherical

47
var/spack/repos/builtin/packages/hepmcanalysis/package.py Normal file
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@@ -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 Hepmcanalysis(MakefilePackage):
"""The HepMCAnalysis Tool is a tool for generator
validation and comparisons."""
homepage = "https://hepmcanalysistool.desy.de/"
url = "https://hepmcanalysistool.desy.de/releases/HepMCAnalysis-00-03-04-13.tar.gz"
version('3.4.13', sha256='be9937c6de493a5671258919493b0caa0cecca77853a2075f5cecce1071e0029')
depends_on('hepmc')
depends_on('fastjet')
depends_on('root')
depends_on('clhep')
variant('cxxstd',
default='11',
values=('11', '14', '17'),
multi=False,
description='Use the specified C++ standard when building.')
patch('lcg.patch')
def edit(self, spec, prefix):
filter_file(r"CXXFLAGS(.*)", r"CXXFLAGS\1 -std=c++" +
self.spec.variants['cxxstd'].value, "config.mk")
def setup_build_environment(self, env):
env.set("HepMCdir", self.spec['hepmc'].prefix)
env.set("FastJetdir", self.spec['fastjet'].prefix)
env.set("CLHEPdir", self.spec['clhep'].prefix)
def url_for_version(self, version):
parts = [int(x) for x in str(version).split('.')]
root = "https://hepmcanalysistool.desy.de/releases/HepMCAnalysis-00-"
return root + "{0:02d}-{1:02d}-{2:02d}.tar.gz".format(*parts)
def install(self, spec, prefix):
install_tree('lib', prefix.lib)
install_tree('include', prefix.include)

4
var/spack/repos/builtin/packages/hpx/package.py
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@@ -65,6 +65,10 @@ class Hpx(CMakePackage, CudaPackage):
depends_on('boost@1.55.0:', when='@:1.1.0')
depends_on('hwloc@1.6:', when='@:1.1.0')
# boost 1.73.0 build problem with HPX 1.4.0 and 1.4.1
# https://github.com/STEllAR-GROUP/hpx/issues/4728#issuecomment-640685308
depends_on('boost@:1.72.0', when='@:1.4')
# CXX Standard
depends_on('boost cxxstd=11', when='cxxstd=11')
depends_on('boost cxxstd=14', when='cxxstd=14')

15
var/spack/repos/builtin/packages/xssp/package.py → var/spack/repos/builtin/packages/hssp/package.py
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@@ -6,12 +6,17 @@
from spack import *
class Xssp(AutotoolsPackage):
"""The source code for building the mkdssp, mkhssp, hsspconv, and hsspsoap
programs is bundled in the xssp project"""
class Hssp(AutotoolsPackage):
"""The source code for building the mkhssp and hsspconv programs is bundled
in the hssp project.
homepage = "https://github.com/cmbi/xssp"
url = "https://github.com/cmbi/xssp/archive/3.0.10.tar.gz"
The mkhssp executable creates stockholm files with hssp annotations in
them. The hsspconv executable converts stockholm to the original hssp
format.
"""
homepage = "https://github.com/cmbi/hssp"
url = "https://github.com/cmbi/hssp/archive/3.0.10.tar.gz"
version('3.0.10', sha256='b475d6fa62098df0e54c8dbdaa0b32de93bf5a393335f73f9b5a7e95f3090d2a')
version('3.0.9', sha256='42a9a93c48d22478212dcaf6ceb3feb64443e4cb2e8cccdd402b47a595d16658')

2
var/spack/repos/builtin/packages/intel-mpi/package.py
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@@ -65,7 +65,7 @@ def setup_dependent_build_environment(self, *args):
})
def setup_run_environment(self, env):
super(self, IntelMpi).setup_run_environment(env)
super(IntelMPI, self).setup_run_environment(env)
for name, value in self.mpi_compiler.wrappers.items():
env.set(name, value)

2
var/spack/repos/builtin/packages/intel-parallel-studio/package.py
View File

@@ -227,7 +227,7 @@ def setup_dependent_build_environment(self, *args):
})
def setup_run_environment(self, env):
super(self, IntelParallelStudio).setup_run_environment(env)
super(IntelParallelStudio, self).setup_run_environment(env)
for name, value in self.mpi_compiler_wrappers.items():
env.set(name, value)

2
var/spack/repos/builtin/packages/intel/package.py
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@@ -13,6 +13,8 @@ class Intel(IntelPackage):
# Same as in ../intel-parallel-studio/package.py, Composer Edition,
# but the version numbering in Spack differs.
version('20.0.1', sha256='26c7e7da87b8a83adfd408b2a354d872be97736abed837364c1bf10f4469b01e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16530/parallel_studio_xe_2020_update1_composer_edition.tgz')
version('20.0.0', sha256='9168045466139b8e280f50f0606b9930ffc720bbc60bc76f5576829ac15757ae', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/parallel_studio_xe_2020_composer_edition.tgz')
version('19.1.1', sha256='26c7e7da87b8a83adfd408b2a354d872be97736abed837364c1bf10f4469b01e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16530/parallel_studio_xe_2020_update1_composer_edition.tgz')
version('19.1.0', sha256='9168045466139b8e280f50f0606b9930ffc720bbc60bc76f5576829ac15757ae', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/parallel_studio_xe_2020_composer_edition.tgz')
version('19.0.5', sha256='e8c8e4b9b46826a02c49325c370c79f896858611bf33ddb7fb204614838ad56c', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15813/parallel_studio_xe_2019_update5_composer_edition.tgz')

4
var/spack/repos/builtin/packages/lapackpp/package.py
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@@ -11,10 +11,10 @@ class Lapackpp(CMakePackage):
of Tennessee)"""
homepage = "https://bitbucket.org/icl/lapackpp"
hg = "https://bitbucket.org/icl/lapackpp"
git = "https://bitbucket.org/icl/lapackpp"
maintainers = ['teonnik', 'Sely85']
version('develop', hg=hg, revision="7ffa486")
version('develop', commit="f878fad")
variant('shared', default=True,
description='Build a shared version of the library')

8
var/spack/repos/builtin/packages/libffi/package.py
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@@ -25,3 +25,11 @@ class Libffi(AutotoolsPackage, SourcewarePackage):
def headers(self):
# The headers are probably in self.prefix.lib but we search everywhere
return find_headers('ffi', self.prefix, recursive=True)
def configure_args(self):
args = []
if self.spec.version >= Version('3.3'):
# Spack adds its own target flags, so tell libffi not to
# second-guess us
args.append('--without-gcc-arch')
return args

2
var/spack/repos/builtin/packages/libnetworkit/package.py
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@@ -31,7 +31,7 @@ class Libnetworkit(CMakePackage):
depends_on('libtlx')
depends_on('py-sphinx', when='+doc', type='build')
patch('0001-Name-agnostic-import-of-tlx-library.patch', when='@6.1')
patch('0001-Name-agnostic-import-of-tlx-library.patch', when='@6.1:')
def cmake_args(self):
spec = self.spec

3
var/spack/repos/builtin/packages/libxsmm/package.py
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@@ -14,10 +14,11 @@ class Libxsmm(MakefilePackage):
and deep learning primitives."""
homepage = 'https://github.com/hfp/libxsmm'
url = 'https://github.com/hfp/libxsmm/archive/1.16.tar.gz'
url = 'https://github.com/hfp/libxsmm/archive/1.16.1.tar.gz'
git = 'https://github.com/hfp/libxsmm.git'
version('master', branch='master')
version('1.16.1', sha256='93dc7a3ec40401988729ddb2c6ea2294911261f7e6cd979cf061b5c3691d729d')
version('1.16', sha256='4f4f2ad97815413af80821d2e306eb6f00541941ad412662da05c02361a20e07')
version('1.15', sha256='499e5adfbf90cd3673309243c2b56b237d54f86db2437e1ac06c8746b55ab91c')
version('1.14', sha256='9c0af4509ea341d1ee2c6c19fc6f19289318c3bd4b17844efeb9e7f9691abf76')

1
var/spack/repos/builtin/packages/nfs-utils/package.py
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@@ -18,6 +18,7 @@ class NfsUtils(AutotoolsPackage):
version('2.4.1', sha256='c0dda96318af554881f4eb1590bfe91f1aba2fba59ed2ac3ba099f80fdf838e9')
version('2.3.4', sha256='36e70b0a583751ead0034ebe5d8826caf2dcc7ee7c0beefe94d6ee5a3b0b2484')
depends_on('pkgconfig', type='build')
depends_on('libtirpc')
depends_on('libevent')
depends_on('libdmx')

1
var/spack/repos/builtin/packages/openfoam/package.py
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@@ -265,6 +265,7 @@ class Openfoam(Package):
version('develop', branch='develop', submodules='True')
version('master', branch='master', submodules='True')
version('2006', sha256='30c6376d6f403985fc2ab381d364522d1420dd58a42cb270d2ad86f8af227edc')
version('1912_200506', sha256='831a39ff56e268e88374d0a3922479fd80260683e141e51980242cc281484121')
version('1912_200403', sha256='1de8f4ddd39722b75f6b01ace9f1ba727b53dd999d1cd2b344a8c677ac2db4c0')
version('1912', sha256='437feadf075419290aa8bf461673b723a60dc39525b23322850fb58cb48548f2')

22
var/spack/repos/builtin/packages/perl-date-manip/package.py Normal file
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@@ -0,0 +1,22 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PerlDateManip(PerlPackage):
"""Date::Manip - Date manipulation routines
Date::Manip is a series of modules designed to make any common date/time
operation easy to do. Operations such as comparing two times,
determining a date a given amount of time from another, or parsing
international times are all easily done. It deals with time as it is
used in the Gregorian calendar (the one currently in use) with full
support for time changes due to daylight saving time."""
homepage = "https://metacpan.org/release/Date-Manip"
url = "https://cpan.metacpan.org/authors/id/S/SB/SBECK/Date-Manip-6.82.tar.gz"
version('6.82', sha256='fa96bcf94c6b4b7d3333f073f5d0faad59f546e5aec13ac01718f2e6ef14672a')

81
var/spack/repos/builtin/packages/postgis/package.py Normal file
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@@ -0,0 +1,81 @@
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Postgis(AutotoolsPackage):
"""
PostGIS is a spatial database extender for PostgreSQL object-relational
database. It adds support for geographic objects allowing location
queries to be run in SQL
"""
homepage = "https://postgis.net/"
url = "https://download.osgeo.org/postgis/source/postgis-2.5.3.tar.gz"
version('3.0.1', sha256='5a5432f95150d9bae9215c6d1c7bb354e060482a7c379daa9b8384e1d03e6353')
version('3.0.0', sha256='c06fd2cd5cea0119106ffe17a7235d893c2bbe6f4b63c8617c767630973ba594')
version('2.5.3', sha256='72e8269d40f981e22fb2b78d3ff292338e69a4f5166e481a77b015e1d34e559a')
variant('gui', default=False, description='Build with GUI support, creating shp2pgsql-gui graphical interface to shp2pgsql')
# Refs:
# https://postgis.net/docs/postgis_installation.html
# https://postgis.net/source/
depends_on('postgresql')
depends_on('geos')
depends_on('proj')
depends_on('gdal')
depends_on('libxml2')
depends_on('json-c')
depends_on('sfcgal')
depends_on('pcre')
depends_on('perl', type=('build', 'run'))
depends_on('protobuf-c')
depends_on('gtkplus@:2.24.32', when='+gui')
def setup_build_environment(self, env):
env.set('POSTGIS_GDAL_ENABLED_DRIVERS', 'ENABLE_ALL')
def setup_run_environment(self, env):
env.set('POSTGIS_GDAL_ENABLED_DRIVERS', 'ENABLE_ALL')
def configure_args(self):
args = []
args.append('--with-sfcgal=' + str(self.spec['sfcgal'].prefix.bin) +
'/sfcgal-config')
if '+gui' in self.spec:
args.append('--with-gui')
return args
# By default package installs under postgresql prefix.
# Apparently this is a known bug:
# https://postgis.net/docs/postgis_installation.html
# The following modifacations that fixed this issue are found in
# Guix recipe for postgis.
# https://git.savannah.gnu.org/cgit/guix.git/tree/gnu/packages/geo.scm#n720
def build(self, spec, prefix):
make('bindir=' + prefix.bin, 'libdir=' + prefix.lib,
'pkglibdir=' + prefix.lib, 'datadir=' + prefix.share,
'docdir=' + prefix.share.doc)
def install(self, spec, prefix):
make('install', 'bindir=' + prefix.bin, 'libdir=' + prefix.lib,
'pkglibdir=' + prefix.lib, 'datadir=' + prefix.share,
'docdir=' + prefix.share.doc)
@run_before('build')
def fix_raster_bindir(self):
makefile = FileFilter('raster/loader/Makefile')
makefile.filter('$(DESTDIR)$(PGSQL_BINDIR)', self.prefix.bin,
string=True)
makefile = FileFilter('raster/scripts/Makefile')
makefile.filter('$(DESTDIR)$(PGSQL_BINDIR)', self.prefix.bin,
string=True)

4
var/spack/repos/builtin/packages/py-crossmap/package.py
View File

@@ -13,6 +13,7 @@ class PyCrossmap(PythonPackage, SourceforgePackage):
homepage = "http://crossmap.sourceforge.net/"
sourceforge_mirror_path = "crossmap/CrossMap-0.3.3.tar.gz"
version('0.3.9', sha256='e20a4653e9fc313ac0f5a6cfc37b42e83c3cf2b42f9483706cfb9ec9ff72c74c')
version('0.3.3', sha256='56d99fd606e13e399b83438953d0d89fc281df1c1e8e47eed7d773e7ec9c88f8')
version('0.2.9', sha256='57243ee5051352c93088874c797ceac0426f249704ba897360fb628b3365d0af')
@@ -20,8 +21,7 @@ class PyCrossmap(PythonPackage, SourceforgePackage):
depends_on('python@2.7:2.8', type=('build', 'run'), when='@:0.2.9')
depends_on('py-setuptools', type='build')
depends_on('py-numpy', type=('build', 'run'))
depends_on('py-cython', type=('build', 'run'))
depends_on('py-cython@0.17:', type=('build', 'run'))
depends_on('py-pysam', type=('build', 'run'))
depends_on('py-bx-python', type=('build', 'run'))

50
var/spack/repos/builtin/packages/py-mdanalysis/package.py
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@@ -16,6 +16,8 @@ class PyMdanalysis(PythonPackage):
homepage = "http://www.mdanalysis.org"
url = "https://pypi.io/packages/source/M/MDAnalysis/MDAnalysis-0.19.2.tar.gz"
version('1.0.0', sha256='f45a024aca45e390ff1c45ca90beb2180b78881be377e2a1aa9cd6c109bcfa81')
version('0.20.1', sha256='d04b71b193b9716d2597ffb9938b93f43487fa535da1bb5c1f2baccf356d7df9')
version('0.19.2', sha256='c5395bbafa5efca2e1aee4715d26129844140c47cb8301da0293106cb969de7d')
version('0.19.1', sha256='ff1d694f8598c0833ec340de6a6adb3b5e62b92d0fa94ee6401718ba972db3cc')
version('0.19.0', sha256='248e3b37fc6150e31c609cc18a3927c32aee37b76d29cbfedf635e7e1aa982cf')
@@ -31,18 +33,42 @@ class PyMdanalysis(PythonPackage):
variant('amber', default=False,
description='Support AMBER netcdf format.')
depends_on('python@2.7:')
depends_on('py-setuptools', type='build')
depends_on('py-cython@0.16:', type='build')
depends_on('py-numpy@1.5.0:', type=('build', 'run'))
depends_on('py-six@1.4.0:', type=('build', 'run'))
depends_on('py-biopython@1.59:', type=('build', 'run'))
depends_on('py-networkx@1.0:', type=('build', 'run'))
depends_on('py-griddataformats@0.3.2:', type=('build', 'run'))
depends_on('python@2.7:', type=('build', 'run'))
depends_on('py-matplotlib', when='+analysis', type=('build', 'run'))
depends_on('py-scipy', when='+analysis', type=('build', 'run'))
depends_on('py-seaborn', when='+analysis', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-cython@0.16:', type='build')
depends_on('py-six@1.4.0:', type=('build', 'run'))
depends_on('py-networkx@1.0:', type=('build', 'run'))
depends_on('py-gsd@1.4.0:', when='@1.17.0:', type=('build', 'run'))
depends_on('py-mmtf-python@1.0.0:', when='@0.16.0:', type=('build', 'run'))
depends_on('py-mock', when='@0.18.0:', type=('build', 'run'))
depends_on('py-tqdm@4.43.0:', when='@1.0.0:', type=('build', 'run'))
depends_on('py-joblib', when='@0.16.0:0.20.1', type=('build', 'run'))
depends_on('py-joblib@0.12:', when='@1.0.0:', type=('build', 'run'))
depends_on('py-numpy@1.5.0:', when='@:0.15.0', type=('build', 'run'))
depends_on('py-numpy@1.10.4:', when='@0.16.0:0.19.2', type=('build', 'run'))
depends_on('py-numpy@1.13.3:', when='@0.20.1:', type=('build', 'run'))
depends_on('py-biopython@1.59:', when='@:0.17.0', type=('build', 'run'))
depends_on('py-biopython@1.71:', when='@0.18.0:', type=('build', 'run'))
depends_on('py-griddataformats@0.3.2:', when='@:0.16.2', type=('build', 'run'))
depends_on('py-griddataformats@0.4:', when='@0.17.0:', type=('build', 'run'))
depends_on('py-matplotlib', when='@:0.15.0+analysis', type=('build', 'run'))
depends_on('py-matplotlib@1.5.1:', when='@0.16.0:0.16.1+analysis', type=('build', 'run'))
depends_on('py-matplotlib@1.5.1:', when='@0.16.2:', type=('build', 'run'))
depends_on('py-scipy', when='@:0.16.1+analysis', type=('build', 'run'))
depends_on('py-scipy', when='@0.16.2:0.17.0', type=('build', 'run'))
depends_on('py-scipy@1.0.0:', when='@0.18.0:', type=('build', 'run'))
depends_on('py-scikit-learn', when='@0.16.0:+analysis', type=('build', 'run'))
depends_on('py-seaborn', when='+analysis', type=('build', 'run'))
depends_on('py-netcdf4@1.0:', when='+amber', type=('build', 'run'))
depends_on('hdf5', when='+amber', type=('run'))
depends_on('hdf5', when='+amber', type=('run'))

5
var/spack/repos/builtin/packages/py-mpi4py/package.py
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@@ -30,3 +30,8 @@ class PyMpi4py(PythonPackage):
def build_args(self, spec, prefix):
return ['--mpicc=%s -shared' % spec['mpi'].mpicc]
@property
def headers(self):
headers = find_all_headers(self.prefix.lib)
return headers

42
var/spack/repos/builtin/packages/py-networkit/package.py Normal file
View File

@@ -0,0 +1,42 @@
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyNetworkit(PythonPackage):
"""NetworKit is a growing open-source toolkit for large-scale network
analysis. Its aim is to provide tools for the analysis of large networks
in the size range from thousands to billions of edges. For this purpose,
it implements efficient graph algorithms, many of them parallel to
utilize multicore architectures. These are meant to compute standard
measures of network analysis, such as degree sequences, clustering
coefficients, and centrality measures. In this respect, NetworKit is
comparable to packages such as NetworkX, albeit with a focus on
parallelism and scalability."""
homepage = "https://networkit.github.io/"
url = "https://pypi.io/packages/source/n/networkit/networkit-6.1.tar.gz"
version('7.0', sha256='eea4b5e565d6990b674e1c7f4d598be9377d57b61d0d82883ecc39edabaf3631')
version('6.1', sha256='f7fcb50dec66a8253f85c10ff9314100de013c7578d531c81d3f71bc6cf8f093')
# Required dependencies
depends_on('cmake', type='build')
depends_on('libnetworkit@7.0', type=('build', 'link'), when='@7.0')
depends_on('libnetworkit@6.1', type=('build', 'link'), when='@6.1')
depends_on('llvm-openmp', when='%apple-clang')
depends_on('ninja', type='build')
depends_on('py-cython', type='build')
depends_on('py-numpy', type=('build', 'run'))
depends_on('py-scipy', type=('build', 'run'))
depends_on('py-setuptools', type='build')
phases = ['build_ext', 'install']
# Overwrite build_ext to enable ext. core-library + parallel build
def build_ext_args(self, spec, prefix):
args = ['--networkit-external-core', '-j{0}'.format(make_jobs)]
return args

8
var/spack/repos/builtin/packages/qgis/package.py
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@@ -17,10 +17,16 @@ class Qgis(CMakePackage):
maintainers = ['adamjstewart', 'Sinan81']
version('3.14.0', sha256='1b76c5278def0c447c3d354149a2afe2562ac26cf0bcbe69b9e0528356d407b8')
version('3.12.3', sha256='c2b53815f9b994e1662995d1f25f90628156b996758f5471bffb74ab29a95220')
version('3.12.2', sha256='501f81715672205afd2c1a289ffc765aff96eaa8ecb49d079a58ef4d907467b8')
version('3.12.1', sha256='a7dc7af768b8960c08ce72a06c1f4ca4664f4197ce29c7fe238429e48b2881a8')
version('3.12.0', sha256='19e9c185dfe88cad7ee6e0dcf5ab7b0bbfe1672307868a53bf771e0c8f9d5e9c')
# Prefer latest long term release
version('3.10.4', sha256='a032e2b8144c2fd825bc26766f586cfb1bd8574bc72efd1aa8ce18dfff8b6c9f', preferred=True)
version('3.10.7', sha256='f6c02489e065bae355d2f4374b84a1624379634c34a770b6d65bf38eb7e71564', preferred=True)
version('3.10.6', sha256='a96791bf6615e4f8ecdbbb9a90a8ef14a12459d8c5c374ab22eb5f776f864bb5')
version('3.10.5', sha256='f3e1cc362941ec69cc21062eeaea160354ef71382b21dc4b3191c315447b4ce1')
version('3.10.4', sha256='a032e2b8144c2fd825bc26766f586cfb1bd8574bc72efd1aa8ce18dfff8b6c9f')
version('3.10.3', sha256='0869704df9120dd642996ff1ed50213ac8247650aa0640b62f8c9c581c05d7a7')
version('3.10.2', sha256='381cb01a8ac2f5379a915b124e9c830d727d2c67775ec49609c7153fe765a6f7')
version('3.10.1', sha256='466ac9fad91f266cf3b9d148f58e2adebd5b9fcfc03e6730eb72251e6c34c8ab')

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