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Merge branch 'develop' into features/shared

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This commit is contained in:
Carson Woods
2020-03-09 23:23:37 +00:00
parent cd54fb95b8 c7dda38826
commit 05fe92e086
203 changed files with 4013 additions and 635 deletions
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29
.github/ISSUE_TEMPLATE/bug_report.md vendored
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@@ -1,14 +1,21 @@
---
name: Bug report
name: "\U0001F41E Bug report"
about: Report a bug in the core of Spack (command not working as expected, etc.)
labels: bug
labels: "bug,triage"
---
<!--
*Explain, in a clear and concise way, the command you ran and the result you were trying to achieve.
Example: "I ran Spack find to list all the installed packages and..."*
-->
### Spack version
<!-- Add the output to the command below -->
```console
$ spack --version
```
### Steps to reproduce the issue
@@ -20,7 +27,7 @@ $ spack <command2> <spec>
### Error Message
If Spack reported an error, provide the error message. If it did not report an error
<!--If Spack reported an error, provide the error message. If it did not report an error
but the output appears incorrect, provide the incorrect output. If there was no error
message and no output but the result is incorrect, describe how it does not match
what you expect. To provide more information you might re-run the commands with
@@ -31,19 +38,27 @@ $ spack -d --stacktrace <command2> <spec>
...
```
that activate the full debug output.
-->
### Information on your system
<!--
This includes:
1. which platform you are using
2. any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.)
-----
-->
### General information
- [ ] I have run `spack --version` and reported the version of Spack
- [ ] I have searched the issues of this repo and believe this is not a duplicate
- [ ] I have run the failing commands in debug mode and reported the output
<!--
We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively!
If you want to ask a question about the tool (how to use it, what it can currently do, etc.), try the `#general` channel on our Slack first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
Other than that, thanks for taking the time to contribute to Spack!
-->

25
.github/ISSUE_TEMPLATE/build_error.md vendored
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@@ -1,19 +1,24 @@
---
name: Build error
name: "\U0001F4A5 Build error"
about: Some package in Spack didn't build correctly
labels: "build-error"
---
*Thanks for taking the time to report this build failure. To proceed with the
<!--*Thanks for taking the time to report this build failure. To proceed with the
report please:*
1. Title the issue "Installation issue: <name-of-the-package>".
2. Provide the information required below.
3. Remove the template instructions before posting the issue.
We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively!
-->
---
### Spack version
<!-- Add the output to the command below -->
```console
$ spack --version
```
### Steps to reproduce the issue
@@ -24,7 +29,7 @@ $ spack install <spec> # Fill in the exact spec you are using
### Platform and user environment
Please report your OS here:
<!-- Please report your OS here:
```commandline
$ uname -a
Linux nuvolari 4.15.0-29-generic #31-Ubuntu SMP Tue Jul 17 15:39:52 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
@@ -37,10 +42,11 @@ and, if relevant, post or attach:
- `compilers.yaml`
to the issue
-->
### Additional information
Sometimes the issue benefits from additional details. In these cases there are
<!--Sometimes the issue benefits from additional details. In these cases there are
a few things we can suggest doing. First of all, you can post the full output of:
```console
$ spack spec --install-status <spec>
@@ -75,4 +81,9 @@ will provide additional debug information. After the failure you will find two f
failed object after Spack's compiler wrapper did its processing
You can post or attach those files to provide maintainers with more information on what
is causing the failure.
is causing the failure.-->
### General information
- [ ] I have run `spack --version` and reported the version of Spack
- [ ] I have searched the issues of this repo and believe this is not a duplicate

21
.github/ISSUE_TEMPLATE/feature_request.md vendored
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@@ -1,28 +1,33 @@
---
name: Feature request
name: "\U0001F38A Feature request"
about: Suggest adding a feature that is not yet in Spack
labels: feature
---
*Please add a concise summary of your suggestion here.*
<!--*Please add a concise summary of your suggestion here.*-->
### Rationale
*Is your feature request related to a problem? Please describe it!*
<!--*Is your feature request related to a problem? Please describe it!*-->
### Description
*Describe the solution you'd like and the alternatives you have considered.*
<!--*Describe the solution you'd like and the alternatives you have considered.*-->
### Additional information
*Add any other context about the feature request here.*
<!--*Add any other context about the feature request here.*-->
-----
### General information
- [ ] I have run `spack --version` and reported the version of Spack
- [ ] I have searched the issues of this repo and believe this is not a duplicate
If you want to ask a question about the tool (how to use it, what it can currently do, etc.), try the `#general` channel on our Slack first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
Other than that, thanks for taking the time to contribute to Spack!
<!--If you want to ask a question about the tool (how to use it, what it can currently do, etc.), try the `#general` channel on our Slack first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
Other than that, thanks for taking the time to contribute to Spack!
-->

2
.github/workflows/linux_build_tests.yaml vendored
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@@ -28,7 +28,7 @@ jobs:
matrix:
package: [lz4, mpich, tut, py-setuptools, openjpeg, r-rcpp]
steps:
- uses: actions/checkout@v1
- uses: actions/checkout@v2
- name: Cache ccache's store
uses: actions/cache@v1
with:

6
etc/spack/defaults/config.yaml
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@@ -75,6 +75,12 @@ config:
misc_cache: ~/.spack/cache
# Timeout in seconds used for downloading sources etc. This only applies
# to the connection phase and can be increased for slow connections or
# servers. 0 means no timeout.
connect_timeout: 10
# If this is false, tools like curl that use SSL will not verify
# certifiates. (e.g., curl will use use the -k option)
verify_ssl: true

24
lib/spack/docs/basic_usage.rst
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@@ -25,6 +25,14 @@ It is recommended that the following be put in your ``.bashrc`` file:
alias less='less -R'
If you do not see colorized output when using ``less -R`` it is because color
is being disabled in the piped output. In this case, tell spack to force
colorized output.
.. code-block:: console
$ spack --color always | less -R
--------------------------
Listing available packages
--------------------------
@@ -45,7 +53,7 @@ can install:
.. command-output:: spack list
:ellipsis: 10
There are thosands of them, so we've truncated the output above, but you
There are thousands of them, so we've truncated the output above, but you
can find a :ref:`full list here <package-list>`.
Packages are listed by name in alphabetical order.
A pattern to match with no wildcards, ``*`` or ``?``,
@@ -267,7 +275,7 @@ the ``spack gc`` ("garbage collector") command, which will uninstall all unneede
-- linux-ubuntu18.04-broadwell / gcc@9.0.1 ----------------------
hdf5@1.10.5 libiconv@1.16 libpciaccess@0.13.5 libszip@2.1.1 libxml2@2.9.9 mpich@3.3.2 openjpeg@2.3.1 xz@5.2.4 zlib@1.2.11
In the example above Spack went through all the packages in the DB
In the example above Spack went through all the packages in the package database
and removed everything that is not either:
1. A package installed upon explicit request of the user
@@ -854,7 +862,7 @@ Variants are named options associated with a particular package. They are
optional, as each package must provide default values for each variant it
makes available. Variants can be specified using
a flexible parameter syntax ``name=<value>``. For example,
``spack install libelf debug=True`` will install libelf build with debug
``spack install libelf debug=True`` will install libelf built with debug
flags. The names of particular variants available for a package depend on
what was provided by the package author. ``spack info <package>`` will
provide information on what build variants are available.
@@ -1067,13 +1075,13 @@ of failing:
In the snippet above, for instance, the microarchitecture was demoted to ``haswell`` when
compiling with ``gcc@4.8`` since support to optimize for ``broadwell`` starts from ``gcc@4.9:``.
Finally if Spack has no information to match compiler and target, it will
Finally, if Spack has no information to match compiler and target, it will
proceed with the installation but avoid injecting any microarchitecture
specific flags.
.. warning::
Currently Spack doesn't print any warning to the user if it has no information
Currently, Spack doesn't print any warning to the user if it has no information
on which optimization flags should be used for a given compiler. This behavior
might change in the future.
@@ -1083,7 +1091,7 @@ specific flags.
Virtual dependencies
--------------------
The dependence graph for ``mpileaks`` we saw above wasn't *quite*
The dependency graph for ``mpileaks`` we saw above wasn't *quite*
accurate. ``mpileaks`` uses MPI, which is an interface that has many
different implementations. Above, we showed ``mpileaks`` and
``callpath`` depending on ``mpich``, which is one *particular*
@@ -1410,12 +1418,12 @@ packages listed as activated:
py-nose@1.3.4 py-numpy@1.9.1 py-setuptools@11.3.1
Now, when a user runs python, ``numpy`` will be available for import
*without* the user having to explicitly loaded. ``python@2.7.8`` now
*without* the user having to explicitly load it. ``python@2.7.8`` now
acts like a system Python installation with ``numpy`` installed inside
of it.
Spack accomplishes this by symbolically linking the *entire* prefix of
the ``py-numpy`` into the prefix of the ``python`` package. To the
the ``py-numpy`` package into the prefix of the ``python`` package. To the
python interpreter, it looks like ``numpy`` is installed in the
``site-packages`` directory.

20
lib/spack/docs/packaging_guide.rst
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@@ -2913,7 +2913,7 @@ discover its dependencies.
If you want to see the environment that a package will build with, or
if you want to run commands in that environment to test them out, you
can use the :ref:`cmd-spack-env` command, documented
can use the :ref:`cmd-spack-build-env` command, documented
below.
^^^^^^^^^^^^^^^^^^^^^
@@ -4332,31 +4332,31 @@ directory, install directory, package directory) and others change to
core spack locations. For example, ``spack cd --module-dir`` will take you to
the main python source directory of your spack install.
.. _cmd-spack-env:
.. _cmd-spack-build-env:
^^^^^^^^^^^^^
``spack env``
^^^^^^^^^^^^^
^^^^^^^^^^^^^^^^^^^
``spack build-env``
^^^^^^^^^^^^^^^^^^^
``spack env`` functions much like the standard unix ``env`` command,
but it takes a spec as an argument. You can use it to see the
``spack build-env`` functions much like the standard unix ``build-env``
command, but it takes a spec as an argument. You can use it to see the
environment variables that will be set when a particular build runs,
for example:
.. code-block:: console
$ spack env mpileaks@1.1%intel
$ spack build-env mpileaks@1.1%intel
This will display the entire environment that will be set when the
``mpileaks@1.1%intel`` build runs.
To run commands in a package's build environment, you can simply
provide them after the spec argument to ``spack env``:
provide them after the spec argument to ``spack build-env``:
.. code-block:: console
$ spack cd mpileaks@1.1%intel
$ spack env mpileaks@1.1%intel ./configure
$ spack build-env mpileaks@1.1%intel ./configure
This will cd to the build directory and then run ``configure`` in the
package's build environment.

2
lib/spack/env/cc vendored
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@@ -43,7 +43,7 @@ parameters=(
# The compiler input variables are checked for sanity later:
# SPACK_CC, SPACK_CXX, SPACK_F77, SPACK_FC
# The default compiler flags are passed from these variables:
# SPACK_CFLAGS, SPACK_CXXFLAGS, SPACK_FCFLAGS, SPACK_FFLAGS,
# SPACK_CFLAGS, SPACK_CXXFLAGS, SPACK_FFLAGS,
# SPACK_LDFLAGS, SPACK_LDLIBS
# Debug env var is optional; set to "TRUE" for debug logging:
# SPACK_DEBUG

1
lib/spack/external/distro.py vendored
View File

@@ -64,6 +64,7 @@
'enterpriseenterprise': 'oracle', # Oracle Enterprise Linux
'redhatenterpriseworkstation': 'rhel', # RHEL 6, 7 Workstation
'redhatenterpriseserver': 'rhel', # RHEL 6, 7 Server
'redhatenterprisecomputenode': 'rhel', # RHEL 6 ComputeNode
}
#: Translation table for normalizing the distro ID derived from the file name

24
lib/spack/spack/binary_distribution.py
View File

@@ -308,7 +308,7 @@ def build_tarball(spec, outdir, force=False, rel=False, unsigned=False,
tmpdir = tempfile.mkdtemp()
cache_prefix = build_cache_prefix(tmpdir)
tarfile_name = tarball_name(spec, '.tar.bz2')
tarfile_name = tarball_name(spec, '.tar.gz')
tarfile_dir = os.path.join(cache_prefix, tarball_directory_name(spec))
tarfile_path = os.path.join(tarfile_dir, tarfile_name)
spackfile_path = os.path.join(
@@ -377,8 +377,8 @@ def build_tarball(spec, outdir, force=False, rel=False, unsigned=False,
shutil.rmtree(tmpdir)
tty.die(e)
# create compressed tarball of the install prefix
with closing(tarfile.open(tarfile_path, 'w:bz2')) as tar:
# create gzip compressed tarball of the install prefix
with closing(tarfile.open(tarfile_path, 'w:gz')) as tar:
tar.add(name='%s' % workdir,
arcname='%s' % os.path.basename(spec.prefix))
# remove copy of install directory
@@ -433,6 +433,9 @@ def build_tarball(spec, outdir, force=False, rel=False, unsigned=False,
web_util.push_to_url(
specfile_path, remote_specfile_path, keep_original=False)
tty.msg('Buildache for "%s" written to \n %s' %
(spec, remote_spackfile_path))
try:
# create an index.html for the build_cache directory so specs can be
# found
@@ -589,16 +592,16 @@ def extract_tarball(spec, filename, allow_root=False, unsigned=False,
stagepath = os.path.dirname(filename)
spackfile_name = tarball_name(spec, '.spack')
spackfile_path = os.path.join(stagepath, spackfile_name)
tarfile_name = tarball_name(spec, '.tar.bz2')
tarfile_name = tarball_name(spec, '.tar.gz')
tarfile_path = os.path.join(tmpdir, tarfile_name)
specfile_name = tarball_name(spec, '.spec.yaml')
specfile_path = os.path.join(tmpdir, specfile_name)
with closing(tarfile.open(spackfile_path, 'r')) as tar:
tar.extractall(tmpdir)
# older buildcache tarfiles use gzip compression
# some buildcache tarfiles use bzip2 compression
if not os.path.exists(tarfile_path):
tarfile_name = tarball_name(spec, '.tar.gz')
tarfile_name = tarball_name(spec, '.tar.bz2')
tarfile_path = os.path.join(tmpdir, tarfile_name)
if not unsigned:
if os.path.exists('%s.asc' % specfile_path):
@@ -799,6 +802,7 @@ def get_specs(force=False, allarch=False):
def get_keys(install=False, trust=False, force=False):
"""
Get pgp public keys available on mirror
with suffix .key or .pub
"""
if not spack.mirror.MirrorCollection():
tty.die("Please add a spack mirror to allow " +
@@ -815,16 +819,18 @@ def get_keys(install=False, trust=False, force=False):
tty.msg("Finding public keys in %s" % mirror_dir)
files = os.listdir(mirror_dir)
for file in files:
if re.search(r'\.key', file):
if re.search(r'\.key', file) or re.search(r'\.pub', file):
link = url_util.join(fetch_url_build_cache, file)
keys.add(link)
else:
tty.msg("Finding public keys at %s" %
url_util.format(fetch_url_build_cache))
p, links = web_util.spider(fetch_url_build_cache, depth=1)
# For s3 mirror need to request index.html directly
p, links = web_util.spider(
url_util.join(fetch_url_build_cache, 'index.html'), depth=1)
for link in links:
if re.search(r'\.key', link):
if re.search(r'\.key', link) or re.search(r'\.pub', link):
keys.add(link)
for link in keys:

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

@@ -263,6 +263,12 @@ def flags_to_build_system_args(self, flags):
if values:
values_str = '{0}={1}'.format(flag.upper(), ' '.join(values))
self.configure_flag_args.append(values_str)
# Spack's fflags are meant for both F77 and FC, therefore we
# additionaly set FCFLAGS if required.
values = flags.get('fflags', None)
if values:
values_str = 'FCFLAGS={0}'.format(' '.join(values))
self.configure_flag_args.append(values_str)
def configure(self, spec, prefix):
"""Runs configure with the arguments specified in

76
lib/spack/spack/build_systems/cuda.py
View File

@@ -13,39 +13,65 @@ class CudaPackage(PackageBase):
"""Auxiliary class which contains CUDA variant, dependencies and conflicts
and is meant to unify and facilitate its usage.
"""
maintainers = ['ax3l', 'svenevs']
# FIXME: keep cuda and cuda_arch separate to make usage easier untill
# https://docs.nvidia.com/cuda/cuda-compiler-driver-nvcc/index.html#gpu-feature-list
# https://developer.nvidia.com/cuda-gpus
# https://en.wikipedia.org/wiki/CUDA#GPUs_supported
cuda_arch_values = [
'10', '11', '12', '13',
'20', '21',
'30', '32', '35', '37',
'50', '52', '53',
'60', '61', '62',
'70', '72', '75',
]
# FIXME: keep cuda and cuda_arch separate to make usage easier until
# Spack has depends_on(cuda, when='cuda_arch!=None') or alike
variant('cuda', default=False,
description='Build with CUDA')
# see http://docs.nvidia.com/cuda/cuda-compiler-driver-nvcc/index.html#gpu-feature-list
# https://developer.nvidia.com/cuda-gpus
variant('cuda_arch',
description='CUDA architecture',
values=spack.variant.any_combination_of(
'20', '30', '32', '35', '50', '52', '53', '60', '61',
'62', '70', '72', '75'
))
values=spack.variant.any_combination_of(*cuda_arch_values))
# see http://docs.nvidia.com/cuda/cuda-compiler-driver-nvcc/index.html#nvcc-examples
# and http://llvm.org/docs/CompileCudaWithLLVM.html#compiling-cuda-code
# https://docs.nvidia.com/cuda/cuda-compiler-driver-nvcc/index.html#nvcc-examples
# https://llvm.org/docs/CompileCudaWithLLVM.html#compiling-cuda-code
@staticmethod
def cuda_flags(arch_list):
return [('--generate-code arch=compute_{0},code=sm_{0} '
'--generate-code arch=compute_{0},code=compute_{0}').format(s)
for s in arch_list]
depends_on("cuda@7:", when='+cuda')
depends_on('cuda', when='+cuda')
# CUDA version vs Architecture
depends_on("cuda@8:", when='cuda_arch=60')
depends_on("cuda@8:", when='cuda_arch=61')
depends_on("cuda@8:", when='cuda_arch=62')
depends_on("cuda@9:", when='cuda_arch=70')
depends_on("cuda@9:", when='cuda_arch=72')
depends_on("cuda@10:", when='cuda_arch=75')
# https://en.wikipedia.org/wiki/CUDA#GPUs_supported
depends_on('cuda@:6.0', when='cuda_arch=10')
depends_on('cuda@:6.5', when='cuda_arch=11')
depends_on('cuda@2.1:6.5', when='cuda_arch=12')
depends_on('cuda@2.1:6.5', when='cuda_arch=13')
depends_on('cuda@:8', when='cuda_arch=20')
depends_on('cuda@3.0:8.0', when='cuda_arch=20')
depends_on('cuda@3.2:8.0', when='cuda_arch=21')
depends_on('cuda@5.0:10.2', when='cuda_arch=30')
depends_on('cuda@5.0:10.2', when='cuda_arch=32')
depends_on('cuda@5.0:10.2', when='cuda_arch=35')
depends_on('cuda@6.5:10.2', when='cuda_arch=37')
depends_on('cuda@6.0:', when='cuda_arch=50')
depends_on('cuda@6.5:', when='cuda_arch=52')
depends_on('cuda@6.5:', when='cuda_arch=53')
depends_on('cuda@8.0:', when='cuda_arch=60')
depends_on('cuda@8.0:', when='cuda_arch=61')
depends_on('cuda@8.0:', when='cuda_arch=62')
depends_on('cuda@9.0:', when='cuda_arch=70')
depends_on('cuda@9.0:', when='cuda_arch=72')
depends_on('cuda@10.0:', when='cuda_arch=75')
# There are at least three cases to be aware of for compiler conflicts
# 1. Linux x86_64
@@ -130,18 +156,8 @@ def cuda_flags(arch_list):
# `clang-apple@x.y.z as a possible fix.
# Compiler conflicts will be eventual taken from here:
# https://docs.nvidia.com/cuda/cuda-installation-guide-mac-os-x/index.html#abstract
conflicts('platform=darwin', when='+cuda ^cuda@11.0:')
# Make sure cuda_arch can not be used without +cuda
conflicts('~cuda', when='cuda_arch=20')
conflicts('~cuda', when='cuda_arch=30')
conflicts('~cuda', when='cuda_arch=32')
conflicts('~cuda', when='cuda_arch=35')
conflicts('~cuda', when='cuda_arch=50')
conflicts('~cuda', when='cuda_arch=52')
conflicts('~cuda', when='cuda_arch=53')
conflicts('~cuda', when='cuda_arch=60')
conflicts('~cuda', when='cuda_arch=61')
conflicts('~cuda', when='cuda_arch=62')
conflicts('~cuda', when='cuda_arch=70')
conflicts('~cuda', when='cuda_arch=72')
conflicts('~cuda', when='cuda_arch=75')
for value in cuda_arch_values:
conflicts('~cuda', when='cuda_arch=' + value)

5
lib/spack/spack/caches.py
View File

@@ -51,8 +51,9 @@ def _fetch_cache():
class MirrorCache(object):
def __init__(self, root):
def __init__(self, root, skip_unstable_versions):
self.root = os.path.abspath(root)
self.skip_unstable_versions = skip_unstable_versions
def store(self, fetcher, relative_dest):
"""Fetch and relocate the fetcher's target into our mirror cache."""
@@ -85,5 +86,3 @@ def symlink(self, mirror_ref):
#: Spack's local cache for downloaded source archives
fetch_cache = llnl.util.lang.Singleton(_fetch_cache)
mirror_cache = None

5
lib/spack/spack/ci.py
View File

@@ -947,8 +947,9 @@ 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, mirror_url, None,
True, True, False, False, True, False)
buildcache._createtarball(env, yaml_path, None, True, False,
mirror_url, None, True, False, False, True,
False)
if build_id:
tty.debug('Writing cdashid ({0}) to remote mirror: {1}'.format(
build_id, mirror_url))

126
lib/spack/spack/cmd/buildcache.py
View File

@@ -52,16 +52,35 @@ def setup_parser(subparser):
create.add_argument('-k', '--key', metavar='key',
type=str, default=None,
help="Key for signing.")
create.add_argument('-d', '--directory', metavar='directory',
type=str, default='.',
help="directory in which to save the tarballs.")
output = create.add_mutually_exclusive_group(required=True)
output.add_argument('-d', '--directory',
metavar='directory',
type=str,
help="local directory where " +
"buildcaches will be written.")
output.add_argument('-m', '--mirror-name',
metavar='mirror-name',
type=str,
help="name of the mirror where " +
"buildcaches will be written.")
output.add_argument('--mirror-url',
metavar='mirror-url',
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('-y', '--spec-yaml', default=None,
help='Create buildcache entry for spec from yaml file')
create.add_argument('--no-deps', action='store_true', default='false',
help='Create buildcache entry wo/ dependencies')
create.add_argument('--only', default='package,dependencies',
dest='things_to_install',
choices=['package', 'dependencies'],
help=('Select the buildcache mode. the default is to'
' build a cache for the package along with all'
' its dependencies. Alternatively, one can'
' decide to build a cache for only the package'
' or only the dependencies'))
arguments.add_common_arguments(create, ['specs'])
create.set_defaults(func=createtarball)
@@ -76,6 +95,10 @@ def setup_parser(subparser):
install.add_argument('-u', '--unsigned', action='store_true',
help="install unsigned buildcache" +
" tarballs for testing")
install.add_argument('-o', '--otherarch', action='store_true',
help="install specs from other architectures" +
" instead of default platform and OS")
arguments.add_common_arguments(install, ['specs'])
install.set_defaults(func=installtarball)
@@ -252,7 +275,8 @@ def find_matching_specs(pkgs, allow_multiple_matches=False, env=None):
return specs_from_cli
def match_downloaded_specs(pkgs, allow_multiple_matches=False, force=False):
def match_downloaded_specs(pkgs, allow_multiple_matches=False, force=False,
other_arch=False):
"""Returns a list of specs matching the not necessarily
concretized specs given from cli
@@ -266,7 +290,7 @@ def match_downloaded_specs(pkgs, allow_multiple_matches=False, force=False):
# List of specs that match expressions given via command line
specs_from_cli = []
has_errors = False
allarch = False
allarch = other_arch
specs = bindist.get_specs(force, allarch)
for pkg in pkgs:
matches = []
@@ -299,8 +323,9 @@ def match_downloaded_specs(pkgs, allow_multiple_matches=False, force=False):
return specs_from_cli
def _createtarball(env, spec_yaml, packages, directory, key, no_deps, force,
rel, unsigned, allow_root, no_rebuild_index):
def _createtarball(env, spec_yaml, packages, add_spec, add_deps,
output_location, key, force, rel, unsigned, allow_root,
no_rebuild_index):
if spec_yaml:
packages = set()
with open(spec_yaml, 'r') as fd:
@@ -320,13 +345,12 @@ def _createtarball(env, spec_yaml, packages, directory, key, no_deps, force,
pkgs = set(packages)
specs = set()
outdir = '.'
if directory:
outdir = directory
mirror = spack.mirror.MirrorCollection().lookup(outdir)
mirror = spack.mirror.MirrorCollection().lookup(output_location)
outdir = url_util.format(mirror.push_url)
msg = 'Buildcache files will be output to %s/build_cache' % outdir
tty.msg(msg)
signkey = None
if key:
signkey = key
@@ -342,14 +366,23 @@ def _createtarball(env, spec_yaml, packages, directory, key, no_deps, force,
tty.debug('skipping external or virtual spec %s' %
match.format())
else:
tty.debug('adding matching spec %s' % match.format())
specs.add(match)
if no_deps is True:
if add_spec:
tty.debug('adding matching spec %s' % match.format())
specs.add(match)
else:
tty.debug('skipping matching spec %s' % match.format())
if not add_deps:
continue
tty.debug('recursing dependencies')
for d, node in match.traverse(order='post',
depth=True,
deptype=('link', 'run')):
# skip root, since it's handled above
if d == 0:
continue
if node.external or node.virtual:
tty.debug('skipping external or virtual dependency %s' %
node.format())
@@ -360,14 +393,10 @@ def _createtarball(env, spec_yaml, packages, directory, key, no_deps, force,
tty.debug('writing tarballs to %s/build_cache' % outdir)
for spec in specs:
tty.msg('creating binary cache file for package %s ' % spec.format())
try:
bindist.build_tarball(spec, outdir, force, rel,
unsigned, allow_root, signkey,
not no_rebuild_index)
except Exception as e:
tty.warn('%s' % e)
pass
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)
def createtarball(args):
@@ -376,9 +405,47 @@ def createtarball(args):
# restrict matching to current environment if one is active
env = ev.get_env(args, 'buildcache create')
_createtarball(env, args.spec_yaml, args.specs, args.directory,
args.key, args.no_deps, args.force, args.rel, args.unsigned,
args.allow_root, args.no_rebuild_index)
output_location = None
if args.directory:
output_location = args.directory
# User meant to provide a path to a local directory.
# Ensure that they did not accidentally pass a URL.
scheme = url_util.parse(output_location, scheme='<missing>').scheme
if scheme != '<missing>':
raise ValueError(
'"--directory" expected a local path; got a URL, instead')
# User meant to provide a path to a local directory.
# Ensure that the mirror lookup does not mistake it for a named mirror.
output_location = 'file://' + output_location
elif args.mirror_name:
output_location = args.mirror_name
# User meant to provide the name of a preconfigured mirror.
# Ensure that the mirror lookup actually returns a named mirror.
result = spack.mirror.MirrorCollection().lookup(output_location)
if result.name == "<unnamed>":
raise ValueError(
'no configured mirror named "{name}"'.format(
name=output_location))
elif args.mirror_url:
output_location = args.mirror_url
# User meant to provide a URL for an anonymous mirror.
# Ensure that they actually provided a URL.
scheme = url_util.parse(output_location, scheme='<missing>').scheme
if scheme == '<missing>':
raise ValueError(
'"{url}" is not a valid URL'.format(url=output_location))
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)
def installtarball(args):
@@ -387,7 +454,8 @@ 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)
matches = match_downloaded_specs(pkgs, args.multiple, args.force,
args.otherarch)
for match in matches:
install_tarball(match, args)

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

@@ -45,7 +45,10 @@ def setup_parser(subparser):
" (this requires significant time and space)")
create_parser.add_argument(
'-f', '--file', help="file with specs of packages to put in mirror")
create_parser.add_argument(
'--skip-unstable-versions', action='store_true',
help="don't cache versions unless they identify a stable (unchanging)"
" source code")
create_parser.add_argument(
'-D', '--dependencies', action='store_true',
help="also fetch all dependencies")
@@ -308,7 +311,8 @@ def mirror_create(args):
existed = web_util.url_exists(directory)
# Actually do the work to create the mirror
present, mirrored, error = spack.mirror.create(directory, mirror_specs)
present, mirrored, error = spack.mirror.create(
directory, mirror_specs, args.skip_unstable_versions)
p, m, e = len(present), len(mirrored), len(error)
verb = "updated" if existed else "created"

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

@@ -154,7 +154,7 @@ def test(parser, args, unknown_args):
# The default is to test the core of Spack. If the option `--extension`
# has been used, then test that extension.
pytest_root = spack.paths.test_path
pytest_root = spack.paths.spack_root
if args.extension:
target = args.extension
extensions = spack.config.get('config:extensions')

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

@@ -97,6 +97,7 @@
config_defaults = {
'config': {
'debug': False,
'connect_timeout': 10,
'verify_ssl': True,
'checksum': True,
'dirty': False,
@@ -279,6 +280,7 @@ def __init__(self, name, data=None):
self.sections = syaml.syaml_dict()
if data:
data = InternalConfigScope._process_dict_keyname_overrides(data)
for section in data:
dsec = data[section]
validate({section: dsec}, section_schemas[section])
@@ -305,6 +307,25 @@ def write_section(self, section):
def __repr__(self):
return '<InternalConfigScope: %s>' % self.name
@staticmethod
def _process_dict_keyname_overrides(data):
"""Turn a trailing `:' in a key name into an override attribute."""
result = {}
for sk, sv in iteritems(data):
if sk.endswith(':'):
key = syaml.syaml_str(sk[:-1])
key.override = True
else:
key = sk
if isinstance(sv, dict):
result[key]\
= InternalConfigScope._process_dict_keyname_overrides(sv)
else:
result[key] = copy.copy(sv)
return result
class Configuration(object):
"""A full Spack configuration, from a hierarchy of config files.
@@ -504,14 +525,14 @@ def set(self, path, value, scope=None):
Accepts the path syntax described in ``get()``.
"""
section, _, rest = path.partition(':')
parts = _process_config_path(path)
section = parts.pop(0)
if not rest:
if not parts:
self.update_config(section, value, scope=scope)
else:
section_data = self.get_config(section, scope=scope)
parts = rest.split(':')
data = section_data
while len(parts) > 1:
key = parts.pop(0)
@@ -611,7 +632,7 @@ def _config():
"""Singleton Configuration instance.
This constructs one instance associated with this module and returns
it. It is bundled inside a function so that configuratoin can be
it. It is bundled inside a function so that configuration can be
initialized lazily.
Return:
@@ -762,17 +783,12 @@ def _merge_yaml(dest, source):
Config file authors can optionally end any attribute in a dict
with `::` instead of `:`, and the key will override that of the
parent instead of merging.
"""
def they_are(t):
return isinstance(dest, t) and isinstance(source, t)
# If both are None, handle specially and return None.
if source is None and dest is None:
return None
# If source is None, overwrite with source.
elif source is None:
if source is None:
return None
# Source list is prepended (for precedence)
@@ -798,8 +814,9 @@ def they_are(t):
# to copy mark information on source keys to dest.
key_marks[sk] = sk
# ensure that keys are marked in the destination. the key_marks dict
# ensures we can get the actual source key objects from dest keys
# ensure that keys are marked in the destination. The
# key_marks dict ensures we can get the actual source key
# objects from dest keys
for dk in list(dest.keys()):
if dk in key_marks and syaml.markable(dk):
syaml.mark(dk, key_marks[dk])
@@ -811,9 +828,34 @@ def they_are(t):
return dest
# In any other case, overwrite with a copy of the source value.
else:
return copy.copy(source)
# If we reach here source and dest are either different types or are
# not both lists or dicts: replace with source.
return copy.copy(source)
#
# Process a path argument to config.set() that may contain overrides ('::' or
# trailing ':')
#
def _process_config_path(path):
result = []
if path.startswith(':'):
raise syaml.SpackYAMLError("Illegal leading `:' in path `{0}'".
format(path), '')
seen_override_in_path = False
while path:
front, sep, path = path.partition(':')
if (sep and not path) or path.startswith(':'):
if seen_override_in_path:
raise syaml.SpackYAMLError("Meaningless second override"
" indicator `::' in path `{0}'".
format(path), '')
path = path.lstrip(':')
front = syaml.syaml_str(front)
front.override = True
seen_override_in_path = True
result.append(front)
return result
#

138
lib/spack/spack/database.py
View File

@@ -18,32 +18,27 @@
as the authoritative database of packages in Spack. This module
provides a cache and a sanity checking mechanism for what is in the
filesystem.
"""
import datetime
import time
import os
import sys
import socket
import contextlib
from six import string_types
from six import iteritems
from ruamel.yaml.error import MarkedYAMLError, YAMLError
import contextlib
import datetime
import os
import socket
import sys
import time
import llnl.util.tty as tty
from llnl.util.filesystem import mkdirp
import spack.store
import six
import spack.repo
import spack.spec
import spack.store
import spack.util.lock as lk
import spack.util.spack_yaml as syaml
import spack.util.spack_json as sjson
from spack.filesystem_view import YamlFilesystemView
from spack.util.crypto import bit_length
from llnl.util.filesystem import mkdirp
from spack.directory_layout import DirectoryLayoutError
from spack.error import SpackError
from spack.filesystem_view import YamlFilesystemView
from spack.util.crypto import bit_length
from spack.version import Version
# TODO: Provide an API automatically retyring a build after detecting and
@@ -284,27 +279,20 @@ def __init__(self, root, db_dir=None, upstream_dbs=None,
exist. This is the ``db_dir``.
The Database will attempt to read an ``index.json`` file in
``db_dir``. If it does not find one, it will fall back to read
an ``index.yaml`` if one is present. If that does not exist, it
will create a database when needed by scanning the entire
Database root for ``spec.yaml`` files according to Spack's
``DirectoryLayout``.
``db_dir``. If that does not exist, it will create a database
when needed by scanning the entire Database root for ``spec.yaml``
files according to Spack's ``DirectoryLayout``.
Caller may optionally provide a custom ``db_dir`` parameter
where data will be stored. This is intended to be used for
where data will be stored. This is intended to be used for
testing the Database class.
"""
self.root = root
if db_dir is None:
# If the db_dir is not provided, default to within the db root.
self._db_dir = os.path.join(self.root, _db_dirname)
else:
# Allow customizing the database directory location for testing.
self._db_dir = db_dir
# If the db_dir is not provided, default to within the db root.
self._db_dir = db_dir or os.path.join(self.root, _db_dirname)
# Set up layout of database files within the db dir
self._old_yaml_index_path = os.path.join(self._db_dir, 'index.yaml')
self._index_path = os.path.join(self._db_dir, 'index.json')
self._lock_path = os.path.join(self._db_dir, 'lock')
@@ -358,8 +346,8 @@ def __init__(self, root, db_dir=None, upstream_dbs=None,
}
try:
sjson.dump(database, f)
except YAMLError as e:
raise syaml.SpackYAMLError(
except Exception as e:
raise Exception(
"error writing YAML database:", str(e))
self.lock = ForbiddenLock()
else:
@@ -572,7 +560,8 @@ def prefix_write_lock(self, spec):
prefix_lock.release_write()
def _write_to_file(self, stream):
"""Write out the databsae to a JSON file.
"""Write out the database in JSON format to the stream passed
as argument.
This function does not do any locking or transactions.
"""
@@ -594,9 +583,8 @@ def _write_to_file(self, stream):
try:
sjson.dump(database, stream)
except YAMLError as e:
raise syaml.SpackYAMLError(
"error writing YAML database:", str(e))
except (TypeError, ValueError) as e:
raise sjson.SpackJSONError("error writing JSON database:", str(e))
def _read_spec_from_dict(self, hash_key, installs):
"""Recursively construct a spec from a hash in a YAML database.
@@ -667,28 +655,15 @@ def _assign_dependencies(self, hash_key, installs, data):
spec._add_dependency(child, dtypes)
def _read_from_file(self, stream, format='json'):
"""
Fill database from file, do not maintain old data
Translate the spec portions from node-dict form to spec form
def _read_from_file(self, filename):
"""Fill database from file, do not maintain old data.
Translate the spec portions from node-dict form to spec form.
Does not do any locking.
"""
if format.lower() == 'json':
load = sjson.load
elif format.lower() == 'yaml':
load = syaml.load
else:
raise ValueError("Invalid database format: %s" % format)
try:
if isinstance(stream, string_types):
with open(stream, 'r') as f:
fdata = load(f)
else:
fdata = load(stream)
except MarkedYAMLError as e:
raise syaml.SpackYAMLError("error parsing YAML database:", str(e))
with open(filename, 'r') as f:
fdata = sjson.load(f)
except Exception as e:
raise CorruptDatabaseError("error parsing database:", str(e))
@@ -700,12 +675,12 @@ def check(cond, msg):
raise CorruptDatabaseError(
"Spack database is corrupt: %s" % msg, self._index_path)
check('database' in fdata, "No 'database' attribute in YAML.")
check('database' in fdata, "no 'database' attribute in JSON DB.")
# High-level file checks
db = fdata['database']
check('installs' in db, "No 'installs' in YAML DB.")
check('version' in db, "No 'version' in YAML DB.")
check('installs' in db, "no 'installs' in JSON DB.")
check('version' in db, "no 'version' in JSON DB.")
installs = db['installs']
@@ -781,7 +756,6 @@ def reindex(self, directory_layout):
"""Build database index from scratch based on a directory layout.
Locks the DB if it isn't locked already.
"""
if self.is_upstream:
raise UpstreamDatabaseLockingError(
@@ -945,7 +919,6 @@ def _write(self, type, value, traceback):
after the start of the next transaction, when it read from disk again.
This routine does no locking.
"""
# Do not write if exceptions were raised
if type is not None:
@@ -970,35 +943,23 @@ def _read(self):
"""Re-read Database from the data in the set location.
This does no locking, with one exception: it will automatically
migrate an index.yaml to an index.json if possible. This requires
taking a write lock.
try to regenerate a missing DB if local. This requires taking a
write lock.
"""
if os.path.isfile(self._index_path):
# Read from JSON file if a JSON database exists
self._read_from_file(self._index_path, format='json')
# Read from file if a database exists
self._read_from_file(self._index_path)
return
elif self.is_upstream:
raise UpstreamDatabaseLockingError(
"No database index file is present, and upstream"
" databases cannot generate an index file")
elif os.path.isfile(self._old_yaml_index_path):
if (not self.is_upstream) and os.access(
self._db_dir, os.R_OK | os.W_OK):
# if we can write, then read AND write a JSON file.
self._read_from_file(self._old_yaml_index_path, format='yaml')
with lk.WriteTransaction(self.lock):
self._write(None, None, None)
else:
# Read chck for a YAML file if we can't find JSON.
self._read_from_file(self._old_yaml_index_path, format='yaml')
else:
if self.is_upstream:
raise UpstreamDatabaseLockingError(
"No database index file is present, and upstream"
" databases cannot generate an index file")
# The file doesn't exist, try to traverse the directory.
# reindex() takes its own write lock, so no lock here.
with lk.WriteTransaction(self.lock):
self._write(None, None, None)
self.reindex(spack.store.layout)
# The file doesn't exist, try to traverse the directory.
# reindex() takes its own write lock, so no lock here.
with lk.WriteTransaction(self.lock):
self._write(None, None, None)
self.reindex(spack.store.layout)
def _add(
self,
@@ -1078,7 +1039,9 @@ def _add(
)
# Connect dependencies from the DB to the new copy.
for name, dep in iteritems(spec.dependencies_dict(_tracked_deps)):
for name, dep in six.iteritems(
spec.dependencies_dict(_tracked_deps)
):
dkey = dep.spec.dag_hash()
upstream, record = self.query_by_spec_hash(dkey)
new_spec._add_dependency(record.spec, dep.deptypes)
@@ -1151,8 +1114,7 @@ def _increment_ref_count(self, spec):
rec.ref_count += 1
def _remove(self, spec):
"""Non-locking version of remove(); does real work.
"""
"""Non-locking version of remove(); does real work."""
key = self._get_matching_spec_key(spec)
rec = self._data[key]

30
lib/spack/spack/fetch_strategy.py
View File

@@ -257,7 +257,7 @@ def __init__(self, url=None, checksum=None, **kwargs):
self.digest = kwargs[h]
self.expand_archive = kwargs.get('expand', True)
self.extra_curl_options = kwargs.get('curl_options', [])
self.extra_options = kwargs.get('fetch_options', [])
self._curl = None
self.extension = kwargs.get('extension', None)
@@ -326,8 +326,6 @@ def _fetch_from_url(self, url):
'-D',
'-', # print out HTML headers
'-L', # resolve 3xx redirects
# Timeout if can't establish a connection after 10 sec.
'--connect-timeout', '10',
url,
]
@@ -339,7 +337,22 @@ def _fetch_from_url(self, url):
else:
curl_args.append('-sS') # just errors when not.
curl_args += self.extra_curl_options
connect_timeout = spack.config.get('config:connect_timeout')
if self.extra_options:
cookie = self.extra_options.get('cookie')
if cookie:
curl_args.append('-j') # junk cookies
curl_args.append('-b') # specify cookie
curl_args.append(cookie)
timeout = self.extra_options.get('timeout')
if timeout:
connect_timeout = max(connect_timeout, int(timeout))
if connect_timeout > 0:
# Timeout if can't establish a connection after n sec.
curl_args.extend(['--connect-timeout', str(connect_timeout)])
# Run curl but grab the mime type from the http headers
curl = self.curl
@@ -1166,6 +1179,15 @@ def fetch(self):
raise FailedDownloadError(self.url)
def stable_target(fetcher):
"""Returns whether the fetcher target is expected to have a stable
checksum. This is only true if the target is a preexisting archive
file."""
if isinstance(fetcher, URLFetchStrategy) and fetcher.cachable:
return True
return False
def from_url(url):
"""Given a URL, find an appropriate fetch strategy for it.
Currently just gives you a URLFetchStrategy that uses curl.

79
lib/spack/spack/installer.py Executable file → Normal file
View File

@@ -651,6 +651,66 @@ def _add_bootstrap_compilers(self, pkg):
if package_id(comp_pkg) not in self.build_tasks:
self._push_task(comp_pkg, is_compiler, 0, 0, STATUS_ADDED)
def _check_db(self, spec):
"""Determine if the spec is flagged as installed in the database
Args:
spec (Spec): spec whose database install status is being checked
Return:
(rec, installed_in_db) tuple where rec is the database record, or
None, if there is no matching spec, and installed_in_db is
``True`` if the spec is considered installed and ``False``
otherwise
"""
try:
rec = spack.store.db.get_record(spec)
installed_in_db = rec.installed if rec else False
except KeyError:
# KeyError is raised if there is no matching spec in the database
# (versus no matching specs that are installed).
rec = None
installed_in_db = False
return rec, installed_in_db
def _check_deps_status(self):
"""Check the install status of the explicit spec's dependencies"""
err = 'Cannot proceed with {0}: {1}'
for dep in self.spec.traverse(order='post', root=False):
dep_pkg = dep.package
dep_id = package_id(dep_pkg)
# Check for failure since a prefix lock is not required
if spack.store.db.prefix_failed(dep):
action = "'spack install' the dependency"
msg = '{0} is marked as an install failure: {1}' \
.format(dep_id, action)
raise InstallError(err.format(self.pkg_id, msg))
# Attempt to get a write lock to ensure another process does not
# uninstall the dependency while the requested spec is being
# installed
ltype, lock = self._ensure_locked('write', dep_pkg)
if lock is None:
msg = '{0} is write locked by another process'.format(dep_id)
raise InstallError(err.format(self.pkg_id, msg))
# Flag external and upstream packages as being installed
if dep_pkg.spec.external or dep_pkg.installed_upstream:
form = 'external' if dep_pkg.spec.external else 'upstream'
tty.debug('Flagging {0} {1} as installed'.format(form, dep_id))
self.installed.add(dep_id)
continue
# Check the database to see if the dependency has been installed
# and flag as such if appropriate
rec, installed_in_db = self._check_db(dep)
if installed_in_db:
tty.debug('Flagging {0} as installed per the database'
.format(dep_id))
self.installed.add(dep_id)
def _prepare_for_install(self, task, keep_prefix, keep_stage,
restage=False):
"""
@@ -680,14 +740,7 @@ def _prepare_for_install(self, task, keep_prefix, keep_stage,
return
# Determine if the spec is flagged as installed in the database
try:
rec = spack.store.db.get_record(task.pkg.spec)
installed_in_db = rec.installed if rec else False
except KeyError:
# KeyError is raised if there is no matching spec in the database
# (versus no matching specs that are installed).
rec = None
installed_in_db = False
rec, installed_in_db = self._check_db(task.pkg.spec)
# Make sure the installation directory is in the desired state
# for uninstalled specs.
@@ -929,6 +982,11 @@ def _init_queue(self, install_deps, install_package):
# Be sure to clear any previous failure
spack.store.db.clear_failure(self.pkg.spec, force=True)
# If not installing dependencies, then determine their
# installation status before proceeding
if not install_deps:
self._check_deps_status()
# Now add the package itself, if appropriate
self._push_task(self.pkg, False, 0, 0, STATUS_ADDED)
@@ -1022,7 +1080,8 @@ def build_process():
configure_args = getattr(pkg, attr)()
configure_args = ' '.join(configure_args)
with open(pkg.configure_args_path, 'w') as args_file:
with open(pkg.configure_args_path, 'w') as \
args_file:
args_file.write(configure_args)
break
@@ -1095,7 +1154,7 @@ def build_process():
except StopIteration as e:
# A StopIteration exception means that do_install was asked to
# stop early from clients.
tty.msg('{0} {1}'.format(self.pid, e.message))
tty.msg('{0} {1}'.format(self.pid, str(e)))
tty.msg('Package stage directory : {0}'
.format(pkg.stage.source_path))

29
lib/spack/spack/mirror.py
View File

@@ -401,7 +401,7 @@ def get_matching_versions(specs, num_versions=1):
return matching
def create(path, specs):
def create(path, specs, skip_unstable_versions=False):
"""Create a directory to be used as a spack mirror, and fill it with
package archives.
@@ -409,6 +409,9 @@ def create(path, specs):
path: Path to create a mirror directory hierarchy in.
specs: Any package versions matching these specs will be added \
to the mirror.
skip_unstable_versions: if true, this skips adding resources when
they do not have a stable archive checksum (as determined by
``fetch_strategy.stable_target``)
Return Value:
Returns a tuple of lists: (present, mirrored, error)
@@ -440,16 +443,14 @@ def create(path, specs):
raise MirrorError(
"Cannot create directory '%s':" % mirror_root, str(e))
mirror_cache = spack.caches.MirrorCache(mirror_root)
mirror_cache = spack.caches.MirrorCache(
mirror_root, skip_unstable_versions=skip_unstable_versions)
mirror_stats = MirrorStats()
try:
spack.caches.mirror_cache = mirror_cache
# Iterate through packages and download all safe tarballs for each
for spec in specs:
mirror_stats.next_spec(spec)
add_single_spec(spec, mirror_root, mirror_stats)
finally:
spack.caches.mirror_cache = None
# Iterate through packages and download all safe tarballs for each
for spec in specs:
mirror_stats.next_spec(spec)
_add_single_spec(spec, mirror_cache, mirror_stats)
return mirror_stats.stats()
@@ -495,7 +496,7 @@ def error(self):
self.errors.add(self.current_spec)
def add_single_spec(spec, mirror_root, mirror_stats):
def _add_single_spec(spec, mirror, mirror_stats):
tty.msg("Adding package {pkg} to mirror".format(
pkg=spec.format("{name}{@version}")
))
@@ -503,10 +504,10 @@ def add_single_spec(spec, mirror_root, mirror_stats):
while num_retries > 0:
try:
with spec.package.stage as pkg_stage:
pkg_stage.cache_mirror(mirror_stats)
pkg_stage.cache_mirror(mirror, mirror_stats)
for patch in spec.package.all_patches():
if patch.cache():
patch.cache().cache_mirror(mirror_stats)
if patch.stage:
patch.stage.cache_mirror(mirror, mirror_stats)
patch.clean()
exception = None
break

7
lib/spack/spack/modules/common.py
View File

@@ -344,7 +344,11 @@ def get_module(module_type, spec, get_full_path, required=True):
The module name or path. May return ``None`` if the module is not
available.
"""
if spec.package.installed_upstream:
try:
upstream = spec.package.installed_upstream
except spack.repo.UnknownPackageError:
upstream, record = spack.store.db.query_by_spec_hash(spec.dag_hash())
if upstream:
module = (spack.modules.common.upstream_module_index
.upstream_module(spec, module_type))
if not module:
@@ -426,6 +430,7 @@ def suffixes(self):
for constraint, suffix in self.conf.get('suffixes', {}).items():
if constraint in self.spec:
suffixes.append(suffix)
suffixes = sorted(set(suffixes))
if self.hash:
suffixes.append(self.hash)
return suffixes

4
lib/spack/spack/package.py
View File

@@ -1135,8 +1135,8 @@ def do_fetch(self, mirror_only=False):
for patch in self.spec.patches:
patch.fetch()
if patch.cache():
patch.cache().cache_local()
if patch.stage:
patch.stage.cache_local()
def do_stage(self, mirror_only=False):
"""Unpacks and expands the fetched tarball."""

6
lib/spack/spack/patch.py
View File

@@ -85,7 +85,8 @@ def apply(self, stage):
apply_patch(stage, self.path, self.level, self.working_dir)
def cache(self):
@property
def stage(self):
return None
def to_dict(self):
@@ -248,9 +249,6 @@ def stage(self):
self._stage.create()
return self._stage
def cache(self):
return self.stage
def clean(self):
self.stage.destroy()

38
lib/spack/spack/relocate.py
View File

@@ -398,10 +398,44 @@ def replace_prefix_text(path_name, old_dir, new_dir):
def replace_prefix_bin(path_name, old_dir, new_dir):
"""
Attempt to replace old install prefix with new install prefix
in binary files by prefixing new install prefix with os.sep
until the lengths of the prefixes are the same.
"""
def replace(match):
occurances = match.group().count(old_dir.encode('utf-8'))
olen = len(old_dir.encode('utf-8'))
nlen = len(new_dir.encode('utf-8'))
padding = (olen - nlen) * occurances
if padding < 0:
return data
return match.group().replace(old_dir.encode('utf-8'),
os.sep.encode('utf-8') * padding +
new_dir.encode('utf-8'))
with open(path_name, 'rb+') as f:
data = f.read()
f.seek(0)
original_data_len = len(data)
pat = re.compile(old_dir.encode('utf-8') + b'([^\0]*?)\0')
if not pat.search(data):
return
ndata = pat.sub(replace, data)
if not len(ndata) == original_data_len:
raise BinaryStringReplacementException(
path_name, original_data_len, len(ndata))
f.write(ndata)
f.truncate()
def replace_prefix_nullterm(path_name, old_dir, new_dir):
"""
Attempt to replace old install prefix with new install prefix
in binary files by replacing with null terminated string
that is the same length unless the old path is shorter
Used on linux to replace mach-o rpaths
"""
def replace(match):
@@ -413,7 +447,6 @@ def replace(match):
return data
return match.group().replace(old_dir.encode('utf-8'),
new_dir.encode('utf-8')) + b'\0' * padding
with open(path_name, 'rb+') as f:
data = f.read()
f.seek(0)
@@ -466,8 +499,7 @@ def relocate_macho_binaries(path_names, old_dir, new_dir, allow_root):
modify_object_macholib(path_name, placeholder, new_dir)
modify_object_macholib(path_name, old_dir, new_dir)
if len(new_dir) <= len(old_dir):
replace_prefix_bin(path_name, old_dir,
new_dir)
replace_prefix_nullterm(path_name, old_dir, new_dir)
else:
tty.warn('Cannot do a binary string replacement'
' with padding for %s'

1
lib/spack/spack/schema/config.py
View File

@@ -55,6 +55,7 @@
},
'source_cache': {'type': 'string'},
'misc_cache': {'type': 'string'},
'connect_timeout': {'type': 'integer', 'minimum': 0},
'verify_ssl': {'type': 'boolean'},
'suppress_gpg_warnings': {'type': 'boolean'},
'install_missing_compilers': {'type': 'boolean'},

8
lib/spack/spack/spec.py
View File

@@ -369,6 +369,10 @@ def _satisfies_target(self, other_target, strict):
if not need_to_check:
return True
# self is not concrete, but other_target is there and strict=True
if self.target is None:
return False
for target_range in str(other_target).split(','):
t_min, sep, t_max = target_range.partition(':')
@@ -1919,9 +1923,7 @@ def from_dict(data):
yaml_deps = node[name]['dependencies']
for dname, dhash, dtypes in Spec.read_yaml_dep_specs(yaml_deps):
# Fill in dependencies by looking them up by name in deps dict
deps[name]._dependencies[dname] = DependencySpec(
deps[name], deps[dname], dtypes)
deps[name]._add_dependency(deps[dname], dtypes)
return spec

21
lib/spack/spack/stage.py
View File

@@ -494,8 +494,14 @@ def cache_local(self):
spack.caches.fetch_cache.store(
self.fetcher, self.mirror_paths.storage_path)
def cache_mirror(self, stats):
"""Perform a fetch if the resource is not already cached"""
def cache_mirror(self, mirror, stats):
"""Perform a fetch if the resource is not already cached
Arguments:
mirror (MirrorCache): the mirror to cache this Stage's resource in
stats (MirrorStats): this is updated depending on whether the
caching operation succeeded or failed
"""
if isinstance(self.default_fetcher, fs.BundleFetchStrategy):
# BundleFetchStrategy has no source to fetch. The associated
# fetcher does nothing but the associated stage may still exist.
@@ -506,20 +512,23 @@ def cache_mirror(self, stats):
# must examine the type of the fetcher.
return
dst_root = spack.caches.mirror_cache.root
if (mirror.skip_unstable_versions and
not fs.stable_target(self.default_fetcher)):
return
absolute_storage_path = os.path.join(
dst_root, self.mirror_paths.storage_path)
mirror.root, self.mirror_paths.storage_path)
if os.path.exists(absolute_storage_path):
stats.already_existed(absolute_storage_path)
else:
self.fetch()
self.check()
spack.caches.mirror_cache.store(
mirror.store(
self.fetcher, self.mirror_paths.storage_path)
stats.added(absolute_storage_path)
spack.caches.mirror_cache.symlink(self.mirror_paths)
mirror.symlink(self.mirror_paths)
def expand_archive(self):
"""Changes to the stage directory and attempt to expand the downloaded

13
lib/spack/spack/test/architecture.py
View File

@@ -214,3 +214,16 @@ def test_optimization_flags_with_custom_versions(
)
opt_flags = target.optimization_flags(compiler)
assert opt_flags == expected_flags
@pytest.mark.regression('15306')
@pytest.mark.parametrize('architecture_tuple,constraint_tuple', [
(('linux', 'ubuntu18.04', None), ('linux', None, 'x86_64')),
(('linux', 'ubuntu18.04', None), ('linux', None, 'x86_64:')),
])
def test_satisfy_strict_constraint_when_not_concrete(
architecture_tuple, constraint_tuple
):
architecture = spack.spec.ArchSpec(architecture_tuple)
constraint = spack.spec.ArchSpec(constraint_tuple)
assert not architecture.satisfies(constraint, strict=True)

15
lib/spack/spack/test/cmd/buildcache.py
View File

@@ -3,6 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import errno
import platform
import pytest
@@ -11,6 +12,7 @@
import spack.binary_distribution
buildcache = spack.main.SpackCommand('buildcache')
install = spack.main.SpackCommand('install')
@pytest.fixture()
@@ -41,3 +43,16 @@ def test_buildcache_list_duplicates(mock_get_specs, capsys):
output = buildcache('list', 'mpileaks', '@2.3')
assert output.count('mpileaks') == 3
def test_buildcache_create_fail_on_perm_denied(
install_mockery, mock_fetch, monkeypatch, tmpdir):
"""Ensure that buildcache create fails on permission denied error."""
install('trivial-install-test-package')
tmpdir.chmod(0)
with pytest.raises(OSError) as error:
buildcache('create', '-d', str(tmpdir),
'--unsigned', 'trivial-install-test-package')
assert error.value.errno == errno.EACCES
tmpdir.chmod(0o700)

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

@@ -672,6 +672,30 @@ def test_install_only_dependencies(tmpdir, mock_fetch, install_mockery):
assert not os.path.exists(root.prefix)
def test_install_only_package(tmpdir, mock_fetch, install_mockery, capfd):
msg = ''
with capfd.disabled():
try:
install('--only', 'package', 'dependent-install')
except spack.installer.InstallError as e:
msg = str(e)
assert 'Cannot proceed with dependent-install' in msg
assert '1 uninstalled dependency' in msg
def test_install_deps_then_package(tmpdir, mock_fetch, install_mockery):
dep = Spec('dependency-install').concretized()
root = Spec('dependent-install').concretized()
install('--only', 'dependencies', 'dependent-install')
assert os.path.exists(dep.prefix)
assert not os.path.exists(root.prefix)
install('--only', 'package', 'dependent-install')
assert os.path.exists(root.prefix)
@pytest.mark.regression('12002')
def test_install_only_dependencies_in_env(tmpdir, mock_fetch, install_mockery,
mutable_mock_env_path):

23
lib/spack/spack/test/cmd/mirror.py
View File

@@ -66,6 +66,29 @@ def test_mirror_from_env(tmpdir, mock_packages, mock_fetch, config,
assert mirror_res == expected
@pytest.fixture
def source_for_pkg_with_hash(mock_packages, tmpdir):
pkg = spack.repo.get('trivial-pkg-with-valid-hash')
local_url_basename = os.path.basename(pkg.url)
local_path = os.path.join(str(tmpdir), local_url_basename)
with open(local_path, 'w') as f:
f.write(pkg.hashed_content)
local_url = "file://" + local_path
pkg.versions[spack.version.Version('1.0')]['url'] = local_url
def test_mirror_skip_unstable(tmpdir_factory, mock_packages, config,
source_for_pkg_with_hash):
mirror_dir = str(tmpdir_factory.mktemp('mirror-dir'))
specs = [spack.spec.Spec(x).concretized() for x in
['git-test', 'trivial-pkg-with-valid-hash']]
spack.mirror.create(mirror_dir, specs, skip_unstable_versions=True)
assert (set(os.listdir(mirror_dir)) - set(['_source-cache']) ==
set(['trivial-pkg-with-valid-hash']))
def test_mirror_crud(tmp_scope, capsys):
with capsys.disabled():
mirror('add', '--scope', tmp_scope, 'mirror', 'http://spack.io')

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

@@ -6,6 +6,7 @@
from spack.main import SpackCommand
spack_test = SpackCommand('test')
cmd_test_py = 'lib/spack/spack/test/cmd/test.py'
def test_list():
@@ -16,13 +17,13 @@ def test_list():
def test_list_with_pytest_arg():
output = spack_test('--list', 'cmd/test.py')
assert output.strip() == "cmd/test.py"
output = spack_test('--list', cmd_test_py)
assert output.strip() == cmd_test_py
def test_list_with_keywords():
output = spack_test('--list', '-k', 'cmd/test.py')
assert output.strip() == "cmd/test.py"
assert output.strip() == cmd_test_py
def test_list_long(capsys):
@@ -44,7 +45,7 @@ def test_list_long(capsys):
def test_list_long_with_pytest_arg(capsys):
with capsys.disabled():
output = spack_test('--list-long', 'cmd/test.py')
output = spack_test('--list-long', cmd_test_py)
assert "test.py::\n" in output
assert "test_list" in output
assert "test_list_with_pytest_arg" in output
@@ -74,7 +75,7 @@ def test_list_names():
def test_list_names_with_pytest_arg():
output = spack_test('--list-names', 'cmd/test.py')
output = spack_test('--list-names', cmd_test_py)
assert "test.py::test_list\n" in output
assert "test.py::test_list_with_pytest_arg\n" in output
assert "test.py::test_list_with_keywords\n" in output

26
lib/spack/spack/test/concretize_preferences.py
View File

@@ -15,15 +15,15 @@
@pytest.fixture()
def concretize_scope(config, tmpdir):
def concretize_scope(mutable_config, tmpdir):
"""Adds a scope for concretization preferences"""
tmpdir.ensure_dir('concretize')
config.push_scope(
mutable_config.push_scope(
ConfigScope('concretize', str(tmpdir.join('concretize'))))
yield
config.pop_scope()
mutable_config.pop_scope()
spack.repo.path._provider_index = None
@@ -84,16 +84,24 @@ def test_preferred_variants(self):
'mpileaks', debug=True, opt=True, shared=False, static=False
)
def test_preferred_compilers(self, mutable_mock_repo):
def test_preferred_compilers(self):
"""Test preferred compilers are applied correctly
"""
update_packages('mpileaks', 'compiler', ['clang@3.3'])
spec = concretize('mpileaks')
assert spec.compiler == spack.spec.CompilerSpec('clang@3.3')
# Need to make sure the test uses an available compiler
compiler_list = spack.compilers.all_compiler_specs()
assert compiler_list
update_packages('mpileaks', 'compiler', ['gcc@4.5.0'])
# Try the first available compiler
compiler = str(compiler_list[0])
update_packages('mpileaks', 'compiler', [compiler])
spec = concretize('mpileaks')
assert spec.compiler == spack.spec.CompilerSpec('gcc@4.5.0')
assert spec.compiler == spack.spec.CompilerSpec(compiler)
# Try the last available compiler
compiler = str(compiler_list[-1])
update_packages('mpileaks', 'compiler', [compiler])
spec = concretize('mpileaks')
assert spec.compiler == spack.spec.CompilerSpec(compiler)
def test_preferred_target(self, mutable_mock_repo):
"""Test preferred compilers are applied correctly

87
lib/spack/spack/test/config.py
View File

@@ -46,7 +46,19 @@
config_override_list = {
'config': {
'build_stage:': ['patha', 'pathb']}}
'build_stage:': ['pathd', 'pathe']}}
config_merge_dict = {
'config': {
'info': {
'a': 3,
'b': 4}}}
config_override_dict = {
'config': {
'info:': {
'a': 7,
'c': 9}}}
@pytest.fixture()
@@ -382,7 +394,7 @@ def test_read_config_override_list(mock_low_high_config, write_config_file):
write_config_file('config', config_override_list, 'high')
assert spack.config.get('config') == {
'install_tree': 'install_tree_path',
'build_stage': ['patha', 'pathb']
'build_stage': config_override_list['config']['build_stage:']
}
@@ -857,3 +869,74 @@ def test_dotkit_in_config_does_not_raise(
# we throw a a deprecation warning without raising
assert '_sp_sys_type' in captured[0] # stdout
assert 'Warning' in captured[1] # stderr
def test_internal_config_section_override(mock_low_high_config,
write_config_file):
write_config_file('config', config_merge_list, 'low')
wanted_list = config_override_list['config']['build_stage:']
mock_low_high_config.push_scope(spack.config.InternalConfigScope
('high', {
'config:': {
'build_stage': wanted_list
}
}))
assert mock_low_high_config.get('config:build_stage') == wanted_list
def test_internal_config_dict_override(mock_low_high_config,
write_config_file):
write_config_file('config', config_merge_dict, 'low')
wanted_dict = config_override_dict['config']['info:']
mock_low_high_config.push_scope(spack.config.InternalConfigScope
('high', config_override_dict))
assert mock_low_high_config.get('config:info') == wanted_dict
def test_internal_config_list_override(mock_low_high_config,
write_config_file):
write_config_file('config', config_merge_list, 'low')
wanted_list = config_override_list['config']['build_stage:']
mock_low_high_config.push_scope(spack.config.InternalConfigScope
('high', config_override_list))
assert mock_low_high_config.get('config:build_stage') == wanted_list
def test_set_section_override(mock_low_high_config, write_config_file):
write_config_file('config', config_merge_list, 'low')
wanted_list = config_override_list['config']['build_stage:']
with spack.config.override('config::build_stage', wanted_list):
assert mock_low_high_config.get('config:build_stage') == wanted_list
assert config_merge_list['config']['build_stage'] == \
mock_low_high_config.get('config:build_stage')
def test_set_list_override(mock_low_high_config, write_config_file):
write_config_file('config', config_merge_list, 'low')
wanted_list = config_override_list['config']['build_stage:']
with spack.config.override('config:build_stage:', wanted_list):
assert wanted_list == mock_low_high_config.get('config:build_stage')
assert config_merge_list['config']['build_stage'] == \
mock_low_high_config.get('config:build_stage')
def test_set_dict_override(mock_low_high_config, write_config_file):
write_config_file('config', config_merge_dict, 'low')
wanted_dict = config_override_dict['config']['info:']
with spack.config.override('config:info:', wanted_dict):
assert wanted_dict == mock_low_high_config.get('config:info')
assert config_merge_dict['config']['info'] == \
mock_low_high_config.get('config:info')
def test_set_bad_path(config):
with pytest.raises(syaml.SpackYAMLError, match='Illegal leading'):
with spack.config.override(':bad:path', ''):
pass
def test_bad_path_double_override(config):
with pytest.raises(syaml.SpackYAMLError,
match='Meaningless second override'):
with spack.config.override('bad::double:override::directive', ''):
pass

1
lib/spack/spack/test/data/modules/tcl/suffix.yaml
View File

@@ -5,3 +5,4 @@ tcl:
suffixes:
'+debug': foo
'~debug': bar
'^mpich': foo

2
lib/spack/spack/test/database.py
View File

@@ -769,7 +769,7 @@ def test_query_spec_with_non_conditional_virtual_dependency(database):
def test_failed_spec_path_error(database):
"""Ensure spec not concrete check is covered."""
s = spack.spec.Spec('a')
with pytest.raises(ValueError, matches='Concrete spec required'):
with pytest.raises(ValueError, match='Concrete spec required'):
spack.store.db._failed_spec_path(s)

96
lib/spack/spack/test/installer.py
View File

@@ -27,6 +27,12 @@ def _none(*args, **kwargs):
return None
def _not_locked(installer, lock_type, pkg):
"""Generic monkeypatch function for _ensure_locked to return no lock"""
tty.msg('{0} locked {1}' .format(lock_type, pkg.spec.name))
return lock_type, None
def _true(*args, **kwargs):
"""Generic monkeypatch function that always returns True."""
return True
@@ -239,7 +245,7 @@ def test_ensure_locked_have(install_mockery, tmpdir):
def test_package_id(install_mockery):
"""Test to cover package_id functionality."""
pkg = spack.repo.get('trivial-install-test-package')
with pytest.raises(ValueError, matches='spec is not concretized'):
with pytest.raises(ValueError, match='spec is not concretized'):
inst.package_id(pkg)
spec = spack.spec.Spec('trivial-install-test-package')
@@ -274,7 +280,7 @@ def _no_compilers(pkg, arch_spec):
# Test up to the dependency check
monkeypatch.setattr(spack.compilers, 'compilers_for_spec', _no_compilers)
with pytest.raises(spack.repo.UnknownPackageError, matches='not found'):
with pytest.raises(spack.repo.UnknownPackageError, match='not found'):
inst._packages_needed_to_bootstrap_compiler(spec.package)
@@ -285,6 +291,57 @@ def test_dump_packages_deps(install_mockery, tmpdir):
inst.dump_packages(spec, '.')
@pytest.mark.tld
def test_check_deps_status_errs(install_mockery, monkeypatch):
"""Test to cover _check_deps_status failures."""
spec, installer = create_installer('a')
# Make sure the package is identified as failed
orig_fn = spack.database.Database.prefix_failed
monkeypatch.setattr(spack.database.Database, 'prefix_failed', _true)
with pytest.raises(inst.InstallError, match='install failure'):
installer._check_deps_status()
monkeypatch.setattr(spack.database.Database, 'prefix_failed', orig_fn)
# Ensure do not acquire the lock
monkeypatch.setattr(inst.PackageInstaller, '_ensure_locked', _not_locked)
with pytest.raises(inst.InstallError, match='write locked by another'):
installer._check_deps_status()
@pytest.mark.tld
def test_check_deps_status_external(install_mockery, monkeypatch):
"""Test to cover _check_deps_status for external."""
spec, installer = create_installer('a')
deps = spec.dependencies()
assert len(deps) > 0
dep_id = 'b'
# Ensure the known dependent is installed if flagged as external
monkeypatch.setattr(spack.spec.Spec, 'external', True)
installer._check_deps_status()
assert dep_id in installer.installed
@pytest.mark.tld
def test_check_deps_status_upstream(install_mockery, monkeypatch):
"""Test to cover _check_deps_status for upstream."""
spec, installer = create_installer('a')
deps = spec.dependencies()
assert len(deps) > 0
dep_id = 'b'
# Ensure the known dependent, b, is installed if flagged as upstream
monkeypatch.setattr(spack.package.PackageBase, 'installed_upstream', True)
installer._check_deps_status()
assert dep_id in installer.installed
def test_add_bootstrap_compilers(install_mockery, monkeypatch):
"""Test to cover _add_bootstrap_compilers."""
def _pkgs(pkg):
@@ -334,6 +391,27 @@ def test_install_task_use_cache(install_mockery, monkeypatch):
assert spec.package.name in installer.installed
def test_install_task_stop_iter(install_mockery, monkeypatch, capfd):
"""Test _install_task to cover the StopIteration exception."""
mock_err_msg = 'mock stop iteration'
def _raise(installer, pkg):
raise StopIteration(mock_err_msg)
spec, installer = create_installer('a')
task = create_build_task(spec.package)
monkeypatch.setattr(spack.package.PackageBase, 'unit_test_check', _true)
monkeypatch.setattr(inst.PackageInstaller, '_setup_install_dir', _raise)
installer._install_task(task)
out = capfd.readouterr()[0]
assert mock_err_msg in out
assert 'Package stage directory' in out
assert spec.package.stage.source_path in out
def test_release_lock_write_n_exception(install_mockery, tmpdir, capsys):
"""Test _release_lock for supposed write lock with exception."""
spec, installer = create_installer('trivial-install-test-package')
@@ -428,7 +506,7 @@ def test_install_uninstalled_deps(install_mockery, monkeypatch, capsys):
monkeypatch.setattr(inst.PackageInstaller, '_update_failed', _noop)
msg = 'Cannot proceed with dependent-install'
with pytest.raises(spack.installer.InstallError, matches=msg):
with pytest.raises(spack.installer.InstallError, match=msg):
installer.install()
out = str(capsys.readouterr())
@@ -446,7 +524,7 @@ def test_install_failed(install_mockery, monkeypatch, capsys):
monkeypatch.setattr(inst.PackageInstaller, '_install_task', _noop)
msg = 'Installation of b failed'
with pytest.raises(spack.installer.InstallError, matches=msg):
with pytest.raises(spack.installer.InstallError, match=msg):
installer.install()
out = str(capsys.readouterr())
@@ -458,10 +536,6 @@ def test_install_lock_failures(install_mockery, monkeypatch, capfd):
def _requeued(installer, task):
tty.msg('requeued {0}' .format(task.pkg.spec.name))
def _not_locked(installer, lock_type, pkg):
tty.msg('{0} locked {1}' .format(lock_type, pkg.spec.name))
return lock_type, None
spec, installer = create_installer('b')
# Ensure never acquire a lock
@@ -485,10 +559,6 @@ def test_install_lock_installed_requeue(install_mockery, monkeypatch, capfd):
def _install(installer, task, **kwargs):
tty.msg('{0} installing'.format(task.pkg.spec.name))
def _not_locked(installer, lock_type, pkg):
tty.msg('{0} locked {1}' .format(lock_type, pkg.spec.name))
return lock_type, None
def _prep(installer, task, keep_prefix, keep_stage, restage):
installer.installed.add('b')
tty.msg('{0} is installed' .format(task.pkg.spec.name))
@@ -573,7 +643,7 @@ def _install(installer, task, **kwargs):
spec, installer = create_installer('b')
with pytest.raises(dl.InstallDirectoryAlreadyExistsError, matches=err):
with pytest.raises(dl.InstallDirectoryAlreadyExistsError, match=err):
installer.install()
assert 'b' in installer.installed

4
lib/spack/spack/test/llnl/util/lock.py
View File

@@ -1272,7 +1272,7 @@ def test_downgrade_write_fails(tmpdir):
lock = lk.Lock('lockfile')
lock.acquire_read()
msg = 'Cannot downgrade lock from write to read on file: lockfile'
with pytest.raises(lk.LockDowngradeError, matches=msg):
with pytest.raises(lk.LockDowngradeError, match=msg):
lock.downgrade_write_to_read()
@@ -1292,5 +1292,5 @@ def test_upgrade_read_fails(tmpdir):
lock = lk.Lock('lockfile')
lock.acquire_write()
msg = 'Cannot upgrade lock from read to write on file: lockfile'
with pytest.raises(lk.LockUpgradeError, matches=msg):
with pytest.raises(lk.LockUpgradeError, match=msg):
lock.upgrade_read_to_write()

9
lib/spack/spack/test/llnl/util/log.py
View File

@@ -32,7 +32,8 @@ def test_log_python_output_with_fd_stream(capfd, tmpdir):
with open('foo.txt') as f:
assert f.read() == 'logged\n'
assert capfd.readouterr() == ('', '')
# Coverage is cluttering stderr during tests
assert capfd.readouterr()[0] == ''
def test_log_python_output_and_echo_output(capfd, tmpdir):
@@ -42,7 +43,8 @@ def test_log_python_output_and_echo_output(capfd, tmpdir):
print('echo')
print('logged')
assert capfd.readouterr() == ('echo\n', '')
# Coverage is cluttering stderr during tests
assert capfd.readouterr()[0] == 'echo\n'
with open('foo.txt') as f:
assert f.read() == 'echo\nlogged\n'
@@ -75,7 +77,8 @@ def test_log_subproc_and_echo_output(capfd, tmpdir):
echo('echo')
print('logged')
assert capfd.readouterr() == ('echo\n', '')
# Coverage is cluttering stderr during tests
assert capfd.readouterr()[0] == 'echo\n'
with open('foo.txt') as f:
assert f.read() == 'logged\n'

2
lib/spack/spack/test/mirror.py
View File

@@ -213,7 +213,7 @@ def test_mirror_cache_symlinks(tmpdir):
"""
cosmetic_path = 'zlib/zlib-1.2.11.tar.gz'
global_path = '_source-cache/archive/c3/c3e5.tar.gz'
cache = spack.caches.MirrorCache(str(tmpdir))
cache = spack.caches.MirrorCache(str(tmpdir), False)
reference = spack.mirror.MirrorReference(cosmetic_path, global_path)
cache.store(MockFetcher(), reference.storage_path)

31
lib/spack/spack/test/modules/common.py
View File

@@ -11,6 +11,7 @@
import spack.spec
import spack.modules.tcl
from spack.modules.common import UpstreamModuleIndex
from spack.spec import Spec
import spack.error
@@ -183,3 +184,33 @@ def test_get_module_upstream():
assert m1_path == '/path/to/a'
finally:
spack.modules.common.upstream_module_index = old_index
def test_load_installed_package_not_in_repo(install_mockery, mock_fetch,
monkeypatch):
# Get a basic concrete spec for the trivial install package.
spec = Spec('trivial-install-test-package')
spec.concretize()
assert spec.concrete
# Get the package
pkg = spec.package
def find_nothing(*args):
raise spack.repo.UnknownPackageError(
'Repo package access is disabled for test')
try:
pkg.do_install()
spec._package = None
monkeypatch.setattr(spack.repo, 'get', find_nothing)
with pytest.raises(spack.repo.UnknownPackageError):
spec.package
module_path = spack.modules.common.get_module('tcl', spec, True)
assert module_path
pkg.do_uninstall()
except Exception:
pkg.remove_prefix()
raise

3
lib/spack/spack/test/modules/tcl.py
View File

@@ -215,9 +215,10 @@ def test_suffixes(self, module_configuration, factory):
writer, spec = factory('mpileaks+debug arch=x86-linux')
assert 'foo' in writer.layout.use_name
assert 'foo-foo' not in writer.layout.use_name
writer, spec = factory('mpileaks~debug arch=x86-linux')
assert 'bar' in writer.layout.use_name
assert 'bar-foo' in writer.layout.use_name
def test_setup_environment(self, modulefile_content, module_configuration):
"""Tests the internal set-up of run-time environment."""

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

@@ -205,6 +205,8 @@ def push_to_url(
# needs to be done in separate steps.
shutil.copy2(local_file_path, remote_file_path)
os.remove(local_file_path)
else:
raise
elif remote_url.scheme == 's3':
if extra_args is None:

2
lib/spack/spack/test/pytest.ini → pytest.ini
View File

@@ -1,7 +1,7 @@
# content of pytest.ini
[pytest]
addopts = --durations=20 -ra
testpaths = .
testpaths = lib/spack/spack/test
python_files = *.py
markers =
db: tests that require creating a DB

8
share/spack/qa/run-unit-tests
View File

@@ -37,16 +37,12 @@ bin/spack -h
bin/spack help -a
# Profile and print top 20 lines for a simple call to spack spec
bin/spack -p --lines 20 spec mpileaks%gcc ^elfutils@0.170
spack -p --lines 20 spec mpileaks%gcc ^elfutils@0.170
#-----------------------------------------------------------
# Run unit tests with code coverage
#-----------------------------------------------------------
extra_args=""
if [[ -n "$@" ]]; then
extra_args="-k $@"
fi
$coverage_run bin/spack test -x --verbose "$extra_args"
$coverage_run $(which spack) test -x --verbose
#-----------------------------------------------------------
# Run tests for setup-env.sh

6
share/spack/spack-completion.bash
View File

@@ -382,7 +382,7 @@ _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 --no-rebuild-index -y --spec-yaml --no-deps"
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"
else
_all_packages
fi
@@ -391,7 +391,7 @@ _spack_buildcache_create() {
_spack_buildcache_install() {
if $list_options
then
SPACK_COMPREPLY="-h --help -f --force -m --multiple -a --allow-root -u --unsigned"
SPACK_COMPREPLY="-h --help -f --force -m --multiple -a --allow-root -u --unsigned -o --otherarch"
else
_all_packages
fi
@@ -1025,7 +1025,7 @@ _spack_mirror() {
_spack_mirror_create() {
if $list_options
then
SPACK_COMPREPLY="-h --help -d --directory -a --all -f --file -D --dependencies -n --versions-per-spec"
SPACK_COMPREPLY="-h --help -d --directory -a --all -f --file --skip-unstable-versions -D --dependencies -n --versions-per-spec"
else
_all_packages
fi

17
var/spack/repos/builtin.mock/packages/trivial-pkg-with-valid-hash/package.py Normal file
View File

@@ -0,0 +1,17 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class TrivialPkgWithValidHash(Package):
url = "http://www.unit-test-should-replace-this-url/trivial_install-1.0"
version('1.0', '6ae8a75555209fd6c44157c0aed8016e763ff435a19cf186f76863140143ff72', expand=False)
hashed_content = "test content"
def install(self, spec, prefix):
pass

20
var/spack/repos/builtin/packages/adios2/package.py
View File

@@ -16,7 +16,7 @@ class Adios2(CMakePackage):
maintainers = ['ax3l', 'chuckatkins', 'williamfgc']
version('develop', branch='master')
version('master', branch='master')
version('2.5.0', sha256='7c8ff3bf5441dd662806df9650c56a669359cb0185ea232ecb3578de7b065329')
version('2.4.0', sha256='50ecea04b1e41c88835b4b3fd4e7bf0a0a2a3129855c9cc4ba6cf6a1575106e2')
version('2.3.1', sha256='3bf81ccc20a7f2715935349336a76ba4c8402355e1dc3848fcd6f4c3c5931893')
@@ -100,8 +100,12 @@ class Adios2(CMakePackage):
extends('python', when='+python')
depends_on('python@2.7:2.8,3.5:',
when='@:2.4.0 +python', type=('build', 'run'))
depends_on('python@3.5:', when='@2.5.0: +python', type=('build', 'run'))
when='@:2.4.0 +python',
type=('build', 'run'))
depends_on('python@3.5:', when='@2.5.0: +python',
type=('build', 'run'))
depends_on('python@2.7:2.8,3.5:', when='@:2.4.0', type='test')
depends_on('python@3.5:', when='@2.5.0:', type='test')
depends_on('py-numpy@1.6.1:', type=('build', 'run'), when='+python')
depends_on('py-mpi4py@2.0.0:', type=('build', 'run'), when='+mpi +python')
@@ -141,9 +145,11 @@ def cmake_args(self):
'ON' if '+fortran' in spec else 'OFF'),
'-DADIOS2_USE_Endian_Reverse={0}'.format(
'ON' if '+endian_reverse' in spec else 'OFF'),
'-DBUILD_TESTING:BOOL={0}'.format(
'ON' if self.run_tests else 'OFF'),
]
if self.spec.version >= Version('2.4.0'):
if spec.version >= Version('2.4.0'):
args.append('-DADIOS2_USE_Blosc={0}'.format(
'ON' if '+blosc' in spec else 'OFF'))
args.append('-DADIOS2_USE_BZip2={0}'.format(
@@ -153,7 +159,7 @@ def cmake_args(self):
args.append('-DADIOS2_USE_SSC={0}'.format(
'ON' if '+ssc' in spec else 'OFF'))
if self.spec.version >= Version('2.5.0'):
if spec.version >= Version('2.5.0'):
args.append('-DADIOS2_USE_DataSpaces={0}'.format(
'ON' if '+dataspaces' in spec else 'OFF'))
@@ -173,8 +179,8 @@ def cmake_args(self):
args.append('-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL={0}'.format(
'ON' if '+pic' in spec else 'OFF'))
if spec.satisfies('+python'):
if spec.satisfies('+python') or self.run_tests:
args.append('-DPYTHON_EXECUTABLE:FILEPATH=%s'
% self.spec['python'].command.path)
% spec['python'].command.path)
return args

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

@@ -18,6 +18,7 @@ class Amrex(CMakePackage):
maintainers = ['mic84', 'asalmgren']
version('develop', branch='development')
version('20.03', sha256='a535dcc016f0d38b55d0ab8e9067c1c53e3686961f6a1fb471cb18a0ebc909e6')
version('20.02', sha256='33529a23694283d12eb37d4682aa86c9cc1240bd50124efcf4464747a7554147')
version('20.01', sha256='f7026d267ca5de79ec7e740264d54230f419776d40feae705e939be0b1d8e0d3')
version('19.10', commit='52844b32b7da11e9733b9a7f4a782e51de7f5e1e') # tag:19.10

6
var/spack/repos/builtin/packages/arpack-ng/package.py
View File

@@ -108,7 +108,11 @@ def install(self, spec, prefix):
if '+mpi' in spec:
options.append('-DMPI=ON')
# TODO: -DINTERFACE64=ON
# If 64-bit BLAS is used:
if (spec.satisfies('^openblas+ilp64') or
spec.satisfies('^intel-mkl+ilp64') or
spec.satisfies('^intel-parallel-studio+mkl+ilp64')):
options.append('-DINTERFACE64=1')
if '+shared' in spec:
options.append('-DBUILD_SHARED_LIBS=ON')

3
var/spack/repos/builtin/packages/aws-parallelcluster/package.py
View File

@@ -12,7 +12,7 @@ class AwsParallelcluster(PythonPackage):
tool to deploy and manage HPC clusters in the AWS cloud."""
homepage = "https://github.com/aws/aws-parallelcluster"
url = "https://pypi.io/packages/source/a/aws-parallelcluster/aws-parallelcluster-2.5.1.tar.gz"
url = "https://pypi.io/packages/source/a/aws-parallelcluster/aws-parallelcluster-2.6.0.tar.gz"
maintainers = [
'sean-smith', 'demartinofra', 'enrico-usai', 'lukeseawalker', 'rexcsn',
@@ -23,6 +23,7 @@ class AwsParallelcluster(PythonPackage):
'pcluster.config', 'pcluster.networking'
]
version('2.6.0', sha256='aaed6962cf5027206834ac24b3d312da91e0f96ae8607f555e12cb124b869f0c')
version('2.5.1', sha256='4fd6e14583f8cf81f9e4aa1d6188e3708d3d14e6ae252de0a94caaf58be76303')
version('2.5.0', sha256='3b0209342ea0d9d8cc95505456103ad87c2d4e35771aa838765918194efd0ad3')

29
var/spack/repos/builtin/packages/bat/package.py Normal file
View File

@@ -0,0 +1,29 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Bat(Package):
"""A cat(1) clone with wings."""
homepage = "https://github.com/sharkdp/bat"
url = "https://github.com/sharkdp/bat/archive/v0.10.0.tar.gz"
version('0.12.1', sha256='1dd184ddc9e5228ba94d19afc0b8b440bfc1819fef8133fe331e2c0ec9e3f8e2')
depends_on('rust')
def install(self, spec, prefix):
cargo = which('cargo')
cargo('install', '--root', prefix, '--path', '.')
# cargo seems to need these to be set so that when it's building
# onig_sys it can run llvm-config and link against libclang.
def setup_build_environment(self, env):
env.append_flags('LLVM_CONFIG_PATH',
join_path(self.spec['llvm'].prefix.libexec.llvm,
'llvm-config'))
env.append_flags('LIBCLANG_PATH', self.spec['llvm'].prefix.lib)

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

@@ -12,6 +12,8 @@ class Bmi(AutotoolsPackage):
homepage = 'https://xgitlab.cels.anl.gov/sds/bmi'
git = 'https://xgitlab.cels.anl.gov/sds/bmi.git'
maintainers = ['carns']
version('develop', branch='master')
depends_on('autoconf', type='build')

9
var/spack/repos/builtin/packages/boost/package.py
View File

@@ -96,8 +96,12 @@ class Boost(Package):
# mpi/python are not installed by default because they pull in many
# dependencies and/or because there is a great deal of customization
# possible (and it would be difficult to choose sensible defaults)
#
# Boost.Container can be both header-only and compiled. '+container'
# indicates the compiled version which requires Extended Allocator
# support. The header-only library is installed when no variant is given.
default_noinstall_libs\
= set(['context', 'coroutine', 'fiber', 'mpi', 'python'])
= set(['container', 'context', 'coroutine', 'fiber', 'mpi', 'python'])
all_libs = default_install_libs | default_noinstall_libs
@@ -174,6 +178,9 @@ def libs(self):
conflicts('+taggedlayout', when='+versionedlayout')
conflicts('+numpy', when='~python')
# Container's Extended Allocators were not added until 1.56.0
conflicts('+container', when='@:1.55.99')
# Patch fix from https://svn.boost.org/trac/boost/ticket/11856
patch('boost_11856.patch', when='@1.60.0%gcc@4.4.7')

2
var/spack/repos/builtin/packages/bowtie2/package.py
View File

@@ -11,7 +11,7 @@ class Bowtie2(Package):
"""Bowtie 2 is an ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences"""
homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
homepage = "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml"
url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.1/bowtie2-2.3.1-source.zip"
version('2.3.5.1', sha256='335c8dafb1487a4a9228ef922fbce4fffba3ce8bc211e2d7085aac092155a53f')

9
var/spack/repos/builtin/packages/bzip2/package.py
View File

@@ -16,9 +16,12 @@ class Bzip2(Package):
homepage = "https://sourceware.org/bzip2/"
url = "https://sourceware.org/pub/bzip2/bzip2-1.0.8.tar.gz"
version('1.0.8', sha256='ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269')
version('1.0.7', sha256='e768a87c5b1a79511499beb41500bcc4caf203726fff46a6f5f9ad27fe08ab2b')
version('1.0.6', sha256='a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd')
# The server is sometimes a bit slow to respond
fetch_options = {'timeout': 60}
version('1.0.8', sha256='ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', fetch_options=fetch_options)
version('1.0.7', sha256='e768a87c5b1a79511499beb41500bcc4caf203726fff46a6f5f9ad27fe08ab2b', fetch_options=fetch_options)
version('1.0.6', sha256='a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', fetch_options=fetch_options)
variant('shared', default=True, description='Enables the build of shared libraries.')

6
var/spack/repos/builtin/packages/caliper/package.py
View File

@@ -64,12 +64,12 @@ class Caliper(CMakePackage):
depends_on('libpfm4@4.8:4.99', when='+libpfm')
depends_on('mpi', when='+mpi')
depends_on('unwind@2018.10.12,1.2:1.99', when='+callpath')
depends_on('unwind@1.2:1.99', when='+callpath')
depends_on('sosflow@spack', when='@1.0:1.99+sosflow')
depends_on('cmake', type='build')
depends_on('python', type='build')
depends_on('python@3:', type='build')
# sosflow support not yet in 2.0
conflicts('+sosflow', '@2.0.0:2.2.99')
@@ -79,6 +79,8 @@ def cmake_args(self):
spec = self.spec
args = [
('-DPYTHON_EXECUTABLE=%s' %
spec['python'].command.path),
'-DBUILD_TESTING=Off',
'-DBUILD_DOCS=Off',
'-DBUILD_SHARED_LIBS=%s' % ('On' if '+shared' in spec else 'Off'),

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

@@ -14,6 +14,8 @@ class Clhep(CMakePackage):
list_url = "https://proj-clhep.web.cern.ch/proj-clhep/"
list_depth = 1
maintainers = ['drbenmorgan']
version('2.4.1.3', sha256='27c257934929f4cb1643aa60aeaad6519025d8f0a1c199bc3137ad7368245913')
version('2.4.1.2', sha256='ff96e7282254164380460bc8cf2dff2b58944084eadcd872b5661eb5a33fa4b8')
version('2.4.1.0', sha256='d14736eb5c3d21f86ce831dc1afcf03d423825b35c84deb6f8fd16773528c54d')

12
var/spack/repos/builtin/packages/cscope/package.py
View File

@@ -10,8 +10,9 @@ class Cscope(AutotoolsPackage):
"""Cscope is a developer's tool for browsing source code."""
homepage = "http://cscope.sourceforge.net/"
url = "http://downloads.sourceforge.net/project/cscope/cscope/15.8b/cscope-15.8b.tar.gz"
url = "https://sourceforge.net/projects/cscope/files/cscope/v15.9/cscope-15.9.tar.gz"
version('15.9', sha256='c5505ae075a871a9cd8d9801859b0ff1c09782075df281c72c23e72115d9f159')
version('15.8b', sha256='4889d091f05aa0845384b1e4965aa31d2b20911fb2c001b2cdcffbcb7212d3af')
depends_on('ncurses')
@@ -20,4 +21,11 @@ class Cscope(AutotoolsPackage):
depends_on('bison', type='build')
depends_on('pkgconfig', type='build')
build_targets = ['CURSES_LIBS=-lncursesw']
build_targets = ['CURSES_LIBS=-lncursesw -ltinfo']
def url_for_version(self, version):
url = "https://sourceforge.net/projects/cscope/files/cscope/{0}{1}/cscope-{1}.tar.gz"
if version >= Version('15.9'):
return url.format('v', version)
else:
return url.format('', version)

2
var/spack/repos/builtin/packages/darshan-runtime/package.py
View File

@@ -18,6 +18,8 @@ class DarshanRuntime(Package):
url = "http://ftp.mcs.anl.gov/pub/darshan/releases/darshan-3.1.0.tar.gz"
git = "https://xgitlab.cels.anl.gov/darshan/darshan.git"
maintainers = ['shanedsnyder', 'carns']
version('develop', branch='master')
version('3.1.7', sha256='9ba535df292727ac1e8025bdf2dc42942715205cad8319d925723fd88709e8d6')
version('3.1.6', sha256='21cb24e2a971c45e04476e00441b7fbea63d2afa727a5cf8b7a4a9d9004dd856')

2
var/spack/repos/builtin/packages/darshan-util/package.py
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@@ -16,6 +16,8 @@ class DarshanUtil(Package):
url = "http://ftp.mcs.anl.gov/pub/darshan/releases/darshan-3.1.0.tar.gz"
git = "https://xgitlab.cels.anl.gov/darshan/darshan.git"
maintainers = ['shanedsnyder', 'carns']
version('develop', branch='master')
version('3.1.7', sha256='9ba535df292727ac1e8025bdf2dc42942715205cad8319d925723fd88709e8d6')
version('3.1.6', sha256='21cb24e2a971c45e04476e00441b7fbea63d2afa727a5cf8b7a4a9d9004dd856')

1
var/spack/repos/builtin/packages/dealii/package.py
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@@ -151,6 +151,7 @@ class Dealii(CMakePackage, CudaPackage):
depends_on('slepc@:3.6.3', when='@:8.4.1+slepc+petsc+mpi')
depends_on('slepc~arpack', when='+slepc+petsc+mpi+int64')
depends_on('sundials@:3~pthread', when='@9.0:+sundials')
depends_on('trilinos gotype=int', when='+trilinos')
# Both Trilinos and SymEngine bundle the Teuchos RCP library.
# This leads to conflicts between macros defined in the included
# headers when they are not compiled in the same mode.

35
var/spack/repos/builtin/packages/ecp-proxy-apps/package.py
View File

@@ -4,31 +4,33 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
from spack import *
class EcpProxyApps(Package):
class EcpProxyApps(BundlePackage):
"""This is a collection of packages that represents the official suite of
DOE/ECP proxy applications. This is a Spack bundle package that
installs the ECP proxy application suite.
"""
tags = ['proxy-app', 'ecp-proxy-app']
maintainers = ['bhatele']
maintainers = ['rspavel']
homepage = "https://proxyapps.exascaleproject.org"
# Dummy url
url = 'https://github.com/exascaleproject/proxy-apps/archive/v1.0.tar.gz'
version('2.1', sha256='604da008fc4ef3bdbc25505088d610333249e3e9745eac7dbfd05b91e33e218d')
version('2.0', sha256='5f3cb3a772224e738c1dab42fb34d40f6b313af51ab1c575fb334e573e41e09a')
version('1.1', sha256='8537e03588c0f46bebf5b7f07146c79812f2ebfb77d29e184baa4dd5f4603ee3')
version('1.0', sha256='13d9795494dabdb4c724d2c0f322c2149b2507d2fd386ced12b54292b7ecf595')
version('3.0')
version('2.1')
version('2.0')
version('1.1')
version('1.0')
variant('candle', default=False,
description='Also build CANDLE Benchmarks')
# Added with release 3.0
depends_on('miniamr@1.4.4', when='@3.0:')
depends_on('xsbench@19', when='@3.0:')
# Added with release 2.1
depends_on('amg@1.2', when='@2.1:')
depends_on('miniamr@1.4.3', when='@2.1:')
@@ -40,15 +42,15 @@ class EcpProxyApps(Package):
depends_on('picsarlite@0.1', when='@2.0:')
depends_on('thornado-mini@1.0', when='@2.0:')
depends_on('candle-benchmarks@0.1', when='+candle @2.0:')
depends_on('candle-benchmarks@0.1', when='+candle @2.0:2.1')
depends_on('laghos@2.0', when='@2.0:')
depends_on('macsio@1.1', when='@2.0:')
depends_on('sw4lite@1.1', when='@2.0:')
depends_on('xsbench@18', when='@2.0:')
depends_on('xsbench@18', when='@2.0:2.1')
# Dependencies for version 2.0
depends_on('amg@1.1', when='@2.0')
depends_on('miniamr@1.4.1', when='@2.0')
depends_on('miniamr@1.4.1', when='@2.0:2.1')
# Added with release 1.1
depends_on('examinimd@1.0', when='@1.1:')
@@ -71,12 +73,3 @@ class EcpProxyApps(Package):
# Removed after release 1.0
depends_on('comd@1.1', when='@1.0')
# Dummy install for now, will be removed when metapackage is available
def install(self, spec, prefix):
with open(os.path.join(spec.prefix, 'package-list.txt'), 'w') as out:
for dep in spec.dependencies(deptype='build'):
out.write("%s\n" % dep.format(
format_string='${PACKAGE} ${VERSION}'))
os.symlink(dep.prefix, os.path.join(spec.prefix, dep.name))
out.close()

27
var/spack/repos/builtin/packages/eigen/find-ptscotch.patch
View File

@@ -1,27 +0,0 @@
Version 3.3.4 contained a bug that prevented it from finding scotch~mpi.
diff --git a/tmp/FindPTSCOTCH.cmake b/cmake/FindPTSCOTCH.cmake
index 1396d05..23451b1 100644
--- a/tmp/FindPTSCOTCH.cmake
+++ b/cmake/FindPTSCOTCH.cmake
@@ -167,11 +167,11 @@ endif()
# If found, add path to cmake variable
# ------------------------------------
+unset(PTSCOTCH_INCLUDE_DIRS)
foreach(ptscotch_hdr ${PTSCOTCH_hdrs_to_find})
if (PTSCOTCH_${ptscotch_hdr}_DIRS)
list(APPEND PTSCOTCH_INCLUDE_DIRS "${PTSCOTCH_${ptscotch_hdr}_DIRS}")
else ()
- set(PTSCOTCH_INCLUDE_DIRS "PTSCOTCH_INCLUDE_DIRS-NOTFOUND")
if (NOT PTSCOTCH_FIND_QUIETLY)
message(STATUS "Looking for ptscotch -- ${ptscotch_hdr} not found")
endif()
@@ -255,7 +255,6 @@ foreach(ptscotch_lib ${PTSCOTCH_libs_to_find})
list(APPEND PTSCOTCH_LIBRARIES "${PTSCOTCH_${ptscotch_lib}_LIBRARY}")
list(APPEND PTSCOTCH_LIBRARY_DIRS "${${ptscotch_lib}_lib_path}")
else ()
- list(APPEND PTSCOTCH_LIBRARIES "${PTSCOTCH_${ptscotch_lib}_LIBRARY}")
if (NOT PTSCOTCH_FIND_QUIETLY)
message(STATUS "Looking for ptscotch -- lib ${ptscotch_lib} not found")
endif()

51
var/spack/repos/builtin/packages/eigen/package.py
View File

@@ -3,8 +3,6 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Eigen(CMakePackage):
"""Eigen is a C++ template library for linear algebra matrices,
@@ -12,41 +10,32 @@ class Eigen(CMakePackage):
"""
homepage = 'http://eigen.tuxfamily.org/'
url = 'https://bitbucket.org/eigen/eigen/get/3.3.4.tar.bz2'
url = 'https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz'
version('3.3.7', sha256='9f13cf90dedbe3e52a19f43000d71fdf72e986beb9a5436dddcd61ff9d77a3ce')
version('3.3.5', sha256='7352bff3ea299e4c7d7fbe31c504f8eb9149d7e685dec5a12fbaa26379f603e2')
version('3.3.4', sha256='dd254beb0bafc695d0f62ae1a222ff85b52dbaa3a16f76e781dce22d0d20a4a6')
version('3.3.3', sha256='a4143fc45e4454b4b98fcea3516b3a79b8cdb3bc7fadf996d088c6a0d805fea1')
version('3.3.1', sha256='a0b4cebaabd8f371d1b364f9723585fbcc7c9640ca60273b99835e6cf115f056')
version('3.2.10', sha256='760e6656426fde71cc48586c971390816f456d30f0b5d7d4ad5274d8d2cb0a6d')
version('3.2.9', sha256='4d1e036ec1ed4f4805d5c6752b76072d67538889f4003fadf2f6e00a825845ff')
version('3.2.8', sha256='722a63d672b70f39c271c5e2a4a43ba14d12015674331790414fcb167c357e55')
version('3.2.7', sha256='e58e1a11b23cf2754e32b3c5990f318a8461a3613c7acbf6035870daa45c2f3e')
version('3.3.7', sha256='d56fbad95abf993f8af608484729e3d87ef611dd85b3380a8bad1d5cbc373a57')
version('3.3.6', sha256='e7cd8c94d6516d1ada9893ccc7c9a400fcee99927c902f15adba940787104dba')
version('3.3.5', sha256='383407ab3d0c268074e97a2cbba84ac197fd24532f014aa2adc522355c1aa2d0')
version('3.3.4', sha256='c5ca6e3442fb48ae75159ca7568854d9ba737bc351460f27ee91b6f3f9fd1f3d')
version('3.3.3', sha256='fd72694390bd8e81586205717d2cf823e718f584b779a155db747d1e68481a2e')
version('3.3.2', sha256='8d7611247fba1236da4dee7a64607017b6fb9ca5e3f0dc44d480e5d33d5663a5')
version('3.3.1', sha256='50dd21a8997fce0857b27a126811ae8ee7619984ab5425ecf33510cec649e642')
version('3.3.0', sha256='de82e01f97e1a95f121bd3ace87aa1237818353c14e38f630a65f5ba2c92f0e1')
version('3.2.10', sha256='0920cb60ec38de5fb509650014eff7cc6d26a097c7b38c7db4b1aa5df5c85042')
version('3.2.9', sha256='f683b20259ad72c3d384c00278166dd2a42d99b78dcd589ed4a6ca74bbb4ca07')
version('3.2.8', sha256='64c54781cfe9eefef2792003ab04b271d4b2ec32eda6e9cdf120d7aad4ebb282')
version('3.2.7', sha256='0ea9df884873275bf39c2965d486fa2d112f3a64b97b60b45b8bc4bb034a36c1')
version('3.2.6', sha256='e097b8dcc5ad30d40af4ad72d7052e3f78639469baf83cffaadc045459cda21f')
version('3.2.5', sha256='8068bd528a2ff3885eb55225c27237cf5cda834355599f05c2c85345db8338b4')
variant('metis', default=False,
description='Enables metis permutations in sparse algebra')
variant('scotch', default=False,
description='Enables scotch/pastix sparse factorization methods')
variant('fftw', default=False,
description='Enables FFTW backend for the FFT plugin')
variant('suitesparse', default=False,
description='Enables SuiteSparse sparse factorization methods')
variant('mpfr', default=False,
description='Enables the multi-precisions floating-point plugin')
# From http://eigen.tuxfamily.org/index.php?title=Main_Page#Requirements
# "Eigen doesn't have any dependencies other than the C++ standard
# library."
variant('build_type', default='RelWithDebInfo',
description='The build type to build',
values=('Debug', 'Release', 'RelWithDebInfo'))
# TODO : dependency on googlehash, superlu, adolc missing
depends_on('metis@5:', when='+metis')
depends_on('scotch', when='+scotch')
depends_on('fftw', when='+fftw')
depends_on('suite-sparse', when='+suitesparse')
depends_on('mpfr@2.3.0:', when='+mpfr')
depends_on('gmp', when='+mpfr')
patch('find-ptscotch.patch', when='@3.3.4')
# TODO: latex and doxygen needed to produce docs with make doc
# TODO: Other dependencies might be needed to test this package
def setup_run_environment(self, env):
env.prepend_path('CPATH', self.prefix.include.eigen3)

21
var/spack/repos/builtin/packages/elfutils/package.py
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@@ -21,15 +21,18 @@ class Elfutils(AutotoolsPackage):
list_url = "https://sourceware.org/elfutils/ftp"
list_depth = 1
version('0.178', sha256='31e7a00e96d4e9c4bda452e1f2cdac4daf8abd24f5e154dee232131899f3a0f2')
version('0.177', sha256='fa489deccbcae7d8c920f60d85906124c1989c591196d90e0fd668e3dc05042e')
version('0.176', sha256='eb5747c371b0af0f71e86215a5ebb88728533c3a104a43d4231963f308cd1023')
version('0.175', sha256='f7ef925541ee32c6d15ae5cb27da5f119e01a5ccdbe9fe57bf836730d7b7a65b')
version('0.174', sha256='cdf27e70076e10a29539d89e367101d516bc4aa11b0d7777fe52139e3fcad08a')
version('0.173', sha256='b76d8c133f68dad46250f5c223482c8299d454a69430d9aa5c19123345a000ff')
version('0.170', sha256='1f844775576b79bdc9f9c717a50058d08620323c1e935458223a12f249c9e066')
version('0.168', sha256='b88d07893ba1373c7dd69a7855974706d05377766568a7d9002706d5de72c276')
version('0.163', sha256='7c774f1eef329309f3b05e730bdac50013155d437518a2ec0e24871d312f2e23')
# Sourceware is often slow to respond.
timeout = {'timeout': 60}
version('0.178', sha256='31e7a00e96d4e9c4bda452e1f2cdac4daf8abd24f5e154dee232131899f3a0f2', fetch_options=timeout)
version('0.177', sha256='fa489deccbcae7d8c920f60d85906124c1989c591196d90e0fd668e3dc05042e', fetch_options=timeout)
version('0.176', sha256='eb5747c371b0af0f71e86215a5ebb88728533c3a104a43d4231963f308cd1023', fetch_options=timeout)
version('0.175', sha256='f7ef925541ee32c6d15ae5cb27da5f119e01a5ccdbe9fe57bf836730d7b7a65b', fetch_options=timeout)
version('0.174', sha256='cdf27e70076e10a29539d89e367101d516bc4aa11b0d7777fe52139e3fcad08a', fetch_options=timeout)
version('0.173', sha256='b76d8c133f68dad46250f5c223482c8299d454a69430d9aa5c19123345a000ff', fetch_options=timeout)
version('0.170', sha256='1f844775576b79bdc9f9c717a50058d08620323c1e935458223a12f249c9e066', fetch_options=timeout)
version('0.168', sha256='b88d07893ba1373c7dd69a7855974706d05377766568a7d9002706d5de72c276', fetch_options=timeout)
version('0.163', sha256='7c774f1eef329309f3b05e730bdac50013155d437518a2ec0e24871d312f2e23', fetch_options=timeout)
# Libraries for reading compressed DWARF sections.
variant('bzip2', default=False,

3
var/spack/repos/builtin/packages/exiv2/package.py
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@@ -15,3 +15,6 @@ class Exiv2(CMakePackage):
url = "https://github.com/Exiv2/exiv2/archive/v0.27.2.tar.gz"
version('0.27.2', sha256='3dbcaf01fbc5b98d42f091d1ff0d4b6cd9750dc724de3d9c0d113948570b2934')
depends_on('zlib', type='link')
depends_on('expat@2.2.6:', type='link')

9
var/spack/repos/builtin/packages/expect/package.py
View File

@@ -66,7 +66,8 @@ def darwin_fix(self):
fix_darwin_install_name(
join_path(self.prefix.lib, 'expect{0}'.format(self.version)))
old = 'libexpect{0}.dylib'.format(self.version)
new = glob.glob(join_path(self.prefix.lib, 'expect*', 'libexpect*'))[0]
install_name_tool = Executable('install_name_tool')
install_name_tool('-change', old, new, self.prefix.bin.expect)
old = 'libexpect{0}.dylib'.format(self.version)
new = glob.glob(join_path(self.prefix.lib, 'expect*',
'libexpect*'))[0]
install_name_tool = Executable('install_name_tool')
install_name_tool('-change', old, new, self.prefix.bin.expect)

2
var/spack/repos/builtin/packages/exuberant-ctags/package.py
View File

@@ -8,7 +8,7 @@
class ExuberantCtags(AutotoolsPackage):
"""The canonical ctags generator"""
homepage = "ctags.sourceforge.net"
homepage = "http://ctags.sourceforge.net"
url = "http://downloads.sourceforge.net/project/ctags/ctags/5.8/ctags-5.8.tar.gz"
version('5.8', sha256='0e44b45dcabe969e0bbbb11e30c246f81abe5d32012db37395eb57d66e9e99c7')

4
var/spack/repos/builtin/packages/f77-zmq/package.py
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@@ -15,10 +15,12 @@ class F77Zmq(MakefilePackage):
maintainers = ['scemama']
version('4.3.2', sha256='f1fb7544d38d9bb7235f98c96f241875ddcb0d37ed950618c23d4e4d666a73ca')
version('4.3.1', sha256='a15d72d93022d3e095528d2808c7767cece974a2dc0e2dd95e4c122f60fcf0a8')
depends_on('libzmq')
depends_on('python', type='build')
depends_on('python@3:', type='build', when="@:4.3.1")
depends_on('python', type='build', when="@4.3.2:")
def setup_build_environment(self, env):
env.append_flags('CFLAGS', '-O3')

17
var/spack/repos/builtin/packages/fairlogger/package.py
View File

@@ -17,7 +17,8 @@ class Fairlogger(CMakePackage):
maintainers = ['dennisklein', 'ChristianTackeGSI']
# generator = 'Ninja'
version('develop', branch='dev')
version('develop', branch='dev', get_full_repo=True)
version('1.6.2', sha256='5c6ef0c0029eb451fee71756cb96e6c5011040a9813e8889667b6f3b6b04ed03')
version('1.6.1', sha256='3894580f4c398d724ba408e410e50f70c9f452e8cfaf7c3ff8118c08df28eaa8')
version('1.6.0', sha256='721e8cadfceb2f63014c2a727e098babc6deba653baab8866445a772385d0f5b')
version('1.5.0', sha256='8e74e0b1e50ee86f4fca87a44c6b393740b32099ac3880046bf252c31c58dd42')
@@ -31,19 +32,22 @@ class Fairlogger(CMakePackage):
values=('Debug', 'Release', 'RelWithDebInfo'),
multi=False,
description='CMake build type')
variant('cxxstd', default='11',
variant('cxxstd', default='default',
values=('11', '14', '17'),
multi=False,
description='Use the specified C++ standard when building.')
variant('pretty',
default=False,
description='Use BOOST_PRETTY_FUNCTION macro.')
description='Use BOOST_PRETTY_FUNCTION macro (Supported by 1.4+).')
conflicts('+pretty', when='@:1.3.99')
depends_on('cmake@3.9.4:', type='build')
depends_on('git', type='build', when='@develop')
depends_on('boost', when='+pretty')
depends_on('fmt@5.3.0:', when='@1.6.0:')
conflicts('^boost@1.70:', when='^cmake@:3.14')
depends_on('fmt@5.3.0:5.99', when='@1.6.0:1.6.1')
depends_on('fmt@5.3.0:', when='@1.6.2:')
def patch(self):
"""FairLogger gets its version number from git.
@@ -55,9 +59,10 @@ def patch(self):
'CMakeLists.txt')
def cmake_args(self):
cxxstd = self.spec.variants['cxxstd'].value
args = []
args.append('-DCMAKE_CXX_STANDARD=%s' % cxxstd)
cxxstd = self.spec.variants['cxxstd'].value
if cxxstd != 'default':
args.append('-DCMAKE_CXX_STANDARD=%s' % cxxstd)
args.append('-DUSE_BOOST_PRETTY_FUNCTION=%s' %
('ON' if '+pretty' in self.spec else 'OFF'))
if self.spec.satisfies('@1.6:'):

1
var/spack/repos/builtin/packages/fast-global-file-status/package.py
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@@ -18,6 +18,7 @@ class FastGlobalFileStatus(AutotoolsPackage):
depends_on('mrnet')
depends_on('mount-point-attributes')
depends_on('mpi')
depends_on('openssl')
def configure_args(self):
spec = self.spec

21
var/spack/repos/builtin/packages/fd-find/package.py Normal file
View File

@@ -0,0 +1,21 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class FdFind(Package):
"""A simple, fast and user-friendly alternative to 'find'."""
homepage = "https://github.com/sharkdp/fd"
url = "https://github.com/sharkdp/fd/archive/v7.3.0.tar.gz"
version('7.4.0', sha256='33570ba65e7f8b438746cb92bb9bc4a6030b482a0d50db37c830c4e315877537')
depends_on('rust')
def install(self, spec, prefix):
cargo = which('cargo')
cargo('install', '--root', prefix, '--path', '.')

13
var/spack/repos/builtin/packages/flatbuffers/package.py
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@@ -17,3 +17,16 @@ class Flatbuffers(CMakePackage):
version('1.10.0', sha256='3714e3db8c51e43028e10ad7adffb9a36fc4aa5b1a363c2d0c4303dd1be59a7c')
version('1.9.0', sha256='5ca5491e4260cacae30f1a5786d109230db3f3a6e5a0eb45d0d0608293d247e3')
version('1.8.0', sha256='c45029c0a0f1a88d416af143e34de96b3091642722aa2d8c090916c6d1498c2e')
variant('shared', default=True,
description='Build shared instead of static libraries')
def cmake_args(self):
args = []
args.append('-DFLATBUFFERS_BUILD_SHAREDLIB={0}'.format(
'ON' if '+shared' in self.spec else 'OFF'))
args.append('-DFLATBUFFERS_BUILD_FLATLIB={0}'.format(
'ON' if '+shared' not in self.spec else 'OFF'))
if 'darwin' in self.spec.architecture:
args.append('-DCMAKE_MACOSX_RPATH=ON')
return args

1
var/spack/repos/builtin/packages/g4abla/package.py
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@@ -11,6 +11,7 @@ class G4abla(Package):
"""Geant4 data for nuclear shell effects in INCL/ABLA hadronic mode"""
homepage = "http://geant4.web.cern.ch"
url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4ABLA.3.0.tar.gz"
maintainers = ['drbenmorgan']
version(
'3.0', sha256='99fd4dcc9b4949778f14ed8364088e45fa4ff3148b3ea36f9f3103241d277014')

1
var/spack/repos/builtin/packages/g4emlow/package.py
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@@ -11,6 +11,7 @@ class G4emlow(Package):
"""Geant4 data files for low energy electromagnetic processes."""
homepage = "http://geant4.web.cern.ch"
url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4EMLOW.6.50.tar.gz"
maintainers = ['drbenmorgan']
version(
'6.50', sha256='c97be73fece5fb4f73c43e11c146b43f651c6991edd0edf8619c9452f8ab1236')

2
var/spack/repos/builtin/packages/g4ensdfstate/package.py
View File

@@ -12,6 +12,8 @@ class G4ensdfstate(Package):
homepage = "http://geant4.web.cern.ch"
url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4ENSDFSTATE.2.1.tar.gz"
maintainers = ['drbenmorgan']
version('2.1', sha256='933e7f99b1c70f24694d12d517dfca36d82f4e95b084c15d86756ace2a2790d9')
version('2.2', sha256='dd7e27ef62070734a4a709601f5b3bada6641b111eb7069344e4f99a01d6e0a6')

2
var/spack/repos/builtin/packages/g4ndl/package.py
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@@ -12,6 +12,8 @@ class G4ndl(Package):
homepage = "http://geant4.web.cern.ch"
url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4NDL.4.5.tar.gz"
maintainers = ['drbenmorgan']
version('4.5', sha256='cba928a520a788f2bc8229c7ef57f83d0934bb0c6a18c31ef05ef4865edcdf8e')
def install(self, spec, prefix):

2
var/spack/repos/builtin/packages/g4neutronxs/package.py
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@@ -13,6 +13,8 @@ class G4neutronxs(Package):
homepage = "http://geant4.web.cern.ch"
url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4NEUTRONXS.1.4.tar.gz"
maintainers = ['drbenmorgan']
version('1.4', sha256='57b38868d7eb060ddd65b26283402d4f161db76ed2169437c266105cca73a8fd')
def install(self, spec, prefix):

2
var/spack/repos/builtin/packages/g4photonevaporation/package.py
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@@ -12,6 +12,8 @@ class G4photonevaporation(Package):
homepage = "http://geant4.web.cern.ch"
url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4PhotonEvaporation.4.3.2.tar.gz"
maintainers = ['drbenmorgan']
version('4.3.2', sha256='d4641a6fe1c645ab2a7ecee09c34e5ea584fb10d63d2838248bfc487d34207c7')
version('5.2', sha256='83607f8d36827b2a7fca19c9c336caffbebf61a359d0ef7cee44a8bcf3fc2d1f')

2
var/spack/repos/builtin/packages/g4pii/package.py
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@@ -12,6 +12,8 @@ class G4pii(Package):
homepage = "http://geant4.web.cern.ch"
url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4PII.1.3.tar.gz"
maintainers = ['drbenmorgan']
version('1.3', sha256='6225ad902675f4381c98c6ba25fc5a06ce87549aa979634d3d03491d6616e926')
def install(self, spec, prefix):

2
var/spack/repos/builtin/packages/g4radioactivedecay/package.py
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@@ -12,6 +12,8 @@ class G4radioactivedecay(Package):
homepage = "http://geant4.web.cern.ch"
url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4RadioactiveDecay.5.1.1.tar.gz"
maintainers = ['drbenmorgan']
version('5.1.1', sha256='f7a9a0cc998f0d946359f2cb18d30dff1eabb7f3c578891111fc3641833870ae')
version('5.2', sha256='99c038d89d70281316be15c3c98a66c5d0ca01ef575127b6a094063003e2af5d')

2
var/spack/repos/builtin/packages/g4realsurface/package.py
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@@ -12,6 +12,8 @@ class G4realsurface(Package):
homepage = "http://geant4.web.cern.ch"
url = "http://geant4-data.web.cern.ch/geant4-data/datasets/RealSurface.1.0.tar.gz"
maintainers = ['drbenmorgan']
version('1.0', sha256='3e2d2506600d2780ed903f1f2681962e208039329347c58ba1916740679020b1')
version('2.1', sha256='2a287adbda1c0292571edeae2082a65b7f7bd6cf2bf088432d1d6f889426dcf3')
version('2.1.1', sha256='90481ff97a7c3fa792b7a2a21c9ed80a40e6be386e581a39950c844b2dd06f50')

2
var/spack/repos/builtin/packages/g4saiddata/package.py
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@@ -12,6 +12,8 @@ class G4saiddata(Package):
homepage = "http://geant4.web.cern.ch"
url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4SAIDDATA.1.1.tar.gz"
maintainers = ['drbenmorgan']
version('1.1', sha256='a38cd9a83db62311922850fe609ecd250d36adf264a88e88c82ba82b7da0ed7f')
def install(self, spec, prefix):

2
var/spack/repos/builtin/packages/g4tendl/package.py
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@@ -12,6 +12,8 @@ class G4tendl(Package):
homepage = "http://geant4.web.cern.ch"
url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4TENDL.1.3.tar.gz"
maintainers = ['drbenmorgan']
version('1.3', sha256='52ad77515033a5d6f995c699809b464725a0e62099b5e55bf07c8bdd02cd3bce')
version('1.3.2', sha256='3b2987c6e3bee74197e3bd39e25e1cc756bb866c26d21a70f647959fc7afb849')

6
var/spack/repos/builtin/packages/gcc/package.py
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@@ -28,6 +28,7 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
version('9.2.0', sha256='ea6ef08f121239da5695f76c9b33637a118dcf63e24164422231917fa61fb206')
version('9.1.0', sha256='79a66834e96a6050d8fe78db2c3b32fb285b230b855d0a66288235bc04b327a0')
version('8.4.0', sha256='e30a6e52d10e1f27ed55104ad233c30bd1e99cfb5ff98ab022dc941edd1b2dd4')
version('8.3.0', sha256='64baadfe6cc0f4947a84cb12d7f0dfaf45bb58b7e92461639596c21e02d97d2c')
version('8.2.0', sha256='196c3c04ba2613f893283977e6011b2345d1cd1af9abeac58e916b1aab3e0080')
version('8.1.0', sha256='1d1866f992626e61349a1ccd0b8d5253816222cdc13390dcfaa74b093aa2b153')
@@ -193,6 +194,11 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
# Binutils can't build ld on macOS
conflicts('+binutils', when='platform=darwin')
# Newer binutils than RHEL's is required to run `as` on some instructions
# generated by new GCC (see https://github.com/spack/spack/issues/12235)
conflicts('~binutils', when='@7: os=rhel6',
msg='New GCC cannot use system assembler on RHEL6')
if sys.platform == 'darwin':
# Fix parallel build on APFS filesystem
# https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81797

2
var/spack/repos/builtin/packages/geant4-data/package.py
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@@ -14,6 +14,8 @@ class Geant4Data(Package):
homepage = "http://geant4.cern.ch"
url = "http://geant4-data.web.cern.ch/geant4-data/ReleaseNotes/ReleaseNotes4.10.3.html"
maintainers = ['drbenmorgan']
version('10.03.p03', sha256='3e0d4d4e6854c8667d930fd5beaec09b7e6ec41f4847935e5d6a2720d0094b30', expand=False)
version('10.04', sha256='f67fb899b99348a1a7e471a05f249f972e7e303c78238fc5f693b99968642255', expand=False)

2
var/spack/repos/builtin/packages/geant4/package.py
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@@ -17,6 +17,8 @@ class Geant4(CMakePackage):
homepage = "http://geant4.cern.ch/"
url = "http://geant4.cern.ch/support/source/geant4.10.01.p03.tar.gz"
maintainers = ['drbenmorgan']
version('10.05.p01', sha256='f4a292220500fad17e0167ce3153e96e3410ecbe96284e572dc707f63523bdff')
version('10.04', sha256='f6d883132f110eb036c69da2b21df51f13c585dc7b99d4211ddd32f4ccee1670')
version('10.03.p03', sha256='a164f49c038859ab675eec474d08c9d02be8c4be9c0c2d3aa8e69adf89e1e138')

36
var/spack/repos/builtin/packages/gengetopt/package.py Normal file
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@@ -0,0 +1,36 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Gengetopt(AutotoolsPackage):
"""Tool to write command line option parsing code for C programs"""
homepage = "https://www.gnu.org/software/gengetopt/gengetopt.html"
url = "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.23.tar.xz"
maintainers = ['rblake-llnl']
version('2.23', sha256='b941aec9011864978dd7fdeb052b1943535824169d2aa2b0e7eae9ab807584ac')
version('2.22.6', sha256='30b05a88604d71ef2a42a2ef26cd26df242b41f5b011ad03083143a31d9b01f7')
version('2.22.5', sha256='3b6fb3240352b0eb0c5b8583b58b62cbba58167cef5a7e82fa08a7f968ed2137')
version('2.22.4', sha256='4edf6b24ec8085929c86835c51d5bf904052cc671530c15f9314d9b87fe54421')
version('2.22.3', sha256='8ce6b3df49cefea97bd522dc054ede2037939978bf23754d5c17311e5a1df3dc')
version('2.22.2', sha256='4bf96bea9f80ac85c716cd07f5fe68602db7f380f6dc2d025f17139aa0b56455')
version('2.22.1', sha256='e8d1de4f8c102263844886a2f2b57d82c291c1eae6307ea406fb96f29a67c3a7')
version('2.22', sha256='b605555e41e9bf7e852a37b051e6a49014e561f21290680e3a60c279488d417e')
version('2.21', sha256='355a32310b2fee5e7289d6d6e89eddd13275a7c85a243dc5dd293a6cb5bb047e')
version('2.20', sha256='4c8b3b42cecff579f5f9de5ccad47e0849e0245e325a04ff5985c248141af1a4')
parallel = False
def url_for_version(self, version):
url = 'ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-{0}.tar.{1}'
if version >= Version('2.23'):
suffix = 'xz'
else:
suffix = 'gz'
return url.format(version, suffix)

39
var/spack/repos/builtin/packages/glfw/package.py Normal file
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@@ -0,0 +1,39 @@
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Glfw(CMakePackage):
"""GLFW is an Open Source, multi-platform library for
OpenGL, OpenGL ES and Vulkan development on the desktop. It
provides a simple API for creating windows, contexts and
surfaces, receiving input and events."""
homepage = "https://www.glfw.org/"
url = "https://github.com/glfw/glfw/archive/3.3.2.tar.gz"
version('3.3.2', sha256='98768e12e615fbe9f3386f5bbfeb91b5a3b45a8c4c77159cef06b1f6ff749537')
version('3.3.1', sha256='6bca16e69361798817a4b62a5239a77253c29577fcd5d52ae8b85096e514177f')
version('3.3', sha256='81bf5fde487676a8af55cb317830703086bb534c53968d71936e7b48ee5a0f3e')
version('3.2.1', sha256='e10f0de1384d75e6fc210c53e91843f6110d6c4f3afbfb588130713c2f9d8fe8')
version('3.2', sha256='cb3aab46757981a39ae108e5207a1ecc4378e68949433a2b040ce2e17d8f6aa6')
version('3.1.2', sha256='6ac642087682aaf7f8397761a41a99042b2c656498217a1c63ba9706d1eef122')
version('3.1.1', sha256='4de311ec9bf43bfdc8423ddf93b91dc54dc73dcfbedfb0991b6fbb3a9baf245f')
version('3.1', sha256='2140f4c532e7ce4c84cb7e4c419d0979d5954fa1ce204b7646491bd2cc5bf308')
version('3.0.4', sha256='a4e7c57db2086803de4fc853bd472ff8b6d2639b9aa16e6ac6b19ffb53958caf')
version('3.0.3', sha256='7a182047ba6b1fdcda778b79aac249bb2328b6d141188cb5df29560715d01693')
depends_on('libxrandr')
depends_on('libxinerama')
depends_on('libxcursor')
depends_on('libxdamage')
depends_on('libxft')
depends_on('libxi')
depends_on('libxmu')
depends_on('freetype')
depends_on('fontconfig')
depends_on('doxygen', type='build')
depends_on('pkgconfig', type='build')

35
var/spack/repos/builtin/packages/gnupg/package.py
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@@ -7,38 +7,49 @@
class Gnupg(AutotoolsPackage):
"""GnuPG is a complete and free implementation of the OpenPGP
standard as defined by RFC4880 """
"""GNU Pretty Good Privacy (PGP) package."""
homepage = "https://gnupg.org/index.html"
url = "https://gnupg.org/ftp/gcrypt/gnupg/gnupg-2.2.17.tar.bz2"
url = "https://gnupg.org/ftp/gcrypt/gnupg/gnupg-2.2.19.tar.bz2"
version('2.2.19', sha256='242554c0e06f3a83c420b052f750b65ead711cc3fddddb5e7274fcdbb4e9dec0')
version('2.2.17', sha256='afa262868e39b651a2db4c071fba90415154243e83a830ca00516f9a807fd514')
version('2.2.15', sha256='cb8ce298d7b36558ffc48aec961b14c830ff1783eef7a623411188b5e0f5d454')
version('2.2.3', sha256='cbd37105d139f7aa74f92b6f65d136658682094b0e308666b820ae4b984084b4')
version('2.1.21', sha256='7aead8a8ba75b69866f583b6c747d91414d523bfdfbe9a8e0fe026b16ba427dd')
depends_on('npth@1.2:')
depends_on('libgpg-error@1.24:')
depends_on('libgcrypt@1.7.0:')
depends_on('libksba@1.3.4:')
depends_on('libassuan@2.4:', when='@:2.2.3')
depends_on('libassuan@2.5:', when='@2.2.15:')
depends_on('libksba@1.3.4:')
depends_on('libgpg-error@1.24:')
depends_on('npth@1.2:')
depends_on('zlib')
depends_on('pinentry', type='run')
depends_on('libiconv')
depends_on('zlib')
def configure_args(self):
return [
'--without-tar',
args = [
'--disable-bzip2',
'--disable-sqlite',
'--disable-ntbtls',
'--disable-gnutls',
'--disable-ldap',
'--disable-regex',
'--with-pinentry-pgm=' + self.spec['pinentry'].command.path,
'--with-libgpg-error-prefix=' + self.spec['libgpg-error'].prefix,
'--with-libgcrypt-prefix=' + self.spec['libgcrypt'].prefix,
'--with-libassuan-prefix=' + self.spec['libassuan'].prefix,
'--with-ksba-prefix=' + self.spec['libksba'].prefix,
'--with-npth-prefix=' + self.spec['npth'].prefix,
'--without-ldap',
'--with-libiconv-prefix=' + self.spec['libiconv'].prefix,
'--without-regex',
'--with-zlib=' + self.spec['zlib'].prefix,
'--without-bzip2',
'--without-tar',
'--without-libiconv-prefix',
'--without-readline',
]
if self.run_tests:
args.append('--enable-all-tests')
return args

1
var/spack/repos/builtin/packages/go/package.py
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@@ -35,6 +35,7 @@ class Go(Package):
extendable = True
version('1.14', sha256='6d643e46ad565058c7a39dac01144172ef9bd476521f42148be59249e4b74389')
version('1.13.8', sha256='b13bf04633d4d8cf53226ebeaace8d4d2fd07ae6fa676d0844a688339debec34')
version('1.13.7', sha256='e4ad42cc5f5c19521fbbbde3680995f2546110b5c6aa2b48c3754ff7af9b41f4')
version('1.13.6', sha256='aae5be954bdc40bcf8006eb77e8d8a5dde412722bc8effcdaf9772620d06420c')

4
var/spack/repos/builtin/packages/gromacs/package.py
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@@ -24,8 +24,10 @@ class Gromacs(CMakePackage):
git = 'https://github.com/gromacs/gromacs.git'
maintainers = ['junghans', 'marvinbernhardt']
version('develop', branch='master')
version('master', branch='master')
version('2020.1', sha256='e1666558831a3951c02b81000842223698016922806a8ce152e8f616e29899cf')
version('2020', sha256='477e56142b3dcd9cb61b8f67b24a55760b04d1655e8684f979a75a5eec40ba01')
version('2019.6', sha256='bebe396dc0db11a9d4cc205abc13b50d88225617642508168a2195324f06a358')
version('2019.5', sha256='438061a4a2d45bbb5cf5c3aadd6c6df32d2d77ce8c715f1c8ffe56156994083a')
version('2019.4', sha256='ba4366eedfc8a1dbf6bddcef190be8cd75de53691133f305a7f9c296e5ca1867')
version('2019.3', sha256='4211a598bf3b7aca2b14ad991448947da9032566f13239b1a05a2d4824357573')

323
var/spack/repos/builtin/packages/gsl/gsl-2.3-cblas.patch Normal file
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@@ -0,0 +1,323 @@
Makefile.am | 8 +-
ax_cblas.m4 | 69 +++++
bspline/Makefile.am | 2 +-
configure.ac | 10 +
eigen/Makefile.am | 2 +-
gsl-config.in | 4 +-
gsl.pc.in | 2 +-
interpolation/Makefile.am | 2 +-
linalg/Makefile.am | 2 +-
multifit/Makefile.am | 4 +-
multimin/Makefile.am | 4 +-
multiroots/Makefile.am | 2 +-
ode-initval/Makefile.am | 2 +-
poly/Makefile.am | 2 +-
specfunc/Makefile.am | 2 +-
wavelet/Makefile.am | 2 +-
31 files changed, 1157 insertions(+), 19 deletions(-)
diff --git a/Makefile.am b/Makefile.am
index c522001..4513bc8 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -19,7 +19,7 @@ EXTRA_DIST = autogen.sh gsl-config.in gsl.pc.in configure.ac THANKS BUGS gsl.spe
lib_LTLIBRARIES = libgsl.la
libgsl_la_SOURCES = version.c
-libgsl_la_LIBADD = $(GSL_LIBADD) $(SUBLIBS)
+libgsl_la_LIBADD = $(GSL_LIBADD) $(SUBLIBS) @CBLAS_LINK_LIBS@
libgsl_la_LDFLAGS = $(GSL_LDFLAGS) -version-info $(GSL_LT_VERSION)
noinst_HEADERS = templates_on.h templates_off.h build.h
@@ -29,10 +29,10 @@ m4data_DATA = gsl.m4
bin_PROGRAMS = gsl-randist gsl-histogram
gsl_randist_SOURCES = gsl-randist.c
-gsl_randist_LDADD = libgsl.la cblas/libgslcblas.la
+gsl_randist_LDADD = libgsl.la
gsl_histogram_SOURCES = gsl-histogram.c
-gsl_histogram_LDADD = libgsl.la cblas/libgslcblas.la
+gsl_histogram_LDADD = libgsl.la
check_SCRIPTS = test_gsl_histogram.sh pkgconfig.test
TESTS = test_gsl_histogram.sh pkgconfig.test
@@ -51,6 +51,8 @@ edit = $(SED) \
-e 's|@GSL_CFLAGS[@]|$(GSL_CFLAGS)|g' \
-e 's|@GSL_LIBM[@]|$(GSL_LIBM)|g' \
-e 's|@GSL_LIBS[@]|$(GSL_LIBS)|g' \
+ -e 's|@CBLAS_CFLAGS[@]|$(CBLAS_CFLAGS)|g' \
+ -e 's|@CBLAS_LIBS[@]|$(CBLAS_LIBS)|g' \
-e 's|@LIBS[@]|$(LIBS)|g' \
-e 's|@VERSION[@]|$(VERSION)|g'
diff --git a/ax_cblas.m4 b/ax_cblas.m4
new file mode 100644
index 0000000..6ef143a
--- /dev/null
+++ b/ax_cblas.m4
@@ -0,0 +1,69 @@
+AC_DEFUN([AX_CBLAS],[
+
+ ext_cblas=no
+ ext_cblas_libs="-lcblas"
+ ext_cblas_cflags=""
+
+ AC_ARG_WITH(cblas-external,
+ [AS_HELP_STRING([--with-cblas-external],
+ [Use external CBLAS library (default is no)])],
+ [with_ext_cblas=$withval],
+ [with_ext_cblas=no])
+
+ case $with_ext_cblas in
+ no) ext_cblas=no ;;
+ yes) ext_cblas=yes ;;
+ -* | */* | *.a | *.so | *.so.* | *.o)
+ ext_cblas=yes
+ ext_cblas_libs="$with_cblas" ;;
+ *) ext_cblas=yes
+ ext_cblas_libs="-l$with_cblas" ;;
+ esac
+
+ AC_ARG_WITH(cblas-external-libs,
+ [AS_HELP_STRING([--with-cblas-external-libs=<libs>],
+ [External cblas libraries to link with (default is "$ext_cblas_libs")])],
+ [ext_cblas_libs=$withval],
+ [])
+
+ AC_ARG_WITH(cblas-external-cflags,
+ [AS_HELP_STRING([--with-cblas-external-cflags=<flags>],
+ [Pre-processing flags to compile with external cblas ("-I<dir>")])],
+ [ext_cblas_cflags=$withval],
+ [])
+
+ if test x$ext_cblas != xno; then
+ if test "x$CBLAS_LIBS" = x; then
+ CBLAS_LIBS="$ext_cblas_libs"
+ fi
+ if test "x$CBLAS_CFLAGS" = x; then
+ CBLAS_CFLAGS="$ext_cblas_cflags"
+ fi
+
+ CFLAGS_sav="$CFLAGS"
+ CFLAGS="$CFLAGS $CBLAS_CFLAGS"
+ AC_CHECK_HEADER(cblas.h, ,
+ [AC_MSG_ERROR([
+ *** Header file cblas.h not found.
+ *** If you installed cblas header in a non standard place,
+ *** specify its install prefix using the following option
+ *** --with-cblas-external-cflags="-I<include_dir>"])
+ ])
+ CFLAGS="$CFLAGS_sav"
+
+ LIBS_sav="$LIBS"
+ LIBS="$LIBS $CBLAS_LIBS -lm"
+ AC_MSG_CHECKING([for cblas_sgemm in $CBLAS_LIBS])
+ AC_TRY_LINK_FUNC(cblas_sgemm, [ext_cblas=yes],
+ [AC_MSG_ERROR([
+ *** Linking with cblas with $LIBS failed.
+ *** If you installed cblas library in a non standard place,
+ *** specify its install prefix using the following option
+ *** --with-cblas-external-libs="-L<lib_dir> -l<lib>"])
+ ])
+ AC_MSG_RESULT($ext_cblas)
+ LIBS="$LIBS_sav"
+ AC_SUBST([CBLAS_CFLAGS])
+ AC_SUBST([CBLAS_LIBS])
+ fi
+])
diff --git a/bspline/Makefile.am b/bspline/Makefile.am
index 3f4f950..d413036 100644
--- a/bspline/Makefile.am
+++ b/bspline/Makefile.am
@@ -12,6 +12,6 @@ check_PROGRAMS = test
TESTS = $(check_PROGRAMS)
-test_LDADD = libgslbspline.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../statistics/libgslstatistics.la
+test_LDADD = libgslbspline.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../statistics/libgslstatistics.la
test_SOURCES = test.c
diff --git a/configure.ac b/configure.ac
index a26fc1e..564d426 100644
--- a/configure.ac
+++ b/configure.ac
@@ -208,6 +208,16 @@ if test "x$LIBS" = "x" ; then
AC_CHECK_LIB(m, cos)
fi
+sinclude(ax_cblas.m4)
+AX_CBLAS
+if test "x$CBLAS_LIBS" != "x"; then
+ CBLAS_LINK_LIBS="$CBLAS_LIBS"
+else
+ CBLAS_LINK_LIBS="\$(top_builddir)/cblas/libgslcblas.la"
+ CBLAS_LIBS="-lgslcblas"
+fi
+AC_SUBST(CBLAS_LINK_LIBS)
+
dnl Remember to put a definition in acconfig.h for each of these
AC_CHECK_DECLS(feenableexcept,,,[#define _GNU_SOURCE 1
#include <fenv.h>])
diff --git a/eigen/Makefile.am b/eigen/Makefile.am
index c28bfde..14197a4 100644
--- a/eigen/Makefile.am
+++ b/eigen/Makefile.am
@@ -11,7 +11,7 @@ noinst_HEADERS = qrstep.c
TESTS = $(check_PROGRAMS)
-test_LDADD = libgsleigen.la ../test/libgsltest.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la ../sort/libgslsort.la
+test_LDADD = libgsleigen.la ../test/libgsltest.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la ../sort/libgslsort.la
test_SOURCES = test.c
diff --git a/gsl-config.in b/gsl-config.in
old mode 100755
new mode 100644
index 3f3fa61..c9c4262
--- a/gsl-config.in
+++ b/gsl-config.in
@@ -58,11 +58,11 @@ while test $# -gt 0; do
;;
--cflags)
- echo @GSL_CFLAGS@
+ echo @GSL_CFLAGS@ @CBLAS_CFLAGS@
;;
--libs)
- : ${GSL_CBLAS_LIB=-lgslcblas}
+ : ${GSL_CBLAS_LIB=@CBLAS_LIBS@}
echo @GSL_LIBS@ $GSL_CBLAS_LIB @GSL_LIBM@
;;
diff --git a/gsl.pc.in b/gsl.pc.in
index 5e9ef21..5a7a0f3 100644
--- a/gsl.pc.in
+++ b/gsl.pc.in
@@ -2,7 +2,7 @@ prefix=@prefix@
exec_prefix=@exec_prefix@
libdir=@libdir@
includedir=@includedir@
-GSL_CBLAS_LIB=-lgslcblas
+GSL_CBLAS_LIB=@CBLAS_LIBS@
Name: GSL
Description: GNU Scientific Library
diff --git a/interpolation/Makefile.am b/interpolation/Makefile.am
index 1d80755..e45bd51 100644
--- a/interpolation/Makefile.am
+++ b/interpolation/Makefile.am
@@ -12,7 +12,7 @@ AM_CPPFLAGS = -I$(top_srcdir)
TESTS = $(check_PROGRAMS)
-test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
+test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
test_SOURCES = test.c
diff --git a/linalg/Makefile.am b/linalg/Makefile.am
index a6c15b0..447ebbe 100644
--- a/linalg/Makefile.am
+++ b/linalg/Makefile.am
@@ -13,4 +13,4 @@ TESTS = $(check_PROGRAMS)
check_PROGRAMS = test
test_SOURCES = test.c
-test_LDADD = libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../rng/libgslrng.la
+test_LDADD = libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../rng/libgslrng.la
diff --git a/multifit/Makefile.am b/multifit/Makefile.am
index 988614e..793b485 100644
--- a/multifit/Makefile.am
+++ b/multifit/Makefile.am
@@ -67,8 +67,8 @@ check_PROGRAMS = test #demo
TESTS = $(check_PROGRAMS)
test_SOURCES = test.c
-test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ../rng/libgslrng.la ../specfunc/libgslspecfunc.la ../min/libgslmin.la
+test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ../rng/libgslrng.la ../specfunc/libgslspecfunc.la ../min/libgslmin.la
#demo_SOURCES = demo.c
-#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la
+#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la
diff --git a/multimin/Makefile.am b/multimin/Makefile.am
index 7071359..65a488a 100644
--- a/multimin/Makefile.am
+++ b/multimin/Makefile.am
@@ -13,8 +13,8 @@ check_PROGRAMS = test #demo
TESTS = $(check_PROGRAMS)
test_SOURCES = test.c test_funcs.c test_funcs.h
-test_LDADD = libgslmultimin.la ../min/libgslmin.la ../poly/libgslpoly.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
+test_LDADD = libgslmultimin.la ../min/libgslmin.la ../poly/libgslpoly.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
#demo_SOURCES = demo.c
-#demo_LDADD = libgslmultimin.la ../min/libgslmin.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
+#demo_LDADD = libgslmultimin.la ../min/libgslmin.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
diff --git a/multiroots/Makefile.am b/multiroots/Makefile.am
index a351c3f..6178448 100644
--- a/multiroots/Makefile.am
+++ b/multiroots/Makefile.am
@@ -15,5 +15,5 @@ check_PROGRAMS = test
TESTS = $(check_PROGRAMS)
test_SOURCES = test.c test_funcs.c test_funcs.h
-test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
+test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
diff --git a/ode-initval/Makefile.am b/ode-initval/Makefile.am
index 9c774b5..346c381 100644
--- a/ode-initval/Makefile.am
+++ b/ode-initval/Makefile.am
@@ -12,7 +12,7 @@ check_PROGRAMS = test
TESTS = $(check_PROGRAMS)
-test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
+test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
test_SOURCES = test.c
diff --git a/poly/Makefile.am b/poly/Makefile.am
index f1dae5d..e0f8e83 100644
--- a/poly/Makefile.am
+++ b/poly/Makefile.am
@@ -10,7 +10,7 @@ noinst_HEADERS = balance.c companion.c qr.c
TESTS = $(check_PROGRAMS)
-check_PROGRAMS = test
+#check_PROGRAMS = test
test_SOURCES = test.c
test_LDADD = libgslpoly.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../sort/libgslsort.la
diff --git a/specfunc/Makefile.am b/specfunc/Makefile.am
index eba9ab2..772cc7e 100644
--- a/specfunc/Makefile.am
+++ b/specfunc/Makefile.am
@@ -12,7 +12,7 @@ TESTS = $(check_PROGRAMS)
check_PROGRAMS = test
-test_LDADD = libgslspecfunc.la ../eigen/libgsleigen.la ../linalg/libgsllinalg.la ../sort/libgslsort.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../block/libgslblock.la ../complex/libgslcomplex.la ../poly/libgslpoly.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
+test_LDADD = libgslspecfunc.la ../eigen/libgsleigen.la ../linalg/libgsllinalg.la ../sort/libgslsort.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../block/libgslblock.la ../complex/libgslcomplex.la ../poly/libgslpoly.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
test_SOURCES = test_sf.c test_sf.h test_airy.c test_bessel.c test_coulomb.c test_dilog.c test_gamma.c test_hyperg.c test_legendre.c test_mathieu.c
diff --git a/wavelet/Makefile.am b/wavelet/Makefile.am
index 9da20d8..8cdbd77 100644
--- a/wavelet/Makefile.am
+++ b/wavelet/Makefile.am
@@ -10,7 +10,7 @@ check_PROGRAMS = test
TESTS = $(check_PROGRAMS)
-test_LDADD = libgslwavelet.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
+test_LDADD = libgslwavelet.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
test_SOURCES = test.c

28
var/spack/repos/builtin/packages/gsl/package.py
View File

@@ -24,3 +24,31 @@ class Gsl(AutotoolsPackage, GNUMirrorPackage):
version('2.1', sha256='59ad06837397617f698975c494fe7b2b698739a59e2fcf830b776428938a0c66')
version('2.0', sha256='e361f0b19199b5e6c21922e9f16adf7eca8dd860842802424906d0f83485ca2d')
version('1.16', sha256='73bc2f51b90d2a780e6d266d43e487b3dbd78945dd0b04b14ca5980fe28d2f53')
variant('external-cblas', default=False, description='Build against external blas')
# from https://dev.gentoo.org/~mgorny/dist/gsl-2.3-cblas.patch.bz2
patch('gsl-2.3-cblas.patch', when="+external-cblas")
conflicts('+external-cblas', when="@:2.2.9999")
depends_on('m4', type='build', when='+external-cblas')
depends_on('autoconf', type='build', when='+external-cblas')
depends_on('automake', type='build', when='+external-cblas')
depends_on('libtool', type='build', when='+external-cblas')
depends_on('blas', when='+external-cblas')
@property
def force_autoreconf(self):
# The external cblas patch touches configure
return self.spec.satisfies('+external-cblas')
def configure_args(self):
configure_args = []
if self.spec.satisfies('+external-cblas'):
configure_args.append('--with-external-cblas')
configure_args.append('CBLAS_CFLAGS=%s'
% self.spec['blas'].headers.include_flags)
configure_args.append('CBLAS_LIBS=%s'
% self.spec['blas'].libs.ld_flags)
return configure_args

31
var/spack/repos/builtin/packages/gunrock/package.py Normal file
View File

@@ -0,0 +1,31 @@
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Gunrock(CMakePackage, CudaPackage):
"""High-Performance Graph Primitives on GPUs"""
homepage = "https://gunrock.github.io/docs/"
git = "https://github.com/gunrock/gunrock.git"
version('master', submodules=True)
version('1.1', submodules=True, tag='v1.1')
version('1.0', submodules=True, tag='v1.0')
version('0.5.1', submodules=True, tag='v0.5.1')
version('0.5', submodules=True, tag='v0.5')
version('0.4', submodules=True, tag='v0.4')
version('0.3.1', submodules=True, tag='v0.3.1')
version('0.3', submodules=True, tag='v0.3')
version('0.2', submodules=True, tag='v0.2')
version('0.1', submodules=True, tag='v0.1')
depends_on('cuda')
def install(self, spec, prefix):
with working_dir(self.build_directory):
install_tree('bin', prefix.bin)
install_tree('lib', prefix.lib)

24
var/spack/repos/builtin/packages/hpctoolkit/package.py
View File

@@ -19,6 +19,7 @@ class Hpctoolkit(AutotoolsPackage):
maintainers = ['mwkrentel']
version('master', branch='master')
version('2020.03.01', commit='94ede4e6fa1e05e6f080be8dc388240ea027f769')
version('2019.12.28', commit='b4e1877ff96069fd8ed0fdf0e36283a5b4b62240')
version('2019.08.14', commit='6ea44ed3f93ede2d0a48937f288a2d41188a277c')
version('2018.12.28', commit='8dbf0d543171ffa9885344f32f23cc6f7f6e39bc')
@@ -52,7 +53,7 @@ class Hpctoolkit(AutotoolsPackage):
'for the compute nodes.')
variant('cuda', default=False,
description='Support CUDA on NVIDIA GPUs (master branch).')
description='Support CUDA on NVIDIA GPUs (2020.03.01 or later).')
boost_libs = (
'+atomic +chrono +date_time +filesystem +system +thread +timer'
@@ -61,18 +62,18 @@ class Hpctoolkit(AutotoolsPackage):
depends_on('binutils+libiberty~nls', type='link')
depends_on('boost' + boost_libs)
depends_on('bzip2', type='link')
depends_on('dyninst')
depends_on('elfutils~nls', type='link')
depends_on('intel-tbb')
depends_on('bzip2+shared', type='link')
depends_on('dyninst@9.3.2:')
depends_on('elfutils+bzip2+xz~nls', type='link')
depends_on('intel-tbb+shared')
depends_on('libdwarf')
depends_on('libmonitor+hpctoolkit')
depends_on('libmonitor+bgq', when='+bgq')
depends_on('libunwind@1.4:')
depends_on('libunwind@1.4: +xz')
depends_on('mbedtls+pic')
depends_on('xerces-c transcoder=iconv')
depends_on('xz', type='link')
depends_on('zlib')
depends_on('zlib+shared')
depends_on('cuda', when='+cuda')
depends_on('intel-xed', when='target=x86_64:')
@@ -83,11 +84,14 @@ class Hpctoolkit(AutotoolsPackage):
conflicts('%gcc@:4.7.99', when='^dyninst@10.0.0:',
msg='hpctoolkit requires gnu gcc 4.8.x or later')
conflicts('%gcc@:4.99.99', when='@master',
msg='the master branch requires gnu gcc 5.x or later')
conflicts('%gcc@:4.99.99', when='@2020.03.01:',
msg='hpctoolkit requires gnu gcc 5.x or later')
conflicts('+cuda', when='@2018.0.0:2019.99.99',
msg='cuda is only available on the master branch')
msg='cuda requires 2020.03.01 or later')
conflicts('+bgq', when='@2020.03.01:',
msg='blue gene requires 2019.12.28 or earlier')
flag_handler = AutotoolsPackage.build_system_flags

6
var/spack/repos/builtin/packages/hpcviewer/package.py
View File

@@ -37,6 +37,9 @@ class Hpcviewer(Package):
maintainers = ['mwkrentel']
viewer_sha = {
('2020.02', 'x86_64'): 'af1f514547a9325aee30eb891b31e38c7ea3f33d2d1978b44f83e7daa3d5de6b',
('2020.02', 'ppc64'): '7bb4926202db663aedd5a6830778c5f73f6b08a65d56861824ea95ba83b1f59c',
('2020.02', 'ppc64le'): 'cfcebb7ba301affd6d21d2afd43c540e6dd4c5bc39b0d20e8bd1e4fed6aa3481',
('2020.01', 'x86_64'): '3cd5a2a382cec1d64c8bd0abaf2b1461dcd4092a4b4074ddbdc1b96d2a0b4220',
('2020.01', 'ppc64'): '814394a5f410033cc1019526c268ef98b5b381e311fcd39ae8b2bde6c6ff017c',
('2020.01', 'ppc64le'): 'e830e956b8088c415fb25ef44a8aca16ebcb27bcd34536866612343217e3f9e4',
@@ -61,6 +64,9 @@ class Hpcviewer(Package):
}
trace_sha = {
('2020.02', 'x86_64'): 'b7b634e91108aa50a2e8647ac6bac87df775ae38aff078545efaa84735e0a666',
('2020.02', 'ppc64'): 'a3e845901689e1b32bc6ab2826c6ac6ed352df4839090fa530b20f747e6e0957',
('2020.02', 'ppc64le'): 'a64a283f61e706d988952a7cede9fac0328b09d2d0b64e4c08acc54e38781c98',
('2020.01', 'x86_64'): '9459177a2445e85d648384e2ccee20524592e91a74d615262f32d0876831cd7c',
('2020.01', 'ppc64'): '02366a2ba30b9b2450d50cf44933288f04fae5bf9868eef7bb2ae1b49d4f454e',
('2020.01', 'ppc64le'): '39970e84e397ed96bc994e7b8db3b7b3aab4e3155fa7ca8e68b9274bb58115f0',

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