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Merge branch 'develop' of https://github.com/LLNL/spack into features/module_refresh

Browse Source 
Conflicts:
	lib/spack/spack/test/__init__.py
This commit is contained in:
alalazo
2016-07-19 09:05:27 +02:00
parent a96eb7096d 7555c3d949
commit acfeb5d043
17 changed files with 421 additions and 220 deletions
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2
.gitignore vendored
View File

@@ -1,7 +1,7 @@
/var/spack/stage
/var/spack/cache
*.pyc
/opt/
/opt
*~
.DS_Store
.idea

49
lib/spack/spack/cmd/bootstrap.py
View File

@@ -23,7 +23,6 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
import os
from subprocess import check_call
import llnl.util.tty as tty
from llnl.util.filesystem import join_path, mkdirp
@@ -31,26 +30,49 @@
import spack
from spack.util.executable import which
_SPACK_UPSTREAM = 'https://github.com/llnl/spack'
description = "Create a new installation of spack in another prefix"
def setup_parser(subparser):
subparser.add_argument('prefix', help="names of prefix where we should install spack")
subparser.add_argument(
'-r', '--remote', action='store', dest='remote',
help="name of the remote to bootstrap from", default='origin')
subparser.add_argument(
'prefix',
help="names of prefix where we should install spack")
def get_origin_url():
def get_origin_info(remote):
git_dir = join_path(spack.prefix, '.git')
git = which('git', required=True)
origin_url = git(
'--git-dir=%s' % git_dir, 'config', '--get', 'remote.origin.url',
output=str)
return origin_url.strip()
try:
branch = git('symbolic-ref', '--short', 'HEAD', output=str)
except ProcessError:
branch = 'develop'
tty.warn('No branch found; using default branch: %s' % branch)
if remote == 'origin' and \
branch not in ('master', 'develop'):
branch = 'develop'
tty.warn('Unknown branch found; using default branch: %s' % branch)
try:
origin_url = git(
'--git-dir=%s' % git_dir,
'config', '--get', 'remote.%s.url' % remote,
output=str)
except ProcessError:
origin_url = _SPACK_UPSTREAM
tty.warn('No git repository found; '
'using default upstream URL: %s' % origin_url)
return (origin_url.strip(), branch.strip())
def bootstrap(parser, args):
origin_url = get_origin_url()
origin_url, branch = get_origin_info(args.remote)
prefix = args.prefix
tty.msg("Fetching spack from origin: %s" % origin_url)
tty.msg("Fetching spack from '%s': %s" % (args.remote, origin_url))
if os.path.isfile(prefix):
tty.die("There is already a file at %s" % prefix)
@@ -62,7 +84,8 @@ def bootstrap(parser, args):
files_in_the_way = os.listdir(prefix)
if files_in_the_way:
tty.die("There are already files there! Delete these files before boostrapping spack.",
tty.die("There are already files there! "
"Delete these files before boostrapping spack.",
*files_in_the_way)
tty.msg("Installing:",
@@ -73,8 +96,10 @@ def bootstrap(parser, args):
git = which('git', required=True)
git('init', '--shared', '-q')
git('remote', 'add', 'origin', origin_url)
git('fetch', 'origin', 'master:refs/remotes/origin/master', '-n', '-q')
git('reset', '--hard', 'origin/master', '-q')
git('fetch', 'origin', '%s:refs/remotes/origin/%s' % (branch, branch),
'-n', '-q')
git('reset', '--hard', 'origin/%s' % branch, '-q')
git('checkout', '-B', branch, 'origin/%s' % branch, '-q')
tty.msg("Successfully created a new spack in %s" % prefix,
"Run %s/bin/spack to use this installation." % prefix)

21
lib/spack/spack/cmd/checksum.py
View File

@@ -42,7 +42,8 @@ def setup_parser(subparser):
'--keep-stage', action='store_true', dest='keep_stage',
help="Don't clean up staging area when command completes.")
subparser.add_argument(
'versions', nargs=argparse.REMAINDER, help='Versions to generate checksums for')
'versions', nargs=argparse.REMAINDER,
help='Versions to generate checksums for')
def get_checksums(versions, urls, **kwargs):
@@ -59,10 +60,10 @@ def get_checksums(versions, urls, **kwargs):
with Stage(url, keep=keep_stage) as stage:
stage.fetch()
if i == 0 and first_stage_function:
first_stage_function(stage)
first_stage_function(stage, url)
hashes.append((version,
spack.util.crypto.checksum(hashlib.md5, stage.archive_file)))
hashes.append((version, spack.util.crypto.checksum(
hashlib.md5, stage.archive_file)))
i += 1
except FailedDownloadError as e:
tty.msg("Failed to fetch %s" % url)
@@ -79,12 +80,12 @@ def checksum(parser, args):
# If the user asked for specific versions, use those.
if args.versions:
versions = {}
for v in args.versions:
v = ver(v)
if not isinstance(v, Version):
for version in args.versions:
version = ver(version)
if not isinstance(version, Version):
tty.die("Cannot generate checksums for version lists or " +
"version ranges. Use unambiguous versions.")
versions[v] = pkg.url_for_version(v)
versions[version] = pkg.url_for_version(version)
else:
versions = pkg.fetch_remote_versions()
if not versions:
@@ -111,5 +112,7 @@ def checksum(parser, args):
if not version_hashes:
tty.die("Could not fetch any versions for %s" % pkg.name)
version_lines = [" version('%s', '%s')" % (v, h) for v, h in version_hashes]
version_lines = [
" version('%s', '%s')" % (v, h) for v, h in version_hashes
]
tty.msg("Checksummed new versions of %s:" % pkg.name, *version_lines)

145
lib/spack/spack/cmd/create.py
View File

@@ -103,6 +103,64 @@ def install(self, spec, prefix):
${install}
""")
# Build dependencies and extensions
dependencies_dict = {
'autotools': "# depends_on('foo')",
'cmake': "depends_on('cmake')",
'scons': "depends_on('scons')",
'python': "extends('python')",
'R': "extends('R')",
'octave': "extends('octave')",
'unknown': "# depends_on('foo')"
}
# Default installation instructions
install_dict = {
'autotools': """\
# FIXME: Modify the configure line to suit your build system here.
configure('--prefix={0}'.format(prefix))
# FIXME: Add logic to build and install here.
make()
make('install')""",
'cmake': """\
with working_dir('spack-build', create=True):
# FIXME: Modify the cmake line to suit your build system here.
cmake('..', *std_cmake_args)
# FIXME: Add logic to build and install here.
make()
make('install')""",
'scons': """\
# FIXME: Add logic to build and install here.
scons('prefix={0}'.format(prefix))
scons('install')""",
'python': """\
# FIXME: Add logic to build and install here.
python('setup.py', 'install', '--prefix={0}'.format(prefix))""",
'R': """\
# FIXME: Add logic to build and install here.
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)""",
'octave': """\
# FIXME: Add logic to build and install here.
octave('--quiet', '--norc',
'--built-in-docstrings-file=/dev/null',
'--texi-macros-file=/dev/null',
'--eval', 'pkg prefix {0}; pkg install {1}'.format(
prefix, self.stage.archive_file))""",
'unknown': """\
# FIXME: Unknown build system
make()
make('install')"""
}
def make_version_calls(ver_hash_tuples):
"""Adds a version() call to the package for each version found."""
@@ -133,60 +191,17 @@ def setup_parser(subparser):
setup_parser.subparser = subparser
class ConfigureGuesser(object):
def __call__(self, stage):
"""Try to guess the type of build system used by the project.
Set any necessary build dependencies or extensions.
Set the appropriate default installation instructions."""
class BuildSystemGuesser(object):
def __call__(self, stage, url):
"""Try to guess the type of build system used by a project based on
the contents of its archive or the URL it was downloaded from."""
# Build dependencies and extensions
dependenciesDict = {
'autotools': "# depends_on('foo')",
'cmake': "depends_on('cmake', type='build')",
'scons': "depends_on('scons', type='build')",
'python': "extends('python', type=nolink)",
'R': "extends('R')",
'unknown': "# depends_on('foo')"
}
# Default installation instructions
installDict = {
'autotools': """\
# FIXME: Modify the configure line to suit your build system here.
configure('--prefix={0}'.format(prefix))
# FIXME: Add logic to build and install here.
make()
make('install')""",
'cmake': """\
with working_dir('spack-build', create=True):
# FIXME: Modify the cmake line to suit your build system here.
cmake('..', *std_cmake_args)
# FIXME: Add logic to build and install here.
make()
make('install')""",
'scons': """\
# FIXME: Add logic to build and install here.
scons('prefix={0}'.format(prefix))
scons('install')""",
'python': """\
# FIXME: Add logic to build and install here.
python('setup.py', 'install', '--prefix={0}'.format(prefix))""",
'R': """\
# FIXME: Add logic to build and install here.
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)""",
'unknown': """\
# FIXME: Unknown build system
make()
make('install')"""
}
# Most octave extensions are hosted on Octave-Forge:
# http://octave.sourceforge.net/index.html
# They all have the same base URL.
if 'downloads.sourceforge.net/octave/' in url:
self.build_system = 'octave'
return
# A list of clues that give us an idea of the build system a package
# uses. If the regular expression matches a file contained in the
@@ -224,12 +239,6 @@ def __call__(self, stage):
self.build_system = build_system
# Set any necessary build dependencies or extensions.
self.dependencies = dependenciesDict[build_system]
# Set the appropriate default installation instructions
self.install = installDict[build_system]
def guess_name_and_version(url, args):
# Try to deduce name and version of the new package from the URL
@@ -334,8 +343,8 @@ def create(parser, args):
# Fetch tarballs (prompting user if necessary)
versions, urls = fetch_tarballs(url, name, version)
# Try to guess what configure system is used.
guesser = ConfigureGuesser()
# Try to guess what build system is used.
guesser = BuildSystemGuesser()
ver_hash_tuples = spack.cmd.checksum.get_checksums(
versions, urls,
first_stage_function=guesser,
@@ -344,13 +353,13 @@ def create(parser, args):
if not ver_hash_tuples:
tty.die("Could not fetch any tarballs for %s" % name)
# Prepend 'py-' to python package names, by convention.
# Add prefix to package name if it is an extension.
if guesser.build_system == 'python':
name = 'py-%s' % name
# Prepend 'r-' to R package names, by convention.
name = 'py-{0}'.format(name)
if guesser.build_system == 'R':
name = 'r-%s' % name
name = 'r-{0}'.format(name)
if guesser.build_system == 'octave':
name = 'octave-{0}'.format(name)
# Create a directory for the new package.
pkg_path = repo.filename_for_package_name(name)
@@ -367,8 +376,8 @@ def create(parser, args):
class_name=mod_to_class(name),
url=url,
versions=make_version_calls(ver_hash_tuples),
dependencies=guesser.dependencies,
install=guesser.install))
dependencies=dependencies_dict[guesser.build_system],
install=install_dict[guesser.build_system]))
# If everything checks out, go ahead and edit.
spack.editor(pkg_path)

24
lib/spack/spack/cmd/package-list.py
View File

@@ -22,10 +22,8 @@
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
import re
import cgi
from StringIO import StringIO
import llnl.util.tty as tty
from llnl.util.tty.colify import *
import spack
@@ -34,21 +32,22 @@
def github_url(pkg):
"""Link to a package file on github."""
return ("https://github.com/llnl/spack/blob/master/var/spack/packages/%s/package.py" %
pkg.name)
url = "https://github.com/llnl/spack/blob/master/var/spack/packages/%s/package.py" # NOQA: ignore=E501
return (url % pkg.name)
def rst_table(elts):
"""Print out a RST-style table."""
cols = StringIO()
ncol, widths = colify(elts, output=cols, tty=True)
header = " ".join("=" * (w-1) for w in widths)
header = " ".join("=" * (w - 1) for w in widths)
return "%s\n%s%s" % (header, cols.getvalue(), header)
def print_rst_package_list():
"""Print out information on all packages in restructured text."""
pkgs = sorted(spack.repo.all_packages(), key=lambda s:s.name.lower())
pkgs = sorted(spack.repo.all_packages(), key=lambda s: s.name.lower())
pkg_names = [p.name for p in pkgs]
print ".. _package-list:"
print
@@ -62,7 +61,7 @@ def print_rst_package_list():
print "Spack currently has %d mainline packages:" % len(pkgs)
print
print rst_table("`%s`_" % p.name for p in pkgs)
print rst_table("`%s`_" % p for p in pkg_names)
print
print "-----"
@@ -79,14 +78,15 @@ def print_rst_package_list():
print
if pkg.versions:
print "Versions:"
print " " + ", ".join(str(v) for v in reversed(sorted(pkg.versions)))
print " " + ", ".join(str(v) for v in
reversed(sorted(pkg.versions)))
for deptype in ('build', 'link', 'run'):
deps = pkg.dependencies(deptype)
for deptype in spack.alldeps:
deps = pkg.dependencies_of_type(deptype)
if deps:
print "%s Dependencies" % deptype.capitalize()
print " " + ", ".join("`%s`_" % d if d != "mpi" else d
for d in build_deps)
print " " + ", ".join("%s_" % d if d in pkg_names
else d for d in deps)
print
print "Description:"

9
lib/spack/spack/platforms/cray_xc.py
View File

@@ -2,6 +2,7 @@
from spack.architecture import Platform, Target
from spack.operating_systems.linux_distro import LinuxDistro
from spack.operating_systems.cnl import Cnl
from spack.util.executable import which
class CrayXc(Platform):
priority = 20
@@ -42,5 +43,11 @@ def __init__(self):
@classmethod
def detect(self):
return os.path.exists('/opt/cray/craype')
if os.path.exists('/cray_home'):
cc_verbose = which('cc')
cc_verbose.add_default_arg('-craype-verbose')
text = cc_verbose(output=str, error=str, ignore_errors=True).split()
if '-D__CRAYXC' in text:
return True
return False

105
lib/spack/spack/preferred_packages.py
View File

@@ -26,8 +26,10 @@
import spack
from spack.version import *
class PreferredPackages(object):
_default_order = {'compiler' : [ 'gcc', 'intel', 'clang', 'pgi', 'xlc' ] } # Arbitrary, but consistent
# Arbitrary, but consistent
_default_order = {'compiler': ['gcc', 'intel', 'clang', 'pgi', 'xlc']}
def __init__(self):
self.preferred = spack.config.get_config('packages')
@@ -35,24 +37,25 @@ def __init__(self):
# Given a package name, sort component (e.g, version, compiler, ...), and
# a second_key (used by providers), return the list
def _order_for_package(self, pkgname, component, second_key, test_all=True):
def _order_for_package(self, pkgname, component, second_key,
test_all=True):
pkglist = [pkgname]
if test_all:
pkglist.append('all')
for pkg in pkglist:
order = self.preferred.get(pkg, {}).get(component, {})
if type(order) is dict:
if isinstance(order, dict) and second_key:
order = order.get(second_key, {})
if not order:
continue
return [str(s).strip() for s in order]
return []
# A generic sorting function. Given a package name and sort
# component, return less-than-0, 0, or greater-than-0 if
# a is respectively less-than, equal to, or greater than b.
def _component_compare(self, pkgname, component, a, b, reverse_natural_compare, second_key):
def _component_compare(self, pkgname, component, a, b,
reverse_natural_compare, second_key):
if a is None:
return -1
if b is None:
@@ -84,92 +87,102 @@ def _component_compare(self, pkgname, component, a, b, reverse_natural_compare,
else:
return 0
# A sorting function for specs. Similar to component_compare, but
# a and b are considered to match entries in the sorting list if they
# satisfy the list component.
def _spec_compare(self, pkgname, component, a, b, reverse_natural_compare, second_key):
if not a or not a.concrete:
def _spec_compare(self, pkgname, component, a, b,
reverse_natural_compare, second_key):
if not a or (not a.concrete and not second_key):
return -1
if not b or not b.concrete:
if not b or (not b.concrete and not second_key):
return 1
specs = self._spec_for_pkgname(pkgname, component, second_key)
a_index = None
b_index = None
reverse = -1 if reverse_natural_compare else 1
for i, cspec in enumerate(specs):
if a_index == None and (cspec.satisfies(a) or a.satisfies(cspec)):
if a_index is None and (cspec.satisfies(a) or a.satisfies(cspec)):
a_index = i
if b_index:
break
if b_index == None and (cspec.satisfies(b) or b.satisfies(cspec)):
if b_index is None and (cspec.satisfies(b) or b.satisfies(cspec)):
b_index = i
if a_index:
break
if a_index != None and b_index == None: return -1
elif a_index == None and b_index != None: return 1
elif a_index != None and b_index == a_index: return -1 * cmp(a, b)
elif a_index != None and b_index != None and a_index != b_index: return cmp(a_index, b_index)
else: return cmp(a, b) * reverse
if a_index is not None and b_index is None:
return -1
elif a_index is None and b_index is not None:
return 1
elif a_index is not None and b_index == a_index:
return -1 * cmp(a, b)
elif (a_index is not None and b_index is not None and
a_index != b_index):
return cmp(a_index, b_index)
else:
return cmp(a, b) * reverse
# Given a sort order specified by the pkgname/component/second_key, return
# a list of CompilerSpecs, VersionLists, or Specs for that sorting list.
def _spec_for_pkgname(self, pkgname, component, second_key):
key = (pkgname, component, second_key)
if not key in self._spec_for_pkgname_cache:
if key not in self._spec_for_pkgname_cache:
pkglist = self._order_for_package(pkgname, component, second_key)
if not pkglist:
if component in self._default_order:
pkglist = self._default_order[component]
if component == 'compiler':
self._spec_for_pkgname_cache[key] = [spack.spec.CompilerSpec(s) for s in pkglist]
self._spec_for_pkgname_cache[key] = \
[spack.spec.CompilerSpec(s) for s in pkglist]
elif component == 'version':
self._spec_for_pkgname_cache[key] = [VersionList(s) for s in pkglist]
self._spec_for_pkgname_cache[key] = \
[VersionList(s) for s in pkglist]
else:
self._spec_for_pkgname_cache[key] = [spack.spec.Spec(s) for s in pkglist]
self._spec_for_pkgname_cache[key] = \
[spack.spec.Spec(s) for s in pkglist]
return self._spec_for_pkgname_cache[key]
def provider_compare(self, pkgname, provider_str, a, b):
"""Return less-than-0, 0, or greater than 0 if a is respecively less-than, equal-to, or
greater-than b. A and b are possible implementations of provider_str.
One provider is less-than another if it is preferred over the other.
For example, provider_compare('scorep', 'mpi', 'mvapich', 'openmpi') would return -1 if
mvapich should be preferred over openmpi for scorep."""
return self._spec_compare(pkgname, 'providers', a, b, False, provider_str)
"""Return less-than-0, 0, or greater than 0 if a is respecively
less-than, equal-to, or greater-than b. A and b are possible
implementations of provider_str. One provider is less-than another
if it is preferred over the other. For example,
provider_compare('scorep', 'mpi', 'mvapich', 'openmpi') would
return -1 if mvapich should be preferred over openmpi for scorep."""
return self._spec_compare(pkgname, 'providers', a, b, False,
provider_str)
def spec_has_preferred_provider(self, pkgname, provider_str):
"""Return True iff the named package has a list of preferred provider"""
return bool(self._order_for_package(pkgname, 'providers', provider_str, False))
"""Return True iff the named package has a list of preferred
providers"""
return bool(self._order_for_package(pkgname, 'providers',
provider_str, False))
def version_compare(self, pkgname, a, b):
"""Return less-than-0, 0, or greater than 0 if version a of pkgname is
respecively less-than, equal-to, or greater-than version b of pkgname.
One version is less-than another if it is preferred over the other."""
respectively less-than, equal-to, or greater-than version b of
pkgname. One version is less-than another if it is preferred over
the other."""
return self._spec_compare(pkgname, 'version', a, b, True, None)
def variant_compare(self, pkgname, a, b):
"""Return less-than-0, 0, or greater than 0 if variant a of pkgname is
respecively less-than, equal-to, or greater-than variant b of pkgname.
One variant is less-than another if it is preferred over the other."""
respectively less-than, equal-to, or greater-than variant b of
pkgname. One variant is less-than another if it is preferred over
the other."""
return self._component_compare(pkgname, 'variant', a, b, False, None)
def architecture_compare(self, pkgname, a, b):
"""Return less-than-0, 0, or greater than 0 if architecture a of pkgname is
respecively less-than, equal-to, or greater-than architecture b of pkgname.
One architecture is less-than another if it is preferred over the other."""
return self._component_compare(pkgname, 'architecture', a, b, False, None)
"""Return less-than-0, 0, or greater than 0 if architecture a of pkgname
is respectively less-than, equal-to, or greater-than architecture b
of pkgname. One architecture is less-than another if it is preferred
over the other."""
return self._component_compare(pkgname, 'architecture', a, b,
False, None)
def compiler_compare(self, pkgname, a, b):
"""Return less-than-0, 0, or greater than 0 if compiler a of pkgname is
respecively less-than, equal-to, or greater-than compiler b of pkgname.
One compiler is less-than another if it is preferred over the other."""
respecively less-than, equal-to, or greater-than compiler b of
pkgname. One compiler is less-than another if it is preferred over
the other."""
return self._spec_compare(pkgname, 'compiler', a, b, False, None)

22
lib/spack/spack/test/__init__.py
View File

@@ -32,17 +32,17 @@
from spack.test.tally_plugin import Tally
"""Names of tests to be included in Spack's test suite"""
test_names = ['architecture', 'versions', 'url_parse', 'url_substitution',
'packages', 'stage',
'spec_syntax', 'spec_semantics', 'spec_dag', 'concretize',
'multimethod', 'install', 'package_sanity', 'config',
'directory_layout', 'pattern', 'python_version', 'git_fetch',
'svn_fetch', 'hg_fetch', 'mirror', 'modules', 'url_extrapolate',
'cc', 'link_tree', 'spec_yaml', 'optional_deps',
'make_executable', 'configure_guess', 'lock', 'database',
'namespace_trie', 'yaml', 'sbang', 'environment', 'cmd.find',
'cmd.uninstall', 'cmd.test_install',
'cmd.test_compiler_cmd', 'cmd.module']
test_names = [
'architecture', 'versions', 'url_parse', 'url_substitution', 'packages',
'stage', 'spec_syntax', 'spec_semantics', 'spec_dag', 'concretize',
'multimethod', 'install', 'package_sanity', 'config', 'directory_layout',
'pattern', 'python_version', 'git_fetch', 'svn_fetch', 'hg_fetch',
'mirror', 'modules', 'url_extrapolate', 'cc', 'link_tree', 'spec_yaml',
'optional_deps', 'make_executable', 'build_system_guess', 'lock',
'database', 'namespace_trie', 'yaml', 'sbang', 'environment', 'cmd.find',
'cmd.uninstall', 'cmd.test_install', 'cmd.test_compiler_cmd',
'cmd.module'
]
def list_tests():

26
lib/spack/spack/test/configure_guess.py → lib/spack/spack/test/build_system_guess.py
View File

@@ -28,14 +28,14 @@
import unittest
from llnl.util.filesystem import *
from spack.cmd.create import ConfigureGuesser
from spack.cmd.create import BuildSystemGuesser
from spack.stage import Stage
from spack.test.mock_packages_test import *
from spack.util.executable import which
class InstallTest(unittest.TestCase):
"""Tests the configure guesser in spack create"""
"""Tests the build system guesser in spack create"""
def setUp(self):
self.tar = which('tar')
@@ -44,12 +44,10 @@ def setUp(self):
os.chdir(self.tmpdir)
self.stage = None
def tearDown(self):
shutil.rmtree(self.tmpdir, ignore_errors=True)
os.chdir(self.orig_dir)
def check_archive(self, filename, system):
mkdirp('archive')
touch(join_path('archive', filename))
@@ -60,24 +58,24 @@ def check_archive(self, filename, system):
with Stage(url) as stage:
stage.fetch()
guesser = ConfigureGuesser()
guesser(stage)
guesser = BuildSystemGuesser()
guesser(stage, url)
self.assertEqual(system, guesser.build_system)
def test_python(self):
self.check_archive('setup.py', 'python')
def test_autotools(self):
self.check_archive('configure', 'autotools')
def test_cmake(self):
self.check_archive('CMakeLists.txt', 'cmake')
def test_scons(self):
self.check_archive('SConstruct', 'scons')
def test_python(self):
self.check_archive('setup.py', 'python')
def test_R(self):
self.check_archive('NAMESPACE', 'R')
def test_unknown(self):
self.check_archive('foobar', 'unknown')

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

@@ -27,7 +27,6 @@
import StringIO
import spack.modules
import unittest
from spack.test.mock_packages_test import MockPackagesTest
FILE_REGISTRY = collections.defaultdict(StringIO.StringIO)
@@ -266,7 +265,7 @@ def test_alter_environment(self):
def test_blacklist(self):
spack.modules.CONFIGURATION = configuration_blacklist
spec = spack.spec.Spec('mpileaks')
spec = spack.spec.Spec('mpileaks ^zmpi')
content = self.get_modulefile_content(spec)
self.assertEqual(len([x for x in content if 'is-loaded' in x]), 1)
self.assertEqual(len([x for x in content if 'module load ' in x]), 1)

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

@@ -30,6 +30,7 @@ class Cmake(Package):
homepage = 'https://www.cmake.org'
url = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
version('3.6.0', 'aa40fbecf49d99c083415c2411d12db9')
version('3.5.2', '701386a1b5ec95f8d1075ecf96383e02')
version('3.5.1', 'ca051f4a66375c89d1a524e726da0296')
version('3.5.0', '33c5d09d4c33d4ffcc63578a6ba8777e')

25
var/spack/repos/builtin/packages/jasper/fix_alpha_channel_assert_fail.patch Normal file
View File

@@ -0,0 +1,25 @@
diff --git a/src/libjasper/jpc/jpc_dec.c b/src/libjasper/jpc/jpc_dec.c
index fa72a0e..1f4845f 100644
--- a/src/libjasper/jpc/jpc_dec.c
+++ b/src/libjasper/jpc/jpc_dec.c
@@ -1069,12 +1069,18 @@ static int jpc_dec_tiledecode(jpc_dec_t *dec, jpc_dec_tile_t *tile)
/* Apply an inverse intercomponent transform if necessary. */
switch (tile->cp->mctid) {
case JPC_MCT_RCT:
- assert(dec->numcomps == 3);
+ if (dec->numcomps != 3 && dec->numcomps != 4) {
+ jas_eprintf("bad number of components (%d)\n", dec->numcomps);
+ return -1;
+ }
jpc_irct(tile->tcomps[0].data, tile->tcomps[1].data,
tile->tcomps[2].data);
break;
case JPC_MCT_ICT:
- assert(dec->numcomps == 3);
+ if (dec->numcomps != 3 && dec->numcomps != 4) {
+ jas_eprintf("bad number of components (%d)\n", dec->numcomps);
+ return -1;
+ }
jpc_iict(tile->tcomps[0].data, tile->tcomps[1].data,
tile->tcomps[2].data);
break;

63
var/spack/repos/builtin/packages/jasper/package.py Normal file
View File

@@ -0,0 +1,63 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class Jasper(Package):
"""Library for manipulating JPEG-2000 images"""
homepage = "https://www.ece.uvic.ca/~frodo/jasper/"
url = "https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip"
version('1.900.1', 'a342b2b4495b3e1394e161eb5d85d754')
variant('shared', default=True,
description='Builds shared versions of the libraries')
variant('debug', default=False,
description='Builds debug versions of the libraries')
depends_on('libjpeg-turbo')
# Fixes a bug (still in upstream as of v.1.900.1) where an assertion fails
# when certain JPEG-2000 files with an alpha channel are processed
# see: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=469786
patch('fix_alpha_channel_assert_fail.patch')
def install(self, spec, prefix):
configure_options = [
'--prefix={0}'.format(prefix),
'--mandir={0}'.format(spec.prefix.man),
]
if '+shared' in spec:
configure_options.append('--enable-shared')
if '+debug' not in spec:
configure_options.append('--disable-debug')
configure(*configure_options)
make()
make('install')

38
var/spack/repos/builtin/packages/mkl/package.py
View File

@@ -9,7 +9,13 @@ class Mkl(IntelInstaller):
Note: You will have to add the download file to a
mirror so that Spack can find it. For instructions on how to set up a
mirror, see http://software.llnl.gov/spack/mirrors.html"""
mirror, see http://software.llnl.gov/spack/mirrors.html.
To set the threading layer at run time set MKL_THREADING_LAYER
variable to one of the following values: INTEL, SEQUENTIAL, PGI.
To set interface layer at run time, use set the MKL_INTERFACE_LAYER
variable to LP64 or ILP64.
"""
homepage = "https://software.intel.com/en-us/intel-mkl"
@@ -18,6 +24,11 @@ class Mkl(IntelInstaller):
version('11.3.3.210', 'f72546df27f5ebb0941b5d21fd804e34',
url="file://%s/l_mkl_11.3.3.210.tgz" % os.getcwd())
# virtual dependency
provides('blas')
provides('lapack')
# TODO: MKL also provides implementation of Scalapack.
def install(self, spec, prefix):
self.intel_prefix = os.path.join(prefix, "pkg")
@@ -26,3 +37,28 @@ def install(self, spec, prefix):
mkl_dir = os.path.join(self.intel_prefix, "mkl")
for f in os.listdir(mkl_dir):
os.symlink(os.path.join(mkl_dir, f), os.path.join(self.prefix, f))
def setup_dependent_package(self, module, dspec):
# For now use Single Dynamic Library:
# To set the threading layer at run time, use the
# mkl_set_threading_layer function or set MKL_THREADING_LAYER
# variable to one of the following values: INTEL, SEQUENTIAL, PGI.
# To set interface layer at run time, use the mkl_set_interface_layer
# function or set the MKL_INTERFACE_LAYER variable to LP64 or ILP64.
# Otherwise one would need to specify several libraries
# (e.g. mkl_intel_lp64;mkl_sequential;mkl_core), which reflect
# different interface and threading layers.
name = 'libmkl_rt.%s' % dso_suffix
libdir = find_library_path(name, self.prefix.lib64, self.prefix.lib)
self.spec.blas_shared_lib = join_path(libdir, name)
self.spec.lapack_shared_lib = self.spec.blas_shared_lib
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
# set up MKLROOT for everyone using MKL package
spack_env.set('MKLROOT', self.prefix)
def setup_environment(self, spack_env, env):
env.set('MKLROOT', self.prefix)

74
var/spack/repos/builtin/packages/mumps/package.py
View File

@@ -23,7 +23,10 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import os, sys, glob
import os
import sys
import glob
class Mumps(Package):
"""MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
@@ -44,13 +47,11 @@ class Mumps(Package):
variant('idx64', default=False, description='Use int64_t/integer*8 as default index type')
variant('shared', default=True, description='Build shared libraries')
depends_on('scotch + esmumps', when='~ptscotch+scotch')
depends_on('scotch + esmumps + mpi', when='+ptscotch')
depends_on('metis@5:', when='+metis')
depends_on('parmetis', when="+parmetis")
depends_on('blas')
depends_on('lapack')
depends_on('scalapack', when='+mpi')
depends_on('mpi', when='+mpi')
@@ -60,42 +61,52 @@ class Mumps(Package):
# end before install
# def patch(self):
def write_makefile_inc(self):
if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec:
raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi')
if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec: # NOQA: ignore=E501
raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') # NOQA: ignore=E501
makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib]
makefile_conf = ["LIBBLAS = %s" % to_link_flags(
self.spec['blas'].blas_shared_lib)
]
orderings = ['-Dpord']
if '+ptscotch' in self.spec or '+scotch' in self.spec:
join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '')
makefile_conf.extend(
["ISCOTCH = -I%s" % self.spec['scotch'].prefix.include,
"LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib,
join_lib,
join_lib.join(['esmumps', 'scotch', 'scotcherr']))])
makefile_conf.extend([
"ISCOTCH = -I%s" % self.spec['scotch'].prefix.include,
"LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib,
join_lib,
join_lib.join(['esmumps',
'scotch',
'scotcherr']))
])
orderings.append('-Dscotch')
if '+ptscotch' in self.spec:
orderings.append('-Dptscotch')
if '+parmetis' in self.spec and '+metis' in self.spec:
libname = 'parmetis' if '+parmetis' in self.spec else 'metis'
makefile_conf.extend(
["IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
"LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')])
makefile_conf.extend([
"IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
"LMETIS = -L%s -l%s -L%s -l%s" % (
self.spec['parmetis'].prefix.lib, 'parmetis',
self.spec['metis'].prefix.lib, 'metis')
])
orderings.append('-Dparmetis')
elif '+metis' in self.spec:
makefile_conf.extend(
["IMETIS = -I%s" % self.spec['metis'].prefix.include,
"LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')])
makefile_conf.extend([
"IMETIS = -I%s" % self.spec['metis'].prefix.include,
"LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')
])
orderings.append('-Dmetis')
makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
# when building shared libs need -fPIC, otherwise
# /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
# /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1'
# can not be used when making a shared object; recompile with -fPIC
fpic = '-fPIC' if '+shared' in self.spec else ''
# TODO: test this part, it needs a full blas, scalapack and
# partitionning environment with 64bit integers
@@ -104,7 +115,7 @@ def write_makefile_inc(self):
# the fortran compilation flags most probably are
# working only for intel and gnu compilers this is
# perhaps something the compiler should provide
['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),
['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), # NOQA: ignore=E501
'OPTL = %s -O ' % fpic,
'OPTC = %s -O -DINTSIZE64' % fpic])
else:
@@ -113,7 +124,6 @@ def write_makefile_inc(self):
'OPTL = %s -O ' % fpic,
'OPTC = %s -O ' % fpic])
if '+mpi' in self.spec:
makefile_conf.extend(
["CC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpicc'),
@@ -134,16 +144,17 @@ def write_makefile_inc(self):
if '+shared' in self.spec:
if sys.platform == 'darwin':
# Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew)
# Building dylibs with mpif90 causes segfaults on 10.8 and
# 10.10. Use gfortran. (Homebrew)
makefile_conf.extend([
'LIBEXT=.dylib',
'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib),
'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'], prefix.lib), # NOQA: ignore=E501
'RANLIB=echo'
])
else:
makefile_conf.extend([
'LIBEXT=.so',
'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,
'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib, # NOQA: ignore=E501
'RANLIB=echo'
])
else:
@@ -153,9 +164,8 @@ def write_makefile_inc(self):
'RANLIB = ranlib'
])
makefile_inc_template = join_path(os.path.dirname(self.module.__file__),
'Makefile.inc')
makefile_inc_template = join_path(
os.path.dirname(self.module.__file__), 'Makefile.inc')
with open(makefile_inc_template, "r") as fh:
makefile_conf.extend(fh.read().split('\n'))
@@ -164,8 +174,6 @@ def write_makefile_inc(self):
makefile_inc = '\n'.join(makefile_conf)
fh.write(makefile_inc)
def install(self, spec, prefix):
make_libs = []
@@ -189,15 +197,15 @@ def install(self, spec, prefix):
install_tree('lib', prefix.lib)
install_tree('include', prefix.include)
if '~mpi' in spec:
if '~mpi' in spec:
lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
install('libseq/libmpiseq%s' % lib_suffix, prefix.lib)
for f in glob.glob(join_path('libseq','*.h')):
for f in glob.glob(join_path('libseq', '*.h')):
install(f, prefix.include)
# FIXME: extend the tests to mpirun -np 2 (or alike) when build with MPI
# FIXME: use something like numdiff to compare blessed output with the current
# FIXME: extend the tests to mpirun -np 2 when build with MPI
# FIXME: use something like numdiff to compare output files
with working_dir('examples'):
if '+float' in spec:
os.system('./ssimpletest < input_simpletest_real')

33
var/spack/repos/builtin/packages/netlib-scalapack/package.py
View File

@@ -25,8 +25,10 @@
from spack import *
import sys
class NetlibScalapack(Package):
"""ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines"""
"""ScaLAPACK is a library of high-performance linear algebra routines for
parallel distributed memory machines"""
homepage = "http://www.netlib.org/scalapack/"
url = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz"
@@ -48,10 +50,22 @@ class NetlibScalapack(Package):
def install(self, spec, prefix):
options = [
"-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else 'OFF'),
"-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else 'ON'),
"-DUSE_OPTIMIZED_LAPACK_BLAS:BOOL=ON", # forces scalapack to use find_package(LAPACK)
]
"-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else
'OFF'),
"-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else
'ON'),
# forces scalapack to use find_package(LAPACK):
"-DUSE_OPTIMIZED_LAPACK_BLAS:BOOL=ON",
]
# Make sure we use Spack's Lapack:
options.extend([
'-DLAPACK_FOUND=true',
'-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include,
'-DLAPACK_LIBRARIES=%s' % (
spec['lapack'].lapack_shared_lib if '+shared' in spec else
spec['lapack'].lapack_static_lib),
])
if '+fpic' in spec:
options.extend([
@@ -66,16 +80,15 @@ def install(self, spec, prefix):
make()
make("install")
# The shared libraries are not installed correctly on Darwin; correct this
# The shared libraries are not installed correctly on Darwin:
if (sys.platform == 'darwin') and ('+shared' in spec):
fix_darwin_install_name(prefix.lib)
def setup_dependent_package(self, module, dependent_spec):
spec = self.spec
lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
lib_suffix = dso_suffix if '+shared' in spec else 'a'
spec.fc_link = '-L%s -lscalapack' % spec.prefix.lib
spec.cc_link = spec.fc_link
spec.libraries = [join_path(spec.prefix.lib, 'libscalapack%s' % lib_suffix)]
spec.libraries = [join_path(spec.prefix.lib,
'libscalapack.%s' % lib_suffix)]

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

@@ -44,6 +44,7 @@ class PyNumpy(Package):
extends('python')
depends_on('py-nose', type='build')
depends_on('py-setuptools', type='build')
depends_on('blas', when='+blas')
depends_on('lapack', when='+lapack')