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Merge remote-tracking branch 'upstream/develop' into develop

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"Updating NERSC branch"
This commit is contained in:
Mario Melara 2016-06-18 00:52:06 -07:00
commit 8af1c5fc8f
22 changed files with 995 additions and 117 deletions
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2
.flake8
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@ -19,5 +19,5 @@
# - F999: name name be undefined or undefined from star imports. # - F999: name name be undefined or undefined from star imports.
# #
[flake8] [flake8]
ignore = E221,E241,E731,F403,F821,F999 ignore = E221,E241,E731,F403,F821,F999,F405
max-line-length = 79 max-line-length = 79

4
lib/spack/llnl/util/tty/__init__.py
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@ -64,12 +64,14 @@ def info(message, *args, **kwargs):
format = kwargs.get('format', '*b') format = kwargs.get('format', '*b')
stream = kwargs.get('stream', sys.stdout) stream = kwargs.get('stream', sys.stdout)
wrap = kwargs.get('wrap', False) wrap = kwargs.get('wrap', False)
break_long_words = kwargs.get('break_long_words', False)
cprint("@%s{==>} %s" % (format, cescape(str(message))), stream=stream) cprint("@%s{==>} %s" % (format, cescape(str(message))), stream=stream)
for arg in args: for arg in args:
if wrap: if wrap:
lines = textwrap.wrap( lines = textwrap.wrap(
str(arg), initial_indent=indent, subsequent_indent=indent) str(arg), initial_indent=indent, subsequent_indent=indent,
break_long_words=break_long_words)
for line in lines: for line in lines:
stream.write(line + '\n') stream.write(line + '\n')
else: else:

6
lib/spack/spack/database.py
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@ -311,7 +311,11 @@ def reindex(self, directory_layout):
for spec in directory_layout.all_specs(): for spec in directory_layout.all_specs():
# Create a spec for each known package and add it. # Create a spec for each known package and add it.
path = directory_layout.path_for_spec(spec) path = directory_layout.path_for_spec(spec)
self._add(spec, path, directory_layout) old_info = old_data.get(spec.dag_hash())
explicit = False
if old_info is not None:
explicit = old_info.explicit
self._add(spec, path, directory_layout, explicit=explicit)
self._check_ref_counts() self._check_ref_counts()

5
lib/spack/spack/hooks/licensing.py
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@ -26,7 +26,7 @@
import spack import spack
import llnl.util.tty as tty import llnl.util.tty as tty
from llnl.util.filesystem import join_path from llnl.util.filesystem import join_path, mkdirp
def pre_install(pkg): def pre_install(pkg):
@ -154,6 +154,9 @@ def symlink_license(pkg):
target = pkg.global_license_file target = pkg.global_license_file
for filename in pkg.license_files: for filename in pkg.license_files:
link_name = join_path(pkg.prefix, filename) link_name = join_path(pkg.prefix, filename)
license_dir = os.path.dirname(link_name)
if not os.path.exists(license_dir):
mkdirp(license_dir)
if os.path.exists(target): if os.path.exists(target):
os.symlink(target, link_name) os.symlink(target, link_name)
tty.msg("Added local symlink %s to global license file" % tty.msg("Added local symlink %s to global license file" %

14
lib/spack/spack/package.py
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@ -397,14 +397,20 @@ def __init__(self, spec):
if self.is_extension: if self.is_extension:
spack.repo.get(self.extendee_spec)._check_extendable() spack.repo.get(self.extendee_spec)._check_extendable()
@property
def global_license_dir(self):
"""Returns the directory where global license files for all
packages are stored."""
spack_root = ancestor(__file__, 4)
return join_path(spack_root, 'etc', 'spack', 'licenses')
@property @property
def global_license_file(self): def global_license_file(self):
"""Returns the path where a global license file should be stored.""" """Returns the path where a global license file for this
particular package should be stored."""
if not self.license_files: if not self.license_files:
return return
spack_root = ancestor(__file__, 4) return join_path(self.global_license_dir, self.name,
global_license_dir = join_path(spack_root, 'etc', 'spack', 'licenses')
return join_path(global_license_dir, self.name,
os.path.basename(self.license_files[0])) os.path.basename(self.license_files[0]))
@property @property

50
var/spack/repos/builtin/packages/bertini/package.py Normal file
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@ -0,0 +1,50 @@
##############################################################################
# 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 Bertini(Package):
"""Bertini is a general-purpose solver, written in C, that was created
for research about polynomial continuation. It solves for the numerical
solution of systems of polynomial equations using homotopy continuation."""
homepage = "https://bertini.nd.edu/"
url = "https://bertini.nd.edu/BertiniSource_v1.5.tar.gz"
version('1.5', 'e3f6cc6e7f9a0cf1d73185e8671af707')
variant('mpi', default=True, description='Compile in parallel')
depends_on('flex')
depends_on('bison')
depends_on('gmp')
depends_on('mpfr')
depends_on('mpi', when='+mpi')
def install(self, spec, prefix):
configure('--prefix=%s' % prefix)
make()
make("install")

28
var/spack/repos/builtin/packages/daal/package.py Normal file
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@ -0,0 +1,28 @@
from spack import *
import os
from spack.pkg.builtin.intel import IntelInstaller
class Daal(IntelInstaller):
"""Intel Data Analytics Acceleration Library.
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"""
homepage = "https://software.intel.com/en-us/daal"
version('2016.2.181', 'aad2aa70e5599ebfe6f85b29d8719d46',
url="file://%s/l_daal_2016.2.181.tgz" % os.getcwd())
version('2016.3.210', 'ad747c0dd97dace4cad03cf2266cad28',
url="file://%s/l_daal_2016.3.210.tgz" % os.getcwd())
def install(self, spec, prefix):
self.intel_prefix = os.path.join(prefix, "pkg")
IntelInstaller.install(self, spec, prefix)
daal_dir = os.path.join(self.intel_prefix, "daal")
for f in os.listdir(daal_dir):
os.symlink(os.path.join(daal_dir, f), os.path.join(self.prefix, f))

24
var/spack/repos/builtin/packages/espresso/package.py
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@ -26,20 +26,28 @@
import os import os
class Espresso(Package): class Espresso(Package):
""" """
QE is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials QE is an integrated suite of Open-Source computer codes for
modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. electronic-structure calculations and materials modeling at
the nanoscale. It is based on density-functional theory, plane
waves, and pseudopotentials.
""" """
homepage = 'http://quantum-espresso.org' homepage = 'http://quantum-espresso.org'
url = 'http://www.qe-forge.org/gf/download/frsrelease/204/912/espresso-5.3.0.tar.gz' url = 'http://www.qe-forge.org/gf/download/frsrelease/204/912/espresso-5.3.0.tar.gz'
version(
'5.4.0',
'8bb78181b39bd084ae5cb7a512c1cfe7',
url='http://www.qe-forge.org/gf/download/frsrelease/211/968/espresso-5.4.0.tar.gz'
)
version('5.3.0', '6848fcfaeb118587d6be36bd10b7f2c3') version('5.3.0', '6848fcfaeb118587d6be36bd10b7f2c3')
variant('mpi', default=True, description='Build Quantum-ESPRESSO with mpi support') variant('mpi', default=True, description='Builds with mpi support')
variant('openmp', default=False, description='Enables openMP support') variant('openmp', default=False, description='Enables openMP support')
variant('scalapack', default=True, description='Enables scalapack support') variant('scalapack', default=True, description='Enables scalapack support')
variant('elpa', default=True, description='Use elpa as an eigenvalue solver') variant('elpa', default=True, description='Uses elpa as an eigenvalue solver')
depends_on('blas') depends_on('blas')
depends_on('lapack') depends_on('lapack')
@ -47,7 +55,12 @@ class Espresso(Package):
depends_on('mpi', when='+mpi') depends_on('mpi', when='+mpi')
depends_on('fftw~mpi', when='~mpi') depends_on('fftw~mpi', when='~mpi')
depends_on('fftw+mpi', when='+mpi') depends_on('fftw+mpi', when='+mpi')
depends_on('scalapack', when='+scalapack+mpi') # TODO : + mpi needed to avoid false dependencies installation # TODO : + mpi needed to avoid false dependencies installation
depends_on('scalapack', when='+scalapack+mpi')
# Spurious problems running in parallel the Makefile
# generated by qe configure
parallel = False
def check_variants(self, spec): def check_variants(self, spec):
error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active' error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active'
@ -93,4 +106,3 @@ def install(self, spec, prefix):
install(filename, prefix.bin) install(filename, prefix.bin)
else: else:
make('install') make('install')

119
var/spack/repos/builtin/packages/hpl/package.py Normal file
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@ -0,0 +1,119 @@
##############################################################################
# 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 *
import os
import platform
class Hpl(Package):
"""HPL is a software package that solves a (random) dense linear system
in double precision (64 bits) arithmetic on distributed-memory computers.
It can thus be regarded as a portable as well as freely available
implementation of the High Performance Computing Linpack Benchmark."""
homepage = "http://www.netlib.org/benchmark/hpl/"
url = "http://www.netlib.org/benchmark/hpl/hpl-2.2.tar.gz"
version('2.2', '0eb19e787c3dc8f4058db22c9e0c5320')
variant('openmp', default=False, description='Enable OpenMP support')
depends_on('mpi@1.1:')
depends_on('blas')
parallel = False
def configure(self, spec, arch):
# List of configuration options
# Order is important
config = []
# OpenMP support
if '+openmp' in spec:
config.append(
'OMP_DEFS = {0}'.format(self.compiler.openmp_flag)
)
config.extend([
# Shell
'SHELL = /bin/sh',
'CD = cd',
'CP = cp',
'LN_S = ln -fs',
'MKDIR = mkdir -p',
'RM = /bin/rm -f',
'TOUCH = touch',
# Platform identifier
'ARCH = {0}'.format(arch),
# HPL Directory Structure / HPL library
'TOPdir = {0}'.format(os.getcwd()),
'INCdir = $(TOPdir)/include',
'BINdir = $(TOPdir)/bin/$(ARCH)',
'LIBdir = $(TOPdir)/lib/$(ARCH)',
'HPLlib = $(LIBdir)/libhpl.a',
# Message Passing library (MPI)
'MPinc = -I{0}'.format(spec['mpi'].prefix.include),
'MPlib = -L{0}'.format(spec['mpi'].prefix.lib),
# Linear Algebra library (BLAS or VSIPL)
'LAinc = {0}'.format(spec['blas'].prefix.include),
'LAlib = {0}'.format(spec['blas'].blas_shared_lib),
# F77 / C interface
'F2CDEFS = -DAdd_ -DF77_INTEGER=int -DStringSunStyle',
# HPL includes / libraries / specifics
'HPL_INCLUDES = -I$(INCdir) -I$(INCdir)/$(ARCH) ' +
'-I$(LAinc) -I$(MPinc)',
'HPL_LIBS = $(HPLlib) $(LAlib) $(MPlib)',
'HPL_OPTS = -DHPL_DETAILED_TIMING -DHPL_PROGRESS_REPORT',
'HPL_DEFS = $(F2CDEFS) $(HPL_OPTS) $(HPL_INCLUDES)',
# Compilers / linkers - Optimization flags
'CC = {0}'.format(spec['mpi'].mpicc),
'CCNOOPT = $(HPL_DEFS)',
'CCFLAGS = $(HPL_DEFS) -O3',
'LINKER = $(CC)',
'LINKFLAGS = $(CCFLAGS) $(OMP_DEFS)',
'ARCHIVER = ar',
'ARFLAGS = r',
'RANLIB = echo'
])
# Write configuration options to include file
with open('Make.{0}'.format(arch), 'w') as makefile:
for var in config:
makefile.write('{0}\n'.format(var))
def install(self, spec, prefix):
# Arch used for file naming purposes only
arch = '{0}-{1}'.format(platform.system(), platform.processor())
# Generate Makefile include
self.configure(spec, arch)
make('arch={0}'.format(arch))
# Manual installation
install_tree(join_path('bin', arch), prefix.bin)
install_tree(join_path('lib', arch), prefix.lib)
install_tree(join_path('include', arch), prefix.include)
install_tree('man', prefix.man)

144
var/spack/repos/builtin/packages/intel-parallel-studio/package.py Normal file
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@ -0,0 +1,144 @@
from spack import *
import os
import re
from spack.pkg.builtin.intel import IntelInstaller, filter_pick, \
get_all_components
class IntelParallelStudio(IntelInstaller):
"""Intel Parallel Studio.
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"""
homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe"
# TODO: can also try the online installer (will download files on demand)
version('composer.2016.2', '1133fb831312eb519f7da897fec223fa',
url="file://%s/parallel_studio_xe_2016_composer_edition_update2.tgz" # NOQA: ignore=E501
% os.getcwd())
version('professional.2016.2', '70be832f2d34c9bf596a5e99d5f2d832',
url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd()) # NOQA: ignore=E501
version('cluster.2016.2', '70be832f2d34c9bf596a5e99d5f2d832',
url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd()) # NOQA: ignore=E501
version('composer.2016.3', '3208eeabee951fc27579177b593cefe9',
url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz" # NOQA: ignore=E501
% os.getcwd())
version('professional.2016.3', 'eda19bb0d0d19709197ede58f13443f3',
url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd()) # NOQA: ignore=E501
version('cluster.2016.3', 'eda19bb0d0d19709197ede58f13443f3',
url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd()) # NOQA: ignore=E501
variant('rpath', default=True, description="Add rpath to .cfg files")
variant('newdtags', default=False,
description="Allow use of --enable-new-dtags in MPI wrappers")
variant('all', default=False,
description="Install all files with the requested edition")
variant('mpi', default=True,
description="Install the Intel MPI library and ITAC tool")
variant('mkl', default=True, description="Install the Intel MKL library")
variant('daal',
default=True, description="Install the Intel DAAL libraries")
variant('ipp', default=True, description="Install the Intel IPP libraries")
variant('tools', default=True, description="""Install the Intel Advisor,\
VTune Amplifier, and Inspector tools""")
provides('mpi', when='@cluster:+mpi')
provides('mkl', when='+mkl')
provides('daal', when='+daal')
provides('ipp', when='+ipp')
def install(self, spec, prefix):
base_components = "ALL" # when in doubt, install everything
mpi_components = ""
mkl_components = ""
daal_components = ""
ipp_components = ""
if spec.satisfies('+all'):
base_components = "ALL"
else:
all_components = get_all_components()
regex = '(comp|openmp|intel-tbb|icc|ifort|psxe|icsxe-pset)'
base_components = \
filter_pick(all_components, re.compile(regex).search)
regex = '(icsxe|imb|mpi|itac|intel-tc|clck)'
mpi_components = \
filter_pick(all_components, re.compile(regex).search)
mkl_components = \
filter_pick(all_components, re.compile('(mkl)').search)
daal_components = \
filter_pick(all_components, re.compile('(daal)').search)
ipp_components = \
filter_pick(all_components, re.compile('(ipp)').search)
regex = '(gdb|vtune|inspector|advisor)'
tool_components = \
filter_pick(all_components, re.compile(regex).search)
components = base_components
if not spec.satisfies('+all'):
if spec.satisfies('+mpi') and 'cluster' in str(spec.version):
components += mpi_components
if spec.satisfies('+mkl'):
components += mkl_components
if spec.satisfies('+daal'):
components += daal_components
if spec.satisfies('+ipp'):
components += ipp_components
if spec.satisfies('+tools') and (spec.satisfies('@cluster') or
spec.satisfies('@professional')):
components += tool_components
self.intel_components = ';'.join(components)
IntelInstaller.install(self, spec, prefix)
absbindir = os.path.dirname(os.path.realpath(os.path.join(
self.prefix.bin, "icc")))
abslibdir = os.path.dirname(os.path.realpath(os.path.join
(self.prefix.lib, "intel64", "libimf.a")))
os.symlink(self.global_license_file, os.path.join(absbindir,
"license.lic"))
if spec.satisfies('+tools') and (spec.satisfies('@cluster') or
spec.satisfies('@professional')):
os.mkdir(os.path.join(self.prefix, "inspector_xe/licenses"))
os.symlink(self.global_license_file, os.path.join(
self.prefix, "inspector_xe/licenses", "license.lic"))
os.mkdir(os.path.join(self.prefix, "advisor_xe/licenses"))
os.symlink(self.global_license_file, os.path.join(
self.prefix, "advisor_xe/licenses", "license.lic"))
os.mkdir(os.path.join(self.prefix, "vtune_amplifier_xe/licenses"))
os.symlink(self.global_license_file, os.path.join(
self.prefix, "vtune_amplifier_xe/licenses", "license.lic"))
if (spec.satisfies('+all') or spec.satisfies('+mpi')) and \
spec.satisfies('@cluster'):
os.symlink(self.global_license_file, os.path.join(
self.prefix, "itac_latest", "license.lic"))
if spec.satisfies('~newdtags'):
wrappers = ["mpif77", "mpif77", "mpif90", "mpif90",
"mpigcc", "mpigcc", "mpigxx", "mpigxx",
"mpiicc", "mpiicc", "mpiicpc", "mpiicpc",
"mpiifort", "mpiifort"]
wrapper_paths = []
for root, dirs, files in os.walk(spec.prefix):
for name in files:
if name in wrappers:
wrapper_paths.append(os.path.join(spec.prefix,
root, name))
for wrapper in wrapper_paths:
filter_file(r'-Xlinker --enable-new-dtags', r' ',
wrapper)
if spec.satisfies('+rpath'):
for compiler_command in ["icc", "icpc", "ifort"]:
cfgfilename = os.path.join(absbindir, "%s.cfg" %
compiler_command)
with open(cfgfilename, "w") as f:
f.write('-Xlinker -rpath -Xlinker %s\n' % abslibdir)
os.symlink(os.path.join(self.prefix.man, "common", "man1"),
os.path.join(self.prefix.man, "man1"))

125
var/spack/repos/builtin/packages/intel/package.py Normal file
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@ -0,0 +1,125 @@
from spack import *
import os
import re
def filter_pick(input_list, regex_filter):
"""Returns the items in input_list that are found in the regex_filter"""
return [l for l in input_list for m in (regex_filter(l),) if m]
def unfilter_pick(input_list, regex_filter):
"""Returns the items in input_list that are not found in the
regex_filter"""
return [l for l in input_list for m in (regex_filter(l),) if not m]
def get_all_components():
"""Returns a list of all the components associated with the downloaded
Intel package"""
all_components = []
with open("pset/mediaconfig.xml", "r") as f:
lines = f.readlines()
for line in lines:
if line.find('<Abbr>') != -1:
component = line[line.find('<Abbr>') + 6:line.find('</Abbr>')]
all_components.append(component)
return all_components
class IntelInstaller(Package):
"""Base package containing common methods for installing Intel software"""
homepage = "https://software.intel.com/en-us"
intel_components = "ALL"
license_required = True
license_comment = '#'
license_files = ['Licenses/license.lic']
license_vars = ['INTEL_LICENSE_FILE']
license_url = \
'https://software.intel.com/en-us/articles/intel-license-manager-faq'
@property
def global_license_file(self):
"""Returns the path where a global license file should be stored."""
if not self.license_files:
return
return join_path(self.global_license_dir, "intel",
os.path.basename(self.license_files[0]))
def install(self, spec, prefix):
# Remove the installation DB, otherwise it will try to install into
# location of other Intel builds
if os.path.exists(os.path.join(os.environ["HOME"], "intel",
"intel_sdp_products.db")):
os.remove(os.path.join(os.environ["HOME"], "intel",
"intel_sdp_products.db"))
if not hasattr(self, "intel_prefix"):
self.intel_prefix = self.prefix
silent_config_filename = 'silent.cfg'
with open(silent_config_filename, 'w') as f:
f.write("""
ACCEPT_EULA=accept
PSET_MODE=install
CONTINUE_WITH_INSTALLDIR_OVERWRITE=yes
PSET_INSTALL_DIR=%s
ACTIVATION_LICENSE_FILE=%s
ACTIVATION_TYPE=license_file
PHONEHOME_SEND_USAGE_DATA=no
CONTINUE_WITH_OPTIONAL_ERROR=yes
COMPONENTS=%s
""" % (self.intel_prefix, self.global_license_file, self.intel_components))
install_script = which("install.sh")
install_script('--silent', silent_config_filename)
class Intel(IntelInstaller):
"""Intel Compilers.
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"""
homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe"
# TODO: can also try the online installer (will download files on demand)
version('16.0.2', '1133fb831312eb519f7da897fec223fa',
url="file://%s/parallel_studio_xe_2016_composer_edition_update2.tgz" # NOQA: ignore=E501
% os.getcwd())
version('16.0.3', '3208eeabee951fc27579177b593cefe9',
url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz" # NOQA: ignore=E501
% os.getcwd())
variant('rpath', default=True, description="Add rpath to .cfg files")
def install(self, spec, prefix):
components = []
all_components = get_all_components()
regex = '(comp|openmp|intel-tbb|icc|ifort|psxe|icsxe-pset)'
components = filter_pick(all_components, re.compile(regex).search)
self.intel_components = ';'.join(components)
IntelInstaller.install(self, spec, prefix)
absbindir = os.path.split(os.path.realpath(os.path.join(
self.prefix.bin, "icc")))[0]
abslibdir = os.path.split(os.path.realpath(os.path.join(
self.prefix.lib, "intel64", "libimf.a")))[0]
# symlink or copy?
os.symlink(self.global_license_file, os.path.join(absbindir,
"license.lic"))
if spec.satisfies('+rpath'):
for compiler_command in ["icc", "icpc", "ifort"]:
cfgfilename = os.path.join(absbindir, "%s.cfg" %
compiler_command)
with open(cfgfilename, "w") as f:
f.write('-Xlinker -rpath -Xlinker %s\n' % abslibdir)
os.symlink(os.path.join(self.prefix.man, "common", "man1"),
os.path.join(self.prefix.man, "man1"))

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from spack import *
import os
from spack.pkg.builtin.intel import IntelInstaller
class Ipp(IntelInstaller):
"""Intel Integrated Performance Primitives.
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"""
homepage = "https://software.intel.com/en-us/intel-ipp"
version('9.0.3.210', '0e1520dd3de7f811a6ef6ebc7aa429a3',
url="file://%s/l_ipp_9.0.3.210.tgz" % os.getcwd())
def install(self, spec, prefix):
self.intel_prefix = os.path.join(prefix, "pkg")
IntelInstaller.install(self, spec, prefix)
ipp_dir = os.path.join(self.intel_prefix, "ipp")
for f in os.listdir(ipp_dir):
os.symlink(os.path.join(ipp_dir, f), os.path.join(self.prefix, f))

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from spack import *
import os
from spack.pkg.builtin.intel import IntelInstaller
class Mkl(IntelInstaller):
"""Intel Math Kernel Library.
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"""
homepage = "https://software.intel.com/en-us/intel-mkl"
version('11.3.2.181', '536dbd82896d6facc16de8f961d17d65',
url="file://%s/l_mkl_11.3.2.181.tgz" % os.getcwd())
version('11.3.3.210', 'f72546df27f5ebb0941b5d21fd804e34',
url="file://%s/l_mkl_11.3.3.210.tgz" % os.getcwd())
def install(self, spec, prefix):
self.intel_prefix = os.path.join(prefix, "pkg")
IntelInstaller.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))

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@ -24,29 +24,38 @@
############################################################################## ##############################################################################
from spack import * from spack import *
class PyAstropy(Package):
"""
The Astropy Project is a community effort to develop a single core
package for Astronomy in Python and foster interoperability between
Python astronomy packages.
"""
homepage = 'http://www.astropy.org/'
class PyAstropy(Package):
"""The Astropy Project is a community effort to develop a single core
package for Astronomy in Python and foster interoperability between
Python astronomy packages."""
homepage = 'http://www.astropy.org/'
url = 'https://pypi.python.org/packages/source/a/astropy/astropy-1.1.2.tar.gz'
version('1.1.2', 'cbe32023b5b1177d1e2498a0d00cda51')
version('1.1.post1', 'b52919f657a37d45cc45f5cb0f58c44d') version('1.1.post1', 'b52919f657a37d45cc45f5cb0f58c44d')
def url_for_version(self, version): # Required dependencies
return 'https://pypi.python.org/packages/source/a/astropy/astropy-{0}.tar.gz'.format(version)
extends('python') extends('python')
depends_on('py-numpy')
# Optional dependencies
depends_on('py-h5py')
depends_on('py-beautifulsoup4')
depends_on('py-pyyaml')
depends_on('py-scipy')
depends_on('libxml2')
depends_on('py-matplotlib')
depends_on('py-pytz')
depends_on('py-scikit-image')
depends_on('py-pandas')
# System dependencies
depends_on('cfitsio') depends_on('cfitsio')
depends_on('expat') depends_on('expat')
depends_on('py-h5py')
depends_on('py-numpy')
depends_on('py-scipy')
def install(self, spec, prefix): def install(self, spec, prefix):
python('setup.py', 'build', '--use-system-cfitsio', python('setup.py', 'build', '--use-system-cfitsio',
'--use-system-expat') '--use-system-expat')
python('setup.py', 'install', '--prefix=' + prefix) python('setup.py', 'install', '--prefix={0}'.format(prefix))

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##############################################################################
# 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 PyBeautifulsoup4(Package):
"""Beautiful Soup is a Python library for pulling data out of HTML and
XML files. It works with your favorite parser to provide idiomatic ways
of navigating, searching, and modifying the parse tree."""
homepage = "https://www.crummy.com/software/BeautifulSoup"
url = "https://pypi.python.org/packages/source/b/beautifulsoup4/beautifulsoup4-4.4.1.tar.gz"
version('4.4.1', '8fbd9a7cac0704645fa20d1419036815')
extends('python')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix={0}'.format(prefix))

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@ -0,0 +1,41 @@
##############################################################################
# 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 PyEmcee(Package):
"""emcee is an MIT licensed pure-Python implementation of Goodman & Weare's
Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler."""
homepage = "http://dan.iel.fm/emcee/current/"
url = "https://pypi.python.org/packages/source/e/emcee/emcee-2.1.0.tar.gz"
version('2.1.0', 'c6b6fad05c824d40671d4a4fc58dfff7')
extends('python')
depends_on('py-numpy')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix={0}'.format(prefix))

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@ -23,23 +23,42 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
############################################################################## ##############################################################################
from spack import * from spack import *
import re
class PyH5py(Package): class PyH5py(Package):
"""The h5py package provides both a high- and low-level interface to the HDF5 library from Python.""" """The h5py package provides both a high- and low-level interface to the
HDF5 library from Python."""
homepage = "https://pypi.python.org/pypi/h5py" homepage = "https://pypi.python.org/pypi/h5py"
url = "https://pypi.python.org/packages/source/h/h5py/h5py-2.4.0.tar.gz" url = "https://pypi.python.org/packages/source/h/h5py/h5py-2.4.0.tar.gz"
version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758') version('2.6.0', 'ec476211bd1de3f5ac150544189b0bf4')
version('2.5.0', '6e4301b5ad5da0d51b0a1e5ac19e3b74') version('2.5.0', '6e4301b5ad5da0d51b0a1e5ac19e3b74')
version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758')
extends('python', ignore=lambda f: re.match(r'bin/cy*', f)) variant('mpi', default=False, description='Build with MPI support')
depends_on('hdf5')
depends_on('py-numpy') extends('python')
depends_on('py-cython')
# Build dependencies
depends_on('py-cython@0.19:')
depends_on('pkg-config')
depends_on('hdf5@1.8.4:+mpi', when='+mpi')
depends_on('hdf5@1.8.4:~mpi', when='~mpi')
depends_on('mpi', when='+mpi')
# Build and runtime dependencies
depends_on('py-numpy@1.6.1:')
# Runtime dependencies
depends_on('py-six') depends_on('py-six')
depends_on('py-pkgconfig')
def install(self, spec, prefix): def install(self, spec, prefix):
python('setup.py', 'configure', '--hdf5=%s' % spec['hdf5'].prefix) python('setup.py', 'configure',
python('setup.py', 'install', '--prefix=%s' % prefix) '--hdf5={0}'.format(spec['hdf5'].prefix))
if '+mpi' in spec:
env['CC'] = spec['mpi'].mpicc
python('setup.py', 'configure', '--mpi')
python('setup.py', 'install', '--prefix={0}'.format(prefix))

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@ -0,0 +1,46 @@
##############################################################################
# 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 PyIminuit(Package):
"""Interactive IPython-Friendly Minimizer based on SEAL Minuit2."""
homepage = "https://pypi.python.org/pypi/iminuit"
url = "https://pypi.python.org/packages/source/i/iminuit/iminuit-1.2.tar.gz"
version('1.2', '4701ec472cae42015e26251703e6e984')
# Required dependencies
extends('python')
depends_on('py-setuptools')
# Optional dependencies
depends_on('py-numpy')
depends_on('py-matplotlib')
depends_on('py-cython')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix={0}'.format(prefix))

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@ -0,0 +1,44 @@
##############################################################################
# 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 PyNestle(Package):
"""Nested sampling algorithms for evaluating Bayesian evidence."""
homepage = "http://kbarbary.github.io/nestle/"
url = "https://pypi.python.org/packages/source/n/nestle/nestle-0.1.1.tar.gz"
version('0.1.1', '4875c0f9a0a8e263c1d7f5fa6ce604c5')
# Required dependencies
extends('python')
depends_on('py-numpy')
# Optional dependencies
depends_on('py-scipy')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix={0}'.format(prefix))

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@ -0,0 +1,51 @@
##############################################################################
# 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 PySncosmo(Package):
"""SNCosmo is a Python library for high-level supernova cosmology
analysis."""
homepage = "http://sncosmo.readthedocs.io/"
url = "https://pypi.python.org/packages/source/s/sncosmo/sncosmo-1.2.0.tar.gz"
version('1.2.0', '028e6d1dc84ab1c17d2f3b6378b2cb1e')
# Required dependencies
# py-sncosmo binaries are duplicates of those from py-astropy
extends('python', ignore=r'bin/.*')
depends_on('py-numpy')
depends_on('py-scipy')
depends_on('py-astropy')
# Recommended dependencies
depends_on('py-matplotlib')
depends_on('py-iminuit')
depends_on('py-emcee')
depends_on('py-nestle')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix={0}'.format(prefix))

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@ -0,0 +1,43 @@
##############################################################################
# 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 PyWcsaxes(Package):
"""WCSAxes is a framework for making plots of Astronomical data
in Matplotlib."""
homepage = "http://wcsaxes.readthedocs.io/en/latest/index.html"
url = "https://github.com/astrofrog/wcsaxes/archive/v0.8.tar.gz"
version('0.8', 'de1c60fdae4c330bf5ddb9f1ab5ab920')
extends('python', ignore=r'bin/pbr')
depends_on('py-numpy')
depends_on('py-matplotlib')
depends_on('py-astropy')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix={0}'.format(prefix))

191
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@ -22,9 +22,6 @@
# License along with this program; if not, write to the Free Software # License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
############################################################################## ##############################################################################
import functools
import glob
import inspect
import os import os
import re import re
from contextlib import closing from contextlib import closing
@ -37,11 +34,10 @@
class Python(Package): class Python(Package):
"""The Python programming language.""" """The Python programming language."""
homepage = "http://www.python.org" homepage = "http://www.python.org"
url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz" url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz"
extendable = True
version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe') version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe')
version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36') version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36')
version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True) version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True)
@ -49,6 +45,8 @@ class Python(Package):
version('2.7.9', '5eebcaa0030dc4061156d3429657fb83') version('2.7.9', '5eebcaa0030dc4061156d3429657fb83')
version('2.7.8', 'd4bca0159acb0b44a781292b5231936f') version('2.7.8', 'd4bca0159acb0b44a781292b5231936f')
extendable = True
depends_on("openssl") depends_on("openssl")
depends_on("bzip2") depends_on("bzip2")
depends_on("readline") depends_on("readline")
@ -64,39 +62,63 @@ def install(self, spec, prefix):
# Rest of install is pretty standard except setup.py needs to # Rest of install is pretty standard except setup.py needs to
# be able to read the CPPFLAGS and LDFLAGS as it scans for the # be able to read the CPPFLAGS and LDFLAGS as it scans for the
# library and headers to build # library and headers to build
configure_args= [ cppflags = ' -I'.join([
"--prefix=%s" % prefix, spec['openssl'].prefix.include, spec['bzip2'].prefix.include,
"--with-threads", spec['readline'].prefix.include, spec['ncurses'].prefix.include,
"--enable-shared", spec['sqlite'].prefix.include, spec['zlib'].prefix.include
"CPPFLAGS=-I%s/include -I%s/include -I%s/include -I%s/include -I%s/include -I%s/include" % ( ])
spec['openssl'].prefix, spec['bzip2'].prefix,
spec['readline'].prefix, spec['ncurses'].prefix, ldflags = ' -L'.join([
spec['sqlite'].prefix, spec['zlib'].prefix), spec['openssl'].prefix.lib, spec['bzip2'].prefix.lib,
"LDFLAGS=-L%s/lib -L%s/lib -L%s/lib -L%s/lib -L%s/lib -L%s/lib" % ( spec['readline'].prefix.lib, spec['ncurses'].prefix.lib,
spec['openssl'].prefix, spec['bzip2'].prefix, spec['sqlite'].prefix.lib, spec['zlib'].prefix.lib
spec['readline'].prefix, spec['ncurses'].prefix, ])
spec['sqlite'].prefix, spec['zlib'].prefix)
] config_args = [
"--prefix={0}".format(prefix),
"--with-threads",
"--enable-shared",
"CPPFLAGS=-I{0}".format(cppflags),
"LDFLAGS=-L{0}".format(ldflags)
]
if spec.satisfies('@3:'): if spec.satisfies('@3:'):
configure_args.append('--without-ensurepip') config_args.append('--without-ensurepip')
configure(*configure_args)
configure(*config_args)
make() make()
make("install") make("install")
# Modify compiler paths in configuration files. This is necessary for self.filter_compilers(spec, prefix)
# building site packages outside of spack
filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)',
(r'\4\5'),
join_path(prefix.lib, 'python%d.%d' % self.version[:2], '_sysconfigdata.py'))
python3_version = '' def filter_compilers(self, spec, prefix):
"""Run after install to tell the configuration files and Makefiles
to use the compilers that Spack built the package with.
If this isn't done, they'll have CC and CXX set to Spack's generic
cc and c++. We want them to be bound to whatever compiler
they were built with."""
kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
dirname = join_path(prefix.lib,
'python{0}'.format(self.version.up_to(2)))
config = 'config'
if spec.satisfies('@3:'): if spec.satisfies('@3:'):
python3_version = '-%d.%dm' % self.version[:2] config = 'config-{0}m'.format(self.version.up_to(2))
makefile_filepath = join_path(prefix.lib, 'python%d.%d' % self.version[:2], 'config%s' % python3_version, 'Makefile')
filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)',
(r'\4\5'),
makefile_filepath)
files = [
'_sysconfigdata.py',
join_path(config, 'Makefile')
]
for filename in files:
filter_file(env['CC'], self.compiler.cc,
join_path(dirname, filename), **kwargs)
filter_file(env['CXX'], self.compiler.cxx,
join_path(dirname, filename), **kwargs)
# ======================================================================== # ========================================================================
# Set up environment to make install easy for python extensions. # Set up environment to make install easy for python extensions.
@ -104,57 +126,59 @@ def install(self, spec, prefix):
@property @property
def python_lib_dir(self): def python_lib_dir(self):
return os.path.join('lib', 'python%d.%d' % self.version[:2]) return join_path('lib', 'python{0}'.format(self.version.up_to(2)))
@property @property
def python_include_dir(self): def python_include_dir(self):
return os.path.join('include', 'python%d.%d' % self.version[:2]) return join_path('include', 'python{0}'.format(self.version.up_to(2)))
@property @property
def site_packages_dir(self): def site_packages_dir(self):
return os.path.join(self.python_lib_dir, 'site-packages') return join_path(self.python_lib_dir, 'site-packages')
def setup_dependent_environment(self, spack_env, run_env, extension_spec): def setup_dependent_environment(self, spack_env, run_env, extension_spec):
# TODO: do this only for actual extensions. """Set PYTHONPATH to include site-packages dir for the
extension and any other python extensions it depends on."""
# Set PYTHONPATH to include site-packages dir for the
# extension and any other python extensions it depends on.
python_paths = [] python_paths = []
for d in extension_spec.traverse(): for d in extension_spec.traverse():
if d.package.extends(self.spec): if d.package.extends(self.spec):
python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) python_paths.append(join_path(d.prefix,
self.site_packages_dir))
pythonpath = ':'.join(python_paths) pythonpath = ':'.join(python_paths)
spack_env.set('PYTHONPATH', pythonpath) spack_env.set('PYTHONPATH', pythonpath)
# For run time environment set only the path for extension_spec and prepend it to PYTHONPATH # For run time environment set only the path for
# extension_spec and prepend it to PYTHONPATH
if extension_spec.package.extends(self.spec): if extension_spec.package.extends(self.spec):
run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir)) run_env.prepend_path('PYTHONPATH', join_path(
extension_spec.prefix, self.site_packages_dir))
def setup_dependent_package(self, module, ext_spec): def setup_dependent_package(self, module, ext_spec):
""" """Called before python modules' install() methods.
Called before python modules' install() methods.
In most cases, extensions will only need to have one line:: In most cases, extensions will only need to have one line::
python('setup.py', 'install', '--prefix=%s' % prefix) python('setup.py', 'install', '--prefix={0}'.format(prefix))"""
"""
# Python extension builds can have a global python executable function # Python extension builds can have a global python executable function
if self.version >= Version("3.0.0") and self.version < Version("4.0.0"): if Version("3.0.0") <= self.version < Version("4.0.0"):
module.python = Executable(join_path(self.spec.prefix.bin, 'python3')) module.python = Executable(join_path(self.spec.prefix.bin,
'python3'))
else: else:
module.python = Executable(join_path(self.spec.prefix.bin, 'python')) module.python = Executable(join_path(self.spec.prefix.bin,
'python'))
# Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs. # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs.
module.python_lib_dir = os.path.join(ext_spec.prefix, self.python_lib_dir) module.python_lib_dir = join_path(ext_spec.prefix,
module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir) self.python_lib_dir)
module.site_packages_dir = os.path.join(ext_spec.prefix, self.site_packages_dir) module.python_include_dir = join_path(ext_spec.prefix,
self.python_include_dir)
module.site_packages_dir = join_path(ext_spec.prefix,
self.site_packages_dir)
# Make the site packages directory for extensions, if it does not exist already. # Make the site packages directory for extensions
if ext_spec.package.is_extension: if ext_spec.package.is_extension:
mkdirp(module.site_packages_dir) mkdirp(module.site_packages_dir)
@ -167,25 +191,28 @@ def python_ignore(self, ext_pkg, args):
ignore_arg = args.get('ignore', lambda f: False) ignore_arg = args.get('ignore', lambda f: False)
# Always ignore easy-install.pth, as it needs to be merged. # Always ignore easy-install.pth, as it needs to be merged.
patterns = [r'easy-install\.pth$'] patterns = [r'site-packages/easy-install\.pth$']
# Ignore pieces of setuptools installed by other packages. # Ignore pieces of setuptools installed by other packages.
# Must include directory name or it will remove all site*.py files.
if ext_pkg.name != 'py-setuptools': if ext_pkg.name != 'py-setuptools':
patterns.append(r'/site[^/]*\.pyc?$') patterns.extend([
patterns.append(r'setuptools\.pth') r'bin/easy_install[^/]*$',
patterns.append(r'bin/easy_install[^/]*$') r'site-packages/setuptools[^/]*\.egg$',
patterns.append(r'setuptools.*egg$') r'site-packages/setuptools\.pth$',
r'site-packages/site[^/]*\.pyc?$',
r'site-packages/__pycache__/site[^/]*\.pyc?$'
])
if ext_pkg.name != 'py-numpy': if ext_pkg.name != 'py-numpy':
patterns.append(r'bin/f2py$') patterns.append(r'bin/f2py$')
return match_predicate(ignore_arg, patterns) return match_predicate(ignore_arg, patterns)
def write_easy_install_pth(self, exts): def write_easy_install_pth(self, exts):
paths = [] paths = []
for ext in sorted(exts.values()): for ext in sorted(exts.values()):
ext_site_packages = os.path.join(ext.prefix, self.site_packages_dir) ext_site_packages = join_path(ext.prefix, self.site_packages_dir)
easy_pth = "%s/easy-install.pth" % ext_site_packages easy_pth = join_path(ext_site_packages, "easy-install.pth")
if not os.path.isfile(easy_pth): if not os.path.isfile(easy_pth):
continue continue
@ -195,15 +222,18 @@ def write_easy_install_pth(self, exts):
line = line.rstrip() line = line.rstrip()
# Skip lines matching these criteria # Skip lines matching these criteria
if not line: continue if not line:
if re.search(r'^(import|#)', line): continue continue
if (ext.name != 'py-setuptools' and if re.search(r'^(import|#)', line):
re.search(r'setuptools.*egg$', line)): continue continue
if ((ext.name != 'py-setuptools' and
re.search(r'setuptools.*egg$', line))):
continue
paths.append(line) paths.append(line)
site_packages = os.path.join(self.prefix, self.site_packages_dir) site_packages = join_path(self.prefix, self.site_packages_dir)
main_pth = "%s/easy-install.pth" % site_packages main_pth = join_path(site_packages, "easy-install.pth")
if not paths: if not paths:
if os.path.isfile(main_pth): if os.path.isfile(main_pth):
@ -211,15 +241,22 @@ def write_easy_install_pth(self, exts):
else: else:
with closing(open(main_pth, 'w')) as f: with closing(open(main_pth, 'w')) as f:
f.write("import sys; sys.__plen = len(sys.path)\n") f.write("""
import sys
sys.__plen = len(sys.path)
""")
for path in paths: for path in paths:
f.write("%s\n" % path) f.write("{0}\n".format(path))
f.write("import sys; new=sys.path[sys.__plen:]; del sys.path[sys.__plen:]; " f.write("""
"p=getattr(sys,'__egginsert',0); sys.path[p:p]=new; sys.__egginsert = p+len(new)\n") new = sys.path[sys.__plen:]
del sys.path[sys.__plen:]
p = getattr(sys, '__egginsert', 0)
sys.path[p:p] = new
sys.__egginsert = p + len(new)
""")
def activate(self, ext_pkg, **args): def activate(self, ext_pkg, **args):
ignore=self.python_ignore(ext_pkg, args) ignore = self.python_ignore(ext_pkg, args)
args.update(ignore=ignore) args.update(ignore=ignore)
super(Python, self).activate(ext_pkg, **args) super(Python, self).activate(ext_pkg, **args)
@ -228,12 +265,12 @@ def activate(self, ext_pkg, **args):
exts[ext_pkg.name] = ext_pkg.spec exts[ext_pkg.name] = ext_pkg.spec
self.write_easy_install_pth(exts) self.write_easy_install_pth(exts)
def deactivate(self, ext_pkg, **args): def deactivate(self, ext_pkg, **args):
args.update(ignore=self.python_ignore(ext_pkg, args)) args.update(ignore=self.python_ignore(ext_pkg, args))
super(Python, self).deactivate(ext_pkg, **args) super(Python, self).deactivate(ext_pkg, **args)
exts = spack.install_layout.extension_map(self.spec) exts = spack.install_layout.extension_map(self.spec)
if ext_pkg.name in exts: # Make deactivate idempotent. # Make deactivate idempotent
if ext_pkg.name in exts:
del exts[ext_pkg.name] del exts[ext_pkg.name]
self.write_easy_install_pth(exts) self.write_easy_install_pth(exts)