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

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This commit is contained in:
Kelly (KT) Thompson 2016-03-28 19:56:07 -06:00
commit 197f07306b
52 changed files with 1022 additions and 281 deletions
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8
etc/spack/modules.yaml Normal file
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@ -0,0 +1,8 @@
# -------------------------------------------------------------------------
# This is the default spack module files generation configuration.
#
# Changes to this file will affect all users of this spack install,
# although users can override these settings in their ~/.spack/modules.yaml.
# -------------------------------------------------------------------------
modules:
enable: ['tcl', 'dotkit']

30
lib/spack/llnl/util/filesystem.py
View file

@ -27,9 +27,10 @@
'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file',
'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
'set_executable', 'copy_mode', 'unset_executable_mode',
'remove_dead_links', 'remove_linked_tree']
'remove_dead_links', 'remove_linked_tree', 'fix_darwin_install_name']
import os
import glob
import sys
import re
import shutil
@ -38,6 +39,7 @@
import getpass
from contextlib import contextmanager, closing
from tempfile import NamedTemporaryFile
import subprocess
import llnl.util.tty as tty
from spack.util.compression import ALLOWED_ARCHIVE_TYPES
@ -392,3 +394,29 @@ def remove_linked_tree(path):
os.unlink(path)
else:
shutil.rmtree(path, True)
def fix_darwin_install_name(path):
"""
Fix install name of dynamic libraries on Darwin to have full path.
There are two parts of this task:
(i) use install_name('-id',...) to change install name of a single lib;
(ii) use install_name('-change',...) to change the cross linking between libs.
The function assumes that all libraries are in one folder and currently won't
follow subfolders.
Args:
path: directory in which .dylib files are alocated
"""
libs = glob.glob(join_path(path,"*.dylib"))
for lib in libs:
# fix install name first:
subprocess.Popen(["install_name_tool", "-id",lib,lib], stdout=subprocess.PIPE).communicate()[0]
long_deps = subprocess.Popen(["otool", "-L",lib], stdout=subprocess.PIPE).communicate()[0].split('\n')
deps = [dep.partition(' ')[0][1::] for dep in long_deps[2:-1]]
# fix all dependencies:
for dep in deps:
for loc in libs:
if dep == os.path.basename(loc):
subprocess.Popen(["install_name_tool", "-change",dep,loc,lib], stdout=subprocess.PIPE).communicate()[0]
break

6
lib/spack/llnl/util/lang.py
View file

@ -117,7 +117,8 @@ def caller_locals():
scope. Yes, this is some black magic, and yes it's useful
for implementing things like depends_on and provides.
"""
stack = inspect.stack()
# Passing zero here skips line context for speed.
stack = inspect.stack(0)
try:
return stack[2][0].f_locals
finally:
@ -128,7 +129,8 @@ def get_calling_module_name():
"""Make sure that the caller is a class definition, and return the
enclosing module's name.
"""
stack = inspect.stack()
# Passing zero here skips line context for speed.
stack = inspect.stack(0)
try:
# Make sure locals contain __module__
caller_locals = stack[2][0].f_locals

54
lib/spack/spack/build_environment.py
View file

@ -225,7 +225,7 @@ def set_module_variables_for_package(pkg, module):
m.spack_cc = join_path(link_dir, pkg.compiler.link_paths['cc'])
m.spack_cxx = join_path(link_dir, pkg.compiler.link_paths['cxx'])
m.spack_f77 = join_path(link_dir, pkg.compiler.link_paths['f77'])
m.spack_f90 = join_path(link_dir, pkg.compiler.link_paths['fc'])
m.spack_fc = join_path(link_dir, pkg.compiler.link_paths['fc'])
# Emulate some shell commands for convenience
m.pwd = os.getcwd
@ -270,32 +270,56 @@ def parent_class_modules(cls):
return result
def setup_package(pkg):
"""Execute all environment setup routines."""
spack_env = EnvironmentModifications()
run_env = EnvironmentModifications()
set_compiler_environment_variables(pkg, spack_env)
set_build_environment_variables(pkg, spack_env)
def setup_module_variables_for_dag(pkg):
"""Set module-scope variables for all packages in the DAG."""
for spec in pkg.spec.traverse(order='post'):
# If a user makes their own package repo, e.g.
# spack.repos.mystuff.libelf.Libelf, and they inherit from
# an existing class like spack.repos.original.libelf.Libelf,
# then set the module variables for both classes so the
# parent class can still use them if it gets called.
modules = parent_class_modules(pkg.__class__)
spkg = spec.package
modules = parent_class_modules(spkg.__class__)
for mod in modules:
set_module_variables_for_package(pkg, mod)
set_module_variables_for_package(spkg, mod)
set_module_variables_for_package(spkg, spkg.module)
def setup_package(pkg):
"""Execute all environment setup routines."""
spack_env = EnvironmentModifications()
run_env = EnvironmentModifications()
# Before proceeding, ensure that specs and packages are consistent
#
# This is a confusing behavior due to how packages are
# constructed. `setup_dependent_package` may set attributes on
# specs in the DAG for use by other packages' install
# method. However, spec.package will look up a package via
# spack.repo, which defensively copies specs into packages. This
# code ensures that all packages in the DAG have pieces of the
# same spec object at build time.
#
# This is safe for the build process, b/c the build process is a
# throwaway environment, but it is kind of dirty.
#
# TODO: Think about how to avoid this fix and do something cleaner.
for s in pkg.spec.traverse(): s.package.spec = s
set_compiler_environment_variables(pkg, spack_env)
set_build_environment_variables(pkg, spack_env)
setup_module_variables_for_dag(pkg)
# Allow dependencies to modify the module
for dependency_spec in pkg.spec.traverse(root=False):
spec = pkg.spec
for dependency_spec in spec.traverse(root=False):
dpkg = dependency_spec.package
dpkg.setup_dependent_python_module(pkg.module, pkg.spec)
dpkg.setup_dependent_package(pkg.module, spec)
# Allow dependencies to set up environment as well
for dependency_spec in pkg.spec.traverse(root=False):
for dependency_spec in spec.traverse(root=False):
dpkg = dependency_spec.package
dpkg.setup_dependent_environment(spack_env, run_env, pkg.spec)
dpkg.setup_dependent_environment(spack_env, run_env, spec)
# Allow the package to apply some settings.
pkg.setup_environment(spack_env, run_env)

4
lib/spack/spack/concretize.py
View file

@ -159,6 +159,10 @@ def concretize_version(self, spec):
if any(v.satisfies(sv) for sv in spec.versions)],
cmp=cmp_versions)
def prefer_key(v):
return pkg.versions.get(Version(v)).get('preferred', False)
valid_versions.sort(key=prefer_key, reverse=True)
if valid_versions:
spec.versions = ver([valid_versions[0]])
else:

28
lib/spack/spack/config.py
View file

@ -237,7 +237,29 @@
'type' : 'object',
'default' : {},
}
},},},},},}
},},},},},},
'modules': {
'$schema': 'http://json-schema.org/schema#',
'title': 'Spack module file configuration file schema',
'type': 'object',
'additionalProperties': False,
'patternProperties': {
r'modules:?': {
'type': 'object',
'default': {},
'additionalProperties': False,
'properties': {
'enable': {
'type': 'array',
'default': [],
'items': {
'type': 'string'
}
}
}
},
},
},
}
"""OrderedDict of config scopes keyed by name.
@ -405,11 +427,11 @@ def _read_config_file(filename, schema):
validate_section(data, schema)
return data
except MarkedYAMLError, e:
except MarkedYAMLError as e:
raise ConfigFileError(
"Error parsing yaml%s: %s" % (str(e.context_mark), e.problem))
except IOError, e:
except IOError as e:
raise ConfigFileError(
"Error reading configuration file %s: %s" % (filename, str(e)))

19
lib/spack/spack/modules.py
View file

@ -48,6 +48,7 @@
import llnl.util.tty as tty
import spack
import spack.config
from llnl.util.filesystem import join_path, mkdirp
from spack.environment import *
@ -56,6 +57,8 @@
# Registry of all types of modules. Entries created by EnvModule's metaclass
module_types = {}
CONFIGURATION = spack.config.get_config('modules')
def print_help():
"""For use by commands to tell user how to activate shell support."""
@ -115,7 +118,7 @@ class EnvModule(object):
class __metaclass__(type):
def __init__(cls, name, bases, dict):
type.__init__(cls, name, bases, dict)
if cls.name != 'env_module':
if cls.name != 'env_module' and cls.name in CONFIGURATION['enable']:
module_types[cls.name] = cls
def __init__(self, spec=None):
@ -158,13 +161,13 @@ def write(self):
# Let the extendee modify their extensions before asking for
# package-specific modifications
for extendee in self.pkg.extendees:
extendee_spec = self.spec[extendee]
extendee_spec.package.modify_module(
self.pkg.module, extendee_spec, self.spec)
spack_env = EnvironmentModifications()
for item in self.pkg.extendees:
package = self.spec[item].package
package.setup_dependent_package(self.pkg.module, self.spec)
package.setup_dependent_environment(spack_env, env, self.spec)
# Package-specific environment modifications
spack_env = EnvironmentModifications()
self.spec.package.setup_environment(spack_env, env)
# TODO : implement site-specific modifications and filters
@ -275,6 +278,6 @@ def write_header(self, module_file):
# Long description
if self.long_description:
module_file.write('proc ModulesHelp { } {\n')
doc = re.sub(r'"', '\"', self.long_description)
module_file.write("puts stderr \"%s\"\n" % doc)
for line in textwrap.wrap(self.long_description, 72):
module_file.write("puts stderr \"%s\"\n" % line)
module_file.write('}\n\n')

2
lib/spack/spack/package.py
View file

@ -1075,7 +1075,7 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
self.setup_environment(spack_env, run_env)
def setup_dependent_python_module(self, module, dependent_spec):
def setup_dependent_package(self, module, dependent_spec):
"""Set up Python module-scope variables for dependent packages.
Called before the install() method of dependents.

9
lib/spack/spack/test/concretize.py
View file

@ -24,6 +24,7 @@
##############################################################################
import spack
from spack.spec import Spec, CompilerSpec
from spack.version import ver
from spack.concretize import find_spec
from spack.test.mock_packages_test import *
@ -77,6 +78,14 @@ def test_concretize_variant(self):
self.check_concretize('mpich')
def test_concretize_preferred_version(self):
spec = self.check_concretize('python')
self.assertEqual(spec.versions, ver('2.7.11'))
spec = self.check_concretize('python@3.5.1')
self.assertEqual(spec.versions, ver('3.5.1'))
def test_concretize_with_virtual(self):
self.check_concretize('mpileaks ^mpi')
self.check_concretize('mpileaks ^mpi@:1.1')

43
var/spack/repos/builtin.mock/packages/python/package.py Normal file
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@ -0,0 +1,43 @@
##############################################################################
# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Written 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 General Public License (as published by
# the Free Software Foundation) version 2.1 dated 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 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 Python(Package):
"""Dummy Python package to demonstrate preferred versions."""
homepage = "http://www.python.org"
url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz"
extendable = True
version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe')
version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36')
version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True)
version('2.7.10', 'd7547558fd673bd9d38e2108c6b42521')
version('2.7.9', '5eebcaa0030dc4061156d3429657fb83')
version('2.7.8', 'd4bca0159acb0b44a781292b5231936f')
def install(self, spec, prefix):
pass

9
var/spack/repos/builtin/packages/arpack-ng/package.py
View file

@ -35,6 +35,10 @@ class ArpackNg(Package):
variant('shared', default=True, description='Enables the build of shared libraries')
variant('mpi', default=False, description='Activates MPI support')
# The function pdlamch10 does not set the return variable. This is fixed upstream
# see https://github.com/opencollab/arpack-ng/issues/34
patch('pdlamch10.patch', when='@3.3:')
depends_on('blas')
depends_on('lapack')
depends_on('mpi', when='+mpi')
@ -46,7 +50,10 @@ def install(self, spec, prefix):
options = ['--prefix=%s' % prefix]
if '+mpi' in spec:
options.append('--enable-mpi')
options.extend([
'--enable-mpi',
'F77=mpif77' #FIXME: avoid hardcoding MPI wrapper names
])
if '~shared' in spec:
options.append('--enable-shared=no')

15
var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch Normal file
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@ -0,0 +1,15 @@
diff --git a/PARPACK/SRC/MPI/pdlamch10.f b/PARPACK/SRC/MPI/pdlamch10.f
index 6571da9..2882c2e 100644
--- a/PARPACK/SRC/MPI/pdlamch10.f
+++ b/PARPACK/SRC/MPI/pdlamch10.f
@@ -86,8 +86,8 @@
TEMP = TEMP1
END IF
*
- PDLAMCH = TEMP
+ PDLAMCH10 = TEMP
*
-* End of PDLAMCH
+* End of PDLAMCH10
*
END

62
var/spack/repos/builtin/packages/atlas/package.py
View file

@ -1,31 +1,36 @@
from spack import *
from spack.util.executable import Executable
import os
import os.path
class Atlas(Package):
"""
Automatically Tuned Linear Algebra Software, generic shared
ATLAS is an approach for the automatic generation and optimization of
numerical software. Currently ATLAS supplies optimized versions for the
complete set of linear algebra kernels known as the Basic Linear Algebra
Subroutines (BLAS), and a subset of the linear algebra routines in the
LAPACK library.
Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and
optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear
algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines
in the LAPACK library.
"""
homepage = "http://math-atlas.sourceforge.net/"
version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da',
url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True)
resource(name='lapack',
url='http://www.netlib.org/lapack/lapack-3.5.0.tgz',
md5='b1d3e3e425b2e44a06760ff173104bdf',
destination='spack-resource-lapack',
when='@3:')
version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825',
url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2/download')
version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da',
url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2')
# TODO: make this provide BLAS once it works better. Create a way
# TODO: to mark "beta" packages and require explicit invocation.
variant('shared', default=True, description='Builds shared library')
# provides('blas')
provides('blas')
provides('lapack')
parallel = False
def patch(self):
# Disable thraed check. LLNL's environment does not allow
# Disable thread check. LLNL's environment does not allow
# disabling of CPU throttling in a way that ATLAS actually
# understands.
filter_file(r'^\s+if \(thrchk\) exit\(1\);', 'if (0) exit(1);',
@ -33,26 +38,21 @@ def patch(self):
# TODO: investigate a better way to add the check back in
# TODO: using, say, MSRs. Or move this to a variant.
@when('@:3.10')
def install(self, spec, prefix):
with working_dir('ATLAS-Build', create=True):
options = []
if '+shared' in spec:
options.append('--shared')
# Lapack resource
lapack_stage = self.stage[1]
lapack_tarfile = os.path.basename(lapack_stage.fetcher.url)
lapack_tarfile_path = join_path(lapack_stage.path, lapack_tarfile)
options.append('--with-netlib-lapack-tarfile=%s' % lapack_tarfile_path)
with working_dir('spack-build', create=True):
configure = Executable('../configure')
configure('--prefix=%s' % prefix, '-C', 'ic', 'cc', '-C', 'if', 'f77', "--dylibs")
make()
make('check')
make('ptcheck')
make('time')
make("install")
def install(self, spec, prefix):
with working_dir('ATLAS-Build', create=True):
configure = Executable('../configure')
configure('--incdir=%s' % prefix.include,
'--libdir=%s' % prefix.lib,
'--cc=cc',
"--shared")
configure('--prefix=%s' % prefix, *options)
make()
make('check')
make('ptcheck')

4
var/spack/repos/builtin/packages/boost/package.py
View file

@ -1,5 +1,6 @@
from spack import *
import spack
import sys
class Boost(Package):
"""Boost provides free peer-reviewed portable C++ source
@ -208,3 +209,6 @@ def install(self, spec, prefix):
for threadingOpt in threadingOpts:
b2('install', 'threading=%s' % threadingOpt, *b2_options)
# The shared libraries are not installed correctly on Darwin; correct this
if (sys.platform == 'darwin') and ('+shared' in spec):
fix_darwin_install_name(prefix.lib)

3
var/spack/repos/builtin/packages/cmake/package.py
View file

@ -38,10 +38,12 @@ class Cmake(Package):
version('2.8.10.2', '097278785da7182ec0aea8769d06860c')
variant('ncurses', default=True, description='Enables the build of the ncurses gui')
variant('openssl', default=True, description="Enables CMake's OpenSSL features")
variant('qt', default=False, description='Enables the build of cmake-gui')
variant('doc', default=False, description='Enables the generation of html and man page documentation')
depends_on('ncurses', when='+ncurses')
depends_on('openssl', when='+openssl')
depends_on('qt', when='+qt')
depends_on('python@2.7.11:', when='+doc')
depends_on('py-sphinx', when='+doc')
@ -77,6 +79,7 @@ def install(self, spec, prefix):
options.append('--sphinx-html')
options.append('--sphinx-man')
if '+openssl' in spec:
options.append('--')
options.append('-DCMAKE_USE_OPENSSL=ON')

10
var/spack/repos/builtin/packages/cryptopp/package.py
View file

@ -8,8 +8,8 @@ class Cryptopp(Package):
public-key encryption (RSA, DSA), and a few obsolete/historical encryption
algorithms (MD5, Panama)."""
homepage = "http://www.cryptopp.com/"
url = "http://www.cryptopp.com/cryptopp563.zip"
homepage = "http://www.cryptopp.com"
base_url = "http://www.cryptopp.com"
version('5.6.3', '3c5b70e2ec98b7a24988734446242d07')
version('5.6.2', '7ed022585698df48e65ce9218f6c6a67')
@ -25,7 +25,5 @@ def install(self, spec, prefix):
install('libcryptopp.a', prefix.lib)
def url_for_version(self, version):
version_tuple = tuple(v for v in iter(version))
version_string = reduce(lambda vs, nv: vs + str(nv), version_tuple, "")
return "%scryptopp%s.zip" % (Cryptopp.homepage, version_string)
version_string = str(version).replace('.', '')
return '%s/cryptopp%s.zip' % (Cryptopp.base_url, version_string)

2
var/spack/repos/builtin/packages/eigen/package.py
View file

@ -48,7 +48,7 @@ class Eigen(Package):
depends_on('metis', when='+metis')
depends_on('scotch', when='+scotch')
depends_on('fftw', when='+fftw')
depends_on('SuiteSparse', when='+suitesparse')
depends_on('suite-sparse', when='+suitesparse')
depends_on('mpfr@2.3.0:') # Eigen 3.2.7 requires at least 2.3.0
depends_on('gmp')

4
var/spack/repos/builtin/packages/espresso/package.py
View file

@ -32,6 +32,10 @@ def check_variants(self, spec):
if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec):
raise RuntimeError(error.format(variant='elpa'))
def setup_environment(self, spack_env, run_env):
# Espresso copies every executable in prefix without creating sub-folders
run_env.prepend_path('PATH', self.prefix)
def install(self, spec, prefix):
self.check_variants(spec)

30
var/spack/repos/builtin/packages/gettext/package.py Normal file
View file

@ -0,0 +1,30 @@
from spack import *
class Gettext(Package):
"""GNU internationalization (i18n) and localization (l10n) library."""
homepage = "https://www.gnu.org/software/gettext/"
url = "http://ftpmirror.gnu.org/gettext/gettext-0.19.7.tar.xz"
version('0.19.7', 'f81e50556da41b44c1d59ac93474dca5')
def install(self, spec, prefix):
options = ['--disable-dependency-tracking',
'--disable-silent-rules',
'--disable-debug',
'--prefix=%s' % prefix,
'--with-included-gettext',
'--with-included-glib',
'--with-included-libcroco',
'--with-included-libunistring',
'--with-emacs',
'--with-lispdir=%s/emacs/site-lisp/gettext' % prefix.share,
'--disable-java',
'--disable-csharp',
'--without-git', # Don't use VCS systems to create these archives
'--without-cvs',
'--without-xz']
configure(*options)
make()
make("install")

10
var/spack/repos/builtin/packages/hypre/package.py
View file

@ -1,5 +1,5 @@
from spack import *
import os
import os, sys
class Hypre(Package):
"""Hypre is a library of high performance preconditioners that
@ -12,7 +12,10 @@ class Hypre(Package):
version('2.10.1', 'dc048c4cabb3cd549af72591474ad674')
version('2.10.0b', '768be38793a35bb5d055905b271f5b8e')
variant('shared', default=True, description="Build shared library version (disables static library)")
# hypre does not know how to build shared libraries on Darwin
variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)")
# SuperluDist have conflicting headers with those in Hypre
variant('internal-superlu', default=True, description="Use internal Superlu routines")
depends_on("mpi")
depends_on("blas")
@ -37,6 +40,9 @@ def install(self, spec, prefix):
if '+shared' in self.spec:
configure_args.append("--enable-shared")
if '~internal-superlu' in self.spec:
configure_args.append("--without-superlu")
# Hypre's source is staged under ./src so we'll have to manually
# cd into it.
with working_dir("src"):

2
var/spack/repos/builtin/packages/libelf/package.py
View file

@ -38,8 +38,6 @@ class Libelf(Package):
provides('elf')
sanity_check_is_file = 'include/libelf.h'
def install(self, spec, prefix):
configure("--prefix=" + prefix,
"--enable-shared",

17
var/spack/repos/builtin/packages/llvm/package.py
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@ -52,7 +52,7 @@ class Llvm(Package):
depends_on('cmake @2.8.12.2:')
# Universal dependency
depends_on('python@2.7:')
depends_on('python@2.7:2.8') # Seems not to support python 3.X.Y
# lldb dependencies
depends_on('ncurses', when='+lldb')
@ -132,6 +132,21 @@ class Llvm(Package):
'llvm-libunwind' : 'http://llvm.org/svn/llvm-project/libunwind/trunk',
}
},
{
'version' : '3.8.0',
'md5':'07a7a74f3c6bd65de4702bf941b511a0',
'resources' : {
'compiler-rt' : 'd6fcbe14352ffb708e4d1ac2e48bb025',
'openmp' : '8fd7cc35d48051613cf1e750e9f22e40',
'polly' : '1b3b20f52d34a4024e21a4ea7112caa7',
'libcxx' : 'd6e0bdbbee39f7907ad74fd56d03b88a',
'libcxxabi' : 'bbe6b4d72c7c5978550d370af529bcf7',
'clang' : 'cc99e7019bb74e6459e80863606250c5',
'clang-tools-extra' : 'c2344f50e0eea0b402f0092a80ddc036',
'lldb' : 'a5da35ed9cc8c8817ee854e3dbfba00e',
'llvm-libunwind' : '162ade468607f153cca12be90b5194fa',
}
},
{
'version' : '3.7.1',
'md5':'bf8b3a2c79e61212c5409041dfdbd319',

22
var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch Normal file
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@ -0,0 +1,22 @@
# HG changeset patch
# User Sean Farley <sean@mcs.anl.gov>
# Date 1332269671 18000
# Tue Mar 20 13:54:31 2012 -0500
# Node ID b95c0c2e1d8bf8e3273f7d45e856f0c0127d998e
# Parent 88049269953c67c3fdcc4309bf901508a875f0dc
cmake: add gklib headers to install into include
diff -r 88049269953c -r b95c0c2e1d8b libmetis/CMakeLists.txt
Index: libmetis/CMakeLists.txt
===================================================================
--- a/libmetis/CMakeLists.txt Tue Mar 20 13:54:29 2012 -0500
+++ b/libmetis/CMakeLists.txt Tue Mar 20 13:54:31 2012 -0500
@@ -12,6 +12,8 @@ endif()
if(METIS_INSTALL)
install(TARGETS metis
LIBRARY DESTINATION lib
RUNTIME DESTINATION lib
ARCHIVE DESTINATION lib)
+ install(FILES gklib_defs.h DESTINATION include)
+ install(FILES gklib_rename.h DESTINATION include)
endif()

15
var/spack/repos/builtin/packages/metis/package.py
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@ -24,7 +24,7 @@
##############################################################################
from spack import *
import glob,sys
class Metis(Package):
"""
@ -49,6 +49,8 @@ class Metis(Package):
depends_on('gdb', when='+gdb')
patch('install_gklib_defs_rename.patch')
def install(self, spec, prefix):
options = []
@ -81,3 +83,14 @@ def install(self, spec, prefix):
cmake(source_directory, *options)
make()
make("install")
# install GKlib headers, which will be needed for ParMETIS
GKlib_dist = join_path(prefix.include,'GKlib')
mkdirp(GKlib_dist)
fs = glob.glob(join_path(source_directory,'GKlib',"*.h"))
for f in fs:
install(f, GKlib_dist)
# The shared library is not installed correctly on Darwin; correct this
if (sys.platform == 'darwin') and ('+shared' in spec):
fix_darwin_install_name(prefix.lib)

2
var/spack/repos/builtin/packages/mpich/package.py
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@ -54,7 +54,7 @@ def setup_dependent_environment(self, env, dependent_spec):
env.set('MPICH_F90', spack_f90)
env.set('MPICH_FC', spack_fc)
def setup_dependent_python_module(self, module, spec, dep_spec):
def setup_dependent_package(self, module, dep_spec):
"""For dependencies, make mpicc's use spack wrapper."""
# FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers?
module.mpicc = join_path(self.prefix.bin, 'mpicc')

19
var/spack/repos/builtin/packages/mumps/package.py
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@ -23,7 +23,7 @@ class Mumps(Package):
depends_on('scotch + esmumps', when='~ptscotch+scotch')
depends_on('scotch + esmumps + mpi', when='+ptscotch')
depends_on('metis', when='~parmetis+metis')
depends_on('metis', when='+metis')
depends_on('parmetis', when="+parmetis")
depends_on('blas')
depends_on('lapack')
@ -54,15 +54,19 @@ def write_makefile_inc(self):
if '+ptscotch' in self.spec:
orderings.append('-Dptscotch')
if '+parmetis' in self.spec or '+metis' in self.spec:
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[libname].prefix.include,
"LMETIS = -L%s -l%s" % (self.spec[libname].prefix.lib, libname)])
["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')])
orderings.append('-Dmetis')
if '+parmetis' in self.spec:
orderings.append('-Dparmetis')
makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
@ -131,7 +135,8 @@ def install(self, spec, prefix):
self.write_makefile_inc()
make(*make_libs)
# Build fails in parallel, at least on OS-X
make(*make_libs, parallel=False)
install_tree('lib', prefix.lib)
install_tree('include', prefix.include)

18
var/spack/repos/builtin/packages/muparser/package.py Normal file
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@ -0,0 +1,18 @@
from spack import *
class Muparser(Package):
"""C++ math expression parser library."""
homepage = "http://muparser.beltoforion.de/"
url = "https://github.com/beltoforion/muparser/archive/v2.2.5.tar.gz"
version('2.2.5', '02dae671aa5ad955fdcbcd3fee313fb7')
def install(self, spec, prefix):
options = ['--disable-debug',
'--disable-dependency-tracking',
'--prefix=%s' % prefix]
configure(*options)
make()
make("install")

15
var/spack/repos/builtin/packages/netcdf-cxx/package.py Normal file
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@ -0,0 +1,15 @@
from spack import *
class NetcdfCxx(Package):
"""C++ compatibility bindings for NetCDF"""
homepage = "http://www.unidata.ucar.edu/software/netcdf"
url = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx-4.2.tar.gz"
version('4.2', 'd32b20c00f144ae6565d9e98d9f6204c')
depends_on('netcdf')
def install(self, spec, prefix):
configure('--prefix=%s' % prefix)
make()
make("install")

7
var/spack/repos/builtin/packages/netcdf/package.py
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@ -43,6 +43,13 @@ def install(self, spec, prefix):
"--enable-dap"
]
# Make sure Netcdf links against Spack's curl
# Otherwise it may pick up system's curl, which could lead to link errors:
# /usr/lib/x86_64-linux-gnu/libcurl.so: undefined reference to `SSL_CTX_use_certificate_chain_file@OPENSSL_1.0.0'
LIBS.append("-lcurl")
CPPFLAGS.append("-I%s" % spec['curl'].prefix.include)
LDFLAGS.append ("-L%s" % spec['curl'].prefix.lib)
if '+mpi' in spec:
config_args.append('--enable-parallel4')

46
var/spack/repos/builtin/packages/netlib-blas/package.py
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@ -1,46 +0,0 @@
from spack import *
import os
class NetlibBlas(Package):
"""Netlib reference BLAS"""
homepage = "http://www.netlib.org/lapack/"
url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
variant('fpic', default=False, description="Build with -fpic compiler option")
# virtual dependency
provides('blas')
# Doesn't always build correctly in parallel
parallel = False
def patch(self):
os.symlink('make.inc.example', 'make.inc')
mf = FileFilter('make.inc')
mf.filter('^FORTRAN.*', 'FORTRAN = f90')
mf.filter('^LOADER.*', 'LOADER = f90')
mf.filter('^CC =.*', 'CC = cc')
if '+fpic' in self.spec:
mf.filter('^OPTS.*=.*', 'OPTS = -O2 -frecursive -fpic')
mf.filter('^CFLAGS =.*', 'CFLAGS = -O3 -fpic')
def install(self, spec, prefix):
make('blaslib')
# Tests that blas builds correctly
make('blas_testing')
# No install provided
mkdirp(prefix.lib)
install('librefblas.a', prefix.lib)
# Blas virtual package should provide blas.a and libblas.a
with working_dir(prefix.lib):
symlink('librefblas.a', 'blas.a')
symlink('librefblas.a', 'libblas.a')

59
var/spack/repos/builtin/packages/netlib-lapack/package.py
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@ -1,13 +1,12 @@
from spack import *
class NetlibLapack(Package):
"""
LAPACK version 3.X is a comprehensive FORTRAN library that does
linear algebra operations including matrix inversions, least
squared solutions to linear sets of equations, eigenvector
analysis, singular value decomposition, etc. It is a very
comprehensive and reputable package that has found extensive
use in the scientific community.
LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations including matrix
inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular value
decomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the
scientific community.
"""
homepage = "http://www.netlib.org/lapack/"
url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
@ -19,42 +18,34 @@ class NetlibLapack(Package):
version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70')
version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
variant('shared', default=False, description="Build shared library version")
variant('debug', default=False, description='Activates the Debug build type')
variant('shared', default=True, description="Build shared library version")
variant('external-blas', default=False, description='Build lapack with an external blas')
variant('lapacke', default=True, description='Activates the build of the LAPACKE C interface')
# virtual dependency
provides('blas', when='~external-blas')
provides('lapack')
# blas is a virtual dependency.
depends_on('blas')
depends_on('cmake')
# Doesn't always build correctly in parallel
parallel = False
@when('^netlib-blas')
def get_blas_libs(self):
blas = self.spec['netlib-blas']
return [join_path(blas.prefix.lib, 'blas.a')]
@when('^atlas')
def get_blas_libs(self):
blas = self.spec['atlas']
return [join_path(blas.prefix.lib, l)
for l in ('libf77blas.a', 'libatlas.a')]
depends_on('blas', when='+external-blas')
def install(self, spec, prefix):
blas_libs = ";".join(self.get_blas_libs())
cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs]
cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
'-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
'-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')]
if '+external-blas' in spec:
# TODO : the mechanism to specify the library should be more general,
# TODO : but this allows to have an hook to an external blas
cmake_args.extend([
'-DUSE_OPTIMIZED_BLAS:BOOL=ON',
'-DBLAS_LIBRARIES:PATH=%s' % join_path(spec['blas'].prefix.lib, 'libblas.a')
])
if '+shared' in spec:
cmake_args.append('-DBUILD_SHARED_LIBS=ON')
cmake_args.extend(std_cmake_args)
cmake_args += std_cmake_args
cmake(*cmake_args)
with working_dir('spack-build', create=True):
cmake('..', *cmake_args)
make()
make("install")

19
var/spack/repos/builtin/packages/netlib-scalapack/package.py
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@ -1,4 +1,5 @@
from spack import *
import sys
class NetlibScalapack(Package):
"""ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines"""
@ -40,10 +41,16 @@ def install(self, spec, prefix):
make()
make("install")
def setup_dependent_python_module(self, module, spec, dependent_spec):
lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
lib_suffix = lib_dsuffix if '+shared' in spec['scalapack'] else '.a'
# The shared libraries are not installed correctly on Darwin; correct this
if (sys.platform == 'darwin') and ('+shared' in spec):
fix_darwin_install_name(prefix.lib)
spec['scalapack'].fc_link = '-L%s -lscalapack' % spec['scalapack'].prefix.lib
spec['scalapack'].cc_link = spec['scalapack'].fc_link
spec['scalapack'].libraries = [join_path(spec['scalapack'].prefix.lib, 'libscalapack%s' % lib_suffix)]
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'
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)]

51
var/spack/repos/builtin/packages/oce/package.py Normal file
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@ -0,0 +1,51 @@
from spack import *
import platform, sys
class Oce(Package):
"""
Open CASCADE Community Edition:
patches/improvements/experiments contributed by users over the official Open CASCADE library.
"""
homepage = "https://github.com/tpaviot/oce"
url = "https://github.com/tpaviot/oce/archive/OCE-0.17.tar.gz"
version('0.17.1', '36c67b87093c675698b483454258af91')
version('0.17' , 'f1a89395c4b0d199bea3db62b85f818d')
version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3')
version('0.16' , '7a4b4df5a104d75a537e25e7dd387eca')
version('0.15' , '7ec541a1c350ca8a684f74980e48801c')
depends_on('cmake@2.8:')
def install(self, spec, prefix):
options = []
options.extend(std_cmake_args)
options.extend([
'-DOCE_INSTALL_PREFIX=%s' % prefix,
'-DOCE_BUILD_SHARED_LIB:BOOL=ON',
'-DOCE_BUILD_TYPE:STRING=Release',
'-DOCE_DATAEXCHANGE:BOOL=ON',
'-DOCE_DISABLE_X11:BOOL=ON',
'-DOCE_DRAW:BOOL=OFF',
'-DOCE_MODEL:BOOL=ON',
'-DOCE_MULTITHREAD_LIBRARY:STRING=NONE', # FIXME: add tbb
'-DOCE_OCAF:BOOL=ON',
'-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=OFF',
'-DOCE_VISUALISATION:BOOL=OFF',
'-DOCE_WITH_FREEIMAGE:BOOL=OFF',
'-DOCE_WITH_GL2PS:BOOL=OFF',
'-DOCE_WITH_OPENCL:BOOL=OFF'
])
if platform.system() == 'Darwin':
options.extend([
'-DOCE_OSX_USE_COCOA:BOOL=ON',
])
cmake('.', *options)
make("install/strip")
# The shared libraries are not installed correctly on Darwin; correct this
if (sys.platform == 'darwin'):
fix_darwin_install_name(prefix.lib)

2
var/spack/repos/builtin/packages/octave/package.py
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@ -62,7 +62,7 @@ class Octave(Package):
depends_on('qrupdate', when='+qrupdate')
#depends_on('qscintilla', when='+qscintilla) # TODO: add package
depends_on('qt', when='+qt')
depends_on('SuiteSparse', when='+suitesparse')
depends_on('suite-sparse',when='+suitesparse')
depends_on('zlib', when='+zlib')

10
var/spack/repos/builtin/packages/openblas/package.py
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@ -6,6 +6,7 @@ class Openblas(Package):
homepage = "http://www.openblas.net"
url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz"
version('0.2.17', '664a12807f2a2a7cda4781e3ab2ae0e1')
version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc')
version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9')
@ -14,7 +15,14 @@ class Openblas(Package):
provides('lapack')
def install(self, spec, prefix):
make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77')
extra=[]
if spec.satisfies('@0.2.16'):
extra.extend([
'BUILD_LAPACK_DEPRECATED=1' # fix missing _dggsvd_ and _sggsvd_
])
make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77',*extra)
make("tests")
make('install', "PREFIX='%s'" % prefix)
lib_dsuffix = 'dylib' if sys.platform == 'darwin' else 'so'

34
var/spack/repos/builtin/packages/p4est/package.py Normal file
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@ -0,0 +1,34 @@
from spack import *
class P4est(Package):
"""Dynamic management of a collection (a forest) of adaptive octrees in parallel"""
homepage = "http://www.p4est.org"
url = "http://p4est.github.io/release/p4est-1.1.tar.gz"
version('1.1', '37ba7f4410958cfb38a2140339dbf64f')
# disable by default to make it work on frontend of clusters
variant('tests', default=False, description='Run small tests')
depends_on('mpi')
def install(self, spec, prefix):
options = ['--enable-mpi',
'--enable-shared',
'--disable-vtk-binary',
'--without-blas',
'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL',
'CFLAGS=-O2',
'CC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # TODO: use ENV variables or MPI class wrappers
'CXX=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
'FC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
'F77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'),
]
configure('--prefix=%s' % prefix, *options)
make()
if '+tests' in self.spec:
make("check")
make("install")

71
var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch Normal file
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@ -0,0 +1,71 @@
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ca945dd..aff8b5f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -23,7 +23,7 @@ else()
set(ParMETIS_LIBRARY_TYPE STATIC)
endif()
-include(${GKLIB_PATH}/GKlibSystem.cmake)
+include_directories(${GKLIB_PATH})
# List of paths that the compiler will search for header files.
# i.e., the -I equivalent
@@ -33,7 +33,7 @@ include_directories(${GKLIB_PATH})
include_directories(${METIS_PATH}/include)
# List of directories that cmake will look for CMakeLists.txt
-add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
+find_library(METIS_LIBRARY metis PATHS ${METIS_PATH}/lib)
add_subdirectory(include)
add_subdirectory(libparmetis)
add_subdirectory(programs)
diff --git a/libparmetis/CMakeLists.txt b/libparmetis/CMakeLists.txt
index 9cfc8a7..e0c4de7 100644
--- a/libparmetis/CMakeLists.txt
+++ b/libparmetis/CMakeLists.txt
@@ -5,7 +5,10 @@ file(GLOB parmetis_sources *.c)
# Create libparmetis
add_library(parmetis ${ParMETIS_LIBRARY_TYPE} ${parmetis_sources})
# Link with metis and MPI libraries.
-target_link_libraries(parmetis metis ${MPI_LIBRARIES})
+target_link_libraries(parmetis ${METIS_LIBRARY} ${MPI_LIBRARIES})
+if(UNIX)
+ target_link_libraries(parmetis m)
+endif()
set_target_properties(parmetis PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}")
install(TARGETS parmetis
diff --git a/libparmetis/parmetislib.h b/libparmetis/parmetislib.h
index c1daeeb..07511f6 100644
--- a/libparmetis/parmetislib.h
+++ b/libparmetis/parmetislib.h
@@ -20,13 +20,12 @@
#include <parmetis.h>
-#include "../metis/libmetis/gklib_defs.h"
+#include <gklib_defs.h>
-#include <mpi.h>
+#include <mpi.h>
#include <rename.h>
#include <defs.h>
#include <struct.h>
#include <macros.h>
#include <proto.h>
-
diff --git a/programs/parmetisbin.h b/programs/parmetisbin.h
index e26cd2d..d156480 100644
--- a/programs/parmetisbin.h
+++ b/programs/parmetisbin.h
@@ -19,7 +19,7 @@
#include <GKlib.h>
#include <parmetis.h>
-#include "../metis/libmetis/gklib_defs.h"
+#include <gklib_defs.h>
#include "../libparmetis/rename.h"
#include "../libparmetis/defs.h"
#include "../libparmetis/struct.h"

36
var/spack/repos/builtin/packages/parmetis/package.py
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@ -24,10 +24,7 @@
##############################################################################
from spack import *
# FIXME : lot of code is duplicated from packages/metis/package.py . Inheriting from there may reduce
# FIXME : the installation rules to just a few lines
import sys
class Parmetis(Package):
"""
@ -43,13 +40,17 @@ class Parmetis(Package):
variant('debug', default=False, description='Builds the library in debug mode')
variant('gdb', default=False, description='Enables gdb support')
variant('idx64', default=False, description='Use int64_t as default index type')
variant('double', default=False, description='Use double precision floating point types')
depends_on('cmake @2.8:') # build dependency
depends_on('mpi')
# FIXME : this should conflict with metis as it builds its own version internally
patch('enable_external_metis.patch')
depends_on('metis')
# bug fixes from PETSc developers
# https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/
patch('pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch')
# https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
depends_on('gdb', when='+gdb')
@ -63,8 +64,8 @@ def install(self, spec, prefix):
# FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case
# FIXME : they use a non-standard name
options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source),
'-DMETIS_PATH:PATH={metis_source}'.format(metis_source=metis_source),
options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=spec['metis'].prefix.include),
'-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix),
'-DCMAKE_C_COMPILER:STRING=mpicc',
'-DCMAKE_CXX_COMPILER:STRING=mpicxx'])
@ -78,18 +79,11 @@ def install(self, spec, prefix):
if '+gdb' in spec:
options.append('-DGDB:BOOL=ON')
metis_header = join_path(metis_source, 'include', 'metis.h')
if '+idx64' in spec:
filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header)
if '+double' in spec:
filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header)
with working_dir(build_directory, create=True):
cmake(source_directory, *options)
make()
make("install")
# Parmetis build system doesn't allow for an external metis to be used, but doesn't copy the required
# metis header either
install(metis_header, self.prefix.include)
# The shared library is not installed correctly on Darwin; correct this
if (sys.platform == 'darwin') and ('+shared' in spec):
fix_darwin_install_name(prefix.lib)

77
var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch Normal file
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@ -0,0 +1,77 @@
From 1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b Mon Sep 17 00:00:00 2001
From: Jed Brown <jed@59A2.org>
Date: Fri, 12 Oct 2012 15:45:10 -0500
Subject: [PATCH] ParMetis bug fixes reported by John Fettig [petsc-maint
#133631]
'''
I have also reported to to Karypis but have received zero
response and he hasn't released any updates to the original release
either. At least he approved my forum posting so that other people
can see the bug and the fix.
http://glaros.dtc.umn.edu/gkhome/node/837
'''
Hg-commit: 1c2b9fe39201d404b493885093b5992028b9b8d4
---
libparmetis/xyzpart.c | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c
index 3a2c289..63abfcb 100644
--- a/libparmetis/xyzpart.c
+++ b/libparmetis/xyzpart.c
@@ -104,7 +104,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
for (i=0; i<nbins; i++)
emarkers[i] = gmin + (gmax-gmin)*i/nbins;
- emarkers[nbins] = gmax*(1.0+2.0*REAL_EPSILON);
+ emarkers[nbins] = gmax*(1.0+copysign(1.0,gmax)*2.0*REAL_EPSILON);
/* get into a iterative backet boundary refinement */
for (l=0; l<5; l++) {
@@ -152,7 +152,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
}
}
nemarkers[0] = gmin;
- nemarkers[nbins] = gmax*(1.0+2.0*REAL_EPSILON);
+ nemarkers[nbins] = gmax*(1.0+copysign(1.0,gmax)*2.0*REAL_EPSILON);
rcopy(nbins+1, nemarkers, emarkers);
}
@@ -218,7 +218,7 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
emarkers[0] = gmin;
emarkers[1] = gsum/gnvtxs;
- emarkers[2] = gmax*(1.0+2.0*REAL_EPSILON);
+ emarkers[2] = gmax*(1.0+(gmax < 0 ? -1. : 1.)*2.0*REAL_EPSILON);
cnbins = 2;
/* get into a iterative backet boundary refinement */
@@ -227,7 +227,7 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
iset(cnbins, 0, lcounts);
rset(cnbins, 0, lsums);
for (j=0, i=0; i<nvtxs;) {
- if (cand[i].key < emarkers[j+1]) {
+ if (cand[i].key <= emarkers[j+1]) {
lcounts[j]++;
lsums[j] += cand[i].key;
i++;
@@ -272,12 +272,12 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
rsorti(cnbins, nemarkers);
rcopy(cnbins, nemarkers, emarkers);
- emarkers[cnbins] = gmax*(1.0+2.0*REAL_EPSILON);
+ emarkers[cnbins] = gmax*(1.0+(gmax < 0 ? -1. : 1.)*2.0*REAL_EPSILON);
}
/* assign the coordinate to the appropriate bin */
for (j=0, i=0; i<nvtxs;) {
- if (cand[i].key < emarkers[j+1]) {
+ if (cand[i].key <= emarkers[j+1]) {
bxyz[cand[i].val*ndims+k] = j;
i++;
}
--
2.1.1.1.g1fb337f

35
var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch Normal file
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@ -0,0 +1,35 @@
From 82409d68aa1d6cbc70740d0f35024aae17f7d5cb Mon Sep 17 00:00:00 2001
From: Sean Farley <sean@mcs.anl.gov>
Date: Tue, 20 Mar 2012 11:59:44 -0500
Subject: [PATCH] parmetis: fix bug reported by jfettig; '<' to '<=' in xyzpart
Hg-commit: 2dd2eae596acaabbc80e0ef875182616f868dbc2
---
libparmetis/xyzpart.c | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c
index 307aed9..3a2c289 100644
--- a/libparmetis/xyzpart.c
+++ b/libparmetis/xyzpart.c
@@ -111,7 +111,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
/* determine bucket counts */
iset(nbins, 0, lcounts);
for (j=0, i=0; i<nvtxs;) {
- if (cand[i].key < emarkers[j+1]) {
+ if (cand[i].key <= emarkers[j+1]) {
lcounts[j]++;
i++;
}
@@ -158,7 +158,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
/* assign the coordinate to the appropriate bin */
for (j=0, i=0; i<nvtxs;) {
- if (cand[i].key < emarkers[j+1]) {
+ if (cand[i].key <= emarkers[j+1]) {
bxyz[cand[i].val*ndims+k] = j;
i++;
}
--
2.1.1.1.g1fb337f

46
var/spack/repos/builtin/packages/petsc/package.py
View file

@ -20,11 +20,15 @@ class Petsc(Package):
variant('shared', default=True, description='Enables the build of shared libraries')
variant('mpi', default=True, description='Activates MPI support')
variant('double', default=True, description='Switches between single and double precision')
variant('complex', default=False, description='Build with complex numbers')
variant('debug', default=False, description='Compile in debug mode')
variant('metis', default=True, description='Activates support for metis and parmetis')
variant('hdf5', default=True, description='Activates support for HDF5 (only parallel)')
variant('boost', default=True, description='Activates support for Boost')
variant('hypre', default=True, description='Activates support for Hypre')
variant('hypre', default=True, description='Activates support for Hypre (only parallel)')
variant('mumps', default=True, description='Activates support for MUMPS (only parallel)')
variant('superlu-dist', default=True, description='Activates support for SuperluDist (only parallel)')
# Virtual dependencies
depends_on('blas')
@ -40,7 +44,13 @@ class Petsc(Package):
depends_on('hdf5+mpi', when='+hdf5+mpi')
depends_on('parmetis', when='+metis+mpi')
depends_on('hypre', when='+hypre+mpi')
# Hypre does not support complex numbers.
# Also PETSc prefer to build it without internal superlu, likely due to conflict in headers
# see https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py
depends_on('hypre~internal-superlu', when='+hypre+mpi~complex')
depends_on('superlu-dist', when='+superlu-dist+mpi')
depends_on('mumps+mpi', when='+mumps+mpi')
depends_on('scalapack', when='+mumps+mpi')
def mpi_dependent_options(self):
if '~mpi' in self.spec:
@ -55,11 +65,20 @@ def mpi_dependent_options(self):
# If mpi is disabled (~mpi), it's an error to have any of these enabled.
# This generates a list of any such errors.
errors = [error_message_fmt.format(library=x)
for x in ('hdf5', 'hypre', 'parmetis')
for x in ('hdf5', 'hypre', 'parmetis','mumps','superlu-dist')
if ('+'+x) in self.spec]
if errors:
errors = ['incompatible variants given'] + errors
raise RuntimeError('\n'.join(errors))
else:
if self.compiler.name == "clang":
compiler_opts = [
'--with-mpi=1',
'--with-cc=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # Avoid confusing PETSc config by clang: warning: argument unused during compilation
'--with-cxx=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
'--with-fc=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
'--with-f77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'),
]
else:
compiler_opts = [
'--with-mpi=1',
@ -68,15 +87,17 @@ def mpi_dependent_options(self):
return compiler_opts
def install(self, spec, prefix):
options = []
options = ['--with-ssl=0']
options.extend(self.mpi_dependent_options())
options.extend([
'--with-precision=%s' % ('double' if '+double' in spec else 'single'),
'--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'),
'--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'),
'--with-debugging=%s' % ('1' if '+debug' in spec else '0'),
'--with-blas-lapack-dir=%s' % spec['lapack'].prefix
])
# Activates library support if needed
for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis'):
for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis','mumps','scalapack'):
options.append(
'--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0'))
)
@ -84,9 +105,24 @@ def install(self, spec, prefix):
options.append(
'--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix)
)
# PETSc does not pick up SuperluDist from the dir as they look for superlu_dist_4.1.a
if 'superlu-dist' in spec:
options.extend([
'--with-superlu_dist-include=%s' % spec['superlu-dist'].prefix.include,
'--with-superlu_dist-lib=%s' % join_path(spec['superlu-dist'].prefix.lib, 'libsuperlu_dist.a'),
'--with-superlu_dist=1'
])
else:
options.append(
'--with-superlu_dist=0'
)
configure('--prefix=%s' % prefix, *options)
# PETSc has its own way of doing parallel make.
make('MAKE_NP=%s' % make_jobs, parallel=False)
make("install")
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
# set up PETSC_DIR for everyone using PETSc package
spack_env.set('PETSC_DIR', self.prefix)

16
var/spack/repos/builtin/packages/py-netcdf/package.py Normal file
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@ -0,0 +1,16 @@
from spack import *
class PyNetcdf(Package):
"""Python interface to the netCDF Library."""
homepage = "http://unidata.github.io/netcdf4-python"
url = "https://github.com/Unidata/netcdf4-python/tarball/v1.2.3.1rel"
version('1.2.3.1', '4fc4320d4f2a77b894ebf8da1c9895af')
extends('python')
depends_on('py-numpy')
depends_on('py-cython')
depends_on('netcdf')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix=%s' % prefix)

33
var/spack/repos/builtin/packages/py-numpy/package.py
View file

@ -1,24 +1,43 @@
from spack import *
class PyNumpy(Package):
"""array processing for numbers, strings, records, and objects."""
homepage = "https://pypi.python.org/pypi/numpy"
"""NumPy is the fundamental package for scientific computing with Python.
It contains among other things: a powerful N-dimensional array object,
sophisticated (broadcasting) functions, tools for integrating C/C++ and
Fortran code, and useful linear algebra, Fourier transform, and random
number capabilities"""
homepage = "http://www.numpy.org/"
url = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz"
version('1.9.1', '78842b73560ec378142665e712ae4ad9')
version('1.10.4', 'aed294de0aa1ac7bd3f9745f4f1968ad')
version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645')
version('1.9.1', '78842b73560ec378142665e712ae4ad9')
variant('blas', default=True)
variant('lapack', default=True)
extends('python')
depends_on('py-nose')
depends_on('netlib-blas+fpic', when='+blas')
depends_on('netlib-lapack+shared', when='+blas')
depends_on('blas', when='+blas')
depends_on('lapack', when='+lapack')
def install(self, spec, prefix):
libraries = []
library_dirs = []
if '+blas' in spec:
libraries.append('blas')
library_dirs.append(spec['blas'].prefix.lib)
if '+lapack' in spec:
libraries.append('lapack')
library_dirs.append(spec['lapack'].prefix.lib)
if '+blas' in spec or '+lapack' in spec:
with open('site.cfg', 'w') as f:
f.write('[DEFAULT]\n')
f.write('libraries=lapack,blas\n')
f.write('library_dirs=%s/lib:%s/lib\n' % (spec['blas'].prefix, spec['lapack'].prefix))
f.write('libraries=%s\n' % ','.join(libraries))
f.write('library_dirs=%s\n' % ':'.join(library_dirs))
python('setup.py', 'install', '--prefix=%s' % prefix)

5
var/spack/repos/builtin/packages/py-scipy/package.py
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@ -2,11 +2,12 @@
class PyScipy(Package):
"""Scientific Library for Python."""
homepage = "https://pypi.python.org/pypi/scipy"
homepage = "http://www.scipy.org/"
url = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz"
version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
version('0.17.0', '5ff2971e1ce90e762c59d2cd84837224')
version('0.15.1', 'be56cd8e60591d6332aac792a5880110')
version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
extends('python')
depends_on('py-nose')

14
var/spack/repos/builtin/packages/python/package.py
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@ -105,10 +105,13 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
pythonpath = ':'.join(python_paths)
spack_env.set('PYTHONPATH', pythonpath)
run_env.set('PYTHONPATH', pythonpath)
# For run time environment set only the path for extension_spec and prepend it to PYTHONPATH
if extension_spec.package.extends(self.spec):
run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir))
def modify_module(self, module, spec, ext_spec):
def setup_dependent_package(self, module, ext_spec):
"""
Called before python modules' install() methods.
@ -118,16 +121,17 @@ def modify_module(self, module, spec, ext_spec):
"""
# Python extension builds can have a global python executable function
if self.version >= Version("3.0.0") and self.version < Version("4.0.0"):
module.python = Executable(join_path(spec.prefix.bin, 'python3'))
module.python = Executable(join_path(self.spec.prefix.bin, 'python3'))
else:
module.python = Executable(join_path(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.
module.python_lib_dir = os.path.join(ext_spec.prefix, self.python_lib_dir)
module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir)
module.site_packages_dir = os.path.join(ext_spec.prefix, self.site_packages_dir)
# Make the site packages directory if it does not exist already.
# Make the site packages directory for extensions, if it does not exist already.
if ext_spec.package.is_extension:
mkdirp(module.site_packages_dir)
# ========================================================================

6
var/spack/repos/builtin/packages/ruby/package.py
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@ -30,7 +30,7 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
# The actual installation path for this gem
spack_env.set('GEM_HOME', extension_spec.prefix)
def modify_module(self, module, spec, ext_spec):
def setup_dependent_package(self, module, ext_spec):
"""Called before ruby modules' install() methods. Sets GEM_HOME
and GEM_PATH to values appropriate for the package being built.
@ -39,5 +39,5 @@ def modify_module(self, module, spec, ext_spec):
gem('install', '<gem-name>.gem')
"""
# Ruby extension builds have global ruby and gem functions
module.ruby = Executable(join_path(spec.prefix.bin, 'ruby'))
module.gem = Executable(join_path(spec.prefix.bin, 'gem'))
module.ruby = Executable(join_path(self.spec.prefix.bin, 'ruby'))
module.gem = Executable(join_path(self.spec.prefix.bin, 'gem'))

23
var/spack/repos/builtin/packages/silo/package.py
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@ -5,24 +5,35 @@ class Silo(Package):
data to binary, disk files."""
homepage = "http://wci.llnl.gov/simulation/computer-codes/silo"
url = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.8/silo-4.8.tar.gz"
base_url = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo"
version('4.10.2', '9ceac777a2f2469ac8cef40f4fab49c8')
version('4.9', 'a83eda4f06761a86726e918fc55e782a')
version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9')
variant('fortran', default=True, description='Enable Fortran support')
variant('silex', default=False, description='Builds Silex, a GUI for viewing Silo files')
depends_on("hdf5")
depends_on('hdf5')
depends_on('qt', when='+silex')
def install(self, spec, prefix):
config_args = [
'--enable-fortran' if '+fortran' in spec else '--disable-fortran',
'--enable-silex' if '+silex' in spec else '--disable-silex',
]
if '+silex' in spec:
config_args.append('--with-Qt-dir=%s' % spec['qt'].prefix)
configure(
"--prefix=%s" % prefix,
"--with-hdf5=%s,%s" % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib),
"--with-zlib=%s,%s" % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib),
'--prefix=%s' % prefix,
'--with-hdf5=%s,%s' % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib),
'--with-zlib=%s,%s' % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib),
*config_args)
make()
make("install")
make('install')
def url_for_version(self, version):
return '%s/silo-%s/silo-%s.tar.gz' % (Silo.base_url, version, version)

49
var/spack/repos/builtin/packages/slepc/package.py Normal file
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@ -0,0 +1,49 @@
import os
from spack import *
class Slepc(Package):
"""
Scalable Library for Eigenvalue Computations.
"""
homepage = "http://www.grycap.upv.es/slepc"
url = "http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz"
version('3.6.2', '2ab4311bed26ccf7771818665991b2ea3a9b15f97e29fd13911ab1293e8e65df')
variant('arpack', default=False, description='Enables Arpack wrappers')
depends_on('petsc')
depends_on('arpack-ng~mpi',when='+arpack^petsc~mpi')
depends_on('arpack-ng+mpi',when='+arpack^petsc+mpi')
def install(self, spec, prefix):
# set SLEPC_DIR for installation
os.environ['SLEPC_DIR'] = self.stage.source_path
options = []
if '+arpack' in spec:
options.extend([
'--with-arpack-dir=%s' % spec['arpack-ng'].prefix.lib,
])
if 'arpack-ng~mpi' in spec:
options.extend([
'--with-arpack-flags=-larpack'
])
else:
options.extend([
'--with-arpack-flags=-lparpack,-larpack'
])
configure('--prefix=%s' % prefix, *options)
make('MAKE_NP=%s' % make_jobs, parallel=False)
#FIXME:
# make('test')
make('install')
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
# set up SLEPC_DIR for everyone using SLEPc package
spack_env.set('SLEPC_DIR', self.prefix)

3
var/spack/repos/builtin/packages/SuiteSparse/package.py → var/spack/repos/builtin/packages/suite-sparse/package.py
View file

@ -1,7 +1,7 @@
from spack import *
class Suitesparse(Package):
class SuiteSparse(Package):
"""
SuiteSparse is a suite of sparse matrix algorithms
"""
@ -24,4 +24,3 @@ def install(self, spec, prefix):
# FIXME : this actually uses the current workaround
# FIXME : (blas / lapack always provide libblas and liblapack as aliases)
make('install', 'INSTALL=%s' % prefix, 'BLAS=-lblas', 'LAPACK=-llapack')

12
var/spack/repos/builtin/packages/superlu-dist/package.py
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@ -1,4 +1,5 @@
from spack import *
import glob
class SuperluDist(Package):
"""A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines."""
@ -52,12 +53,13 @@ def install(self, spec, prefix):
# system "make"
# need to install by hand
headers_location = join_path(self.prefix.include,'superlu_dist')
headers_location = self.prefix.include
mkdirp(headers_location)
# FIXME: fetch all headers in the folder automatically
for header in ['Cnames.h','cublas_utils.h','dcomplex.h','html_mainpage.h','machines.h','old_colamd.h','psymbfact.h','superlu_ddefs.h','superlu_defs.h','superlu_enum_consts.h','superlu_zdefs.h','supermatrix.h','util_dist.h']:
superludist_header = join_path(self.stage.source_path, 'SRC/',header)
install(superludist_header, headers_location)
mkdirp(prefix.lib)
headers = glob.glob(join_path(self.stage.source_path, 'SRC','*.h'))
for h in headers:
install(h,headers_location)
superludist_lib = join_path(self.stage.source_path, 'lib/libsuperlu_dist.a')
install(superludist_lib,self.prefix.lib)

79
var/spack/repos/builtin/packages/tbb/package.py Normal file
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@ -0,0 +1,79 @@
from spack import *
import os
import glob
class Tbb(Package):
"""Widely used C++ template library for task parallelism.
Intel Threading Building Blocks (Intel TBB) lets you easily write parallel
C++ programs that take full advantage of multicore performance, that are
portable and composable, and that have future-proof scalability.
"""
homepage = "http://www.threadingbuildingblocks.org/"
# Only version-specific URL's work for TBB
version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz')
def coerce_to_spack(self,tbb_build_subdir):
for compiler in ["icc","gcc","clang"]:
fs = glob.glob(join_path(tbb_build_subdir,"*.%s.inc" % compiler ))
for f in fs:
lines = open(f).readlines()
of = open(f,"w")
for l in lines:
if l.strip().startswith("CPLUS ="):
of.write("# coerced to spack\n")
of.write("CPLUS = $(CXX)\n")
elif l.strip().startswith("CPLUS ="):
of.write("# coerced to spack\n")
of.write("CONLY = $(CC)\n")
else:
of.write(l);
def install(self, spec, prefix):
#
# we need to follow TBB's compiler selection logic to get the proper build + link flags
# but we still need to use spack's compiler wrappers
# to accomplish this, we do two things:
#
# * Look at the spack spec to determine which compiler we should pass to tbb's Makefile
#
# * patch tbb's build system to use the compiler wrappers (CC, CXX) for
# icc, gcc, clang
# (see coerce_to_spack())
#
self.coerce_to_spack("build")
if spec.satisfies('%clang'):
tbb_compiler = "clang"
elif spec.satisfies('%intel'):
tbb_compiler = "icc"
else:
tbb_compiler = "gcc"
mkdirp(prefix)
mkdirp(prefix.lib)
#
# tbb does not have a configure script or make install target
# we simply call make, and try to put the pieces together
#
make("compiler=%s" %(tbb_compiler))
# install headers to {prefix}/include
install_tree('include',prefix.include)
# install libs to {prefix}/lib
tbb_lib_names = ["libtbb",
"libtbbmalloc",
"libtbbmalloc_proxy"]
for lib_name in tbb_lib_names:
# install release libs
fs = glob.glob(join_path("build","*release",lib_name + ".*"))
for f in fs:
install(f, prefix.lib)
# install debug libs if they exist
fs = glob.glob(join_path("build","*debug",lib_name + "_debug.*"))
for f in fs:
install(f, prefix.lib)