Merge branch 'features/cantera' of https://github.com/adamjstewart/spack into adamjstewart-features/cantera

This commit is contained in:
Todd Gamblin
2016-06-20 23:53:48 -07:00
9 changed files with 748 additions and 70 deletions

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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 *
import os
class Cantera(Package):
"""Cantera is a suite of object-oriented software tools for problems
involving chemical kinetics, thermodynamics, and/or transport processes."""
homepage = "http://www.cantera.org/docs/sphinx/html/index.html"
url = "https://github.com/Cantera/cantera/archive/v2.2.1.tar.gz"
version('2.2.1', '9d1919bdef39ddec54485fc8a741a3aa')
variant('lapack', default=True, description='Build with external BLAS/LAPACK libraries')
variant('threadsafe', default=True, description='Build threadsafe, requires Boost')
variant('sundials', default=True, description='Build with external Sundials')
variant('python', default=False, description='Build the Cantera Python module')
variant('matlab', default=False, description='Build the Cantera Matlab toolbox')
# Required dependencies
depends_on('scons')
# Recommended dependencies
depends_on('blas', when='+lapack')
depends_on('lapack', when='+lapack')
depends_on('boost', when='+threadsafe')
depends_on('sundials', when='+sundials') # must be compiled with -fPIC
# Python module dependencies
extends('python', when='+python')
depends_on('py-numpy', when='+python')
depends_on('py-scipy', when='+python')
depends_on('py-cython', when='+python')
depends_on('py-3to2', when='+python')
# TODO: these "when" specs don't actually work
# depends_on('py-unittest2', when='+python^python@2.6')
# depends_on('py-unittest2py3k', when='+python^python@3.1')
# Matlab toolbox dependencies
# TODO: add Matlab package
# TODO: allow packages to extend multiple other packages
# extends('matlab', when='+matlab')
def install(self, spec, prefix):
# Required options
options = [
'prefix={0}'.format(prefix),
'CC={0}'.format(os.environ['CC']),
'CXX={0}'.format(os.environ['CXX']),
'F77={0}'.format(os.environ['F77']),
'FORTRAN={0}'.format(os.environ['FC']),
'cc_flags=-fPIC',
# Allow Spack environment variables to propagate through to SCons
'env_vars=all'
]
# BLAS/LAPACK support
if '+lapack' in spec:
options.extend([
'blas_lapack_libs=lapack,blas',
'blas_lapack_dir={0}'.format(spec['lapack'].prefix.lib)
])
# Threadsafe build, requires Boost
if '+threadsafe' in spec:
options.extend([
'build_thread_safe=yes',
'boost_inc_dir={0}'.format(spec['boost'].prefix.include),
'boost_lib_dir={0}'.format(spec['boost'].prefix.lib),
'boost_thread_lib=boost_thread-mt,boost_system-mt'
])
else:
options.append('build_thread_safe=no')
# Sundials support
if '+sundials' in spec:
options.extend([
'use_sundials=y',
'sundials_include={0}'.format(spec['sundials'].prefix.include),
'sundials_libdir={0}'.format(spec['sundials'].prefix.lib),
'sundials_license={0}'.format(
join_path(spec['sundials'].prefix, 'LICENSE'))
])
else:
options.append('use_sundials=n')
# Python module
if '+python' in spec:
options.extend([
'python_package=full',
'python_cmd={0}'.format(
join_path(spec['python'].prefix.bin, 'python')),
'python_array_home={0}'.format(spec['py-numpy'].prefix)
])
if spec['python'].satisfies('@3'):
options.extend([
'python3_package=y',
'python3_cmd={0}'.format(
join_path(spec['python'].prefix.bin, 'python')),
'python3_array_home={0}'.format(spec['py-numpy'].prefix)
])
else:
options.append('python3_package=n')
else:
options.append('python_package=none')
options.append('python3_package=n')
# Matlab toolbox
if '+matlab' in spec:
options.extend([
'matlab_toolbox=y',
'matlab_path={0}'.format(spec['matlab'].prefix)
])
else:
options.append('matlab_toolbox=n')
scons('build', *options)
if '+python' in spec:
# Tests will always fail if Python dependencies aren't built
# In addition, 3 of the tests fail when run in parallel
scons('test', parallel=False)
scons('install')
self.filter_compilers()
def filter_compilers(self):
"""Run after install to tell the Makefile and SConstruct files to use
the compilers that Spack built the package with.
If this isn't done, they'll have CC, CXX, F77, and FC set to Spack's
generic cc, c++, f77, and f90. We want them to be bound to whatever
compiler they were built with."""
kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
dirname = os.path.join(self.prefix, 'share/cantera/samples')
cc_files = [
'cxx/rankine/Makefile', 'cxx/NASA_coeffs/Makefile',
'cxx/kinetics1/Makefile', 'cxx/flamespeed/Makefile',
'cxx/combustor/Makefile', 'f77/SConstruct'
]
cxx_files = [
'cxx/rankine/Makefile', 'cxx/NASA_coeffs/Makefile',
'cxx/kinetics1/Makefile', 'cxx/flamespeed/Makefile',
'cxx/combustor/Makefile'
]
f77_files = [
'f77/Makefile', 'f77/SConstruct'
]
fc_files = [
'f90/Makefile', 'f90/SConstruct'
]
for filename in cc_files:
filter_file(os.environ['CC'], self.compiler.cc,
os.path.join(dirname, filename), **kwargs)
for filename in cxx_files:
filter_file(os.environ['CXX'], self.compiler.cxx,
os.path.join(dirname, filename), **kwargs)
for filename in f77_files:
filter_file(os.environ['F77'], self.compiler.f77,
os.path.join(dirname, filename), **kwargs)
for filename in fc_files:
filter_file(os.environ['FC'], self.compiler.fc,
os.path.join(dirname, filename), **kwargs)

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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 Py3to2(Package):
"""lib3to2 is a set of fixers that are intended to backport code written
for Python version 3.x into Python version 2.x."""
homepage = "https://pypi.python.org/pypi/3to2"
url = "https://pypi.python.org/packages/source/3/3to2/3to2-1.1.1.zip"
version('1.1.1', 'cbeed28e350dbdaef86111ace3052824')
extends('python')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix=%s' % 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 PyUnittest2(Package):
"""unittest2 is a backport of the new features added to the unittest
testing framework in Python 2.7 and onwards."""
homepage = "https://pypi.python.org/pypi/unittest2"
url = "https://pypi.python.org/packages/source/u/unittest2/unittest2-1.1.0.tar.gz"
version('1.1.0', 'f72dae5d44f091df36b6b513305ea000')
extends('python')
depends_on('py-setuptools')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix=%s' % 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 PyUnittest2py3k(Package):
"""unittest2 is a backport of the new features added to the unittest
testing framework in Python 2.7 and 3.2. This is a Python 3 compatible
version of unittest2."""
homepage = "https://pypi.python.org/pypi/unittest2py3k"
url = "https://pypi.python.org/packages/source/u/unittest2py3k/unittest2py3k-0.5.1.tar.gz"
version('0.5.1', '8824ff92044310d9365f90d892bf0f09')
extends('python')
depends_on('py-setuptools')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix=%s' % prefix)

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@@ -28,10 +28,11 @@
class Serf(Package):
"""Apache Serf - a high performance C-based HTTP client library
built upon the Apache Portable Runtime (APR) library"""
homepage = 'https://serf.apache.org/'
url = 'https://archive.apache.org/dist/serf/serf-1.3.8.tar.bz2'
version('1.3.8', '1d45425ca324336ce2f4ae7d7b4cfbc5567c5446')
version('1.3.8', '1d45425ca324336ce2f4ae7d7b4cfbc5567c5446')
depends_on('apr')
depends_on('apr-util')
@@ -41,8 +42,6 @@ class Serf(Package):
depends_on('zlib')
def install(self, spec, prefix):
scons = which("scons")
options = ['PREFIX=%s' % prefix]
options.append('APR=%s' % spec['apr'].prefix)
options.append('APU=%s' % spec['apr-util'].prefix)

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@@ -23,17 +23,151 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import os
class Sundials(Package):
"""SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers)"""
"""SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation
Solvers)"""
homepage = "http://computation.llnl.gov/casc/sundials/"
url = "http://computation.llnl.gov/casc/sundials/download/code/sundials-2.5.0.tar.gz"
url = "http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/download/sundials-2.6.2.tar.gz"
version('2.5.0', 'aba8b56eec600de3109cfb967aa3ba0f')
version('2.6.2', '3deeb0ede9f514184c6bd83ecab77d95')
depends_on("mpi")
variant('mpi', default=True, description='Enable MPI support')
variant('lapack', default=True, description='Build with external BLAS/LAPACK libraries')
variant('klu', default=False, description='Build with SuiteSparse KLU libraries')
variant('superlu', default=False, description='Build with SuperLU_MT libraries')
variant('openmp', default=False, description='Enable OpenMP support')
variant('pthread', default=True, description='Enable POSIX threads support')
depends_on('mpi', when='+mpi')
depends_on('blas', when='+lapack')
depends_on('lapack', when='+lapack')
depends_on('suite-sparse', when='+klu')
depends_on('superlu-mt+openmp', when='+superlu+openmp')
depends_on('superlu-mt+pthread', when='+superlu+pthread')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
make()
make("install")
cmake_args = std_cmake_args[:]
cmake_args.extend([
'-DBUILD_SHARED_LIBS=ON',
'-DCMAKE_C_FLAGS=-fPIC',
'-DCMAKE_Fortran_FLAGS=-fPIC',
'-DEXAMPLES_ENABLE=ON',
'-DEXAMPLES_INSTALL=ON',
'-DFCMIX_ENABLE=ON'
])
# MPI support
if '+mpi' in spec:
cmake_args.extend([
'-DMPI_ENABLE=ON',
'-DMPI_MPICC={0}'.format(spec['mpi'].mpicc),
'-DMPI_MPIF77={0}'.format(spec['mpi'].mpif77)
])
else:
cmake_args.append('-DMPI_ENABLE=OFF')
# Building with LAPACK and BLAS
if '+lapack' in spec:
cmake_args.extend([
'-DLAPACK_ENABLE=ON',
'-DLAPACK_LIBRARIES={0};{1}'.format(
spec['lapack'].lapack_shared_lib,
spec['blas'].blas_shared_lib
)
])
else:
cmake_args.append('-DLAPACK_ENABLE=OFF')
# Building with KLU
if '+klu' in spec:
cmake_args.extend([
'-DKLU_ENABLE=ON',
'-DKLU_INCLUDE_DIR={0}'.format(
spec['suite-sparse'].prefix.include),
'-DKLU_LIBRARY_DIR={0}'.format(
spec['suite-sparse'].prefix.lib)
])
else:
cmake_args.append('-DKLU_ENABLE=OFF')
# Building with SuperLU_MT
if '+superlu' in spec:
cmake_args.extend([
'-DSUPERLUMT_ENABLE=ON',
'-DSUPERLUMT_INCLUDE_DIR={0}'.format(
spec['superlu-mt'].prefix.include),
'-DSUPERLUMT_LIBRARY_DIR={0}'.format(
spec['superlu-mt'].prefix.lib)
])
if '+openmp' in spec:
cmake_args.append('-DSUPERLUMT_THREAD_TYPE=OpenMP')
elif '+pthread' in spec:
cmake_args.append('-DSUPERLUMT_THREAD_TYPE=Pthread')
else:
msg = 'You must choose either +openmp or +pthread when '
msg += 'building with SuperLU_MT'
raise RuntimeError(msg)
else:
cmake_args.append('-DSUPERLUMT_ENABLE=OFF')
# OpenMP support
if '+openmp' in spec:
cmake_args.append('-DOPENMP_ENABLE=ON')
else:
cmake_args.append('-DOPENMP_ENABLE=OFF')
# POSIX threads support
if '+pthread' in spec:
cmake_args.append('-DPTHREAD_ENABLE=ON')
else:
cmake_args.append('-DPTHREAD_ENABLE=OFF')
with working_dir('build', create=True):
cmake('..', *cmake_args)
make()
make('install')
install('LICENSE', prefix)
self.filter_compilers()
def filter_compilers(self):
"""Run after install to tell the Makefiles to use
the compilers that Spack built the package with.
If this isn't done, they'll have CC, CPP, and F77 set to
Spack's generic cc and f77. We want them to be bound to
whatever compiler they were built with."""
kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
dirname = os.path.join(self.prefix, 'examples')
cc_files = [
'arkode/C_serial/Makefile', 'arkode/C_parallel/Makefile',
'cvode/serial/Makefile', 'cvode/parallel/Makefile',
'cvodes/serial/Makefile', 'cvodes/parallel/Makefile',
'ida/serial/Makefile', 'ida/parallel/Makefile',
'idas/serial/Makefile', 'idas/parallel/Makefile',
'kinsol/serial/Makefile', 'kinsol/parallel/Makefile',
'nvector/serial/Makefile', 'nvector/parallel/Makefile',
'nvector/pthreads/Makefile'
]
f77_files = [
'arkode/F77_serial/Makefile', 'cvode/fcmix_serial/Makefile',
'ida/fcmix_serial/Makefile', 'ida/fcmix_pthreads/Makefile',
'kinsol/fcmix_serial/Makefile'
]
for filename in cc_files:
filter_file(os.environ['CC'], self.compiler.cc,
os.path.join(dirname, filename), **kwargs)
for filename in f77_files:
filter_file(os.environ['F77'], self.compiler.f77,
os.path.join(dirname, filename), **kwargs)

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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 *
import glob
import os
class SuperluMt(Package):
"""SuperLU is a general purpose library for the direct solution of large,
sparse, nonsymmetric systems of linear equations on high performance
machines. SuperLU_MT is designed for shared memory parallel machines."""
homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/#superlu_mt"
url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_mt_3.1.tar.gz"
version('3.1', '06ac62f1b4b7d17123fffa0d0c315e91')
variant('blas', default=True, description='Build with external BLAS library')
# Must choose one or the other
variant('openmp', default=False, description='Build with OpenMP support')
variant('pthread', default=True, description='Build with POSIX threads support')
# NOTE: must link with a single-threaded BLAS library
depends_on('blas', when='+blas')
# Cannot be built in parallel
parallel = False
def configure(self, spec):
# Validate chosen variants
if '+openmp' in spec and '+pthread' in spec:
msg = 'You cannot choose both +openmp and +pthread'
raise RuntimeError(msg)
if '~openmp' in spec and '~pthread' in spec:
msg = 'You must choose either +openmp or +pthread'
raise RuntimeError(msg)
# List of configuration options
config = []
# The machine (platform) identifier to append to the library names
if '+openmp' in spec:
# OpenMP
config.extend([
'PLAT = _OPENMP',
'TMGLIB = libtmglib.a',
'MPLIB = {0}'.format(self.compiler.openmp_flag),
'CFLAGS = {0}'.format(self.compiler.openmp_flag),
'FFLAGS = {0}'.format(self.compiler.openmp_flag)
])
elif '+pthread' in spec:
# POSIX threads
config.extend([
'PLAT = _PTHREAD',
'TMGLIB = libtmglib$(PLAT).a',
'MPLIB = -lpthread'
])
# The BLAS library
# NOTE: must link with a single-threaded BLAS library
if '+blas' in spec:
config.extend([
'BLASDEF = -DUSE_VENDOR_BLAS',
'BLASLIB = -L{0} -lblas'.format(spec['blas'].prefix.lib)
])
else:
config.append('BLASLIB = ../lib/libblas$(PLAT).a')
# Generic options
config.extend([
# The name of the libraries to be created/linked to
'SUPERLULIB = libsuperlu_mt$(PLAT).a',
'MATHLIB = -lm',
# The archiver and the flag(s) to use when building archives
'ARCH = ar',
'ARCHFLAGS = cr',
'RANLIB = {0}'.format('ranlib' if which('ranlib') else 'echo'),
# Definitions used by CPP
'PREDEFS = -D_$(PLAT)',
# Compilers and flags
'CC = {0}'.format(os.environ['CC']),
'CFLAGS += $(PREDEFS) -D_LONGINT',
'NOOPTS = -O0',
'FORTRAN = {0}'.format(os.environ['FC']),
'LOADER = {0}'.format(os.environ['CC']),
# C preprocessor defs for compilation
'CDEFS = -DAdd_'
])
# Write configuration options to include file
with open('make.inc', 'w') as inc:
for option in config:
inc.write('{0}\n'.format(option))
def install(self, spec, prefix):
# Set up make include file manually
self.configure(spec)
# BLAS needs to be compiled separately if using internal BLAS library
if '+blas' not in spec:
make('blaslib')
make()
# Install manually
install_tree('lib', prefix.lib)
headers = glob.glob(join_path('SRC', '*.h'))
mkdir(prefix.include)
for h in headers:
install(h, prefix.include)