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Lafnetscha/foam extend (#35)
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* First try at OpenFOAM-extend

* limiting package to foam-extend to start

* Ignoring the flake8 error for a line too long

* First try at OpenFOAM-extend

* limiting package to foam-extend to start

* Removing extra dependencies + minor fix according to remarks on spack#1002

* removing useless selfs

* changes to use from_sourcing_file

* correcting flake8

* Changes for flex 2.6.0 and intel mpi

* correction for paraview paths
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@nrichart @alalazo
nrichart authored and alalazo committed Sep 30, 2016
1 parent baf5eca commit 92311e8
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254 changes: 254 additions & 0 deletions var/spack/repos/builtin/packages/foam-extend/package.py
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from spack import *
from spack.environment import *

import multiprocessing
import os


class FoamExtend(Package):
"""The foam-extend project is a fork of the OpenFOAM open source library
for Computational Fluid Dynamics (CFD)."""

homepage = "http://www.extend-project.de/"

version('3.2', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.2')
version('3.1', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.1')
version('3.0', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.0')

variant('paraview', default=False, description='Enable ParaFOAM')
variant('scotch', default=True, description='Activate Scotch as a possible decomposition library')
variant('ptscotch', default=True, description='Activate PT-Scotch as a possible decomposition library')
variant('metis', default=True, description='Activate Metis as a possible decomposition library')
variant('parmetis', default=True, description='Activate Parmetis as a possible decomposition library')
variant('parmgridgen', default=True, description='Activate Parmgridgen support')
variant('source', default=True, description='Installs also the source folder')

supported_compilers = {'clang': 'Clang', 'gcc': 'Gcc', 'intel': 'Icc'}

depends_on('mpi')
depends_on('python')
#depends_on('flex@:2.5.99')
depends_on('flex')
depends_on('zlib')

depends_on('scotch ~ metis', when='~ptscotch+scotch')
depends_on('scotch ~ metis + mpi', when='+ptscotch')
depends_on('metis@5:', when='+metis')
depends_on('parmetis', when='+parmetis')
depends_on('parmgridgen', when='+parmgridgen')

depends_on('paraview', when='+paraview')

def set_arch(self):
(sysname, nodename, release, version, machine) = os.uname()

if self.compiler.name not in self.supported_compilers:
raise RuntimeError('{0} is not a supported compiler \
to compile OpenFOAM'.format(self.compiler.name))

foam_compiler = self.supported_compilers[self.compiler.name]
if sysname == 'Linux':
arch = 'linux'
if foam_compiler == 'Clang':
raise RuntimeError('OS, compiler combination not\
supported ({0} {1})'.format(sysname, foam_compiler))
elif sysname == 'Darwin':
if machine == 'x86_64':
arch = 'darwinIntel'
if foam_compiler == 'Icc':
raise RuntimeError('OS, compiler combination not\
supported ({0} {1})'.format(sysname, foam_compiler))
else:
raise RuntimeError('{0} {1} is not a \
supported architecture'.format(sysname, machine))

return (arch, foam_compiler)

def get_openfoam_environment(self):
return EnvironmentModifications.from_sourcing_files(
join_path(self.stage.source_path,
'etc/bashrc'))

def patch(self):
# change names to match the package and not the one patch in
# the Third-Party of foam-extend
if '+parmgridgen' in self.spec:
filter_file(r'-lMGridGen',
r'-lmgrid',
'src/dbns/Make/options')
filter_file(r'-lMGridGen',
r'-lmgrid',
'src/fvAgglomerationMethods/MGridGenGamgAgglomeration/Make/options')

# Get the wmake arch and compiler
(arch, foam_compiler) = self.set_arch()

prefs_dict = {
'compilerInstall': 'System',
'WM_COMPILER': foam_compiler,
'WM_ARCH_OPTION': '64',
'WM_PRECISION_OPTION': 'DP',
'WM_COMPILE_OPTION': 'SPACKOpt',
'WM_MPLIB': 'SPACK',

'CMAKE_DIR': self.spec['cmake'].prefix,
'CMAKE_BIN_DIR': self.spec['cmake'].prefix.bin,
'PYTHON_DIR': self.spec['python'].prefix,
'PYTHON_BIN_DIR': self.spec['python'].prefix.bin,

'FLEX_SYSTEM': 1,
'FLEX_DIR': self.spec['flex'].prefix,

'BISON_SYSTEM': 1,
'BISON_DIR': self.spec['flex'].prefix,

'ZLIB_SYSTEM': 1,
'ZLIB_DIR': self.spec['zlib'].prefix,
}

if '+scotch' in self.spec or '+ptscotch' in self.spec:
prefs_dict['SCOTCH_SYSTEM'] = 1
prefs_dict['SCOTCH_DIR'] = self.spec['scotch'].prefix
prefs_dict['SCOTCH_BIN_DIR'] = self.spec['scotch'].prefix.bin
prefs_dict['SCOTCH_LIB_DIR'] = self.spec['scotch'].prefix.lib
prefs_dict['SCOTCH_INCLUDE_DIR'] = \
self.spec['scotch'].prefix.include

if '+metis' in self.spec:
prefs_dict['METIS_SYSTEM'] = 1
prefs_dict['METIS_DIR'] = self.spec['metis'].prefix
prefs_dict['METIS_BIN_DIR'] = self.spec['metis'].prefix.bin
prefs_dict['METIS_LIB_DIR'] = self.spec['metis'].prefix.lib
prefs_dict['METIS_INCLUDE_DIR'] = self.spec['metis'].prefix.include

if '+parmetis' in self.spec:
prefs_dict['PARMETIS_SYSTEM'] = 1
prefs_dict['PARMETIS_DIR'] = self.spec['parmetis'].prefix
prefs_dict['PARMETIS_BIN_DIR'] = self.spec['parmetis'].prefix.bin
prefs_dict['PARMETIS_LIB_DIR'] = self.spec['parmetis'].prefix.lib
prefs_dict['PARMETIS_INCLUDE_DIR'] = \
self.spec['parmetis'].prefix.include

if '+parmgridgen' in self.spec:
prefs_dict['PARMGRIDGEN_SYSTEM'] = 1
prefs_dict['PARMGRIDGEN_DIR'] = self.spec['parmgridgen'].prefix
prefs_dict['PARMGRIDGEN_BIN_DIR'] = \
self.spec['parmgridgen'].prefix.bin
prefs_dict['PARMGRIDGEN_LIB_DIR'] = \
self.spec['parmgridgen'].prefix.lib
prefs_dict['PARMGRIDGEN_INCLUDE_DIR'] = \
self.spec['parmgridgen'].prefix.include

if '+paraview' in self.spec:
prefs_dict['PARAVIEW_SYSTEM'] = 1
prefs_dict['PARAVIEW_DIR'] = self.spec['paraview'].prefix
prefs_dict['PARAVIEW_BIN_DIR'] = self.spec['paraview'].prefix.bin
prefs_dict['QT_SYSTEM'] = 1
prefs_dict['QT_DIR'] = self.spec['qt'].prefix
prefs_dict['QT_BIN_DIR'] = self.spec['qt'].prefix.bin

# write the prefs files to define the configuration needed,
# only the prefs.sh is used by this script but both are
# installed for end users
with working_dir('.'):
with open("etc/prefs.sh", "w") as fh:
for key in sorted(prefs_dict):
fh.write('export {0}={1}\n'.format(key, prefs_dict[key]))

with open("etc/prefs.csh", "w") as fh:
for key in sorted(prefs_dict):
fh.write('setenv {0}={1}\n'.format(key, prefs_dict[key]))

# Defining a different mpi and optimisation file to be able to
# make wmake get spack info with minimum modifications on
# configurations scripts
if 'intelmpi' in self.spec:
mpi_info = [
'PFLAGS = -DMPICH_IGNORE_CXX_SEEK',
'PINC = -I{0}'.format(join_path(self.spec['mpi'].prefix,'include64')),
'PLIBS = -L{0} -lmpi'.format(self.spec['mpi'].prefix.lib64)
]
else:
mpi_info = [
'PFLAGS = -DOMPI_SKIP_MPICXX -DMPICH_IGNORE_CXX_SEEK',
'PINC = -I{0}'.format(self.spec['mpi'].prefix.include),
'PLIBS = -L{0} -lmpi'.format(self.spec['mpi'].prefix.lib)
]

arch_path = ''.join([arch, prefs_dict['WM_ARCH_OPTION'],
foam_compiler])
option_path = ''.join([arch_path,
prefs_dict['WM_PRECISION_OPTION'],
prefs_dict['WM_COMPILE_OPTION']])
rule_path = join_path("wmake", "rules", arch_path)
build_path = join_path(self.stage.source_path, 'lib', option_path)
install_path = \
join_path(self.prefix,
'foam-extend-{0}'.format(self.version.up_to(2)),
option_path)

rpaths_foam = ' '.join([
'{0}{1}'.format(self.compiler.cxx_rpath_arg,
install_path),
'{0}{1}'.format(self.compiler.cxx_rpath_arg,
build_path)
])

compiler_flags = {
'DBUG': rpaths_foam,
'OPT': '-O3',
}

with working_dir(rule_path):
with open('mplibSPACK', "w") as fh:
fh.write('\n'.join(mpi_info))

for comp in ['c', 'c++']:
with open('{0}SPACKOpt'.format(comp), "w") as fh:
for key, val in compiler_flags.iteritems():
fh.write('{0}{1} = {2}\n'.format(comp, key, val))

for _file in ['src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinLexer.L',
'src/surfMesh/surfaceFormats/stl/STLsurfaceFormatASCII.L',
'src/meshTools/triSurface/triSurface/interfaces/STL/readSTLASCII.L',
'applications/utilities/preProcessing/fluentDataToFoam/fluentDataToFoam.L',
'applications/utilities/mesh/conversion/gambitToFoam/gambitToFoam.L',
'applications/utilities/mesh/conversion/fluent3DMeshToFoam/fluent3DMeshToFoam.L',
'applications/utilities/mesh/conversion/ansysToFoam/ansysToFoam.L',
'applications/utilities/mesh/conversion/fluentMeshToFoam/fluentMeshToFoam.L',
'applications/utilities/mesh/conversion/fluent3DMeshToElmer/fluent3DMeshToElmer.L']:
filter_file(r'#if YY_FLEX_SUBMINOR_VERSION < 34',
r'#if YY_FLEX_MAJOR_VERSION <= 2 && YY_FLEX_MINOR_VERSION <= 5 && YY_FLEX_SUBMINOR_VERSION < 34',
_file)

def setup_environment(self, spack_env, run_env):
with working_dir(self.stage.path):
spack_env.set('FOAM_INST_DIR', os.path.abspath('.'))

(arch, foam_compiler) = self.set_arch()

run_env.set('FOAM_INST_DIR', self.prefix)

def install(self, spec, prefix):
env_openfoam = self.get_openfoam_environment()
env_openfoam.apply_modifications()

if self.parallel:
os.environ['WM_NCOMPPROCS'] = str(self.make_jobs) \
if self.make_jobs else str(multiprocessing.cpu_count())

allwmake = Executable('./Allwmake')
allwmake()

install_path = \
join_path(self.prefix,
'foam-extend-{0}'.format(self.version.up_to(2)))

if '+source' in spec:
install_tree('src', join_path(install_path, 'src'))

install_tree('lib', join_path(install_path, 'lib'))
install_tree('bin', join_path(install_path, 'bin'))
install_tree('applications', join_path(install_path, 'applications'))
install_tree('etc', join_path(install_path, 'etc'))
install_tree('wmake', join_path(install_path, 'wmake'))
71 changes: 71 additions & 0 deletions var/spack/repos/builtin/packages/parmgridgen/package.py
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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 Parmgridgen(Package):
"""MGRIDGEN is a serial library written entirely in ANSI C that implements
(serial) algorithms for obtaining a sequence of successive coarse grids
that are well-suited for geometric multigrid methods.
ParMGridGen is the parallel version of MGridGen
"""

homepage = "http://www-users.cs.umn.edu/~moulitsa/software.html"
url = "http://www-users.cs.umn.edu/~moulitsa/download/ParMGridGen-1.0.tar.gz"

version('1.0', '2872fa95b7fb91d6bd525490eed62038')

depends_on('mpi')

def install(self, spec, prefix):
make_opts = [
'make=make',
'COPTIONS=-fPIC',
'LDOPTIONS=-fPIC',
'CC={0}'.format(self.compiler.cc),
'PARCC={0}'.format(spec['mpi'].mpicc),
'LD={0}'.format(self.compiler.cc),
'PARLD={0}'.format(spec['mpi'].mpicc),
'LIBDIR=-L../..',
'PARLIBS=-L../../ -lparmgrid -lmgrid -lm',
'LIBS=-L../../ -lmgrid -lm',
'parallel'
]

make(*make_opts, parallel=False)

mkdirp(prefix.include, prefix.lib, prefix.bin)

install("mgridgen.h", prefix.include)
install("parmgridgen.h", prefix.include)

install("MGridGen/IMlib/libIMlib.a",
join_path(prefix.lib, 'libIMlib.a'))
install("libmgrid.a", prefix.lib)
install("libparmgrid.a", prefix.lib)

install("mgridgen", prefix.bin)
install("parmgridgen", prefix.bin)
12 changes: 5 additions & 7 deletions var/spack/repos/builtin/packages/scotch/package.py
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Expand Up @@ -171,24 +171,22 @@ def install(self, spec, prefix):
target == 'ptscotch'))
make(target, parallel=can_make_parallel)

# todo change this to take into account darwin systems
lib_ext = '.so' if '+shared' in self.spec else '.a'
lib_ext = dso_suffix if '+shared' in self.spec else 'a'
# It seams easier to remove metis wrappers from the folder that will be
# installed than to tweak the Makefiles
if '+metis' not in self.spec:
with working_dir('lib'):
lib_ext = '.so' if '+shared' in self.spec else '.a'
force_remove('libscotchmetis{0}'.format(lib_ext))
force_remove('libptscotchparmetis{0}'.format(lib_ext))
force_remove('libscotchmetis.{0}'.format(lib_ext))
force_remove('libptscotchparmetis.{0}'.format(lib_ext))

with working_dir('include'):
force_remove('metis.h')
force_remove('parmetis.h')

if '~esmumps' in self.spec and self.spec.version < Version('6.0.0'):
with working_dir('lib'):
force_remove('libesmumps{0}'.format(lib_ext))
force_remove('libptesmumps{0}'.format(lib_ext))
force_remove('libesmumps.{0}'.format(lib_ext))
force_remove('libptesmumps.{0}'.format(lib_ext))

with working_dir('include'):
force_remove('esmumps.h')
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