# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import os
import shutil
class Mfem(Package):
"""Free, lightweight, scalable C++ library for finite element methods."""
tags = ['FEM', 'finite elements', 'high-order', 'AMR', 'HPC']
homepage = 'http://www.mfem.org'
git = 'https://github.com/mfem/mfem.git'
maintainers = ['goxberry', 'tzanio', 'markcmiller86', 'acfisher',
'v-dobrev']
# Recommended mfem builds to test when updating this file: see the shell
# script 'test_builds.sh' in the same directory as this file.
# mfem is downloaded from a URL shortener at request of upstream
# author Tzanio Kolev <tzanio@llnl.gov>. See here:
# https://github.com/mfem/mfem/issues/53
#
# The following procedure should be used to verify security when a
# new version is added:
#
# 1. Verify that no checksums on old versions have changed.
#
# 2. Verify that the shortened URL for the new version is listed at:
# http://mfem.org/download/
#
# 3. Use http://getlinkinfo.com or similar to verify that the
# underling download link for the latest version comes has the
# prefix: http://mfem.github.io/releases
#
# If this quick verification procedure fails, additional discussion
# will be required to verify the new version.
# 'develop' is a special version that is always larger (or newer) than any
# other version.
version('develop', branch='master')
# Tagged development version used by the laghos package:
version('3.4.1-laghos-v2.0', tag='laghos-v2.0')
version('3.4.0',
'4e73e4fe0482636de3c5dc983cd395839a83cb16f6f509bd88b053e8b3858e05',
url='https://bit.ly/mfem-3-4', extension='.tar.gz',
preferred=True)
version('3.3.2',
'b70fa3c5080b9ec514fc05f4a04ff74322b99ac4ecd6d99c229f0ed5188fc0ce',
url='https://goo.gl/Kd7Jk8', extension='.tar.gz')
# Tagged development version used by the laghos package:
version('3.3.1-laghos-v1.0', tag='laghos-v1.0')
version('3.3',
'b17bd452593aada93dc0fee748fcfbbf4f04ce3e7d77fdd0341cc9103bcacd0b',
url='http://goo.gl/Vrpsns', extension='.tar.gz')
version('3.2',
'2938c3deed4ec4f7fd5b5f5cfe656845282e86e2dcd477d292390058b7b94340',
url='http://goo.gl/Y9T75B', extension='.tar.gz')
version('3.1',
'841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57',
url='http://goo.gl/xrScXn', extension='.tar.gz')
variant('static', default=True,
description='Build static library')
variant('shared', default=False,
description='Build shared library')
variant('mpi', default=True,
description='Enable MPI parallelism')
# Can we make the default value for 'metis' to depend on the 'mpi' value?
variant('metis', default=True,
description='Enable METIS support')
# TODO: The 'hypre' variant is the same as 'mpi', we may want to remove it.
# For now, keep the 'hypre' variant while ignoring its setting. This
# is done to preserve compatibility with other packages that refer to
# it, e.g. xSDK.
variant('hypre', default=True,
description='Required for MPI parallelism')
variant('openmp', default=False,
description='Enable OpenMP parallelism')
variant('threadsafe', default=False,
description=('Enable thread safe features.'
' Required for OpenMP.'
' May cause minor performance issues.'))
variant('superlu-dist', default=False,
description='Enable MPI parallel, sparse direct solvers')
# Placeholder for STRUMPACK, support added in mfem v3.3.2:
# variant('strumpack', default=False,
# description='Enable support for STRUMPACK')
variant('suite-sparse', default=False,
description='Enable serial, sparse direct solvers')
variant('petsc', default=False,
description='Enable PETSc solvers, preconditioners, etc.')
variant('sundials', default=False,
description='Enable Sundials time integrators')
variant('pumi', default=False,
description='Enable functionality based on PUMI')
variant('mpfr', default=False,
description='Enable precise, 1D quadrature rules')
variant('lapack', default=False,
description='Use external blas/lapack routines')
variant('debug', default=False,
description='Build debug instead of optimized version')
variant('netcdf', default=False,
description='Enable Cubit/Genesis reader')
variant('conduit', default=False,
description='Enable binary data I/O using Conduit')
variant('gzstream', default=True,
description='Support zip\'d streams for I/O')
variant('gnutls', default=False,
description='Enable secure sockets using GnuTLS')
variant('libunwind', default=False,
description='Enable backtrace on error support using Libunwind')
variant('timer', default='auto',
values=('auto', 'std', 'posix', 'mac', 'mpi'),
description='Timing functions to use in mfem::StopWatch')
variant('examples', default=False,
description='Build and install examples')
variant('miniapps', default=False,
description='Build and install miniapps')
conflicts('+shared', when='@:3.3.2')
conflicts('~static~shared')
conflicts('~threadsafe', when='+openmp')
conflicts('+netcdf', when='@:3.1')
conflicts('+superlu-dist', when='@:3.1')
conflicts('+gnutls', when='@:3.1')
conflicts('+gzstream', when='@:3.2')
conflicts('+mpfr', when='@:3.2')
conflicts('+petsc', when='@:3.2')
conflicts('+sundials', when='@:3.2')
conflicts('+pumi', when='@:3.3.2')
conflicts('timer=mac', when='@:3.3.0')
conflicts('timer=mpi', when='@:3.3.0')
conflicts('~metis+mpi', when='@:3.3.0')
conflicts('+metis~mpi', when='@:3.3.0')
conflicts('+conduit', when='@:3.3.2')
conflicts('+superlu-dist', when='~mpi')
conflicts('+petsc', when='~mpi')
conflicts('+pumi', when='~mpi')
conflicts('timer=mpi', when='~mpi')
conflicts('+pumi', when='+shared')
depends_on('mpi', when='+mpi')
depends_on('hypre@2.10.0:2.13.999', when='@:3.3.999+mpi')
depends_on('hypre', when='@3.4:+mpi')
depends_on('metis', when='+metis')
depends_on('blas', when='+lapack')
depends_on('lapack', when='+lapack')
depends_on('sundials@2.7.0', when='@:3.3.0+sundials~mpi')
depends_on('sundials@2.7.0+mpi+hypre', when='@:3.3.0+sundials+mpi')
depends_on('sundials@2.7.0:', when='@3.3.2:+sundials~mpi')
depends_on('sundials@2.7.0:+mpi+hypre', when='@3.3.2:+sundials+mpi')
depends_on('pumi', when='+pumi')
depends_on('suite-sparse', when='+suite-sparse')
depends_on('superlu-dist', when='+superlu-dist')
# The PETSc tests in MFEM will fail if PETSc is not configured with
# SuiteSparse and MUMPS. On the other hand, if we require the variants
# '+suite-sparse+mumps' of PETSc, the xsdk package concretization fails.
depends_on('petsc@3.8:+mpi+double+hypre', when='+petsc')
# Recommended when building outside of xsdk:
# depends_on('petsc@3.8:+mpi+double+hypre+suite-sparse+mumps',
# when='+petsc')
depends_on('mpfr', when='+mpfr')
depends_on('netcdf', when='+netcdf')
depends_on('unwind', when='+libunwind')
depends_on('zlib', when='+gzstream')
depends_on('gnutls', when='+gnutls')
depends_on('conduit@0.3.1:,master:', when='+conduit')
depends_on('conduit+mpi', when='+conduit+mpi')
patch('mfem_ppc_build.patch', when='@3.2:3.3.0 arch=ppc64le')
patch('mfem-3.4.patch', when='@3.4.0')
patch('mfem-3.3-3.4-petsc-3.9.patch',
when='@3.3.0:3.4.0 +petsc ^petsc@3.9.0:')
phases = ['configure', 'build', 'install']
def setup_environment(self, spack_env, run_env):
spack_env.unset('MFEM_DIR')
spack_env.unset('MFEM_BUILD_DIR')
#
# Note: Although MFEM does support CMake configuration, MFEM
# development team indicates that vanilla GNU Make is the
# preferred mode of configuration of MFEM and the mode most
# likely to be up to date in supporting *all* of MFEM's
# configuration options. So, don't use CMake
#
def configure(self, spec, prefix):
def yes_no(varstr):
return 'YES' if varstr in self.spec else 'NO'
# We need to add rpaths explicitly to allow proper export of link flags
# from within MFEM.
# Similar to spec[pkg].libs.ld_flags but prepends rpath flags too.
def ld_flags_from_library_list(libs_list):
flags = ['-Wl,-rpath,%s' % dir for dir in libs_list.directories]
flags += [libs_list.ld_flags]
return ' '.join(flags)
def ld_flags_from_dirs(pkg_dirs_list, pkg_libs_list):
flags = ['-Wl,-rpath,%s' % dir for dir in pkg_dirs_list]
flags += ['-L%s' % dir for dir in pkg_dirs_list]
flags += ['-l%s' % lib for lib in pkg_libs_list]
return ' '.join(flags)
def find_optional_library(name, prefix):
for shared in [True, False]:
for path in ['lib64', 'lib']:
lib = find_libraries(name, join_path(prefix, path),
shared=shared, recursive=False)
if lib:
return lib
return LibraryList([])
metis5_str = 'NO'
if ('+metis' in spec) and spec['metis'].satisfies('@5:'):
metis5_str = 'YES'
options = [
'PREFIX=%s' % prefix,
'MFEM_USE_MEMALLOC=YES',
'MFEM_DEBUG=%s' % yes_no('+debug'),
# NOTE: env['CXX'] is the spack c++ compiler wrapper. The real
# compiler is defined by env['SPACK_CXX'].
'CXX=%s' % env['CXX'],
'MFEM_USE_LIBUNWIND=%s' % yes_no('+libunwind'),
'MFEM_USE_GZSTREAM=%s' % yes_no('+gzstream'),
'MFEM_USE_METIS=%s' % yes_no('+metis'),
'MFEM_USE_METIS_5=%s' % metis5_str,
'MFEM_THREAD_SAFE=%s' % yes_no('+threadsafe'),
'MFEM_USE_MPI=%s' % yes_no('+mpi'),
'MFEM_USE_LAPACK=%s' % yes_no('+lapack'),
'MFEM_USE_SUPERLU=%s' % yes_no('+superlu-dist'),
'MFEM_USE_SUITESPARSE=%s' % yes_no('+suite-sparse'),
'MFEM_USE_SUNDIALS=%s' % yes_no('+sundials'),
'MFEM_USE_PETSC=%s' % yes_no('+petsc'),
'MFEM_USE_PUMI=%s' % yes_no('+pumi'),
'MFEM_USE_NETCDF=%s' % yes_no('+netcdf'),
'MFEM_USE_MPFR=%s' % yes_no('+mpfr'),
'MFEM_USE_GNUTLS=%s' % yes_no('+gnutls'),
'MFEM_USE_OPENMP=%s' % yes_no('+openmp'),
'MFEM_USE_CONDUIT=%s' % yes_no('+conduit')]
cxxflags = spec.compiler_flags['cxxflags']
if cxxflags:
# The cxxflags are set by the spack c++ compiler wrapper. We also
# set CXXFLAGS explicitly, for clarity, and to properly export the
# cxxflags in the variable MFEM_CXXFLAGS in config.mk.
options += ['CXXFLAGS=%s' % ' '.join(cxxflags)]
if '~static' in spec:
options += ['STATIC=NO']
if '+shared' in spec:
options += ['SHARED=YES', 'PICFLAG=%s' % self.compiler.pic_flag]
if '+mpi' in spec:
options += ['MPICXX=%s' % spec['mpi'].mpicxx]
hypre = spec['hypre']
# The hypre package always links with 'blas' and 'lapack'.
all_hypre_libs = hypre.libs + hypre['lapack'].libs + \
hypre['blas'].libs
options += [
'HYPRE_OPT=-I%s' % hypre.prefix.include,
'HYPRE_LIB=%s' % ld_flags_from_library_list(all_hypre_libs)]
if '+metis' in spec:
options += [
'METIS_OPT=-I%s' % spec['metis'].prefix.include,
'METIS_LIB=%s' %
ld_flags_from_dirs([spec['metis'].prefix.lib], ['metis'])]
if '+lapack' in spec:
lapack_blas = spec['lapack'].libs + spec['blas'].libs
options += [
# LAPACK_OPT is not used
'LAPACK_LIB=%s' % ld_flags_from_library_list(lapack_blas)]
if '+superlu-dist' in spec:
lapack_blas = spec['lapack'].libs + spec['blas'].libs
options += [
'SUPERLU_OPT=-I%s -I%s' %
(spec['superlu-dist'].prefix.include,
spec['parmetis'].prefix.include),
'SUPERLU_LIB=-L%s -L%s -lsuperlu_dist -lparmetis %s' %
(spec['superlu-dist'].prefix.lib,
spec['parmetis'].prefix.lib,
ld_flags_from_library_list(lapack_blas))]
if '+suite-sparse' in spec:
ss_spec = 'suite-sparse:' + self.suitesparse_components
options += [
'SUITESPARSE_OPT=-I%s' % spec[ss_spec].prefix.include,
'SUITESPARSE_LIB=%s' %
ld_flags_from_library_list(spec[ss_spec].libs)]
if '+sundials' in spec:
sun_spec = 'sundials:' + self.sundials_components
options += [
'SUNDIALS_OPT=%s' % spec[sun_spec].headers.cpp_flags,
'SUNDIALS_LIB=%s' %
ld_flags_from_library_list(spec[sun_spec].libs)]
if '+petsc' in spec:
# options += ['PETSC_DIR=%s' % spec['petsc'].prefix]
options += [
'PETSC_OPT=%s' % spec['petsc'].headers.cpp_flags,
'PETSC_LIB=%s' %
ld_flags_from_library_list(spec['petsc'].libs)]
if '+pumi' in spec:
options += ['PUMI_DIR=%s' % spec['pumi'].prefix]
if '+netcdf' in spec:
options += [
'NETCDF_OPT=-I%s' % spec['netcdf'].prefix.include,
'NETCDF_LIB=%s' %
ld_flags_from_dirs([spec['netcdf'].prefix.lib], ['netcdf'])]
if '+gzstream' in spec:
if "@:3.3.2" in spec:
options += ['ZLIB_DIR=%s' % spec['zlib'].prefix]
else:
options += [
'ZLIB_OPT=-I%s' % spec['zlib'].prefix.include,
'ZLIB_LIB=%s' %
ld_flags_from_library_list(spec['zlib'].libs)]
if '+mpfr' in spec:
options += [
'MPFR_OPT=-I%s' % spec['mpfr'].prefix.include,
'MPFR_LIB=%s' %
ld_flags_from_dirs([spec['mpfr'].prefix.lib], ['mpfr'])]
if '+gnutls' in spec:
options += [
'GNUTLS_OPT=-I%s' % spec['gnutls'].prefix.include,
'GNUTLS_LIB=%s' %
ld_flags_from_dirs([spec['gnutls'].prefix.lib], ['gnutls'])]
if '+libunwind' in spec:
libunwind = spec['unwind']
headers = find_headers('libunwind', libunwind.prefix.include)
headers.add_macro('-g')
libs = find_optional_library('libunwind', libunwind.prefix)
# When mfem uses libunwind, it also needs 'libdl'.
libs += LibraryList(find_system_libraries('libdl'))
options += [
'LIBUNWIND_OPT=%s' % headers.cpp_flags,
'LIBUNWIND_LIB=%s' % ld_flags_from_library_list(libs)]
if '+openmp' in spec:
options += ['OPENMP_OPT=%s' % self.compiler.openmp_flag]
timer_ids = {'std': '0', 'posix': '2', 'mac': '4', 'mpi': '6'}
timer = spec.variants['timer'].value
if timer != 'auto':
options += ['MFEM_TIMER_TYPE=%s' % timer_ids[timer]]
if '+conduit' in spec:
conduit = spec['conduit']
headers = HeaderList(find(conduit.prefix.include, 'conduit.hpp',
recursive=True))
conduit_libs = ['libconduit', 'libconduit_relay',
'libconduit_blueprint']
libs = find_libraries(conduit_libs, conduit.prefix.lib,
shared=('+shared' in conduit))
libs += LibraryList(find_system_libraries('libdl'))
if '+hdf5' in conduit:
hdf5 = conduit['hdf5']
headers += find_headers('hdf5', hdf5.prefix.include)
libs += hdf5.libs
options += [
'CONDUIT_OPT=%s' % headers.cpp_flags,
'CONDUIT_LIB=%s' % ld_flags_from_library_list(libs)]
make('config', *options, parallel=False)
make('info', parallel=False)
def build(self, spec, prefix):
make('lib')
@run_after('build')
def check_or_test(self):
# Running 'make check' or 'make test' may fail if MFEM_MPIEXEC or
# MFEM_MPIEXEC_NP are not set appropriately.
if not self.run_tests:
# check we can build ex1 (~mpi) or ex1p (+mpi).
make('-C', 'examples', 'ex1p' if ('+mpi' in self.spec) else 'ex1',
parallel=False)
# make('check', parallel=False)
else:
make('all')
make('test', parallel=False)
def install(self, spec, prefix):
make('install', parallel=False)
# TODO: The way the examples and miniapps are being installed is not
# perfect. For example, the makefiles do not work.
install_em = ('+examples' in spec) or ('+miniapps' in spec)
if install_em and ('+shared' in spec):
make('examples/clean', 'miniapps/clean')
# This is a hack to get the examples and miniapps to link with the
# installed shared mfem library:
with working_dir('config'):
os.rename('config.mk', 'config.mk.orig')
copy(str(self.config_mk), 'config.mk')
shutil.copystat('config.mk.orig', 'config.mk')
prefix_share = join_path(prefix, 'share', 'mfem')
if '+examples' in spec:
make('examples')
install_tree('examples', join_path(prefix_share, 'examples'))
if '+miniapps' in spec:
make('miniapps')
install_tree('miniapps', join_path(prefix_share, 'miniapps'))
if install_em:
install_tree('data', join_path(prefix_share, 'data'))
@property
def suitesparse_components(self):
"""Return the SuiteSparse components needed by MFEM."""
ss_comps = 'umfpack,cholmod,colamd,amd,camd,ccolamd,suitesparseconfig'
if self.spec.satisfies('@3.2:'):
ss_comps = 'klu,btf,' + ss_comps
return ss_comps
@property
def sundials_components(self):
"""Return the SUNDIALS components needed by MFEM."""
sun_comps = 'arkode,cvode,nvecserial,kinsol'
if '+mpi' in self.spec:
sun_comps += ',nvecparhyp,nvecparallel'
return sun_comps
@property
def headers(self):
"""Export the main mfem header, mfem.hpp.
"""
hdrs = HeaderList(find(self.prefix.include, 'mfem.hpp',
recursive=False))
return hdrs or None
@property
def libs(self):
"""Export the mfem library file.
"""
libs = find_libraries('libmfem', root=self.prefix.lib,
shared=('+shared' in self.spec), recursive=False)
return libs or None
@property
def config_mk(self):
"""Export the location of the config.mk file.
This property can be accessed using spec['mfem'].package.config_mk
"""
dirs = [self.prefix, self.prefix.share.mfem]
for d in dirs:
f = join_path(d, 'config.mk')
if os.access(f, os.R_OK):
return FileList(f)
return FileList(find(self.prefix, 'config.mk', recursive=True))
@property
def test_mk(self):
"""Export the location of the test.mk file.
This property can be accessed using spec['mfem'].package.test_mk.
In version 3.3.2 and newer, the location of test.mk is also defined
inside config.mk, variable MFEM_TEST_MK.
"""
dirs = [self.prefix, self.prefix.share.mfem]
for d in dirs:
f = join_path(d, 'test.mk')
if os.access(f, os.R_OK):
return FileList(f)
return FileList(find(self.prefix, 'test.mk', recursive=True))