diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/mfem')
4 files changed, 525 insertions, 139 deletions
diff --git a/var/spack/repos/builtin/packages/mfem/mfem-3.3-3.4-petsc-3.9.patch b/var/spack/repos/builtin/packages/mfem/mfem-3.3-3.4-petsc-3.9.patch new file mode 100644 index 0000000000..dcf4870a25 --- /dev/null +++ b/var/spack/repos/builtin/packages/mfem/mfem-3.3-3.4-petsc-3.9.patch @@ -0,0 +1,71 @@ +diff --git a/examples/petsc/rc_ex3p b/examples/petsc/rc_ex3p +index 2cbe07ef2..c585d9b52 100644 +--- a/examples/petsc/rc_ex3p ++++ b/examples/petsc/rc_ex3p +@@ -6,4 +6,4 @@ + # it needs PETSc configured with MUMPS + + -solver_pc_type cholesky +--solver_pc_factor_mat_solver_package mumps ++-solver_pc_factor_mat_solver_type mumps +diff --git a/examples/petsc/rc_ex3p_bddc b/examples/petsc/rc_ex3p_bddc +index ea887bb29..2e1eba0d5 100644 +--- a/examples/petsc/rc_ex3p_bddc ++++ b/examples/petsc/rc_ex3p_bddc +@@ -16,7 +16,7 @@ + #-pc_bddc_adaptive_threshold 10 + + # Customization of the local solvers +-#-pc_bddc_neumann_pc_factor_mat_solver_package mumps +-#-pc_bddc_dirichlet_pc_factor_mat_solver_package mumps ++#-pc_bddc_neumann_pc_factor_mat_solver_type mumps ++#-pc_bddc_dirichlet_pc_factor_mat_solver_type mumps + #-pc_bddc_coarse_pc_type cholesky +-#-pc_bddc_coarse_pc_factor_mat_solver_package mumps ++#-pc_bddc_coarse_pc_factor_mat_solver_type mumps +diff --git a/examples/petsc/rc_ex4p b/examples/petsc/rc_ex4p +index f734f35fe..64fbe9427 100644 +--- a/examples/petsc/rc_ex4p ++++ b/examples/petsc/rc_ex4p +@@ -2,4 +2,4 @@ + # it needs PETSc configured with MUMPS + + -solver_pc_type cholesky +--solver_pc_factor_mat_solver_package mumps ++-solver_pc_factor_mat_solver_type mumps +diff --git a/examples/petsc/rc_ex4p_bddc b/examples/petsc/rc_ex4p_bddc +index 9507ad431..e8ef99db7 100644 +--- a/examples/petsc/rc_ex4p_bddc ++++ b/examples/petsc/rc_ex4p_bddc +@@ -13,7 +13,7 @@ + #-pc_bddc_adaptive_threshold 10 + + # Customization of the local solvers +-#-pc_bddc_neumann_pc_factor_mat_solver_package mumps +-#-pc_bddc_dirichlet_pc_factor_mat_solver_package mumps ++#-pc_bddc_neumann_pc_factor_mat_solver_type mumps ++#-pc_bddc_dirichlet_pc_factor_mat_solver_type mumps + #-pc_bddc_coarse_pc_type cholesky +-#-pc_bddc_coarse_pc_factor_mat_solver_package mumps ++#-pc_bddc_coarse_pc_factor_mat_solver_type mumps +diff --git a/examples/petsc/rc_ex5p_bddc b/examples/petsc/rc_ex5p_bddc +index b243c53c8..a4bc899c3 100644 +--- a/examples/petsc/rc_ex5p_bddc ++++ b/examples/petsc/rc_ex5p_bddc +@@ -28,13 +28,13 @@ + # local solvers (needs PETSc compiled with support for SuiteSparse) + # default solvers will fail + -prec_pc_bddc_neumann_pc_type lu +--prec_pc_bddc_neumann_pc_factor_mat_solver_package umfpack ++-prec_pc_bddc_neumann_pc_factor_mat_solver_type umfpack + -prec_pc_bddc_dirichlet_pc_type lu +--prec_pc_bddc_dirichlet_pc_factor_mat_solver_package umfpack ++-prec_pc_bddc_dirichlet_pc_factor_mat_solver_type umfpack + + # coarse solver (needs PETSc compiled with support for MUMPS) + # default solver may fail +--prec_pc_bddc_coarse_pc_factor_mat_solver_package mumps ++-prec_pc_bddc_coarse_pc_factor_mat_solver_type mumps + -prec_pc_bddc_coarse_pc_type cholesky + + # deluxe scaling (needs PETSc compiled with support for MUMPS) diff --git a/var/spack/repos/builtin/packages/mfem/mfem-3.4.patch b/var/spack/repos/builtin/packages/mfem/mfem-3.4.patch new file mode 100644 index 0000000000..465e0525ea --- /dev/null +++ b/var/spack/repos/builtin/packages/mfem/mfem-3.4.patch @@ -0,0 +1,36 @@ +diff --git a/config/test.mk b/config/test.mk +index 4821b084d..62479fc63 100644 +--- a/config/test.mk ++++ b/config/test.mk +@@ -14,11 +14,13 @@ + # Colors used below: + # green '\033[0;32m' + # red '\033[0;31m' ++# yellow '\033[0;33m' + # no color '\033[0m' + COLOR_PRINT = if [ -t 1 ]; then \ + printf $(1)$(2)'\033[0m'$(3); else printf $(2)$(3); fi + PRINT_OK = $(call COLOR_PRINT,'\033[0;32m',OK," ($$1 $$2)\n") + PRINT_FAILED = $(call COLOR_PRINT,'\033[0;31m',FAILED," ($$1 $$2)\n") ++PRINT_SKIP = $(call COLOR_PRINT,'\033[0;33m',SKIP,"\n") + + # Timing support + define TIMECMD_detect +diff --git a/examples/pumi/makefile b/examples/pumi/makefile +index 2f98eeca7..5ff652aca 100644 +--- a/examples/pumi/makefile ++++ b/examples/pumi/makefile +@@ -51,6 +51,13 @@ endif + MFEM_TESTS = EXAMPLES + include $(MFEM_TEST_MK) + ++ifneq (,$(filter test%,$(MAKECMDGOALS))) ++ ifeq (,$(wildcard ../../data/pumi)) ++ $(info PUMI data directory not found. The PUMI tests will be SKIPPED.) ++ mfem-test = printf " $(3) [$(2) $(1) ... ]: "; $(PRINT_SKIP) ++ endif ++endif ++ + # Testing: Parallel vs. serial runs + RUN_MPI_NP = $(MFEM_MPIEXEC) $(MFEM_MPIEXEC_NP) + RUN_MPI = $(RUN_MPI_NP) $(MFEM_MPI_NP) diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py index 3afbd4ca2f..d6f55b6566 100644 --- a/var/spack/repos/builtin/packages/mfem/package.py +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -1,43 +1,33 @@ -############################################################################## -# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. # -# 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 -############################################################################## -import re +# 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' - url = 'https://github.com/mfem/mfem' + 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 verison is added: + # new version is added: # # 1. Verify that no checksums on old versions have changed. # @@ -51,13 +41,20 @@ class Mfem(Package): # If this quick verification procedure fails, additional discussion # will be required to verify the new version. - version('3.3.2', - '01a762a5d0a2bc59ce4e2f59009045a4', - url='https://goo.gl/Kd7Jk8', extension='.tar.gz', + # 'develop' is a special version that is always larger (or newer) than any + # other version. + version('develop', branch='master') + + version('3.4.0', + '4e73e4fe0482636de3c5dc983cd395839a83cb16f6f509bd88b053e8b3858e05', + url='https://bit.ly/mfem-3-4', extension='.tar.gz', preferred=True) - version('laghos-v1.0', git='https://github.com/mfem/mfem', - tag='laghos-v1.0') + version('3.3.2', + 'b70fa3c5080b9ec514fc05f4a04ff74322b99ac4ecd6d99c229f0ed5188fc0ce', + url='https://goo.gl/Kd7Jk8', extension='.tar.gz') + + version('laghos-v1.0', tag='laghos-v1.0') version('3.3', 'b17bd452593aada93dc0fee748fcfbbf4f04ce3e7d77fdd0341cc9103bcacd0b', @@ -71,8 +68,19 @@ class Mfem(Package): '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, @@ -83,12 +91,17 @@ class Mfem(Package): ' 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..') + 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, @@ -97,43 +110,87 @@ class Mfem(Package): 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('+mpi', when='~hypre') - conflicts('+suite-sparse', when='~lapack') - conflicts('+superlu-dist', when='@:3.1') + 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('hypre', when='+hypre') + 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('blas', when='+suite-sparse') depends_on('lapack', when='+lapack') - depends_on('lapack', when='+suite-sparse') - - depends_on('mpi', when='+mpi') - depends_on('metis') - depends_on('parmetis', when='+superlu-dist') - depends_on('metis@5:', when='+superlu-dist') - depends_on('metis@5:', when='+suite-sparse ^suite-sparse@4.5:') - depends_on('sundials@2.7:+hypre', when='+sundials') + 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='@3.2: +superlu-dist') - depends_on('petsc@3.8:', when='+petsc') - + 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='@3.2: +netcdf') - depends_on('zlib', when='@3.2: +netcdf') - depends_on('hdf5', when='@3.2: +netcdf') - depends_on('libunwind', when='+debug') + 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:', 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:') - patch('mfem_ppc_build.patch', when='@3.2:3.3 arch=ppc64le') + 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 @@ -142,144 +199,230 @@ class Mfem(Package): # likely to be up to date in supporting *all* of MFEM's # configuration options. So, don't use CMake # - def install(self, spec, prefix): + def configure(self, spec, prefix): def yes_no(varstr): return 'YES' if varstr in self.spec else 'NO' - metis5_str = 'NO' - if '+superlu-dist' in spec or \ - spec.satisfies('+suite-sparse ^suite-sparse@4.5:') or \ - spec['metis'].satisfies('@5:'): - metis5_str = 'YES' + # 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([]) - threadsafe_str = 'NO' - if '+openmp' in spec or '+threadsafe' in spec: - threadsafe_str = 'YES' + 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('+debug'), + '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' % threadsafe_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_OPENMP=%s' % yes_no('+openmp')] + '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 '+hypre' in spec: + if '+metis' in spec: options += [ - 'HYPRE_DIR=%s' % spec['hypre'].prefix, - 'HYPRE_OPT=-I%s' % spec['hypre'].prefix.include, - 'HYPRE_LIB=-L%s' % spec['hypre'].prefix.lib + ' -lHYPRE'] + '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_lib = (spec['lapack'].libs + spec['blas'].libs).ld_flags # NOQA: ignore=E501 + lapack_blas = spec['lapack'].libs + spec['blas'].libs options += [ - 'LAPACK_OPT=-I%s' % spec['lapack'].prefix.include, - 'LAPACK_LIB=%s' % lapack_lib] + # LAPACK_OPT is not used + 'LAPACK_LIB=%s' % ld_flags_from_library_list(lapack_blas)] if '+superlu-dist' in spec: - metis_lib = '-L%s -lparmetis -lmetis' % spec['parmetis'].prefix.lib - options += [ - 'METIS_DIR=%s' % spec['parmetis'].prefix, - 'METIS_OPT=-I%s' % spec['parmetis'].prefix.include, - 'METIS_LIB=%s' % metis_lib] - superlu_lib = '-L%s' % spec['superlu-dist'].prefix.lib - superlu_lib += ' -lsuperlu_dist' + lapack_blas = spec['lapack'].libs + spec['blas'].libs options += [ - 'SUPERLU_DIR=%s' % spec['superlu-dist'].prefix, - 'SUPERLU_OPT=-I%s' % spec['superlu-dist'].prefix.include, - 'SUPERLU_LIB=%s' % superlu_lib] - else: - metis_lib = '-L%s -lmetis' % spec['metis'].prefix.lib - options += [ - 'METIS_DIR=%s' % spec['metis'].prefix, - 'METIS_OPT=-I%s' % spec['metis'].prefix.include, - 'METIS_LIB=%s' % metis_lib] + '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: - ssp = spec['suite-sparse'].prefix - ss_lib = '-L%s' % ssp.lib - if '@3.2:' in spec: - ss_lib += ' -lklu -lbtf' - ss_lib += (' -lumfpack -lcholmod -lcolamd' + - ' -lamd -lcamd -lccolamd -lsuitesparseconfig') - no_rt = spec.satisfies('platform=darwin') - if not no_rt: - ss_lib += ' -lrt' - ss_lib += (' ' + metis_lib + ' ' + lapack_lib) + ss_spec = 'suite-sparse:' + self.suitesparse_components options += [ - 'SUITESPARSE_DIR=%s' % ssp, - 'SUITESPARSE_OPT=-I%s' % ssp.include, - 'SUITESPARSE_LIB=%s' % ss_lib] + '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: - sundials_libs = ( - '-lsundials_arkode -lsundials_cvode' - ' -lsundials_nvecserial -lsundials_kinsol') - if '+mpi' in spec: - sundials_libs += ( - ' -lsundials_nvecparhyp -lsundials_nvecparallel') + sun_spec = 'sundials:' + self.sundials_components options += [ - 'SUNDIALS_DIR=%s' % spec['sundials'].prefix, - 'SUNDIALS_OPT=-I%s' % spec['sundials'].prefix.include, - 'SUNDIALS_LIB=-L%s %s' % (spec['sundials'].prefix.lib, - sundials_libs)] + '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: - f = open('%s/lib/pkgconfig/PETSc.pc' % spec['petsc'].prefix, 'r') - for line in f: - if re.search('^\s*Cflags: ', line): - petsc_opts = re.sub('^\s*Cflags: (.*)', '\\1', line) - elif re.search('^\s*Libs.*: ', line): - petsc_libs = re.sub('^\s*Libs.*: (.*)', '\\1', line) - f.close() + # options += ['PETSC_DIR=%s' % spec['petsc'].prefix] options += [ - 'PETSC_DIR=%s' % spec['petsc'].prefix, - 'PETSC_OPT=%s' % petsc_opts, - 'PETSC_LIB=-L%s -lpetsc %s' % - (spec['petsc'].prefix.lib, petsc_libs)] + '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: - np = spec['netcdf'].prefix - zp = spec['zlib'].prefix - h5p = spec['hdf5'].prefix - nlib = '-L%s -lnetcdf ' % np.lib - nlib += '-L%s -lhdf5_hl -lhdf5 ' % h5p.lib - nlib += '-L%s -lz' % zp.lib options += [ - 'NETCDF_DIR=%s' % np, - 'HDF5_DIR=%s' % h5p, - 'ZLIB_DIR=%s' % zp, - 'NETCDF_OPT=-I%s' % np.include, - 'NETCDF_LIB=%s' % nlib] + '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_LIB=-L%s -lmpfr' % spec['mpfr'].prefix.lib] + 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] + 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) - make('config', *options) + def build(self, spec, prefix): make('lib') - if self.run_tests: - make('check') + @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) - make('install') + # 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') if '+examples' in spec: make('examples') @@ -288,3 +431,64 @@ class Mfem(Package): if '+miniapps' in spec: make('miniapps') install_tree('miniapps', join_path(prefix, 'miniapps')) + + if install_em: + install_tree('data', join_path(prefix, '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)) diff --git a/var/spack/repos/builtin/packages/mfem/test_builds.sh b/var/spack/repos/builtin/packages/mfem/test_builds.sh new file mode 100755 index 0000000000..125fa0055c --- /dev/null +++ b/var/spack/repos/builtin/packages/mfem/test_builds.sh @@ -0,0 +1,75 @@ +#!/bin/bash + +builds=( + # preferred version: + 'mfem' + 'mfem~mpi~metis~gzstream' + 'mfem+mpi+superlu-dist+suite-sparse+petsc \ + +sundials+pumi+mpfr+netcdf+gzstream+gnutls+libunwind \ + ^hypre~internal-superlu ^petsc+suite-sparse+mumps' + 'mfem~mpi+suite-sparse+sundials+mpfr+netcdf \ + +gzstream+gnutls+libunwind' + # develop version: + 'mfem@develop+shared~static' + 'mfem@develop+shared~static~mpi~metis~gzstream' + # TODO: Replace '^conduit~python~hdf5' with '^conduit~python' when conduit + # is fixed to accept '^hdf5+mpi'. + # NOTE: Skip PUMI since it conflicts with '+shared'. + 'mfem@develop+shared~static+mpi \ + +superlu-dist+suite-sparse+petsc+sundials+mpfr+netcdf+gzstream \ + +gnutls+libunwind+conduit ^hypre~internal-superlu \ + ^petsc+suite-sparse+mumps ^conduit~python~hdf5' + # TODO: The options '^netcdf~mpi ^hdf5@1.8.19~mpi' are added just to make + # conduit happy. + 'mfem@develop+shared~static~mpi \ + +suite-sparse+sundials+mpfr+netcdf+gzstream+gnutls+libunwind \ + +conduit ^conduit~python ^netcdf~mpi ^hdf5@1.8.19~mpi' +) + +builds2=( + # preferred version + 'mfem+superlu-dist' + 'mfem+suite-sparse~mpi' + 'mfem+suite-sparse' + 'mfem+sundials~mpi' + 'mfem+sundials' + 'mfem+pumi' + 'mfem+netcdf~mpi' + 'mfem+netcdf' + 'mfem+mpfr' + 'mfem+gnutls' + 'mfem+petsc+mpi ^hypre~internal-superlu ^petsc+suite-sparse+mumps' + # develop version + 'mfem@develop+superlu-dist' + 'mfem@develop+suite-sparse~mpi' + 'mfem@develop+suite-sparse' + 'mfem@develop+sundials~mpi' + 'mfem@develop+sundials' + 'mfem@develop+pumi' + 'mfem@develop+netcdf~mpi' + 'mfem@develop+netcdf' + 'mfem@develop+mpfr' + 'mfem@develop+gnutls' + 'mfem@develop+conduit~mpi ^conduit~python' + 'mfem@develop+conduit ^conduit~python' + 'mfem@develop+petsc+mpi ^hypre~internal-superlu \ + ^petsc+suite-sparse+mumps' +) + +trap 'printf "\nScript interrupted.\n"; exit 33' INT + +SEP='==========================================================================' +sep='--------------------------------------------------------------------------' + +for bld in "${builds[@]}" "${builds2[@]}"; do + printf "\n%s\n" "${SEP}" + printf " %s\n" "${bld}" + printf "%s\n" "${SEP}" + eval bbb="\"${bld}\"" + spack spec -I $bbb || exit 1 + printf "%s\n" "${sep}" + spack install --test=root $bbb || exit 2 +done + +# Uninstall all mfem builds: +# spack uninstall --all mfem |