diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/amrex/package.py | 3 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/mfem/package.py | 262 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/sundials/package.py | 71 |
3 files changed, 205 insertions, 131 deletions
diff --git a/var/spack/repos/builtin/packages/amrex/package.py b/var/spack/repos/builtin/packages/amrex/package.py index a13200b3e0..772bbce3a5 100644 --- a/var/spack/repos/builtin/packages/amrex/package.py +++ b/var/spack/repos/builtin/packages/amrex/package.py @@ -33,8 +33,9 @@ class Amrex(CMakePackage): homepage = "https://ccse.lbl.gov/AMReX/index.html" url = "https://github.com/AMReX-Codes/amrex.git" - version('develop', git='https://github.com/AMReX-Codes/amrex.git', tag='master') version('17.06', git='https://github.com/AMReX-Codes/amrex.git', commit='836d3c7') + version('master', git='https://github.com/AMReX-Codes/amrex.git', tag='master') + version('develop', git='https://github.com/AMReX-Codes/amrex.git', tag='develop') variant('dims', default='3', diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py index 2848d77887..ffd3233a9f 100644 --- a/var/spack/repos/builtin/packages/mfem/package.py +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -23,6 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +import re class Mfem(Package): @@ -62,132 +63,194 @@ class Mfem(Package): '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57', url='http://goo.gl/xrScXn', extension='.tar.gz') - variant('metis', default=False, description='Activate support for metis') - variant('hypre', default=False, description='Activate support for hypre') - variant('suite-sparse', default=False, - description='Activate support for SuiteSparse') - variant('mpi', default=True, description='Activate support for MPI') + variant('mpi', default=True, + description='Enable MPI parallelism') + 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='Activate support for SuperLU_Dist') - variant('lapack', default=False, description='Activate support for LAPACK') - variant('debug', default=False, description='Build debug version') - variant('netcdf', default=False, description='Activate NetCDF support') + description='Enable MPI parallel, sparse direct solvers') + 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('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('gzstream', default=True, + description='Support zip\'d streams for I/O') + 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('+netcdf', when='@:3.1') 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', when='+mpi') - depends_on('hypre', when='+mpi') - - depends_on('hypre', when='+hypre') - - depends_on('metis@4:', when='+metis') - - depends_on('suite-sparse', when='+suite-sparse') - depends_on('blas', when='+suite-sparse') - depends_on('lapack', when='+suite-sparse') + 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('cmake', when='^metis@5:', type='build') + depends_on('hypre~internal-superlu', when='+mpi') + depends_on('hypre@develop~internal-superlu', when='+petsc +hypre') + depends_on('sundials@2.7:+hypre', when='+sundials') + depends_on('suite-sparse', when='+suite-sparse') depends_on('superlu-dist', when='@3.2: +superlu-dist') + depends_on('petsc@develop', when='+petsc') + depends_on('mpfr', when='+mpfr') + depends_on('cmake', when='^metis@5:', type='build') 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('zlib', when='+gzstream') patch('mfem_ppc_build.patch', when='@3.2:3.3 arch=ppc64le') def check_variants(self, spec): - if '+mpi' in spec and ('+hypre' not in spec or '+metis' not in spec): - raise InstallError('mfem+mpi must be built with +hypre ' + - 'and +metis!') - if '+suite-sparse' in spec and ('+metis' not in spec or - '+lapack' not in spec): - raise InstallError('mfem+suite-sparse must be built with ' + - '+metis and +lapack!') if 'metis@5:' in spec and '%clang' in spec and ( '^cmake %gcc' not in spec): raise InstallError('To work around CMake bug with clang, must ' + 'build mfem with mfem[+variants] %clang ' + '^cmake %gcc to force CMake to build with gcc') - if '@:3.1' in spec and '+superlu-dist' in spec: - raise InstallError('MFEM does not support SuperLU_DIST for ' + - 'versions 3.1 and earlier') - if '@:3.1' in spec and '+netcdf' in spec: - raise InstallError('MFEM does not support NetCDF for versions' + - '3.1 and earlier') return + # + # 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 install(self, spec, prefix): self.check_variants(spec) - options = ['PREFIX=%s' % prefix] - - if '+lapack' in spec: - lapack_lib = (spec['lapack'].libs + spec['blas'].libs).ld_flags # NOQA: ignore=E501 - options.extend([ - 'MFEM_USE_LAPACK=YES', - 'LAPACK_OPT=-I%s' % spec['lapack'].prefix.include, - 'LAPACK_LIB=%s' % lapack_lib]) + 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' + + threadsafe_str = 'NO' + if '+openmp' in spec or '+threadsafe' in spec: + threadsafe_str = 'YES' + + options = [ + 'PREFIX=%s' % prefix, + 'MFEM_USE_MEMALLOC=YES', + 'MFEM_DEBUG=%s' % yes_no('+debug'), + 'MFEM_USE_LIBUNWIND=%s' % yes_no('+debug'), + 'MFEM_USE_GZSTREAM=%s' % yes_no('+gzstream'), + 'MFEM_USE_METIS_5=%s' % metis5_str, + 'MFEM_THREAD_SAFE=%s' % threadsafe_str, + '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_NETCDF=%s' % yes_no('+netcdf'), + 'MFEM_USE_MPFR=%s' % yes_no('+mpfr'), + 'MFEM_USE_OPENMP=%s' % yes_no('+openmp')] if '+hypre' in spec: - options.extend([ + options += [ 'HYPRE_DIR=%s' % spec['hypre'].prefix, 'HYPRE_OPT=-I%s' % spec['hypre'].prefix.include, - 'HYPRE_LIB=-L%s' % spec['hypre'].prefix.lib + - ' -lHYPRE']) + 'HYPRE_LIB=-L%s' % spec['hypre'].prefix.lib + ' -lHYPRE'] - if 'parmetis' in spec: - metis_lib = '-L%s -lparmetis -lmetis' % spec['parmetis'].prefix.lib - metis_str = 'MFEM_USE_METIS_5=YES' - options.extend([metis_str, - 'METIS_DIR=%s' % spec['parmetis'].prefix, - 'METIS_OPT=-I%s' % spec['parmetis'].prefix.include, - 'METIS_LIB=%s' % metis_lib]) - elif 'metis' in spec: - metis_lib = '-L%s -lmetis' % spec['metis'].prefix.lib - if spec['metis'].satisfies('@5:'): - metis_str = 'MFEM_USE_METIS_5=YES' - else: - metis_str = 'MFEM_USE_METIS_5=NO' - options.extend([ - metis_str, - 'METIS_DIR=%s' % spec['metis'].prefix, - 'METIS_OPT=-I%s' % spec['metis'].prefix.include, - 'METIS_LIB=%s' % metis_lib]) - - if 'mpi' in spec: - options.extend(['MFEM_USE_MPI=YES']) + if '+lapack' in spec: + lapack_lib = (spec['lapack'].libs + spec['blas'].libs).ld_flags # NOQA: ignore=E501 + options += [ + 'LAPACK_OPT=-I%s' % spec['lapack'].prefix.include, + 'LAPACK_LIB=%s' % lapack_lib] 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' - sl_inc = 'SUPERLU_OPT=-I%s' % spec['superlu-dist'].prefix.include - options.extend(['MFEM_USE_SUPERLU=YES', - 'SUPERLU_DIR=%s' % spec['superlu-dist'].prefix, - sl_inc, - 'SUPERLU_LIB=%s' % superlu_lib]) + 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] 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) - - options.extend(['MFEM_USE_SUITESPARSE=YES', - 'SUITESPARSE_DIR=%s' % ssp, - 'SUITESPARSE_OPT=-I%s' % ssp.include, - 'SUITESPARSE_LIB=%s' % ss_lib]) + options += [ + 'SUITESPARSE_DIR=%s' % ssp, + 'SUITESPARSE_OPT=-I%s' % ssp.include, + 'SUITESPARSE_LIB=%s' % ss_lib] + + if '+sundials' in spec: + sundials_libs = ( + '-lsundials_arkode -lsundials_cvode' + ' -lsundials_nvecserial -lsundials_kinsol') + if '+mpi' in spec: + sundials_libs += ( + ' -lsundials_nvecparhyp -lsundials_nvecparallel') + 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)] + + 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, + 'PETSC_OPT=%s' % petsc_opts, + 'PETSC_LIB=-L%s -lpetsc %s' % + (spec['petsc'].prefix.lib, petsc_libs)] if '+netcdf' in spec: np = spec['netcdf'].prefix @@ -196,28 +259,31 @@ class Mfem(Package): nlib = '-L%s -lnetcdf ' % np.lib nlib += '-L%s -lhdf5_hl -lhdf5 ' % h5p.lib nlib += '-L%s -lz' % zp.lib - options.extend(['MFEM_USE_NETCDF=YES', - 'NETCDF_DIR=%s' % np, - 'HDF5_DIR=%s' % h5p, - 'ZLIB_DIR=%s' % zp, - 'NETCDF_OPT=-I%s' % np.include, - 'NETCDF_LIB=%s' % nlib]) + options += [ + 'NETCDF_DIR=%s' % np, + 'HDF5_DIR=%s' % h5p, + 'ZLIB_DIR=%s' % zp, + 'NETCDF_OPT=-I%s' % np.include, + 'NETCDF_LIB=%s' % nlib] - if '+debug' in spec: - options.extend(['MFEM_DEBUG=YES']) + if '+mpfr' in spec: + options += ['MPFR_LIB=-L%s -lmpfr' % spec['mpfr'].prefix.lib] + + if '+openmp' in spec: + options += ['OPENMP_OPT = %s' % self.compiler.openmp_flag] make('config', *options) - make('all') - - # Run a small test before installation - args = ['-m', join_path('data', 'star.mesh'), '--no-visualization'] - if '+mpi' in spec: - Executable(join_path(spec['mpi'].prefix.bin, - 'mpirun'))('-np', - '4', - join_path('examples', 'ex1p'), - *args) - else: - Executable(join_path('examples', 'ex1'))(*args) + make('lib') + + if self.run_tests: + make('check') make('install') + + if '+examples' in spec: + make('examples') + install_tree('examples', join_path(prefix, 'examples')) + + if '+miniapps' in spec: + make('miniapps') + install_tree('miniapps', join_path(prefix, 'miniapps')) diff --git a/var/spack/repos/builtin/packages/sundials/package.py b/var/spack/repos/builtin/packages/sundials/package.py index 18c3d409f8..66f385f29f 100644 --- a/var/spack/repos/builtin/packages/sundials/package.py +++ b/var/spack/repos/builtin/packages/sundials/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * import os +import sys class Sundials(Package): @@ -33,21 +34,28 @@ class Sundials(Package): homepage = "http://computation.llnl.gov/casc/sundials/" url = "http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/download/sundials-2.6.2.tar.gz" + version('2.7.0', 'c304631b9bc82877d7b0e9f4d4fd94d3') version('2.6.2', '3deeb0ede9f514184c6bd83ecab77d95') - variant('mpi', default=True, description='Enable MPI support') + variant('mpi', default=True, + description='Enable MPI parallelism') variant('lapack', default=True, - description='Build with external BLAS/LAPACK libraries') + description='Use external BLAS/LAPACK libraries') variant('klu', default=False, - description='Build with SuiteSparse KLU libraries') + description='Enable KLU sparse, direct solver') variant('superlu', default=False, - description='Build with SuperLU_MT libraries') - variant('openmp', default=False, description='Enable OpenMP support') + description='Enable SuperLU_MT sparse, direct solver') + variant('openmp', default=False, + description='Enable OpenMP parallelism') variant('pthread', default=True, - description='Enable POSIX threads support') + description='Enable Pthreads parallelism') + variant('hypre', default=False, + description='Enable Hypre parallel vector for MPI parallelism') - depends_on('cmake', type='build') + depends_on('cmake', type='build') depends_on('mpi', when='+mpi') + depends_on('mpi', when='@2.7:+hypre') + depends_on('hypre', when='@2.7:+hypre') depends_on('blas', when='+lapack') depends_on('lapack', when='+lapack') depends_on('suite-sparse', when='+klu') @@ -55,6 +63,10 @@ class Sundials(Package): depends_on('superlu-mt+pthread', when='+superlu+pthread') def install(self, spec, prefix): + + def on_off(varstr): + return 'ON' if varstr in self.spec else 'OFF' + cmake_args = std_cmake_args[:] cmake_args.extend([ '-DBUILD_SHARED_LIBS=ON', @@ -62,47 +74,53 @@ class Sundials(Package): '-DCMAKE_Fortran_FLAGS={0}'.format(self.compiler.pic_flag), '-DEXAMPLES_ENABLE=ON', '-DEXAMPLES_INSTALL=ON', - '-DFCMIX_ENABLE=ON' + '-DFCMIX_ENABLE=ON', + '-DMPI_ENABLE=%s' % on_off('+mpi'), + '-DLAPACK_ENABLE=%s' % on_off('+lapack'), + '-DKLU_ENABLE=%s' % on_off('+klu'), + '-DHYPRE_ENABLE=%s' % on_off('+hypre'), + '-DSUPERLUMT_ENABLE=%s' % on_off('+superlu'), + '-DOPENMP_ENABLE=%s' % on_off('+openmp'), + '-DPTHREAD_ENABLE=%s' % on_off('+pthread') ]) # 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 Hypre + if '+hypre' in spec and spec.satisfies('@2.7:'): + cmake_args.extend([ + '-DHYPRE_INCLUDE_DIR={0}'.format( + spec['hypre'].prefix.include), + '-DHYPRE_LIBRARY_DIR={0}'.format( + spec['hypre'].prefix.lib) + ]) # Building with LAPACK and BLAS if '+lapack' in spec: cmake_args.extend([ - '-DLAPACK_ENABLE=ON', '-DLAPACK_LIBRARIES={0}'.format( (spec['lapack'].libs + spec['blas'].libs).joined(';') ) ]) - 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( @@ -116,20 +134,6 @@ class Sundials(Package): 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) @@ -137,6 +141,9 @@ class Sundials(Package): make() make('install') + if (sys.platform == 'darwin'): + fix_darwin_install_name(prefix.lib) + install('LICENSE', prefix) self.filter_compilers() |