a2220f3150
- Fix trailing whitespace missed by the bug described in #12755. - Fix other style issues that have crept in over time (this can happen when flake8 adds new checks with new versions)
501 lines
20 KiB
Python
501 lines
20 KiB
Python
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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import os
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import shutil
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class Mfem(Package):
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"""Free, lightweight, scalable C++ library for finite element methods."""
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tags = ['FEM', 'finite elements', 'high-order', 'AMR', 'HPC']
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homepage = 'http://www.mfem.org'
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git = 'https://github.com/mfem/mfem.git'
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maintainers = ['goxberry', 'tzanio', 'markcmiller86', 'acfisher',
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'v-dobrev']
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# Recommended mfem builds to test when updating this file: see the shell
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# script 'test_builds.sh' in the same directory as this file.
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# mfem is downloaded from a URL shortener at request of upstream
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# author Tzanio Kolev <tzanio@llnl.gov>. See here:
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# https://github.com/mfem/mfem/issues/53
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#
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# The following procedure should be used to verify security when a
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# new version is added:
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#
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# 1. Verify that no checksums on old versions have changed.
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#
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# 2. Verify that the shortened URL for the new version is listed at:
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# http://mfem.org/download/
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#
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# 3. Use http://getlinkinfo.com or similar to verify that the
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# underling download link for the latest version comes has the
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# prefix: http://mfem.github.io/releases
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#
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# If this quick verification procedure fails, additional discussion
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# will be required to verify the new version.
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# 'develop' is a special version that is always larger (or newer) than any
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# other version.
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version('develop', branch='master')
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# Tagged development version used by the laghos package:
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version('3.4.1-laghos-v2.0', tag='laghos-v2.0')
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version('3.4.0',
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'4e73e4fe0482636de3c5dc983cd395839a83cb16f6f509bd88b053e8b3858e05',
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url='https://bit.ly/mfem-3-4', extension='.tar.gz',
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preferred=True)
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version('3.3.2',
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'b70fa3c5080b9ec514fc05f4a04ff74322b99ac4ecd6d99c229f0ed5188fc0ce',
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url='https://goo.gl/Kd7Jk8', extension='.tar.gz')
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# Tagged development version used by the laghos package:
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version('3.3.1-laghos-v1.0', tag='laghos-v1.0')
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version('3.3',
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'b17bd452593aada93dc0fee748fcfbbf4f04ce3e7d77fdd0341cc9103bcacd0b',
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url='http://goo.gl/Vrpsns', extension='.tar.gz')
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version('3.2',
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'2938c3deed4ec4f7fd5b5f5cfe656845282e86e2dcd477d292390058b7b94340',
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url='http://goo.gl/Y9T75B', extension='.tar.gz')
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version('3.1',
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'841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57',
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url='http://goo.gl/xrScXn', extension='.tar.gz')
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variant('static', default=True,
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description='Build static library')
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variant('shared', default=False,
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description='Build shared library')
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variant('mpi', default=True,
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description='Enable MPI parallelism')
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# Can we make the default value for 'metis' to depend on the 'mpi' value?
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variant('metis', default=True,
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description='Enable METIS support')
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# TODO: The 'hypre' variant is the same as 'mpi', we may want to remove it.
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# For now, keep the 'hypre' variant while ignoring its setting. This
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# is done to preserve compatibility with other packages that refer to
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# it, e.g. xSDK.
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variant('hypre', default=True,
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description='Required for MPI parallelism')
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variant('openmp', default=False,
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description='Enable OpenMP parallelism')
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variant('threadsafe', default=False,
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description=('Enable thread safe features.'
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' Required for OpenMP.'
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' May cause minor performance issues.'))
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variant('superlu-dist', default=False,
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description='Enable MPI parallel, sparse direct solvers')
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# Placeholder for STRUMPACK, support added in mfem v3.3.2:
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# variant('strumpack', default=False,
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# description='Enable support for STRUMPACK')
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variant('suite-sparse', default=False,
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description='Enable serial, sparse direct solvers')
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variant('petsc', default=False,
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description='Enable PETSc solvers, preconditioners, etc.')
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variant('sundials', default=False,
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description='Enable Sundials time integrators')
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variant('pumi', default=False,
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description='Enable functionality based on PUMI')
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variant('mpfr', default=False,
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description='Enable precise, 1D quadrature rules')
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variant('lapack', default=False,
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description='Use external blas/lapack routines')
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variant('debug', default=False,
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description='Build debug instead of optimized version')
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variant('netcdf', default=False,
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description='Enable Cubit/Genesis reader')
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variant('conduit', default=False,
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description='Enable binary data I/O using Conduit')
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variant('gzstream', default=True,
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description='Support zip\'d streams for I/O')
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variant('gnutls', default=False,
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description='Enable secure sockets using GnuTLS')
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variant('libunwind', default=False,
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description='Enable backtrace on error support using Libunwind')
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variant('timer', default='auto',
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values=('auto', 'std', 'posix', 'mac', 'mpi'),
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description='Timing functions to use in mfem::StopWatch')
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variant('examples', default=False,
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description='Build and install examples')
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variant('miniapps', default=False,
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description='Build and install miniapps')
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conflicts('+shared', when='@:3.3.2')
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conflicts('~static~shared')
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conflicts('~threadsafe', when='+openmp')
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conflicts('+netcdf', when='@:3.1')
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conflicts('+superlu-dist', when='@:3.1')
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conflicts('+gnutls', when='@:3.1')
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conflicts('+gzstream', when='@:3.2')
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conflicts('+mpfr', when='@:3.2')
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conflicts('+petsc', when='@:3.2')
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conflicts('+sundials', when='@:3.2')
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conflicts('+pumi', when='@:3.3.2')
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conflicts('timer=mac', when='@:3.3.0')
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conflicts('timer=mpi', when='@:3.3.0')
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conflicts('~metis+mpi', when='@:3.3.0')
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conflicts('+metis~mpi', when='@:3.3.0')
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conflicts('+conduit', when='@:3.3.2')
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conflicts('+superlu-dist', when='~mpi')
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conflicts('+petsc', when='~mpi')
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conflicts('+pumi', when='~mpi')
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conflicts('timer=mpi', when='~mpi')
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conflicts('+pumi', when='+shared')
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depends_on('mpi', when='+mpi')
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depends_on('hypre@2.10.0:2.13.999', when='@:3.3.999+mpi')
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depends_on('hypre', when='@3.4:+mpi')
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depends_on('metis', when='+metis')
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depends_on('blas', when='+lapack')
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depends_on('lapack', when='+lapack')
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depends_on('sundials@2.7.0', when='@:3.3.0+sundials~mpi')
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depends_on('sundials@2.7.0+mpi+hypre', when='@:3.3.0+sundials+mpi')
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depends_on('sundials@2.7.0:', when='@3.3.2:+sundials~mpi')
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depends_on('sundials@2.7.0:+mpi+hypre', when='@3.3.2:+sundials+mpi')
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depends_on('pumi', when='+pumi')
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depends_on('suite-sparse', when='+suite-sparse')
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depends_on('superlu-dist', when='+superlu-dist')
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# The PETSc tests in MFEM will fail if PETSc is not configured with
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# SuiteSparse and MUMPS. On the other hand, if we require the variants
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# '+suite-sparse+mumps' of PETSc, the xsdk package concretization fails.
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depends_on('petsc@3.8:+mpi+double+hypre', when='+petsc')
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# Recommended when building outside of xsdk:
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# depends_on('petsc@3.8:+mpi+double+hypre+suite-sparse+mumps',
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# when='+petsc')
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depends_on('mpfr', when='+mpfr')
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depends_on('netcdf', when='+netcdf')
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depends_on('unwind', when='+libunwind')
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depends_on('zlib', when='+gzstream')
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depends_on('gnutls', when='+gnutls')
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depends_on('conduit@0.3.1:,master:', when='+conduit')
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depends_on('conduit+mpi', when='+conduit+mpi')
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patch('mfem_ppc_build.patch', when='@3.2:3.3.0 arch=ppc64le')
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patch('mfem-3.4.patch', when='@3.4.0')
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patch('mfem-3.3-3.4-petsc-3.9.patch',
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when='@3.3.0:3.4.0 +petsc ^petsc@3.9.0:')
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phases = ['configure', 'build', 'install']
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def setup_environment(self, spack_env, run_env):
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spack_env.unset('MFEM_DIR')
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spack_env.unset('MFEM_BUILD_DIR')
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#
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# Note: Although MFEM does support CMake configuration, MFEM
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# development team indicates that vanilla GNU Make is the
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# preferred mode of configuration of MFEM and the mode most
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# likely to be up to date in supporting *all* of MFEM's
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# configuration options. So, don't use CMake
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#
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def configure(self, spec, prefix):
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def yes_no(varstr):
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return 'YES' if varstr in self.spec else 'NO'
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# We need to add rpaths explicitly to allow proper export of link flags
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# from within MFEM.
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# Similar to spec[pkg].libs.ld_flags but prepends rpath flags too.
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def ld_flags_from_library_list(libs_list):
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flags = ['-Wl,-rpath,%s' % dir for dir in libs_list.directories]
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flags += [libs_list.ld_flags]
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return ' '.join(flags)
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def ld_flags_from_dirs(pkg_dirs_list, pkg_libs_list):
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flags = ['-Wl,-rpath,%s' % dir for dir in pkg_dirs_list]
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flags += ['-L%s' % dir for dir in pkg_dirs_list]
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flags += ['-l%s' % lib for lib in pkg_libs_list]
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return ' '.join(flags)
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def find_optional_library(name, prefix):
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for shared in [True, False]:
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for path in ['lib64', 'lib']:
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lib = find_libraries(name, join_path(prefix, path),
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shared=shared, recursive=False)
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if lib:
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return lib
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return LibraryList([])
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metis5_str = 'NO'
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if ('+metis' in spec) and spec['metis'].satisfies('@5:'):
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metis5_str = 'YES'
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options = [
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'PREFIX=%s' % prefix,
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'MFEM_USE_MEMALLOC=YES',
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'MFEM_DEBUG=%s' % yes_no('+debug'),
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# NOTE: env['CXX'] is the spack c++ compiler wrapper. The real
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# compiler is defined by env['SPACK_CXX'].
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'CXX=%s' % env['CXX'],
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'MFEM_USE_LIBUNWIND=%s' % yes_no('+libunwind'),
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'MFEM_USE_GZSTREAM=%s' % yes_no('+gzstream'),
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'MFEM_USE_METIS=%s' % yes_no('+metis'),
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'MFEM_USE_METIS_5=%s' % metis5_str,
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'MFEM_THREAD_SAFE=%s' % yes_no('+threadsafe'),
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'MFEM_USE_MPI=%s' % yes_no('+mpi'),
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'MFEM_USE_LAPACK=%s' % yes_no('+lapack'),
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'MFEM_USE_SUPERLU=%s' % yes_no('+superlu-dist'),
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'MFEM_USE_SUITESPARSE=%s' % yes_no('+suite-sparse'),
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'MFEM_USE_SUNDIALS=%s' % yes_no('+sundials'),
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'MFEM_USE_PETSC=%s' % yes_no('+petsc'),
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'MFEM_USE_PUMI=%s' % yes_no('+pumi'),
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'MFEM_USE_NETCDF=%s' % yes_no('+netcdf'),
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'MFEM_USE_MPFR=%s' % yes_no('+mpfr'),
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'MFEM_USE_GNUTLS=%s' % yes_no('+gnutls'),
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'MFEM_USE_OPENMP=%s' % yes_no('+openmp'),
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'MFEM_USE_CONDUIT=%s' % yes_no('+conduit')]
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cxxflags = spec.compiler_flags['cxxflags']
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if cxxflags:
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# The cxxflags are set by the spack c++ compiler wrapper. We also
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# set CXXFLAGS explicitly, for clarity, and to properly export the
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# cxxflags in the variable MFEM_CXXFLAGS in config.mk.
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options += ['CXXFLAGS=%s' % ' '.join(cxxflags)]
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if '~static' in spec:
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options += ['STATIC=NO']
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if '+shared' in spec:
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options += ['SHARED=YES', 'PICFLAG=%s' % self.compiler.pic_flag]
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if '+mpi' in spec:
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options += ['MPICXX=%s' % spec['mpi'].mpicxx]
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hypre = spec['hypre']
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# The hypre package always links with 'blas' and 'lapack'.
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all_hypre_libs = hypre.libs + hypre['lapack'].libs + \
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hypre['blas'].libs
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options += [
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'HYPRE_OPT=-I%s' % hypre.prefix.include,
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'HYPRE_LIB=%s' % ld_flags_from_library_list(all_hypre_libs)]
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if '+metis' in spec:
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options += [
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'METIS_OPT=-I%s' % spec['metis'].prefix.include,
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'METIS_LIB=%s' %
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ld_flags_from_dirs([spec['metis'].prefix.lib], ['metis'])]
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if '+lapack' in spec:
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lapack_blas = spec['lapack'].libs + spec['blas'].libs
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options += [
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# LAPACK_OPT is not used
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'LAPACK_LIB=%s' % ld_flags_from_library_list(lapack_blas)]
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if '+superlu-dist' in spec:
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lapack_blas = spec['lapack'].libs + spec['blas'].libs
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options += [
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'SUPERLU_OPT=-I%s -I%s' %
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(spec['superlu-dist'].prefix.include,
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spec['parmetis'].prefix.include),
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'SUPERLU_LIB=-L%s -L%s -lsuperlu_dist -lparmetis %s' %
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(spec['superlu-dist'].prefix.lib,
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spec['parmetis'].prefix.lib,
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ld_flags_from_library_list(lapack_blas))]
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if '+suite-sparse' in spec:
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ss_spec = 'suite-sparse:' + self.suitesparse_components
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options += [
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'SUITESPARSE_OPT=-I%s' % spec[ss_spec].prefix.include,
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'SUITESPARSE_LIB=%s' %
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ld_flags_from_library_list(spec[ss_spec].libs)]
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if '+sundials' in spec:
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sun_spec = 'sundials:' + self.sundials_components
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options += [
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'SUNDIALS_OPT=%s' % spec[sun_spec].headers.cpp_flags,
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'SUNDIALS_LIB=%s' %
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ld_flags_from_library_list(spec[sun_spec].libs)]
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if '+petsc' in spec:
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# options += ['PETSC_DIR=%s' % spec['petsc'].prefix]
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options += [
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'PETSC_OPT=%s' % spec['petsc'].headers.cpp_flags,
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'PETSC_LIB=%s' %
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ld_flags_from_library_list(spec['petsc'].libs)]
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if '+pumi' in spec:
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options += ['PUMI_DIR=%s' % spec['pumi'].prefix]
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if '+netcdf' in spec:
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options += [
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'NETCDF_OPT=-I%s' % spec['netcdf'].prefix.include,
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'NETCDF_LIB=%s' %
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ld_flags_from_dirs([spec['netcdf'].prefix.lib], ['netcdf'])]
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if '+gzstream' in spec:
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if "@:3.3.2" in spec:
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options += ['ZLIB_DIR=%s' % spec['zlib'].prefix]
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else:
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options += [
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'ZLIB_OPT=-I%s' % spec['zlib'].prefix.include,
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'ZLIB_LIB=%s' %
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ld_flags_from_library_list(spec['zlib'].libs)]
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if '+mpfr' in spec:
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options += [
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'MPFR_OPT=-I%s' % spec['mpfr'].prefix.include,
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'MPFR_LIB=%s' %
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ld_flags_from_dirs([spec['mpfr'].prefix.lib], ['mpfr'])]
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if '+gnutls' in spec:
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options += [
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'GNUTLS_OPT=-I%s' % spec['gnutls'].prefix.include,
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'GNUTLS_LIB=%s' %
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ld_flags_from_dirs([spec['gnutls'].prefix.lib], ['gnutls'])]
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if '+libunwind' in spec:
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libunwind = spec['unwind']
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headers = find_headers('libunwind', libunwind.prefix.include)
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headers.add_macro('-g')
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libs = find_optional_library('libunwind', libunwind.prefix)
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# When mfem uses libunwind, it also needs 'libdl'.
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libs += LibraryList(find_system_libraries('libdl'))
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options += [
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'LIBUNWIND_OPT=%s' % headers.cpp_flags,
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'LIBUNWIND_LIB=%s' % ld_flags_from_library_list(libs)]
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if '+openmp' in spec:
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options += ['OPENMP_OPT=%s' % self.compiler.openmp_flag]
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timer_ids = {'std': '0', 'posix': '2', 'mac': '4', 'mpi': '6'}
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timer = spec.variants['timer'].value
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if timer != 'auto':
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options += ['MFEM_TIMER_TYPE=%s' % timer_ids[timer]]
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if '+conduit' in spec:
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conduit = spec['conduit']
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headers = HeaderList(find(conduit.prefix.include, 'conduit.hpp',
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recursive=True))
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conduit_libs = ['libconduit', 'libconduit_relay',
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'libconduit_blueprint']
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libs = find_libraries(conduit_libs, conduit.prefix.lib,
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shared=('+shared' in conduit))
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libs += LibraryList(find_system_libraries('libdl'))
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if '+hdf5' in conduit:
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hdf5 = conduit['hdf5']
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headers += find_headers('hdf5', hdf5.prefix.include)
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libs += hdf5.libs
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options += [
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'CONDUIT_OPT=%s' % headers.cpp_flags,
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'CONDUIT_LIB=%s' % ld_flags_from_library_list(libs)]
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make('config', *options, parallel=False)
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make('info', parallel=False)
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def build(self, spec, prefix):
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make('lib')
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@run_after('build')
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def check_or_test(self):
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# Running 'make check' or 'make test' may fail if MFEM_MPIEXEC or
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# MFEM_MPIEXEC_NP are not set appropriately.
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if not self.run_tests:
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# check we can build ex1 (~mpi) or ex1p (+mpi).
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make('-C', 'examples', 'ex1p' if ('+mpi' in self.spec) else 'ex1',
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parallel=False)
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# make('check', parallel=False)
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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))
|