73c978ddd9
Replace use of `shutil.copytree` with `copy_tree` and `install_tree` functions in `llnl.util.filesystem`. - `copy_tree` copies without setting permissions. It should be used to copy files around in the build directory. - `install_tree` copies files and sets permissions. It should be used to copy files into the installation directory. - `install` and `copy` are analogous single-file functions. - add more extensive tests for these functions - update packages to use these functions.
514 lines
21 KiB
Python
514 lines
21 KiB
Python
##############################################################################
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# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/spack/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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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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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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version('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:', 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
|
|
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')
|
|
|
|
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'))
|
|
|
|
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))
|