455 lines
20 KiB
Python
455 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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class Dealii(CMakePackage, CudaPackage):
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"""C++ software library providing well-documented tools to build finite
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element codes for a broad variety of PDEs."""
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homepage = "https://www.dealii.org"
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url = "https://github.com/dealii/dealii/releases/download/v8.4.1/dealii-8.4.1.tar.gz"
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git = "https://github.com/dealii/dealii.git"
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maintainers = ['davydden', 'jppelteret']
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# Don't add RPATHs to this package for the full build DAG.
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# only add for immediate deps.
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transitive_rpaths = False
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version('develop', branch='master')
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version('9.1.1', sha256='fc5b483f7fe58dfeb52d05054011280f115498e337af3e085bf272fd1fd81276')
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version('9.1.0', sha256='5b070112403f8afbb72345c1bb24d2a38d11ce58891217e353aab97957a04600')
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version('9.0.1', sha256='df2f0d666f2224be07e3741c0e8e02132fd67ea4579cd16a2429f7416146ee64')
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version('9.0.0', sha256='c918dc5c1a31d62f6eea7b524dcc81c6d00b3c378d4ed6965a708ab548944f08')
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version('8.5.1', sha256='d33e812c21a51f7e5e3d3e6af86aec343155650b611d61c1891fbc3cabce09ae')
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version('8.5.0', sha256='e6913ff6f184d16bc2598c1ba31f879535b72b6dff043e15aef048043ff1d779')
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version('8.4.2', sha256='ec7c00fadc9d298d1a0d16c08fb26818868410a9622c59ba624096872f3058e4')
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version('8.4.1', sha256='00a0e92d069cdafd216816f1aff460f7dbd48744b0d9e0da193287ebf7d6b3ad')
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version('8.4.0', sha256='36a20e097a03f17b557e11aad1400af8c6252d25f7feca40b611d5fc16d71990')
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version('8.3.0', sha256='4ddf72632eb501e1c814e299f32fc04fd680d6fda9daff58be4209e400e41779')
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version('8.2.1', sha256='d75674e45fe63cd9fa294460fe45228904d51a68f744dbb99cd7b60720f3b2a0')
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version('8.1.0', sha256='d666bbda2a17b41b80221d7029468246f2658051b8c00d9c5907cd6434c4df99')
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variant('mpi', default=True, description='Compile with MPI')
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variant('assimp', default=True,
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description='Compile with Assimp')
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variant('arpack', default=True,
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description='Compile with Arpack and PArpack (only with MPI)')
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variant('adol-c', default=True,
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description='Compile with Adol-c')
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variant('doc', default=False,
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description='Compile with documentation')
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variant('ginkgo', default=True, description='Compile with Ginkgo')
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variant('gmsh', default=True, description='Compile with GMSH')
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variant('gsl', default=True, description='Compile with GSL')
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variant('hdf5', default=True,
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description='Compile with HDF5 (only with MPI)')
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variant('metis', default=True, description='Compile with Metis')
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variant('muparser', default=True, description='Compile with muParser')
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variant('nanoflann', default=True, description='Compile with Nanoflann')
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variant('netcdf', default=True,
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description='Compile with Netcdf (only with MPI)')
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variant('oce', default=True, description='Compile with OCE')
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variant('p4est', default=True,
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description='Compile with P4est (only with MPI)')
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variant('petsc', default=True,
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description='Compile with Petsc (only with MPI)')
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variant('scalapack', default=True,
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description='Compile with ScaLAPACK (only with MPI)')
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variant('sundials', default=True,
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description='Compile with Sundials')
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variant('slepc', default=True,
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description='Compile with Slepc (only with Petsc and MPI)')
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variant('symengine', default=True,
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description='Compile with SymEngine')
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variant('trilinos', default=True,
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description='Compile with Trilinos (only with MPI)')
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variant('python', default=False,
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description='Compile with Python bindings')
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variant('int64', default=False,
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description='Compile with 64 bit indices support')
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variant('optflags', default=False,
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description='Compile using additional optimization flags')
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variant('build_type', default='DebugRelease',
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description='The build type to build',
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values=('Debug', 'Release', 'DebugRelease'))
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# required dependencies, light version
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depends_on('blas')
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# Boost 1.58 is blacklisted, require at least 1.59, see
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# https://github.com/dealii/dealii/issues/1591
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# There are issues with 1.65.1 and 1.65.0:
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# https://github.com/dealii/dealii/issues/5262
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# we take the patch from https://github.com/boostorg/serialization/pull/79
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# more precisely its variation https://github.com/dealii/dealii/pull/5572#issuecomment-349742019
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# 1.68.0 has issues with serialization https://github.com/dealii/dealii/issues/7074
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# adopt https://github.com/boostorg/serialization/pull/105 as a fix
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depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:+thread+system+serialization+iostreams',
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patches=[patch('boost_1.65.1_singleton.patch',
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level=1,
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when='@1.65.1'),
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patch('boost_1.68.0.patch',
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level=1,
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when='@1.68.0'),
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],
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when='~python')
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depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:+thread+system+serialization+iostreams+python',
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patches=[patch('boost_1.65.1_singleton.patch',
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level=1,
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when='@1.65.1'),
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patch('boost_1.68.0.patch',
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level=1,
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when='@1.68.0'),
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],
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when='+python')
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# bzip2 is not needed since 9.0
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depends_on('bzip2', when='@:8.99')
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depends_on('lapack')
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depends_on('suite-sparse')
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depends_on('tbb')
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depends_on('zlib')
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# optional dependencies
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depends_on('mpi', when='+mpi')
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depends_on('adol-c@2.6.4:', when='@9.0:+adol-c')
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depends_on('arpack-ng+mpi', when='+arpack+mpi')
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depends_on('assimp', when='@9.0:+assimp')
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depends_on('doxygen+graphviz', when='+doc')
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depends_on('graphviz', when='+doc')
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depends_on('ginkgo', when='@9.1:+ginkgo')
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depends_on('gmsh+tetgen+netgen+oce', when='@9.0:+gmsh', type=('build', 'run'))
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depends_on('gsl', when='@8.5.0:+gsl')
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# FIXME: next line fixes concretization with petsc
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depends_on('hdf5+mpi+hl+fortran', when='+hdf5+mpi+petsc')
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depends_on('hdf5+mpi+hl', when='+hdf5+mpi~petsc')
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depends_on('cuda@8:', when='+cuda')
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depends_on('cmake@3.9:', when='+cuda', type='build')
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# older version of deal.II do not build with Cmake 3.10, see
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# https://github.com/dealii/dealii/issues/5510
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depends_on('cmake@:3.9.99', when='@:8.99', type='build')
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# FIXME: concretizer bug. The two lines mimic what comes from PETSc
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# but we should not need it
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depends_on('metis@5:+int64', when='+metis+int64')
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depends_on('metis@5:~int64', when='+metis~int64')
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depends_on('muparser', when='+muparser')
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depends_on('nanoflann', when='@9.0:+nanoflann')
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depends_on('netcdf+mpi', when='+netcdf+mpi')
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depends_on('netcdf-cxx', when='+netcdf+mpi')
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depends_on('oce', when='+oce')
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depends_on('p4est', when='+p4est+mpi')
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depends_on('petsc+mpi~int64', when='+petsc+mpi~int64')
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depends_on('petsc+mpi+int64', when='+petsc+mpi+int64')
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depends_on('petsc@:3.6.4', when='@:8.4.1+petsc+mpi')
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depends_on('python', when='@8.5.0:+python')
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depends_on('scalapack', when='@9.0:+scalapack')
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depends_on('slepc', when='+slepc+petsc+mpi')
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depends_on('slepc@:3.6.3', when='@:8.4.1+slepc+petsc+mpi')
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depends_on('slepc~arpack', when='+slepc+petsc+mpi+int64')
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depends_on('sundials@:3~pthread', when='@9.0:+sundials')
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# Both Trilinos and SymEngine bundle the Teuchos RCP library.
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# This leads to conflicts between macros defined in the included
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# headers when they are not compiled in the same mode.
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# See https://github.com/symengine/symengine/issues/1516
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# FIXME: uncomment when the following is fixed
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# https://github.com/spack/spack/issues/11160
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# depends_on("symengine@0.4: build_type=Release", when="@9.1:+symengine+trilinos^trilinos~debug") # NOQA: ignore=E501
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# depends_on("symengine@0.4: build_type=Debug", when="@9.1:+symengine+trilinos^trilinos+debug") # NOQA: ignore=E501
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depends_on('symengine@0.4:', when='@9.1:+symengine')
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# do not require +rol to make concretization of xsdk possible
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depends_on('trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos', when='+trilinos+mpi~int64~cuda')
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depends_on('trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos~hypre', when='+trilinos+mpi+int64~cuda')
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# FIXME: temporary disable Tpetra when using CUDA due to
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# namespace "Kokkos::Impl" has no member "cuda_abort"
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depends_on('trilinos@master+amesos+aztec+epetra+ifpack+ml+muelu+rol+sacado+teuchos~amesos2~ifpack2~intrepid2~kokkos~tpetra~zoltan2', when='+trilinos+mpi~int64+cuda')
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depends_on('trilinos@master+amesos+aztec+epetra+ifpack+ml+muelu+rol+sacado+teuchos~hypre~amesos2~ifpack2~intrepid2~kokkos~tpetra~zoltan2', when='+trilinos+mpi+int64+cuda')
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# Explicitly provide a destructor in BlockVector,
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# otherwise deal.II may fail to build with Intel compilers.
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patch('https://github.com/dealii/dealii/commit/a89d90f9993ee9ad39e492af466b3595c06c3e25.patch',
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sha256='4282b32e96f2f5d376eb34f3fddcc4615fcd99b40004cca784eb874288d1b31c',
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when='@9.0.1')
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# https://github.com/dealii/dealii/pull/7935
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patch('https://github.com/dealii/dealii/commit/f8de8c5c28c715717bf8a086e94f071e0fe9deab.patch',
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sha256='61f217744b70f352965be265d2f06e8c1276685e2944ca0a88b7297dd55755da',
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when='@9.0.1 ^boost@1.70.0:')
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# check that the combination of variants makes sense
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# 64-bit BLAS:
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for p in ['openblas', 'intel-mkl', 'intel-parallel-studio+mkl']:
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conflicts('^{0}+ilp64'.format(p), when='@:8.5.1',
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msg='64bit BLAS is only supported from 9.0.0')
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# interfaces added in 9.0.0:
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for p in ['assimp', 'gmsh', 'nanoflann', 'scalapack', 'sundials',
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'adol-c']:
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conflicts('+{0}'.format(p), when='@:8.5.1',
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msg='The interface to {0} is supported from version 9.0.0 '
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'onwards. Please explicitly disable this variant '
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'via ~{0}'.format(p))
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# interfaces added in 9.1.0:
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for p in ['ginkgo', 'symengine']:
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conflicts('+{0}'.format(p), when='@:9.0',
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msg='The interface to {0} is supported from version 9.1.0 '
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'onwards. Please explicitly disable this variant '
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'via ~{0}'.format(p))
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conflicts('+slepc', when='~petsc',
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msg='It is not possible to enable slepc interfaces '
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'without petsc.')
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conflicts('+adol-c', when='^trilinos+chaco',
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msg='symbol clash between the ADOL-C library and '
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'Trilinos SEACAS Chaco.')
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# interfaces added in 8.5.0:
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for p in ['gsl', 'python']:
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conflicts('+{0}'.format(p), when='@:8.4.2',
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msg='The interface to {0} is supported from version 8.5.0 '
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'onwards. Please explicitly disable this variant '
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'via ~{0}'.format(p))
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# MPI requirements:
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for p in ['arpack', 'hdf5', 'netcdf', 'p4est', 'petsc', 'scalapack',
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'slepc', 'trilinos']:
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conflicts('+{0}'.format(p), when='~mpi',
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msg='To enable {0} it is necessary to build deal.II with '
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'MPI support enabled.'.format(p))
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def cmake_args(self):
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spec = self.spec
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options = []
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# release flags
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cxx_flags_release = []
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# debug and release flags
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cxx_flags = []
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lapack_blas_libs = spec['lapack'].libs + spec['blas'].libs
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lapack_blas_headers = spec['lapack'].headers + spec['blas'].headers
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options.extend([
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'-DDEAL_II_COMPONENT_EXAMPLES=ON',
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'-DDEAL_II_WITH_THREADS:BOOL=ON',
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'-DBOOST_DIR=%s' % spec['boost'].prefix,
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# CMake's FindBlas/Lapack may pickup system's blas/lapack instead
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# of Spack's. Be more specific to avoid this.
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# Note that both lapack and blas are provided in -DLAPACK_XYZ.
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'-DLAPACK_FOUND=true',
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'-DLAPACK_INCLUDE_DIRS=%s' % ';'.join(
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lapack_blas_headers.directories),
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'-DLAPACK_LIBRARIES=%s' % lapack_blas_libs.joined(';'),
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'-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
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'-DZLIB_DIR=%s' % spec['zlib'].prefix,
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'-DDEAL_II_ALLOW_BUNDLED=OFF'
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])
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if (spec.satisfies('^intel-parallel-studio+tbb')):
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# deal.II/cmake will have hard time picking up TBB from Intel.
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tbb_ver = '.'.join(('%s' % spec['tbb'].version).split('.')[1:])
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options.extend([
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'-DTBB_FOUND=true',
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'-DTBB_VERSION=%s' % tbb_ver,
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'-DTBB_INCLUDE_DIRS=%s' % ';'.join(
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spec['tbb'].headers.directories),
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'-DTBB_LIBRARIES=%s' % spec['tbb'].libs.joined(';')
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])
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else:
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options.append('-DTBB_DIR=%s' % spec['tbb'].prefix)
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if (spec.satisfies('^openblas+ilp64') or
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spec.satisfies('^intel-mkl+ilp64') or
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spec.satisfies('^intel-parallel-studio+mkl+ilp64')):
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options.append('-DLAPACK_WITH_64BIT_BLAS_INDICES=ON')
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if spec.satisfies('@:8.99'):
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options.extend([
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# Cmake may still pick up system's bzip2, fix this:
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'-DBZIP2_FOUND=true',
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'-DBZIP2_INCLUDE_DIRS=%s' % spec['bzip2'].prefix.include,
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'-DBZIP2_LIBRARIES=%s' % spec['bzip2'].libs.joined(';')
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])
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# Set recommended flags for maximum (matrix-free) performance, see
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# https://groups.google.com/forum/?fromgroups#!topic/dealii/3Yjy8CBIrgU
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if spec.satisfies('%gcc'):
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cxx_flags_release.extend(['-O3'])
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cxx_flags.extend(['-march=native'])
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elif spec.satisfies('%intel'):
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cxx_flags_release.extend(['-O3'])
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cxx_flags.extend(['-march=native'])
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elif spec.satisfies('%clang'):
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cxx_flags_release.extend(['-O3', '-ffp-contract=fast'])
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cxx_flags.extend(['-march=native'])
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# Python bindings
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if spec.satisfies('@8.5.0:'):
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options.extend([
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'-DDEAL_II_COMPONENT_PYTHON_BINDINGS=%s' %
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('ON' if '+python' in spec else 'OFF')
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])
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if '+python' in spec:
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python_exe = spec['python'].command.path
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python_library = spec['python'].libs[0]
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python_include = spec['python'].headers.directories[0]
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options.extend([
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'-DPYTHON_EXECUTABLE=%s' % python_exe,
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'-DPYTHON_INCLUDE_DIR=%s' % python_include,
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'-DPYTHON_LIBRARY=%s' % python_library
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])
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# Set directory structure:
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if spec.satisfies('@:8.2.1'):
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options.extend(['-DDEAL_II_COMPONENT_COMPAT_FILES=OFF'])
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else:
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options.extend([
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'-DDEAL_II_EXAMPLES_RELDIR=share/deal.II/examples',
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'-DDEAL_II_DOCREADME_RELDIR=share/deal.II/',
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'-DDEAL_II_DOCHTML_RELDIR=share/deal.II/doc'
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])
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# CUDA
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if '+cuda' in spec:
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options.append(
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'-DDEAL_II_WITH_CUDA=ON'
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)
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if not spec.satisfies('^cuda@9:'):
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options.append('-DDEAL_II_WITH_CXX14=OFF')
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cuda_arch = spec.variants['cuda_arch'].value
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if cuda_arch != 'none':
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if len(cuda_arch) > 1:
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raise InstallError(
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'deal.II only supports compilation for a single GPU!'
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)
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flags = '-arch=sm_{0}'.format(cuda_arch[0])
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# FIXME: there are some compiler errors in dealii
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# with: flags = ' '.join(self.cuda_flags(cuda_arch))
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# Stick with -arch=sm_xy for now.
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options.append(
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'-DDEAL_II_CUDA_FLAGS={0}'.format(flags)
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)
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else:
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options.extend([
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'-DDEAL_II_WITH_CUDA=OFF',
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])
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# MPI
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if '+mpi' in spec:
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options.extend([
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'-DDEAL_II_WITH_MPI:BOOL=ON',
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'-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
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'-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
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'-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
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])
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else:
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options.extend([
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'-DDEAL_II_WITH_MPI:BOOL=OFF',
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])
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# Optional dependencies for which library names are the same as CMake
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# variables:
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for library in (
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'gsl', 'hdf5', 'p4est', 'petsc', 'slepc', 'trilinos', 'metis',
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'sundials', 'nanoflann', 'assimp', 'gmsh', 'muparser',
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'symengine', 'ginkgo'):
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if ('+' + library) in spec:
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options.extend([
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'-D%s_DIR=%s' % (library.upper(), spec[library].prefix),
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'-DDEAL_II_WITH_%s:BOOL=ON' % library.upper()
|
|
])
|
|
else:
|
|
options.extend([
|
|
'-DDEAL_II_WITH_%s:BOOL=OFF' % library.upper()
|
|
])
|
|
|
|
# adol-c
|
|
if '+adol-c' in spec:
|
|
options.extend([
|
|
'-DADOLC_DIR=%s' % spec['adol-c'].prefix,
|
|
'-DDEAL_II_WITH_ADOLC=ON'
|
|
])
|
|
else:
|
|
options.extend([
|
|
'-DDEAL_II_WITH_ADOLC=OFF'
|
|
])
|
|
|
|
# doxygen
|
|
options.extend([
|
|
'-DDEAL_II_COMPONENT_DOCUMENTATION=%s' %
|
|
('ON' if '+doc' in spec else 'OFF'),
|
|
])
|
|
|
|
# arpack
|
|
if '+arpack' in spec and '+mpi' in spec:
|
|
options.extend([
|
|
'-DARPACK_DIR=%s' % spec['arpack-ng'].prefix,
|
|
'-DDEAL_II_WITH_ARPACK=ON',
|
|
'-DDEAL_II_ARPACK_WITH_PARPACK=ON'
|
|
])
|
|
else:
|
|
options.extend([
|
|
'-DDEAL_II_WITH_ARPACK=OFF'
|
|
])
|
|
|
|
# since Netcdf is spread among two, need to do it by hand:
|
|
if '+netcdf' in spec and '+mpi' in spec:
|
|
netcdf = spec['netcdf-cxx'].libs + spec['netcdf'].libs
|
|
options.extend([
|
|
'-DNETCDF_FOUND=true',
|
|
'-DNETCDF_LIBRARIES=%s' % netcdf.joined(';'),
|
|
'-DNETCDF_INCLUDE_DIRS=%s;%s' % (
|
|
spec['netcdf-cxx'].prefix.include,
|
|
spec['netcdf'].prefix.include),
|
|
])
|
|
else:
|
|
options.extend([
|
|
'-DDEAL_II_WITH_NETCDF=OFF'
|
|
])
|
|
|
|
if '+scalapack' in spec:
|
|
scalapack = spec['scalapack'].libs
|
|
options.extend([
|
|
'-DSCALAPACK_FOUND=true',
|
|
'-DSCALAPACK_INCLUDE_DIRS=%s' % (
|
|
spec['scalapack'].prefix.include),
|
|
'-DSCALAPACK_LIBRARIES=%s' % scalapack.joined(';'),
|
|
'-DDEAL_II_WITH_SCALAPACK=ON'
|
|
])
|
|
else:
|
|
options.extend([
|
|
'-DDEAL_II_WITH_SCALAPACK=OFF'
|
|
])
|
|
|
|
# Open Cascade
|
|
if '+oce' in spec:
|
|
options.extend([
|
|
'-DOPENCASCADE_DIR=%s' % spec['oce'].prefix,
|
|
'-DDEAL_II_WITH_OPENCASCADE=ON'
|
|
])
|
|
else:
|
|
options.extend([
|
|
'-DDEAL_II_WITH_OPENCASCADE=OFF'
|
|
])
|
|
|
|
# 64 bit indices
|
|
options.extend([
|
|
'-DDEAL_II_WITH_64BIT_INDICES=%s' % ('+int64' in spec)
|
|
])
|
|
|
|
# collect CXX flags:
|
|
if len(cxx_flags_release) > 0 and '+optflags' in spec:
|
|
options.extend([
|
|
'-DCMAKE_CXX_FLAGS_RELEASE:STRING=%s' % (
|
|
' '.join(cxx_flags_release)),
|
|
'-DCMAKE_CXX_FLAGS:STRING=%s' % (
|
|
' '.join(cxx_flags))
|
|
])
|
|
|
|
return options
|
|
|
|
def setup_environment(self, spack_env, run_env):
|
|
run_env.set('DEAL_II_DIR', self.prefix)
|