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|
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import os
class Dealii(CMakePackage, CudaPackage):
"""C++ software library providing well-documented tools to build finite
element codes for a broad variety of PDEs."""
homepage = "https://www.dealii.org"
url = "https://github.com/dealii/dealii/releases/download/v8.4.1/dealii-8.4.1.tar.gz"
git = "https://github.com/dealii/dealii.git"
maintainers = ['davydden', 'jppelteret', 'luca-heltai']
# Don't add RPATHs to this package for the full build DAG.
# only add for immediate deps.
transitive_rpaths = False
generator = 'Ninja'
version('master', branch='master')
version('9.2.0', sha256='d05a82fb40f1f1e24407451814b5a6004e39366a44c81208b1ae9d65f3efa43a')
version('9.1.1', sha256='fc5b483f7fe58dfeb52d05054011280f115498e337af3e085bf272fd1fd81276')
version('9.1.0', sha256='5b070112403f8afbb72345c1bb24d2a38d11ce58891217e353aab97957a04600')
version('9.0.1', sha256='df2f0d666f2224be07e3741c0e8e02132fd67ea4579cd16a2429f7416146ee64')
version('9.0.0', sha256='c918dc5c1a31d62f6eea7b524dcc81c6d00b3c378d4ed6965a708ab548944f08')
version('8.5.1', sha256='d33e812c21a51f7e5e3d3e6af86aec343155650b611d61c1891fbc3cabce09ae')
version('8.5.0', sha256='e6913ff6f184d16bc2598c1ba31f879535b72b6dff043e15aef048043ff1d779')
version('8.4.2', sha256='ec7c00fadc9d298d1a0d16c08fb26818868410a9622c59ba624096872f3058e4')
version('8.4.1', sha256='00a0e92d069cdafd216816f1aff460f7dbd48744b0d9e0da193287ebf7d6b3ad')
version('8.4.0', sha256='36a20e097a03f17b557e11aad1400af8c6252d25f7feca40b611d5fc16d71990')
version('8.3.0', sha256='4ddf72632eb501e1c814e299f32fc04fd680d6fda9daff58be4209e400e41779')
version('8.2.1', sha256='d75674e45fe63cd9fa294460fe45228904d51a68f744dbb99cd7b60720f3b2a0')
version('8.1.0', sha256='d666bbda2a17b41b80221d7029468246f2658051b8c00d9c5907cd6434c4df99')
# Configuration variants
variant('build_type', default='DebugRelease',
description='The build type to build',
values=('Debug', 'Release', 'DebugRelease'))
variant('cxxstd', default='default', multi=False,
description='Compile using the specified C++ standard',
values=('default', '11', '14', '17'))
variant('doc', default=False,
description='Compile with documentation')
variant('examples', default=True,
description='Compile tutorial programs')
variant('int64', default=False,
description='Compile with 64 bit indices support')
variant('mpi', default=True,
description='Compile with MPI')
variant('optflags', default=False,
description='Compile using additional optimization flags')
variant('python', default=False,
description='Compile with Python bindings')
# Package variants
variant('assimp', default=True,
description='Compile with Assimp')
variant('arpack', default=True,
description='Compile with Arpack and PArpack (only with MPI)')
variant('adol-c', default=True,
description='Compile with ADOL-C')
variant('ginkgo', default=True,
description='Compile with Ginkgo')
variant('gmsh', default=True,
description='Compile with GMSH')
variant('gsl', default=True,
description='Compile with GSL')
variant('hdf5', default=True,
description='Compile with HDF5 (only with MPI)')
variant('metis', default=True,
description='Compile with Metis')
variant('muparser', default=True,
description='Compile with muParser')
variant('nanoflann', default=True,
description='Compile with Nanoflann')
variant('netcdf', default=False,
description='Compile with Netcdf (only with MPI)')
variant('oce', default=True,
description='Compile with OCE')
variant('p4est', default=True,
description='Compile with P4est (only with MPI)')
variant('petsc', default=True,
description='Compile with Petsc (only with MPI)')
variant('scalapack', default=True,
description='Compile with ScaLAPACK (only with MPI)')
variant('sundials', default=True,
description='Compile with Sundials')
variant('slepc', default=True,
description='Compile with Slepc (only with Petsc and MPI)')
variant('symengine', default=True,
description='Compile with SymEngine')
variant('threads', default=True,
description='Compile with multi-threading via TBB')
variant('trilinos', default=True,
description='Compile with Trilinos (only with MPI)')
# Required dependencies: Light version
depends_on('blas')
# Boost 1.58 is blacklisted, require at least 1.59, see
# https://github.com/dealii/dealii/issues/1591
# There are issues with 1.65.1 and 1.65.0:
# https://github.com/dealii/dealii/issues/5262
# we take the patch from https://github.com/boostorg/serialization/pull/79
# more precisely its variation https://github.com/dealii/dealii/pull/5572#issuecomment-349742019
# 1.68.0 has issues with serialization https://github.com/dealii/dealii/issues/7074
# adopt https://github.com/boostorg/serialization/pull/105 as a fix
depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:+thread+system+serialization+iostreams',
patches=[patch('boost_1.65.1_singleton.patch',
level=1,
when='@1.65.1'),
patch('boost_1.68.0.patch',
level=1,
when='@1.68.0'),
],
when='~python')
depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:+thread+system+serialization+iostreams+python',
patches=[patch('boost_1.65.1_singleton.patch',
level=1,
when='@1.65.1'),
patch('boost_1.68.0.patch',
level=1,
when='@1.68.0'),
],
when='+python')
# The std::auto_ptr is removed in the C++ 17 standard.
# See https://github.com/dealii/dealii/issues/4662
# and related topics discussed for other software libraries.
depends_on('boost cxxstd=11', when='cxxstd=11')
depends_on('boost cxxstd=14', when='cxxstd=14')
depends_on('boost cxxstd=17', when='cxxstd=17')
depends_on('bzip2', when='@:8.99')
depends_on('lapack')
depends_on('ninja', type='build')
depends_on('suite-sparse')
depends_on('zlib')
# Optional dependencies: Configuration
depends_on('cuda@8:', when='+cuda')
depends_on('cmake@3.9:', when='+cuda', type='build')
# Older version of deal.II do not build with Cmake 3.10, see
# https://github.com/dealii/dealii/issues/5510
depends_on('cmake@:3.9.99', when='@:8.99', type='build')
depends_on('mpi', when='+mpi')
depends_on('python', when='@8.5.0:+python')
# Optional dependencies: Packages
depends_on('adol-c@2.6.4:', when='@9.0:+adol-c')
depends_on('arpack-ng+mpi', when='+arpack+mpi')
depends_on('assimp', when='@9.0:+assimp')
depends_on('doxygen+graphviz', when='+doc')
depends_on('graphviz', when='+doc')
depends_on('ginkgo', when='@9.1:+ginkgo')
depends_on('gmsh+tetgen+netgen+oce', when='@9.0:+gmsh', type=('build', 'run'))
depends_on('gsl', when='@8.5.0:+gsl')
# FIXME: next line fixes concretization with petsc
depends_on('hdf5+mpi+hl+fortran', when='+hdf5+mpi+petsc')
depends_on('hdf5+mpi+hl', when='+hdf5+mpi~petsc')
# FIXME: concretizer bug. The two lines mimic what comes from PETSc
# but we should not need it
depends_on('metis@5:+int64', when='+metis+int64')
depends_on('metis@5:~int64', when='+metis~int64')
depends_on('muparser', when='+muparser')
# Nanoflann support has been removed after 9.2.0
depends_on('nanoflann', when='@9.0:9.2+nanoflann')
depends_on('netcdf-c+mpi', when='+netcdf+mpi')
depends_on('netcdf-cxx', when='+netcdf+mpi')
depends_on('oce', when='+oce')
depends_on('p4est', when='+p4est+mpi')
depends_on('petsc+mpi~int64', when='+petsc+mpi~int64')
depends_on('petsc+mpi+int64', when='+petsc+mpi+int64')
depends_on('petsc@:3.6.4', when='@:8.4.1+petsc+mpi')
depends_on('scalapack', when='@9.0:+scalapack')
depends_on('slepc', when='+slepc+petsc+mpi')
depends_on('slepc@:3.6.3', when='@:8.4.1+slepc+petsc+mpi')
depends_on('slepc~arpack', when='+slepc+petsc+mpi+int64')
depends_on('sundials@:3~pthread', when='@9.0:+sundials')
depends_on('trilinos gotype=int', when='+trilinos@12.18.1:')
# Both Trilinos and SymEngine bundle the Teuchos RCP library.
# This leads to conflicts between macros defined in the included
# headers when they are not compiled in the same mode.
# See https://github.com/symengine/symengine/issues/1516
# FIXME: uncomment when the following is fixed
# https://github.com/spack/spack/issues/11160
# depends_on("symengine@0.4: build_type=Release", when="@9.1:+symengine+trilinos^trilinos~debug") # NOQA: ignore=E501
# depends_on("symengine@0.4: build_type=Debug", when="@9.1:+symengine+trilinos^trilinos+debug") # NOQA: ignore=E501
depends_on('symengine@0.4:', when='@9.1:+symengine')
depends_on('symengine@0.6:', when='@9.2:+symengine')
depends_on('tbb', when='+threads')
# do not require +rol to make concretization of xsdk possible
depends_on('trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos', when='+trilinos+mpi~int64~cuda')
depends_on('trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos~hypre', when='+trilinos+mpi+int64~cuda')
# FIXME: temporary disable Tpetra when using CUDA due to
# namespace "Kokkos::Impl" has no member "cuda_abort"
depends_on('trilinos@master+amesos+aztec+epetra+ifpack+ml+muelu+rol+sacado+teuchos~amesos2~ifpack2~intrepid2~kokkos~tpetra~zoltan2', when='+trilinos+mpi~int64+cuda')
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')
# Explicitly provide a destructor in BlockVector,
# otherwise deal.II may fail to build with Intel compilers.
patch('https://github.com/dealii/dealii/commit/a89d90f9993ee9ad39e492af466b3595c06c3e25.patch',
sha256='4282b32e96f2f5d376eb34f3fddcc4615fcd99b40004cca784eb874288d1b31c',
when='@9.0.1')
# https://github.com/dealii/dealii/pull/7935
patch('https://github.com/dealii/dealii/commit/f8de8c5c28c715717bf8a086e94f071e0fe9deab.patch',
sha256='61f217744b70f352965be265d2f06e8c1276685e2944ca0a88b7297dd55755da',
when='@9.0.1 ^boost@1.70.0:')
# Fix TBB version check
# https://github.com/dealii/dealii/pull/9208
patch('https://github.com/dealii/dealii/commit/80b13fe5a2eaefc77fa8c9266566fa8a2de91edf.patch',
sha256='6f876dc8eadafe2c4ec2a6673864fb451c6627ca80511b6e16f3c401946fdf33',
when='@9.0.0:9.1.1')
# Check for sufficiently modern versions
conflicts('cxxstd=98', when='@9.0:')
conflicts('cxxstd=11', when='@9.3:')
# Interfaces added in 8.5.0:
for p in ['gsl', 'python']:
conflicts('+{0}'.format(p), when='@:8.4.2',
msg='The interface to {0} is supported from version 8.5.0 '
'onwards. Please explicitly disable this variant '
'via ~{0}'.format(p))
# Interfaces added in 9.0.0:
for p in ['assimp', 'gmsh', 'nanoflann', 'scalapack', 'sundials',
'adol-c']:
conflicts('+{0}'.format(p), when='@:8.5.1',
msg='The interface to {0} is supported from version 9.0.0 '
'onwards. Please explicitly disable this variant '
'via ~{0}'.format(p))
# interfaces added in 9.1.0:
for p in ['ginkgo', 'symengine']:
conflicts('+{0}'.format(p), when='@:9.0',
msg='The interface to {0} is supported from version 9.1.0 '
'onwards. Please explicitly disable this variant '
'via ~{0}'.format(p))
# Interfaces removed in 9.3.0:
conflicts('+nanoflann', when='@9.3.0:',
msg='The interface to Nanoflann was removed from version 9.3.0. '
'Please explicitly disable this variant via ~nanoflann')
# Check that the combination of variants makes sense
# 64-bit BLAS:
for p in ['openblas', 'intel-mkl', 'intel-parallel-studio+mkl']:
conflicts('^{0}+ilp64'.format(p), when='@:8.5.1',
msg='64bit BLAS is only supported from 9.0.0')
# MPI requirements:
for p in ['arpack', 'hdf5', 'netcdf', 'p4est', 'petsc', 'scalapack',
'slepc', 'trilinos']:
conflicts('+{0}'.format(p), when='~mpi',
msg='To enable {0} it is necessary to build deal.II with '
'MPI support enabled.'.format(p))
# Optional dependencies:
conflicts('+adol-c', when='^trilinos+chaco',
msg='symbol clash between the ADOL-C library and '
'Trilinos SEACAS Chaco.')
conflicts('+slepc', when='~petsc',
msg='It is not possible to enable slepc interfaces '
'without petsc.')
def cmake_args(self):
spec = self.spec
options = []
# Release flags
cxx_flags_release = []
# Debug and release flags
cxx_flags = []
# Set directory structure:
if spec.satisfies('@:8.2.1'):
options.append(
self.define('DEAL_II_COMPONENT_COMPAT_FILES', False)
)
else:
options.extend([
self.define(
'DEAL_II_EXAMPLES_RELDIR', 'share/deal.II/examples'
),
self.define('DEAL_II_DOCREADME_RELDIR', 'share/deal.II/'),
self.define('DEAL_II_DOCHTML_RELDIR', 'share/deal.II/doc')
])
# Required dependencies
lapack_blas_libs = spec['lapack'].libs + spec['blas'].libs
lapack_blas_headers = spec['lapack'].headers + spec['blas'].headers
options.extend([
self.define('BOOST_DIR', spec['boost'].prefix),
# CMake's FindBlas/Lapack may pickup system's blas/lapack instead
# of Spack's. Be more specific to avoid this.
# Note that both lapack and blas are provided in -DLAPACK_XYZ.
self.define('LAPACK_FOUND', True),
self.define(
'LAPACK_INCLUDE_DIRS',
';'.join(lapack_blas_headers.directories)
),
self.define('LAPACK_LIBRARIES', lapack_blas_libs.joined(';')),
self.define('UMFPACK_DIR', spec['suite-sparse'].prefix),
self.define('ZLIB_DIR', spec['zlib'].prefix),
self.define('DEAL_II_ALLOW_BUNDLED', False)
])
if spec.satisfies('@:8.99'):
options.extend([
# Cmake may still pick up system's bzip2, fix this:
self.define('BZIP2_FOUND', True),
self.define(
'BZIP2_INCLUDE_DIRS', spec['bzip2'].prefix.include
),
self.define('BZIP2_LIBRARIES', spec['bzip2'].libs.joined(';'))
])
# Doxygen documentation
options.append(self.define_from_variant(
'DEAL_II_COMPONENT_DOCUMENTATION', 'doc'
))
# Examples / tutorial programs
options.append(self.define_from_variant(
'DEAL_II_COMPONENT_EXAMPLES', 'examples'
))
# Enforce the specified C++ standard
if spec.variants['cxxstd'].value != 'default':
cxxstd = spec.variants['cxxstd'].value
options.append(
self.define('DEAL_II_WITH_CXX{0}'.format(cxxstd), True)
)
# Performance
# Set recommended flags for maximum (matrix-free) performance, see
# https://groups.google.com/forum/?fromgroups#!topic/dealii/3Yjy8CBIrgU
if spec.satisfies('%gcc'):
cxx_flags_release.extend(['-O3'])
elif spec.satisfies('%intel'):
cxx_flags_release.extend(['-O3'])
elif spec.satisfies('%clang') or spec.satisfies('%apple-clang'):
cxx_flags_release.extend(['-O3', '-ffp-contract=fast'])
# 64 bit indices
options.append(self.define_from_variant(
'DEAL_II_WITH_64BIT_INDICES', 'int64'
))
if (spec.satisfies('^openblas+ilp64') or
spec.satisfies('^intel-mkl+ilp64') or
spec.satisfies('^intel-parallel-studio+mkl+ilp64')):
options.append(
self.define('LAPACK_WITH_64BIT_BLAS_INDICES', True)
)
# CUDA
options.append(self.define_from_variant(
'DEAL_II_WITH_CUDA', 'cuda'
))
if '+cuda' in spec:
if not spec.satisfies('^cuda@9:'):
options.append('-DDEAL_II_WITH_CXX14=OFF')
cuda_arch = spec.variants['cuda_arch'].value
if cuda_arch != 'none':
if len(cuda_arch) > 1:
raise InstallError(
'deal.II only supports compilation for a single GPU!'
)
flags = '-arch=sm_{0}'.format(cuda_arch[0])
# FIXME: there are some compiler errors in dealii
# with: flags = ' '.join(self.cuda_flags(cuda_arch))
# Stick with -arch=sm_xy for now.
options.append(
self.define('DEAL_II_CUDA_FLAGS', flags)
)
# MPI
options.append(self.define_from_variant(
'DEAL_II_WITH_MPI', 'mpi'
))
if '+mpi' in spec:
options.extend([
self.define('CMAKE_C_COMPILER', spec['mpi'].mpicc),
self.define('CMAKE_CXX_COMPILER', spec['mpi'].mpicxx),
self.define('CMAKE_Fortran_COMPILER', spec['mpi'].mpifc),
self.define('MPI_C_COMPILER', spec['mpi'].mpicc),
self.define('MPI_CXX_COMPILER', spec['mpi'].mpicxx),
self.define('MPI_Fortran_COMPILER', spec['mpi'].mpifc)
])
if '+cuda' in spec:
options.extend([
self.define('DEAL_II_MPI_WITH_CUDA_SUPPORT',
spec['mpi'].satisfies('+cuda')),
self.define('CUDA_HOST_COMPILER', spec['mpi'].mpicxx)
])
# Python bindings
if spec.satisfies('@8.5.0:'):
options.append(self.define_from_variant(
'DEAL_II_COMPONENT_PYTHON_BINDINGS', 'python'
))
if '+python' in spec:
python_exe = spec['python'].command.path
python_library = spec['python'].libs[0]
python_include = spec['python'].headers.directories[0]
options.extend([
self.define('PYTHON_EXECUTABLE', python_exe),
self.define('PYTHON_INCLUDE_DIR', python_include),
self.define('PYTHON_LIBRARY', python_library)
])
# Threading
options.append(self.define_from_variant(
'DEAL_II_WITH_THREADS', 'threads'
))
if '+threads' in spec:
if (spec.satisfies('^intel-parallel-studio+tbb')):
# deal.II/cmake will have hard time picking up TBB from Intel.
tbb_ver = '.'.join(('%s' % spec['tbb'].version).split('.')[1:])
options.extend([
self.define('TBB_FOUND', True),
self.define('TBB_VERSION', tbb_ver),
self.define(
'TBB_INCLUDE_DIRS',
';'.join(spec['tbb'].headers.directories)
),
self.define('TBB_LIBRARIES', spec['tbb'].libs.joined(';'))
])
else:
options.append(
self.define('TBB_DIR', spec['tbb'].prefix)
)
# Optional dependencies for which library names are the same as CMake
# variables:
for library in (
'gsl', 'hdf5', 'p4est', 'petsc', 'slepc', 'trilinos', 'metis',
'sundials', 'nanoflann', 'assimp', 'gmsh', 'muparser',
'symengine', 'ginkgo'):
options.append(self.define_from_variant(
'DEAL_II_WITH_{0}'.format(library.upper()), library
))
if ('+' + library) in spec:
options.append(self.define(
'{0}_DIR'.format(library.upper()), spec[library].prefix
))
# Optional dependencies that do not fit the above pattern:
# ADOL-C
options.append(self.define_from_variant(
'DEAL_II_WITH_ADOLC', 'adol-c'
))
if '+adol-c' in spec:
options.append(
self.define('ADOLC_DIR', spec['adol-c'].prefix)
)
# ARPACK
options.append(self.define_from_variant(
'DEAL_II_WITH_ARPACK', 'arpack'
))
if '+arpack' in spec and '+mpi' in spec:
options.extend([
self.define('ARPACK_DIR', spec['arpack-ng'].prefix),
self.define('DEAL_II_ARPACK_WITH_PARPACK', True)
])
# NetCDF
# since Netcdf is spread among two, need to do it by hand:
if '+netcdf' in spec and '+mpi' in spec:
netcdf_libs = spec['netcdf-cxx'].libs + spec['netcdf-c'].libs
options.extend([
self.define('NETCDF_FOUND', True),
self.define('NETCDF_INCLUDE_DIRS', '{0};{1}'.format(
spec['netcdf-cxx'].prefix.include,
spec['netcdf-c'].prefix.include
)),
self.define('NETCDF_LIBRARIES', netcdf_libs.joined(';'))
])
else:
options.append(
self.define('DEAL_II_WITH_NETCDF', False)
)
# ScaLAPACK
options.append(self.define_from_variant(
'DEAL_II_WITH_SCALAPACK', 'scalapack'
))
if '+scalapack' in spec:
scalapack_libs = spec['scalapack'].libs
options.extend([
self.define('SCALAPACK_FOUND', True),
self.define(
'SCALAPACK_INCLUDE_DIRS', spec['scalapack'].prefix.include
),
self.define('SCALAPACK_LIBRARIES', scalapack_libs.joined(';'))
])
# Open Cascade
options.append(self.define_from_variant(
'DEAL_II_WITH_OPENCASCADE', 'oce'
))
if '+oce' in spec:
options.append(
self.define('OPENCASCADE_DIR', spec['oce'].prefix)
)
# As a final step, collect CXX flags that may have been
# added anywhere above:
if len(cxx_flags_release) > 0 and '+optflags' in spec:
options.extend([
self.define(
'CMAKE_CXX_FLAGS_RELEASE', ' '.join(cxx_flags_release)
),
self.define('CMAKE_CXX_FLAGS', ' '.join(cxx_flags))
])
# Add flags for machine vectorization, used when tutorials
# and user code is built.
# See https://github.com/dealii/dealii/issues/9164
options.append(
self.define('DEAL_II_CXX_FLAGS', os.environ['SPACK_TARGET_ARGS'])
)
return options
def setup_run_environment(self, env):
env.set('DEAL_II_DIR', self.prefix)
def setup_build_environment(self, env):
spec = self.spec
if '+cuda' in spec and '+mpi' in spec:
env.set('CUDAHOSTCXX', spec['mpi'].mpicxx)
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