spack/var/spack/repos/builtin/packages/dealii/package.py
2019-05-28 15:22:39 -05:00

455 lines
20 KiB
Python

# Copyright 2013-2019 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 *
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']
# Don't add RPATHs to this package for the full build DAG.
# only add for immediate deps.
transitive_rpaths = False
version('develop', branch='master')
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')
variant('mpi', default=True, description='Compile with MPI')
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('doc', default=False,
description='Compile with documentation')
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=True,
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('trilinos', default=True,
description='Compile with Trilinos (only with MPI)')
variant('python', default=False,
description='Compile with Python bindings')
variant('int64', default=False,
description='Compile with 64 bit indices support')
variant('optflags', default=False,
description='Compile using additional optimization flags')
variant('build_type', default='DebugRelease',
description='The build type to build',
values=('Debug', 'Release', 'DebugRelease'))
# 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')
# bzip2 is not needed since 9.0
depends_on('bzip2', when='@:8.99')
depends_on('lapack')
depends_on('suite-sparse')
depends_on('tbb')
depends_on('zlib')
# optional dependencies
depends_on('mpi', when='+mpi')
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')
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')
# 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')
depends_on('nanoflann', when='@9.0:+nanoflann')
depends_on('netcdf+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('python', when='@8.5.0:+python')
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')
# 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')
# 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:')
# 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')
# 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))
conflicts('+slepc', when='~petsc',
msg='It is not possible to enable slepc interfaces '
'without petsc.')
conflicts('+adol-c', when='^trilinos+chaco',
msg='symbol clash between the ADOL-C library and '
'Trilinos SEACAS Chaco.')
# 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))
# 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))
def cmake_args(self):
spec = self.spec
options = []
# release flags
cxx_flags_release = []
# debug and release flags
cxx_flags = []
lapack_blas_libs = spec['lapack'].libs + spec['blas'].libs
lapack_blas_headers = spec['lapack'].headers + spec['blas'].headers
options.extend([
'-DDEAL_II_COMPONENT_EXAMPLES=ON',
'-DDEAL_II_WITH_THREADS:BOOL=ON',
'-DBOOST_DIR=%s' % 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.
'-DLAPACK_FOUND=true',
'-DLAPACK_INCLUDE_DIRS=%s' % ';'.join(
lapack_blas_headers.directories),
'-DLAPACK_LIBRARIES=%s' % lapack_blas_libs.joined(';'),
'-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
'-DZLIB_DIR=%s' % spec['zlib'].prefix,
'-DDEAL_II_ALLOW_BUNDLED=OFF'
])
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([
'-DTBB_FOUND=true',
'-DTBB_VERSION=%s' % tbb_ver,
'-DTBB_INCLUDE_DIRS=%s' % ';'.join(
spec['tbb'].headers.directories),
'-DTBB_LIBRARIES=%s' % spec['tbb'].libs.joined(';')
])
else:
options.append('-DTBB_DIR=%s' % spec['tbb'].prefix)
if (spec.satisfies('^openblas+ilp64') or
spec.satisfies('^intel-mkl+ilp64') or
spec.satisfies('^intel-parallel-studio+mkl+ilp64')):
options.append('-DLAPACK_WITH_64BIT_BLAS_INDICES=ON')
if spec.satisfies('@:8.99'):
options.extend([
# Cmake may still pick up system's bzip2, fix this:
'-DBZIP2_FOUND=true',
'-DBZIP2_INCLUDE_DIRS=%s' % spec['bzip2'].prefix.include,
'-DBZIP2_LIBRARIES=%s' % spec['bzip2'].libs.joined(';')
])
# 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'])
cxx_flags.extend(['-march=native'])
elif spec.satisfies('%intel'):
cxx_flags_release.extend(['-O3'])
cxx_flags.extend(['-march=native'])
elif spec.satisfies('%clang'):
cxx_flags_release.extend(['-O3', '-ffp-contract=fast'])
cxx_flags.extend(['-march=native'])
# Python bindings
if spec.satisfies('@8.5.0:'):
options.extend([
'-DDEAL_II_COMPONENT_PYTHON_BINDINGS=%s' %
('ON' if '+python' in spec else 'OFF')
])
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([
'-DPYTHON_EXECUTABLE=%s' % python_exe,
'-DPYTHON_INCLUDE_DIR=%s' % python_include,
'-DPYTHON_LIBRARY=%s' % python_library
])
# Set directory structure:
if spec.satisfies('@:8.2.1'):
options.extend(['-DDEAL_II_COMPONENT_COMPAT_FILES=OFF'])
else:
options.extend([
'-DDEAL_II_EXAMPLES_RELDIR=share/deal.II/examples',
'-DDEAL_II_DOCREADME_RELDIR=share/deal.II/',
'-DDEAL_II_DOCHTML_RELDIR=share/deal.II/doc'
])
# CUDA
if '+cuda' in spec:
options.append(
'-DDEAL_II_WITH_CUDA=ON'
)
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(
'-DDEAL_II_CUDA_FLAGS={0}'.format(flags)
)
else:
options.extend([
'-DDEAL_II_WITH_CUDA=OFF',
])
# MPI
if '+mpi' in spec:
options.extend([
'-DDEAL_II_WITH_MPI:BOOL=ON',
'-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
'-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
'-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
])
else:
options.extend([
'-DDEAL_II_WITH_MPI:BOOL=OFF',
])
# 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'):
if ('+' + library) in spec:
options.extend([
'-D%s_DIR=%s' % (library.upper(), spec[library].prefix),
'-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)