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Update formatting to meet code style requirements.

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Kelly (KT) Thompson 2016-06-12 19:56:29 -06:00
parent b89bcdff62
commit 31d2c38687
1 changed files with 113 additions and 80 deletions
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193
var/spack/repos/builtin/packages/trilinos/package.py
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@ -23,18 +23,23 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import os, sys, glob
import os
import sys
# Trilinos is complicated to build, as an inspiration a couple of links to other repositories which build it:
# Trilinos is complicated to build, as an inspiration a couple of links to
# other repositories which build it:
# https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/t/trilinos.py#L111
# https://github.com/koecher/candi/blob/master/deal.II-toolchain/packages/trilinos.package
# https://gitlab.com/configurations/cluster-config/blob/master/trilinos.sh
# https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb
# and some relevant documentation/examples:
# https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb and some
# relevant documentation/examples:
# https://github.com/trilinos/Trilinos/issues/175
class Trilinos(Package):
"""The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented
software framework for the solution of large-scale, complex multi-physics engineering and scientific problems.
"""The Trilinos Project is an effort to develop algorithms and enabling
technologies within an object-oriented software framework for the solution
of large-scale, complex multi-physics engineering and scientific problems.
A unique design feature of Trilinos is its focus on packages.
"""
homepage = "https://trilinos.org/"
@ -54,7 +59,8 @@ class Trilinos(Package):
variant('hypre', default=True, description='Compile with Hypre preconditioner')
variant('hdf5', default=True, description='Compile with HDF5')
variant('suite-sparse', default=True, description='Compile with SuiteSparse solvers')
# not everyone has py-numpy activated, keep it disabled by default to avoid configure errors
# not everyone has py-numpy activated, keep it disabled by default to avoid
# configure errors
variant('python', default=False, description='Build python wrappers')
variant('shared', default=True, description='Enables the build of shared libraries')
variant('debug', default=False, description='Builds a debug version of the libraries')
@ -67,37 +73,37 @@ class Trilinos(Package):
depends_on('matio')
depends_on('glm')
depends_on('swig')
depends_on('metis@5:',when='+metis')
depends_on('suite-sparse',when='+suite-sparse')
depends_on('metis@5:', when='+metis')
depends_on('suite-sparse', when='+suite-sparse')
# MPI related dependencies
depends_on('mpi')
depends_on('netcdf+mpi')
depends_on('parmetis',when='+metis')
# Trilinos' Tribits config system is limited which makes it
# very tricky to link Amesos with static MUMPS, see
depends_on('parmetis', when='+metis')
# Trilinos' Tribits config system is limited which makes it very tricky to
# link Amesos with static MUMPS, see
# https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html
# One could work it out by getting linking flags from mpif90 --showme:link (or alike)
# and adding results to -DTrilinos_EXTRA_LINK_FLAGS
# together with Blas and Lapack and ScaLAPACK and Blacs and -lgfortran and
# it may work at the end. But let's avoid all this by simply using shared libs
depends_on('mumps@5.0:+mpi+shared',when='+mumps')
depends_on('scalapack',when='+mumps')
depends_on('superlu-dist',when='+superlu-dist')
depends_on('hypre~internal-superlu',when='+hypre')
depends_on('hdf5+mpi',when='+hdf5')
depends_on('python',when='+python')
# One could work it out by getting linking flags from mpif90 --showme:link
# (or alike) and adding results to -DTrilinos_EXTRA_LINK_FLAGS together
# with Blas and Lapack and ScaLAPACK and Blacs and -lgfortran and it may
# work at the end. But let's avoid all this by simply using shared libs
depends_on('mumps@5.0:+mpi+shared', when='+mumps')
depends_on('scalapack', when='+mumps')
depends_on('superlu-dist', when='+superlu-dist')
depends_on('hypre~internal-superlu', when='+hypre')
depends_on('hdf5+mpi', when='+hdf5')
depends_on('python', when='+python')
patch('umfpack_from_suitesparse.patch')
# check that the combination of variants makes sense
def variants_check(self):
if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'):
# For Trilinos v11 we need to force SuperLUDist=OFF,
# since only the deprecated SuperLUDist v3.3 together with an Amesos patch
# is working.
raise RuntimeError('The superlu-dist variant can only be used with Trilinos @12.0.1:')
# For Trilinos v11 we need to force SuperLUDist=OFF, since only the
# deprecated SuperLUDist v3.3 together with an Amesos patch is
# working.
raise RuntimeError('The superlu-dist variant can only be used' +
' with Trilinos @12.0.1:')
def install(self, spec, prefix):
self.variants_check()
@ -107,27 +113,32 @@ def install(self, spec, prefix):
options.extend(std_cmake_args)
mpi_bin = spec['mpi'].prefix.bin
options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
'-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
'-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF',
'-DTrilinos_ENABLE_TESTS:BOOL=OFF',
'-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
'-DCMAKE_BUILD_TYPE:STRING=%s' % ('DEBUG' if '+debug' in spec else 'RELEASE'),
'-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
'-DTPL_ENABLE_MPI:BOOL=ON',
'-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
'-DTPL_ENABLE_BLAS=ON',
'-DBLAS_LIBRARY_NAMES=blas', # FIXME: don't hardcode names
'-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib,
'-DTPL_ENABLE_LAPACK=ON',
'-DLAPACK_LIBRARY_NAMES=lapack',
'-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix,
'-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
'-DTrilinos_ENABLE_CXX11:BOOL=ON',
'-DTPL_ENABLE_Netcdf:BOOL=ON',
'-DTPL_ENABLE_HYPRE:BOOL=%s' % ('ON' if '+hypre' in spec else 'OFF'),
'-DTPL_ENABLE_HDF5:BOOL=%s' % ('ON' if '+hdf5' in spec else 'OFF'),
])
options.extend([
'-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
'-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
'-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF',
'-DTrilinos_ENABLE_TESTS:BOOL=OFF',
'-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
'-DCMAKE_BUILD_TYPE:STRING=%s' % (
'DEBUG' if '+debug' in spec else 'RELEASE'),
'-DBUILD_SHARED_LIBS:BOOL=%s' % (
'ON' if '+shared' in spec else 'OFF'),
'-DTPL_ENABLE_MPI:BOOL=ON',
'-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
'-DTPL_ENABLE_BLAS=ON',
'-DBLAS_LIBRARY_NAMES=blas', # FIXME: don't hardcode names
'-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib,
'-DTPL_ENABLE_LAPACK=ON',
'-DLAPACK_LIBRARY_NAMES=lapack',
'-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix,
'-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
'-DTrilinos_ENABLE_CXX11:BOOL=ON',
'-DTPL_ENABLE_Netcdf:BOOL=ON',
'-DTPL_ENABLE_HYPRE:BOOL=%s' % (
'ON' if '+hypre' in spec else 'OFF'),
'-DTPL_ENABLE_HDF5:BOOL=%s' % (
'ON' if '+hdf5' in spec else 'OFF'),
])
if '+boost' in spec:
options.extend([
@ -137,29 +148,40 @@ def install(self, spec, prefix):
])
else:
options.extend(['-DTPL_ENABLE_Boost:BOOL=OFF'])
# Fortran lib
libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read())
libgfortran = os.path.dirname(os.popen(
'%s --print-file-name libgfortran.a' %
join_path(mpi_bin, 'mpif90')).read())
options.extend([
'-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran,
'-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % (
libgfortran),
'-DTrilinos_ENABLE_Fortran=ON'
])
# for build-debug only:
#options.extend([
# '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
#])
# options.extend([
# '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
# ])
# suite-sparse related
if '+suite-sparse' in spec:
options.extend([
'-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file?
#'-DTPL_ENABLE_Cholmod:BOOL=ON',
#'-DCholmod_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
#'-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
# FIXME: Trilinos seems to be looking for static libs only,
# patch CMake TPL file?
'-DTPL_ENABLE_Cholmod:BOOL=OFF',
# '-DTPL_ENABLE_Cholmod:BOOL=ON',
# '-DCholmod_LIBRARY_DIRS:PATH=%s' % (
# spec['suite-sparse'].prefix.lib,
# '-DCholmod_INCLUDE_DIRS:PATH=%s' % (
# spec['suite-sparse'].prefix.include,
'-DTPL_ENABLE_UMFPACK:BOOL=ON',
'-DUMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
'-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
'-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
'-DUMFPACK_LIBRARY_DIRS:PATH=%s' % (
spec['suite-sparse'].prefix.lib),
'-DUMFPACK_INCLUDE_DIRS:PATH=%s' % (
spec['suite-sparse'].prefix.include),
'-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;' +
'suitesparseconfig'
])
else:
options.extend([
@ -175,9 +197,11 @@ def install(self, spec, prefix):
'-DMETIS_LIBRARY_NAMES=metis',
'-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include,
'-DTPL_ENABLE_ParMETIS:BOOL=ON',
'-DParMETIS_LIBRARY_DIRS=%s;%s' % (spec['parmetis'].prefix.lib,spec['metis'].prefix.lib),
'-DParMETIS_LIBRARY_DIRS=%s;%s' % (
spec['parmetis'].prefix.lib, spec['metis'].prefix.lib),
'-DParMETIS_LIBRARY_NAMES=parmetis;metis',
'-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include
'-DTPL_ParMETIS_INCLUDE_DIRS=%s' % (
spec['parmetis'].prefix.include)
])
else:
options.extend([
@ -190,11 +214,14 @@ def install(self, spec, prefix):
options.extend([
'-DTPL_ENABLE_MUMPS:BOOL=ON',
'-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
'-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord', # order is important!
# order is important!
'-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord',
'-DTPL_ENABLE_SCALAPACK:BOOL=ON',
'-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
# FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
'-DSCALAPACK_LIBRARY_NAMES=scalapack'
])
# see https://github.com/trilinos/Trilinos/blob/master/packages/amesos/README-MUMPS
# see
# https://github.com/trilinos/Trilinos/blob/master/packages/amesos/README-MUMPS
cxx_flags.extend([
'-DMUMPS_5_0'
])
@ -207,16 +234,20 @@ def install(self, spec, prefix):
# superlu-dist:
if '+superlu-dist' in spec:
# Amesos, conflicting types of double and complex SLU_D
# see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
# and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
# see
# https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
# and
# https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
options.extend([
'-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
'-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
])
options.extend([
'-DTPL_ENABLE_SuperLUDist:BOOL=ON',
'-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib,
'-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include
'-DSuperLUDist_LIBRARY_DIRS=%s' %
spec['superlu-dist'].prefix.lib,
'-DSuperLUDist_INCLUDE_DIRS=%s' %
spec['superlu-dist'].prefix.include
])
if spec.satisfies('^superlu-dist@4.0:'):
options.extend([
@ -227,7 +258,6 @@ def install(self, spec, prefix):
'-DTPL_ENABLE_SuperLUDist:BOOL=OFF',
])
# python
if '+python' in spec:
options.extend([
@ -254,23 +284,26 @@ def install(self, spec, prefix):
'-DTrilinos_ENABLE_FEI=OFF'
])
with working_dir('spack-build', create=True):
cmake('..', *options)
make()
make('install')
# When trilinos is built with Python, libpytrilinos is included through
# cmake configure files. Namely, Trilinos_LIBRARIES in TrilinosConfig.cmake
# contains pytrilinos. This leads to a run-time error:
# Symbol not found: _PyBool_Type
# and prevents Trilinos to be used in any C++ code, which links executable
# against the libraries listed in Trilinos_LIBRARIES.
# See https://github.com/Homebrew/homebrew-science/issues/2148#issuecomment-103614509
# When trilinos is built with Python, libpytrilinos is included
# through cmake configure files. Namely, Trilinos_LIBRARIES in
# TrilinosConfig.cmake contains pytrilinos. This leads to a
# run-time error: Symbol not found: _PyBool_Type and prevents
# Trilinos to be used in any C++ code, which links executable
# against the libraries listed in Trilinos_LIBRARIES. See
# https://github.com/Homebrew/homebrew-science/issues/2148#issuecomment-103614509
# A workaround it to remove PyTrilinos from the COMPONENTS_LIST :
if '+python' in self.spec:
filter_file(r'(SET\(COMPONENTS_LIST.*)(PyTrilinos;)(.*)', (r'\1\3'), '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib)
filter_file(r'(SET\(COMPONENTS_LIST.*)(PyTrilinos;)(.*)',
(r'\1\3'),
'%s/cmake/Trilinos/TrilinosConfig.cmake' %
prefix.lib)
# The shared libraries are not installed correctly on Darwin; correct this
# The shared libraries are not installed correctly on Darwin;
# correct this
if (sys.platform == 'darwin') and ('+shared' in spec):
fix_darwin_install_name(prefix.lib)