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Merge pull request #1207 from davydden/pkg/dealii_update_petsc37

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dealii: update for petsc37
This commit is contained in:
Todd Gamblin 2016-07-11 15:32:32 -07:00 committed by GitHub
commit 15790d7018
1 changed files with 112 additions and 98 deletions
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210
var/spack/repos/builtin/packages/dealii/package.py
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@ -37,7 +37,7 @@ class Dealii(Package):
version('8.3.0', 'fc6cdcb16309ef4bea338a4f014de6fa') version('8.3.0', 'fc6cdcb16309ef4bea338a4f014de6fa')
version('8.2.1', '71c728dbec14f371297cd405776ccf08') version('8.2.1', '71c728dbec14f371297cd405776ccf08')
version('8.1.0', 'aa8fadc2ce5eb674f44f997461bf668d') version('8.1.0', 'aa8fadc2ce5eb674f44f997461bf668d')
version('dev', git='https://github.com/dealii/dealii.git') version('develop', git='https://github.com/dealii/dealii.git')
variant('mpi', default=True, description='Compile with MPI') variant('mpi', default=True, description='Compile with MPI')
variant('arpack', default=True, description='Compile with Arpack and PArpack (only with MPI)') variant('arpack', default=True, description='Compile with Arpack and PArpack (only with MPI)')
@ -73,20 +73,21 @@ class Dealii(Package):
depends_on("doxygen+graphviz", when='+doc') depends_on("doxygen+graphviz", when='+doc')
depends_on("graphviz", when='+doc') depends_on("graphviz", when='+doc')
depends_on("gsl", when='@8.5.0:+gsl') depends_on("gsl", when='@8.5.0:+gsl')
depends_on("gsl", when='@dev+gsl')
depends_on("hdf5+mpi", when='+hdf5+mpi') depends_on("hdf5+mpi", when='+hdf5+mpi')
depends_on("metis@5:", when='+metis') depends_on("metis@5:", when='+metis')
depends_on("netcdf+mpi", when="+netcdf+mpi") depends_on("netcdf+mpi", when="+netcdf+mpi")
depends_on("netcdf-cxx", when='+netcdf+mpi') depends_on("netcdf-cxx", when='+netcdf+mpi')
depends_on("oce", when='+oce') depends_on("oce", when='+oce')
depends_on("p4est", when='+p4est+mpi') depends_on("p4est", when='+p4est+mpi')
depends_on("petsc@:3.6.4+mpi", when='+petsc+mpi') # FIXME: update after 3.7 is supported upstream. # NOQA: ignore=E501 depends_on("petsc+mpi", when='@8.5.0:+petsc+mpi')
depends_on("slepc@:3.6.3", when='+slepc+petsc+mpi') depends_on("slepc", when='@8.5.0:+slepc+petsc+mpi')
depends_on("petsc@:3.6.4+mpi", when='@:8.4.1+petsc+mpi')
depends_on("slepc@:3.6.3", when='@:8.4.1+slepc+petsc+mpi')
depends_on("trilinos", when='+trilinos+mpi') depends_on("trilinos", when='+trilinos+mpi')
# developer dependnecies # developer dependnecies
depends_on("numdiff", when='@dev') depends_on("numdiff", when='@develop')
depends_on("astyle@2.04", when='@dev') depends_on("astyle@2.04", when='@develop')
def install(self, spec, prefix): def install(self, spec, prefix):
options = [] options = []
@ -119,6 +120,16 @@ def install(self, spec, prefix):
'-DZLIB_DIR=%s' % spec['zlib'].prefix '-DZLIB_DIR=%s' % spec['zlib'].prefix
]) ])
# 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'
])
# MPI # MPI
if '+mpi' in spec: if '+mpi' in spec:
options.extend([ options.extend([
@ -193,115 +204,118 @@ def install(self, spec, prefix):
]) ])
cmake('.', *options) cmake('.', *options)
make() make()
make("test") if self.run_tests:
make("test")
make("install") make("install")
# run some MPI examples with different solvers from PETSc and Trilinos # run some MPI examples with different solvers from PETSc and Trilinos
env['DEAL_II_DIR'] = prefix if self.run_tests:
print('=====================================') env['DEAL_II_DIR'] = prefix
print('============ EXAMPLES ===============')
print('=====================================')
# take bare-bones step-3
print('=====================================')
print('============ Step-3 =================')
print('=====================================')
with working_dir('examples/step-3'):
cmake('.')
make('release')
make('run', parallel=False)
# An example which uses Metis + PETSc
# FIXME: switch step-18 to MPI
with working_dir('examples/step-18'):
print('=====================================') print('=====================================')
print('============= Step-18 ===============') print('============ EXAMPLES ===============')
print('=====================================') print('=====================================')
# list the number of cycles to speed up # take bare-bones step-3
filter_file(r'(end_time = 10;)', ('end_time = 3;'), 'step-18.cc') print('=====================================')
if '^petsc' in spec and '^metis' in spec: print('============ Step-3 =================')
print('=====================================')
with working_dir('examples/step-3'):
cmake('.') cmake('.')
make('release') make('release')
make('run', parallel=False) make('run', parallel=False)
# take step-40 which can use both PETSc and Trilinos # An example which uses Metis + PETSc
# FIXME: switch step-40 to MPI run # FIXME: switch step-18 to MPI
with working_dir('examples/step-40'): with working_dir('examples/step-18'):
print('=====================================')
print('========== Step-40 PETSc ============')
print('=====================================')
# list the number of cycles to speed up
filter_file(r'(const unsigned int n_cycles = 8;)',
('const unsigned int n_cycles = 2;'), 'step-40.cc')
cmake('.')
if '^petsc' in spec:
make('release')
make('run', parallel=False)
print('=====================================')
print('========= Step-40 Trilinos ==========')
print('=====================================')
# change Linear Algebra to Trilinos
# The below filter_file should be different for versions
# before and after 8.4.0
if spec.satisfies('@8.4.0:') or spec.satisfies('@dev'):
filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)',
('#define FORCE_USE_OF_TRILINOS'), 'step-40.cc')
else:
filter_file(r'(#define USE_PETSC_LA.*)',
('// #define USE_PETSC_LA'), 'step-40.cc')
if '^trilinos+hypre' in spec:
make('release')
make('run', parallel=False)
# the rest of the tests on step 40 only works for
# dealii version 8.4.0 and after
if spec.satisfies('@8.4.0:') or spec.satisfies('@dev'):
print('=====================================') print('=====================================')
print('=== Step-40 Trilinos SuperluDist ====') print('============= Step-18 ===============')
print('=====================================') print('=====================================')
# change to direct solvers # list the number of cycles to speed up
filter_file(r'(LA::SolverCG solver\(solver_control\);)', ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc') # NOQA: ignore=E501 filter_file(r'(end_time = 10;)', ('end_time = 3;'),
filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)', 'step-18.cc')
(''), 'step-40.cc') if '^petsc' in spec and '^metis' in spec:
filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)', # NOQA: ignore=E501 cmake('.')
(''), 'step-40.cc')
filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', # NOQA: ignore=E501
(''), 'step-40.cc')
filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc') # NOQA: ignore=E501
filter_file(r'(preconditioner\);)', (''), 'step-40.cc')
if '^trilinos+superlu-dist' in spec:
make('release')
make('run', paralle=False)
print('=====================================')
print('====== Step-40 Trilinos MUMPS =======')
print('=====================================')
# switch to Mumps
filter_file(r'(Amesos_Superludist)',
('Amesos_Mumps'), 'step-40.cc')
if '^trilinos+mumps' in spec:
make('release') make('release')
make('run', parallel=False) make('run', parallel=False)
print('=====================================') # take step-40 which can use both PETSc and Trilinos
print('============ Step-36 ================') # FIXME: switch step-40 to MPI run
print('=====================================') with working_dir('examples/step-40'):
with working_dir('examples/step-36'): print('=====================================')
if 'slepc' in spec: print('========== Step-40 PETSc ============')
print('=====================================')
# list the number of cycles to speed up
filter_file(r'(const unsigned int n_cycles = 8;)',
('const unsigned int n_cycles = 2;'), 'step-40.cc')
cmake('.') cmake('.')
make('release') if '^petsc' in spec:
make('run', parallel=False) make('release')
make('run', parallel=False)
print('=====================================') print('=====================================')
print('============ Step-54 ================') print('========= Step-40 Trilinos ==========')
print('=====================================') print('=====================================')
with working_dir('examples/step-54'): # change Linear Algebra to Trilinos
if 'oce' in spec: # The below filter_file should be different for versions
cmake('.') # before and after 8.4.0
make('release') if spec.satisfies('@8.4.0:'):
make('run', parallel=False) filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)',
('#define FORCE_USE_OF_TRILINOS'),
'step-40.cc')
else:
filter_file(r'(#define USE_PETSC_LA.*)',
('// #define USE_PETSC_LA'), 'step-40.cc')
if '^trilinos+hypre' in spec:
make('release')
make('run', parallel=False)
# the rest of the tests on step 40 only works for
# dealii version 8.4.0 and after
if spec.satisfies('@8.4.0:'):
print('=====================================')
print('=== Step-40 Trilinos SuperluDist ====')
print('=====================================')
# change to direct solvers
filter_file(r'(LA::SolverCG solver\(solver_control\);)', ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc') # NOQA: ignore=E501
filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)',
(''), 'step-40.cc')
filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)', # NOQA: ignore=E501
(''), 'step-40.cc')
filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', # NOQA: ignore=E501
(''), 'step-40.cc')
filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc') # NOQA: ignore=E501
filter_file(r'(preconditioner\);)', (''), 'step-40.cc')
if '^trilinos+superlu-dist' in spec:
make('release')
make('run', paralle=False)
print('=====================================')
print('====== Step-40 Trilinos MUMPS =======')
print('=====================================')
# switch to Mumps
filter_file(r'(Amesos_Superludist)',
('Amesos_Mumps'), 'step-40.cc')
if '^trilinos+mumps' in spec:
make('release')
make('run', parallel=False)
print('=====================================')
print('============ Step-36 ================')
print('=====================================')
with working_dir('examples/step-36'):
if 'slepc' in spec:
cmake('.')
make('release')
make('run', parallel=False)
print('=====================================')
print('============ Step-54 ================')
print('=====================================')
with working_dir('examples/step-54'):
if 'oce' in spec:
cmake('.')
make('release')
make('run', parallel=False)
def setup_environment(self, spack_env, env): def setup_environment(self, spack_env, env):
env.set('DEAL_II_DIR', self.prefix) env.set('DEAL_II_DIR', self.prefix)