def test_slepc(backends):
"""Check for petsc + slepc."""
from dolfin import has_linear_algebra_backend, has_slepc
if has_linear_algebra_backend("PETSc") and has_slepc():
backends.append("petsc")
else:
print "Petsc + slepc not found."
def setup_fenics(simulation):
"""
Setup FEniCS parameters like linear algebra backend
"""
# Test for PETSc linear algebra backend
if not dolfin.has_linear_algebra_backend("PETSc"):
ocellaris_error(
'Missing PETSc',
'DOLFIN has not been configured with PETSc ' 'which is needed by Ocellaris.',
)
dolfin.parameters['linear_algebra_backend'] = 'PETSc'
# Form compiler "uflacs" needed for isoparametric elements
form_compiler = simulation.input.get_value('solver/form_compiler', 'auto', 'string')
dolfin.parameters['form_compiler']['representation'] = form_compiler
from setuptools import setup, find_packages
from os import path
from io import open
import re
try:
from dolfin import __version__ as dolfin_version
from dolfin import has_linear_algebra_backend, has_slepc
except ImportError:
raise
else:
fenics_version_major = int(dolfin_version[0:4])
if (fenics_version_major < 2016 or fenics_version_major >= 2018):
raise Exception(
'hIPPYlib requires FEniCS versions 2016.x.x or 2017.x.x')
if not has_linear_algebra_backend("PETSc"):
raise Exception(
'hIPPYlib requires FEniCS to be installed with PETSc support')
if not has_slepc():
raise Exception(
'hIPPYlib requires FEniCS to be installed with SLEPc support')
here = path.abspath(path.dirname(__file__))
with open(path.join(here, 'README.md'), encoding='utf-8') as f:
long_description = f.read()
version = {}
with open(path.join(here, 'hippylib/version.py')) as f:
exec(f.read(), version)
VERSION = version['__version__']
import numpy as np
from spuq.utils.testing import *
try:
import dolfin
from dolfin import (UnitSquare, FunctionSpace, Expression, interpolate, dx,
inner, nabla_grad, TrialFunction, TestFunction,
assemble, Constant, DirichletBC, Mesh, PETScMatrix,
SLEPcEigenSolver, Function, solve)
from spuq.fem.fenics.fenics_basis import FEniCSBasis
from spuq.fem.fenics.fenics_vector import FEniCSVector
from spuq.fem.fenics.fenics_operator import FEniCSOperator, FEniCSSolveOperator
HAVE_FENICS = True
# Test for PETSc and SLEPc
HAVE_SLEPC = dolfin.has_linear_algebra_backend("PETSc") and dolfin.has_slepc()
TestFunction = no_test(TestFunction)
except:
HAVE_FENICS = False
def homogeneous_bc(V):
# define boundary conditions
def u0_boundary(x, on_boundary):
return on_boundary
u0 = Constant(0.0)
bc = DirichletBC(V, u0, u0_boundary)
return bc
def assemble_lhs(coeff, V):
"""Assemble the discrete problem (i.e. the stiffness matrix)."""
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# RBniCS is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with RBniCS. If not, see <http://www.gnu.org/licenses/>.
#
# Check that dolfin has been compiled with PETSc and SLEPc
from dolfin import has_petsc, has_linear_algebra_backend, parameters, has_slepc
assert has_petsc()
assert has_linear_algebra_backend("PETSc")
assert parameters["linear_algebra_backend"] == "PETSc"
assert has_slepc()
# Import modules
from rbnics.backends.dolfin.abs import abs
from rbnics.backends.dolfin.affine_expansion_storage import AffineExpansionStorage
from rbnics.backends.dolfin.assign import assign
from rbnics.backends.dolfin.basis_functions_matrix import BasisFunctionsMatrix
from rbnics.backends.dolfin.copy import copy
from rbnics.backends.dolfin.eigen_solver import EigenSolver
from rbnics.backends.dolfin.evaluate import evaluate
from rbnics.backends.dolfin.export import export
from rbnics.backends.dolfin.function import Function
from rbnics.backends.dolfin.functions_list import FunctionsList
from rbnics.backends.dolfin.gram_schmidt import GramSchmidt
"geometry": ["BoundingBoxTree"]
}
# FIXME: Graph tests disabled for now since SCOTCH is now required
# Run both C++ and Python tests as default
only_python = False
# Check if we should run only Python tests, use for quick testing
if len(sys.argv) == 2 and sys.argv[1] == "--only-python":
only_python = True
# Build prefix list
prefixes = [""]
if has_mpi() and (has_parmetis() or has_scotch()) and \
(has_linear_algebra_backend("Epetra") or has_linear_algebra_backend("PETSc")):
prefixes.append("mpirun -np 3 ")
else:
print "DOLFIN has not been compiled with MPI and/or ParMETIS/SCOTCH. Unit tests will not be run in parallel."
# Allow to disable parallel testing
if "DISABLE_PARALLEL_TESTING" in os.environ:
prefixes = [""]
# Set non-interactive
os.putenv('DOLFIN_NOPLOT', '1')
failed = []
# Run tests in serial, then in parallel
for prefix in prefixes:
for test, subtests in tests.items():
"parameter": ["Parameters"],
"python-extras": ["test"],
"refinement": ["refine"],
}
# Run both C++ and Python tests as default
only_python = False
# Check if we should run only Python tests, use for quick testing
if len(sys.argv) == 2 and sys.argv[1] == "--only-python":
only_python = True
# Build prefix list
prefixes = [""]
if has_mpi() and (has_parmetis() or has_scotch()) and \
(has_linear_algebra_backend("Epetra") or \
has_linear_algebra_backend("PETSc")):
prefixes.append("mpirun -np 3 ")
else:
print "DOLFIN has not been compiled with MPI and/or ParMETIS/SCOTCH. " \
"Unit tests will not be run in parallel."
# Allow to disable parallel testing
if "DISABLE_PARALLEL_TESTING" in os.environ:
prefixes = [""]
# Set non-interactive
os.putenv('DOLFIN_NOPLOT', '1')
failed = []
# Run tests in serial, then in parallel
"""This is a cluster-executable version of the Stokes flow PDE solution"""
import numpy as np
import dolfin as df
import time
import scipy.io as sio
import os
import socket
import sys
# Test for PETSc or Epetra
if not df.has_linear_algebra_backend("PETSc") and not df.has_linear_algebra_backend("Epetra"):
df.info("DOLFIN has not been configured with Trilinos or PETSc. Exiting.")
exit()
if df.has_krylov_solver_method("minres"):
krylov_method = "minres"
elif df.has_krylov_solver_method("tfqmr"):
krylov_method = "tfqmr"
else:
df.info("Default linear algebra backend was not compiled with MINRES or TFQMR "
"Krylov subspace method. Terminating.")
exit()
# general parameters
meshes = np.arange(0, 10000) # vector of random meshes to load
porousMedium = 'nonOverlappingCircles' # circles or randomField
nElements = 256
# Define physical parameters
mu = 1 # viscosity