def test_mpi_atomicity(tempdir):
comm_world = MPI.comm_world
if MPI.size(comm_world) > 1:
filename = os.path.join(tempdir, "mpiatomic.h5")
with HDF5File(MPI.comm_world, filename, "w") as f:
assert f.get_mpi_atomicity() is False
f.set_mpi_atomicity(True)
assert f.get_mpi_atomicity() is True
# Copyright (C) 2014-2014 Aslak Wigdahl Bergersen
#
# This file is part of DOLFINX (https://www.fenicsproject.org)
#
# SPDX-License-Identifier: LGPL-3.0-or-later
"""Shared skips for unit tests involving dolfinx."""
import pytest
from dolfinx import MPI
from dolfinx.common import has_petsc_complex
# Skips with respect to parallel or serial
xfail_in_parallel = pytest.mark.xfail(
MPI.size(MPI.comm_world) > 1,
reason="This test does not yet work in parallel.")
skip_in_parallel = pytest.mark.skipif(
MPI.size(MPI.comm_world) > 1,
reason="This test should only be run in serial.")
# Skips with respect to the scalar type
skip_if_complex = pytest.mark.skipif(
has_petsc_complex, reason="This test does not work in complex mode.")
xfail_if_complex = pytest.mark.xfail(
has_petsc_complex, reason="This test does not work in complex mode.")
vertices_fiat = np.sort(
vertex_global_indices[np.array(entity_topology)])
assert all(vertices_fiat == vertices_dolfin)
def test_mesh_topology_lifetime():
"""Check that lifetime of Mesh.topology is bound to underlying mesh object"""
mesh = UnitSquareMesh(MPI.comm_world, 4, 4)
rc = sys.getrefcount(mesh)
topology = mesh.topology
assert sys.getrefcount(mesh) == rc + 1
del topology
assert sys.getrefcount(mesh) == rc
@pytest.mark.xfail(condition=MPI.size(MPI.comm_world) > 1,
reason="Small meshes fail in parallel")
def test_small_mesh():
mesh3d = UnitCubeMesh(MPI.comm_world, 1, 1, 1)
gdim = mesh3d.geometry.dim
assert mesh3d.num_entities_global(gdim) == 6
mesh2d = UnitSquareMesh(MPI.comm_world, 1, 1)
gdim = mesh2d.geometry.dim
assert mesh2d.num_entities_global(gdim) == 2
mesh1d = UnitIntervalMesh(MPI.comm_world, 2)
gdim = mesh1d.geometry.dim
assert mesh1d.num_entities_global(gdim) == 2
import pytest
from petsc4py import PETSc
from dolfinx import (MPI, Function, FunctionSpace, Mesh, MeshFunction,
MeshValueCollection, TensorFunctionSpace, UnitCubeMesh,
UnitIntervalMesh, UnitSquareMesh, VectorFunctionSpace,
cpp, has_petsc_complex)
from dolfinx.cpp.mesh import CellType
from dolfinx.io import XDMFFile
from dolfinx_utils.test.fixtures import tempdir
from ufl import FiniteElement, VectorElement
assert (tempdir)
# Supported XDMF file encoding
if MPI.size(MPI.comm_world) > 1:
encodings = (XDMFFile.Encoding.HDF5, )
else:
encodings = (XDMFFile.Encoding.HDF5, XDMFFile.Encoding.ASCII)
# Data types supported in templating
data_types = (('int', int), ('size_t', int), ('double', float))
# Finite elements tested
fe_1d_shapes = ["interval"]
fe_2d_shapes = ["triangle"]
fe_3d_shapes = ["tetrahedron"]
fe_families = ["CG", "DG"]
fe_degrees = [0, 1, 3]
topological_dim = [1, 2, 3]
number_cells = [6, 10]
def dS_from_measure(mesh):
boundaries = MeshFunction("size_t", mesh, mesh.topology.dim - 1, 1)
dS = Measure("dS")(subdomain_data=boundaries, domain=mesh)
return dS
def dS_from_measure_and_subdomain(mesh):
dS = dS_from_measure(mesh)
return dS(1)
@pytest.mark.parametrize("mode", [
pytest.param(GhostMode.none),
pytest.param(GhostMode.shared_facet,
marks=pytest.mark.xfail(
condition=MPI.size(MPI.comm_world) == 1,
reason="Shared ghost modes fail in serial")),
pytest.param(GhostMode.shared_vertex,
marks=pytest.mark.xfail(
condition=MPI.size(MPI.comm_world) == 1,
reason="Shared ghost modes fail in serial"))
])
@pytest.mark.parametrize(
"dx", [dx_from_ufl, dx_from_measure, dx_from_measure_and_subdomain])
@pytest.mark.parametrize(
"ds", [ds_from_ufl, ds_from_measure, ds_from_measure_and_subdomain])
def test_ghost_mesh_assembly(mode, dx, ds):
mesh = UnitSquareMesh(MPI.comm_world, 12, 12, ghost_mode=mode)
V = FunctionSpace(mesh, ("Lagrange", 1))
u, v = ufl.TrialFunction(V), ufl.TestFunction(V)
dx = dx(mesh)
def test_manufactured_poisson_dg(degree, filename, datadir):
""" Manufactured Poisson problem, solving u = x[component]**n, where n is the
degree of the Lagrange function space.
"""
with XDMFFile(MPI.comm_world, os.path.join(datadir, filename)) as xdmf:
if MPI.size(MPI.comm_world) == 1: # Serial
mesh = xdmf.read_mesh(GhostMode.none)
else:
mesh = xdmf.read_mesh(GhostMode.shared_facet)
V = FunctionSpace(mesh, ("DG", degree))
u, v = TrialFunction(V), TestFunction(V)
# Exact solution
x = SpatialCoordinate(mesh)
u_exact = x[1] ** degree
# Coefficient
k = Function(V)
k.vector.set(2.0)
k.vector.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
# Source term
f = - div(k * grad(u_exact))
# Mesh normals and element size
n = FacetNormal(mesh)
h = CellDiameter(mesh)
h_avg = (h("+") + h("-")) / 2.0
# Penalty parameter
alpha = 32
dx_ = dx(metadata={"quadrature_degree": -1})
ds_ = ds(metadata={"quadrature_degree": -1})
dS_ = dS(metadata={"quadrature_degree": -1})
a = inner(k * grad(u), grad(v)) * dx_ \
- k("+") * inner(avg(grad(u)), jump(v, n)) * dS_ \
- k("+") * inner(jump(u, n), avg(grad(v))) * dS_ \
+ k("+") * (alpha / h_avg) * inner(jump(u, n), jump(v, n)) * dS_ \
- inner(k * grad(u), v * n) * ds_ \
- inner(u * n, k * grad(v)) * ds_ \
+ (alpha / h) * inner(k * u, v) * ds_
L = inner(f, v) * dx_ - inner(k * u_exact * n, grad(v)) * ds_ \
+ (alpha / h) * inner(k * u_exact, v) * ds_
for integral in a.integrals():
integral.metadata()["quadrature_degree"] = ufl.algorithms.estimate_total_polynomial_degree(a)
for integral in L.integrals():
integral.metadata()["quadrature_degree"] = ufl.algorithms.estimate_total_polynomial_degree(L)
b = assemble_vector(L)
b.ghostUpdate(addv=PETSc.InsertMode.ADD, mode=PETSc.ScatterMode.REVERSE)
A = assemble_matrix(a, [])
A.assemble()
# Create LU linear solver
solver = PETSc.KSP().create(MPI.comm_world)
solver.setType(PETSc.KSP.Type.PREONLY)
solver.getPC().setType(PETSc.PC.Type.LU)
solver.setOperators(A)
# Solve
uh = Function(V)
solver.solve(b, uh.vector)
uh.vector.ghostUpdate(addv=PETSc.InsertMode.INSERT,
mode=PETSc.ScatterMode.FORWARD)
error = assemble_scalar((u_exact - uh)**2 * dx)
error = MPI.sum(mesh.mpi_comm(), error)
assert np.absolute(error) < 1.0e-14