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
def test_save_and_read_mesh_3D(tempdir):
filename = os.path.join(tempdir, "mesh3d.h5")
# Write to file
mesh0 = UnitCubeMesh(MPI.comm_world, 10, 10, 10)
mesh_file = HDF5File(mesh0.mpi_comm(), filename, "w")
mesh_file.write(mesh0, "/my_mesh")
mesh_file.close()
# Read from file
mesh_file = HDF5File(mesh0.mpi_comm(), filename, "r")
mesh1 = mesh_file.read_mesh("/my_mesh", False, cpp.mesh.GhostMode.none)
mesh_file.close()
assert mesh0.num_entities_global(0) == mesh1.num_entities_global(0)
dim = mesh0.topology.dim
assert mesh0.num_entities_global(dim) == mesh1.num_entities_global(dim)
def test_save_and_read_vector(tempdir):
filename = os.path.join(tempdir, "vector.h5")
# Write to file
local_range = MPI.local_range(MPI.comm_world, 305)
x = PETSc.Vec()
x.create(MPI.comm_world)
x.setSizes((local_range[1] - local_range[0], None))
x.setFromOptions()
x.set(1.2)
with HDF5File(MPI.comm_world, filename, "w") as vector_file:
vector_file.write(x, "/my_vector")
# Read from file
with HDF5File(MPI.comm_world, filename, "r") as vector_file:
y = vector_file.read_vector(MPI.comm_world, "/my_vector", False)
assert y.getSize() == x.getSize()
x.axpy(-1.0, y)
assert x.norm() == 0.0
def test_save_and_read_mesh_value_collection_with_only_one_marked_entity(
tempdir):
ndiv = 2
filename = os.path.join(tempdir, "mesh_value_collection.h5")
mesh = UnitCubeMesh(MPI.comm_world, ndiv, ndiv, ndiv)
mvc = MeshValueCollection("size_t", mesh, 3)
mesh.create_entities(3)
if MPI.rank(mesh.mpi_comm()) == 0:
mvc.set_value(0, 1)
# write to file
with HDF5File(mesh.mpi_comm(), filename, 'w') as f:
f.write(mvc, "/mesh_value_collection")
# read from file
with HDF5File(mesh.mpi_comm(), filename, 'r') as f:
mvc = f.read_mvc_size_t(mesh, "/mesh_value_collection")
assert MPI.sum(mesh.mpi_comm(), mvc.size()) == 1
if MPI.rank(mesh.mpi_comm()) == 0:
assert mvc.get_value(0, 0) == 1
def test_save_and_read_function(tempdir):
filename = os.path.join(tempdir, "function.h5")
mesh = UnitSquareMesh(MPI.comm_world, 10, 10)
Q = FunctionSpace(mesh, ("CG", 3))
F0 = Function(Q)
F1 = Function(Q)
E = Expression("x[0]", degree=1)
F0.interpolate(E)
# Save to HDF5 File
hdf5_file = HDF5File(mesh.mpi_comm(), filename, "w")
hdf5_file.write(F0, "/function")
hdf5_file.close()
# Read back from file
hdf5_file = HDF5File(mesh.mpi_comm(), filename, "r")
F1 = hdf5_file.read_function(Q, "/function")
F0.vector().axpy(-1.0, F1.vector())
assert F0.vector().norm(dolfin.cpp.la.Norm.l2) < 1.0e-12
hdf5_file.close()
def test_save_and_read_meshfunction_2D(tempdir):
filename = os.path.join(tempdir, "meshfn-2d.h5")
# Write to file
mesh = UnitSquareMesh(MPI.comm_world, 20, 20)
with HDF5File(mesh.mpi_comm(), filename, "w") as mf_file:
# save meshfuns to compare when reading back
meshfunctions = []
for i in range(0, 3):
mf = MeshFunction('double', mesh, i, 0.0)
# NB choose a value to set which will be the same on every
# process for each entity
mf.values[:] = cpp.mesh.midpoints(mesh, i,
range(mesh.num_entities(i)))[:,
0]
meshfunctions.append(mf)
mf_file.write(mf, "/meshfunction/meshfun%d" % i)
# Read back from file
with HDF5File(mesh.mpi_comm(), filename, "r") as mf_file:
for i in range(0, 3):
mf2 = mf_file.read_mf_double(mesh, "/meshfunction/meshfun%d" % i)
assert numpy.all(meshfunctions[i].values == mf2.values)
def test_save_and_read_meshfunction_2D(tempdir):
filename = os.path.join(tempdir, "meshfn-2d.h5")
# Write to file
mesh = UnitSquareMesh(MPI.comm_world, 20, 20)
with HDF5File(mesh.mpi_comm(), filename, "w") as mf_file:
# save meshfuns to compare when reading back
meshfunctions = []
for i in range(0, 3):
mf = MeshFunction('double', mesh, i, 0.0)
# NB choose a value to set which will be the same
# on every process for each entity
for cell in MeshEntities(mesh, i):
mf[cell] = cell.midpoint()[0]
meshfunctions.append(mf)
mf_file.write(mf, "/meshfunction/meshfun%d" % i)
# Read back from file
with HDF5File(mesh.mpi_comm(), filename, "r") as mf_file:
for i in range(0, 3):
mf2 = mf_file.read_mf_double(mesh, "/meshfunction/meshfun%d" % i)
for cell in MeshEntities(mesh, i):
assert meshfunctions[i][cell] == mf2[cell]
def test_parallel(tempdir):
filename = os.path.join(tempdir, "y.h5")
hdf5 = HDF5File(MPI.comm_world, filename, "w")
assert (hdf5)
def test_save_vector(tempdir):
filename = os.path.join(tempdir, "x.h5")
x = PETScVector(MPI.comm_world, [0, 305], [], 1)
x[:] = 1.0
with HDF5File(MPI.comm_world, filename, "w") as vector_file:
vector_file.write(x, "/my_vector")