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"""Unit tests for the HDF5 io library"""
# Copyright (C) 2012 Garth N. Wells
#
# This file is part of DOLFIN.
#
# DOLFIN is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# DOLFIN 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 DOLFIN. If not, see <http://www.gnu.org/licenses/>.
#
# Modified by Chris Richardson 2013
import pytest
import os
from dolfin import *
from dolfin_utils.test import skip_if_not_HDF5, fixture, tempdir, xfail_with_serial_hdf5_in_parallel
@skip_if_not_HDF5
@xfail_with_serial_hdf5_in_parallel
def test_parallel(tempdir):
filename = os.path.join(tempdir, "y.h5")
have_parallel = has_hdf5_parallel()
hdf5 = HDF5File(MPI.comm_world, filename, "w")
@skip_if_not_HDF5
@xfail_with_serial_hdf5_in_parallel
def test_save_vector(tempdir):
filename = os.path.join(tempdir, "x.h5")
x = Vector(MPI.comm_world, 305)
x[:] = 1.0
with HDF5File(x.mpi_comm(), filename, "w") as vector_file:
vector_file.write(x, "/my_vector")
@skip_if_not_HDF5
@xfail_with_serial_hdf5_in_parallel
def test_save_and_read_vector(tempdir):
filename = os.path.join(tempdir, "vector.h5")
# Write to file
x = Vector(MPI.comm_world, 305)
x[:] = 1.2
with HDF5File(x.mpi_comm(), filename, "w") as vector_file:
vector_file.write(x, "/my_vector")
# Read from file
y = Vector()
with HDF5File(x.mpi_comm(), filename, "r") as vector_file:
vector_file.read(y, "/my_vector", False)
assert y.size() == x.size()
assert (x - y).norm("l1") == 0.0
@skip_if_not_HDF5
@xfail_with_serial_hdf5_in_parallel
def test_save_and_read_meshfunction_2D(tempdir):
filename = os.path.join(tempdir, "meshfn-2d.h5")
# Write to file
mesh = UnitSquareMesh(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)
# NB choose a value to set which will be the same
# on every process for each entity
for cell in entities(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 = MeshFunction('double', mesh, i)
mf_file.read(mf2, "/meshfunction/meshfun%d" % i)
for cell in entities(mesh, i):
assert meshfunctions[i][cell] == mf2[cell]
@skip_if_not_HDF5
@xfail_with_serial_hdf5_in_parallel
def test_save_and_read_meshfunction_3D(tempdir):
filename = os.path.join(tempdir, "meshfn-3d.h5")
# Write to file
mesh = UnitCubeMesh(10, 10, 10)
mf_file = HDF5File(mesh.mpi_comm(), filename, "w")
# save meshfuns to compare when reading back
meshfunctions = []
for i in range(0,4):
mf = MeshFunction('double', mesh, i)
# NB choose a value to set which will be the same
# on every process for each entity
for cell in entities(mesh, i):
mf[cell] = cell.midpoint()[0]
meshfunctions.append(mf)
mf_file.write(mf, "/meshfunction/group/%d/meshfun"%i)
mf_file.close()
# Read back from file
mf_file = HDF5File(mesh.mpi_comm(), filename, "r")
for i in range(0,4):
mf2 = MeshFunction('double', mesh, i)
mf_file.read(mf2, "/meshfunction/group/%d/meshfun"%i)
for cell in entities(mesh, i):
assert meshfunctions[i][cell] == mf2[cell]
mf_file.close()
@skip_if_not_HDF5
@xfail_with_serial_hdf5_in_parallel
def test_save_and_read_mesh_value_collection(tempdir):
ndiv = 5
filename = os.path.join(tempdir, "mesh_value_collection.h5")
mesh = UnitCubeMesh(ndiv, ndiv, ndiv)
point2list = lambda p : [ p.x(), p.y(), p.z() ]
# write to file
with HDF5File(mesh.mpi_comm(), filename, 'w') as f :
for dim in range(mesh.topology().dim()) :
mvc = MeshValueCollection("size_t", mesh, dim)
mesh.init(dim)
for e in entities(mesh, dim) :
# this can be easily computed to the check the value
val = int(ndiv*sum(point2list(e.midpoint()))) + 1
mvc.set_value(e.index(), val)
f.write(mvc, "/mesh_value_collection_{}".format(dim))
# read from file
with HDF5File(mesh.mpi_comm(), filename, 'r') as f :
for dim in range(mesh.topology().dim()) :
mvc = MeshValueCollection("size_t", mesh, dim)
f.read(mvc, "/mesh_value_collection_{}".format(dim))
# check the values
for (cell, lidx), val in mvc.values().items() :
eidx = Cell(mesh, cell).entities(dim)[lidx]
mid = point2list(MeshEntity(mesh, dim, eidx).midpoint())
assert val == int(ndiv*sum(mid)) + 1
@skip_if_not_HDF5
@xfail_with_serial_hdf5_in_parallel
def test_save_and_read_mesh_value_collection_with_only_one_marked_entity(tempdir):
ndiv = 5
filename = os.path.join(tempdir, "mesh_value_collection.h5")
mesh = UnitCubeMesh(ndiv, ndiv, ndiv)
mvc = MeshValueCollection("size_t", mesh, 3)
mesh.init(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 = MeshValueCollection("size_t", mesh, 3)
f.read(mvc, "/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
@skip_if_not_HDF5
@xfail_with_serial_hdf5_in_parallel
def test_save_and_read_function(tempdir):
filename = os.path.join(tempdir, "function.h5")
mesh = UnitSquareMesh(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")
hdf5_file.read(F1, "/function")
result = F0.vector() - F1.vector()
assert len(result.get_local().nonzero()[0]) == 0
hdf5_file.close()
@skip_if_not_HDF5
@xfail_with_serial_hdf5_in_parallel
def test_save_and_read_mesh_2D(tempdir):
filename = os.path.join(tempdir, "mesh2d.h5")
# Write to file
mesh0 = UnitSquareMesh(20, 20)
mesh_file = HDF5File(mesh0.mpi_comm(), filename, "w")
mesh_file.write(mesh0, "/my_mesh")
mesh_file.close()
# Read from file
mesh1 = Mesh()
mesh_file = HDF5File(mesh0.mpi_comm(), filename, "r")
mesh_file.read(mesh1, "/my_mesh", False)
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)
@skip_if_not_HDF5
@xfail_with_serial_hdf5_in_parallel
def test_save_and_read_mesh_3D(tempdir):
filename = os.path.join(tempdir, "mesh3d.h5")
# Write to file
mesh0 = UnitCubeMesh(10, 10, 10)
mesh_file = HDF5File(mesh0.mpi_comm(), filename, "w")
mesh_file.write(mesh0, "/my_mesh")
mesh_file.close()
# Read from file
mesh1 = Mesh()
mesh_file = HDF5File(mesh0.mpi_comm(), filename, "r")
mesh_file.read(mesh1, "/my_mesh", False)
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)
@skip_if_not_HDF5
@xfail_with_serial_hdf5_in_parallel
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
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