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import typing
from collections import ChainMap
from mpi4py import MPI
import dolfinx
import ipyparallel as ipp
import numpy as np
import numpy.typing
import numpy.typing as npt
import pytest
import io4dolfinx
def find_backends():
backends = []
try:
import adios2
if adios2.is_built_with_mpi:
backends.append("adios2")
except ModuleNotFoundError:
pass
try:
import h5py
if h5py.get_config().mpi:
backends.append("h5py")
except ModuleNotFoundError:
pass
return backends
@pytest.fixture(params=find_backends(), scope="function")
def backend(request):
yield request.param
@pytest.fixture(scope="module")
def cluster():
cluster = ipp.Cluster(engines="mpi", n=2)
rc = cluster.start_and_connect_sync()
rc.wait_for_engines(n=2)
yield rc
cluster.stop_cluster_sync()
@pytest.fixture(scope="function")
def write_function(tmp_path):
def _write_function(
mesh,
el,
f,
dtype,
backend: typing.Literal["adios2", "h5py"],
name="uh",
append: bool = False,
) -> str:
V = dolfinx.fem.functionspace(mesh, el)
uh = dolfinx.fem.Function(V, dtype=dtype)
uh.interpolate(f)
uh.name = name
el_hash = (
io4dolfinx.utils.element_signature(V)
.replace(" ", "")
.replace(",", "")
.replace("(", "")
.replace(")", "")
.replace("[", "")
.replace("]", "")
)
# Consistent tmp dir across processes
f_path = MPI.COMM_WORLD.bcast(tmp_path, root=0)
file_hash = f"{el_hash}_{np.dtype(dtype).name}"
if backend == "adios2":
suffix = ".bp"
else:
suffix = ".h5"
filename = (f_path / f"mesh_{file_hash}").with_suffix(suffix)
if mesh.comm.size != 1:
if not append:
io4dolfinx.write_mesh(filename, mesh, backend=backend)
io4dolfinx.write_function(filename, uh, time=0.0, backend=backend)
else:
if MPI.COMM_WORLD.rank == 0:
if not append:
io4dolfinx.write_mesh(filename, mesh, backend=backend)
io4dolfinx.write_function(filename, uh, time=0.0, backend=backend)
return filename
return _write_function
@pytest.fixture(scope="function")
def read_function():
def _read_function(
comm, el, f, path, dtype, backend: typing.Literal["adios2", "h5py"], name="uh"
):
mesh = io4dolfinx.read_mesh(
path,
comm,
ghost_mode=dolfinx.mesh.GhostMode.shared_facet,
backend=backend,
)
V = dolfinx.fem.functionspace(mesh, el)
v = dolfinx.fem.Function(V, dtype=dtype)
v.name = name
io4dolfinx.read_function(path, v, backend=backend)
v_ex = dolfinx.fem.Function(V, dtype=dtype)
v_ex.interpolate(f)
res = np.finfo(dtype).resolution
np.testing.assert_allclose(v.x.array, v_ex.x.array, atol=10 * res, rtol=10 * res)
return _read_function
@pytest.fixture(scope="function")
def get_dtype():
def _get_dtype(in_dtype: np.dtype, is_complex: bool):
dtype: numpy.typing.DTypeLike
if in_dtype == np.float32:
if is_complex:
dtype = np.complex64
else:
dtype = np.float32
elif in_dtype == np.float64:
if is_complex:
dtype = np.complex128
else:
dtype = np.float64
else:
raise ValueError("Unsuported dtype")
return dtype
return _get_dtype
@pytest.fixture(scope="function")
def write_function_time_dep(tmp_path):
def _write_function_time_dep(
mesh, el, f0, f1, t0, t1, dtype, backend: typing.Literal["adios2", "h5py"]
) -> str:
V = dolfinx.fem.functionspace(mesh, el)
uh = dolfinx.fem.Function(V, dtype=dtype)
uh.interpolate(f0)
el_hash = (
io4dolfinx.utils.element_signature(V)
.replace(" ", "")
.replace(",", "")
.replace("(", "")
.replace(")", "")
.replace("[", "")
.replace("]", "")
)
file_hash = f"{el_hash}_{np.dtype(dtype).name}"
# Consistent tmp dir across processes
f_path = MPI.COMM_WORLD.bcast(tmp_path, root=0)
if backend == "adios2":
suffix = ".bp"
else:
suffix = ".h5"
filename = (f_path / f"mesh_{file_hash}").with_suffix(suffix)
if mesh.comm.size != 1:
io4dolfinx.write_mesh(filename, mesh, backend=backend)
io4dolfinx.write_function(filename, uh, time=t0, backend=backend)
uh.interpolate(f1)
io4dolfinx.write_function(filename, uh, time=t1, backend=backend)
else:
if MPI.COMM_WORLD.rank == 0:
io4dolfinx.write_mesh(filename, mesh, backend=backend)
io4dolfinx.write_function(filename, uh, time=t0, backend=backend)
uh.interpolate(f1)
io4dolfinx.write_function(filename, uh, time=t1, backend=backend)
return filename
return _write_function_time_dep
@pytest.fixture(scope="function")
def read_function_time_dep():
def _read_function_time_dep(
comm, el, f0, f1, t0, t1, path, dtype, backend: typing.Literal["adios2", "h5py"]
):
mesh = io4dolfinx.read_mesh(
path,
comm,
ghost_mode=dolfinx.mesh.GhostMode.shared_facet,
backend=backend,
)
V = dolfinx.fem.functionspace(mesh, el)
v = dolfinx.fem.Function(V, dtype=dtype)
io4dolfinx.read_function(path, v, time=t1, backend=backend)
v_ex = dolfinx.fem.Function(V, dtype=dtype)
v_ex.interpolate(f1)
res = np.finfo(dtype).resolution
assert np.allclose(v.x.array, v_ex.x.array, atol=10 * res, rtol=10 * res)
io4dolfinx.read_function(path, v, time=t0, backend=backend)
v_ex = dolfinx.fem.Function(V, dtype=dtype)
v_ex.interpolate(f0)
res = np.finfo(dtype).resolution
assert np.allclose(v.x.array, v_ex.x.array, atol=10 * res, rtol=10 * res)
return _read_function_time_dep
def _generate_reference_map(
mesh: dolfinx.mesh.Mesh,
meshtag: dolfinx.mesh.MeshTags,
comm: MPI.Intracomm,
root: int,
) -> typing.Optional[dict[str, tuple[int, npt.NDArray]]]:
"""
Helper function to generate map from meshtag value to its corresponding index and midpoint.
Args:
mesh: The mesh
meshtag: The associated meshtag
comm: MPI communicator to gather the map from all processes with
root (int): Rank to store data on
Returns:
Root rank returns the map, all other ranks return None
"""
mesh.topology.create_connectivity(meshtag.dim, mesh.topology.dim)
midpoints = dolfinx.mesh.compute_midpoints(mesh, meshtag.dim, meshtag.indices)
e_map = mesh.topology.index_map(meshtag.dim)
value_to_midpoint = {}
for index, value in zip(meshtag.indices, meshtag.values):
value_to_midpoint[value] = (
int(e_map.local_range[0] + index),
midpoints[index],
)
global_map = comm.gather(value_to_midpoint, root=root)
if comm.rank == root:
return dict(ChainMap(*global_map)) # type: ignore
return None
@pytest.fixture
def generate_reference_map():
return _generate_reference_map
|
