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from __future__ import annotations
import itertools
from mpi4py import MPI
import dolfinx
import numpy as np
import pytest
import io4dolfinx
root = 0
dtypes: list["str"] = ["float64", "float32"] # Mesh geometry dtypes
write_comm: list[MPI.Intracomm] = [
MPI.COMM_SELF,
MPI.COMM_WORLD,
] # Communicators for creating mesh
read_modes: list[dolfinx.mesh.GhostMode] = [
dolfinx.mesh.GhostMode.none,
dolfinx.mesh.GhostMode.shared_facet,
]
# Cell types of different dimensions
two_dimensional_cell_types: list[dolfinx.mesh.CellType] = [
dolfinx.mesh.CellType.triangle,
dolfinx.mesh.CellType.quadrilateral,
]
three_dimensional_cell_types: list[dolfinx.mesh.CellType] = [
dolfinx.mesh.CellType.tetrahedron,
dolfinx.mesh.CellType.hexahedron,
]
one_dim_combinations = itertools.product(dtypes, write_comm)
two_dim_combinations = itertools.product(dtypes, two_dimensional_cell_types, write_comm)
three_dim_combinations = itertools.product(dtypes, three_dimensional_cell_types, write_comm)
@pytest.fixture(params=one_dim_combinations, scope="module")
def mesh_1D(request):
dtype, write_comm = request.param
mesh = dolfinx.mesh.create_unit_interval(write_comm, 8, dtype=np.dtype(dtype))
return mesh
@pytest.fixture(params=two_dim_combinations, scope="module")
def mesh_2D(request):
dtype, cell_type, write_comm = request.param
mesh = dolfinx.mesh.create_unit_square(
write_comm, 10, 7, cell_type=cell_type, dtype=np.dtype(dtype)
)
return mesh
@pytest.fixture(params=three_dim_combinations, scope="module")
def mesh_3D(request):
dtype, cell_type, write_comm = request.param
mesh = dolfinx.mesh.create_unit_cube(
write_comm, 5, 7, 3, cell_type=cell_type, dtype=np.dtype(dtype)
)
return mesh
@pytest.mark.parametrize("read_mode", read_modes)
@pytest.mark.parametrize("read_comm", [MPI.COMM_SELF, MPI.COMM_WORLD])
def test_checkpointing_meshtags_1D(
mesh_1D, read_comm, read_mode, tmp_path, backend, generate_reference_map
):
mesh = mesh_1D
# Write unique mesh file for each combination of MPI communicator and dtype
hash = f"{mesh.comm.size}_{mesh.geometry.x.dtype}"
fname = MPI.COMM_WORLD.bcast(tmp_path, root=0)
suffix = ".bp" if backend == "adios" else ".h5"
filename = (fname / f"{backend}_meshtags_1D_{hash}").with_suffix(suffix)
# If mesh communicator is more than a self communicator or serial write on all processes.
# If serial or self communicator, only write on root rank
if mesh.comm.size != 1:
io4dolfinx.write_mesh(filename, mesh, backend=backend)
else:
if MPI.COMM_WORLD.rank == root:
io4dolfinx.write_mesh(filename, mesh, backend=backend)
# Create meshtags labeling each entity (of each co-dimension) with a
# unique number (their initial global index).
org_maps = []
for dim in range(mesh.topology.dim + 1):
mesh.topology.create_connectivity(dim, mesh.topology.dim)
e_map = mesh.topology.index_map(dim)
num_entities_local = e_map.size_local
entities = np.arange(num_entities_local, dtype=np.int32)
ft = dolfinx.mesh.meshtags(mesh, dim, entities, e_map.local_range[0] + entities)
ft.name = f"entity_{dim}"
# If parallel write on all processes, else write on root rank
if mesh.comm.size != 1:
io4dolfinx.write_meshtags(filename, mesh, ft, backend=backend)
# Create map from mesh tag value to its corresponding index and midpoint
org_map = generate_reference_map(mesh, ft, mesh.comm, root)
org_maps.append(org_map)
else:
if MPI.COMM_WORLD.rank == root:
io4dolfinx.write_meshtags(filename, mesh, ft, backend=backend)
# Create map from mesh tag value to its corresponding index and midpoint
org_map = generate_reference_map(mesh, ft, MPI.COMM_SELF, root)
org_maps.append(org_map)
del ft
del mesh
MPI.COMM_WORLD.Barrier()
# Read mesh on testing communicator
new_mesh = io4dolfinx.read_mesh(filename, read_comm, ghost_mode=read_mode, backend=backend)
for dim in range(new_mesh.topology.dim + 1):
# Read meshtags on all processes if testing communicator has multiple ranks
# else read on root 0
if read_comm.size != 1:
new_ft = io4dolfinx.read_meshtags(
filename,
new_mesh,
meshtag_name=f"entity_{dim}",
backend=backend,
)
# Generate meshtags map from mesh tag value to its corresponding index and midpoint
# and gather on root process
read_map = generate_reference_map(new_mesh, new_ft, new_mesh.comm, root)
else:
if MPI.COMM_WORLD.rank == root:
new_ft = io4dolfinx.read_meshtags(
filename,
new_mesh,
meshtag_name=f"entity_{dim}",
backend=backend,
)
read_map = generate_reference_map(new_mesh, new_ft, read_comm, root)
# On root process, check that midpoints are the same for each value in the meshtag
if MPI.COMM_WORLD.rank == root:
org_map = org_maps[dim]
assert len(org_map) == len(read_map)
for value, (_, midpoint) in org_map.items():
_, read_midpoint = read_map[value]
np.testing.assert_allclose(read_midpoint, midpoint)
@pytest.mark.parametrize("read_mode", read_modes)
@pytest.mark.parametrize("read_comm", [MPI.COMM_SELF, MPI.COMM_WORLD])
def test_checkpointing_meshtags_2D(
mesh_2D, read_comm, read_mode, tmp_path, backend, generate_reference_map
):
mesh = mesh_2D
hash = f"{mesh.comm.size}_{mesh.topology.cell_name()}_{mesh.geometry.x.dtype}"
fname = MPI.COMM_WORLD.bcast(tmp_path, root=0)
filename = fname / f"meshtags_1D_{hash}.bp"
if mesh.comm.size != 1:
io4dolfinx.write_mesh(filename, mesh, backend=backend)
else:
if MPI.COMM_WORLD.rank == root:
io4dolfinx.write_mesh(filename, mesh, backend=backend)
org_maps = []
for dim in range(mesh.topology.dim + 1):
mesh.topology.create_connectivity(dim, mesh.topology.dim)
e_map = mesh.topology.index_map(dim)
num_entities_local = e_map.size_local
entities = np.arange(num_entities_local, dtype=np.int32)
ft = dolfinx.mesh.meshtags(mesh, dim, entities, e_map.local_range[0] + entities)
ft.name = f"entity_{dim}"
if mesh.comm.size != 1:
io4dolfinx.write_meshtags(filename, mesh, ft, backend=backend)
org_map = generate_reference_map(mesh, ft, mesh.comm, root)
org_maps.append(org_map)
else:
if MPI.COMM_WORLD.rank == root:
io4dolfinx.write_meshtags(filename, mesh, ft, backend=backend)
org_map = generate_reference_map(mesh, ft, MPI.COMM_SELF, root)
org_maps.append(org_map)
del ft
del mesh
MPI.COMM_WORLD.Barrier()
new_mesh = io4dolfinx.read_mesh(filename, read_comm, ghost_mode=read_mode, backend=backend)
for dim in range(new_mesh.topology.dim + 1):
if read_comm.size != 1:
new_ft = io4dolfinx.read_meshtags(
filename,
new_mesh,
meshtag_name=f"entity_{dim}",
backend=backend,
)
read_map = generate_reference_map(new_mesh, new_ft, new_mesh.comm, root)
else:
if MPI.COMM_WORLD.rank == root:
new_ft = io4dolfinx.read_meshtags(
filename,
new_mesh,
meshtag_name=f"entity_{dim}",
backend=backend,
)
read_map = generate_reference_map(new_mesh, new_ft, read_comm, root)
if MPI.COMM_WORLD.rank == root:
org_map = org_maps[dim]
assert len(org_map) == len(read_map)
for value, (_, midpoint) in org_map.items():
_, read_midpoint = read_map[value]
np.testing.assert_allclose(read_midpoint, midpoint)
@pytest.mark.parametrize("read_mode", read_modes)
@pytest.mark.parametrize("read_comm", [MPI.COMM_SELF, MPI.COMM_WORLD])
def test_checkpointing_meshtags_3D(
mesh_3D, read_comm, read_mode, tmp_path, backend, generate_reference_map
):
mesh = mesh_3D
hash = f"{mesh.comm.size}_{mesh.topology.cell_name()}_{mesh.geometry.x.dtype}"
fname = MPI.COMM_WORLD.bcast(tmp_path, root=0)
filename = fname / f"meshtags_1D_{hash}.bp"
if mesh.comm.size != 1:
io4dolfinx.write_mesh(filename, mesh, backend=backend)
else:
if MPI.COMM_WORLD.rank == root:
io4dolfinx.write_mesh(filename, mesh, backend=backend)
org_maps = []
for dim in range(mesh.topology.dim + 1):
mesh.topology.create_connectivity(dim, mesh.topology.dim)
e_map = mesh.topology.index_map(dim)
num_entities_local = e_map.size_local
entities = np.arange(num_entities_local, dtype=np.int32)
ft = dolfinx.mesh.meshtags(mesh, dim, entities, e_map.local_range[0] + entities)
ft.name = f"entity_{dim}"
if mesh.comm.size != 1:
io4dolfinx.write_meshtags(filename, mesh, ft, backend=backend)
org_map = generate_reference_map(mesh, ft, mesh.comm, root)
org_maps.append(org_map)
else:
if MPI.COMM_WORLD.rank == root:
io4dolfinx.write_meshtags(filename, mesh, ft, backend=backend)
org_map = generate_reference_map(mesh, ft, MPI.COMM_SELF, root)
org_maps.append(org_map)
del ft
del mesh
MPI.COMM_WORLD.Barrier()
new_mesh = io4dolfinx.read_mesh(filename, read_comm, ghost_mode=read_mode, backend=backend)
for dim in range(new_mesh.topology.dim + 1):
if read_comm.size != 1:
new_ft = io4dolfinx.read_meshtags(
filename,
new_mesh,
meshtag_name=f"entity_{dim}",
backend=backend,
)
read_map = generate_reference_map(new_mesh, new_ft, new_mesh.comm, root)
else:
if MPI.COMM_WORLD.rank == root:
new_ft = io4dolfinx.read_meshtags(
filename,
new_mesh,
meshtag_name=f"entity_{dim}",
backend=backend,
)
read_map = generate_reference_map(new_mesh, new_ft, MPI.COMM_SELF, root)
if MPI.COMM_WORLD.rank == root:
org_map = org_maps[dim]
assert len(org_map) == len(read_map)
for value, (_, midpoint) in org_map.items():
_, read_midpoint = read_map[value]
np.testing.assert_allclose(read_midpoint, midpoint)
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