Storing mesh partition

Storing mesh partition#

This data is re-ordered when reading in a mesh, as the mesh is partitioned. This means that when storing the mesh to disk from DOLFINx, the geometry and connectivity arrays are re-ordered. If we want to avoid to re-partition the mesh every time you run a simulation (on a fixed number of processes), one can store the partitioning of the mesh in the checkpoint.

import logging
from pathlib import Path

import ipyparallel as ipp

def write_partitioned_mesh(filename: Path):
    import subprocess

    from mpi4py import MPI

    import dolfinx

    import adios4dolfinx

    # Create a simple unit square mesh
    mesh = dolfinx.mesh.create_unit_square(
        MPI.COMM_WORLD,
        10,
        10,
        cell_type=dolfinx.mesh.CellType.quadrilateral,
        ghost_mode=dolfinx.mesh.GhostMode.shared_facet,
    )

    # Write mesh checkpoint
    adios4dolfinx.write_mesh(filename, mesh, engine="BP4", store_partition_info=True)
    # Inspect checkpoint on rank 0 with `bpls`
    if mesh.comm.rank == 0:
        output = subprocess.run(["bpls", "-a", "-l", filename], capture_output=True)
        print(output.stdout.decode("utf-8"))

We inspect the partitioned mesh

mesh_file = Path("partitioned_mesh.bp")
n = 3

with ipp.Cluster(engines="mpi", n=n, log_level=logging.ERROR) as cluster:
    query = cluster[:].apply_async(write_partitioned_mesh, mesh_file)
    query.wait()
    assert query.successful(), query.error
    print("".join(query.stdout))

  string   CellType            attr   = "quadrilateral"
  int32_t  Degree              attr   = 1
  int32_t  LagrangeVariant     attr   = 2
  double   MeshTime            {1} = 0 / 0
  int32_t  PartitionProcesses  attr   = 3
  int32_t  PartitioningData    {134} = 0 / 2
  int32_t  PartitioningOffset  {101} = 0 / 134
  double   Points              {121, 2} = 0 / 1
  int64_t  Topology            {100, 4} = 0 / 120

Reading a partitioned mesh#

If we try to read the mesh in on a different number of processes, we will get an error

def read_partitioned_mesh(filename: Path, read_from_partition: bool = True):
    from mpi4py import MPI

    import adios4dolfinx

    prefix = f"{MPI.COMM_WORLD.rank + 1}/{MPI.COMM_WORLD.size}: "
    try:
        mesh = adios4dolfinx.read_mesh(
            filename, comm=MPI.COMM_WORLD, engine="BP4", read_from_partition=read_from_partition
        )
        print(f"{prefix} Mesh: {mesh.name} read successfully with {read_from_partition=}")
    except ValueError as e:
        print(f"{prefix} Caught exception: ", e)

with ipp.Cluster(engines="mpi", n=n + 1, log_level=logging.ERROR) as cluster:
    # Read mesh from file with different number of processes
    query = cluster[:].apply_async(read_partitioned_mesh, mesh_file)
    query.wait()
    assert query.successful(), query.error
    print("".join(query.stdout))

1/4:  Caught exception:  Number of processes in file (3)!=(comm.size=4)
2/4:  Caught exception:  Number of processes in file (3)!=(comm.size=4)
3/4:  Caught exception:  Number of processes in file (3)!=(comm.size=4)
4/4:  Caught exception:  Number of processes in file (3)!=(comm.size=4)

Read mesh from file with different number of processes (not using partitioning information).

with ipp.Cluster(engines="mpi", n=n + 1, log_level=logging.ERROR) as cluster:
    query = cluster[:].apply_async(read_partitioned_mesh, mesh_file, False)
    query.wait()
    assert query.successful(), query.error
    print("".join(query.stdout))

1/4:  Mesh: mesh read successfully with read_from_partition=False
2/4:  Mesh: mesh read successfully with read_from_partition=False
3/4:  Mesh: mesh read successfully with read_from_partition=False
4/4:  Mesh: mesh read successfully with read_from_partition=False

Read mesh from file with same number of processes as was written, re-using partitioning information.

with ipp.Cluster(engines="mpi", n=n, log_level=logging.ERROR) as cluster:
    query = cluster[:].apply_async(read_partitioned_mesh, mesh_file, True)
    query.wait()
    assert query.successful(), query.error
    print("".join(query.stdout))

1/3:  Mesh: mesh read successfully with read_from_partition=True
2/3:  Mesh: mesh read successfully with read_from_partition=True
3/3:  Mesh: mesh read successfully with read_from_partition=True
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