Parallel function saving and reading it back using PETSc or adios4dolfinx

Ekrem_Ekici · February 7, 2024, 7:43pm

I changed it to

and it still gives;

Mesh written to checkpoint_0.bp on comm 1/3

Mesh written to checkpoint_0.bp on comm 2/3

Mesh written to checkpoint_0.bp on comm 3/3

Mesh read from checkpoint_0.bp on comm 1/2
Function written to checkpoint_1.bp on comm 1/2

Mesh read from checkpoint_0.bp on comm 2/2
Function written to checkpoint_1.bp on comm 2/2

Traceback (most recent call last):
  File "demo.py", line 114, in <module>
    assert query_3.successful(), query_3.error
AssertionError: [<RemoteError[ ]:Exception(MPI_ERR_TRUNCATE: message truncated)>]
Stopping cluster <Cluster(cluster_id='1707334019-xzjr', profile='default', controller=<running>, engine_sets=['1707334020'])>

there is some problem during function reading. I did trying my tests again for v0.7.2. When I run mesh with;

# adios_mesh.py
from dolfinx.mesh import create_unit_square
import adios4dolfinx
from mpi4py import MPI
import shutil

mesh = create_unit_square(MPI.COMM_WORLD, 30, 30)
shutil.rmtree("mesh", ignore_errors=True)
adios4dolfinx.write_mesh(mesh, "mesh")

and write function with;

# adios_write.py
import numba
import numpy as np
from dolfinx.fem import (Function, FunctionSpace, locate_dofs_geometrical)
from dolfinx.mesh import locate_entities
from ufl import FiniteElement
from mpi4py import MPI
import dolfinx.fem
import dolfinx.io
import adios4dolfinx
import os
import pathlib
import shutil

def export_function(function: dolfinx.fem.Function, directory: str, filename: str) -> None:

    comm = function.function_space.mesh.comm
    visualization_directory = os.path.join(directory, filename + ".bp")
    checkpointing_directory = os.path.join(
        directory, filename + "_checkpoint.bp")

    shutil.rmtree(visualization_directory, ignore_errors=True)
    os.makedirs(visualization_directory, exist_ok=True)
    print(visualization_directory)
    # Export for visualization
    with dolfinx.io.VTXWriter(comm, visualization_directory, function, "bp4") as vtx_file:
        vtx_file.write(0)
    # Export for checkpointing
    adios4dolfinx.write_function(function, pathlib.Path(visualization_directory), "bp4")

mesh = adios4dolfinx.read_mesh(MPI.COMM_WORLD, "mesh", engine='BP4', ghost_mode=dolfinx.mesh.GhostMode.shared_facet)

v_cg = FiniteElement("CG", mesh.ufl_cell(), 2)
Q = FunctionSpace(mesh, v_cg)

def Omega_0(x):
    return x[1] <= 0.3

def Omega_1(x):
    return x[1] >= 0.7

kappa = Function(Q)
cells_0 = locate_entities(mesh, mesh.topology.dim, Omega_0)
cells_1 = locate_entities(mesh, mesh.topology.dim, Omega_1)

@numba.njit
def unroll_dofmap(dofs, bs):
    dofs_unrolled = np.zeros(bs*len(dofs), dtype=np.int32)
    for i, dof in enumerate(dofs):
        for b in range(bs):
            dofs_unrolled[i*bs+b] = dof*bs+b
    return dofs_unrolled

dofs_0 = locate_dofs_geometrical(Q, Omega_0)
dofs_1 = locate_dofs_geometrical(Q, Omega_1)
dofmap_bs = Q.dofmap.bs
kappa.x.array[unroll_dofmap(dofs_0, dofmap_bs)] = 1
kappa.x.array[unroll_dofmap(dofs_1, dofmap_bs)] = 0.1

export_function(kappa, "adios_dir", "test_export")

and finally testing the export with;

# assert.py
import numba
import numpy as np
from dolfinx.fem import (Function, FunctionSpace, locate_dofs_geometrical)
from dolfinx.mesh import create_unit_square, locate_entities
from ufl import FiniteElement
from mpi4py import MPI
import dolfinx.fem
import dolfinx.io
import adios4dolfinx
import os
import pathlib

mesh = adios4dolfinx.read_mesh(MPI.COMM_WORLD, "mesh", engine='BP4', ghost_mode=dolfinx.mesh.GhostMode.shared_facet)

v_cg = FiniteElement("CG", mesh.ufl_cell(), 2)
Q = FunctionSpace(mesh, v_cg)

def Omega_0(x):
    return x[1] <= 0.3

def Omega_1(x):
    return x[1] >= 0.7

kappa = Function(Q)
cells_0 = locate_entities(mesh, mesh.topology.dim, Omega_0)
cells_1 = locate_entities(mesh, mesh.topology.dim, Omega_1)

@numba.njit
def unroll_dofmap(dofs, bs):
    dofs_unrolled = np.zeros(bs*len(dofs), dtype=np.int32)
    for i, dof in enumerate(dofs):
        for b in range(bs):
            dofs_unrolled[i*bs+b] = dof*bs+b
    return dofs_unrolled

dofs_0 = locate_dofs_geometrical(Q, Omega_0)
dofs_1 = locate_dofs_geometrical(Q, Omega_1)
dofmap_bs = Q.dofmap.bs
kappa.x.array[unroll_dofmap(dofs_0, dofmap_bs)] = 1
kappa.x.array[unroll_dofmap(dofs_1, dofmap_bs)] = 0.1

def import_function(function_space: dolfinx.fem.FunctionSpace, directory: str, filename: str) -> dolfinx.fem.Function:

    function = dolfinx.fem.Function(function_space)
    checkpointing_directory = os.path.join(directory, filename + ".bp")
    adios4dolfinx.read_function(function, pathlib.Path(checkpointing_directory), "bp4")
    return function

kappa_import = import_function(Q, "adios_dir", "test_export")

print("original", np.count_nonzero(kappa.vector.array))
print("imported", np.count_nonzero(kappa_import.vector.array))

assert np.allclose(kappa.vector.array, kappa_import.vector.array)

gives;

Traceback (most recent call last):
  File "assert.py", line 50, in <module>
    kappa_import = import_function(Q, "adios_dir", "test_export")
  File "assert.py", line 47, in import_function
    adios4dolfinx.read_function(function, pathlib.Path(checkpointing_directory), "bp4")
  File "/home/ee331/Dev/Venvs/v073complex/lib/python3.8/site-packages/adios4dolfinx/checkpointing.py", line 337, in read_function
    inc_cells, inc_perms = send_and_recv_cell_perm(
  File "/home/ee331/Dev/Venvs/v073complex/lib/python3.8/site-packages/adios4dolfinx/comm_helpers.py", line 203, in send_and_recv_cell_perm
    mesh_to_data.Neighbor_alltoall(out_size, recv_size)
  File "mpi4py/MPI/Comm.pyx", line 2154, in mpi4py.MPI.Topocomm.Neighbor_alltoall
mpi4py.MPI.Exception: MPI_ERR_TRUNCATE: message truncated

what does
mesh_to_data.Neighbor_alltoall(out_size, recv_size)
do?

dokken · February 7, 2024, 7:51pm

It communicates how much data should be passed from one process to the other.

Are you using openmpi or MPICH?
Could you also add a print-statement printing source and dest from:

github.com

jorgensd/adios4dolfinx/blob/377541633dd5c3de441dd0ffeb1c5869c6702f8f/src/adios4dolfinx/comm_helpers.py#L164C4-L164C21


      
          source, dest, _ = mesh_to_data.Get_dist_neighbors()

with print(f"{MPI.COMM_WORLD.rank}, {source=} {dest=}", flush=True)

Ekrem_Ekici · February 7, 2024, 7:57pm

I am using openmpi.

it gives;

0, source=[0] dest=[0]

dokken · February 7, 2024, 7:58pm

Again, for this code to work you should store the function and mesh in the same file.

dokken · February 7, 2024, 8:11pm

Please also print (out_size) and (recv_size) prior to the all_to_all.

Ekrem_Ekici · February 7, 2024, 8:16pm

It seems that nothing changed. Here is another MWE;

# adios_write.py
import numba
import numpy as np
from dolfinx.fem import (Function, FunctionSpace, locate_dofs_geometrical)
from dolfinx.mesh import locate_entities
from ufl import FiniteElement
from mpi4py import MPI
import dolfinx.fem
import dolfinx.io
import adios4dolfinx
import os
import pathlib
import shutil

def export_function(function: dolfinx.fem.Function, directory: str, filename: str) -> None:

    comm = function.function_space.mesh.comm
    visualization_directory = os.path.join(directory, filename + ".bp")

    shutil.rmtree(visualization_directory, ignore_errors=True)
    os.makedirs(visualization_directory, exist_ok=True)
    print(visualization_directory)
    
    # Export for visualization
    with dolfinx.io.VTXWriter(comm, visualization_directory, function, "bp4") as vtx_file:
        vtx_file.write(0)
    # Export mesh
    adios4dolfinx.write_mesh(function.function_space.mesh, pathlib.Path(visualization_directory))
    # Export for checkpointing
    adios4dolfinx.write_function(function, pathlib.Path(visualization_directory), "bp4")


from dolfinx.mesh import create_unit_square

mesh_dolfinx = create_unit_square(MPI.COMM_WORLD, 30, 30)
shutil.rmtree("adios_dir/test_export.bp", ignore_errors=True)
adios4dolfinx.write_mesh(mesh_dolfinx, "adios_dir/test_export.bp")

mesh = adios4dolfinx.read_mesh(MPI.COMM_WORLD, "adios_dir/test_export.bp", engine='BP4', ghost_mode=dolfinx.mesh.GhostMode.shared_facet)

v_cg = FiniteElement("CG", mesh.ufl_cell(), 2)
Q = FunctionSpace(mesh, v_cg)

def Omega_0(x):
    return x[1] <= 0.3

def Omega_1(x):
    return x[1] >= 0.7

kappa = Function(Q)
cells_0 = locate_entities(mesh, mesh.topology.dim, Omega_0)
cells_1 = locate_entities(mesh, mesh.topology.dim, Omega_1)

@numba.njit
def unroll_dofmap(dofs, bs):
    dofs_unrolled = np.zeros(bs*len(dofs), dtype=np.int32)
    for i, dof in enumerate(dofs):
        for b in range(bs):
            dofs_unrolled[i*bs+b] = dof*bs+b
    return dofs_unrolled

dofs_0 = locate_dofs_geometrical(Q, Omega_0)
dofs_1 = locate_dofs_geometrical(Q, Omega_1)
dofmap_bs = Q.dofmap.bs
kappa.x.array[unroll_dofmap(dofs_0, dofmap_bs)] = 1
kappa.x.array[unroll_dofmap(dofs_1, dofmap_bs)] = 0.1

export_function(kappa, "adios_dir", "test_export")

then read and test it with;

# assert.py
import numba
import numpy as np
from dolfinx.fem import (Function, FunctionSpace, locate_dofs_geometrical)
from dolfinx.mesh import create_unit_square, locate_entities
from ufl import FiniteElement
from mpi4py import MPI
import dolfinx.fem
import dolfinx.io
import adios4dolfinx
import os
import pathlib

mesh = adios4dolfinx.read_mesh(MPI.COMM_WORLD, "adios_dir/test_export.bp", engine='BP4', ghost_mode=dolfinx.mesh.GhostMode.shared_facet)

v_cg = FiniteElement("CG", mesh.ufl_cell(), 2)
Q = FunctionSpace(mesh, v_cg)

def Omega_0(x):
    return x[1] <= 0.3

def Omega_1(x):
    return x[1] >= 0.7

kappa = Function(Q)
cells_0 = locate_entities(mesh, mesh.topology.dim, Omega_0)
cells_1 = locate_entities(mesh, mesh.topology.dim, Omega_1)

@numba.njit
def unroll_dofmap(dofs, bs):
    dofs_unrolled = np.zeros(bs*len(dofs), dtype=np.int32)
    for i, dof in enumerate(dofs):
        for b in range(bs):
            dofs_unrolled[i*bs+b] = dof*bs+b
    return dofs_unrolled

dofs_0 = locate_dofs_geometrical(Q, Omega_0)
dofs_1 = locate_dofs_geometrical(Q, Omega_1)
dofmap_bs = Q.dofmap.bs
kappa.x.array[unroll_dofmap(dofs_0, dofmap_bs)] = 1
kappa.x.array[unroll_dofmap(dofs_1, dofmap_bs)] = 0.1

def import_function(function_space: dolfinx.fem.FunctionSpace, directory: str, filename: str) -> dolfinx.fem.Function:

    function = dolfinx.fem.Function(function_space)
    checkpointing_directory = os.path.join(directory, filename + ".bp")
    adios4dolfinx.read_function(function, pathlib.Path(checkpointing_directory), "bp4")
    return function

kappa_import = import_function(Q, "adios_dir", "test_export")

print("original", np.count_nonzero(kappa.vector.array))
print("imported", np.count_nonzero(kappa_import.vector.array))

assert np.allclose(kappa.vector.array, kappa_import.vector.array)

gives

0, source=[0] dest=[0]
out_size, recv_size [1800] [0]
Traceback (most recent call last):
  File "assert.py", line 50, in <module>
    kappa_import = import_function(Q, "adios_dir", "test_export")
  File "assert.py", line 47, in import_function
    adios4dolfinx.read_function(function, pathlib.Path(checkpointing_directory), "bp4")
  File "/home/ee331/Dev/Venvs/v073complex/lib/python3.8/site-packages/adios4dolfinx/checkpointing.py", line 337, in read_function
    inc_cells, inc_perms = send_and_recv_cell_perm(
  File "/home/ee331/Dev/Venvs/v073complex/lib/python3.8/site-packages/adios4dolfinx/comm_helpers.py", line 204, in send_and_recv_cell_perm
    mesh_to_data.Neighbor_alltoall(out_size, recv_size)
  File "mpi4py/MPI/Comm.pyx", line 2154, in mpi4py.MPI.Topocomm.Neighbor_alltoall
mpi4py.MPI.Exception: MPI_ERR_TRUNCATE: message truncated

out_size is 1800 but recv_size is 0. Not sure how to interpret.

dokken · February 7, 2024, 8:31pm

That makes sense to me, as you are filling in recv_size with the alltoall call.
There seems to be some issue with your MPI installation that I’ve not encountered myself.

You could simply try the following MWE (in serial):

from mpi4py import MPI
import numpy as np
comm = MPI.COMM_WORLD
assert comm.size == 1, "This should only run in serial"
dest_ranks = [0]
mesh_to_data = comm.Create_dist_graph(
    [0], [len(dest_ranks)], dest_ranks, reorder=False)
in_size = np.empty(1, dtype=np.int32)
out_size = np.array([10], dtype=np.int32)
mesh_to_data.Neighbor_alltoall(out_size, in_size)
print(in_size)

Ekrem_Ekici · February 7, 2024, 8:52pm

Thank you. What would you recommend then? Which version of openmpi/mpich are your using?

dokken · February 7, 2024, 8:52pm

Did you run the snippet above? what did it return?

dokken · February 7, 2024, 8:53pm

I’m using Mpich 4.1.2, as that is what comes with Docker.
What openmpi version are you using?

Ekrem_Ekici · February 7, 2024, 8:56pm

My openmpi version is

export OPENMPI_SERIES=4.1
export OPENMPI_PATCH=6

and relevant python binding is

mpi4py 3.1.5
This configuration can run all parallel stuff in dolfinx but sadly did not work for adios4dolfinx.

dokken · February 7, 2024, 9:07pm

adios4dolfinx does nothing special. It uses standard MPI neighbourhood communicators.
The snippet I posted above is an illustration of what happens internally in adios4dolfinx in the call you are referring to.

It could be related to: Find cell tags from two overlapped meshes with different resolutions - #11 by dokken
but it is hard for me to work with when I cannot reproduce your error.

Ekrem_Ekici · February 7, 2024, 11:27pm

The issue was openmpi. I installed mpich from scratch and hence dolfinx and adios4dolfinx.

And the demo file runs fine, but I have another problem now. When I try to open the .bp file the paraview 5.12.0 RC1 says;

terminate called after throwing an instance of 'std::runtime_error'
  what():  ERROR: neither vtk.xml file or bp attribute was found in adios_dir/test_export.bp

I cannot view the solution.

dokken · February 8, 2024, 4:26am

Checkpoints are not possible to visualize in Paraview.

The reason for this is:

they contain information specific to Dolfinx
VTXReader in Paraview is missing features for global arrays. VTK support for unstructured grids with global arrays. · Issue #3688 · ornladios/ADIOS2 · GitHub

The latter point stops any efficient implementation of N to M checkpointing (write with M processes, read with N), especially in cases where N<<M or N>>M

francesco-ballarin · February 8, 2024, 6:31am

That’s the reason there is also have a VTXFile.write in my RBniCSx snippet.

francesco-ballarin · February 8, 2024, 9:04am

Sorry guys @Ekrem_Ekici @dokken , I spoke too soon

I didn’t realize that yesterday I was running @dokken’s test in a terminal with adios4dolfinx before v0.7.2, rather than v0.7.2.
Now that I am actually importing v0.7.2 I can confirm that I have the same error as @Ekrem_Ekici

It seems to be specific about openmpi. I reported this at `v0.7.2` incompatible with openmpi · Issue #55 · jorgensd/adios4dolfinx · GitHub

Ekrem_Ekici · February 8, 2024, 1:40pm

Thank you. Now, I am trying the simplify your demo further; Here is the minimal example;

# demo.py
from dolfinx.mesh import create_unit_square
import adios4dolfinx
from dolfinx.fem import Function, FunctionSpace
from ufl import FiniteElement
import numpy as np
from mpi4py import MPI
import dolfinx

path = "checkpoint0.bp"
path_out = "checkpoint1.bp"

mesh = create_unit_square(MPI.COMM_WORLD, 30, 30)
adios4dolfinx.write_mesh(mesh, path, engine='BP4')

def f(x):
    return x[0]**2+x[1]

mesh = adios4dolfinx.read_mesh(MPI.COMM_WORLD, path, engine='BP4', ghost_mode=dolfinx.mesh.GhostMode.shared_facet)

v_cg = FiniteElement("CG", mesh.ufl_cell(), 1)
V = FunctionSpace(mesh, v_cg)

kappa = Function(V)
kappa.interpolate(f)

adios4dolfinx.write_mesh(mesh, path_out, engine="BP4")
adios4dolfinx.write_function(kappa, path_out, engine="BP4")

kappa_import = Function(V)

adios4dolfinx.read_function(kappa_import, path_out, engine="BP4")

np.testing.assert_allclose(kappa.x.array, kappa_import.x.array, atol=1e-15)

It does work for single process but running it in parallel (2 procs) gives;

AssertionError: 
Not equal to tolerance rtol=1e-07, atol=1e-15

Mismatched elements: 523 / 523 (100%)
Max absolute difference: 1.41
Max relative difference: 68.375
 x: array([0.934444+0.j, 1.      +0.j, 1.033333+0.j, 0.967778+0.j,
       0.871111+0.j, 1.066667+0.j, 0.904444+0.j, 1.001111+0.j,
       0.81    +0.j, 1.1     +0.j, 0.843333+0.j, 0.937778+0.j,...
 y: array([0.09    +0.j, 0.111111+0.j, 0.144444+0.j, 0.071111+0.j,
       0.156667+0.j, 0.123333+0.j, 0.234444+0.j, 0.211111+0.j,
       0.137778+0.j, 0.19    +0.j, 0.211111+0.j, 0.073g.py:441: RuntimeWarning: mpi4py.MPI.File size changed

What is wrong here?

dokken · February 8, 2024, 1:56pm

Ekrem_Ekici:

adios4dolfinx.write_mesh(mesh, path_out, engine="BP4")
adios4dolfinx.write_function(kappa, path_out, engine="BP4")

kappa_import = Function(V)

adios4dolfinx.read_function(kappa_import, path_out, engine="BP4")

np.testing.assert_allclose(kappa.x.array, kappa_import.x.array, atol=1e-15)

If you want to re-use the function inside the same script, you should use the snapshot checkpoints, not the recoverable checkpoint: checkpointing slides

Note that I’ve also fixed the openmpi issue (new release 0.7.3 at adios4dolfinx · PyPI)

Ekrem_Ekici · February 8, 2024, 2:03pm

It does not work for separated files too. I build the mesh with;

# adios_mesh.py
from dolfinx.mesh import create_unit_square
import adios4dolfinx
from mpi4py import MPI
from pathlib import Path

path = Path("adios_dir/mesh.bp")
mesh = create_unit_square(MPI.COMM_WORLD, 30, 30)
adios4dolfinx.write_mesh(mesh, path, engine='BP4')

then read the mesh and write the function with;

# adios_write.py
from dolfinx.fem import (Function, FunctionSpace, locate_dofs_geometrical)
from ufl import FiniteElement
from mpi4py import MPI
import dolfinx.fem
import dolfinx.io
import adios4dolfinx
from pathlib import Path

def f(x):
    return x[0]**2+x[1]

path = Path("adios_dir/mesh.bp")
path_out = Path("adios_dir/checkpoint.bp")

mesh = adios4dolfinx.read_mesh(MPI.COMM_WORLD, path, engine='BP4', ghost_mode=dolfinx.mesh.GhostMode.shared_facet)

v_cg = FiniteElement("CG", mesh.ufl_cell(), 1)
V = FunctionSpace(mesh, v_cg)

kappa = Function(V)
kappa.interpolate(f)

adios4dolfinx.write_mesh(mesh, path_out, engine="BP4")
adios4dolfinx.write_function(kappa, path_out, engine="BP4")

then finally read that function with;

# adios_read.py
import dolfinx.fem
from dolfinx.fem import (Function, FunctionSpace)
from ufl import FiniteElement
from mpi4py import MPI
import adios4dolfinx
import dolfinx
import numpy as np
from pathlib import Path

def f(x):
    return x[0]**2+x[1]
    
path = Path("adios_dir/mesh.bp")
path_out = "adios_dir/checkpoint.bp"

mesh = adios4dolfinx.read_mesh(MPI.COMM_WORLD, path, engine='BP4', ghost_mode=dolfinx.mesh.GhostMode.shared_facet)

v_cg = FiniteElement("CG", mesh.ufl_cell(), 1)
V = FunctionSpace(mesh, v_cg)

kappa = Function(V)
kappa.interpolate(f)


kappa_import = Function(V)

adios4dolfinx.read_function(kappa_import, path_out, engine="BP4")

np.testing.assert_allclose(kappa.x.array, kappa_import.x.array, atol=1e-15)

gives;

AssertionError: 
Not equal to tolerance rtol=1e-07, atol=1e-15

Mismatched elements: 961 / 961 (100%)
Max absolute difference: 1.46555556
Max relative difference: 1319.
 x: array([9.344444e-01+0.j, 1.000000e+00+0.j, 1.033333e+00+0.j,
       9.677778e-01+0.j, 8.711111e-01+0.j, 1.066667e+00+0.j,
       9.044444e-01+0.j, 1.001111e+00+0.j, 8.100000e-01+0.j,...
 y: array([2.833333e-01+0.j, 2.500000e-01+0.j, 2.177778e-01+0.j,
       2.511111e-01+0.j, 3.166667e-01+0.j, 1.877778e-01+0.j,
       2.844444e-01+0.j, 2.211111e-01+0.j, 3.500000e-01+0.j,...

with the configuration below;

python3 adios_mesh.py
mpirun -np 2 python3 adios_write.py
mpirun -np 1 python3 adios_read.py

I almost copied everything from your demo as separate files but these files above are not working for some reason. Do they work as expected in your system?

dokken · February 8, 2024, 2:10pm

Ekrem_Ekici:

# adios_read.py
import dolfinx.fem
from dolfinx.fem import (Function, FunctionSpace)
from ufl import FiniteElement
from mpi4py import MPI
import adios4dolfinx
import dolfinx
import numpy as np
from pathlib import Path

def f(x):
    return x[0]**2+x[1]
    
path = Path("adios_dir/mesh.bp")
path_out = "adios_dir/checkpoint.bp"

mesh = adios4dolfinx.read_mesh(MPI.COMM_WORLD, path, engine='BP4', ghost_mode=dolfinx.mesh.GhostMode.shared_facet)

Again, read the mesh from the checkpoint in the third file. That was the whole point of

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