Paraview crash when exporting XDMF or VTX files

dolfinx
, ,
1

Dear FEniCS community,

I’m facing a Paraview crash when exporting files from the latest stable release of Dolfinx. Even the most simple example is failing. For instance, the Poisson_demo taken from Dolfinx repo:

from petsc4py.PETSc import ScalarType  # type: ignore

# +
import numpy as np

import ufl
from dolfinx import fem, io, mesh, plot
from dolfinx.fem.petsc import LinearProblem
from ufl import ds, dx, grad, inner

# +
msh = mesh.create_rectangle(comm=MPI.COMM_WORLD,
                            points=((0.0, 0.0), (2.0, 1.0)), n=(32, 16),
                            cell_type=mesh.CellType.triangle)
V = fem.functionspace(msh, ("Lagrange", 1))


facets = mesh.locate_entities_boundary(msh, dim=(msh.topology.dim - 1),
                                       marker=lambda x: np.logical_or(np.isclose(x[0], 0.0),
                                                                      np.isclose(x[0], 2.0)))


dofs = fem.locate_dofs_topological(V=V, entity_dim=1, entities=facets)


bc = fem.dirichletbc(value=ScalarType(0), dofs=dofs, V=V)

# +
u = ufl.TrialFunction(V)
v = ufl.TestFunction(V)
x = ufl.SpatialCoordinate(msh)
f = 10 * ufl.exp(-((x[0] - 0.5) ** 2 + (x[1] - 0.5) ** 2) / 0.02)
g = ufl.sin(5 * x[0])
a = inner(grad(u), grad(v)) * dx
L = inner(f, v) * dx + inner(g, v) * ds
# -

# +
problem = LinearProblem(a, L, bcs=[bc], petsc_options={
                        "ksp_type": "preonly", "pc_type": "lu"})
uh = problem.solve()
# -


# +
with io.XDMFFile(msh.comm, "out_poisson/poisson.xdmf", "w") as file:
    file.write_mesh(msh)
    file.write_function(uh)

make Paraview crash. If I only do file.write_mesh(msh), then it works. Something fails on my side when using file.write_function(uh).

I have tested the following dolfinx builds:

Docker image dolfinx/dolfinx:v0.7.3
Dolfinx intalled on docker image ubuntu:jammy using PPA
Anaconda env fenics-dolfinx

Paraview versions tested are 5.11.0, 5.11.1, 5.11.2 and 5.12.0RC on Linux, Windows and MACOS with X86 and ARM systems.

I could upload the crash report from Paraview but I don’t know how. I put a link to share:

crash report

I appreciate any help.

2

What XDMF reader are you using in paraview to open the files?
I cannot reproduce the issue with the docker image you refer to on ubuntu 22.04 with Paraview 5.11.0

Could you please check if you can open:


# +
from mpi4py import MPI
from dolfinx import fem, io, mesh

# +
msh = mesh.create_rectangle(comm=MPI.COMM_WORLD,
                            points=((0.0, 0.0), (2.0, 1.0)), n=(2, 2),
                            cell_type=mesh.CellType.triangle)
V = fem.functionspace(msh, ("Lagrange", 1))
uh = fem.Function(V)
uh.interpolate(lambda x: x[0])


with io.XDMFFile(msh.comm, "out_poisson/poisson.xdmf", "w", encoding=io.XDMFFile.Encoding.ASCII) as file:
    file.write_mesh(msh)
    file.write_function(uh)

and add data in out_poisson/poisson.xdmf to your reply:

<?xml version="1.0"?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="3.0" xmlns:xi="https://www.w3.org/2001/XInclude">
  <Domain>
    <Grid Name="mesh" GridType="Uniform">
      <Topology TopologyType="Triangle" NumberOfElements="8" NodesPerElement="3">
        <DataItem Dimensions="8 3" NumberType="Int" Format="XML">0 1 2
0 3 2
4 0 3
3 2 5
4 6 3
3 7 5
6 3 7
6 8 7
</DataItem>
      </Topology>
      <Geometry GeometryType="XY">
        <DataItem Dimensions="9 2" Format="XML">1 0
2 0
2 0.5
1 0.5
0 0
2 1
0 0.5
1 1
0 1
</DataItem>
      </Geometry>
    </Grid>
    <Grid Name="f" GridType="Collection" CollectionType="Temporal">
      <Grid Name="f" GridType="Uniform">
        <xi:include xpointer="xpointer(/Xdmf/Domain/Grid[@GridType='Uniform'][1]/*[self::Topology or self::Geometry])" />
        <Time Value="0" />
        <Attribute Name="f" AttributeType="Scalar" Center="Node">
          <DataItem Dimensions="9 1" Format="XML">1
2
2
1
2.154228071576087e-17
2
2.154228071576087e-17
1
-2.154228071576087e-17
</DataItem>
        </Attribute>
      </Grid>
    </Grid>
  </Domain>
</Xdmf>

in my case

3

Dear dokken, thanks for your reply.

I have tried to use XDMF3 READER, XDMF3 READER S and XDMF3 READER T. All of them crash. The same happen when I export to VTX and use ADIOS reader.

The data in out_poisson/poisson.xdmf is the following:

<?xml version="1.0"?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="3.0" xmlns:xi="https://www.w3.org/2001/XInclude">
  <Domain>
    <Grid Name="mesh" GridType="Uniform">
      <Topology TopologyType="Triangle" NumberOfElements="8" NodesPerElement="3">
        <DataItem Dimensions="8 3" NumberType="Int" Format="XML">0 1 2
0 3 2
4 0 3
3 2 5
4 6 3
3 7 5
6 3 7
6 8 7
</DataItem>
      </Topology>
      <Geometry GeometryType="XY">
        <DataItem Dimensions="9 2" Format="XML">1 0
2 0
2 0.5
1 0.5
0 0
2 1
0 0.5
1 1
0 1
</DataItem>
      </Geometry>
    </Grid>
    <Grid Name="f" GridType="Collection" CollectionType="Temporal">
      <Grid Name="f" GridType="Uniform">
        <xi:include xpointer="xpointer(/Xdmf/Domain/Grid[@GridType='Uniform'][1]/*[self::Topology or self::Geometry])" />
        <Time Value="0" />
        <Attribute Name="f" AttributeType="Scalar" Center="Node">
          <DataItem Dimensions="9 1" Format="XML">1
2
2
1
2.154228071576087e-17
2
2.154228071576087e-17
1
-2.154228071576087e-17
</DataItem>
        </Attribute>
      </Grid>
    </Grid>
  </Domain>
</Xdmf>

EDIT: I was able to open the file when using XDMF3 READER S.

4

As this file is exactly the same as mine (and runs on my system), there must be an issue with how you install Paraview.

5

I’m still facing an error when exporting using VTK. The MWE is as follows.

# +
from mpi4py import MPI
from dolfinx import fem, io, mesh

# +
msh = mesh.create_rectangle(comm=MPI.COMM_WORLD,
                            points=((0.0, 0.0), (2.0, 1.0)), n=(2, 2),
                            cell_type=mesh.CellType.triangle)
V = fem.functionspace(msh, ("DG", 1))
uh = fem.Function(V)
uh.interpolate(lambda x: x[0])


with io.VTKFile(msh.comm, "out_poisson/poisson.vtk", "w") as file:
    file.write_mesh(msh)
    file.write_function(uh)

EDIT: change from VTX to VTK.

6

Thanks @dokken , I was able to fix the XMDF output.

7

You say VTX, but send code for VTK:

Anyhow, the VTKFile extensions is .pvd, not .vtk.

8

Post edited. Using .pvd as the extension fix the problem. Thank you very much.