Cannot open .xdmf files in legacy version of fenics + latest Paraview

General
1

Any help would be much appreciated as I cannot get this to work no matter what. I am running FEniCS 2019.1.0 (legacy latest version) in ubuntu 22.04.01 with anaconda. I installed using conda-forge in the ubuntu terminal.

Whenever I try to open a .xdmf file in any version of Paraview (tried numerous versions), Paraview crashes using the XDMFReaderS or T options, and doesn’t crash with just XDMFReader - but produces this error when I hit apply:

ERROR: In vtkXdmfReader.cxx, line 487
vtkXdmfReader (00000282C61832C0): Failed to read data.

ERROR: In vtkExecutive.cxx, line 741
vtkPVCompositeDataPipeline (00000282C580C470): Algorithm vtkFileSeriesReader (00000282D4036890) returned failure for request: vtkInformation (00000282FC6AE360)
Debug: Off
Modified Time: 420096
Reference Count: 1
Registered Events: (none)
Request: REQUEST_DATA
FORWARD_DIRECTION: 0
ALGORITHM_AFTER_FORWARD: 1
FROM_OUTPUT_PORT: 0

ERROR: In vtkXdmfReader.cxx, line 487
vtkXdmfReader (00000282FE17C690): Failed to read data.

ERROR: In vtkExecutive.cxx, line 741
vtkPVCompositeDataPipeline (00000282FD1E4E50): Algorithm vtkFileSeriesReader (00000282FC902380) returned failure for request: vtkInformation (00000282FDDD6AC0)
Debug: Off
Modified Time: 1145751
Reference Count: 1
Registered Events: (none)
Request: REQUEST_DATA
FORWARD_DIRECTION: 0
ALGORITHM_AFTER_FORWARD: 1
FROM_OUTPUT_PORT: 0

Here is my MWE:

from fenics import *

mesh = UnitSquareMesh(32, 32)
V = FunctionSpace(mesh, “Lagrange”, 1)

def boundary(x):
return x[0] < DOLFIN_EPS or x[0] > 1.0 - DOLFIN_EPS

u0 = Constant(0.0)
bc = DirichletBC(V, u0, boundary)

u = TrialFunction(V)
v = TestFunction(V)
f = Expression(“10exp(-(pow(x[0] - 0.5, 2) + pow(x[1] - 0.5, 2)) / 0.02)", degree=2)
g = Expression("sin(5x[0])”, degree=2)
a = inner(grad(u), grad(v))dx
L = fvdx + gv*ds

u = Function(V)
solve(a == L, u, bc)

file = File(“poisson.pvd”)
file << u

poissonfile = XDMFFile(“poissonFile.xdmf”)
poissonfile.write(u)

I have tried many different programs with xdmf files and all do the same issue. PVDs work fine. Please can anyone help?

2

Please post the contents of the XDMFFile?

Additionally, could you use ascii encoding and add the output of your xdmf file, i.e.

encoding = XDMFFile.Encoding.ASCII
file = XDMFFile("poissonFile.xdmf")
file.write(u,encoding=encoding)
3

Dokken, thank you very much. That made it work and I can now open and view it after hours of banging my head at this problem.

4

I wouldnt call it a solution. It was supposed to help debugging the code.

Using ascii will slow down the code in parallel.

Probably, as it is related to xdmf with h5 encoding, it was adressed at https://bitbucket.org/fenics-project/dolfin/commits/6fbc9fb8e1272c4cdd73d7e2e432dc29ebfe03ac
and
backport xdmf+boost patch (#169) · conda-forge/fenics-feedstock@3ea2183 · GitHub

5

I see, thanks. I am not sure how to upload the contents of the xdmf file with the ascii encoding here. Is this patch able to be applied to legacy fenics 2019.1.0?

6

This patch is for 2019.1.0 (the one on fenics-feedstock).

Ascii encoding is plaintext, simply open the xdmf file in a text editor, and copy the content of the file here, encapsulated with 3x`, i.e.

```
add contents here
```
7

Thats great thanks for the patch. Here is the file contents - I reduced the mesh to 14x14 to make the file shorter to be able to post here.

<?xml version="1.0"?>
<Xdmf Version="3.0">
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</DataItem>
      </Attribute>
    </Grid>
  </Domain>
</Xdmf>
8

As the ascii format works, i am more interested in the content of the xdmf file if you use the hdf5 encoding. Then the file should be significantly shorter, as it should contain pointers to the h5 file.

9

Ah sorry. Here is what the hdf5 encoded xdmf looks like (14x14 mesh)


<?xml version="1.0"?>
<Xdmf Version="3.0">
  <Domain>
    <Grid Name="mesh" GridType="Uniform">
      <Topology NumberOfElements="392" TopologyType="Triangle" NodesPerElement="3">
        <DataItem Dimensions="392 3" NumberType="UInt" Format="HDF">poissonFile.h5</DataItem>
      </Topology>
      <Geometry GeometryType="XY">
        <DataItem Dimensions="225 2" Format="HDF">poissonFile.h5</DataItem>
      </Geometry>
      <Attribute Name="f_9" AttributeType="Scalar" Center="Node">
        <DataItem Dimensions="225 1" Format="HDF">poissonFile.h5</DataItem>
      </Attribute>
    </Grid>
  </Domain>
</Xdmf>
10

The issue is here, there should be something appended after .h5, which is what

is resolving.

11

Thank you very much for your help, appreciate it.