failure to read xdmf files generated by Fenics

ParaView Support
1

I am using Paraview-5.8.1-RC2 with a MacOS Mojave 10.14.5 with 16Gb Ram

I get errors message (see below) when I open the attached xdmf file (generated by Fenics). velocity.xdmf (24.1 KB)
The velocity.h5 companion file is present in the same directory. It is 9Mo so I don’t include it here. I can provide a link if necessary.

I tried to open the file with Paraview-5.8.0 and Paraview-5.6.2 and got the same issue.
I could not find an answer in the posts about xdmf.
Any help appreciated.

ERROR: In /Users/kitware/dashboards/buildbot-slave/88b2a88f/build/superbuild/paraview/src/VTK/IO/Xdmf2/vtkXdmfReader.cxx, line 476
vtkXdmfReader (0x7fbb45582580): Failed to read data.

ERROR: In /Users/kitware/dashboards/buildbot-slave/88b2a88f/build/superbuild/paraview/src/VTK/Common/ExecutionModel/vtkExecutive.cxx, line 753
vtkPVCompositeDataPipeline (0x600002298a80): Algorithm vtkFileSeriesReader(0x60000266cf00) returned failure for request: vtkInformation (0x60000059b780)
Debug: Off
Modified Time: 330481
Reference Count: 1
Registered Events: (none)
Request: REQUEST_DATA
FROM_OUTPUT_PORT: 0
ALGORITHM_AFTER_FORWARD: 1
FORWARD_DIRECTION: 0

2

Use the XDMF3 reader option.

3

I can choose between XDMF Reader or xdmf3ReaderS or xdfmf3ReaderT.
But the last two make Paraview crash. So I can only open with XDMF Reader and I still have the same problem.

4

Seems I didn’t generate the xdmf file correctly.
I did it in python with the following commands:

First I create the file before my time loop

xdmffile_u = XDMFFile(‘velocity.xdmf’)

then I save the time values within the time loop to file (XDMF/HDF5)

xdmffile_u.write(u, t)

Thanks to https://fenicsproject.discourse.group/t/loading-xdmf-file-in-paraview/2291

I solved the issue inserting the command

xdmffile_u.parameters[“flush_output”] = True

just after the file creation:

xdmffile_u = XDMFFile(‘velocity.xdmf’)
xdmffile_u.parameters[“flush_output”] = True

Now all three xdmf readers work correctly. No need to use xdfm3 btw.

1 Like
5

Could you go through step by step on how to use this command. I’m currently extracting an xdmf file from a fenicsproject machine and I desperately need help on this topic. If you could please go through step by step on how to make this work that would be great.