Error reading HDF5 file

Question

I'm trying to read a mesh into my program using HDF5File. This is my code:

f = HDF5File(mpi_comm_world(),'trmesh.h5', 'r')
mesh = Mesh()
f.read(mesh, 'mesh', False)

I get the following error when i try to run the code:

Error:   Unable to complete call to function has_dataset().
Reason:  Assertion link_status >= 0 failed.

I got this code from this question: http://fenicsproject.org/qa/274/consistent-io-of-mesh-and-function-in-parallel but somehow, they don't get this error.

What am I doing wrong?

Thanks!

Comments

Can you have a look in your hdf5 file using

h5ls -r trmesh.h5

What does that show?

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The output of that command is the following:

/                        Group
/Data0                   Dataset {1670, 3} 
/Data1                   Dataset {944, 3}
/Data2                   Dataset {1670}
/Data3                   Dataset {1670}
/Data4                   Dataset {1670}
/Data5                   Dataset {944, 3}

Answer 1

OK, so there is no dataset or group in your hdf5 file called "mesh". If you are trying to
read a mesh, it must exist in the hdf5 file with the name used in the f.read() line.
How did you create the file trmesh.h5?

Answer 2

I used ParaView to create this xdmf file, but it seems that paraview didn't export the file well. If I export a mesh using FEniCS and import it afterwards, the code runs just fine. This question can be closed. Thank you.

Comments

It's not really paraview's fault - it just isn't explained anywhere that the hdf5/xdmf output from
paraview is not FEniCS compatible...

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Ok, this makes sense. Will this be fixed in the (near) future?

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It's not on the radar.
If you want to raise an issue on bitbucket.org/fenics-project/dolfin, you can.