key error when using petsc_gen_xdmf.py

[Zhenhua Li]

Hi Salvus,

I was following the instruction of Salvus from Scratch, and obtained the file movie.h5.
Then when I use petsc_gen_xdmf.py by typing python petsc_gen_xdmf.py movie.h5, I got a key error b'vector'.
I am brand new to this field so could you please tell me where to locate the error? I checked petsc_gen_xdmf.py and found nothing useful.
Thank you,

Zhenhua

[Lion Krischer]

Hi Zhenhua,

are you running Python 2 or 3? Here is a version of petsc_gen_xdmf.py that should work for both. If it still does not work: can you send us the full error log?

Cheers!

Lion

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[Zhenhua Li]

Hi Lion,

I am using python3.6. The new file you sent me worked! Thank you!

Cheers!
Zhenhua

On Tuesday, October 17, 2017 at 1:17:00 PM UTC-6, Lion Krischer wrote:

Hi Zhenhua,

are you running Python 2 or 3? Here is a version of petsc_gen_xdmf.py that should work for both. If it still does not work: can you send us the full error log?

Cheers!

Lion

On 17.10.17 19:04, Zhenhua Li wrote:

Hi Salvus,

I was following the instruction of Salvus from Scratch, and obtained the file movie.h5.
Then when I use petsc_gen_xdmf.py by typing python petsc_gen_xdmf.py movie.h5, I got a key error b'vector'.
I am brand new to this field so could you please tell me where to locate the error? I checked petsc_gen_xdmf.py and found nothing useful.
Thank you,

Zhenhua

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[Saikiran Tharimena]

Hi Lion,

I had a similar issue and used the version of petsc_gen_xdmf.py that you attached above. Although the code executed without errors, I am unable to open the movie.xmf file using paraview. I get the following error:

ERROR: In /build/paraview-arsa8T/paraview-5.0.1+dfsg1/ParaViewCore/ServerImplementation/Core/vtkSIProxy.cxx, line 310

vtkSISourceProxy (0x36c4e30): Failed to create vtkXdmfReader. Aborting for debugging purposes.

Aborted (core dumped)

My suspicion is that movie.xmf file did not get written correctly. The movie.h5 file is about 17 Gb while the movie.xmf file is about 153 kb!

The model I ran is on a spherical 3D chunk with topography and max-colatitude of 40 degree from center of mesh, and dominant period of 25 seconds. I used salvus_seismo.Source and *.Receiver to define my source and 1 receiver.

Thanks,

Sai.

[Saikiran Tharimena]

Just an update. After searching online, apparently there is some problem with paraview5.0 reading xmf files. I originally installed paraview in ubuntu using apt-get and it still seems to point 5.0.1 as the latest version.

After installing a copy of paraview5.4 from paraview[.]org, everything seems to be working fine.

Cheers,

Sai.

[Michael Afanasiev]

Hi Sai,

Good to hear the update fixed the issue. Just FYI: we expect the .xmf file to be so small. All it contains is some meta information which tells Paraview how to interpret the data stored in the movie.h5 file.

Cheers,

Mike.

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[Saikiran Tharimena]

Thanks for the info about xmf file Mike, good to know the details.

I am going a bit off topic - do you guys have any plans for Salvus workshop in the future or at AGU'17?

Cheers,

Sai.

[Michael Afanasiev]

Hi Sai,

We are certainly thinking about Salvus workshops, although nothing is planned at the moment. Good to know there is interest! Do you have some ideas on what topics would be useful to cover?

Cheers,

Mike

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