[petsc-dev] DMPlexCreateMedFromFile broken

[Matthew Knepley]

On Tue, Nov 7, 2017 at 11:44 AM, Vaclav Hapla <vaclav.hapla at erdw.ethz.ch>
wrote:

> Nico Schlömer just introduced MED support into his meshio tool, based on
> my issue request. When I convert blockcylinder-50.exo directly to the MED
> format with meshio, the result can be loaded into GMSH and looks
> reasonable. But DMPlexCreateMedFromFile denies to open it with the
> following error:
>
> _MEDmeshAdvancedRd236.c [285] : Erreur de valeur invalide du filtre
> _MEDmeshAdvancedRd236.c [285] :
> _MEDmeshAdvancedRd236.c [286] : geotype = 0
> _MEDmeshAdvancedRd236.c [286] : meshname = "mesh0"
> _MEDmeshAdvancedRd236.c [286] : _datagroupname2 = "NOE"
> _MEDmeshAdvancedRd236.c [287] : (*_filter).storagemode = 2
> [0]PETSC ERROR: #1 DMPlexCreateMedFromFile() line 86 in
> /scratch/petsc-dev/src/dm/impls/plex/plexmed.c
> [0]PETSC ERROR: #2 DMPlexCreateFromFile() line 2815 in
> /scratch/petsc-dev/src/dm/impls/plex/plexcreate.c
> [0]PETSC ERROR: #3 main() line 38 in /scratch/petsc-dev/src/dm/
> impls/plex/examples/tutorials/ex5.c
>
> Can you see whether it's a bug in DMPlexCreateMedFromFile or the MED file
> is broken?
>

It appears to be an MED incompatibility


https://bitbucket.org/petsc/petsc/src/17bd883d72f40a596f2d89b5afda5a233b621464/src/dm/impls/plex/plexmed.c?at=master&fileviewer=file-view-default#plexmed.c-86

We should ask Nico about it.

  Thanks,

     Matt


> Thanks
>
> Vaclav
>
>
> 5. 11. 2017 v 18:48, Matthew Knepley <knepley at gmail.com>:
>
> On Thu, Nov 2, 2017 at 12:08 PM, Vaclav Hapla <vaclav.hapla at erdw.ethz.ch>
> wrote:
>
>> It seems that DMPlexCreateMedFromFile leaves out some mesh elements. I
>> found it out when investigating why ParMetis redistribution crashes.
>>
>> I attach the datafile $PETSC_DIR/share/petsc/datafiles/meshes/blockcylinder-50.exo
>> converted to GMSH and MED format.
>> The conversion EXO to GMSH was done by meshio (github.com/nschloe/meshio),
>> and GMSH to MED by GMSH itself.
>>
>> I did:
>>
>> cd $PETSC_DIR/src/dm/impls/plex/examples/tutorials
>> make ex5
>> FILE=blockcylinder-50.exo && ./ex5 -filename $FILE -dm_view hdf5:$FILE.h5
>> && $PETSC_DIR/bin/petsc_gen_xdmf.py $FILE.h5
>> FILE=blockcylinder-50.msh && ./ex5 -filename $FILE -dm_view hdf5:$FILE.h5
>> && $PETSC_DIR/bin/petsc_gen_xdmf.py $FILE.h5
>> FILE=blockcylinder-50.med && ./ex5 -filename $FILE -dm_view hdf5:$FILE.h5
>> && $PETSC_DIR/bin/petsc_gen_xdmf.py $FILE.h5
>>
>> While the output from blockcylinder-50.exo and blockcylinder-50.msh looks
>> OK, that from blockcylinder-50.med is corrupted.
>>
>> I also attach my HDF5/XDMF outputs and screenshots from ParaView.
>
>
> It appears that MED, at least coming from GMsh, inverts hexes just like
> GMsh does. I have fixed this in branch
>
>   knepley/fix-plex-med-orientation
>
> If you run your test in this, everything should be fine.
>
> Michael, can you check whether this is a general fix, or it only applied
> to MED from GMsh?
>
>   Thanks,
>
>      Matt
>
>
>>
>> Vaclav
>>
>>
>>
>>
>>
>>
>>
>>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
>
>
>


-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
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