[petsc-dev] DMPlexCreateMedFromFile broken

[Matthew Knepley]

On Thu, Nov 9, 2017 at 11:15 AM, Vaclav Hapla <vaclav.hapla at erdw.ethz.ch>
wrote:

>
> 7. 11. 2017 v 19:51, Matthew Knepley <knepley at gmail.com>:
>
> 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/impl
>> s/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/17bd883d72f40a596f2d89b5afda5a
> 233b621464/src/dm/impls/plex/plexmed.c?at=master&
> fileviewer=file-view-default#plexmed.c-86
>
> We should ask Nico about it.
>
>
> I tried to load the MED file from meshio (attached) by the MED-supplied
> test $PETSC_ARCH/externalpackages/med-3.2.0/tests/c/test5.c, and it
> didn't complain. I compared it with DMPlexCreateMedFromFile, replaced
> MED_COMPACT_STMODE flag by MED_GLOBAL_PFLMODE in MEDfilterBlockOfEntityCr
> calls (patch attached), and it started to work magically.
>

The people who write MED should be shot, or at least severely beaten so
they can still document this stuff. Here is code using COMPACT


https://github.com/cycheung/gmsh/blob/master/Post/PViewDataGModelIO.cpp#L581

I am reluctant to change things without a reason.

   Matt


> But I have no idea what's the meaning of this flag - I found no
> documentation of the MED library.
>
> Note also that your knepley/fix-plex-med-orientation fix is still needed
> so I mean this should be applied generally - Nico's meshio is independent
> of GMSH.
>
> Vaclav
>
>
>
>
>
>   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/>
>
>
>
>


-- 
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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