[petsc-users] [DMCreate from a Gmsh with mixed mesh crash for DMPlex]

[Mike Michell]

Attached is a mixed mesh file that I am testing. I cannot see any special
marker for pyramid cells. Version of gmsh is 4.9.0.

Thanks,



> On Wed, Jul 13, 2022 at 10:41 AM Mike Michell <mi.mike1021 at gmail.com>
> wrote:
>
>> Thank you for the quick response. Below is the full error message I get.
>>
>>
>> [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [0]PETSC ERROR: Argument out of range
>> [0]PETSC ERROR: No face description for cell type unknown
>>
>
> Here is the problem. The pyramid (or some other cell) was classified as
> "unknown". First, make sure the Gmsh file is version 4.1.
> If that fails, send the Gmsh file and I will try to figure out why the
> cell is not coming up as a pyramid.
>
>   Thanks,
>
>      Matt
>
>
>> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
>> [0]PETSC ERROR: Petsc Release Version 3.17.0, unknown
>> [0]PETSC ERROR: /home/Mike/Workspace/test on a named Mike Wed Jul 13
>> 10:38:31 2022
>> [0]PETSC ERROR: Configure options
>> --prefix=/home/Mike/Library/petsc_partition/install-intel
>> PETSC_ARCH=linux-gnu-intel --with-cc=mpiicc --with-cxx=mpiicpc
>> --with-fc=mpiifort --download-fblaslapack --download-metis
>> --download-parmetis --download-eigen --download-pragmatic --download-hdf5
>> --download-triangle --with-debugging=1 COPTFLAGS="-O3 -mtune=native"
>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
>> [0]PETSC ERROR: #1 DMPlexGetRawFaces_Internal() at
>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexinterpolate.c:312
>> [0]PETSC ERROR: #2 DMPlexInterpolateFaces_Internal() at
>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexinterpolate.c:350
>> [0]PETSC ERROR: #3 DMPlexInterpolate() at
>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexinterpolate.c:1327
>> [0]PETSC ERROR: #4 DMPlexCreateGmsh() at
>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexgmsh.c:1634
>> [0]PETSC ERROR: #5 DMPlexCreateGmshFromFile() at
>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexgmsh.c:1418
>> [0]PETSC ERROR: #6 DMPlexCreateFromFile() at
>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexcreate.c:4721
>> [0]PETSC ERROR: #7 DMPlexCreateFromOptions_Internal() at
>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexcreate.c:3212
>> [0]PETSC ERROR: #8 DMSetFromOptions_Plex() at
>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexcreate.c:3433
>> [0]PETSC ERROR: #9 DMSetFromOptions() at
>> /home/Mike/Library/petsc_partition/src/dm/interface/dm.c:887
>> [0]PETSC ERROR: #10 User provided function() at User file:0
>> Abort(63) on node 0 (rank 0 in comm 16): application called
>> MPI_Abort(MPI_COMM_SELF, 63) - process 0
>>
>> Thanks,
>> Mike
>>
>>
>>> On Wed, Jul 13, 2022 at 10:30 AM Mike Michell <mi.mike1021 at gmail.com>
>>> wrote:
>>>
>>>> Hi, DMCreate() is used to load/distribute grid built from gmsh, and the
>>>> function crashes when a mixed mesh of tetra and pyramids in 3D. It looks
>>>> PETSc can handle the cell types of
>>>> Tetra/Hexa/Prism/Pyramids/Polygon/Polyhedra in 3D. Thus I am unsure why it
>>>> crashes when pyramids included in gmsh file.
>>>>
>>>> Below functions are used to mesh distribution.
>>>> call DMCreate(PETSC_COMM_WORLD, dm_g, ierr);CHKERRA(ierr)
>>>> call DMSetType(dm_g, DMPLEX, ierr);CHKERRA(ierr)
>>>> call DMSetFromOptions(dm_g, ierr);CHKERRA(ierr)
>>>>
>>>> Below error messages got from run.
>>>>
>>>
>>> I need the complete error message. This is only the stack. I cannot see
>>> the error message, or the version of PETSc you are using.
>>>
>>> This should work, so I do not immediately know what is wrong.
>>>
>>>   Thanks,
>>>
>>>      Matt
>>>
>>>
>>>> [0]PETSC ERROR: #1 DMPlexGetRawFaces_Internal() at
>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexinterpolate.c:312
>>>> [0]PETSC ERROR: #2 DMPlexInterpolateFaces_Internal() at
>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexinterpolate.c:350
>>>> [0]PETSC ERROR: #3 DMPlexInterpolate() at
>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexinterpolate.c:1327
>>>> [0]PETSC ERROR: #4 DMPlexCreateGmsh() at
>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexgmsh.c:1634
>>>> [0]PETSC ERROR: #5 DMPlexCreateGmshFromFile() at
>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexgmsh.c:1418
>>>> [0]PETSC ERROR: #6 DMPlexCreateFromFile() at
>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexcreate.c:4721
>>>> [0]PETSC ERROR: #7 DMPlexCreateFromOptions_Internal() at
>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexcreate.c:3212
>>>> [0]PETSC ERROR: #8 DMSetFromOptions_Plex() at
>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexcreate.c:3433
>>>> [0]PETSC ERROR: #9 DMSetFromOptions() at
>>>> /home/Mike/Library/petsc_partition/src/dm/interface/dm.c:887
>>>> [0]PETSC ERROR: #10 User provided function() at User file:0
>>>> Abort(63) on node 0 (rank 0 in comm 16): application called
>>>> MPI_Abort(MPI_COMM_SELF, 63) - process 0
>>>>
>>>> Can I get any comments on that?
>>>>
>>>> Thanks,
>>>>
>>>>
>>>>
>>>
>>> --
>>> 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.cse.buffalo.edu/~knepley/>
>>>
>>
>
> --
> 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.cse.buffalo.edu/~knepley/>
>
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