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

Matthew Knepley knepley at gmail.com
Wed Jul 13 12:40:30 CDT 2022 

On Wed, Jul 13, 2022 at 11:18 AM Mike Michell <mi.mike1021 at gmail.com> wrote:

> 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.
>

You are correct. Pyramids were disabled. I have activated them here:

  https://gitlab.com/petsc/petsc/-/merge_requests/5422

You mesh runs fine after this for me. I am not sure things like geometry
will work for pyramids. However, if you find something
broken, just let me know.

   Thanks,

      Matt


> 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/>
>>
>

-- 
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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