[petsc-users] [DMCreate from a Gmsh with mixed mesh crash for DMPlex]
Mike Michell
mi.mike1021 at gmail.com
Wed Jul 13 16:17:47 CDT 2022
Before your pull request merged to main, I copied your change to my local
/src/dm/impls/plex/plexgmsh.c to test pyramids.
Loading DMPlex with the mesh including pyramids works okay, but printing
out the solution field to .vtk or .vtu format causes a problem with
"Unknown Cell Type Error" from post-processing tools (such as tecplot or
paraview).
I had a look at /src/dm/impls/plex/plexvtk.c the function,
DMPlexVTKGetCellType_Internal() seems not explicitly including a cellType
marker for prism and pyramids. Probably, "VTK_WEDGE" is prism with
triangular base, but still, there seems no pyramids marker.
Thanks,
> 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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