[petsc-users] [DMCreate from a Gmsh with mixed mesh crash for DMPlex]
Mike Michell
mi.mike1021 at gmail.com
Thu Jul 14 18:32:55 CDT 2022
VTK format itself supports pyramids for sure. But I do not think PETSc
output part through VTK format does not. Is there any possibility to debug
this issue?
Thanks,
> On Wed, Jul 13, 2022 at 4:18 PM Mike Michell <mi.mike1021 at gmail.com>
> wrote:
>
>> 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.
>>
>
> Yes, I am not sure it supports pyramids. Will have to look.
>
> Thanks,
>
> Matt
>
>
>> 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/>
>>>
>>
>
> --
> 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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