[petsc-users] [DMCreate from a Gmsh with mixed mesh crash for DMPlex]
Matthew Knepley
knepley at gmail.com
Wed Jul 13 16:45:39 CDT 2022
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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