[petsc-users] DMPlexInterpolate error nonconforming object sizes

[Matthew Knepley]

On Sat, Jul 2, 2022 at 7:34 AM Matthew Knepley <knepley at gmail.com> wrote:

> On Sat, Jul 2, 2022 at 7:15 AM Prateek Gupta <prateekgupta1709 at gmail.com>
> wrote:
>
>> Hi Matt,
>> you are right about the first DM being invalid. I wasn't reading the
>> cells properly. But now that I have fixed it, the code seems to hang in an
>> infinite loop in DMPlexStratify. I am attaching the working snippet which
>> exhibits the issue.
>>
>
> Your depth ranges overlap:
>
> [0]PETSC ERROR: Petsc has generated inconsistent data
> [0]PETSC ERROR: New depth 2 range [0,4) overlaps with depth 1 range [0,4)
> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.17.1-558-g510ea5c820e
>  GIT Date: 2022-06-08 21:35:46 -0400
> [0]PETSC ERROR: ./dmplex_dist on a arch-master-debug named
> MacBook-Pro.fios-router.home by knepley Sat Jul  2 07:33:55 2022
> [0]PETSC ERROR: Configure options --PETSC_ARCH=arch-master-debug
> --download-bamg --download-chaco --download-ctetgen --download-egads
> --download-eigen --download-exodusii --download-fftw --download-hpddm
> --download-ks --download-libceed --download-libpng --download-metis
> --download-ml --download-mmg --download-mumps --download-netcdf
> --download-opencascade --download-p4est --download-parmetis
> --download-parmmg --download-pnetcdf --download-pragmatic
> --download-ptscotch --download-scalapack --download-slepc
> --download-suitesparse --download-superlu_dist --download-tetgen
> --download-triangle --with-cmake-exec=/PETSc3/petsc/apple/bin/cmake
> --with-ctest-exec=/PETSc3/petsc/apple/bin/ctest
> --with-hdf5-dir=/PETSc3/petsc/apple --with-mpi-dir=/PETSc3/petsc/apple
> --with-petsc4py=1 --with-shared-libraries --with-slepc --with-zlib
> --download-bison
> [0]PETSC ERROR: #1 DMPlexCreateDepthStratum() at
> /PETSc3/petsc/petsc-dev/src/dm/impls/plex/plex.c:3864
> [0]PETSC ERROR: #2 DMPlexStratify() at
> /PETSc3/petsc/petsc-dev/src/dm/impls/plex/plex.c:3984
> [0]PETSC ERROR: #3 main() at
> /Users/knepley/Downloads/tmp/Prateek/dmplex_dist.cpp:167
> [0]PETSC ERROR: PETSc Option Table entries:
> [0]PETSC ERROR: -malloc_debug
>
> I will try to figure out why.
>

The problem is that vertices are numbered _after_ cells, so you need to add
n_elements to every vertex number. Or you could consider calling


https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexCreateFromCellListPetsc/

  Thanks,

      Matt


>   Thanks,
>
>      Matt
>
>
>> Thanks for your help!
>>
>>
>> Sincerely,
>> Prateek Gupta, PhD
>>
>>
>> On Sat, Jul 2, 2022 at 4:37 PM Matthew Knepley <knepley at gmail.com> wrote:
>>
>>> On Sat, Jul 2, 2022 at 3:11 AM Prateek Gupta <prateekgupta1709 at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>> I am trying to create a minimal example of reading nodes and elements
>>>> from a text file and creating dmplex mesh. So far I am following the
>>>> procedure as in plexfluent.c. However, while trying to interpolate the
>>>> mesh, I get the error,
>>>>
>>>> [0]PETSC ERROR: Nonconforming object sizes
>>>> [0]PETSC ERROR: The number of vertices in first DM 20 != 0 in the
>>>> second DM
>>>>
>>>> The call trace looks like this,
>>>> [0]PETSC ERROR: #1 DMPlexCopyCoordinates() line 1448 in
>>>> /build/petsc-zg3KH7/petsc-3.12.4+dfsg1/src/dm/impls/plex/plexinterpolate.c
>>>> [0]PETSC ERROR: #2 DMPlexInterpolate() line 1394 in
>>>> /build/petsc-zg3KH7/petsc-3.12.4+dfsg1/src/dm/impls/plex/plexinterpolate.c
>>>>
>>>> The code snippet for interpolation is exactly same as in plexfluent.c
>>>> except for the petscCall function,
>>>>
>>>> --------------------------------------------------
>>>>   if (interpolate) {
>>>>     DM idm;
>>>>     PetscCall(DMPlexInterpolate(*dm, &idm));
>>>>     PetscCall(DMDestroy(dm));
>>>>     dm  = idm;
>>>>   }
>>>> --------------------------------------------------
>>>>
>>>> dm is the DM object declared within main only. Any help will be
>>>> appreciated. I can guess that the idm object doesn't have memory allocated
>>>> for copying the vertices, but my question is how come it works off-the-bat
>>>> for fluent/gmsh files using functions in plexfluent.c and plexgmsh.c. Is
>>>> there a way to allocate just the vertices? Or do I need to use
>>>> DMPlexSetChart for idm object before interpolating?
>>>>
>>>
>>> My guess is that the first DM is invalid. If you send the code, I will
>>> go through it.
>>>
>>>   Thanks,
>>>
>>>      Matt
>>>
>>>
>>>> Thank you.
>>>> Sincerely,
>>>> Prateek Gupta, PhD
>>>>
>>>
>>>
>>> --
>>> 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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