[petsc-users] DMPlexInterpolate error nonconforming object sizes

Sat Jul 2 08:37:17 CDT 2022

Thanks Matt. Fixed it now!

Thank you.
Sincerely,
Prateek Gupta, PhD

On Sat, Jul 2, 2022 at 5:10 PM Matthew Knepley <knepley at gmail.com> wrote:

> 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/>
>
-- 
Thank you.
Sincerely,
Prateek Gupta, PhD
Phone:- +91 92891 88977
             +91 9999812651
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