[petsc-dev] DMPlexCreateGlobalToNaturalSF and partitioners

Fri Dec 17 16:44:28 CST 2021

On Fri, Dec 17, 2021 at 3:04 PM Alexis Marboeuf <marboeua at mcmaster.ca>
wrote:

> Dear PETSc Team,
>
> Following the merge request !4547 for fixing the Global To Natural map, I
> am implementing modifications to introduce a "natural" DM (i.e. the DM used
> for IO): see the discussion in
> https://gitlab.com/petsc/petsc/-/merge_requests/4547. I am writing an
> example for that, very similar to src/dm/impls/plex/tests/ex44.c added by
> the merge request, and running on 2 processors. The idea is to: (i) create
> a DM (the same distributed 2x5 mesh of ex44.c); (ii) call multiple times
> DMPlexDistribute with different partitioners and set one of the DMs as the
> "natural" DM; and (iii) see if we can reconstruct correctly the "natural"
> ordering and distribution from the last DM and the Global To Natural map. I
> am having some troubles however with at least parmetis and ptscotch
> partitioners which raise an error inside DMPlexCreateGlobalToNatural. Here
> is the error:
>

The easiest thing to do here is to start a branch from the !4547 branch
that I can checkout, and then tell me how to run what you are running.

  Thanks,

     Matt

> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [1]PETSC ERROR: Invalid argument
>
> [1]PETSC ERROR: Input array needs to be sorted
>
> Invalid argument
>
> [0]PETSC ERROR: Input array needs to be sorted
>
> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
>
> [0]PETSC ERROR: [1]PETSC ERROR: See https://petsc.org/release/faq/ for
> trouble shooting.
>
> [1]PETSC ERROR: Petsc Development GIT revision: v3.16.1-435-g007f11b901  GIT
> Date: 2021-12-01 14:31:21 +0000
>
> Petsc Development GIT revision: v3.16.1-435-g007f11b901  GIT Date:
> 2021-12-01 14:31:21 +0000
>
> [0]PETSC ERROR: ../ex47 on a arch-darwin-c-debug named
> marboeua-1.math.mcmaster.ca by alexismarboeuf Thu Dec 16 22:39:20 2021
>
> [1]PETSC ERROR: ../ex47 on a arch-darwin-c-debug named
> marboeua-1.math.mcmaster.ca by alexismarboeuf Thu Dec 16 22:39:20 2021
>
> [1]PETSC ERROR: [0]PETSC ERROR: Configure options --force
> --download-fblaslapack=1 --download-exodusii=1 --download-hdf5=1
> --download-chaco=1 --download-metis=1 --download-parmetis=1
> -download-ptscotch=1 --download-sowing=1 --download-hypre=1 --download-ml=1
> --download-netcdf=1 --download-yaml=1 --download-zlib=1
> --download-pnetcdf=1 --download-sieve=1 --with-boost=1
> --with-boost-dir=/opt/homebrew/Cellar/boost/1.76.0 with-clanguage=C++
> --with-c2html=0 --with-fortran-datatypes=1
> --with-mpi-dir=/opt/homebrew/Cellar/mpich/3.4.2 --with-debugging=1
> --with-ranlib=ranlib --with-x11=1
>
> [0]PETSC ERROR: Configure options --force --download-fblaslapack=1
> --download-exodusii=1 --download-hdf5=1 --download-chaco=1
> --download-metis=1 --download-parmetis=1 -download-ptscotch=1
> --download-sowing=1 --download-hypre=1 --download-ml=1 --download-netcdf=1
> --download-yaml=1 --download-zlib=1 --download-pnetcdf=1 --download-sieve=1
> --with-boost=1 --with-boost-dir=/opt/homebrew/Cellar/boost/1.76.0
> with-clanguage=C++ --with-c2html=0 --with-fortran-datatypes=1
> --with-mpi-dir=/opt/homebrew/Cellar/mpich/3.4.2 --with-debugging=1
> --with-ranlib=ranlib --with-x11=1
>
> [1]PETSC ERROR: #1 PetscSortedRemoveDupsInt() at
> /Users/alexismarboeuf/Documents/petsc2/src/sys/utils/sorti.c:308
>
> [0]PETSC ERROR: #2 PetscSFCreateEmbeddedLeafSF() at
> /Users/alexismarboeuf/Documents/petsc2/src/vec/is/sf/interface/sf.c:1409
>
> [0]PETSC ERROR: #1 PetscSortedRemoveDupsInt() at
> /Users/alexismarboeuf/Documents/petsc2/src/sys/utils/sorti.c:308
>
> [1]PETSC ERROR: #2 PetscSFCreateEmbeddedLeafSF() at
> /Users/alexismarboeuf/Documents/petsc2/src/vec/is/sf/interface/sf.c:1409
>
> [1]PETSC ERROR: #3 DMPlexCreateGlobalToNaturalSF() at
> /Users/alexismarboeuf/Documents/petsc2/src/dm/impls/plex/plexnatural.c:173
>
> [1]PETSC ERROR: #4 DMPlexDistribute() at
> /Users/alexismarboeuf/Documents/petsc2/src/dm/impls/plex/plexdistribute.c:1755
>
> [1]PETSC ERROR: #5 main() at
> /Users/alexismarboeuf/Documents/petsc2/src/dm/impls/plex/tests/ex47.c:289
>
> [1]PETSC ERROR: PETSc Option Table entries:
>
> [1]PETSC ERROR: -petscpartitioner_type ptscotch
>
> [1]PETSC ERROR: ----------------End of Error Message -------send entire
> error message to petsc-maint at mcs.anl.gov----------
>
> Abort(62) on node 1 (rank 1 in comm 0): application called
> MPI_Abort(MPI_COMM_WORLD, 62) - process 1
>
> #3 DMPlexCreateGlobalToNaturalSF() at
> /Users/alexismarboeuf/Documents/petsc2/src/dm/impls/plex/plexnatural.c:173
>
> [0]PETSC ERROR: #4 DMPlexDistribute() at
> /Users/alexismarboeuf/Documents/petsc2/src/dm/impls/plex/plexdistribute.c:1755
>
> [0]PETSC ERROR: #5 main() at
> /Users/alexismarboeuf/Documents/petsc2/src/dm/impls/plex/tests/ex47.c:289
>
> [0]PETSC ERROR: PETSc Option Table entries:
>
> [0]PETSC ERROR: -petscpartitioner_type ptscotch
>
> [0]PETSC ERROR: ----------------End of Error Message -------send entire
> error message to petsc-maint at mcs.anl.gov----------
>
> Abort(62) on node 0 (rank 0 in comm 0): application called
> MPI_Abort(MPI_COMM_WORLD, 62) - process 0
>
> Thanks all for your help.
> -------------------------------------------------------------------
> Alexis Marboeuf
> Postdoctoral fellow, Department of Mathematics & Statistics
> Hamilton Hall room 409B, McMaster University
> 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
> EMail: marboeua at mcmaster.ca
> Tel. +1 (905) 525 9140 ext. 27031
> -------------------------------------------------------------------
>

-- 
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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