[petsc-dev] Possible SF bug

Thu Apr 1 17:23:57 CDT 2021

Matt,
It is easy for me to know it is not an SF bug, since the code passes a null
pointer (as leafdata) to an SF with 9 roots and leaves. But I could not
figure out what the root reason is.  Here is my finding.
In DMSetUp(forest) >> DMSetUp_p4est >> DMPforestGetPlex
>> DMConvert_pforest_plex >> .. >> DMShareDiscretization,  we have
     dmB->sectionSF = dmA->sectionSF;
Which makes the two DMs,  forest, and  ((DM_Forest_pforest*) ((DM_Forest*)
forest->data)->data)->plex, share the same sectionSF. But in the test,
there are two places to populate the sectionSF based on different DMs.

1) In DMGlobalToLocal(forest, g, INSERT_VALUES, l), the SF is built based
on forest and its local/globalSection.
2) In VecView(g, viewer), which does
             ierr = VecGetDM(vec,&dm);CHKERRQ(ierr);

  ierr = DMPforestGetPlex(dm,&plex);CHKERRQ(ierr);
  ierr = VecSetDM(vec,plex);CHKERRQ(ierr);
  ierr = VecView_Plex(vec,viewer);CHKERRQ(ierr);
  ierr = VecSetDM(vec,dm);CHKERRQ(ierr);

VecView_Plex() calls VecView_Plex_HDF5_Internal(), which builds the SF
based on plex's local/globalSection.

Depending on which function is called first, we get different SFs. The
crashed one did 1) first and then 2). The 'good'  one did 2) and then 1).
But  even the good one is wrong, since it gives an empty SF (thus not
crashing the code).

--Junchao Zhang

On Tue, Mar 30, 2021 at 5:44 AM Matthew Knepley <knepley at gmail.com> wrote:

> On Mon, Mar 29, 2021 at 11:05 PM Junchao Zhang <junchao.zhang at gmail.com>
> wrote:
>
>> Matt,
>>   I can reproduce the error. Let me see what is wrong.
>>
>
> Thanks! It might be a bug in Plex or Forest as well, but it is hard for me
> to tell.
>
>    Matt
>
>
>>   Thanks.
>> --Junchao Zhang
>>
>>
>> On Mon, Mar 29, 2021 at 2:16 PM Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> Junchao,
>>>
>>> I have an SF problem, which I think is a caching bug, but it is hard to
>>> see what is happening in the internals. I have made a small example which
>>> should help you see what is wrong. It is attached.
>>>
>>> If you run without arguments, you get
>>>
>>> master *:~/Downloads/tmp/Salac$ ./forestHDF
>>> [0]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> [0]PETSC ERROR: Null argument, when expecting valid pointer
>>> [0]PETSC ERROR: Trying to copy to a null pointer
>>> [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html
>>> for trouble shooting.
>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.14.5-879-g03cacdc99d
>>>  GIT Date: 2021-03-22 01:02:08 +0000
>>> [0]PETSC ERROR: ./forestHDF on a arch-master-debug named
>>> MacBook-Pro.fios-router.home by knepley Mon Mar 29 15:14:16 2021
>>> [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-libpng --download-metis --download-ml --download-mumps
>>> --download-netcdf --download-opencascade --download-p4est
>>> --download-parmetis --download-pnetcdf --download-scalapack
>>> --download-slepc --download-suitesparse --download-superlu_dist
>>> --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-shared-libraries --with-slepc --with-zlib --download-tetgen
>>> [0]PETSC ERROR: #1 PetscMemcpy() at
>>> /PETSc3/petsc/petsc-dev/include/petscsys.h:1798
>>> [0]PETSC ERROR: #2 UnpackAndInsert_PetscReal_1_1() at
>>> /PETSc3/petsc/petsc-dev/src/vec/is/sf/impls/basic/sfpack.c:426
>>> [0]PETSC ERROR: #3 ScatterAndInsert_PetscReal_1_1() at
>>> /PETSc3/petsc/petsc-dev/src/vec/is/sf/impls/basic/sfpack.c:426
>>> [0]PETSC ERROR: #4 PetscSFLinkScatterLocal() at
>>> /PETSc3/petsc/petsc-dev/src/vec/is/sf/impls/basic/sfpack.c:1248
>>> [0]PETSC ERROR: #5 PetscSFBcastBegin_Basic() at
>>> /PETSc3/petsc/petsc-dev/src/vec/is/sf/impls/basic/sfbasic.c:193
>>> [0]PETSC ERROR: #6 PetscSFBcastWithMemTypeBegin() at
>>> /PETSc3/petsc/petsc-dev/src/vec/is/sf/interface/sf.c:1493
>>> [0]PETSC ERROR: #7 DMGlobalToLocalBegin() at
>>> /PETSc3/petsc/petsc-dev/src/dm/interface/dm.c:2565
>>> [0]PETSC ERROR: #8 VecView_Plex_HDF5_Internal() at
>>> /PETSc3/petsc/petsc-dev/src/dm/impls/plex/plexhdf5.c:251
>>> [0]PETSC ERROR: #9 VecView_Plex() at
>>> /PETSc3/petsc/petsc-dev/src/dm/impls/plex/plex.c:385
>>> [0]PETSC ERROR: #10 VecView_p4est() at
>>> /PETSc3/petsc/petsc-dev/src/dm/impls/forest/p4est/pforest.c:4922
>>> [0]PETSC ERROR: #11 VecView() at
>>> /PETSc3/petsc/petsc-dev/src/vec/vec/interface/vector.c:613
>>> [0]PETSC ERROR: #12 main() at
>>> /Users/knepley/Downloads/tmp/Salac/forestHDF.c:53
>>> [0]PETSC ERROR: PETSc Option Table entries:
>>> [0]PETSC ERROR: -malloc_debug
>>> [0]PETSC ERROR: ----------------End of Error Message -------send entire
>>> error message to petsc-maint at mcs.anl.gov----------
>>> application called MPI_Abort(MPI_COMM_SELF, 53001) - process 0
>>> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=53001
>>>
>>> If you run with
>>>
>>>   ./forestHDF -write_early
>>>
>>> or
>>>
>>>   ./forestHDF -no_g2l
>>>
>>> Then it is fine. Thus it appears to me that if you run a G2L at the
>>> wrong time, something is incorrectly cached.
>>>
>>>   Thanks,
>>>
>>>     Matt
>>>
>>> --
>>> 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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