[petsc-dev] Possible SF bug
Matthew Knepley
knepley at gmail.com
Thu Apr 1 20:28:22 CDT 2021
On Thu, Apr 1, 2021 at 6:24 PM Junchao Zhang <junchao.zhang at gmail.com>
wrote:
> 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.
>
Junchao, thanks so much for looking at this. With what you show below, I
think I can figure it out now.
Thanks,
Matt
> 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/>
>>
>
--
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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