[petsc-dev] Possible SF bug
Matthew Knepley
knepley at gmail.com
Fri Apr 2 08:19:52 CDT 2021
On Thu, Apr 1, 2021 at 9:28 PM Matthew Knepley <knepley at gmail.com> wrote:
> 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.
>
I think I have the fix: https://gitlab.com/petsc/petsc/-/merge_requests/3805
THanks,
Matt
> 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/>
>
--
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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