[petsc-users] Tough to reproduce petsctablefind error

Thu Aug 13 12:14:45 CDT 2020

Thanks for the update. Let's assume it is a bug in MPI :)
--Junchao Zhang

On Thu, Aug 13, 2020 at 11:15 AM Chris Hewson <chris at resfrac.com> wrote:

> Just as an update to this, I can confirm that using the mpich version
> (3.3.2) downloaded with the petsc download solved this issue on my end.
>
> *Chris Hewson*
> Senior Reservoir Simulation Engineer
> ResFrac
> +1.587.575.9792
>
>
> On Thu, Jul 23, 2020 at 5:58 PM Junchao Zhang <junchao.zhang at gmail.com>
> wrote:
>
>> On Mon, Jul 20, 2020 at 7:05 AM Barry Smith <bsmith at petsc.dev> wrote:
>>
>>>
>>>     Is there a comprehensive  MPI test suite (perhaps from MPICH)? Is
>>> there any way to run this full test suite under the problematic MPI and see
>>> if it detects any problems?
>>>
>>>      Is so, could someone add it to the FAQ in the debugging section?
>>>
>> MPICH does have a test suite. It is at the subdir test/mpi of downloaded
>> mpich <http://www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz>.
>> It annoyed me since it is not user-friendly.  It might be helpful in
>> catching bugs at very small scale. But say if I want to test allreduce on
>> 1024 ranks on 100 doubles, I have to hack the test suite.
>> Anyway, the instructions are here.
>>
>> For the purpose of petsc, under test/mpi one can configure it with
>> $./configure CC=mpicc CXX=mpicxx FC=mpifort --enable-strictmpi
>> --enable-threads=funneled --enable-fortran=f77,f90 --enable-fast
>> --disable-spawn --disable-cxx --disable-ft-tests  // It is weird I disabled
>> cxx but I had to set CXX!
>> $make -k -j8  // -k is to keep going and ignore compilation errors, e.g.,
>> when building tests for MPICH extensions not in MPI standard, but your MPI
>> is OpenMPI.
>> $ // edit testlist, remove lines mpi_t, rma, f77, impls. Those are
>> sub-dirs containing tests for MPI routines Petsc does not rely on.
>> $ make testings or directly './runtests -tests=testlist'
>>
>> On a batch system,
>> $export MPITEST_BATCHDIR=`pwd`/btest       // specify a batch dir, say
>> btest,
>> $./runtests -batch -mpiexec=mpirun -np=1024 -tests=testlist   // Use 1024
>> ranks if a test does no specify the number of processes.
>> $ // It copies test binaries to the batch dir and generates a
>> script runtests.batch there.  Edit the script to fit your batch system and
>> then submit a job and wait for its finish.
>> $ cd btest && ../checktests --ignorebogus
>>
>>
>> PS: Fande, changing an MPI fixed your problem does not necessarily mean
>> the old MPI has bugs. It is complicated. It could be a petsc bug.  You need
>> to provide us a code to reproduce your error. It does not matter if the
>> code is big.
>>
>>
>>>     Thanks
>>>
>>>       Barry
>>>
>>>
>>> On Jul 20, 2020, at 12:16 AM, Fande Kong <fdkong.jd at gmail.com> wrote:
>>>
>>> Trace could look like this:
>>>
>>> [640]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> [640]PETSC ERROR: Argument out of range
>>> [640]PETSC ERROR: key 45226154 is greater than largest key allowed 740521
>>> [640]PETSC ERROR: See
>>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
>>> shooting.
>>> [640]PETSC ERROR: Petsc Release Version 3.13.3, unknown
>>> [640]PETSC ERROR: ../../griffin-opt on a arch-moose named r6i5n18 by
>>> wangy2 Sun Jul 19 17:14:28 2020
>>> [640]PETSC ERROR: Configure options --download-hypre=1
>>> --with-debugging=no --with-shared-libraries=1 --download-fblaslapack=1
>>> --download-metis=1 --download-ptscotch=1 --download-parmetis=1
>>> --download-superlu_dist=1 --download-mumps=1 --download-scalapack=1
>>> --download-slepc=1 --with-mpi=1 --with-cxx-dialect=C++11
>>> --with-fortran-bindings=0 --with-sowing=0 --with-64-bit-indices
>>> --download-mumps=0
>>> [640]PETSC ERROR: #1 PetscTableFind() line 132 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/include/petscctable.h
>>> [640]PETSC ERROR: #2 MatSetUpMultiply_MPIAIJ() line 33 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/mat/impls/aij/mpi/mmaij.c
>>> [640]PETSC ERROR: #3 MatAssemblyEnd_MPIAIJ() line 876 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/mat/impls/aij/mpi/mpiaij.c
>>> [640]PETSC ERROR: #4 MatAssemblyEnd() line 5347 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/mat/interface/matrix.c
>>> [640]PETSC ERROR: #5 MatPtAPNumeric_MPIAIJ_MPIXAIJ_allatonce() line 901
>>> in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/mat/impls/aij/mpi/mpiptap.c
>>> [640]PETSC ERROR: #6 MatPtAPNumeric_MPIAIJ_MPIMAIJ_allatonce() line 3180
>>> in /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/mat/impls/maij/maij.c
>>> [640]PETSC ERROR: #7 MatProductNumeric_PtAP() line 704 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/mat/interface/matproduct.c
>>> [640]PETSC ERROR: #8 MatProductNumeric() line 759 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/mat/interface/matproduct.c
>>> [640]PETSC ERROR: #9 MatPtAP() line 9199 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/mat/interface/matrix.c
>>> [640]PETSC ERROR: #10 MatGalerkin() line 10236 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/mat/interface/matrix.c
>>> [640]PETSC ERROR: #11 PCSetUp_MG() line 745 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/ksp/pc/impls/mg/mg.c
>>> [640]PETSC ERROR: #12 PCSetUp_HMG() line 220 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/ksp/pc/impls/hmg/hmg.c
>>> [640]PETSC ERROR: #13 PCSetUp() line 898 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/ksp/pc/interface/precon.c
>>> [640]PETSC ERROR: #14 KSPSetUp() line 376 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/ksp/ksp/interface/itfunc.c
>>> [640]PETSC ERROR: #15 KSPSolve_Private() line 633 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/ksp/ksp/interface/itfunc.c
>>> [640]PETSC ERROR: #16 KSPSolve() line 853 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/ksp/ksp/interface/itfunc.c
>>> [640]PETSC ERROR: #17 SNESSolve_NEWTONLS() line 225 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/snes/impls/ls/ls.c
>>> [640]PETSC ERROR: #18 SNESSolve() line 4519 in
>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/snes/interface/snes.c
>>>
>>> On Sun, Jul 19, 2020 at 11:13 PM Fande Kong <fdkong.jd at gmail.com> wrote:
>>>
>>>> I am not entirely sure what is happening, but we encountered similar
>>>> issues recently.  It was not reproducible. It might occur at different
>>>> stages, and errors could be weird other than "ctable stuff." Our code was
>>>> Valgrind clean since every PR in moose needs to go through rigorous
>>>> Valgrind checks before it reaches the devel branch.  The errors happened
>>>> when we used mvapich.
>>>>
>>>> We changed to use HPE-MPT (a vendor stalled MPI), then everything was
>>>> smooth.  May you try a different MPI? It is better to try a system carried
>>>> one.
>>>>
>>>> We did not get the bottom of this problem yet, but we at least know
>>>> this is kind of MPI-related.
>>>>
>>>> Thanks,
>>>>
>>>> Fande,
>>>>
>>>>
>>>> On Sun, Jul 19, 2020 at 3:28 PM Chris Hewson <chris at resfrac.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I am having a bug that is occurring in PETSC with the return string:
>>>>>
>>>>> [7]PETSC ERROR: PetscTableFind() line 132 in
>>>>> /home/chewson/petsc-3.13.2/include/petscctable.h key 7556 is greater than
>>>>> largest key allowed 5693
>>>>>
>>>>> This is using petsc-3.13.2, compiled and running using mpich with -O3
>>>>> and debugging turned off tuned to the haswell architecture and
>>>>> occurring either before or during a KSPBCGS solve/setup or during a MUMPS
>>>>> factorization solve (I haven't been able to replicate this issue with the
>>>>> same set of instructions etc.).
>>>>>
>>>>> This is a terrible way to ask a question, I know, and not very helpful
>>>>> from your side, but this is what I have from a user's run and can't
>>>>> reproduce on my end (either with the optimization compilation or with
>>>>> debugging turned on). This happens when the code has run for quite some
>>>>> time and is happening somewhat rarely.
>>>>>
>>>>> More than likely I am using a static variable (code is written in c++)
>>>>> that I'm not updating when the matrix size is changing or something silly
>>>>> like that, but any help or guidance on this would be appreciated.
>>>>>
>>>>> *Chris Hewson*
>>>>> Senior Reservoir Simulation Engineer
>>>>> ResFrac
>>>>> +1.587.575.9792
>>>>>
>>>>
>>>
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