[petsc-users] Tough to reproduce petsctablefind error

Thu Aug 13 11:15:23 CDT 2020

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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