[petsc-users] Tough to reproduce petsctablefind error

Junchao Zhang junchao.zhang at gmail.com
Thu Aug 13 17:21:02 CDT 2020 

That is a great idea. I'll figure it out.
--Junchao Zhang


On Thu, Aug 13, 2020 at 4:31 PM Barry Smith <bsmith at petsc.dev> wrote:

>
>   Junchao,
>
>     Any way in the PETSc configure to warn that MPICH version is "bad" or
> "untrustworthy" or even the vague "we have suspicians about this version
> and recommend avoiding it"? A lot of time could be saved if others don't
> deal with the same problem.
>
>     Maybe add arrays of suspect_versions for OpenMPI, MPICH, etc and
> always check against that list and print a boxed warning at configure time?
> Better you could somehow generalize it and put it in package.py for use by
> all packages, then any package can included lists of "suspect" versions.
> (There are definitely HDF5 versions that should be avoided :-)).
>
>     Barry
>
>
> On Aug 13, 2020, at 12:14 PM, Junchao Zhang <junchao.zhang at gmail.com>
> wrote:
>
> 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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