[petsc-users] Tough to reproduce petsctablefind error
Matthew Knepley
knepley at gmail.com
Thu Sep 24 12:35:45 CDT 2020
On Thu, Sep 24, 2020 at 1:22 PM Chris Hewson <chris at resfrac.com> wrote:
> Hi Guys,
>
> Thanks for all of the prompt responses, very helpful and appreciated.
>
> By "when debugging", did you mean when configure petsc --with-debugging=1
> COPTFLAGS=-O0 -g etc or when you attached a debugger?
> - Both, I have run with a debugger attached and detached, all compiled
> with the following flags "--with-debugging=1 COPTFLAGS=-O0 -g"
>
> 1) Try OpenMPI (probably won't help, but worth trying)
> - Worth a try for sure
>
> 2) Find which part of the simulation makes it non-deterministic. Is it the
> mesh partitioning (parmetis)? Then try to make it deterministic.
> - Good tip, it is the mesh partitioning and along the lines of a question
> from Barry, the matrix size is changing. I will make this deterministic and
> give it a try
>
> 3) Dump matrices, vectors, etc and see when it fails, you can quickly
> reproduce the error by reading in the intermediate data.
> - Also a great suggestion, will give it a try
>
> The full stack would be really useful here. I am guessing this happens on
> MatMult(), but I do not know.
> - Agreed, I am currently running it so that the full stack will be
> produced, but waiting for it to fail, had compiled with all available
> optimizations on, but downside is of course if there is a failure.
> As a general question, roughly what's the performance impact on petsc with
> -o1/-o2/-o0 as opposed to -o3? Performance impact of --with-debugging = 1?
> Obviously problem/machine dependant, wondering on guidance more for this
> than anything
>
> Is the nonzero structure of your matrices changing or is it fixed for the
> entire simulation?
> The non-zero structure is changing, although the structures are reformed
> when this happens and this happens thousands of time before the failure has
> occured.
>
Okay, this is the most likely spot for a bug. How are you changing the
matrix? It should be impossible to put in an invalid column index when
using MatSetValues()
because we check all the inputs. However, I do not think we check when you
just yank out the arrays.
Thanks,
Matt
> Does this particular run always crash at the same place? Similar place?
> Doesn't always crash?
> Doesn't always crash, but other similar runs have crashed in different
> spots, which makes it difficult to resolve. I am going to try out a few of
> the strategies suggested above and will let you know what comes of that.
>
> *Chris Hewson*
> Senior Reservoir Simulation Engineer
> ResFrac
> +1.587.575.9792
>
>
> On Thu, Sep 24, 2020 at 11:05 AM Barry Smith <bsmith at petsc.dev> wrote:
>
>> Chris,
>>
>> We realize how frustrating this type of problem is to deal with.
>>
>> Here is the code:
>>
>> ierr =
>> PetscTableCreate(aij->B->rmap->n,mat->cmap->N+1,&gid1_lid1);CHKERRQ(ierr);
>> for (i=0; i<aij->B->rmap->n; i++) {
>> for (j=0; j<B->ilen[i]; j++) {
>> PetscInt data,gid1 = aj[B->i[i] + j] + 1;
>> ierr = PetscTableFind(gid1_lid1,gid1,&data);CHKERRQ(ierr);
>> if (!data) {
>> /* one based table */
>> ierr =
>> PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);CHKERRQ(ierr);
>> }
>> }
>> }
>>
>> It is simply looping over the rows of the sparse matrix putting the
>> columns it finds into the hash table.
>>
>> aj[B->i[i] + j] are the column entries, the number of columns in the
>> matrix is mat->cmap->N so the column entries should always be
>> less than the number of columns. The code is crashing when column entry
>> 24443 which is larger than the number of columns 23988.
>>
>> So either the aj[B->i[i] + j] + 1 are incorrect or the mat->cmap->N is
>> incorrect.
>>
>> 640]PETSC ERROR: #3 MatAssemblyEnd_MPIAIJ() line 876 in
>>>>>>> /home/wangy2/trunk/sawtooth/griffin/moose/petsc/src/mat/impls/aij/mpi/mpiaij.c
>>>>>>>
>>>>>>>
>> if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) {
>> ierr = MatSetUpMultiply_MPIAIJ(mat);CHKERRQ(ierr);
>> }
>>
>> Seems to indicate it is setting up a new multiple because it is either
>> the first time into the algorithm or the nonzero structure changed on some
>> rank requiring a new assembly process.
>>
>> Is the nonzero structure of your matrices changing or is it fixed for
>> the entire simulation?
>>
>> Since the code has been running for a very long time already I have to
>> conclude that this is not the first time through and so something has
>> changed in the matrix?
>>
>> I think we have to put more diagnostics into the library to provide more
>> information before or at the time of the error detection.
>>
>> Does this particular run always crash at the same place? Similar
>> place? Doesn't always crash?
>>
>> Barry
>>
>>
>>
>>
>> On Sep 24, 2020, at 8:46 AM, Chris Hewson <chris at resfrac.com> wrote:
>>
>> After about a month of not having this issue pop up, it has come up again
>>
>> We have been struggling with a similar PETSc Error for awhile now, the
>> error message is as follows:
>>
>> [7]PETSC ERROR: PetscTableFind() line 132 in
>> /home/chewson/petsc-3.13.3/include/petscctable.h key 24443 is greater than
>> largest key allowed 23988
>>
>> It is a particularly nasty bug as it doesn't reproduce itself when
>> debugging and doesn't happen all the time with the same inputs either. The
>> problem occurs after a long runtime of the code (12-40 hours) and we are
>> using a ksp solve with KSPBCGS.
>>
>> The PETSc compilation options that are used are:
>>
>> --download-metis
>> --download-mpich
>> --download-mumps
>> --download-parmetis
>> --download-ptscotch
>> --download-scalapack
>> --download-suitesparse
>> --prefix=/opt/anl/petsc-3.13.3
>> --with-debugging=0
>> --with-mpi=1
>> COPTFLAGS=-O3 -march=haswell -mtune=haswell
>> CXXOPTFLAGS=-O3 -march=haswell -mtune=haswell
>> FOPTFLAGS=-O3 -march=haswell -mtune=haswell
>>
>> This is being run across 8 processes and is failing consistently on the
>> rank 7 process. We also use openmp outside of PETSC and the linear solve
>> portion of the code. The rank 0 process is always using compute, during
>> this the slave processes use an MPI_Wait call to wait for the collective
>> parts of the code to be called again. All PETSC calls are done across all
>> of the processes.
>>
>> We are using mpich version 3.3.2, downloaded with the petsc 3.13.3
>> package.
>>
>> At every PETSC call we are checking the error return from the function
>> collectively to ensure that no errors have been returned from PETSC.
>>
>> Some possible causes that I can think of are as follows:
>> 1. Memory leak causing a corruption either in our program or in petsc or
>> with one of the petsc objects. This seems unlikely as we have checked runs
>> with the option -malloc_dump for PETSc and using valgrind.
>>
>> 2. Optimization flags set for petsc compilation are causing variables
>> that go out of scope to be optimized out.
>>
>> 3. We are giving the wrong number of elements for a process or the value
>> is changing during the simulation. This seems unlikely as there is nothing
>> overly unique about these simulations and it's not reproducing itself.
>>
>> 4. An MPI channel or socket error causing an error in the collective
>> values for PETSc.
>>
>> Any input on this issue would be greatly appreciated.
>>
>> *Chris Hewson*
>> Senior Reservoir Simulation Engineer
>> ResFrac
>> +1.587.575.9792
>>
>>
>> On Thu, Aug 13, 2020 at 4:21 PM Junchao Zhang <junchao.zhang at gmail.com>
>> wrote:
>>
>>> 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
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>
>>
--
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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