[petsc-users] Tough to reproduce petsctablefind error
Mark McClure
mark at resfrac.com
Sat Sep 26 10:17:14 CDT 2020
Thank you, all for the explanations.
Following Matt's suggestion, we'll use -g (and not use -with-debugging=0)
all future compiles to all users, so in future, we can provide better
information.
Second, Chris is going to boil our function down to minimum stub and share
in case there is some subtle issue with the way the functions are being
called.
Third, I have question/request - Petsc is, in fact, detecting an error. As
far as I can tell, this is not an uncontrolled 'seg fault'. It seems to me
that maybe Petsc could choose to return out from the function when it
detects this error, returning an error code, rather than dumping the core
and terminating the program. If Petsc simply returned out with an error
message, this would resolve the problem for us. After the Petsc call, we
check for Petsc error messages. If Petsc returns an error - that's fine -
we use a direct solver as a backup, and the simulation continues. So - I am
not sure whether this is feasible - but if Petsc could return out with an
error message - rather than dumping the core and terminating the program -
then that would effectively resolve the issue for us. Would this change be
possible?
Mark
On Fri, Sep 25, 2020 at 2:08 PM Barry Smith <bsmith at petsc.dev> wrote:
>
> I May 2019 Lisandro changed the versions of Metis and ParMetis that
> PETSc uses to use a portable machine independent random number generator so
> if you are having PETSc install Metis then its random number generator
> should generate the exact same random numbers on repeated identical runs on
> the same machine or different machines. If this does not appear to be the
> case please let us know. PETSc doesn't use random numbers much but when it
> does they are all portable and machine independent and produce identical
> results for identical runs.
>
> Due to the non-commutativity of floating point arithmetic with
> parallelism (numbers arrive in different orders on identical runs) the
> numerical results will differ and hence decisions (iteration convergence
> etc) will differ so the "results" can vary a great deal in different
> identical runs.
>
> We did have a user getting "random" errors only after very long runs
> that were due to "hardware errors" perhaps due to overheating so it is also
> possible your problems are not due directly to memory corruption, PETSc or
> MPI or even OS software. This may be too complicated for your work flow but
> perhaps if you restricted your jobs to shorter times with a restart
> mechanism these problems would not appear.
>
> Barry
>
> Truly random "hardware" errors often produce just wildly crazy numbers,
> in your report the numbers are off but not absurdly large which points to
> possible software errors.
>
>
>
>
> On Sep 25, 2020, at 12:02 PM, Mark McClure <mark at resfrac.com> wrote:
>
> Hello,
>
> I work with Chris, and have a few comments, hopefully helpful. Thank you
> all, for your help.
>
> Our program is unfortunately behaving a little bit nondeterministically. I
> am not sure why because for the OpenMP parts, I test it for race conditions
> using Intel Inspector and see none. We are using Metis, not Parmetis. Do
> Petsc or Metis have any behavior that is nondeterministic? We will continue
> to investigate the cause of the nondeterminism. But that is a challenge for
> us reproducing this problem because we can run the same simulation 10
> times, and we do not get precisely the same result each time. In fact, for
> this bug, Chris did run it 10 times and did not reproduce.
>
> Every month, 1000s of hours of this simulator are being run on the
> Azure cluster. This crash has been occurring for months, but at infrequent
> intervals, and have never been able to reproduce it. As such, we can't
> generate an error dump, unless we gave all users a Petsc build with no
> optimization and waited weeks until a problem cropped up.
>
> Here's what we'll do - we'll internally make a build with debug and then
> run a large number of simulations until the problem reproduces and we get
> the error dump. That will take us some time, but we'll do it.
>
> Here is a bit more background that might be helpful. At first, we used
> OpenMPI 2.1.1-8 with Petsc 3.13.2. With that combo, we observed a memory
> leak, and simulations failed when the node ran out of RAM. Then we switched
> to MPICH3.3a2 and Petsc 3.13.3. The memory leak went away. That's when we
> started seeing this bug "greater than largest key allowed". It was
> unreproducible, but happening relatively more often than it is now (I
> think) - I was getting a couple user reports a week. Then, we updated to
> MPICH 3.3.2 and the same Petsc version (3.13.3). The problem seems to be
> less common - hadn't happened for the past month. But then it happened four
> times this week.
>
> Other background to note - our linear system very frequently changes
> size/shape. There will be 10,000s of Petsc solves with different matrices
> (different positions of nonzero values) over the course of a simulation. As
> far as we can tell, the crash only occurs only after the simulator has run
> for a long time, 10+ hours. Having said that, it does not appear to be a
> memory leak - at least, the node has plenty of remaining RAM when these
> crashes are occurring.
>
> Mark
>
>
> On Thu, Sep 24, 2020 at 4:41 PM Mark Adams <mfadams at lbl.gov> wrote:
>
>> You might add code here like:
>>
>> if (ierr) {
>> for (; i<aij->B->rmap->n; i++) {
>> for ( j<B->ilen[i]; j++) {
>> PetscInt data,gid1 = aj[B->i[i] + j] + 1; // don't use ierr
>> print rank, gid1;
>> }
>> CHKERRQ(ierr);
>>
>> I am guessing that somehow you have a table that is bad and too small. It
>> failed on an index not much bigger than the largest key allowed. Maybe just
>> compute the max and see if it goes much larger than the largest key allowed.
>>
>> If your mesh just changed to you know if it got bigger or smaller...
>>
>> Anyway just some thoughts,
>> Mark
>>
>>
>>
>> On Thu, Sep 24, 2020 at 4:18 PM Barry Smith <bsmith at petsc.dev> wrote:
>>
>>>
>>>
>>> On Sep 24, 2020, at 2:47 PM, Matthew Knepley <knepley at gmail.com> wrote:
>>>
>>> On Thu, Sep 24, 2020 at 3:42 PM Barry Smith <bsmith at petsc.dev> wrote:
>>>
>>>>
>>>> The stack is listed below. It crashes inside MatPtAP().
>>>>
>>>
>>> What about just checking that the column indices that PtAP receives are
>>> valid? Are we not doing that?
>>>
>>>
>>> The code that checks for column too large in MatSetValues_MPIXXAIJ()
>>> is turned off for optimized builds, I am making a MR to always have it on.
>>> But I doubt this is the problem, other, more harsh crashes, are likely if
>>> the column index is too large.
>>>
>>> This is difficult to debug because all we get is a stack trace. It
>>> would be good if we produce some information about the current state of the
>>> objects when the error is detected. We should think about what light-weight
>>> stuff we could report when errors are detected.
>>>
>>>
>>> Barry
>>>
>>>
>>> Matt
>>>
>>>
>>>> It is possible there is some subtle bug in the rather complex PETSc
>>>> code for MatPtAP() but I am included to blame MPI again.
>>>>
>>>> I think we should add some simple low-overhead always on
>>>> communication error detecting code to PetscSF where some check sums are
>>>> also communicated at the highest level of PetscSF().
>>>>
>>>> I don't know how but perhaps when the data is packed per destination
>>>> rank a checksum is computed and when unpacked the checksum is compared
>>>> using extra space at the end of the communicated packed array to store and
>>>> send the checksum. Yes, it is kind of odd for a high level library like
>>>> PETSc to not trust the communication channel but MPI implementations have
>>>> proven themselves to not be trustworthy and adding this to PetscSF is not
>>>> intrusive to the PETSc API or user. Plus it gives a definitive yes or no as
>>>> to the problem being from an error in the communication.
>>>>
>>>> Barry
>>>>
>>>> On Sep 24, 2020, at 12:35 PM, Matthew Knepley <knepley at gmail.com>
>>>> wrote:
>>>>
>>>> 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/>
>>>>
>>>>
>>>>
>>>
>>> --
>>> 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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