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 <ch...@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.zh...@gmail.com> > wrote: > >> On Mon, Jul 20, 2020 at 7:05 AM Barry Smith <bsm...@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...@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...@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 <ch...@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 >>>>> >>>> >>>
