[petsc-users] MPI Iterative solver crash on HPC

Mon Jan 14 10:36:31 CST 2019

This time, it crashes at
[6]PETSC ERROR: #1 MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ() line 1989 in /lustre/home/vef002/petsc/src/mat/impls/aij/mpi/mpimatmatmult.c
ierr      = PetscMalloc1(bi[pn]+1,&bj);
which allocates local portion of B^T*A.
You may also try to increase number of cores to reduce local matrix size.
Hong

On Mon, Jan 14, 2019 at 7:42 AM Mark Adams <mfadams at lbl.gov<mailto:mfadams at lbl.gov>> wrote:
The memory requested is an insane number. You may need to use 64 bit integers.

On Mon, Jan 14, 2019 at 8:06 AM Sal Am via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
I ran it by: mpiexec -n 8 valgrind --tool=memcheck -q --num-callers=20 --log-file=valgrind.log-osa.%p ./solveCSys -malloc off -ksp_type bcgs -pc_type gamg -mattransposematmult_via scalable -ksp_monitor -log_view
The error:

[6]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[6]PETSC ERROR: Out of memory. This could be due to allocating
[6]PETSC ERROR: too large an object or bleeding by not properly
[6]PETSC ERROR: destroying unneeded objects.
[6]PETSC ERROR: Memory allocated 0 Memory used by process 39398023168
[6]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
[6]PETSC ERROR: Memory requested 18446744066024411136
[6]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[6]PETSC ERROR: Petsc Release Version 3.10.2, unknown
[6]PETSC ERROR: ./solveCSys on a linux-cumulus-debug named r02g03 by vef002 Mon Jan 14 08:54:45 2019
[6]PETSC ERROR: Configure options PETSC_ARCH=linux-cumulus-debug --with-cc=/usr/local/depot/openmpi-3.1.1-gcc-7.3.0/bin/mpicc --with-fc=/usr/local/depot/openmpi-3.1.1-gcc-7.3.0/bin/mpifort --with-cxx=/usr/local/depot/openmpi-3.1.1-gcc-7.3.0/bin/mpicxx --download-parmetis --download-metis --download-ptscotch --download-superlu_dist --download-mumps --with-scalar-type=complex --with-debugging=yes --download-scalapack --download-superlu --download-fblaslapack=1 --download-cmake
[6]PETSC ERROR: #1 MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ() line 1989 in /lustre/home/vef002/petsc/src/mat/impls/aij/mpi/mpimatmatmult.c
[6]PETSC ERROR: #2 PetscMallocA() line 397 in /lustre/home/vef002/petsc/src/sys/memory/mal.c
[6]PETSC ERROR: #3 MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ() line 1989 in /lustre/home/vef002/petsc/src/mat/impls/aij/mpi/mpimatmatmult.c
[6]PETSC ERROR: #4 MatTransposeMatMult_MPIAIJ_MPIAIJ() line 1203 in /lustre/home/vef002/petsc/src/mat/impls/aij/mpi/mpimatmatmult.c
[6]PETSC ERROR: #5 MatTransposeMatMult() line 9984 in /lustre/home/vef002/petsc/src/mat/interface/matrix.c
[6]PETSC ERROR: #6 PCGAMGCoarsen_AGG() line 882 in /lustre/home/vef002/petsc/src/ksp/pc/impls/gamg/agg.c
[6]PETSC ERROR: #7 PCSetUp_GAMG() line 522 in /lustre/home/vef002/petsc/src/ksp/pc/impls/gamg/gamg.c
[6]PETSC ERROR: #8 PCSetUp() line 932 in /lustre/home/vef002/petsc/src/ksp/pc/interface/precon.c
[6]PETSC ERROR: #9 KSPSetUp() line 391 in /lustre/home/vef002/petsc/src/ksp/ksp/interface/itfunc.c
[6]PETSC ERROR: #10 main() line 68 in /home/vef002/debugenv/tests/solveCmplxLinearSys.cpp
[6]PETSC ERROR: PETSc Option Table entries:
[6]PETSC ERROR: -ksp_monitor
[6]PETSC ERROR: -ksp_type bcgs
[6]PETSC ERROR: -log_view
[6]PETSC ERROR: -malloc off
[6]PETSC ERROR: -mattransposematmult_via scalable
[6]PETSC ERROR: -pc_type gamg
[6]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 6 in communicator MPI_COMM_WORLD
with errorcode 55.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

Memory requested error seems astronomical though.... This was done on a machine with 500GB of memory, during my last check it was using 30GB mem/processor not sure if it increased suddenly. The file size of the matrix is 40GB still same matrix
2 122 821 366 (non-zero elements)
25 947 279 x 25 947 279

On Fri, Jan 11, 2019 at 5:34 PM Zhang, Hong <hzhang at mcs.anl.gov<mailto:hzhang at mcs.anl.gov>> wrote:
Add option '-mattransposematmult_via scalable'
Hong

On Fri, Jan 11, 2019 at 9:52 AM Zhang, Junchao via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
I saw the following error message in your first email.
[0]PETSC ERROR: Out of memory. This could be due to allocating
[0]PETSC ERROR: too large an object or bleeding by not properly
[0]PETSC ERROR: destroying unneeded objects.
Probably the matrix is too large. You can try with more compute nodes, for example, use 8 nodes instead of 2, and see what happens.

--Junchao Zhang

On Fri, Jan 11, 2019 at 7:45 AM Sal Am via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
Using a larger problem set with 2B non-zero elements and a matrix of 25M x 25M I get the following error:
[4]PETSC ERROR: ------------------------------------------------------------------------
[4]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[4]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[4]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[4]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[4]PETSC ERROR: likely location of problem given in stack below
[4]PETSC ERROR: ---------------------  Stack Frames ------------------------------------
[4]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[4]PETSC ERROR:       INSTEAD the line number of the start of the function
[4]PETSC ERROR:       is given.
[4]PETSC ERROR: [4] MatCreateSeqAIJWithArrays line 4422 /lustre/home/vef002/petsc/src/mat/impls/aij/seq/aij.c
[4]PETSC ERROR: [4] MatMatMultSymbolic_SeqAIJ_SeqAIJ line 747 /lustre/home/vef002/petsc/src/mat/impls/aij/seq/matmatmult.c
[4]PETSC ERROR: [4] MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable line 1256 /lustre/home/vef002/petsc/src/mat/impls/aij/mpi/mpimatmatmult.c
[4]PETSC ERROR: [4] MatTransposeMatMult_MPIAIJ_MPIAIJ line 1156 /lustre/home/vef002/petsc/src/mat/impls/aij/mpi/mpimatmatmult.c
[4]PETSC ERROR: [4] MatTransposeMatMult line 9950 /lustre/home/vef002/petsc/src/mat/interface/matrix.c
[4]PETSC ERROR: [4] PCGAMGCoarsen_AGG line 871 /lustre/home/vef002/petsc/src/ksp/pc/impls/gamg/agg.c
[4]PETSC ERROR: [4] PCSetUp_GAMG line 428 /lustre/home/vef002/petsc/src/ksp/pc/impls/gamg/gamg.c
[4]PETSC ERROR: [4] PCSetUp line 894 /lustre/home/vef002/petsc/src/ksp/pc/interface/precon.c
[4]PETSC ERROR: [4] KSPSetUp line 304 /lustre/home/vef002/petsc/src/ksp/ksp/interface/itfunc.c
[4]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[4]PETSC ERROR: Signal received
[4]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[4]PETSC ERROR: Petsc Release Version 3.10.2, unknown
[4]PETSC ERROR: ./solveCSys on a linux-cumulus-debug named r02g03 by vef002 Fri Jan 11 09:13:23 2019
[4]PETSC ERROR: Configure options PETSC_ARCH=linux-cumulus-debug --with-cc=/usr/local/depot/openmpi-3.1.1-gcc-7.3.0/bin/mpicc --with-fc=/usr/local/depot/openmpi-3.1.1-gcc-7.3.0/bin/mpifort --with-cxx=/usr/local/depot/openmpi-3.1.1-gcc-7.3.0/bin/mpicxx --download-parmetis --download-metis --download-ptscotch --download-superlu_dist --download-mumps --with-scalar-type=complex --with-debugging=yes --download-scalapack --download-superlu --download-fblaslapack=1 --download-cmake
[4]PETSC ERROR: #1 User provided function() line 0 in  unknown file
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 4 in communicator MPI_COMM_WORLD
with errorcode 59.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind

Using Valgrind on only one of the valgrind files the following error was written:

==9053== Invalid read of size 4
==9053==    at 0x5B8067E: MatCreateSeqAIJWithArrays (aij.c:4445)
==9053==    by 0x5BC2608: MatMatMultSymbolic_SeqAIJ_SeqAIJ (matmatmult.c:790)
==9053==    by 0x5D106F8: MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable (mpimatmatmult.c:1337)
==9053==    by 0x5D0E84E: MatTransposeMatMult_MPIAIJ_MPIAIJ (mpimatmatmult.c:1186)
==9053==    by 0x5457C57: MatTransposeMatMult (matrix.c:9984)
==9053==    by 0x64DD99D: PCGAMGCoarsen_AGG (agg.c:882)
==9053==    by 0x64C7527: PCSetUp_GAMG (gamg.c:522)
==9053==    by 0x6592AA0: PCSetUp (precon.c:932)
==9053==    by 0x66B1267: KSPSetUp (itfunc.c:391)
==9053==    by 0x4019A2: main (solveCmplxLinearSys.cpp:68)
==9053==  Address 0x8386997f4 is not stack'd, malloc'd or (recently) free'd
==9053==

On Fri, Jan 11, 2019 at 8:41 AM Sal Am <tempohoper at gmail.com<mailto:tempohoper at gmail.com>> wrote:
Thank you Dave,

I reconfigured PETSc with valgrind and debugging mode, I ran the code again with the following options:
mpiexec -n 8 valgrind --tool=memcheck -q --num-callers=20 --log-file=valgrind.log.%p ./solveCSys -malloc off -ksp_type bcgs -pc_type gamg -log_view
(as on the petsc website you linked)

It finished solving using the iterative solver, but the resulting valgrind.log.%p files (all 8 corresponding to each processor) are all empty. And it took a whooping ~15hours, for what used to take ~10-20min. Maybe this is because of valgrind? I am not sure. Attached is the log_view.

On Thu, Jan 10, 2019 at 8:59 AM Dave May <dave.mayhem23 at gmail.com<mailto:dave.mayhem23 at gmail.com>> wrote:

On Thu, 10 Jan 2019 at 08:55, Sal Am via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
I am not sure what is exactly is wrong as the error changes slightly every time I run it (without changing the parameters).

This likely implies that you have a memory error in your code (a memory leak would not cause this behaviour).
I strongly suggest you make sure your code is free of memory errors.
You can do this using valgrind. See here

https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind

for an explanation of how to use valgrind.

I have attached the first two run's errors and my code.

Is there a memory leak somewhere? I have tried running it with -malloc_dump, but not getting anything printed out, however, when run with -log_view I see that Viewer is created 4 times, but destroyed 3 times. The way I see it, I have destroyed it where I see I no longer have use for it so not sure if I am wrong. Could this be the reason why it keeps crashing? It crashes as soon as it reads the matrix, before entering the solving mode (I have a print statement before solving starts that never prints).

how I run it in the job script on 2 node with 32 processors using the clusters OpenMPI.

mpiexec ./solveCSys -ksp_type bcgs -pc_type gamg -ksp_converged_reason -ksp_monitor_true_residual -log_view -ksp_error_if_not_converged -ksp_monitor -malloc_log -ksp_view

the matrix:
2 122 821 366 (non-zero elements)
25 947 279 x 25 947 279

Thanks and all the best
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20190114/2a5b5d82/attachment-0001.html>