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 <mfad...@lbl.gov<mailto:mfad...@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@mcs.anl.gov<mailto:petsc-users@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-ma...@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 <hzh...@mcs.anl.gov<mailto:hzh...@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@mcs.anl.gov<mailto:petsc-users@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@mcs.anl.gov<mailto:petsc-users@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 <tempoho...@gmail.com<mailto:tempoho...@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.mayhe...@gmail.com<mailto:dave.mayhe...@gmail.com>> wrote: On Thu, 10 Jan 2019 at 08:55, Sal Am via petsc-users <petsc-users@mcs.anl.gov<mailto:petsc-users@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