[petsc-users] PETSC MPI error on PetscGatherMessageLengths2

[Sun, Hui]

I'm running some code written by myself, using PETSC with MPI. It runs fine with less than or equal to 12 cores. However, if I ran it with 16 cores, it gives me an error. By looking at the error message, it seems that the error happens at a line where I have something like this:


ierr = MatTransposeMatMult(C,B,MAT_INITIAL_MATRIX,1,&A);CHKERRQ(ierr);

And I have attached the error message here. Does anyone sort of having an idea of what might be causing the problem here? Or is there any hint of what might be a direction for looking into this bug?


[hus003 at tscc-login2 test]$ cat /home/hus003/output/errFluid3d | grep '\[4\]'

[4]PETSC ERROR: ------------------------------------------------------------------------

[4]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end

[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] PetscGatherMessageLengths2 line 180 /state/partition1/jjh/All-Rolls/math-roll/BUILD/sdsc-petsc_intel_openmpi_ib-3.5.2/petsc-3.5.2/src/sys/utils/mpimesg.c

[4]PETSC ERROR: [4] MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ line 1573 /state/partition1/jjh/All-Rolls/math-roll/BUILD/sdsc-petsc_intel_openmpi_ib-3.5.2/petsc-3.5.2/src/mat/impls/aij/mpi/mpimatmatmult.c

[4]PETSC ERROR: [4] MatTransposeMatMult_MPIAIJ_MPIAIJ line 812 /state/partition1/jjh/All-Rolls/math-roll/BUILD/sdsc-petsc_intel_openmpi_ib-3.5.2/petsc-3.5.2/src/mat/impls/aij/mpi/mpimatmatmult.c

[4]PETSC ERROR: [4] MatTransposeMatMult line 8945 /state/partition1/jjh/All-Rolls/math-roll/BUILD/sdsc-petsc_intel_openmpi_ib-3.5.2/petsc-3.5.2/src/mat/interface/matrix.c

[4]PETSC ERROR: [4] Schur_Prec line 2885 /home/hus003/DISM/LSM_DISM3D/test/../Stokes3D.h

[4]PETSC ERROR: [4] StokesSetup line 140 /home/hus003/DISM/LSM_DISM3D/test/../Stokes3D.h

[4]PETSC ERROR: [4] test line 102 /home/hus003/DISM/LSM_DISM3D/test/test.cpp

[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 3.5.2, Sep, 08, 2014

[4]PETSC ERROR: ./test on a intel-openmpi_ib named tscc-gpu-6-5.sdsc.edu by hus003 Mon Jul 13 23:57:09 2015

[4]PETSC ERROR: Configure options CFLAGS= FFLAGS= CXXFLAGS= --prefix=/opt/petsc/intel/openmpi_ib --with-mpi=1 --download-pastix=../pastix_5.2.2.12.tar.bz2 --download-ptscotch=../scotch_6.0.0_esmumps.tar.gz --with-blas-lib="-Wl,--start-group /opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_intel_lp64.a            /opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_sequential.a /opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_core.a            -Wl,--end-group -lpthread -lm" --with-lapack-lib="-Wl,--start-group /opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_intel_lp64.a            /opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_sequential.a /opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_core.a            -Wl,--end-group -lpthread -lm" --with-superlu_dist-include=/opt/superlu/intel/openmpi_ib/include --with-superlu_dist-lib="-L/opt/superlu/intel/openmpi_ib/lib -lsuperlu" --with-parmetis-dir=/opt/parmetis/intel/openmpi_ib --with-metis-dir=/opt/parmetis/intel/openmpi_ib --with-mpi-dir=/opt/openmpi/intel/ib --with-scalapack-dir=/opt/scalapack/intel/openmpi_ib --download-mumps=../MUMPS_4.10.0-p3.tar.gz --download-blacs=../blacs-dev.tar.gz --download-fblaslapack=../fblaslapack-3.4.2.tar.gz --with-pic=1 --with-shared-libraries=1

[4]PETSC ERROR: #1 User provided function() line 0 in  unknown file


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