[petsc-users] signal received error; MatNullSpaceTest; Stokes flow solver with pc fieldsplit and schur complement

Barry Smith bsmith at mcs.anl.gov
Thu Oct 17 10:30:18 CDT 2013

On Oct 17, 2013, at 9:26 AM, Bishesh Khanal <bisheshkh at gmail.com> wrote:
> --------------------------------------------------------------------------
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 15 Terminate: Somet 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[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
> [0]PETSC ERROR: likely location of problem given in stack below
> [0]PETSC ERROR: ---------------------  Stack Frames ------------------------------------
> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> [0]PETSC ERROR:       INSTEAD the line number of the start of the function
> [0]PETSC ERROR:       is given.
> [0]PETSC ERROR: [0] MatSetValues_MPIAIJ line 505 /tmp/petsc-3.4.3/src/mat/impls/aij/mpi/mpiaij.c
> [0]PETSC ERROR: [0] MatSetValues line 1071 /tmp/petsc-3.4.3/src/mat/interface/matrix.c
> [0]PETSC ERROR: [0] MatSetValuesLocal line 1935 /tmp/petsc-3.4.3/src/mat/interface/matrix.c
> [0]PETSC ERROR: [0] DMCreateMatrix_DA_3d_MPIAIJ line 1051 /tmp/petsc-3.4.3/src/dm/impls/da/fdda.c
> [0]PETSC ERROR: [0] DMCreateMatrix_DA line 627 /tmp/petsc-3.4.3/src/dm/impls/da/fdda.c
> [0]PETSC ERROR: [0] DMCreateMatrix line 900 /tmp/petsc-3.4.3/src/dm/interface/dm.c
> [0]PETSC ERROR: [0] KSPSetUp line 192 /tmp/petsc-3.4.3/src/ksp/ksp/interface/itfunc.c
> [0]PETSC ERROR: [0] solveModel line 122 "unknowndirectory/"/epi/asclepios2/bkhanal/works/AdLemModel/src/PetscAdLemTaras3D.cxx
> [0]PETSC ERROR: --------------------- Error Message ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 3.4.3, Oct, 15, 2013 
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: /epi/asclepios2/bkhanal/works/AdLemModel/build/src/AdLemMain on a arch-linux2-cxx-debug named nef002 by bkhanal Thu Oct 17 15:55:33 2013
> [0]PETSC ERROR: Libraries linked from /epi/asclepios2/bkhanal/petscDebug/lib
> [0]PETSC ERROR: Configure run at Wed Oct 16 14:18:48 2013
> [0]PETSC ERROR: Configure options --with-mpi-dir=/opt/openmpi-gcc/current/ --with-shared-libraries --prefix=/epi/asclepios2/bkhanal/petscDebug -download-f-blas-lapack=1 --download-metis --download-parmetis --download-superlu_dist --download-scalapack --download-mumps --download-hypre --with-clanguage=cxx
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
> ==47363== 
> ==47363== HEAP SUMMARY:
> ==47363==     in use at exit: 10,939,838,029 bytes in 8,091 blocks
> ==47363==   total heap usage: 1,936,963 allocs, 1,928,872 frees, 11,530,164,042 bytes allocated
> ==47363== 
> Does it mean it is crashing near MatSetValues_MPIAIJ ?

> It is not really "crashing" here. The most likely cause is that the OS has run out of memory to provide so it has started shutting down processes; this is the "unfriendly" way that Unix handles "running out of memory".  A much less likely possibility (since the program has just started) is that the process has run out of allocated time and the OS is shutting it down.   

   I am confident in this case it is simply a mater of the system running out of memory.  What happens if you run the exact same job without the valgrind? Please send the ENTIRE error message.


More information about the petsc-users mailing list