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

[Barry Smith]

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.

   Barry