On Thu, Oct 17, 2013 at 5:30 PM, Barry Smith <[email protected]> wrote:
> > On Oct 17, 2013, at 9:26 AM, Bishesh Khanal <[email protected]> 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]PETSCERROR: 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. > Thanks!! Yes it seems that it was because of the running out of the memory. I realized that in the job script I submitted to the cluster I had limited the memory to a certain value. I deleted that line and resubmitted the job, now I the job gets killed because of the wall time (of 3 hours) being exceeded unlike the previous case where the mpiexec killed the job quite quickly. Now I will run the job again by increasing the wall time and see if it gives results or not and get back here. Thanks again! > > Barry > > > > >
