<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Oct 17, 2013 at 3:47 PM, Bishesh Khanal <span dir="ltr"><<a href="mailto:bisheshkh@gmail.com" target="_blank">bisheshkh@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote"><div class="im">On Thu, Oct 17, 2013 at 3:00 PM, Jed Brown <span dir="ltr"><<a href="mailto:jedbrown@mcs.anl.gov" target="_blank">jedbrown@mcs.anl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>Bishesh Khanal <<a href="mailto:bisheshkh@gmail.com" target="_blank">bisheshkh@gmail.com</a>> writes:<br>
> The program crashes only for a bigger domain size. Even in the cluster, it<br>
> does not crash for the domain size up to a certain size. So I need to run<br>
> in the debugger for the case when it crashes to get the stack trace from<br>
> the SEGV, right ? I do not know how to attach a debugger when submitting a<br>
> job to the cluster if that is possible at all!<br>
<br>
</div>Most machines allow you to get "interactive" sessions. You can usually<br>
run debuggers within those. Some facilities also have commercial<br>
debuggers.<br></blockquote></div><div><br>Thanks, I'll have a look at that.<br> <br></div><div class="im"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div><br>
> Or are you asking me to run the program in the debugger in my laptop<br>
> for the biggest size ? (I have not tried running the code for the<br>
> biggest size in my laptop fearing it might take forever)<br>
<br>
</div>Your laptop probably doesn't have enough memory for that.<br></blockquote><div><br></div></div><div>Yes, I tried it just a while ago and this is happened I think. (Just to confirm, I have put the error message for this case at the very end of this reply.*)<br>
</div><div class="im"><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
Can you try running on the cluster with one MPI rank per node? We<br>
should rule out simple out-of-memory problems, confirm that the code<br>
executes correctly with MPICH, and finally figure out why it fails with<br>
Open MPI (assuming that the previous hunch was correct).<br>
<br>
</blockquote></div></div><br></div></div></blockquote><div>I tried running on the cluster with one core per node with 4 nodes and I got the following errors (note: using valgrind, and openmpi of the cluster) at the very end after the many usual "unconditional jump ... errors" which might be interesting<br>
<br>mpiexec: killing job...<br><br>mpiexec: abort is already in progress...hit ctrl-c again to forcibly terminate<br><br>--------------------------------------------------------------------------<br>MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD <br>
with errorcode 59.<br><br>NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>You may or may not see output from other processes, depending on<br>exactly when Open MPI kills them.<br>--------------------------------------------------------------------------<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>[0]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end<br>[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<br>
[0]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC</a> ERROR: or try <a href="http://valgrind.org">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors<br>
[0]PETSC ERROR: likely location of problem given in stack below<br>[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------<br>[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,<br>
[0]PETSC ERROR: INSTEAD the line number of the start of the function<br>[0]PETSC ERROR: is given.<br>[0]PETSC ERROR: [0] MatSetValues_MPIAIJ line 505 /tmp/petsc-3.4.3/src/mat/impls/aij/mpi/mpiaij.c<br>[0]PETSC ERROR: [0] MatSetValues line 1071 /tmp/petsc-3.4.3/src/mat/interface/matrix.c<br>
[0]PETSC ERROR: [0] MatSetValuesLocal line 1935 /tmp/petsc-3.4.3/src/mat/interface/matrix.c<br>[0]PETSC ERROR: [0] DMCreateMatrix_DA_3d_MPIAIJ line 1051 /tmp/petsc-3.4.3/src/dm/impls/da/fdda.c<br>[0]PETSC ERROR: [0] DMCreateMatrix_DA line 627 /tmp/petsc-3.4.3/src/dm/impls/da/fdda.c<br>
[0]PETSC ERROR: [0] DMCreateMatrix line 900 /tmp/petsc-3.4.3/src/dm/interface/dm.c<br>[0]PETSC ERROR: [0] KSPSetUp line 192 /tmp/petsc-3.4.3/src/ksp/ksp/interface/itfunc.c<br>[0]PETSC ERROR: [0] solveModel line 122 "unknowndirectory/"/epi/asclepios2/bkhanal/works/AdLemModel/src/PetscAdLemTaras3D.cxx<br>
[0]PETSC ERROR: --------------------- Error Message ------------------------------------<br>[0]PETSC ERROR: Signal received!<br>[0]PETSC ERROR: ------------------------------------------------------------------------<br>[0]PETSC ERROR: Petsc Release Version 3.4.3, Oct, 15, 2013 <br>
[0]PETSC ERROR: See docs/changes/index.html for recent updates.<br>[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.<br>[0]PETSC ERROR: See docs/index.html for manual pages.<br>[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[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<br>[0]PETSC ERROR: Libraries linked from /epi/asclepios2/bkhanal/petscDebug/lib<br>
[0]PETSC ERROR: Configure run at Wed Oct 16 14:18:48 2013<br>[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<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file<br>==47363== <br>==47363== HEAP SUMMARY:<br>==47363== in use at exit: 10,939,838,029 bytes in 8,091 blocks<br>
==47363== total heap usage: 1,936,963 allocs, 1,928,872 frees, 11,530,164,042 bytes allocated<br>==47363== <br><br></div><div>Does it mean it is crashing near MatSetValues_MPIAIJ ?<br></div><div> <br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr"><div class="gmail_extra"></div><div class="gmail_extra">I'm sorry but I'm a complete beginner with MPI and clusters; so what does one MPI rank per node means and what should I do to do that ? My guess is that I set one core per node and use multiple nodes in my job script file ? Or do I need to do something in the petsc code ? <br>
<br></div><div class="gmail_extra">*Here is the error I get when running for the full domain size in my laptop:<br>[3]PETSC ERROR: --------------------- Error Message ------------------------------------<br>[3]PETSC ERROR: Out of memory. This could be due to allocating<br>
[3]PETSC ERROR: too large an object or bleeding by not properly<br>[3]PETSC ERROR: destroying unneeded objects.<br>[1]PETSC ERROR: Memory allocated 0 Memory used by process 1700159488<br>[1]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.<br>
[1]PETSC ERROR: Memory requested 6234924800!<br>[1]PETSC ERROR: ------------------------------------------------------------------------<br>[1]PETSC ERROR: Petsc Release Version 3.4.3, Oct, 15, 2013 <br>[1]PETSC ERROR: See docs/changes/index.html for recent updates.<br>
[1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.<br>[1]PETSC ERROR: See docs/index.html for manual pages.<br>[1]PETSC ERROR: ------------------------------------------------------------------------<br>
[1]PETSC ERROR: [2]PETSC ERROR: Memory allocated 0 Memory used by process 1695793152<br>
[2]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.<br>[2]PETSC ERROR: Memory requested 6223582208!<br>[2]PETSC ERROR: ------------------------------------------------------------------------<br>[2]PETSC ERROR: Petsc Release Version 3.4.3, Oct, 15, 2013 <br>
[2]PETSC ERROR: See docs/changes/index.html for recent updates.<br>[2]PETSC ERROR: See docs/faq.html for hints about trouble shooting.<br>[2]PETSC ERROR: See docs/index.html for manual pages.<br>[2]PETSC ERROR: ------------------------------------------------------------------------<br>
[2]PETSC ERROR: src/AdLemMain on a arch-linux2-cxx-debug named edwards by bkhanal Thu Oct 17 15:19:22 2013<br>[1]PETSC ERROR: Libraries linked from /home/bkhanal/Documents/softwares/petsc-3.4.3/arch-linux2-cxx-debug/lib<br>
[1]PETSC ERROR: Configure run at Wed Oct 16 15:13:05 2013<br>[1]PETSC ERROR: Configure options --download-mpich -download-f-blas-lapack=1 --download-metis --download-parmetis --download-superlu_dist --download-scalapack --download-mumps --download-hypre --with-clanguage=cxx<br>
[1]PETSC ERROR: ------------------------------------------------------------------------<br>[1]PETSC ERROR: PetscMallocAlign() line 46 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/sys/memory/mal.c<br>src/AdLemMain on a arch-linux2-cxx-debug named edwards by bkhanal Thu Oct 17 15:19:22 2013<br>
[2]PETSC ERROR: Libraries linked from /home/bkhanal/Documents/softwares/petsc-3.4.3/arch-linux2-cxx-debug/lib<br>[2]PETSC ERROR: Configure run at Wed Oct 16 15:13:05 2013<br>[2]PETSC ERROR: Configure options --download-mpich -download-f-blas-lapack=1 --download-metis --download-parmetis --download-superlu_dist --download-scalapack --download-mumps --download-hypre --with-clanguage=cxx<br>
[2]PETSC ERROR: ------------------------------------------------------------------------<br>[2]PETSC ERROR: PetscMallocAlign() line 46 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/sys/memory/mal.c<br>[1]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 3551 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/seq/aij.c<br>
[1]PETSC ERROR: MatSeqAIJSetPreallocation() line 3496 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/seq/aij.c<br>[2]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 3551 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/seq/aij.c<br>
[2]PETSC ERROR: MatSeqAIJSetPreallocation() line 3496 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/seq/aij.c<br>[1]PETSC ERROR: MatMPIAIJSetPreallocation_MPIAIJ() line 3307 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/mpi/mpiaij.c<br>
[1]PETSC ERROR: MatMPIAIJSetPreallocation() line 4015 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/mpi/mpiaij.c<br>[2]PETSC ERROR: MatMPIAIJSetPreallocation_MPIAIJ() line 3307 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/mpi/mpiaij.c<br>
[2]PETSC ERROR: MatMPIAIJSetPreallocation() line 4015 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/mpi/mpiaij.c<br>[0]PETSC ERROR: --------------------- Error Message ------------------------------------<br>
[0]PETSC ERROR: Out of memory. This could be due to allocating<br>[0]PETSC ERROR: too large an object or bleeding by not properly<br>[0]PETSC ERROR: destroying unneeded objects.<br>[2]PETSC ERROR: [1]PETSC ERROR: DMCreateMatrix_DA_3d_MPIAIJ() line 1101 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/dm/impls/da/fdda.c<br>
[1]PETSC ERROR: DMCreateMatrix_DA_3d_MPIAIJ() line 1101 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/dm/impls/da/fdda.c<br>[2]PETSC ERROR: DMCreateMatrix_DA() line 771 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/dm/impls/da/fdda.c<br>
DMCreateMatrix_DA() line 771 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/dm/impls/da/fdda.c<br>[3]PETSC ERROR: Memory allocated 0 Memory used by process 1675407360<br>[3]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.<br>
[3]PETSC ERROR: Memory requested 6166659200!<br>[3]PETSC ERROR: ------------------------------------------------------------------------<br>[3]PETSC ERROR: Petsc Release Version 3.4.3, Oct, 15, 2013 <br>[3]PETSC ERROR: See docs/changes/index.html for recent updates.<br>
[3]PETSC ERROR: See docs/faq.html for hints about trouble shooting.<br>[3]PETSC ERROR: See docs/index.html for manual pages.<br>[3]PETSC ERROR: ------------------------------------------------------------------------<br>
[3]PETSC ERROR: src/AdLemMain on a arch-linux2-cxx-debug named edwards by bkhanal Thu Oct 17 15:19:22 2013<br>
[3]PETSC ERROR: Libraries linked from /home/bkhanal/Documents/softwares/petsc-3.4.3/arch-linux2-cxx-debug/lib<br>[3]PETSC ERROR: Configure run at Wed Oct 16 15:13:05 2013<br>[3]PETSC ERROR: Configure options --download-mpich -download-f-blas-lapack=1 --download-metis --download-parmetis --download-superlu_dist --download-scalapack --download-mumps --download-hypre --with-clanguage=cxx<br>
[3]PETSC ERROR: ------------------------------------------------------------------------<br>[3]PETSC ERROR: [1]PETSC ERROR: DMCreateMatrix() line 910 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/dm/interface/dm.c<br>
[2]PETSC ERROR: DMCreateMatrix() line 910 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/dm/interface/dm.c<br>PetscMallocAlign() line 46 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/sys/memory/mal.c<br>[3]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 3551 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/seq/aij.c<br>
[3]PETSC ERROR: MatSeqAIJSetPreallocation() line 3496 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/seq/aij.c<br>[1]PETSC ERROR: KSPSetUp() line 207 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/ksp/ksp/interface/itfunc.c<br>
[2]PETSC ERROR: KSPSetUp() line 207 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/ksp/ksp/interface/itfunc.c<br>[3]PETSC ERROR: MatMPIAIJSetPreallocation_MPIAIJ() line 3307 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/mpi/mpiaij.c<br>
[3]PETSC ERROR: MatMPIAIJSetPreallocation() line 4015 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/mpi/mpiaij.c<br>[3]PETSC ERROR: DMCreateMatrix_DA_3d_MPIAIJ() line 1101 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/dm/impls/da/fdda.c<br>
[3]PETSC ERROR: DMCreateMatrix_DA() line 771 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/dm/impls/da/fdda.c<br>[3]PETSC ERROR: DMCreateMatrix() line 910 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/dm/interface/dm.c<br>
[3]PETSC ERROR: KSPSetUp() line 207 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/ksp/ksp/interface/itfunc.c<br>[1]PETSC ERROR: solveModel() line 128 in "unknowndirectory/"/user/bkhanal/home/works/AdLemModel/src/PetscAdLemTaras3D.cxx<br>
[2]PETSC ERROR: solveModel() line 128 in "unknowndirectory/"/user/bkhanal/home/works/AdLemModel/src/PetscAdLemTaras3D.cxx<br>[3]PETSC ERROR: solveModel() line 128 in "unknowndirectory/"/user/bkhanal/home/works/AdLemModel/src/PetscAdLemTaras3D.cxx<br>
[0]PETSC ERROR: Memory allocated 0 Memory used by process 1711476736<br>[0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.<br>[0]PETSC ERROR: Memory requested 6292477952!<br>[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: Petsc Release Version 3.4.3, Oct, 15, 2013 <br>[0]PETSC ERROR: See docs/changes/index.html for recent updates.<br>[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.<br>[0]PETSC ERROR: See docs/index.html for manual pages.<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>[0]PETSC ERROR: src/AdLemMain on a arch-linux2-cxx-debug named edwards by bkhanal Thu Oct 17 15:19:22 2013<br>[0]PETSC ERROR: Libraries linked from /home/bkhanal/Documents/softwares/petsc-3.4.3/arch-linux2-cxx-debug/lib<br>
[0]PETSC ERROR: Configure run at Wed Oct 16 15:13:05 2013<br>[0]PETSC ERROR: Configure options --download-mpich -download-f-blas-lapack=1 --download-metis --download-parmetis --download-superlu_dist --download-scalapack --download-mumps --download-hypre --with-clanguage=cxx<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>[0]PETSC ERROR: PetscMallocAlign() line 46 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/sys/memory/mal.c<br>[0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 3551 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/seq/aij.c<br>
[0]PETSC ERROR: MatSeqAIJSetPreallocation() line 3496 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/seq/aij.c<br>[0]PETSC ERROR: MatMPIAIJSetPreallocation_MPIAIJ() line 3307 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/mpi/mpiaij.c<br>
[0]PETSC ERROR: MatMPIAIJSetPreallocation() line 4015 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/mat/impls/aij/mpi/mpiaij.c<br>[0]PETSC ERROR: DMCreateMatrix_DA_3d_MPIAIJ() line 1101 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/dm/impls/da/fdda.c<br>
[0]PETSC ERROR: DMCreateMatrix_DA() line 771 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/dm/impls/da/fdda.c<br>[0]PETSC ERROR: DMCreateMatrix() line 910 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/dm/interface/dm.c<br>
[0]PETSC ERROR: KSPSetUp() line 207 in /home/bkhanal/Documents/softwares/petsc-3.4.3/src/ksp/ksp/interface/itfunc.c<br>[0]PETSC ERROR: solveModel() line 128 in "unknowndirectory/"/user/bkhanal/home/works/AdLemModel/src/PetscAdLemTaras3D.cxx<br>
--9345:0:aspacem Valgrind: FATAL: VG_N_SEGMENTS is too low.<br>--9345:0:aspacem Increase it and rebuild. Exiting now.<br>--9344:0:aspacem Valgrind: FATAL: VG_N_SEGMENTS is too low.<br>--9344:0:aspacem Increase it and rebuild. Exiting now.<br>
--9343:0:aspacem Valgrind: FATAL: VG_N_SEGMENTS is too low.<br>--9343:0:aspacem Increase it and rebuild. Exiting now.<br>--9346:0:aspacem Valgrind: FATAL: VG_N_SEGMENTS is too low.<br>--9346:0:aspacem Increase it and rebuild. Exiting now.<br>
<br>===================================================================================<br>= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES<br>= EXIT CODE: 1<br>= CLEANING UP REMAINING PROCESSES<br>= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES<br>
===================================================================================<br><br><br></div></div>
</blockquote></div><br></div></div>