[petsc-users] Segmentation Violation for SNES ex12

Tue Jan 13 12:25:12 CST 2015

On Sun, Jan 11, 2015 at 10:05 PM, Justin Chang <jychang48 at gmail.com> wrote:

> Hi all,
>
> Our research group recently got access to a relatively new HPC cluster
> (with SLURM scheduler) and I am trying to run some test examples with it on
> multiple processors. When I run SNES ex12 serially it works. However when i
> run it on two processes, I get the following error:
>

Yes, this was a bug in the big refactoring push that just went in. We did
not catch it somehow in the tests. I have
pushed a fix, and now it works for me. It is in next.

  Thanks,

    Matt

> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [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] DMLabelMakeInvalid_Private line 81
> /home/jchang23/petsc/src/dm/impls/plex/plexlabel.c
> [0]PETSC ERROR: [0] DMLabelSetValue line 466
> /home/jchang23/petsc/src/dm/impls/plex/plexlabel.c
> [0]PETSC ERROR: [0] DMPlexLabelComplete line 72
> /home/jchang23/petsc/src/dm/impls/plex/plexsubmesh.c
> [0]PETSC ERROR: [0] DMCreateDefaultSection_Plex line 5368
> /home/jchang23/petsc/src/dm/impls/plex/plex.c
> [0]PETSC ERROR: [0] DMGetDefaultSection line 2974
> /home/jchang23/petsc/src/dm/interface/dm.c
> [0]PETSC ERROR: [0] DMGetDefaultGlobalSection line 3129
> /home/jchang23/petsc/src/dm/interface/dm.c
> [0]PETSC ERROR: [0] DMCreateGlobalVector_Section_Private line 12
> /home/jchang23/petsc/src/dm/interface/dmi.c
> [0]PETSC ERROR: [0] DMCreateGlobalVector_Plex line 1152
> /home/jchang23/petsc/src/dm/impls/plex/plexcreate.c
> [0]PETSC ERROR: [0] DMCreateGlobalVector line 683
> /home/jchang23/petsc/src/dm/interface/dm.c
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Signal received
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.5.2-1351-g37b8796  GIT
> Date: 2015-01-11 11:57:24 -0600
> [0]PETSC ERROR: ./petsc/src/snes/examples/tutorials/ex12 on a
> arch-linux2-c-opt named compute-0-0.local by jchang23 Sun Jan 11 21:55:42
> 2015
> [0]PETSC ERROR: Configure options --download-fblaslapack --download-hdf5
> --download-metis --download-parmetis --with-c=gcc --with-cmake=cmake
> --with-debugging=1 --with-fc-gfortran
> --with-mpi-dir=/share/apps/openmpi-1.8.3/
> CPPFLAGS=-I/share/apps/openmpi-1.8.3/include
> LDFLAGS=-L/share/apps/openmpi-1.8.3/lib PETSC_ARCH=arch-linux2-c-opt
> download-chaco --download-triangle
> [0]PETSC ERROR: #1 User provided function() line 0 in  unknown file
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [1]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> [1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
> [1]PETSC ERROR: likely location of problem given in stack below
> [1]PETSC ERROR: ---------------------  Stack Frames
> ------------------------------------
> [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> [1]PETSC ERROR:       INSTEAD the line number of the start of the function
> [1]PETSC ERROR:       is given.
> [1]PETSC ERROR: [1] DMLabelMakeInvalid_Private line 81
> /home/jchang23/petsc/src/dm/impls/plex/plexlabel.c
> [1]PETSC ERROR: [1] DMLabelSetValue line 466
> /home/jchang23/petsc/src/dm/impls/plex/plexlabel.c
> [1]PETSC ERROR: [1] DMPlexLabelComplete line 72
> /home/jchang23/petsc/src/dm/impls/plex/plexsubmesh.c
> [1]PETSC ERROR: [1] DMCreateDefaultSection_Plex line 5368
> /home/jchang23/petsc/src/dm/impls/plex/plex.c
> [1]PETSC ERROR: [1] DMGetDefaultSection line 2974
> /home/jchang23/petsc/src/dm/interface/dm.c
> [1]PETSC ERROR: [1] DMGetDefaultGlobalSection line 3129
> /home/jchang23/petsc/src/dm/interface/dm.c
> [1]PETSC ERROR: [1] DMCreateGlobalVector_Section_Private line 12
> /home/jchang23/petsc/src/dm/interface/dmi.c
> [1]PETSC ERROR: [1] DMCreateGlobalVector_Plex line 1152
> /home/jchang23/petsc/src/dm/impls/plex/plexcreate.c
> [1]PETSC ERROR: [1] DMCreateGlobalVector line 683
> /home/jchang23/petsc/src/dm/interface/dm.c
> [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [1]PETSC ERROR: Signal received
> [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [1]PETSC ERROR: Petsc Development GIT revision: v3.5.2-1351-g37b8796  GIT
> Date: 2015-01-11 11:57:24 -0600
> [1]PETSC ERROR: ./petsc/src/snes/examples/tutorials/ex12 on a
> arch-linux2-c-opt named compute-2-7.local by jchang23 Sun Jan 11 21:55:42
> 2015
> [1]PETSC ERROR: Configure options --download-fblaslapack --download-hdf5
> --download-metis --download-parmetis --with-c=gcc --with-cmake=cmake
> --with-debugging=1 --with-fc-gfortran
> --with-mpi-dir=/share/apps/openmpi-1.8.3/
> CPPFLAGS=-I/share/apps/openmpi-1.8.3/include
> LDFLAGS=-L/share/apps/openmpi-1.8.3/lib PETSC_ARCH=arch-linux2-c-opt
> download-chaco --download-triangle
> [1]PETSC ERROR: #1 User provided function() line 0 in  unknown file
> --------------------------------------------------------------------------
>
> I have no idea what this means. Here is the script file used to run the
> problem with:
>
> #!/bin/bash
> #SBATCH -J test
> #SBATCH -o test.txt
> #SBATCH -N 2
>
> mpirun -np 2 ./ex12 -run_type full -refinement_limit 0.00015625
> -interpolate 1 -petscspace_order 2 -pc_type gamg -ksp_rtol 1.0e-10
> -ksp_monitor_short -ksp_converged_reason -snes_monitor_short
> -snes_converged_reason -petscpartitioner_type parmetis
>
> ---
>
> Any help appreciated it, thanks
>
> Justin
>
>

-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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