[petsc-users] Segmentation Violation for SNES ex12

Sun Jan 11 22:05:05 CST 2015

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:

[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
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