[petsc-users] Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

[Barry Smith]

  Segmentation Violation's are due to illegal memory access. They can be found with a debugger or with valgrind. There really is no other way. Debug on a workstation not on a cluster with a batch system.


   Barry

> On Nov 16, 2016, at 10:47 AM, Beheshti, Mohammadali <Mohammadali.Beheshti at uhn.ca> wrote:
> 
> Hi,
> 
> I am running a simulation using a software that solves a FEM problem. My job script is as follows:
> 
> #!/bin/bash
> #PBS -N myjob
> #PBS -l nodes=1:ppn=8
> #PBS -l walltime=120:00:00
> #PBS -l mem=32000MB
> module load openmpi/2.0.0
> cd /cluster/home/t48263uhn/Carp/PlosOneData/
> mpirun -np 8 carp.debug.petsc.pt +F /cluster/home/t48263uhn/Carp/PlosOneData/parameters_ECG_adjust.par
> 
> When I run this job I get following PETSC error:
> 
> [5]PETSC ERROR: ------------------------------------------------------------------------
> [5]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
> [5]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [5]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> [5]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
> [5]PETSC ERROR: likely location of problem given in stack below
> [5]PETSC ERROR: ---------------------  Stack Frames ------------------------------------
> [5]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> [5]PETSC ERROR:       INSTEAD the line number of the start of the function
> [5]PETSC ERROR:       is given.
> [5]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [5]PETSC ERROR: Signal received
> [5]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> [5]PETSC ERROR: Petsc Release Version 3.7.3, Jul, 24, 2016
> [5]PETSC ERROR: carp.debug.petsc.pt on a linux-gnu named node46.uhnh4h.cluster by t48263uhn Wed Nov 16 10:50:03 2016
> [5]PETSC ERROR: Configure options --with-petsc-arch=linux-gnu --with-debugging=yes --with-mpi-dir=/cluster/tools/software/openmpi/2.0.0/ --download-ml=yes --download-fblaspack=yes -PETSC_ARCH=linux-gnu --download-superlu_dist=yes --download-superlu=yes --download-hypre=yes --download-mumps=yes --download-scalapack=yes --download-blacs=yes --download-hdf5=yes --download-metis=yes --download-parmetis=yes --download-pastix=yes --download-ptscotch=yes --download-sundials=yes --with-shared-libraries=1
> [5]PETSC ERROR: #1 User provided function() line 0 in  unknown file
> 
> I appreciate any help in finding the cause of the error.
> 
> Best Regards,
> 
> Ali
> 
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