[petsc-users] Segmentation Violation

[Peter Zhoujie Lu]

Dear all,

I have some issue with my code using petsc. The exact same code runs fine
on a linux box with ifort. Is that still be a possible memory corruption? I
have some issue with getting valgrind working on 10.7. Is there any better
way to debug this? Thanks. Here is the error message I got for OSX 10.7
with gcc.

Peter

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] VecCreateMPIWithArray line 312
/Users/lvzhoujie/Work/petsc-3.3-p2/src/vec/vec/impls/mpi/pbvec.c
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 59.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

p.s. I also found /src/ksp/pc/examples/test/ex7.c not working on my
computer. Here is the error message:

[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Object is in wrong state!
[0]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on
argument 1 "mat" before MatSetValues()!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 2, Fri Jul 13 15:42:00
CDT 2012
[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: ./ex7 on a linux-ifo named peter-lu by plu Fri Aug 10
21:06:23 2012
[0]PETSC ERROR: Libraries linked from
/Users/lvzhoujie/Work/petsc-3.3-p2/linux-ifort-opt/lib
[0]PETSC ERROR: Configure run at Fri Aug 10 10:44:21 2012
[0]PETSC ERROR: Configure options --with-pic --download-openmpi=1
--with-fortran=1 --with-debugging=1 --with-shared-libraries=1
--download-superlu_dist=yes --with-fortran-interfaces=1
--with-scalar-type=real --download-f-blas-lapack --with-cc=gcc
--with-fc=gfortran --with-cxx=c++ --with-petsc-arch=linux-ifort-opt
--download-parmetis=yes --download-metis
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: MatSetValues() line 993 in
/Users/lvzhoujie/Work/petsc-3.3-p2/src/mat/interface/matrix.c
[0]PETSC ERROR: main() line 25 in src/ksp/pc/examples/tests/ex7.c
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 73.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
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