[Libmesh-users] Getting PETSc error after modifying the stiffness matrix

[Omar Al-A. <oma...@gm...>]

Hi everyone,

I am trying to add a term to a the stiffness matrix which is V and it
appears as follows:

 for (unsigned int i=0; i<phi.size(); i++){
          for (unsigned int j=0; j<phi.size(); j++)
            {
              Me(i,j) += JxW[qp]*phi[i][qp]*phi[j][qp];
              Ke(i,j) += JxW[qp]*(dphi[i][qp]*dphi[j][qp] +
phi[i][qp]*phi[j][qp]* V );
             }

The error that I am getting is:

[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/petsc-as/documentation/troubleshooting.html#Signal[0]PETSCERROR:
or try
http://valgrind.org on GNU/linux and Apple Mac OS X to find memory
corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 3, Fri Jun  4 15:34:52
CDT 2010
[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: ./ex100-opt on a linux-gnu named ubuntu by omabbasi Wed Apr
13 17:19:17 2011
[0]PETSC ERROR: Libraries linked from
/build/buildd/petsc-3.1.dfsg/linux-gnu-c-opt/lib
[0]PETSC ERROR: Configure run at Fri Sep 10 05:10:39 2010
[0]PETSC ERROR: Configure options --with-shared --with-debugging=0
--useThreads 0 --with-clanguage=C++ --with-c-support
--with-fortran-interfaces=1 --with-mpi-dir=/usr/lib/openmpi
--with-mpi-shared=1 --with-blas-lib=-lblas --with-lapack-lib=-llapack
--with-umfpack=1 --with-umfpack-include=/usr/include/suitesparse
--with-umfpack-lib="[/usr/lib/libumfpack.so,/usr/lib/libamd.so]"
--with-spooles=1 --with-spooles-include=/usr/include/spooles
--with-spooles-lib=/usr/lib/libspooles.so --with-hypre=1
--with-hypre-dir=/usr --with-scotch=1
--with-scotch-include=/usr/include/scotch
--with-scotch-lib=/usr/lib/libscotch.so --with-hdf5=1 --with-hdf5-dir=/usr
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown
file
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM
0
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.
--------------------------------------------------------------------------

I expect that I am getting this error because V is not written in a way that
PETSc recognize. I would appreciate any suggestions.


Not sure if this piece of information is important but let me write it
anyway. V is calculated by the following code:

       Real sigma   = 3.1575;
       Real epsilon = 0.0450;
       Real V1[131];
       Real V;
        const Real x = q_point[qp](0);
        const Real y = q_point[qp](1);
        const Real z = q_point[qp](2);

        for (int i=0; i<nr; i++){
        V1[i] = -4 * epsilon * pow(sigma,6)  /
sqrt((pow(x-xx[i][0],2))+(pow(x-xx[i][1],2))+(pow(x-xx[i][2],2)))
                +4 * epsilon * pow(sigma,12) /
sqrt((pow(x-xx[i][0],2))+(pow(x-xx[i][1],2))+(pow(x-xx[i][2],2)));
        }

        for(int i = 0; i<nr; ++i) {
            V += V1[i];
      }
    if (V > 1.e8){ V = 1.e8;}

Thanks in advance,
Omar