Error when solving eqns with PETSc

[Matthew Knepley]

Memory is being garbaged somewhere. I suggest using valgrind as it says
in the error message. However, I also have a guess. Are you sure that the
AIJ arrays that you provided to the constructor are using 0-offset numbering?
I suspect that it would be 1-offset for both ia_spar and ja_spar which would
cause problems.

  Matt

On 8/14/07, Ben Tay <zonexo at gmail.com> wrote:
> Hi,
>
> I am currently using the following way to solve my poisson eqn
>
> in global.F (global variables)
>
> implicit none
>
> save
>
> Mat    A_mat
> Vec    xx,b_rhs
> KSP   ksp
> PC    pc
> PCType      ptype
> KSPType        ksptype
>
> then they are initialized
>
> call PetscInitialize(PETSC_NULL_CHARACTER,ierr)
> call
> MatCreateSeqAIJ(PETSC_COMM_SELF,size_x*size_y,size_x*size_y,13,PETSC_NULL_INTEGER,A_mat,ierr)
> call VecCreateSeq(PETSC_COMM_SELF,size_x*size_y,b_rhs,ierr)
> call VecDuplicate(b_rhs,xx,ierr)
> call KSPCreate(PETSC_COMM_SELF,ksp,ierr)
> call VecAssemblyBegin(b_rhs,ierr)
> call VecAssemblyEnd(b_rhs,ierr)
> call VecAssemblyBegin(xx,ierr)
> call VecAssemblyEnd(xx,ierr)
>
> My original matrix is stored as ITPACK format so I used ellcsr from
> SPARSKIT to convert to CSR format and use
>
> call
> ellcsr(total_k,big_A,int_a,total_k,13,A_spar,ja_spar,ia_spar,nzmax,ierr)
> ...
> call
> MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,Ntot,Ntot,ia_spar,ja_spar,A_spar,A_mat,ierr)
> call MatAssemblyBegin(A_mat,MAT_FINAL_ASSEMBLY,ierr)
> call MatAssemblyEnd(A_mat,MAT_FINAL_ASSEMBLY,ierr)
>
> to read into PETSc. Then read in the RHS as well
>
> do k=1,Ntot
>     II=k-1
>     call VecSetValue(b_rhs,II,q_p(k),INSERT_VALUES,ierr)
> end do
>
> Finally the matrix is solved using
>
> call KSPSolve(ksp,b_rhs,xx,ierr).
>
> This works but the A_mat matrix is not changing with time. Hence I tried
> to call the above sentences only at the 1st time step. However I got
> this error when KSPSolve is called:
>
> [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]PETSC
> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple 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 2.3.3, Patch 4, Tue Aug  7
> 17:36:16 CDT 2007 HG revision: ee49636ddd90fb72d14b79fa8180225eb4257c59
> [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: ./a.out on a atlas3 named atlas3-c01 by g0306332 Tue Aug
> 14 18:13:09 2007
> [0]PETSC ERROR: Libraries linked from
> /lsftmp/g0306332/petsc-2.3.3-p4/lib/atlas3
> [0]PETSC ERROR: Configure run at Sat Aug 11 08:25:45 2007
> [0]PETSC ERROR: Configure options --with-cc=icc --with-fc=ifort
> --with-x=0 --download-hypre=1 --download-mumps=1 --download-scalapack=1
> --download-blacs=1 --with-debugging=0
> --with-blas-lapack-dir=/opt/intel/cmkl/8.1.1/ --with-shared
> --with-mpi-dir=/lsftmp/g0306332/mpich2/
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
> I thought I've delcared A_mat as a global variable so after filling up
> values using MatCreateSeqAIJWithArrays, MatAssemblyBegin,
> MatAssemblyEnd, I only need to update the RHS vector. It seems that I'm
> missing out something.
>
>


-- 
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