Error when solving eqns with PETSc

Tue Aug 14 10:15:53 CDT 2007

On 8/14/07, Ben Tay <zonexo at gmail.com> wrote:
> Oh, I will check up valgrind since I've not used it b4. The original
> converter starts from 1 so I've done a -1 offset. If I call converter,
> MatCreateSeqAIJWithArrays, MatAssemblyBegin,MatAssemblyEnd at every time
> step, it works perfectly and the answers are very close with another
> solver. However, if I only called it once, the error appears the moment
> I try to call KSPSolve.
>
> One qn is if I declare A_mat as a global variable, once I finalise it
> with MatAssemblyBegin,MatAssemblyEnd, it should remain as global
> variable? I don't 've to do any more manipulation.

Are you sure you are not calling MatDestroy?

  Matt

> I just 've to update the RHS vector and I can call KSPSolve to get the
> solution. Is that correct?
>
> Thanks
>
> Matthew Knepley wrote:
> > 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.
> >>
> >>
> >>
> >
> >
> >
>
>

-- 
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experiments is infinitely more interesting than any results to which
their experiments lead.
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