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Re: Error when solving eqns with PETSc

Well, I did call MatDestroy, but that's at the very last step when everything's over. It's ok. I'll give to figure out where the problem occurs.

Thanks

Matthew Knepley wrote:
On 8/14/07, Ben Tay <zonexo@xxxxxxxxx> 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@xxxxxxxxx> 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.