Error when solving eqns with PETSc

[Ben Tay]

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.

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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