Error when solving eqns with PETSc

[Ben Tay]

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 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.
>>>>
>>>>
>>>>
>>>>         
>>>
>>>       
>>     
>
>
>