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
