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. > >> > >> > >> > > > > > > > > -- 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
