[petsc-users] Argument out of range error in MatPermute
Eda Oktay
eda.oktay at metu.edu.tr
Mon Apr 22 03:28:03 CDT 2019
Thank you for your answers. I figured out that for a matrix of size
4253*4253, local size of Mat is 2127 and 2127 for 2 processors. However, I
wrote the program such that the local sizes of IS 2127 and 2126.
Is local size of Mat being 2127 on both processors correct? If it is, then
I will change the local size of IS but then it will exceed the global size
of Mat. Isn't this also a problem?
Thanks a lot,
Eda
Smith, Barry F. <bsmith at mcs.anl.gov>, 9 Nis 2019 Sal, 00:31 tarihinde şunu
yazdı:
>
> Suggest printing out the IS with ISView after it is created and
> confirming that 1) it is a permutation and 2) that the size of the IS on
> each process matches the number of rows on that process.
>
> Note from the manual page: The index sets should be on the same
> communicator as Mat and have the same local sizes.
>
> Barry
>
>
> > On Apr 8, 2019, at 3:21 AM, Eda Oktay via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
> >
> > Hello again,
> >
> > I solved the problem for even numbered sized matrices. However when the
> matrix size is odd, then number of elements in each index set at each
> processor are different. (For example, for size 4253*4253 and 2 processors,
> size of index set at processor 0 is 2127 where at processor 1, it is 2126)
> I think this is why, MatPermute again gives the same "Argument out of
> range" error. Index sets look like correct but I still did not get why I
> get this error.
> >
> > This is the part of my program:
> >
> > PetscMPIInt rank,size;
> > MPI_Comm_rank(PETSC_COMM_WORLD, &rank);
> > MPI_Comm_size(PETSC_COMM_WORLD, &size);
> >
> > PetscInt mod;
> > mod = siz % size;
> >
> > PetscInt *idxx,ss;
> > ss = (siz-mod)/size;
>
> >
> > if (mod != 0){
> > if (rank<mod){
> > PetscMalloc1(ss+1,&idxx);
> > } else{
> > PetscMalloc1(ss,&idxx);
> > }
> > }
> >
> > if (rank != size-1) {
> > j =0;
> > for (i=rank*ss; i<(rank+1)*ss; i++) {
> > idxx[j] = idx[i];
> > j++;
> > }
> >
> > } else {
> >
> > j =0;
> > for (i=rank*ss; i<siz; i++) {
> > idxx[j] = idx[i];
> > j++;
> > }
> >
> > }
> >
> > if (mod != 0){
> > if (rank<mod){
> > idxx[ss+1] = idx[ss*size+rank+1];
> > }
> > }
> >
> > /*Permute matrix L (spy(A(p1,p1))*/
> >
> > if (mod != 0){
> > if (rank<mod){
> > ierr =
> ISCreateGeneral(PETSC_COMM_WORLD,ss+1,idxx,PETSC_COPY_VALUES,&is);CHKERRQ(ierr);
> > } else{
> > ierr =
> ISCreateGeneral(PETSC_COMM_WORLD,ss,idxx,PETSC_COPY_VALUES,&is);CHKERRQ(ierr);
> > }
> > }
> > ierr = ISSetPermutation(is);CHKERRQ(ierr);
> >
> > ierr = MatPermute(A,is,is,&PL);CHKERRQ(ierr);
> >
> > And I get the following error even if I use MatSetOption :
> >
> > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > [0]PETSC ERROR: Argument out of range
> > [0]PETSC ERROR: New nonzero at (0,4252) caused a malloc
> > Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to turn
> off this check
> > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> > [0]PETSC ERROR: Petsc Release Version 3.10.3, Dec, 18, 2018
> > [0]PETSC ERROR: ./SON_YENI_DENEME_TEMIZ_ENYENI_FINAL on a
> arch-linux2-c-debug named dd2b.wls.metu.edu.tr by edaoktay Mon Apr 8
> 11:10:59 2019
> > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --with-cxx-dialect=C++11 --download-openblas
> --download-metis --download-parmetis --download-superlu_dist
> --download-slepc --download-mpich
> > [0]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 617 in
> /home/edaoktay/petsc-3.10.3/src/mat/impls/aij/mpi/mpiaij.c
> > [0]PETSC ERROR: #2 MatSetValues() line 1349 in
> /home/edaoktay/petsc-3.10.3/src/mat/interface/matrix.c
> > [0]PETSC ERROR: #3 MatPermute_MPIAIJ() line 1714 in
> /home/edaoktay/petsc-3.10.3/src/mat/impls/aij/mpi/mpiaij.c
> > [0]PETSC ERROR: #4 MatPermute() line 4997 in
> /home/edaoktay/petsc-3.10.3/src/mat/interface/matrix.c
> > [0]PETSC ERROR: #5 main() line 352 in
> /home/edaoktay/petsc-3.10.3/arch-linux2-c-debug/share/slepc/examples/src/eda/SON_YENI_DENEME_TEMIZ_ENYENI_FINAL.c
> > [0]PETSC ERROR: PETSc Option Table entries:
> > [0]PETSC ERROR: -f
> /home/edaoktay/petsc-3.10.3/share/petsc/datafiles/matrices/binary_files/airfoil1_binary
> > [0]PETSC ERROR: -mat_partitioning_type parmetis
> > [0]PETSC ERROR: -unweighted
> > [0]PETSC ERROR: ----------------End of Error Message -------send entire
> error message to petsc-maint at mcs.anl.gov----------
> >
> > Thanks!
> >
> > Eda
> >
> > Eda Oktay <eda.oktay at metu.edu.tr>, 25 Mar 2019 Pzt, 13:53 tarihinde
> şunu yazdı:
> > I attached whole program I wrote where the problem is in line 285. One
> of the matrices I used was airfoil1_binary, included in the folder. Also, I
> included makefile. Is that what you want?
> >
> > Matthew Knepley <knepley at gmail.com>, 25 Mar 2019 Pzt, 13:41 tarihinde
> şunu yazdı:
> > That should not happen. Can you send in a small example that we can
> debug.
> >
> > Thanks,
> >
> > Matt
> >
> > On Mon, Mar 25, 2019 at 12:38 AM Eda Oktay via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
> > Hello,
> >
> > I am trying to permute a vector A using following lines:
> >
> > ierr =
> ISCreateGeneral(PETSC_COMM_SELF,siz,idx,PETSC_COPY_VALUES,&is);CHKERRQ(ierr);
> > ierr = ISSetPermutation(is);CHKERRQ(ierr);
> > ierr = ISDuplicate(is,&newIS);CHKERRQ(ierr);
> > ierr =
> MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
> > ierr = MatPermute(A,is,newIS,&PL);CHKERRQ(ierr);
> >
> > However, in MatPermute line, I get the following error even if I used
> MatSetOption before this line:
> >
> > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > [0]PETSC ERROR: Argument out of range
> > [0]PETSC ERROR: New nonzero at (0,485) caused a malloc
> > Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to turn
> off this check
> > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> > [0]PETSC ERROR: Petsc Release Version 3.10.3, Dec, 18, 2018
> > [0]PETSC ERROR: ./DENEME_TEMIZ_ENYENI_FINAL on a arch-linux2-c-debug
> named 1232.wls.metu.edu.tr by edaoktay Mon Mar 25 12:15:14 2019
> > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --with-cxx-dialect=C++11 --download-openblas
> --download-metis --download-parmetis --download-superlu_dist
> --download-slepc --download-mpich
> > [0]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 579 in
> /home/edaoktay/petsc-3.10.3/src/mat/impls/aij/mpi/mpiaij.c
> > [0]PETSC ERROR: #2 MatAssemblyEnd_MPIAIJ() line 807 in
> /home/edaoktay/petsc-3.10.3/src/mat/impls/aij/mpi/mpiaij.c
> > [0]PETSC ERROR: #3 MatAssemblyEnd() line 5340 in
> /home/edaoktay/petsc-3.10.3/src/mat/interface/matrix.c
> > [0]PETSC ERROR: #4 MatPermute_MPIAIJ() line 1723 in
> /home/edaoktay/petsc-3.10.3/src/mat/impls/aij/mpi/mpiaij.c
> > [0]PETSC ERROR: #5 MatPermute() line 4997 in
> /home/edaoktay/petsc-3.10.3/src/mat/interface/matrix.c
> > [0]PETSC ERROR: #6 main() line 285 in
> /home/edaoktay/petsc-3.10.3/arch-linux2-c-debug/share/slepc/examples/src/eda/DENEME_TEMIZ_ENYENI_FINAL.c
> > [0]PETSC ERROR: PETSc Option Table entries:
> > [0]PETSC ERROR: -f
> /home/edaoktay/petsc-3.10.3/share/petsc/datafiles/matrices/binary_files/airfoil1_binary
> > [0]PETSC ERROR: -mat_partitioning_type parmetis
> > [0]PETSC ERROR: -weighted
> > [0]PETSC ERROR: ----------------End of Error Message -------send entire
> error message to petsc-maint at mcs.anl.gov----------
> >
> > I'll be glad if you can help me.
> >
> > Thanks!
> >
> > Eda
> >
> >
> > --
> > 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
> >
> > https://www.cse.buffalo.edu/~knepley/
>
>
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