[petsc-users] Argument out of range error in MatPermute
Stefano Zampini
stefano.zampini at gmail.com
Mon Apr 22 10:13:37 CDT 2019
If you are using PETSC_DECIDE for the local sizes in MatSetSizes, the
default local sizes should be 2127 and 2126.
Il giorno lun 22 apr 2019 alle ore 11:28 Eda Oktay via petsc-users <
petsc-users at mcs.anl.gov> ha scritto:
> 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/
>>
>>
--
Stefano
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