[petsc-users] Argument out of range error in MatPermute

Mark Adams mfadams at lbl.gov
Mon Apr 8 08:46:36 CDT 2019 

Note, it does not look like "is" gets created and idxx gets allocated if
mod==0.

Are you sure 'idx' is a valid permutation? You might try replacing idx[i]
with i for debugging, and test with mod==0

On Mon, Apr 8, 2019 at 4:21 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/
>>> <http://www.cse.buffalo.edu/~knepley/>
>>>
>>
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