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

Stefano Zampini stefano.zampini at gmail.com
Wed Apr 24 05:14:53 CDT 2019 

I don't understand your code. However, I suspect we have a bug here
https://bitbucket.org/petsc/petsc/src/dba4d5898a4236b42fbe8dff209f1243d2f2582a/src/mat/impls/aij/mpi/mpiaij.c#lines-1652
The code assumes the number of leaves is A->rmap->n (the row local size of
the matrix). Shouldn't this be the local size of the IS (rowp)? Barry?

Il giorno mer 24 apr 2019 alle ore 13:03 Eda Oktay <eda.oktay at metu.edu.tr>
ha scritto:

> Dear Stefano,
>
> Thank you for answering. When I used MatSetSizes, I got an error since the
> matrix is read from outside, but from the error I understood that actually
> the local sizes are 2127 and 2126, so I misunderstood the problem. I am
> sorry for my mistake.
>
> However, I still cannot understand where is the error. Because both
> communicators and local sizes of IS and the matrix are the same. I still
> get the same error in MatPermute:
>
> [0]PETSC ERROR: Argument out of range
> [0]PETSC ERROR: Index -1081207334 is out of range
> [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: ./TEKRAR_TEK_SAYI_SON_YENI_DENEME_TEMIZ_ENYENI_FINAL on a
> arch-linux2-c-debug named 53d.wls.metu.edu.tr by edaoktay Wed Apr 24
> 11:22:15 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 PetscLayoutFindOwner() line 248 in
> /home/edaoktay/petsc-3.10.3/include/petscis.h
> [0]PETSC ERROR: #2 MatPermute_MPIAIJ() line 1685 in
> /home/edaoktay/petsc-3.10.3/src/mat/impls/aij/mpi/mpiaij.c
> [0]PETSC ERROR: #3 MatPermute() line 4997 in
> /home/edaoktay/petsc-3.10.3/src/mat/interface/matrix.c
> [0]PETSC ERROR: #4 main() line 361 in
> /home/edaoktay/petsc-3.10.3/arch-linux2-c-debug/share/slepc/examples/src/eda/TEKRAR_TEK_SAYI_SON_YENI_DENEME_TEMIZ_ENYENI_FINAL.c
>
> This is the part of my program:
>
>   ierr = MatCreateVecs(L,&vr,NULL);CHKERRQ(ierr);
>   ierr = EPSGetEigenpair(eps,0,&kr,NULL,vr,NULL);
>   ierr = PetscPrintf(PETSC_COMM_WORLD," The second smallest eigenvalue:
> %g\n",kr);CHKERRQ(ierr);
>
>   /* sort second smallest eigenvector */
>
>   ierr = VecGetSize(vr,&siz);CHKERRQ(ierr);
>   ierr = PetscMalloc1(siz,&idx);CHKERRQ(ierr);
>   for (i=0; i<siz;i++) idx[i] = i;
>
>   VecScatter ctx;
>   Vec vout;
>   VecScatterCreateToAll(vr,&ctx,&vout);
>   VecScatterBegin(ctx,vr,vout,INSERT_VALUES,SCATTER_FORWARD);
>   VecScatterEnd(ctx,vr,vout,INSERT_VALUES,SCATTER_FORWARD);
>   VecScatterDestroy(&ctx);
>
>   PetscScalar *avr;
>   ierr = VecGetArray(vout,&avr);CHKERRQ(ierr);
>   ierr = PetscSortRealWithPermutation(siz,avr,idx);CHKERRQ(ierr);
>
>   /*Select out a piece of the resulting indices idx on each process; for
> example with two processes I think rank = 0 would get the first half of the
> idx and rank = 1 would get the second half.*/
>
>   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);
>     }
>   } else{
>       PetscMalloc1(ss,&idxx);
>   }
>
>
>     j =0;
>     for (i=rank*ss; i<(rank+1)*ss; i++) {
>       idxx[j] = idx[i];
>      //PetscPrintf(PETSC_COMM_WORLD," idxx: %D\n",idxx[j]);
>       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);
>         }
>
>     }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);
>
> I printed IS and idxx, IS is a permutation and numbers seem to be correct.
> The program also works when mod==0.
>
> Thanks,
>
> Eda
>
> Stefano Zampini <stefano.zampini at gmail.com>, 22 Nis 2019 Pzt, 18:13
> tarihinde şunu yazdı:
>
>> 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
>>
>

-- 
Stefano
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