[petsc-users] Argument out of range error in MatPermute
Matthew Knepley
knepley at gmail.com
Wed Apr 24 06:30:00 CDT 2019
On Wed, Apr 24, 2019 at 6:35 AM Stefano Zampini via petsc-users <
petsc-users at mcs.anl.gov> wrote:
> Dump the index sets and the matrix in binary and send them
>
First, reduce your problem size to about 10.
Matt
> Il giorno mer 24 apr 2019 alle ore 13:21 Eda Oktay <eda.oktay at metu.edu.tr>
> ha scritto:
>
>> Since I am using square matrix, isn't the row local size of the matrix
>> equal to the local size of IS? They are both 2127 and 2126.
>>
>> Stefano Zampini <stefano.zampini at gmail.com>, 24 Nis 2019 Çar, 13:15
>> tarihinde şunu yazdı:
>>
>>> 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
>>>
>>
>
> --
> Stefano
>
--
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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