[petsc-users] Argument out of range error in MatPermute
Eda Oktay
eda.oktay at metu.edu.tr
Wed Apr 24 07:24:50 CDT 2019
Dear Matt,
I solved my problem by trying with 9*9 matrix as you said. I made indexing
mistake.
Thank you for answering.
Eda
Matthew Knepley <knepley at gmail.com>, 24 Nis 2019 Çar, 14:30 tarihinde şunu
yazdı:
> 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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