[petsc-users] Argument out of range error in MatPermute
Eda Oktay
eda.oktay at metu.edu.tr
Wed Apr 24 05:21:33 CDT 2019
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
>
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