[petsc-users] Building MatIS with dense local matrix ?

Stefano Zampini stefano.zampini at gmail.com
Mon Jun 19 15:46:07 CDT 2017 

Franck,

Thanks. I'll​ get back soon with a fix.

Stefano


Il 19 Giu 2017 18:17, "Franck Houssen" <franck.houssen at inria.fr> ha scritto:

> The problem was difficult to reduce as reducing make things disappear...
> Luckily, I believe I got it (or at least, it looks "like" the one I
> "really" have...).
>
> Seems that for square matrix, it works fine for csr and dense matrix. But,
> If I am not mistaken, it does not for dense rectangular matrix (still OK
> for csr).
>
> matISCSRDenseSquare.cpp: 2 procs, global 3x3 matrix, each proc adds a 2x2
> local matrix in the global matrix.
> matISCSRDenseRect.cpp: 2 procs, global *2*x3 matrix, each proc adds a *1*x2
> local *vector* in the global matrix.
>
> reminder: running debian/testing with gcc-6.3 + petsc-3.7.6
>
> Franck
>
> >> mpirun -n 2 ./matISCSRDenseSquare.exe csr; mpirun -n 2
> ./matISCSRDenseSquare.exe dense
> csr
> csr
> Mat Object: 2 MPI processes
>   type: is
>   Mat Object:   1 MPI processes
>     type: seqaij
> row 0: (0, 1.)  (1, 0.)
> row 1: (0, 0.)  (1, 1.)
>   Mat Object:   1 MPI processes
>     type: seqaij
> row 0: (0, 1.)  (1, 0.)
> row 1: (0, 0.)  (1, 1.)
> dense
> dense
> Mat Object: 2 MPI processes
>   type: is
>   Mat Object:   1 MPI processes
>     type: seqdense
> 1.0000000000000000e+00 0.0000000000000000e+00
> 0.0000000000000000e+00 1.0000000000000000e+00
>   Mat Object:   1 MPI processes
>     type: seqdense
> 1.0000000000000000e+00 0.0000000000000000e+00
> 0.0000000000000000e+00 1.0000000000000000e+00
>
> >> mpirun -n 2 ./matISCSRDenseRect.exe csr; mpirun -n 2
> ./matISCSRDenseRect.exe dense
> csr
> csr
> Mat Object: 2 MPI processes
>   type: is
>   Mat Object:   1 MPI processes
>     type: seqaij
> row 0: (0, 1.)  (1, 0.)
>   Mat Object:   1 MPI processes
>     type: seqaij
> row 0: (0, 1.)  (1, 0.)
> dense
> dense
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Argument out of range
> [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [1]PETSC ERROR: Argument out of range
> [1]PETSC ERROR: New nonzero at (0,1) caused a malloc
> Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to turn
> off this check
> [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [1]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
> [1]PETSC ERROR: ./matISCSRDenseRect.exe on a arch-linux2-c-debug named
> yoda by fghoussen Mon Jun 19 18:08:58 2017
> New nonzero at (0,1) 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 3.7.6, Apr, 24, 2017
> [1]PETSC ERROR: Configure options --prefix=/home/fghoussen/
> Documents/INRIA/petsc-3.7.6/local --with-mpi=1 --with-pthread=1
> --download-f2cblaslapack=yes --download-mumps=yes --download-scalapack=yes
> --download-superlu=yes --download-suitesparse=yes
> [1]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 616 in
> /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/impls/aij/mpi/mpiaij.c
> [1]PETSC ERROR: #2 MatSetValues() line 1190 in /home/fghoussen/Documents/
> INRIA/petsc-3.7.6/src/mat/interface/matrix.c
> [1]PETSC ERROR: #3 MatSetValuesLocal() line 2053 in
> /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/interface/matrix.c
> [1]PETSC ERROR: #4 MatISGetMPIXAIJ_IS() line 365 in
> /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/impls/is/matis.c
> [1]PETSC ERROR: #5 MatISGetMPIXAIJ() line 437 in /home/fghoussen/Documents/
> INRIA/petsc-3.7.6/src/mat/impls/is/matis.c
> [0]PETSC ERROR: ./matISCSRDenseRect.exe on a arch-linux2-c-debug named
> yoda by fghoussen Mon Jun 19 18:08:58 2017
> [0]PETSC ERROR: Configure options --prefix=/home/fghoussen/
> Documents/INRIA/petsc-3.7.6/local --with-mpi=1 --with-pthread=1
> --download-f2cblaslapack=yes --download-mumps=yes --download-scalapack=yes
> --download-superlu=yes --download-suitesparse=yes
> [0]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 582 in
> /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/impls/aij/mpi/mpiaij.c
> [0]PETSC ERROR: #2 MatSetValues() line 1190 in /home/fghoussen/Documents/
> INRIA/petsc-3.7.6/src/mat/interface/matrix.c
> [0]PETSC ERROR: #3 MatSetValuesLocal() line 2053 in
> /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/interface/matrix.c
> [0]PETSC ERROR: #4 MatISGetMPIXAIJ_IS() line 365 in
> /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/impls/is/matis.c
> [0]PETSC ERROR: #5 MatISGetMPIXAIJ() line 437 in /home/fghoussen/Documents/
> INRIA/petsc-3.7.6/src/mat/impls/is/matis.c
> Mat Object: 2 MPI processes
>   type: is
>   Mat Object:   1 MPI processes
>     type: seqdense
> 1.0000000000000000e+00 0.0000000000000000e+00
>   Mat Object:   1 MPI processes
>     type: seqdense
> 1.0000000000000000e+00 0.0000000000000000e+00
>
> >> diff matISCSRDenseSquare.cpp matISCSRDenseRect.cpp
> 3c3
> < // ~> g++ -o matISCSRDenseSquare.exe matISCSRDenseSquare.cpp -lpetsc
> -lm; mpirun -n 2 matISCSRDenseSquare.exe
> ---
> > // ~> g++ -o matISCSRDenseRect.exe matISCSRDenseRect.cpp -lpetsc -lm;
> mpirun -n 2 matISCSRDenseRect.exe
> 24c24
> <   ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD, 1, 2, localIdx,
> PETSC_COPY_VALUES, &rmap);
> ---
> >   ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD, 1, 1, &rank,
> PETSC_COPY_VALUES, &rmap);
> 29c29
> <   MatCreateIS(PETSC_COMM_WORLD, 1, PETSC_DECIDE, PETSC_DECIDE, 3, 3,
> rmap, cmap, &A);
> ---
> >   MatCreateIS(PETSC_COMM_WORLD, 1, PETSC_DECIDE, PETSC_DECIDE, 2, 3,
> rmap, cmap, &A);
> 32,33c32,33
> <   if (matType == "csr") {cout << matType << endl;
> MatCreateSeqAIJ(PETSC_COMM_SELF, 2, 2, 2, NULL, &Aloc);}
> <   else {cout << matType << endl; MatCreateSeqDense(PETSC_COMM_SELF, 2,
> 2, NULL, &Aloc);}
> ---
> >   if (matType == "csr") {cout << matType << endl;
> MatCreateSeqAIJ(PETSC_COMM_SELF, 1, 2, 2, NULL, &Aloc);}
> >   else {cout << matType << endl; MatCreateSeqDense(PETSC_COMM_SELF, 1,
> 2, NULL, &Aloc);}
> 35,36c35,36
> <   PetscScalar localVal[4] = {1., 0., 0., 1.};
> <   MatSetValues(Aloc, 2, localIdx, 2, localIdx, localVal, ADD_VALUES); //
> Add local 2x2 matrix
> ---
> >   PetscScalar localVal[2] = {1., 0.}; PetscInt oneLocalRow = 0;
> >   MatSetValues(Aloc, 1, &oneLocalRow, 2, localIdx, localVal,
> ADD_VALUES); // Add local row
>
> ------------------------------
>
> *De: *"Stefano Zampini" <stefano.zampini at gmail.com>
> *À: *"Franck Houssen" <franck.houssen at inria.fr>
> *Cc: *"PETSc users list" <petsc-users at mcs.anl.gov>
> *Envoyé: *Lundi 19 Juin 2017 15:25:35
> *Objet: *Re: [petsc-users] Building MatIS with dense local matrix ?
>
> Can you send a minimal working example so that I can fix the code?
>
> Thanks
> Stefano
>
> Il 19 Giu 2017 15:20, "Franck Houssen" <franck.houssen at inria.fr> ha
> scritto:
>
>> Hi,
>>
>> I try to call MatISGetMPIXAIJ on a MatIS (A) that has been feed locally
>> by sequential (Aloc) dense matrix.
>> Seems this ends up with this error: [0]PETSC ERROR: New nonzero at (0,1)
>> caused a malloc. Is this a known error / limitation ? (not supposed to work
>> with dense matrix ?)
>>
>> This (pseudo code) works fine:
>> MatCreateIS(..., A)
>> MatCreateSeqAIJ(..., Aloc)
>> MatISSetLocalMat(pcA, pcALoc)
>> MatISGetMPIXAIJ(A, ...) // OK !
>>
>> When I try to replace MatCreateSeqAIJ(..., Aloc) with
>> MatCreateSeqDense(..., Aloc), it does no more work.
>>
>> Franck
>>
>> PS: running debian/testing with gcc-6.3 + petsc-3.7.6
>>
>
>
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