[petsc-users] How to extract array portions
Dave May
dave.mayhem23 at gmail.com
Wed Apr 6 04:16:43 CDT 2016
On 6 April 2016 at 11:08, FRANCAVILLA MATTEO ALESSANDRO <d019598 at polito.it>
wrote:
> Hi,
>
> I'm trying to set a linear problem with a 2x2 block matrix (say A=[A11
> A12; A21 A22] in matlab notation). Obviously I could generate a single
> matrix, but I would like to keep it as a 2x2 block matrix with the 4 blocks
> generated and used independently (e.g., because at some point I need to
> change some of those blocks to matrix-free). My plan was then to generate a
> MatShell and set a MATOP_MULT shell operation to explicitly compute y=A*x
> by splitting x=[x1;x2] and y=[y1;y2] and carrying out the single
> matrix-vector multiplications, and reassembling the final result.
Take a look at MatNest - it does exactly what you want.
http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatCreateNest.html
http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MATNEST.html#MATNEST
Thanks,
Dave
> My problem is that my efforts in extracting x1 and x2 from the original x
> vector have failed. The following Fortran code is what seemed to me the
> most reasonable thing to do to set the matrix-vector multiplication, but it
> does not work
>
>
> !======================================================
> subroutine MyMult(A,x,y,IERR)
>
> implicit none
>
> #include <petsc/finclude/petscsys.h>
> #include <petsc/finclude/petscvec.h>
> #include <petsc/finclude/petscvec.h90>
> #include <petsc/finclude/petscmat.h>
>
> Mat A
> Vec x,y, x1, x2, y1, y2
> IS :: ix1, ix2, iy1, iy2
> PetscErrorCode ierr
> PetscInt M, N, II, NumberOfUnknowns, NumberOfMeasures
> PetscInt, ALLOCATABLE :: INDICES(:)
> PetscMPIInt :: RANK
>
> CALL VecGetSize(x,N,IERR)
> NumberOfUnknowns = N / 2
> CALL VecGetSize(y,N,IERR)
> NumberOfMeasures = N - NumberOfUnknowns
>
> N = NumberOfUnknowns + MAX(NumberOfUnknowns,NumberOfMeasures)
> ALLOCATE(INDICES(N))
> INDICES = (/ (ii, ii=0, N-1) /)
>
> CALL
> ISCreateGeneral(MPI_COMM_SELF,NumberOfUnknowns,INDICES(1:NumberOfUnknowns),PETSC_COPY_VALUES,ix1,IERR)
> CALL VecGetSubVector(x,ix1,x1,IERR)
> CALL
> ISCreateGeneral(MPI_COMM_SELF,NumberOfUnknowns,INDICES(NumberOfUnknowns+1:2*NumberOfUnknowns),PETSC_COPY_VALUES,ix2,IERR)
> CALL VecGetSubVector(x,ix2,x2,IERR)
> CALL
> ISCreateGeneral(MPI_COMM_SELF,NumberOfUnknowns,INDICES(1:NumberOfUnknowns),PETSC_COPY_VALUES,iy1,IERR)
> CALL VecGetSubVector(y,iy1,y1,IERR)
> CALL
> ISCreateGeneral(MPI_COMM_SELF,NumberOfUnknowns,INDICES(NumberOfUnknowns+1:NumberOfUnknowns+NumberOfMeasures),PETSC_COPY_VALUES,iy2,IERR)
> CALL VecGetSubVector(y,iy2,y2,IERR)
>
> CALL MatMult(L_discretized,x1,y1,IERR)
> CALL MatMultAdd(K_discretized,x2,y1,y1,IERR)
> CALL MatMult(L_MR,x1,y2,IERR)
> CALL MatMultAdd(K_MR,x2,y2,y2,IERR)
>
> CALL VecRestoreSubVector(y,iy1,y1,IERR)
> CALL VecRestoreSubVector(y,iy2,y2,IERR)
>
> return
> end subroutine MyMult
> !======================================================
>
>
> Obviously the sequence of calls to ISCreateGeneral and VecGetSubVector
> does not do what I expect, as the errors I'm getting are in the following
> MatMult multiplications (the global sizes of x1 and x2 SHOULD BE both 771,
> while y1 and y2 should be 771 and 2286):
>
> 1) executed with 1 MPI process:
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Nonconforming object sizes
> [0]PETSC ERROR: Mat mat,Vec y: global dim 2286 771
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015
> [0]PETSC ERROR: ./ISS on a arch-linux2-c-debug named
> alessandro-HP-ProDesk-490-G2-MT by alessandro Wed Apr 6 10:54:03 2016
> [0]PETSC ERROR: Configure options
> --with-blas-lapack-dir=/opt/intel/composer_xe_2015.2.164/mkl
> --with-mpi-cc=/home/alessandro/.openmpi-1.8.3/bin/mpicc
> --with-mpi-f90=/home/alessandro/.openmpi-1.8.3/bin/mpif90
> --with-mpiexec=/home/alessandro/.openmpi-1.8.3/bin/mpiexec
> --with-scalar-type=complex
> [0]PETSC ERROR: #1 MatMult() line 2215 in
> /home/alessandro/CODE/PETSc/petsc-3.6.3/src/mat/interface/matrix.c
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Nonconforming object sizes
> [0]PETSC ERROR: Mat mat,Vec v3: local dim 2286 771
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015
> [0]PETSC ERROR: ./ISS on a arch-linux2-c-debug named
> alessandro-HP-ProDesk-490-G2-MT by alessandro Wed Apr 6 10:54:03 2016
> [0]PETSC ERROR: Configure options
> --with-blas-lapack-dir=/opt/intel/composer_xe_2015.2.164/mkl
> --with-mpi-cc=/home/alessandro/.openmpi-1.8.3/bin/mpicc
> --with-mpi-f90=/home/alessandro/.openmpi-1.8.3/bin/mpif90
> --with-mpiexec=/home/alessandro/.openmpi-1.8.3/bin/mpiexec
> --with-scalar-type=complex
> [0]PETSC ERROR: #2 MatMultAdd() line 2396 in
> /home/alessandro/CODE/PETSc/petsc-3.6.3/src/mat/interface/matrix.c
>
>
>
> 2) executed with 4 MPI processes (I'm copying the output of process 0
> only, they're all the same):
>
> ....
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Nonconforming object sizes
> [0]PETSC ERROR: Mat mat,Vec x: global dim 771 3084
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015
> [0]PETSC ERROR: ./ISS on a arch-linux2-c-debug named
> alessandro-HP-ProDesk-490-G2-MT by alessandro Wed Apr 6 10:49:13 2016
> [0]PETSC ERROR: Configure options
> --with-blas-lapack-dir=/opt/intel/composer_xe_2015.2.164/mkl
> --with-mpi-cc=/home/alessandro/.openmpi-1.8.3/bin/mpicc
> --with-mpi-f90=/home/alessandro/.openmpi-1.8.3/bin/mpif90
> --with-mpiexec=/home/alessandro/.openmpi-1.8.3/bin/mpiexec
> --with-scalar-type=complex
> [0]PETSC ERROR: #1 MatMult() line 2214 in
> /home/alessandro/CODE/PETSc/petsc-3.6.3/src/mat/interface/matrix.c
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Nonconforming object sizes
> [0]PETSC ERROR: Mat mat,Vec v1: global dim 771 3084
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015
> [0]PETSC ERROR: ./ISS on a arch-linux2-c-debug named
> alessandro-HP-ProDesk-490-G2-MT by alessandro Wed Apr 6 10:49:13 2016
> [0]PETSC ERROR: Configure options
> --with-blas-lapack-dir=/opt/intel/composer_xe_2015.2.164/mkl
> --with-mpi-cc=/home/alessandro/.openmpi-1.8.3/bin/mpicc
> --with-mpi-f90=/home/alessandro/.openmpi-1.8.3/bin/mpif90
> --with-mpiexec=/home/alessandro/.openmpi-1.8.3/bin/mpiexec
> --with-scalar-type=complex
> [0]PETSC ERROR: #2 MatMultAdd() line 2393 in
> /home/alessandro/CODE/PETSc/petsc-3.6.3/src/mat/interface/matrix.c
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Nonconforming object sizes
> [0]PETSC ERROR: Mat mat,Vec x: global dim 771 3084
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015
> [0]PETSC ERROR: ./ISS on a arch-linux2-c-debug named
> alessandro-HP-ProDesk-490-G2-MT by alessandro Wed Apr 6 10:49:13 2016
> [0]PETSC ERROR: Configure options
> --with-blas-lapack-dir=/opt/intel/composer_xe_2015.2.164/mkl
> --with-mpi-cc=/home/alessandro/.openmpi-1.8.3/bin/mpicc
> --with-mpi-f90=/home/alessandro/.openmpi-1.8.3/bin/mpif90
> --with-mpiexec=/home/alessandro/.openmpi-1.8.3/bin/mpiexec
> --with-scalar-type=complex
> [0]PETSC ERROR: #3 MatMult() line 2214 in
> /home/alessandro/CODE/PETSc/petsc-3.6.3/src/mat/interface/matrix.c
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Nonconforming object sizes
> [0]PETSC ERROR: Mat mat,Vec v1: global dim 771 3084
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015
> [0]PETSC ERROR: ./ISS on a arch-linux2-c-debug named
> alessandro-HP-ProDesk-490-G2-MT by alessandro Wed Apr 6 10:49:13 2016
> [0]PETSC ERROR: Configure options
> --with-blas-lapack-dir=/opt/intel/composer_xe_2015.2.164/mkl
> --with-mpi-cc=/home/alessandro/.openmpi-1.8.3/bin/mpicc
> --with-mpi-f90=/home/alessandro/.openmpi-1.8.3/bin/mpif90
> --with-mpiexec=/home/alessandro/.openmpi-1.8.3/bin/mpiexec
> --with-scalar-type=complex
> [0]PETSC ERROR: #4 MatMultAdd() line 2393 in
> /home/alessandro/CODE/PETSc/petsc-3.6.3/src/mat/interface/matrix.c
> ....
>
>
> Any idea? I would like to keep the flexibility of having a sequence of
> mat-vec multiplications as in
>
> CALL MatMult(L_discretized,x1,y1,IERR)
> CALL MatMultAdd(K_discretized,x2,y1,y1,IERR)
> CALL MatMult(L_MR,x1,y2,IERR)
> CALL MatMultAdd(K_MR,x2,y2,y2,IERR)
>
> but for doing that I need to be able to extract x1 and x2, and to
> reassemble the partial results into y.
>
> Thanks in advance,
> Alessandro
>
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