[petsc-users] block matrix without MatCreateNest
Klaij, Christiaan
C.Klaij at marin.nl
Sat Jul 30 09:41:58 CDT 2016
Anyone?
(my guess is an if-statement, something like "if type nest then
setup nest"...)
> Date: Thu, 28 Jul 2016 08:38:54 +0000
> From: "Klaij, Christiaan" <C.Klaij at marin.nl>
> To: "petsc-users at mcs.anl.gov" <petsc-users at mcs.anl.gov>
> Subject: [petsc-users] block matrix without MatCreateNest
> Message-ID: <1469695134232.97712 at marin.nl>
> Content-Type: text/plain; charset="utf-8"
>
> I'm trying to understand how to assemble a block matrix in a
> format-independent manner, so that I can switch between types
> mpiaij and matnest.
>
> The manual states that the key to format-independent assembly is
> to use MatGetLocalSubMatrix. So, in the code below, I'm using
> this to assemble a 3-by-3 block matrix A and setting the diagonal
> of block A02. This seems to work for type mpiaij, but not for
> type matnest. What am I missing?
>
> Chris
>
>
> $ cat mattry.F90
> program mattry
>
> use petscksp
> implicit none
> #include <petsc/finclude/petsckspdef.h>
>
> PetscInt :: n=4 ! setting 4 cells per process
>
> PetscErrorCode :: ierr
> PetscInt :: size,rank,i
> Mat :: A,A02
> IS :: isg0,isg1,isg2
> IS :: isl0,isl1,isl2
> ISLocalToGlobalMapping :: map
>
> integer, allocatable, dimension(:) :: idx
>
> call PetscInitialize(PETSC_NULL_CHARACTER,ierr); CHKERRQ(ierr)
> call MPI_Comm_size(PETSC_COMM_WORLD,size,ierr); CHKERRQ(ierr)
> call MPI_Comm_rank(PETSC_COMM_WORLD,rank,ierr);CHKERRQ(ierr)
>
> ! local index sets for 3 fields
> allocate(idx(n))
> idx=(/ (i-1, i=1,n) /)
> call ISCreateGeneral(PETSC_COMM_WORLD,n,idx,PETSC_COPY_VALUES,isl0,ierr);CHKERRQ(ierr)
> call ISCreateGeneral(PETSC_COMM_WORLD,n,idx+n,PETSC_COPY_VALUES,isl1,ierr);CHKERRQ(ierr)
> call ISCreateGeneral(PETSC_COMM_WORLD,n,idx+2*n,PETSC_COPY_VALUES,isl2,ierr);CHKERRQ(ierr)
> ! call ISView(isl3,PETSC_VIEWER_STDOUT_WORLD,ierr); CHKERRQ(ierr)
> deallocate(idx)
>
> ! global index sets for 3 fields
> allocate(idx(n))
> idx=(/ (i-1+rank*3*n, i=1,n) /)
> call ISCreateGeneral(PETSC_COMM_WORLD,n,idx,PETSC_COPY_VALUES,isg0,ierr);CHKERRQ(ierr)
> call ISCreateGeneral(PETSC_COMM_WORLD,n,idx+n,PETSC_COPY_VALUES,isg1,ierr); CHKERRQ(ierr)
> call ISCreateGeneral(PETSC_COMM_WORLD,n,idx+2*n,PETSC_COPY_VALUES,isg2,ierr); CHKERRQ(ierr)
> ! call ISView(isg3,PETSC_VIEWER_STDOUT_WORLD,ierr); CHKERRQ(ierr)
> deallocate(idx)
>
> ! local-to-global mapping
> allocate(idx(3*n))
> idx=(/ (i-1+rank*3*n, i=1,3*n) /)
> call ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD,1,3*n,idx,PETSC_COPY_VALUES,map,ierr); CHKERRQ(ierr)
> ! call ISLocalToGlobalMappingView(map,PETSC_VIEWER_STDOUT_WORLD,ierr); CHKERRQ(ierr)
> deallocate(idx)
>
> ! create the 3-by-3 block matrix
> call MatCreate(PETSC_COMM_WORLD,A,ierr); CHKERRQ(ierr)
> call MatSetSizes(A,3*n,3*n,PETSC_DECIDE,PETSC_DECIDE,ierr); CHKERRQ(ierr)
> ! call MatSetType(A,MATNEST,ierr); CHKERRQ(ierr)
> call MatSetUp(A,ierr); CHKERRQ(ierr)
> call MatSetOptionsPrefix(A,"A_",ierr); CHKERRQ(ierr)
> call MatSetLocalToGlobalMapping(A,map,map,ierr); CHKERRQ(ierr)
> call MatSetFromOptions(A,ierr); CHKERRQ(ierr)
>
> ! set diagonal of block A02 to 0.65
> call MatGetLocalSubmatrix(A,isl0,isl2,A02,ierr); CHKERRQ(ierr)
> do i=1,n
> call MatSetValuesLocal(A02,1,i-1,1,i-1,0.65d0,INSERT_VALUES,ierr); CHKERRQ(ierr)
> end do
> call MatRestoreLocalSubMatrix(A,isl0,isl2,A02,ierr); CHKERRQ(ierr)
> call MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
> call MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
>
> ! verify
> call MatGetSubmatrix(A,isg0,isg2,MAT_INITIAL_MATRIX,A02,ierr); CHKERRQ(ierr)
> call MatView(A02,PETSC_VIEWER_STDOUT_WORLD,ierr);CHKERRQ(ierr)
>
> call PetscFinalize(ierr)
>
> end program mattry
>
> $ mpiexec -n 2 ./mattry -A_mat_type mpiaij
> Mat Object: 2 MPI processes
> type: mpiaij
> row 0: (0, 0.65)
> row 1: (1, 0.65)
> row 2: (2, 0.65)
> row 3: (3, 0.65)
> row 4: (4, 0.65)
> row 5: (5, 0.65)
> row 6: (6, 0.65)
> row 7: (7, 0.65)
>
> $ mpiexec -n 2 ./mattry -A_mat_type nest
> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [0]PETSC ERROR: Null argument, when expecting valid pointer
> [0]PETSC ERROR: Null Pointer: Parameter # 3
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.7.3, Jul, 24, 2016
> [0]PETSC ERROR: ./mattry on a linux_64bit_debug named lin0322.marin.local by cklaij Thu Jul 28 10:31:04 2016
> [0]PETSC ERROR: Configure options --with-mpi-dir=/home/cklaij/ReFRESCO/Dev/trunk/Libs/install/openmpi/1.8.7 --with-clanguage=c++ --with-x=1 --with-debugging=1 --with-blas-lapack-dir=/opt/intel/composer_xe_2015.1.133/mkl --with-shared-libraries=0
> [0]PETSC ERROR: #1 MatNestFindIS() line 298 in /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/mat/impls/nest/matnest.c
> [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [1]PETSC ERROR: Null argument, when expecting valid pointer
> [1]PETSC ERROR: Null Pointer: Parameter # 3
> [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> [1]PETSC ERROR: Petsc Release Version 3.7.3, Jul, 24, 2016
> [1]PETSC ERROR: ./mattry on a linux_64bit_debug named lin0322.marin.local by cklaij Thu Jul 28 10:31:04 2016
> [1]PETSC ERROR: Configure options --with-mpi-dir=/home/cklaij/ReFRESCO/Dev/trunk/Libs/install/openmpi/1.8.7 --with-clanguage=c++ --with-x=1 --with-debugging=1 --with-blas-lapack-dir=/opt/intel/composer_xe_2015.1.133/mkl --with-shared-libraries=0
> [1]PETSC ERROR: #1 MatNestFindIS() line 298 in /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/mat/impls/nest/matnest.c
> [1]PETSC ERROR: #2 MatNestFindSubMat() line 371 in /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/mat/impls/nest/matnest.c
> [1]PETSC ERROR: #3 MatGetLocalSubMatrix_Nest() line 414 in /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/mat/impls/nest/matnest.c
> [1]PETSC ERROR: #4 MatGetLocalSubMatrix() line 10099 in /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/mat/interface/matrix.c
> #2 MatNestFindSubMat() line 371 in /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/mat/impls/nest/matnest.c
> [0]PETSC ERROR: #3 MatGetLocalSubMatrix_Nest() line 414 in /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/mat/impls/nest/matnest.c
> [0]PETSC ERROR: #4 MatGetLocalSubMatrix() line 10099 in /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/mat/interface/matrix.c
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> with errorcode 85.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> [lin0322.marin.local:11985] 1 more process has sent help message help-mpi-api.txt / mpi-abort
> [lin0322.marin.local:11985] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
> $
>
>
> dr. ir. Christiaan Klaij | CFD Researcher | Research & Development
> MARIN | T +31 317 49 33 44 | mailto:C.Klaij at marin.nl | http://www.marin.nl
>
> MARIN news: http://www.marin.nl/web/News/News-items/Ship-design-in-EU-project-Holiship.htm
>
dr. ir. Christiaan Klaij | CFD Researcher | Research & Development
MARIN | T +31 317 49 33 44 | mailto:C.Klaij at marin.nl | http://www.marin.nl
MARIN news: http://www.marin.nl/web/News/News-items/Joint-Industry-Project-LifeLine-kicks-off.htm
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