You need to call MatNestSetSubMats() after you set the mattype. Yes the manual pages are missing needed cross links.
> On Jul 30, 2016, at 9:41 AM, Klaij, Christiaan <[email protected]> wrote: > > 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" <[email protected]> >> To: "[email protected]" <[email protected]> >> Subject: [petsc-users] block matrix without MatCreateNest >> Message-ID: <[email protected]> >> 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:[email protected] | 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:[email protected] | http://www.marin.nl > > MARIN news: > http://www.marin.nl/web/News/News-items/Joint-Industry-Project-LifeLine-kicks-off.htm >
