The fix for MAT_NEW_NONZERO_LOCATIONS, thanks again. I have yet another question, sorry. The recent version of MUMPS supports distributed and sparse RHS is there any chance that this will be supported in PETSc in the near future?
> On May 30, 2018, at 6:55 PM, Marius Buerkle <[email protected]> wrote: > > Thanks for the quick fix, I will test it and report back. > I have another maybe related question, if MAT_NEW_NONZERO_LOCATIONS is true > and let's say 1 new nonzero position is created it does not allocated 1 but > several new nonzeros but only use 1. Correct > I think that is normal, right? Yes > But, at least as far as I understand the manual, a subsequent call of mat > assemble with > MAT_FINAL_ASSEMBLY should compress out the unused allocations and release the > memory, is this correct? It "compresses it out" (by shifting all the nonzero entries to the beginning of the internal i, j, and a arrays), but does NOT release any memory. Since the values are stored in one big contiguous array (obtained with a single malloc) it cannot just free part of the array, so the extra locations just sit harmlessly at the end if the array unused. > If so, this did not work for me, even after doing > MAT_FINAL_ASSEMBLY the unused nonzero allocations remain. Is this normal? Yes, Barry > >> >> Fixed in the branch barry/fix-mat-new-nonzero-locations/maint >> >> Once this passes testing it will go into the maint branch and then the next >> patch release but you can use it now in the branch >> barry/fix-mat-new-nonzero-locations/maint >> >> Thanks for the report and reproducible example >> >> Barry >> >> >>> On May 29, 2018, at 7:51 PM, Marius Buerkle <[email protected]> wrote: >>> >>> Sure, I made a small reproducer, it is Fortran though I hope that is ok. If >>> MAT_NEW_NONZERO_LOCATIONS is set to false I get an error, if it is set to >>> true the new nonzero element is inserted, if MAT_NEW_NONZERO_LOCATIONS is >>> false and either MAT_NEW_NONZERO_LOCATION_ERR or >>> MAT_NEW_NONZERO_ALLOCATION_ERR is set to false afterwards then the new >>> nonzero is also created without an error, but if MAT_NEW_NONZERO_LOCATIONS >>> is set to false after >>> MAT_NEW_NONZERO_LOCATION_ERR/MAT_NEW_NONZERO_ALLOCATION_ERR have been set >>> to false I get an error again. >>> >>> >>> program newnonzero >>> #include <petsc/finclude/petscmat.h> >>> use petscmat >>> implicit none >>> >>> Mat :: A >>> PetscInt :: dnnz,onnz,n,m,idxm(1),idxn(1),nl1,nl2 >>> PetscScalar :: v(1) >>> PetscReal :: info(MAT_INFO_SIZE) >>> PetscErrorCode :: ierr >>> >>> integer :: nproc,iproc,i >>> >>> call PetscInitialize(PETSC_NULL_CHARACTER,ierr) >>> >>> call MPI_COMM_SIZE(PETSC_COMM_WORLD, nproc,ierr) >>> >>> call MPI_Comm_rank( PETSC_COMM_WORLD, iproc, ierr ) >>> >>> n=3 >>> m=n >>> call >>> MatCreateAIJ(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,n,m,1,PETSC_NULL_INTEGER,0,PETSC_NULL_INTEGER,A,ierr) >>> >>> >>> call MatGetOwnershipRange(A,nl1,nl2,ierr) >>> do i=nl1,nl2-1 >>> idxn(1)=i >>> idxm(1)=i >>> v(1)=1d0 >>> call MatSetValues(A,1,idxn,1,idxm, v,INSERT_VALUES,ierr) >>> end do >>> call MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY,ierr) >>> call MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY,ierr) >>> >>> call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE,ierr) >>> !~ call MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE,ierr) >>> !~ call MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR ,PETSC_FALSE,ierr) >>> !~ call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE,ierr) >>> >>> >>> idxn(1)=0 >>> idxm(1)=n-1 >>> if ((idxn(1).ge.nl1).and.(idxn(1).le.nl2-1)) then >>> v(1)=2d0 >>> call MatSetValues(A,1,idxn,1,idxm, v,INSERT_VALUES,ierr) >>> end if >>> call MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY,ierr) >>> call MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY,ierr) >>> >>> if ((idxn(1).ge.nl1).and.(idxn(1).le.nl2-1)) then >>> v(1)=2d0 >>> call MatGetValues(A,1,idxn,1,idxm, v,ierr) >>> write(6,*) v >>> end if >>> >>> call PetscFinalize(ierr) >>> >>> end program newnonzero >>> >>> >>> >>> $ mpiexec.hydra -n 3 ./a.out >>> [0]PETSC ERROR: --------------------- Error Message >>> -------------------------------------------------------------- >>> [0]PETSC ERROR: Argument out of range >>> [0]PETSC ERROR: Inserting a new nonzero at global row/column (0, 2) into >>> matrix >>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for >>> trouble shooting. >>> [0]PETSC ERROR: Petsc Release Version 3.9.2, May, 20, 2018 >>> [0]PETSC ERROR: ./a.out on a named tono-hpc1 by marius Wed May 30 09:42:40 >>> 2018 >>> [0]PETSC ERROR: Configure options --prefix=/home/marius/prog/petsc/3.9.2 >>> --download-elemental=yes --download-metis=yes --download-parmetis=yes >>> --download-mumps=yes >>> --with-scalapack-lib="/home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a >>> -Wl,--start-group >>> /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_intel_lp64.a >>> >>> /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_sequential.a >>> >>> /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_core.a >>> >>> /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a >>> -Wl,--end-group -lpthread -lm -ldl" --FC=mpiifort --CC=mpicc --CXX=mpicxx >>> --with-scalar-type=complex --with-mpi-dir= >>> --with-blaslapack-lib="/home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a >>> -Wl,--start-group >>> /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_intel_lp64.a >>> >>> /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_sequential.a >>> >>> /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_core.a >>> >>> /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a >>> -Wl,--end-group -lpthread -lm -ldl" --with-cxx-dialect=C++11 >>> --download-superlu_dist=yes --download-ptscotch=yes --with-x >>> --with-debugging=1 --download-superlu=yes --with-mkl_cpardiso=1 >>> --with-mkl_pardiso=1 --with-scalapack=1 >>> [0]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 607 in >>> /home/marius/prog/petsc/petsc-3.9.2/src/mat/impls/aij/mpi/mpiaij.c >>> [0]PETSC ERROR: #2 MatSetValues() line 1312 in >>> /home/marius/prog/petsc/petsc-3.9.2/src/mat/interface/matrix.c >>> (0.000000000000000E+000,0.000000000000000E+000) >>> >>> >>> >>> Please send complete error message; type of matrix used etc. Ideally code >>> that demonstrates the problem. >>> >>> Barry >>> >>> >>>> On May 29, 2018, at 3:31 AM, Marius Buerkle <[email protected]> wrote: >>>> >>>> >>>> Hi, >>>> >>>> I tried to set MAT_NEW_NONZERO_LOCATIONS to false, as far as I understood >>>> MatSetValues should simply ignore entries which would give rise to new >>>> nonzero values not creating a new entry and not cause an error, but I get >>>> "[1]PETSC ERROR: Inserting a new nonzero at global row/column". Is this >>>> option supposed to work or not? >>> >> >>
