The current version of the MUMPS code in PETSc supports sparse right hand sides for sequential solvers. You can call MatMatSolve(A,X,B) with B of type MATTRANSPOSE, with the inner matrix being a MATSEQAIJ
2018-05-31 10:37 GMT+03:00 Marius Buerkle <[email protected]>: > 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? > >>> > >> > >> > > -- Stefano
