[petsc-users] MAT_NEW_NONZERO_LOCATIONS working?

Thu May 31 03:21:27 CDT 2018

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 <mbuerkle at web.de>:

> 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 <mbuerkle at web.de> 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 <mbuerkle at web.de> 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 <mbuerkle at web.de> 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
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