[petsc-users] MAT_NEW_NONZERO_LOCATIONS working?

Thu May 31 11:25:05 CDT 2018

  Hong,

    Can you see about adding support for distributed right hand side?

    Thanks

      Barry


> On May 31, 2018, at 2:37 AM, Marius Buerkle <mbuerkle at web.de> wrote:
> 
> 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?
>>>> 
>>> 
>>> 
>