[petsc-users] MAT_NEW_NONZERO_LOCATIONS working?

Wed May 30 18:55:16 CDT 2018

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. I think that is normal, right? 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? If so, this did not work for me, even after doing 
MAT_FINAL_ASSEMBLY the unused nonzero allocations remain. Is this normal?

> 
>    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?
> >  
> 
>