[petsc-users] MAT_NEW_NONZERO_LOCATIONS working?

Wed May 30 19:07:42 CDT 2018

> 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?
>>> 
>> 
>> 