[petsc-users] MatCopy question

Junchao Zhang junchao.zhang at gmail.com
Thu Sep 26 13:36:27 CDT 2024 

No, Setting a bigger matrix size won't have a negative impact.  Only the
actual number of nonzeros matters.

--Junchao Zhang


On Thu, Sep 26, 2024 at 1:33 PM Frank Bramkamp <bramkamp at nsc.liu.se> wrote:

> Thanks for the reply,
>
> when setting the size larger than needed, would that have any negative
> impact somewhere else ?!
> We typically pre-determine how many non-zero elements are present, when
> using MatCreate.
>
> Then, the smaller size needs the same memory as the larger matrix ?!
>
> Thanks, Frank
>
>
>
>
> On 26 Sep 2024, at 20:27, Junchao Zhang <junchao.zhang at gmail.com> wrote:
>
> Is it possible to set the size of the COMPACT matrix as large as the WIDE
> matrix, then do MatAYPX(WIDE, 0, COMPACT, SUBSET_NONZERO_PATTERN), i.e,
> WIDE = 0*WIDE + COMPACT?  You need to build WIDE upfront once, but if you
> repeat, the other MatAYPX will be fast.
>
> --Junchao Zhang
>
>
> On Thu, Sep 26, 2024 at 1:13 PM Barry Smith <bsmith at petsc.dev> wrote:
>
>>
>>   Frank,
>>
>>    Sorry for the confusion. MatCopy() and MatAXPY() only work for
>> identically sized matrices.
>>
>>    Even if the two matrices are the same size but one, say A, has a
>> subset of nonzeros than the other, say B, what you want to do is
>> non-trivial. This is because to do a copy you must MatAssembly the matrix
>> first and this squeezes out the zero locations that you would like to fill
>> in B.
>>
>>    A simple solution is in the code that computes the subset of entries,
>> call MatSetValues() twice, once for A and once for B. Not entirely
>> satisfying but it will work and be reasonably efficient.
>>
>>
>>   Barry
>>
>>
>> > On Sep 26, 2024, at 1:50 PM, Frank Bramkamp <bramkamp at nsc.liu.se>
>> wrote:
>> >
>> > Dear PETSc team,
>> >
>> >
>> > I would like to create two matrices. The first matrix is based on a
>> compact stencil (COMPACT), and the second one has an extended stencil (WIDE)
>> > So the non-zero elements of the  COMPACT matrix is contained in the
>> WIDE matrix as well. But the WIDE matrix shall contain some additional
>> elements.
>> > I try to create the COMPACT matrix first, then copy it to the WIDE
>> matrix and then add some more terms to the WIDE matrix.
>> > We want to create a matrix that is based on a lower order approximation
>> of our scheme which serves as basis matrix for preconditioning,
>> > where we want to have a more accurate jacobian which has a larger
>> stencil, that is based on the lower approximation plus some additional
>> non-zero elements.
>> > We want to avoid that we have to call the same routines twice to setup
>> the more accurate matrix, but copy the elements from the lower order
>> (compact) matrix.
>> >
>> >
>> > I try to use MatCopy to copy the COMPACT matrix into the WIDE matrix.
>> Somehow I cannot figure out to do this,
>> > since there is always a problem wirh non conforming sizes
>> >
>> > [0]PETSC ERROR: Nonconforming object sizes
>> > [0]PETSC ERROR: Mat A,Mat B: global dim (4,8) (4,8)
>> >
>> >
>> > Here is a basic example that I try.
>> > Adding additional elements to the WIDE matrix is disabled right now,
>> since MatCopy already gives a problem.
>> > I thought that in MatCopy(COMPACT, WIDE, DIFFERENT_NONZERO_PATTERN,
>> ierr)
>> > the option DIFFERENT_NONZERO_PATTERN should enable to copy different
>> matrix sizes into each other.
>> > Or is that not possible to do ?!
>> >
>> > Here the COMPACT matrix is a 4x4 matrix and the WIDE matrix 8x8, for a
>> basic test.
>> >
>> > Thanks, Frank Bramkamp
>> >
>> >
>> >
>> >
>> > program petsc_matrix_example
>> > #include <petsc/finclude/petsc.h>
>> >  use petsc
>> >  implicit none
>> >
>> >  PetscErrorCode :: ierr
>> >  Mat :: COMPACT, WIDE
>> >  PetscInt :: m, n, MM, NN, d_nz
>> >  PetscInt :: i, j
>> >  PetscScalar :: additional_value
>> >
>> > ! Initialize PETSc
>> >  call PetscInitialize(PETSC_NULL_CHARACTER, ierr)
>> >
>> > ! Set dimensions for COMPACT matrix
>> >  m = 4  ! Local rows
>> >  n = 4  ! Local columns
>> >  MM = 4  ! Global rows
>> >  NN = 4  ! Global columns
>> >  d_nz = 4 ! Estimated non-zeros per row (diagonal) o_nz = 0 ! Estimated
>> non-zeros per row (off-diagonal)
>> >
>> > ! Create COMPACT matrix
>> >  call MatCreateSeqAIJ(PETSC_COMM_SELF, MM, NN, PETSC_DECIDE,
>> PETSC_NULL_INTEGER, COMPACT, ierr)
>> >
>> > ! Set some values in COMPACT matrix (example) do i = 0, M-1
>> >  do i = 0, NN-1
>> >     !do j = max(0, i-1), min(NN-1, i+1)
>> >     do j = 0,NN-1
>> >      call MatSetValue(COMPACT, i, j, 1.0_PETSC_REAL_KIND,
>> INSERT_VALUES, ierr)
>> >    end do
>> >  end do
>> >
>> > ! Assemble COMPACT matrix
>> >  call MatAssemblyBegin(COMPACT, MAT_FINAL_ASSEMBLY, ierr)
>> >  call MatAssemblyEnd(COMPACT, MAT_FINAL_ASSEMBLY, ierr)
>> >
>> > ! Set dimensions for WIDE matrix
>> >  n = 8  ! Increase local columns
>> >  NN = 8  ! Increase global columns
>> >  m  = 8
>> >  MM = 8
>> >  d_nz = 8
>> >
>> > ! Create WIDE matrix
>> >  call MatCreateSeqAIJ(PETSC_COMM_SELF, MM, NN, PETSC_DECIDE,
>> PETSC_NULL_INTEGER, WIDE, ierr)
>> >
>> >  ! Assemble WIDE matrix: MUST WE ASSMBLE THE MATRIX BEFORE MatCOPY ?!
>> >  call MatAssemblyBegin(WIDE, MAT_FINAL_ASSEMBLY, ierr)
>> >  call MatAssemblyEnd(WIDE, MAT_FINAL_ASSEMBLY, ierr)
>> >
>> > ! Copy elements from COMPACT to WIDE
>> >  call MatCopy(COMPACT, WIDE, DIFFERENT_NONZERO_PATTERN, ierr)
>> >
>> >
>> >
>> >  !call MatAssemblyBegin(WIDE, MAT_FINAL_ASSEMBLY, ierr)
>> >
>> >  ! Add additional elements to WIDE matrix
>> > !!$  additional_value = 10.0
>> > !!$
>> > !!$  ! original
>> > !!$  !do i = 0, MM-1
>> > !!$  !  do j = NN/2, NN-1
>> > !!$  !    call MatSetValue(WIDE, i, j, additional_value, INSERT_VALUES,
>> ierr)
>> > !!$  !  end do
>> > !!$ !end do
>> > !!$
>> > !!$  do i = 0, NN-1
>> > !!$    do j = max(0, i-1), min(NN-1, i+1)
>> > !!$      call MatSetValue(WIDE, i, j, 10.0_PETSC_REAL_KIND, ADD_VALUES,
>> ierr)
>> > !!$    end do
>> > !!$  end do
>> >
>> >
>> > ! Assemble WIDE matrix again
>> >  call MatAssemblyBegin(WIDE, MAT_FINAL_ASSEMBLY, ierr)
>> >  call MatAssemblyEnd(WIDE, MAT_FINAL_ASSEMBLY, ierr)
>> >
>> > ! View matrices (optional)
>> >  call PetscPrintf(PETSC_COMM_WORLD, "COMPACT matrix:\n", ierr)
>> >  call MatView(COMPACT, PETSC_VIEWER_STDOUT_WORLD, ierr)
>> >  call PetscPrintf(PETSC_COMM_WORLD, "WIDE matrix:\n", ierr)
>> >  call MatView(WIDE, PETSC_VIEWER_STDOUT_WORLD, ierr)
>> >
>> > ! Clean up
>> >  call MatDestroy(COMPACT, ierr)
>> >  call MatDestroy(WIDE, ierr)
>> >
>> > ! Finalize PETSc
>> >  call PetscFinalize(ierr)
>> >
>> > end program petsc_matrix_example
>> >
>> >
>>
>>
>
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