[petsc-users] MatCreateSBAIJ

[Sam Guo]

I am most interested in how the lower triangular part is redistributed. It
seems that SBAJI saves memory but requires more communication than BAIJ.

On Mon, Mar 21, 2022 at 11:27 AM Sam Guo <sam.guo at cd-adapco.com> wrote:

> Mark, thanks for the quick response. I am more interested in parallel
> implementation of MatMult for SBAIJ. I found following
>
> 1094: *PetscErrorCode <https://petsc.org/main/docs/manualpages/Sys/PetscErrorCode.html#PetscErrorCode> MatMult_MPISBAIJ(Mat <https://petsc.org/main/docs/manualpages/Mat/Mat.html#Mat> A,Vec <https://petsc.org/main/docs/manualpages/Vec/Vec.html#Vec> xx,Vec <https://petsc.org/main/docs/manualpages/Vec/Vec.html#Vec> yy)*1095: {1096:   Mat_MPISBAIJ      *a = (Mat_MPISBAIJ*)A->data;1097:   PetscErrorCode <https://petsc.org/main/docs/manualpages/Sys/PetscErrorCode.html#PetscErrorCode>    ierr;1098:   PetscInt <https://petsc.org/main/docs/manualpages/Sys/PetscInt.html#PetscInt>          mbs=a->mbs,bs=A->rmap->bs;1099:   PetscScalar <https://petsc.org/main/docs/manualpages/Sys/PetscScalar.html#PetscScalar>       *from;1100:   const PetscScalar <https://petsc.org/main/docs/manualpages/Sys/PetscScalar.html#PetscScalar> *x;
> 1103:   /* diagonal part */1104:   (*a->A->ops->mult)(a->A,xx,a->slvec1a);1105:   VecSet <https://petsc.org/main/docs/manualpages/Vec/VecSet.html#VecSet>(a->slvec1b,0.0);
> 1107:   /* subdiagonal part */1108:   (*a->B->ops->multtranspose)(a->B,xx,a->slvec0b);
> 1110:   /* copy x into the vec slvec0 */1111:   VecGetArray <https://petsc.org/main/docs/manualpages/Vec/VecGetArray.html#VecGetArray>(a->slvec0,&from);1112:   VecGetArrayRead <https://petsc.org/main/docs/manualpages/Vec/VecGetArrayRead.html#VecGetArrayRead>(xx,&x);
> 1114:   PetscArraycpy <https://petsc.org/main/docs/manualpages/Sys/PetscArraycpy.html#PetscArraycpy>(from,x,bs*mbs);1115:   VecRestoreArray <https://petsc.org/main/docs/manualpages/Vec/VecRestoreArray.html#VecRestoreArray>(a->slvec0,&from);1116:   VecRestoreArrayRead <https://petsc.org/main/docs/manualpages/Vec/VecRestoreArrayRead.html#VecRestoreArrayRead>(xx,&x);
> 1118:   VecScatterBegin <https://petsc.org/main/docs/manualpages/PetscSF/VecScatterBegin.html#VecScatterBegin>(a->sMvctx,a->slvec0,a->slvec1,ADD_VALUES <https://petsc.org/main/docs/manualpages/Sys/ADD_VALUES.html#ADD_VALUES>,SCATTER_FORWARD <https://petsc.org/main/docs/manualpages/Vec/SCATTER_FORWARD.html#SCATTER_FORWARD>);1119:   VecScatterEnd <https://petsc.org/main/docs/manualpages/PetscSF/VecScatterEnd.html#VecScatterEnd>(a->sMvctx,a->slvec0,a->slvec1,ADD_VALUES <https://petsc.org/main/docs/manualpages/Sys/ADD_VALUES.html#ADD_VALUES>,SCATTER_FORWARD <https://petsc.org/main/docs/manualpages/Vec/SCATTER_FORWARD.html#SCATTER_FORWARD>);1120:   /* supperdiagonal part */1121:   (*a->B->ops->multadd)(a->B,a->slvec1b,a->slvec1a,yy);1122:   return(0);1123: }
>
>   I try to understand the algorithm.
>
>
> Thanks,
>
> Sam
>
>
> On Mon, Mar 21, 2022 at 11:14 AM Mark Adams <mfadams at lbl.gov> wrote:
>
>> This code looks fine to me and the code is
>> in src/mat/impls/sbaij/seq/sbaij2.c
>>
>> On Mon, Mar 21, 2022 at 2:02 PM Sam Guo <sam.guo at cd-adapco.com> wrote:
>>
>>> Dear PETSc dev team,
>>>    The documentation about MatCreateSBAIJ has following
>>> "It is recommended that one use the MatCreate
>>> <https://petsc.org/main/docs/manualpages/Mat/MatCreate.html#MatCreate>
>>> (), MatSetType
>>> <https://petsc.org/main/docs/manualpages/Mat/MatSetType.html#MatSetType>()
>>> and/or MatSetFromOptions
>>> <https://petsc.org/main/docs/manualpages/Mat/MatSetFromOptions.html#MatSetFromOptions>(),
>>> MatXXXXSetPreallocation() paradigm instead of this routine directly.
>>> [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation
>>> <https://petsc.org/main/docs/manualpages/Mat/MatSeqAIJSetPreallocation.html#MatSeqAIJSetPreallocation>
>>> ]"
>>>    I currently call MatCreateSBAIJ directly as follows:
>>> MatCreateSBAIJ (with d_nnz and o_nnz)
>>> MatSetValues (to add row by row)
>>> MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
>>> MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
>>> MatSetOption(A, MAT_SYMMETRIC, PETSC_TRUE);
>>>
>>>    Two questions:
>>>    (1) I am wondering whether what I am doing is the most efficient.
>>>
>>>    (2) I try to find out how the matrix vector multiplication is
>>> implemented in PETSc for SBAIJ storage.
>>>
>>> Thanks,
>>> Sam
>>>
>>
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