[petsc-users] MatZeroRows changes my sparsity pattern

[Alexander Lindsay]

On Thu, Jul 15, 2021 at 8:46 AM Fande Kong <fdkong.jd at gmail.com> wrote:

> "if (a->keepnonzeropattern)" branch does not change ilen so that
> A->ops->assemblyend will be fine. It would help if you made sure that
> elements have been inserted for these rows before you call MatZeroRows.
>

So this is the crux of the problem. In ex11 let's say that I had not insert
a value at (0,5) but I know I'm going to later and I've preallocated the
space for it. MatZeroValues will erase that preallocation with its call to
MatAssemblyEnd with MAT_FINAL_ASSEMBLY regardless of the value of
keepnonzeropattern.


> However, I am not sure it is necessary to call  A->ops->assemblyend if we
> already require a->keepnonzeropattern. That being said, we might have
> something like this
>
>
> *diff --git a/src/mat/impls/aij/seq/aij.c b/src/mat/impls/aij/seq/aij.c*
>
> *index 42c93a82b1..3f20a599d6 100644*
>
> *--- a/src/mat/impls/aij/seq/aij.c*
>
> *+++ b/src/mat/impls/aij/seq/aij.c*
>
> @@ -2203,7 +2203,9 @@ PetscErrorCode MatZeroRows_SeqAIJ(Mat A,PetscInt
> N,const PetscInt rows[],PetscSc
>
>  #if defined(PETSC_HAVE_DEVICE)
>
>    if (A->offloadmask != PETSC_OFFLOAD_UNALLOCATED) A->offloadmask =
> PETSC_OFFLOAD_CPU;
>
>  #endif
>
> -  ierr = (*A->ops->assemblyend)(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>
> +  if (!a->keepnonzeropattern) {
>
> +    ierr = (*A->ops->assemblyend)(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>
> +  }
>
>    PetscFunctionReturn(0);
>
>  }
>
>
> Fande
>
> On Thu, Jul 15, 2021 at 9:30 AM Stefano Zampini <stefano.zampini at gmail.com>
> wrote:
>
>> Alexander
>>
>> Do you have a small code to reproduce the issue?
>>
>> Below is the output using a PETSc example (src/mat/tests/ex11). The
>> pattern is kept.
>>
>> kl-18448:tests szampini$ ./ex11
>> Mat Object: 1 MPI processes
>>   type: seqaij
>> row 0: (0, 5.)
>> row 1: (0, -1.)  (1, 4.)  (2, -1.)  (6, -1.)
>> row 2: (2, 5.)
>> row 3: (2, -1.)  (3, 4.)  (4, -1.)  (8, -1.)
>> row 4: (4, 5.)
>> row 5: (0, -1.)  (5, 4.)  (6, -1.)  (10, -1.)
>> row 6: (6, 5.)
>> row 7: (2, -1.)  (6, -1.)  (7, 4.)  (8, -1.)  (12, -1.)
>> row 8: (8, 5.)
>> row 9: (4, -1.)  (8, -1.)  (9, 4.)  (14, -1.)
>> row 10: (10, 5.)
>> row 11: (6, -1.)  (10, -1.)  (11, 4.)  (12, -1.)  (16, -1.)
>> row 12: (12, 5.)
>> row 13: (8, -1.)  (12, -1.)  (13, 4.)  (14, -1.)  (18, -1.)
>> row 14: (14, 5.)
>> row 15: (10, -1.)  (15, 4.)  (16, -1.)  (20, -1.)
>> row 16: (16, 5.)
>> row 17: (12, -1.)  (16, -1.)  (17, 4.)  (18, -1.)  (22, -1.)
>> row 18: (18, 5.)
>> row 19: (14, -1.)  (18, -1.)  (19, 4.)  (24, -1.)
>> row 20: (20, 5.)
>> row 21: (16, -1.)  (20, -1.)  (21, 4.)  (22, -1.)
>> row 22: (22, 5.)
>> row 23: (18, -1.)  (22, -1.)  (23, 4.)  (24, -1.)
>> row 24: (19, -1.)  (23, -1.)  (24, 4.)
>> kl-18448:tests szampini$ ./ex11 -keep_nonzero_pattern
>> Mat Object: 1 MPI processes
>>   type: seqaij
>> row 0: (0, 5.)  (1, 0.)  (5, 0.)
>> row 1: (0, -1.)  (1, 4.)  (2, -1.)  (6, -1.)
>> row 2: (1, 0.)  (2, 5.)  (3, 0.)  (7, 0.)
>> row 3: (2, -1.)  (3, 4.)  (4, -1.)  (8, -1.)
>> row 4: (3, 0.)  (4, 5.)  (9, 0.)
>> row 5: (0, -1.)  (5, 4.)  (6, -1.)  (10, -1.)
>> row 6: (1, 0.)  (5, 0.)  (6, 5.)  (7, 0.)  (11, 0.)
>> row 7: (2, -1.)  (6, -1.)  (7, 4.)  (8, -1.)  (12, -1.)
>> row 8: (3, 0.)  (7, 0.)  (8, 5.)  (9, 0.)  (13, 0.)
>> row 9: (4, -1.)  (8, -1.)  (9, 4.)  (14, -1.)
>> row 10: (5, 0.)  (10, 5.)  (11, 0.)  (15, 0.)
>> row 11: (6, -1.)  (10, -1.)  (11, 4.)  (12, -1.)  (16, -1.)
>> row 12: (7, 0.)  (11, 0.)  (12, 5.)  (13, 0.)  (17, 0.)
>> row 13: (8, -1.)  (12, -1.)  (13, 4.)  (14, -1.)  (18, -1.)
>> row 14: (9, 0.)  (13, 0.)  (14, 5.)  (19, 0.)
>> row 15: (10, -1.)  (15, 4.)  (16, -1.)  (20, -1.)
>> row 16: (11, 0.)  (15, 0.)  (16, 5.)  (17, 0.)  (21, 0.)
>> row 17: (12, -1.)  (16, -1.)  (17, 4.)  (18, -1.)  (22, -1.)
>> row 18: (13, 0.)  (17, 0.)  (18, 5.)  (19, 0.)  (23, 0.)
>> row 19: (14, -1.)  (18, -1.)  (19, 4.)  (24, -1.)
>> row 20: (15, 0.)  (20, 5.)  (21, 0.)
>> row 21: (16, -1.)  (20, -1.)  (21, 4.)  (22, -1.)
>> row 22: (17, 0.)  (21, 0.)  (22, 5.)  (23, 0.)
>> row 23: (18, -1.)  (22, -1.)  (23, 4.)  (24, -1.)
>> row 24: (19, -1.)  (23, -1.)  (24, 4.)
>>
>> On Jul 15, 2021, at 4:41 PM, Alexander Lindsay <alexlindsay239 at gmail.com>
>> wrote:
>>
>> My interpretation of the documentation page of MatZeroRows is that if
>> I've set MAT_KEEP_NONZERO_PATTERN to true, then my sparsity pattern
>> shouldn't be changed by a call to it, e.g. a->imax should not change.
>> However, at least for sequential matrices, MatAssemblyEnd is called with
>> MAT_FINAL_ASSEMBLY at the end of MatZeroRows_SeqAIJ and that does indeed
>> change my sparsity pattern. Is my interpretation of the documentation page
>> wrong?
>>
>> Alex
>>
>>
>>
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