Because I completely forgot that this option existed, and the LLM didn't save
me from embarrassing myself.
I see that this option sets mat->force_diagonals, but this variable is never
used in the mat assembly routines, meaning it will not help in this situation.
Presumably, MatAssemblyXXX_YYY() could/should be fixed to respect this flag?
Then it would help the Olivier.
Barry
> On Jun 27, 2025, at 7:49 AM, Pierre Jolivet <pie...@joliv.et> wrote:
>
>
>
>> On 27 Jun 2025, at 1:33 PM, Barry Smith <bsm...@petsc.dev> wrote:
>>
>>
>>
>> Handling empty diagonal entries on matrices is often problematic, just as
>> you describe.
>>
>> I suggest placing explicit zeros on the diagonal first before providing
>> the other entries, which might be the cleanest and most efficient approach.
>> So have each MPI rank loop over its local rows and call MatSetValue() for
>> each diagonal entry and then continue with your other MatSetValues(). Do not
>> call MatAssemblyBegin/End() after you have provided the zeros on the
>> diagonal just chug straight into setting the other values.
>>
>> Barry
>>
>> As you observed, trying to add the zero entries in the matrix after it is
>> assembled is terribly inefficient and not the way to go.
>>
>> I've considered adding a matrix option to force zero entries on the
>> diagonal, but I never completed my consideration. For example,
>> MatSetOption(A, MAT_NONEMPTY_DIAGONAL,PETSC_TRUE);
>
> Why would you need another option when there is already
> MAT_FORCE_DIAGONAL_ENTRIES?
>
> Thanks,
> Pierre
>
>> and when this option is set, MatAssemblyBegin fills up any empty diagonal
>> entries automatically.
>>
>>
>>
>>> On Jun 27, 2025, at 6:26 AM, JAMOND Olivier <olivier.jam...@cea.fr> wrote:
>>>
>>> Hello,
>>>
>>> I am working on a PDE solver which uses petsc to solve its sparse
>>> distributed linear systems. I am mainly dealing with MPIAIJ matrices.
>>>
>>> In some situations, it may happen that the matrices considered does not
>>> have non-zero term on the diagonal. For instance I work on a case which
>>> have a stokes like saddle-point structure (in a MPIAIJ, not a MATNEST):
>>>
>>> [A Bt][U]=[F]
>>> [B 0 ][L] [0]
>>>
>>> I do not insert null terms in the zero block.
>>>
>>> In some cases, I use the function `MatZeroRowsColumns` to handle
>>> "Dirichlet" boundary conditions. In this particular case, I apply Dirichlet
>>> BCs only on dofs of "U". But I get an error `Matrix is missing diagonal
>>> entry in row X` from the function `MatZeroRowsColumns`, where X is a row
>>> related to "L".
>>>
>>> My first question is: is it normal that I get an error for a missing
>>> diagonal in the function `MatZeroRowsColumns`entry for a dof that is not
>>> involved in the list of dofs that I pass to `MatZeroRowsColumns`?
>>>
>>> I then tried to make my code to detect that there are some missing diagonal
>>> entries, and add an explicit zero to them. My code which adds the missing
>>> diagonal entries looks like what follows. This is certainly not the best
>>> way to do that, as in my test case about ~80% of the total computation time
>>> is spent in this piece of code (more precisely in `MatSetValue(D, k, k, 0.,
>>> ADD_VALUES)`).
>>> So my second question is: what would be the most efficient way to detect
>>> the missing diagonal entries, and ad explicit zeros on the diagonal at
>>> these places?
>>>
>>> Many thanks,
>>> Olivier
>>>
>>> ...
>>> MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
>>> MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
>>>
>>> Mat D;
>>> MatGetDiagonalBlock(A, &D);
>>>
>>> PetscBool missing;
>>> MatMissingDiagonal(D, &missing, NULL);
>>>
>>> if (missing) {
>>>
>>> IS missingDiagEntryRows;
>>> MatFindZeroDiagonals(D, &missingDiagEntryRows)
>>>
>>> PetscInt size;
>>> ISGetLocalSize(missingDiagEntryRows, &size);
>>> const PetscInt *ptr;
>>> ISGetIndices(missingDiagEntryRows, &ptr);
>>>
>>> for (Index i = 0; i < size; ++i) {
>>> PetscInt k = ptr[i];
>>> MatSetValue(D, k, k, 0., ADD_VALUES);
>>> }
>>> MatAssemblyBegin(D, MAT_FINAL_ASSEMBLY);
>>> MatAssemblyEnd(D, MAT_FINAL_ASSEMBLY);
>>>
>>> ISRestoreIndices(missingDiagEntryRows, &ptr);
>>> }
>>>
>>>
>>> _________________________________________
>>> Olivier Jamond
>>> Research Engineer
>>> French Atomic Energy and Alternative Energies Commission
>>> DES/ISAS/DM2S/SEMT/DYN
>>> 91191 Gif sur Yvette, Cedex, France
>>> Email: olivier.jamond <mailto:olivier.jam...@cea.fr>@cea.fr
>>> <mailto:olivier.jam...@cea.fr> Phone: +336.78.18.18.25
>>
