[petsc-users] MatCreateBAIJ, SNES, Preallocation...

[Mark Adams]

Oh, this is BAIJ. Sure.

On Fri, May 17, 2019 at 11:01 AM Smith, Barry F. <bsmith at mcs.anl.gov> wrote:

>
>   BAIJ and SBAIJ it is the number of block rows, so the row sizes divided
> by the bs. For AIJ the number of rows.
>
> > On May 17, 2019, at 9:55 AM, William Coirier <
> William.Coirier at kratosdefense.com> wrote:
> >
> > Mark:
> >
> > Should the size of d_nnz and o_nnz be the number of rows accessed on
> this processor or the number of block rows?
> > ________________________________________
> > From: Smith, Barry F. [bsmith at mcs.anl.gov]
> > Sent: Friday, May 17, 2019 9:15 AM
> > To: Mark Adams
> > Cc: William Coirier; petsc-users at mcs.anl.gov; Michael Robinson; Andrew
> Holm
> > Subject: Re: [petsc-users] MatCreateBAIJ, SNES, Preallocation...
> >
> >  I don't understand. For BAIJ and SBAIJ it is the number of block
> nonzeros in the two parts of the matrix. It is not the number of nonzeros
> per row.
> > For Mat[MPI]AIJSetPreallocation() it is the number of nonzeros (even if
> a block size has been set) because for AIJ matrices the block size does not
> affect the storage of the matrix and it is merely informative.
> >
> >   For MatXAIJSetPreallocation() however (which can be used with AIJ,
> BAIJ, and SBAIJ) the nonzero blocks are for all three matrix formats.
> MatXAIJSetPreallocation is a convenience function that allows the user to
> avoid needing to allocate three sets of arrays and fill them up separately
> for each of the AIJ, BAIJ, and SBAIJ formats.
> >
> >   Is everything now clear, if not please feel free to ask more specific
> questions to clarify.
> >
> >  Barry
> >
> >> On May 17, 2019, at 6:16 AM, Mark Adams <mfadams at lbl.gov> wrote:
> >>
> >>
> >>
> >> On Thu, May 16, 2019 at 6:28 PM William Coirier via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
> >> Ok, got it. My misinterpretation was how to fill the d_nnz and o_nnz
> arrays.
> >>
> >> Thank you for your help!
> >>
> >> Might I make a suggestion related to the documentation? Perhaps I have
> not fully read the page on the MatMPIBAIJSetPreallocation so you can simply
> disregard and I'm ok with that! The documentation has for the d_nnz:
> >>
> >> d_nnz   - array containing the number of block nonzeros in the various
> block rows of the in diagonal portion of the local (possibly different for
> each block row) or NULL. If you plan to factor the matrix you must leave
> room for the diagonal entry and set it even if it is zero.
> >>
> >> Am I correct in that this array should be of size numRows, where
> numRows is found from  calling MatGetOwnershipRange(J,&iLow,&iHigh) so
> numRows=iHigh-iLow.
> >>
> >> yes, this interface does not change if you set the block size or not.
> It is at the equation level.
> >>
> >>
> >> I think my error was allocating this only to be numRows/bs since I
> thought it's a block size thing.
> >>
> >>
> >> This documentation looks wrong to me, and at least confusing. "number
> of block nonzeros" reads wrong to me. We now have:
> >>
> >> d_nz- number of block nonzeros per block row in diagonal portion of
> local submatrix (same for all local rows)
> >> d_nnz- array containing the number of block nonzeros in the various
> block rows of the in diagonal portion of the local (possibly different for
> each block row) or NULL. If you plan to factor the matrix you must leave
> room for the diagonal entry and set it even if it is zero.
> >> o_nz- number of block nonzeros per block row in the off-diagonal
> portion of local submatrix (same for all local rows).
> >> o_nnz- array containing the number of nonzeros in the various block
> rows of the off-diagonal portion of the local submatrix (possibly different
> for each block row) or NULL.
> >>
> >> I can suggest:
> >>
> >> d_nz- number of nonzeros per row in diagonal portion of local submatrix
> (same for all local rows)
> >> d_nnz- array containing the number of nonzeros in each row of the
> diagonal portion of the local matrix (the same for each row within a block)
> or NULL. You must have a diagonal entry and set it even if it is zero if
> you plan to factor the matrix.
> >> o_nz- number of nonzeros per row in the off-diagonal portion of local
> submatrix (same for all local rows).
> >> o_nnz- array containing the number of nonzeros in each row of the
> off-diagonal portion of the local submatrix (the same for each row within a
> block) or NULL.
> >>
> >> I can change this if this is acceptable.
> >
>
>
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