[petsc-users] DAGetMatrix with extra nonzeros: memory preallocation

[Jed Brown]

On Sat, Sep 10, 2011 at 12:36, Mohamad M. Nasr-Azadani <mmnasr at gmail.com>wrote:

> I am setting up a matrix (parallel) using DA's in 3D.
> DA is built upon a width=1, STAR_STENCIL type.
> The nonzero structure of the resulting matrix is hepta-diagonal for the
> most part, however, since I am imposing boundary conditions using
> interpolation methods, for some boundary nodes, it is possible that some
> extra nonzeros are added into new locations.
> This obviously reduces the matrix setup and assembly efficiency since the
> new nonzeros are not preallocated.
> Is there any way that I could do it myself, i.e. preallocate the new
> nonzeros before matrix setup to get the best performance?
>

Unfortunately there is not a convenient way to express this such that
DMGetMatrix() will preallocate for those entries. You can preallocate your
own matrix without calling DMGetMatrix(). It's not very hard for a stencil
width of 1 with STAR, but it is still some code to write.
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