[petsc-users] questions about matrix preallocation

[Jed Brown]

On Thu, Nov 24, 2011 at 07:46, Dominik Szczerba <dominik at itis.ethz.ch>wrote:

> Yes, that is true, but 1) within the overshot preallocation margin 2)
> I do it at each execution of the loop, so I do not see why only the
> second time there are mallocs. I display mallocs directly before
> KSPSolve().
>

The matrix is compacted. The implementation
(MatSeqAIJSetPreallocation_SeqAIJ) could be changed to analyze the newly
prescribed preallocation relative to the old allocation and determine that
it can fit within the old storage. The problem here is that someone might
specifically preallocate smaller because they want to free the old storage.
So maybe we should just recognize an exact match, but what if the user
called MatCreateMPIAIJWithSplitArrays() (so they still own the arrays) and
they are calling this preallocation routine because they want to reuse the
arrays for something else?

If we can settle on some understandable semantics for when freeing and
reallocating makes sense, then we can put it in.

Or you could insert zeros into those locations that might be used later.


>
> > I suggest assembling all possible entries (even the ones that happen to
> be
> > zero) in the first assembly. Then there will be space and you can reuse
> the
> > data structure.
>
> This will require a bigger change in my code. Is always calling
> MatMPIAIJSetPreallocation a bad (inefficient) alternative?
>

Depends on the availability of memory, but probably not. Always profile.
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