Re: Dynamic allocation of Non zeros?

[Zhifeng Sheng <z.sheng@xxxxxxxxxxxxxx>]

Barry Smith wrote:

> Zhifeng,
>
> We already do this; it helps with the time, but still results in very 
> inefficient runs if your preallocation is zero entries.
>
> Perhaps you could describe how your matrix entries are generated and 
> we can suggest a
> preallocation scheme?
>
> Barry
>
>
> On Nov 1, 2007, at 7:52 AM, Zhifeng Sheng wrote:
>
> > Dear all
> >
> > It is always not easy to determine the number of nonzeros in a row 
> > without any cost.
> >
> > I wonder if I can make dynamic allocation, for instance, if one found 
> > the nonzeros of a row overflow the pre-allocated space, then the 
> > space shall be doubled.
> >
> > This may waste some memory but it may not be that bad. Or maybe this 
> > is already done in Petsc?
> >
> > Could please tell what happens if I assign the nozero number in rows 
> > to be zeros and let the programme fills in the nonzeros ?
> >
> > Best regards
> > Zhifeng Sheng
In that case I'd better do some preallocation. I am working on 3D FEM 
code with unstructured tetrahedron mesh, and on each node, we can have 3 
to arround 12 unknowns, at this moment I assigned 50 nonzeros to each 
rows, and it is sufficient... just half of the memory assigned went 
wasted. Then I tried 25 nonzeros in a row, but this is not enough and 
the performance is terrible.

So... do I really need to compute the nonzero pattern?

Ps. my matrix is SeqSBAIJ with block size 1, so I am wondering when I 
specify the nonzeros in a row, does it mean the actually nonzeros 
numbers or the memory that is needed? (for instance, for SeqSBAIJ, the 
actual nonzeros in a row would twice as much as memory needed)

Thank you
Best regards
Zhifeng