slow access to consecutive matrix elements

[Jaroslav Hajek]

On Sat, Oct 11, 2008 at 10:22 AM, Francesco Potorti`
<Potorti at isti.cnr.it> wrote:
> This is a real life example that demonstrates how access to matrix
> elements is not optimised for the case of complete ranges in the first
> dimensions.  I am sending it here and not to the bug list because this
> example may be useful to others, at least until this cases is optimised
> in the sources.
>
> # This is a big 5-dim matrix, about 100MB size
> octave> kk=rand(156,222,1,44,8);
>
> # I access a slice of it, which is sequential in memory
> octave> t=cputime; for ii=1:44, for jj=1:8
>  mm=kk(:,:,:,ii,jj); endfor, endfor, cputime-t
> ans =  5.9124
>
> # Using a linear index is much faster
> octave> span=(1:156*222);
>        t=cputime; for ii=1:44, for jj=1:8
>  mm=kk(sub2ind(size(kk),1,1,1,ii,jj)+span-1); endfor, endfor, cputime-t
> ans =  2.6642
>
> # Removing the call to sub2ind reaches top speed
> octave> cp=[1,cumprod(size(kk)(1:end-1))]; span=(1:156*222);
>        t=cputime; for ii=1:44, for jj=1:8
>  mm=kk(sum(([1,1,1,ii,jj]-1).*cp)+span); endfor, endfor, cputime-t
> ans =  1.4001
>
> Still, I wish access were faster yet.  Is there a reason why copying
> consecutive memory is so slow?  I wish I could help with optimising
> this, even if I am certainly not the most qualified person to do it.
>

I guess the indexing routines do deserve some attention w.r.t
performance. Reducing code duplication would also be nice. I have this
on my TODO list, but I don't think it's a good idea to do it before
3.2.x is forked, as such changes are, IMO, likely to introduce bugs.


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-- 
RNDr. Jaroslav Hajek
computing expert
Aeronautical Research and Test Institute (VZLU)
Prague, Czech Republic
url: www.highegg.matfyz.cz