[Numpy-discussion] Large symmetrical matrix
Bruce Southey
bsouthey at gmail.com
Wed Jun 11 13:12:23 EDT 2008
Charles R Harris wrote:
>
>
> On Wed, Jun 11, 2008 at 9:33 AM, Simon Palmer <simon.palmer at gmail.com
> <mailto:simon.palmer at gmail.com>> wrote:
>
> Pretty simple. I don't do any transformations. It is a euclidean
> distance matrix between n vectors in my data space, so I use it
> for lookup of minima and I recalculate portions of it during the
> processing of my algorithm.
>
> It is the single largest limitation of my code, both in terms of
> performance and scalability. A fast and efficient solution to
> this issue would make a huge difference to me.
>
>
> So are you doing hierarchical clustering?
>
> Chuck
>
>
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Lapack supports symmetric matrices (http://en.wikipedia.org/wiki/LAPACK)
but, to my knowledge, these are not implemented in SciPy (and I am not
sure if sparse will help). So you have the memory penalty or
performance penalty unless you create the bindings necessary that you need.
Bruce
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