[Numpy-discussion] Large symmetrical matrix

Bruce Southey bsouthey@gmail....
Wed Jun 11 12:12:23 CDT 2008


Charles R Harris wrote:
>
>
> On Wed, Jun 11, 2008 at 9:33 AM, Simon Palmer <simon.palmer@gmail.com 
> <mailto:simon.palmer@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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