[R] Computing very large distance matrix
Prof Brian Ripley
ripley at stats.ox.ac.uk
Wed Feb 25 20:12:25 CET 2004
On Wed, 25 Feb 2004, Arnav Sheth wrote:
> Hello All,
> I have a 131072x132 matrix for which I need to compute a regular euclidean distance matrix, which I then need to transform and run agnes() on this transformed matrix. I am having trouble computing the distance matrix as it is fairly large and I am sure I have gone over the max.
> The specific error I am getting is:
> Error in vector("double", length) : negative length vectors are not allowed
We've improved that message for the next release.
> I have increased the memory limit to the maximum capacity of my hard
> drive (which is around 20gb), with no success.
You'd need to increase the 32-bit limit of Windows, too ....
> I am running the RGUI on Windows XP with 512 mb of RAM.
> Would anyone have any suggestions as to how I can overcome this problem?
> I would be most grateful for any help.
No. The distance matrix is 8Gb all by itself.
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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