[R] Run out of memory

Prof Brian D Ripley ripley at stats.ox.ac.uk
Mon Apr 2 23:45:41 CEST 2001

On Mon, 2 Apr 2001, Hongli Li wrote:

> I am trying to use R to cluster 7129 samples, my data set is a 7129 x 38
matrix,  when I trying to get the distance matrix using function dist( ), the
memory exhausted, and I tried to set the memory when I run R by
> R --vsize=250M --nsize=1000k

That's not the way to do it in recent versions of R.

> no matter what I set for vsize the result is the same, it says:
> Error: heap memory (256000kb) exhausted [need 198498Kb more]
>                                                                         (this
doesn't change)
> What can I do to solve this?

Upgrade your R and your computer's RAM?   To store the result needs
200Mb on my calculation, and then you need to do something with it.
It worked in about 5 minutes and 400Mb on a 1Gb 600MHz Linux machine.

However, what are you then going to do with this?  Hierarchical clustering
on 7000 points is not very sensible, and kmeans does not need a distance

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 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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