Run out of memory
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 matrix.
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 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._