Re: [R] 64 bit Linux/Ubuntu memory limit problem?

From: IAIN GALLAGHER <iaingallagher_at_btopenworld.com>
Date: Thu, 24 Apr 2008 14:57:08 +0100 (BST)


Hi Zack.

I don't know how helpful this is but I use R on 64bit ubuntu for the analysis of large microarray datasets. R may well be taking advantage of all your memory but the objects it's creating are too big. You could run 'top' in another terminal window to examine this behaviour. If R is using all your memory then I suppose you'll have to install some more.

Cheers

iain

zack holden <zack_holden_at_hotmail.com> wrote: Dear list,  

I've recently installed R on a 64 bit machine with 8 GB of RAM. I set this computer up as a dual-boot system, with windows XP 64 and Ubuntu 7.10. I downloaded the Linux 64 bit version of R and installed it.  

I'm trying to run rather large Random forest models and was running into severe memory limitations with my old windows 32 bit machines.  

When I run Random Forest models on my new machine, I get the error message: Error: cannot allocate vector of size 2.1 GB.  

I'm a new Linux user, but I thought that R under Linux would by default take advantage of all available memory. I've searched previous posts and found only 1 thread (posted by David Katz) that didn't really help.  

Do I need to specify that the Ubuntu/Linux OS use all 8 Gigs of RAM? Could I have done something wrong when I downloaded and installed R?  

I'd appreciate any advice.  

Thanks in advance,  

Zack
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