Are you paging? That might explain the long run times. How much space are your other objects taking up? The matrix by itself should only require about 13MB if it is numeric. I would guess it is some of the other objects that you have in your working space. Put some gc() in your loop to see how much space is being used. Run it with a subset of the data and see how long it takes. This might give you an estimate of the time, and space, that might be needed for the entire dataset.
Do a 'ps' to see how much memory your process is using. Do one every couple of minutes to see if it is growing. You can alway use Rprof() to get an idea of where time is being spent (use it on a small subset). On 7/18/07, zhihua li <[EMAIL PROTECTED]> wrote:
Hi netters, I'm using the 64-bit R-2.5.0 on a x86-64 cpu, with an RAM of 2 GB. The operating system is SUSE 10. The system information is: -uname -a Linux someone 2.6.13-15.15-smp #1 SMP Mon Feb 26 14:11:33 UTC 2007 x86_64 x86_64 x86_64 GNU/Linux I used heatmap to process a matrix of the dim [16000,100]. After 3 hours of desperating waiting, R told me: cannot allocate vector of size 896 MB. I know the matrix is very big, but since I have 2 GB of RAM and in a 64-bit system, there should be no problem to deal with a vector smaller than 1 GB? (I was not running any other applications in my system) Does anyone know what's going on? Is there a hardware limit where I have to add more RAM, or is there some way to resolve it softwarely? Also is it possible to speed up the computing (I don't wanna wait another 3 hours to know I get another error message) Thank you in advance! _________________________________________________________________ 享用世界上最大的电子邮件系统― MSN Hotmail。 http://www.hotmail.com ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
