The dist object for the rows of the matrix will be 16000x16000, which if there are any copies will easily suck up all of your RAM.
A more pertinent question is what use would a heatmap of that size be? How do you plan to visualize 16000 rows? In a pdf? You certainly couldn't publish such a thing, nor would it be useful as a picture in a presentation. You would probably be better off filtering down to a more reasonable number of rows (say 500 or less), and using that to make your heatmap. Best, Jim jim holtman wrote: > 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! >> >> _________________________________________________________________ >> ?????????????? 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. >> >> > > > > ------------------------------------------------------------------------ > > ______________________________________________ > 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. -- James W. MacDonald, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. ______________________________________________ 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.