[R] memory error with 64-bit R in linux

[jim holtman]

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 <lzhtom at hotmail.com> 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!
>
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-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?