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

[Paul Gilbert]

You might try running top while R runs, to get a better idea of what is
happening. 64-bit R takes more memory than 32-bit (longer pointers) and
for a large problem I would say that 2GB RAM is a minimum if you want
any speed. Slowness is likely related to needing to use swap space. The
"cannot allocate" error is because you run out of both RAM and swap. If
you are close to finishing your calculation you may resolve things by
increasing swap, but don't expect it to be fast.

There is also a possibility that your user id is restricted, but I'm not
sure how that works anymore. It used to be controlled by ulimit, but
that does not seem to be the case in newer versions of Linux.

If you are still debugging your code, and there is some chance you are
just gobbling up memory endlessly until it runs out, then you can speed
things up (i.e. fail more quickly) by turning swap off. There are
debugging situations where this turns out to be useful.

HTH,
Paul

zhihua li 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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