[BioC] how to set R memory limit

[Steve Lianoglou]

Hi,

On Mon, Jan 9, 2012 at 10:49 PM, wang peter <wng.peter at gmail.com> wrote:
> i have 64 G memory server
> only run one R program
> but it reported
>  cannot relocate 5.2G memory

Someone sometime ago on R-help (can't remember who) put it best, which
I'll paraphrase here: The "cannot relocate XXX memory" error is fired
when the "last straw is drawn which breaks the camel's back"

So although you have a 64GB server and assuming you are running in
64bit mode, this error doesn't tell you that your server doesn't have
5.4GB memory in it, it means that R (or something else) has been
chewing up your memory and R tried to get a 5.4G contiguous block of
it, and apparently there isn't any free block of that size left.

Use your favorite process monitoring tool for your OS to keep on eye
on your CPU's memory usage to confirm.

Also, as Sean suggests, sessionInfo output is always helpful.

HTH,

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact