[BioC] how to set R memory limit

[Sebastian Thieme]

Hello,

I had such a problem several times ago. Look at the option() parameter
there you can set the RAM limit. e.g. options(java.parameters =
"-Xmx8192m") to allocate 8GB RAM. the default is 1024MB I think.

Best regards

Basti

2012/1/10 Steve Lianoglou <mailinglist.honeypot at gmail.com>:
> 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
>
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