[BioC] how to set R memory limit

[Sean Davis]

On Tue, Jan 10, 2012 at 3:30 AM, Sebastian Thieme
<thieme at mi.fu-berlin.de> wrote:
> 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.

Hi, Sebastian.  This option sets the java heap space and does not
affect R memory size.  I would not expect setting this option to fix
the original poster's problem (but the report was not very detailed),
but if one is using a package that uses the JVM, this is a useful
parameter to set.

Sean


> 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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