[R] Problems with R memory usage on Linux

[Prof Brian Ripley]

Or ?"Memory-limits" (and the posting guide of course).

On Wed, 15 Oct 2008, Prof Brian Ripley wrote:

> See ?"Memory-size"
>
> On Wed, 15 Oct 2008, B. Bogart wrote:
>
>> Hello all,
>> 
>> I'm working with a large data-set, and upgraded my RAM to 4GB to help
>> with the mem use.
>> 
>> I've got a 32bit kernel with 64GB memory support compiled in.
>> 
>> gnome-system-monitor and free both show the full 4GB as being available.
>> 
>> In R I was doing some processing and I got the following message (when
>> collecting 100 307200*8 dataframes into a single data-frame (for plotting):
>> 
>> Error: cannot allocate vector of size 2.3 Mb
>> 
>> So I checked the R memory usage:
>> 
>> $ ps -C R -o size
>>   SZ
>> 3102548
>> 
>> I tried removing some objects and running gc() R then shows much less
>> memory being used:
>> 
>> $ ps -C R -o size
>>   SZ
>> 2732124
>> 
>> Which should give me an extra 300MB in R.
>> 
>> I still get the same error about R being unable to allocate another 2.3MB.
>> 
>> I deleted well over 2.3MB of objects...
>> 
>> Any suggestions as to get around this?
>> 
>> Is the only way to use all 4GB in R to use a 64bit kernel?
>> 
>> Thanks all,
>> B. Bogart
>> 
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide 
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>> 
>
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595