Re: [R] gc() and memory efficiency

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Tue, 5 Feb 2008 06:06:51 +0000 (GMT)

  1. See ?"Memory-limits": it is almost certainly memory fragmentation. You don't need to give the memory back to the OS (and few OSes actually do so).
  2. I've never seen this running a 64-bit version of R.
  3. You can easily write a script to do this. Indeed, you could write an R script to run multiple R scripts in separate processes in turn (via system("Rscript fileN.R") ). For example. Uwe Ligges uses R to script building and testing of packages on Windows.

On Mon, 4 Feb 2008, Doran, Harold wrote:

> I have a program which reads in a very large data set, performs some
> analyses, and then repeats this process with another data set. As soon
> as the first set of analyses are complete, I remove the very large
> object and clean up to try and make memory available in order to run the
> second set of analyses. The process looks something like this:
>
> 1) read in data set 1 and perform analyses
> rm(list=ls())
> gc()
> 2) read in data set 2 and perform analyses
> rm(list=ls())
> gc()
> ...
>
> But, it appears that I am not making the memory that was consumed in
> step 1 available back to the OS as R complains that it cannot allocate a
> vector of size X as the process tries to repeat in step 2.
>
> So, I close and reopen R and then drop in the code to run the second
> analysis. When this is done, I close and reopen R and run the third
> analysis.
>
> This is terribly inefficient. Instead I would rather just source in the
> R code and let the analyses run over night.
>
> Is there a way that I can use gc() or some other function more
> efficiently rather than having to close and reopen R at each iteration?
>
> I'm using Windows XP and r 2.6.1
>
> Harold
>
> [[alternative HTML version deleted]]
>
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>

-- 
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

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Received on Tue 05 Feb 2008 - 06:14:19 GMT

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