[R] Memory issues..

JFRI (Jesper Frickman) jfri at novozymes.com
Thu Nov 13 17:02:57 CET 2003

I tried first to increase --min-vsize to 2G (which I assume means as
much of the 512M RAM available on my system as possible). The idea was
to allocate all the heap memory in one huge chunk to avoid
fragmentation. It actually brought the number of assays completed up
from 11 to 13 before it stopped with the usual error. Then I increased
--max-memory-size to 2G, and when I came in this morning it was still
running. However, it would probably take days instead of hours to
complete the last couple of assays! So it is easier to restart a couple
of times...

Do you think that running R on Linux would fix the problem? I use Linux
on my private home PC, and I might get a permission to try it out on the
company network... If I have a good reason to do so!


-----Original Message-----
From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk] 
Sent: Wednesday, November 12, 2003 10:55 AM
To: JFRI (Jesper Frickman)
Cc: r-help at stat.math.ethz.ch
Subject: RE: [R] Memory issues..

On Wed, 12 Nov 2003, JFRI (Jesper Frickman) wrote:

> How much processing takes place before you get to the lme call? Maybe 
> R has just used up the memory on something else. I think there is a 
> fair amount of memory leak, as I get similar problems with my program.

> I use

Windows, right?  I don't think this is memory leak, but rather
fragmentation.  Hopefully the memory management in R-devel will ease
and you might like to compile that up and try it.

On R 1.8.0 on Windows you have to be able to find a block of contiguous 
memory of the needed size, so fragmentation can kill you.  Try
--max-memory-size unless you are near 2Gb.

> R 1.8.0. My program goes as follows.
> 1. Use RODBC to get a data.frame containing assays to analyze (17 
> assays are found). 2. Define an AnalyzeAssay(assay, suffix) function 
> to do the following:
> 	a) Use RODBC to get data.
> 	b) Store dataset "limsdata" in workspace using the <<- operator
> avoid the following error in qqnorm.lme: Error in eval(expr, envir,
> enclos) : Object "limsdata" not found, when I call it with a grouping 
> formula like: ~ resid(.) | ORDCURV.
> 	c) Call lme to analyze data.
> 	d) Produce some diagnostic plots. Record them by setting
> on the trellis.device
> 	e) Save the plots on win.metafile using replayPlot(...)
> 	f) Save text to a file using sink(...)
> 3. Call the function for each assay using the code:
> # Analyze each assay
> for(i in 1:length(assays[,1]))
> {
> 	writeLines(paste("Analyzing ", assays$DILUTION[i], " ", 
> assays$PROFNO[i], "...", sep=""))
> 	flush.console()
> 	AnalyzeAssay(assays$DILUTION[i], assays$PROFNO[i])
> 	# Clean up memory
> 	rm(limsdata)
> 	gc()
> }
> As you can see, I try to remove the dataset stored in workspace and 
> then call gc() to clean up my memory as I go.
> Nevertheless, when I come to assay 11 out of 17, it stops with a 
> memory allocation error. I have to quit R, and start again with assay 
> 11, then it stops again with assay 15 and finally 17. The last assays 
> have much more data than the first ones, but all assays can be 
> completed as long as I keep restarting...
> Maybe restarting the job can help you getting it done?

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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