Re: [R] locfit and memory allocation

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Tue 05 Apr 2005 - 17:25:10 EST

Calling gc() before starting a memory-intensive task is normally a good idea, as it helps avoid memory fragmentation (which is possibly a problem in a 32-bit OS, but you did not say). R 2.1.0 beta has some dodges to help, so you may find if helpful to try that out.

On Mon, 4 Apr 2005, Mike Hickerson wrote:

> Hello
>
> I am getting memory allocation errors when running a function that uses
> locfit within a for loop. After 25 or so loops, it gives this error.
>
> "Error: cannot allocate vector of size 281250 Kb"
>
> Running on linux cluster with a Gb of RAM. Problem never happens on my
> OS X (less memory). The total data is 130 cols by 5000 rows
> The first 129 cols are response variables, the 130th is the parameter
> The function fits a local regression between the 129 variables in the
> ith row of m[ ] to the 129 variables in 5000 rows after m was fed into
> 130 different vectors called Var1, .....Var129, and PARAMETER.
>
> array <- scan(("DataFile"),nlines=5000)
> m<-matrix(array,ncol=130,byrow=T)
>
> for (i in 1:200)
> {
> result<-
> function(m[i,c(1,....,129)],PARAMETER,cbind(Var1,...,Var129)seq(1,len=50
> 00),F)
> }
>
> Any ideas on how to avoid this memory allocation problem would be
> greatly appreciated. Garbage collection? (or is that too slow?)
>
> Many Thanks in Advance!
>
> Mike
>
>
>
>
> Mike Hickerson
> University of California
> Museum of Vertebrate Zoology
> 3101 Valley Life Sciences Building
> Berkeley, California  94720-3160  USA
> voice 510-642-8911
> cell: 510-701-0861
> fax 510-643-8238
> mhick@berkeley.edu
>
> [[alternative text/enriched version deleted]]
>
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-- 
Brian D. Ripley,                  ripley@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 Apr 05 17:37:01 2005

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