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Re: error: memory exhausted -- trying to return to prompt


From: Dirk Eddelbuettel
Subject: Re: error: memory exhausted -- trying to return to prompt
Date: Sat, 9 Aug 2003 16:38:41 -0500
User-agent: Mutt/1.3.28i

On Sat, Aug 09, 2003 at 01:37:03PM -0700, Ian Garcia wrote:
>  I' have an array of length=19200;
>  I'm trying to use the statistical function ranks
>  on it but I get this error
> 
>  error: memory exhausted -- trying to return to prompt
> 
>  Is there any way to solve this ?
[...]
> octave:1>R = pgnumdata("marray", ["select mean from
> arrays where array_id=1 order by gene_id "]);

Nice to see my old pgnumdata function at work :)

> octave:2>length(R)
> ans=19200
> 
> octave:3>R=ranks(R)
> 
>  error: memory exhausted -- trying to return to prompt

Looks like you are out of luck with the combination of
a) ram and b) swap size on your computer as well as c) the particular
implementation.

You can alter either one (or more) of a), b) or c):

a) buy more ram
b) add another swap partition (or file, which is easier) and endure the
swapping 
c-1) use something else -- given that you are having Postgres as the backend,
and that your other post revealed that you use Debian, you could use the fact
that we ship the 'R as an embedded procedural Postgres' language package. See
     $ apt-cache show postgresql-plr
as this has the advantage of doing R's computing _inside_ the dbms saving
you a lot of I/O.
c-2) find or invent a less memory intensive algorithm     
     
Dirk     

-- 
Those are my principles, and if you don't like them... well, I have others.
                                                -- Groucho Marx



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