From ripley at stats.ox.ac.uk  Fri Jan  6 09:44:28 2006
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Fri, 6 Jan 2006 08:44:28 +0000 (GMT)
Subject: [Rd] Q: R 2.2.1:  Memory Management Issues?
In-Reply-To: <7BB23955-EC08-43D3-9465-AD12540C17A3@r-project.org>
References: <3CB6B0EE6816B142859B24E77724A8B8F87DDD@sccsmxsusr05.pharma.aventis.com>
	<7BB23955-EC08-43D3-9465-AD12540C17A3@r-project.org>
Message-ID: <Pine.LNX.4.61.0601060834460.18569@gannet.stats>

On Thu, 5 Jan 2006, Simon Urbanek wrote:

> Karen,
>
> On Jan 5, 2006, at 5:18 PM, <Karen.Green at sanofi-aventis.com>
> <Karen.Green at sanofi-aventis.com> wrote:
>
>> I am trying to run a R script which makes use of the MCLUST package.
>> The script can successfully read in the approximately 17000 data
>> points ok, but then throws an error:
>> --------------------------------------------------------
>> Error:  cannot allocate vector of size 1115070Kb
>
> This is 1.1GB of RAM to allocate alone for one vector(!). As you
> stated yourself the total upper limit is 2GB, so you cannot even fit
> two of those in memory anyway - not much you can do with it even if
> it is allocated.

Just in case people missed this (Simon as a MacOS user has no reason to 
know this), the Windows limit is in fact 3Gb if you tell your OS to allow 
it.  (How is in the quoted rw-FAQ, Q2.9, and from 2.2.1 R will 
automatically notice this whereas earlier versions needed to be told.)

However, there is another problem with a 32-bit OS:  you can only fit 2 
1.1Gb objects in a 3Gb address space if they are in specific positions, 
and fragmentation is often a big problem.

I believe a 64-bit OS with 4Gb of RAM would handle such problems much 
more comfortably.  The alternative is to find (or write) more efficient 
mixture-fitting software than mclust.

-- 
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



[Rd] Q: R 2.2.1: Memory Management Issues?
Prof Brian Ripley