Re: [R] Memory Problem

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Fri, 21 Mar 2008 16:13:56 +0000 (GMT)

On Fri, 21 Mar 2008, Georgios Marentakis wrote:

> Dear all,
> I am having a memory problem when analyzing a rather large data set with
> nested factors in R.
> The model is of the form X~A*B*(C/D/F) A,B,C,D,F being the independent
> variables some of which are nested.
> The problem occurs when using aov but also when using glm or lme.
> In particular I get the following response,
>
> Error: cannot allocate vector of size 1.6 Gb
> R(311,0xa000d000) malloc: *** vm_allocate(size=1733365760) failed (error
> code=3)
> R(311,0xa000d000) malloc: *** error: can't allocate region
> R(311,0xa000d000) malloc: *** set a breakpoint in szone_error to debug
> R(311,0xa000d000) malloc: *** vm_allocate(size=1733365760) failed (error
> code=3)
> R(311,0xa000d000) malloc: *** error: can't allocate region
> R(311,0xa000d000) malloc: *** set a breakpoint in szone_error to debug
>
> This is on an Intel Mac with 2 GBytes of RAM running MacOS X vs. 10.4.11
> The very same result appears on an 8 core Intel Mac with 6 Gbytes of RAM and
> on a Linux Box with 2 GBytes of RAM.
> Is there a way to bypass this and let R allocate the necessary memory? Is
> this a system problem? Would it be resolved in a mainframe for example?

It is not R which is failing to allocate the memory, but the OS.

Most likely it is a 32-bit address space issue (1.6Gb is a large hole to find in a (probably) 3Gb address space), so you need a 64-bit OS (e.g. Mac OS 10.5) and a 64-bit version of R.

>
> thank you very much for your time,
> georgios
>
> [[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 Fri 21 Mar 2008 - 16:27:33 GMT

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