From tlumley at u.washington.edu  Mon Mar  6 18:13:07 2006
From: tlumley at u.washington.edu (Thomas Lumley)
Date: Mon, 6 Mar 2006 09:13:07 -0800 (PST)
Subject: [Rd] Running R on dual/quad Opteron machines
In-Reply-To: <3c12769c0603060850pd3bbc73gb40a5e9f324d8050@mail.gmail.com>
References: <3c12769c0603060850pd3bbc73gb40a5e9f324d8050@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0603060906130.24583@homer24.u.washington.edu>

On Mon, 6 Mar 2006, Simone Giannerini wrote:
> The environment will probably be either Unix/Linux or Solaris and the
> amount of RAM will be 8-16Gb, depending on the number of processors.
> My main concerns are the following:
>
> 1. How much does R  benefit from passing from one processor to
> two/four processor machines? Consider that the typical intensive use
> of the server
> will be represented by simulation studies with many repeated loops.

The typical way that R is used on multiprocessor systems is running more 
than one program, rather than parallel processing. If four people are 
using the computer or if one person splits 10,000 iterations of a 
simulation into 4 sets of 2,500 you will be using all four processors.

> 2. How does R cope with parallelization and/or parallelized compiled code ?
>

It doesn't really.  There are interfaces to MPI and PVM and there is the 
possibility of using a parallel BLAS to speed up linear algebra.  These 
won't help much unless the server is under fairly low load so that a 
single program can use more than 100% of a single processor.  Our 
multiprocessor Opteron servers are rarely that underutilized.

 	-thomas

Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle



[Rd] Running R on dual/quad Opteron machines
Thomas Lumley