From chris.jewell at warwick.ac.uk  Mon Dec  6 20:58:36 2010
From: chris.jewell at warwick.ac.uk (Chris Jewell)
Date: Mon, 6 Dec 2010 19:58:36 +0000
Subject: [Rd] R with ATLAS avoids Linux cpu affinity
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	<19709.2360.287048.26325@max.nulle.part>
Message-ID: <408D77D5-A33A-455E-99C8-6608EACE6F3A@warwick.ac.uk>


On 6 Dec 2010, at 16:03, Dirk Eddelbuettel wrote:
> AFAICT R should not alter CPU affinity.  So if I were you I'd swap the BLAS
> implementation and try again.  As you are on Ubuntu, you can try the MKL that
> comes with the (now a littler older) Revolution R in Ubuntu 9.10; otherwise I
> can highly recommend the GotoBLAS2 helper package listed in my paper for a
> local GotoBLAS2 built.   The script may be out of sync with the fairly recent
> license change of GotoBLAS2 (to the more liberal BSD license permitting
> redistribution).  With some luck we will GotoBLAS2 deb packages in future
> Debian and Ubuntu releases.


Thanks for the comments, Dirk.  I take your point about ATLAS having the cores compiled in.  I have replaced ATLAS with ACML, and all works fine.

Cheers,

Chris


--
Dr Chris Jewell
Department of Statistics
University of Warwick
Coventry
CV4 7AL
UK
Tel: +44 (0)24 7615 0778



[Rd] R with ATLAS avoids Linux cpu affinity
Chris Jewell