R with ATLAS avoids Linux cpu affinity
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