Andrew Crane-Droesch
2014-Aug-21 11:53 UTC
[R] bam (mgcv) not using the specified number of cores
I am getting strange behavior when trying to fit models to large datasets using bam. I am working on a 4-core machine, but I think that there may be 2 physical cores that the computer uses as 4 cores in some sense that I don't understand. When I run the bam using makeCluster(3), the model runs on one core. But when I run it on makeCluster(2), top shoes me that three of my cores are taken up to full capacity, and my computer slows down or crashes. How can I get it to truly run on 2 cores? I'm on a thinkpad X230, running ubuntu. Thanks, Andrew
Hi Andrew, Could you provide a bit more information, please. In particular the results of sessionInfo() and the code that caused this weird behaviour (+ an indication of dataset size). best, Simon On 21/08/14 12:53, Andrew Crane-Droesch wrote:> I am getting strange behavior when trying to fit models to large > datasets using bam. I am working on a 4-core machine, but I think that > there may be 2 physical cores that the computer uses as 4 cores in some > sense that I don't understand. > > When I run the bam using makeCluster(3), the model runs on one core. But > when I run it on makeCluster(2), top shoes me that three of my cores are > taken up to full capacity, and my computer slows down or crashes. > > How can I get it to truly run on 2 cores? > > I'm on a thinkpad X230, running ubuntu. > > Thanks, > Andrew > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- Simon Wood, Mathematical Science, University of Bath BA2 7AY UK +44 (0)1225 386603 http://people.bath.ac.uk/sw283