Hi all, I have a problem with cpu affinity in my R-2.11.1 installation compiled against ATLAS running on a Linux (Ubuntu 10.04) cluster under GridEngine. I wish to use Grid Engine's core binding feature to bind user processes into the number of cores they request on the cluster, thus preventing badly behaved multi-threaded libraries from consuming more cores than requested. An example of this is R compiled against multithreaded ATLAS, which needs to be bound into a single core if a user submits a 1 core job. Grid Engine achieves this through the sched_setaffinity system call under Linux 2.6. For most applications (including if I write a test C program that uses ATLAS BLAS), this works well, and prevents threads from 'leaking' outside the cpu set they are assigned. However, R appears to be able to avoid the core binding. This is *very* strange as I was under the impression that any child processes or threads inherit the cpu affinity of the parent.
Does anyone have experience of this and could offer a comment or solution? Thanks, Chris -- Dr Chris Jewell Department of Statistics University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 7615 0778 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
