News & Announcements
R 'multicore' package now available (Biowulf)
Date: 19 March 2009 09:03:54From: Susan Chacko (susanc@HELIX.NIH.GOV)
The R package 'multicore' has been installed on the Biowulf cluster.
multicore is an R package that provides functions for parallel
execution of R code on machines with multiple cores or CPUs. Unlike
other parallel processing methods all jobs share the full state of R
when spawned, so no data or code needs to be initialized. The actual
spawning is very fast as well since no new R instance needs to be
started.
This package should be used to utilize all the processors on a node
for a single job. Users should be aware that the cluster includes
single-core (2 processors per node) and dual-core (4 processors per
node) nodes. It is simplest to assume 4p per node and always submit to
the dual-core ('dc') nodes.
If you are submitting a swarm of R jobs that each use multicore, each
node should run only a single R command, since the multicore
paralellization will utilize all the processors on that node. Thus,
the swarm command should be :
swarm -n 1 -f myswarmfile -l nodes=1:dc
More information on the Biowulf R page: http://biowulf.nih.gov/apps/R.html

