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R on Biowulf

R (the R Project) is a language and environment for statistical computing and graphics. R is similar to the award-winning S system, which was developed at Bell Laboratories by John Chambers et al. It provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, ...).

R is designed as a true computer language with control-flow constructions for iteration and alternation, and it allows users to add additional functionality by defining new functions. For computationally intensive tasks, C, C++ and Fortran code can be linked and called at run time.

Submitting R jobs

For basic information about setting up an R job, see the R documentation listed at the end of this page. Also see the Batch Queuing System in the Biowulf user guide.

Create a script such as the following: 

                   script file /home/username/runR
--------------------------------------------------------------------------
#!/bin/tcsh
# This file is runR
#
#PBS -N R
#PBS -m be
#PBS -k oe
date

/usr/local/bin/R --vanilla < /data/username/R/Rtest.r > /data/username/R/Rtest.out
--------------------------------------------------------------------------

Submit the script using the 'qsub' command, e.g. 

qsub -v -l nodes=1 /home/username/runR

Running a 'swarm' of R jobs

The swarm program is a convenient way to submit large numbers of jobs. Create a swarm command file containing a single job on each line, e.g. 
                 swarm command file /home/username/Rjobs
--------------------------------------------------------------------------
/usr/local/bin/R --vanilla < /data/username/R/R1 > /data/username/R/R1.out
/usr/local/bin/R --vanilla < /data/username/R/R2 > /data/username/R/R2.out
/usr/local/bin/R --vanilla < /data/username/R/R3 > /data/username/R/R3.out
/usr/local/bin/R --vanilla < /data/username/R/R4 > /data/username/R/R4.out
/usr/local/bin/R --vanilla < /data/username/R/R5 > /data/username/R/R5.out
....
--------------------------------------------------------------------------
Submit this by typing: 
swarm -f /home/username/Rjobs
Swarm will run 2 jobs per node, since the Biowulf nodes are all 2-processor. See the Swarm documentation for more information.

Documentation
This document is available as http://biowulf.nih.gov/apps/r.html
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