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support:hpc:software:r

The R Project for Statistical Computing

R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS.

We have installed the latest stable R v2.15 version compiled with current compilers and with added modules as well as the default CentOS version.

Prerequisites

Below is a list of prerequisites for using R:

Using

The CentOS R is in the default path. To use the CSE version say:

module load R

To use submit a serial job:

#!/bin/bash -l
#SBATCH -J MyJob

module load R
R CMD BATCH --no-save --no-restore <name of R scripts>.R

Then to run the above example:

$ sbatch -p serial <scriptname.sh>

To submit a R+Rmpi parallel job:

#!/bin/bash -l
#SBATCH -J MyJob
module load R Rmpi
R CMD BATCH --no-save --no-restore brute_force.R

Then to submit the job:

$ sbatch -p serial -n 11 <scriptname.sh>

The example code is available at: http://math.acadiau.ca/ACMMaC/Rmpi/brute_force.R

After the job is run in the directory you ran it from you should find a file of the form <scriptname>.o<jobID> containing the output of the job, as well as a PDF file named Rplots.pdf.

support/hpc/software/r.txt · Last modified: 2014/03/26 11:42 by bill