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R is a free software environment for statistical computing. It provides rich data analysis functionalites and sophiscated graphical capabilities.

Versions and Availability

Module Names for R on philip
Machine Version Module Name
philip 3.1.3 r/3.1.3/INTEL-15.0.3
philip 8.2.3 raxml/8.2.3/INTEL-15.0.3-mt-sse3
philip 2.2 repet/2.2
philip 2.0.5_06 rum/2.0.5_06
▶ Module FAQ?

The information here is applicable to LSU HPC and LONI systems.


A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.


System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.profile

When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is set automatically using SoftEnv. See below for more information.


The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.


Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.

Default Setup

When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.

Viewing Available Modules

The command

$ module avail

displays a list of all the modules available. The list will look something like:

--- some stuff deleted ---

---------------- /usr/local/packages/Modules/modulefiles/admin -----------------
EasyBuild/1.11.1       GCC/4.9.0              INTEL-140-MPICH/3.1.1
EasyBuild/1.13.0       INTEL/14.0.2           INTEL-140-MVAPICH2/2.0
--- some stuff deleted ---

The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).

Managing Modules

Besides avail, there are other basic module commands to use for manipulating the environment. These include:

add/load mod1 mod2 ... modn . . . Add modules
rm/unload mod1 mod2 ... modn  . . Remove modules
switch/swap mod . . . . . . . . . Switch or swap one module for another
display/show  . . . . . . . . . . List modules loaded in the environment
avail . . . . . . . . . . . . . . List available module names
whatis mod1 mod2 ... modn . . . . Describe listed modules

The -h option to module will list all available commands.

Module is currently available only on SuperMIC.


R may be run either interactively via the R console, or as a batch process reading commands from a script file.

To launch the R console, simply execute the R command. After the console is launched, users can run R commands at the prompt:

$ R

R version 3.1.0 (2014-04-10) -- "Spring Dance"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> x <- 5
> x
[1] 5
> m <- matrix(1:6,2,3)
> m
     [,1] [,2] [,3]
[1,]    1    3    5
[2,]    2    4    6

Rscript, on the other hand, can be used to run a R scirpt in which a sequence of R commands has been saved. The syntax is:

	$ Rscript <options> <name of the R script>

For example:

	$ cat hello.R 
	print("Hello World!")
	$ Rscript hello.R 
	[1] "Hello World!"

▶ QSub FAQ?

Portable Batch System: qsub


All HPC@LSU clusters use the Portable Batch System (PBS) for production processing. Jobs are submitted to PBS using the qsub command. A PBS job file is basically a shell script which also contains directives for PBS.

$ qsub job_script

Where job_script is the name of the file containing the script.

PBS Directives

PBS directives take the form:

#PBS -X value

Where X is one of many single letter options, and value is the desired setting. All PBS directives must appear before any active shell statement.

Example Job Script
 # Use "workq" as the job queue, and specify the allocation code.
 #PBS -q workq
 #PBS -A your_allocation_code
 # Assuming you want to run 16 processes, and each node supports 4 processes, 
 # you need to ask for a total of 4 nodes. The number of processes per node 
 # will vary from machine to machine, so double-check that your have the right 
 # values before submitting the job.
 #PBS -l nodes=4:ppn=4
 # Set the maximum wall-clock time. In this case, 10 minutes.
 #PBS -l walltime=00:10:00
 # Specify the name of a file which will receive all standard output,
 # and merge standard error with standard output.
 #PBS -o /scratch/myName/parallel/output
 #PBS -j oe
 # Give the job a name so it can be easily tracked with qstat.
 #PBS -N MyParJob
 # That is it for PBS instructions. The rest of the file is a shell script.
 #   1. Copy the necessary files from your home directory to your scratch directory.
 #   2. Execute in your scratch directory.
 #   3. Copy any necessary files back to your home directory.

 # Let's mark the time things get started.


 # Set some handy environment variables.

 export HOME_DIR=/home/$USER/parallel
 export WORK_DIR=/scratch/myName/parallel
 # Set a variable that will be used to tell MPI how many processes will be run.
 # This makes sure MPI gets the same information provided to PBS above.

 export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`

 # Copy the files, jump to WORK_DIR, and execute! The program is named "hydro".

 cp $HOME_DIR/hydro $WORK_DIR
 mpirun -machinefile $PBS_NODEFILE -np $NPROCS $WORK_DIR/hydro

 # Mark the time processing ends.

 # And we're out'a here!

 exit 0


Last modified: June 26 2015 14:09:16.