R on Pegasus

R is available on Pegasus through the module command. You can load R into your environment by typing the following on the commandline:

[username@pegasus ~]$ module load R

This loads the default version of R, currently 4.1.0. To load a specific version of R, say, 3.6.3, you can type the following:

[username@pegasus ~]$ module load R/3.6.3

To see a list of available software, including R versions, use the command module avail. For more information about software available on Pegasus, see Software on the Pegasus Cluster.

Batch R

To run a batch R file on the compute nodes on Pegasus, submit the file to LSF with R CMD BATCH filename.R, with filename being the name of your R script. This can be done using the following (two) commands:

[username@pegasus ~]$ module load R/4.1.0
[username@pegasus ~]$ bsub -q general -P projectID R CMD BATCH filename.R
Job is submitted to <projectID> project.
Job <6101046> is submitted to queue <general>.

Batch jobs can also be submitted to LSF with script files, such as example.job shown below.

example.job
#!/bin/bash
#BSUB -J R_job            # name of your job
#BSUB -e filename.e%J     # file that will contain any error messages
#BSUB -o filename.o%J     # file that will contain standard output
#BSUB -R "span[hosts=1]"  # request run script on one node
#BSUB -q general          # request run on general queue
#BSUB -n 1                # request 1 core
#BSUB -W 2                # request 2 minutes of runtime
#BSUB -P projectID        # your projectID
R CMD BATCH filename.R    # R command and your batch R file

When using such a script file, the batch job can be submitted by typing the following on the commandline

[username@pegasus ~]$ bsub < example.job

Interactive R

R can also be run interactively by requesting resources on the interactive queue. This can be done by first loading R into your environment

[username@pegasus ~]$ module load R/4.1.0

and then requesting an interactive R session by typing on the commandline

[username@pegasus ~]$ bsub -Is -q interactive R

or

[username@pegasus ~]$ bsub -Is -P ProjectID R

making sure to replace ProjectID with the actual name of your project.

Installing additional R packages

To install additional R packages, you’ll need to confirm that your package’s pre-requisites are met by inspecting and modifying your local environment as needed or by loading the appropriate modules. See Pegasus Cluster Software Installation for help with complex requirements.

From the R prompt, install any R package to your personal R library with the standard install.package() R command. For instance, to install the doParallel package, a parallel backend for the foreach function, one would type the following on the commandline in an interactive session of R.

>  install.packages("doParallel", repos="http://R-Forge.R-project.org")

The result would be as follows:

Installing package into ‘/nethome/CaneID/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'http://R-Forge.R-project.org/src/contrib/doParallel_1.0.14.tar.gz'
Content type 'application/x-gzip' length 173692 bytes (169 KB)
==================================================
downloaded 169 KB

* installing *source* package ‘doParallel’ ...
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (doParallel)

The downloaded source packages are in
        ‘/tmp/RtmpnBwmdD/downloaded_packages’
>

Contact IDSC ACS to review any core library pre-requisites and dependencies, for cluster-wide installation.

A Sample R script

Below is a sample R script which creates a graphical output file after it has been run.

example1.R

---

 # create graphical output file
pdf("example1.pdf")

# Define two vectors v1 and v2
v1 <- c(1, 4, 7, 8, 10, 12)
v2 <- c(2, 8, 9, 10, 11, 15)

# Creat some graphs
hist(v1)
hist(v2)
pie(v1)
barplot(v2)

# close the file
dev.off()

Such a script can be run as a batch job. After the script has run, the graphical output file can be transferred to a local computer using FileZilla or scp, in order to be viewed.