R on Pegasus

To run the R programming language on Pegasus, first load an R module with module load R/version. Use the command module avail to see a list of available software, including R versions. For more information about Pegasus software, see Software on the Pegasus Cluster.

Batch R

To run a batch R file on Pegasus compute nodes, submit the file to LSF with R CMD BATCH filename.R. Remember to include the -P flag and your project, if you have one.

[username@pegasus ~]$ module load R/2.15.2
[username@pegasus ~]$ bsub -q general -P projectID R CMD BATCH example1.R
Job is submitted to <projectID> project.
Job <6101046> is submitted to queue <general>.

See example1.R below. For more information about bsub and scheduling jobs, see Scheduling Jobs on the Pegasus Cluster.

Batch jobs can also be submitted to LSF with script files.

example.job
#!/bin/bash
#BSUB -J R_job            # name of your job
#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 example1.R    # R command and your batch R file



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

Interactive R

Load an R module, then submit an interactive R session with bsub -Is. Specify your project with the -P flag.

[username@pegasus ~]$ module load R/2.15.2
[username@pegasus ~]$ bsub -Is -q interactive R
or
[username@pegasus ~]$ bsub -Is -P hpc R

R packages

Confirm that your R package’s pre-requisites are met, either in your local environment or as a module on the cluster. You will need to load any cluster modules that are pre-requisites, and install locally any other pre-requisites. 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. Choose y when asked about using a personal library, and y again if asked to create one.

>  install.packages("doParallel", repos="http://R-Forge.R-project.org")
Warning in install.packages("doParallel", repos = "http://R-Forge.R-project.org") :
  'lib = "/share/opt/R/3.1.2/lib64/R/library"' is not writable
Would you like to use a personal library instead?  (y/n) y
Would you like to create a personal library
~/R/x86_64-unknown-linux-gnu-library/3.1
to install packages into?  (y/n) y
...

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

R file examples

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()

If you have forwarded your display, open the pdf from the Pegasus prompt with evince.

[username@pegasus ~]$ evince example1.pdf
example1.png

example1.png