Hoffman2:R

Back to all things Hoffman2

R is a great statistics and graphics tool. Here's how to run it on the cluster. See the official info from ATS here.

Interactively

1. On the cluster, check out an interactive node.
2. Execute the following so the node knows how to speak R

   $ module load R

3. Execute

   $ R

4. And you'll now be in an interactive R session. If you have no idea what to do with R, we suggest looking here. To see all the installed packages, execute

   > library()

Batch

1. On the cluster, check out an interactive node.
2. Execute the following so the node know how to speak R

    $ module load R

3. Execute an R script using the following commands

    $ R CMD BATCH /path/to/R/script /path/to/output/file

/path/to/R/script

This argument is necessary because it is the file you are running

/path/to/output/file

This argument is optional. If you don't specify this argument, the output will be dumped into a file in the current working directory named for the script run with "out" appended to it. (e.g. if you ran the script sampleRscript.R, the generic output file would be named sampleRscript.Rout)

Job

R.q

Similar to job.q, there is an R.q for building command files for jobs that use R. It's a fairly simple step-by-step program that will guide you through making an SGE command file.

But for the less than patient, we'll run through an example case now.

Example

1. Once on Hoffman2, you'll need to edit one file so pull out your favorite text editor and edit the file

   ~/.queuerc

2. Add the line (if it isn't already there)

   set qqodir = ~/job-output

3. You've just set the default directory where your job command files will be created. Save the configuration file and close your text editor.
4. Make that directory using the command

   $ mkdir ~/job-output

5. Now execute

   $ R.q

6. Press enter to acknowledge the message that appears (READ IT FIRST THOUGH).
7. Type Build <ENTER> to begin creating an SGE command file.
8. The program now asks you which script you'd like to run, enter the following text to use our example script

   /u/home/FMRI/apps/examples/qsub/sampleR.R

9. The program now asks how much memory the job will need (in Megabytes). This script is really simple, but go ahead with the default value.
10. The program now asks how long will the job take (in hours). Go with the minimum 1 hour; it will complete in much less than this.
11. The program now asks if your job should be limited to only your resource group's cores. Answer n because you do not need to be limiting yourself here and the job is not going to be running for more than 24 hours.
12. Soon, the program will tell you that sampleR.cmd has been built and saved.
13. When it asks you if you would like to submit your job, say no. Then type Quit <ENTER> to leave the program.
14. Now you should be able to run

    ls ~/job-output

    and see R.cmd. This file will stay there until you delete it and can be run over and over again. Making a command file like this is especially useful if there is a task you'll be running repeatedly on Hoffman2. But if this is something you only need to run once, you should delete the file so you don't needlessly approach your quota.

15. The time has come to actually run the program (thought we'd never get to that, didn't you?). Type

    $ qsub job-output/R.cmd

    and after hitting enter, a message similar to this will pop up:

    Your job 1882940 ("R.cmd") has been submitted

    where the number is your JobID, a unique numerical identifier for the computer job you have submitted to the queue.

16. Now you can check if the job has finished running by doing

    $ ls ~/job-output

17. When two files named R.out.[JOBID] and R.joblog.[JOBID] (where JOBID is your job's unique identifier) appear, your job has run.

    R.out.[JOBID]

    This file has all the standard output generated by your script.

    R.joblog.[JOBID]

    This file has all the details about when, where, and how your job was processed. Useful information if you are going to be running this job over and over and need to fine tune the resources it uses.

18. Better ways of checking on your job can be found here.
19. The script you ran is an example taken from [1] which we found by Googling "R example scripts."
20. Finally, go check the inbox of the email you used to sign up for your Hoffman2 account. There will be two emails from "root@mail.hoffman2.idre.ucla.edu" that indicate when the job was started and when the job was completed. This is one of the neat features of the queue so that you can be alerted about the progress of your job without having to stay logged into Hoffman2 and checking on it constantly.

By hand

You could also make a shell script that contains

#!/bin/bash
module load R
R CMD BATCH /path/to/R/script

and submit this shell script using qsub or q.sh to achieve similar results.

Different Versions

Different versions of R are maintained on Hoffman2. To see which versions are installed, use the command

module available R

To load a specific version, use the command

module load R/<version>

where you replace <version> with the numerical version name e.g.

module load R/2.12.2

will load version 2.12.2

External Links

• R on Hoffman2, official description
• The R Project
• Example R Script