Using R on the CCS cluster

• If you don't already have one, obtain a CCS account (username). Let Keith know, so he can add you to the econ workgroup on the server.


• Write your R script (helloworld.r). Example:

#Hello World example
a <- c("Hello, world!")
print(a)




• Write a script for the CCS queueing system (helloworld.sh). Example:

#PBS -q econ_long
#PBS -N myscript
#PBS -d /scratch03/username
#PBS -l nodes=1:ppn=2,walltime=10:00:00,mem=1gb
#PBS -j oe
#PBS -M username@tulane.edu
#PBS -m abe
#PBS -o helloworld.log

module load intel
module load R-2.14.0

echo Start Job
cd /scratch03/username
date
pwd
R --vanilla --slave < helloworld.r > helloworld.out
echo End Job


This script requests that the contents be added to the econ_long queue. It will let the script run for up to 10 hours on 2 processors using 1GB of memory and send out an email when it begins, finishes, or aborts.



• Upload your do-file and queue script to sphynx.ccs.tulane.edu using secure FTP (SFTP).

To do this, you need an FTP program, like Filezilla. The server address is sphynx.ccs.tulane.edu. Specify SFTP and use your CCS username and password. Once you login, change the directory to /scratch03/username. Then, upload helloworld.m and helloworld.sh to that directory.



• Login to sphynx.ccs.tulane.edu via SSH

To do this from Windows, you need an SSH terminal, like Putty. To do this from Mac OS, you can use the built-in Terminal. The server address is sphynx.ccs.tulane.edu. Specify SSH and use your CCS username and password. For example, in Terminal:

username$ssh sphynx.ccs.tulane.edu
username@sphynx.ccs.tulane.edu's password:
username@sphynx>




• Change directory to /scratch03/username.

username@login-02-01>cd /scratch03/username




• Add your job to the PBS queue.

username@login-02-01>qsub helloworld.sh
jobid




• Check the status of your job.

username@login-02-01>qstat




• Check the status of the nodes. (The econ nodes are compute-01-200 through compute-01-204.)

username@login-02-01>qnodes




• Kill your job if necessary.

username@login-02-01>qdel jobid




• Other information about the queuing system can be found here.