shadow_tr

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 /econ/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 /econ/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 /econ/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 /econ/username.
  • username@login-02-01>cd /econ/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.

206 Tilton Hall, Tulane University, New Orleans, LA 70118 tel 504-865-5321 fax 504-865-5869 pwatson@tulane.edu