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!")

  • Write a script for the CCS queueing system ( 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
    #PBS -m abe
    #PBS -o helloworld.log

    module load intel
    module load R-2.14.0

    echo Start Job
    cd /econ/username
    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 using secure FTP (SFTP).
  • To do this, you need an FTP program, like Filezilla. The server address is Specify SFTP and use your CCS username and password. Once you login, change the directory to /econ/username. Then, upload helloworld.m and to that directory.

  • Login to 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 Specify SSH and use your CCS username and password. For example, in Terminal:

    username$ssh's password:

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

  • Add your job to the PBS queue.
  • username@login-02-01>qsub

  • 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.

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