shadow_tr

Using Stata 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 Stata do-file (mydofile.do). Example:
  • log using mydofile.log, text replace
    set mem 300m
    sysuse auto
    generate weightsq = weight^2
    regress mpg weight weightsq foreign
    log close
    exit


  • Write a script for the CCS queueing system (myscript.sh). Example:
  • #PBS -q econ_long
    #PBS -N mydofile
    #PBS -d /econ/username
    #PBS -j oe
    #PBS -o stdlog.log
    #PBS -l nodes=1:ppn=2,walltime=5:00:00,mem=1gb
    #PBS -M username@tulane.edu
    #PBS -m abe

    module load intel
    module load stata

    echo Start Job
    cd /econ/username
    date
    pwd
    /usr/local/opt/stata/stata-mp -b do mydofile
    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 5 hours, on 2 processors, on 1 node, using 1 GB 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 mydofile.do and myscript.sh to that directory.


  • Login to spynhx.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 myscript.sh
    jobid


  • Check the status of your job.
  • username@login-02-01>qstat


  • Check the status of the nodes.
  • 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