Using matlab on ccs server

• 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 Matlab m-file (mymfile.m). Example:

n=20;
m=100;
A=randn(n,m);
B=rand(n,m);
save test A B;
quit;




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

#PBS -q econ_main
#PBS -N mymfile
#PBS -l walltime=10:00:00
#PBS -j oe
#PBS -M username@tulane.edu
#PBS -m abe
#PBS -e stderr.txt
#PBS -o stdlog.txt

echo Start Job
cd /econ_00/username
date
pwd
matlab -nodisplay -nosplash < mymfile.m
echo End Job


This script requests that the contents be added to the econ_main queue. It will let the script run for up to 10 hours and send out an email when it begins, finishes, or aborts.



• Upload your do-file and queue script to ccs1.ccs.tulane.edu using secure FTP (SFTP).

To do this, you need an FTP program, like Filezilla. The server address is ccs1.ccs.tulane.edu. Specify SFTP and use your CCS username and password. Once you login, change the directory to /econ_00/username. Then, upload mymfile.m and myscript.sh to that directory.



• Login to ccs1.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 ccs1.ccs.tulane.edu. Specify SSH and use your CCS username and password. For example, in Terminal:

username$ssh ccs1.ccs.tulane.edu
username@ccs1.ccs.tulane.edu's password:
username@ccs1>




• During that SSH session, login to the CCS ares cluster and change directories to /econ_00/username.

username@ccs1>ssh ares
username@login-02-01>cd /econ_00/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. (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.