Getting Started with Stella

Pre-requisites

The first thing you need is a local account on Stella.
You can ask me (lilian.janin@manchester.ac.uk) or Kostas (nikask@cs.man.ac.uk) to create one for you, or you can follow the instructions for administrators.
You should then be able to use ssh to log onto stella.cs.man.ac.uk.
Your local directory is /users/<login_name> and is aliased to /home/stella/<login_name>.

Note: For security reasons, Stella is configured to be only accessible from inside the university campus. If you need to access it from home, you will need to log first on your university computer and then on stella.

Submitting your first job, command line version

From your linux box, ssh to stella:

user@linuxbox:~> ssh stella
Password: ********
user@stella:~>

We will submit the following script to the Grid Engine job manager:

#!/bin/bash
hostname       # print the name of the compute node chosen for execution (it can be anything from comp00 to comp05)
date           # print the date and time
sleep 30       # wait for 30 seconds to leave you some time to admire your job in the queue
date           # print the date and time before finishing, to prove that it lasted for 30 seconds

Save these commands in a script file or use /users/scripts/examples/hostname_sleep30, and submit it:

user@stella:~> qsub /users/scripts/examples/hostname_sleep30
Your job 1122 ("hostname_sleep30") has been submitted

Your job is now queued for execution. If a queue is available to run it, it will be scheduled and run. Using the command qstat, you can see the status of Grid Engine jobs and queues:

user@stella:~> qstat
job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID 
-----------------------------------------------------------------------------------------------------------------
   1122 10.01000 hostname_s user       r     12/05/2006 11:15:28 serial.q@comp01.cs.man.ac.uk       1        

The previous screen shows that your job is running (state=r) in the queue serial.q on the compute node comp01.
The output of the script is redirected by default to two files in your home directory called <script_name>.o<job_number> (for stdout) and <script_name>.e<job_number> (for stderr).

user@stella:~> cat ~/hostname_sleep30.o1122
comp01
Tue Dec  5 11:15:29 GMT 2006
Tue Dec  5 11:15:59 GMT 2006

Setting up ssh

For some application (matlab for example), you also need to setup ssh to work without password between stella and the compute nodes. This can be done like that:

user@stella:~> mkdir .ssh
user@stella:~> cd .ssh
user@stella:~/.ssh> ssh-keygen -t dsa
user@stella:~/.ssh> ssh-keygen -t rsa
user@stella:~/.ssh> cat id_rsa.pub id_dsa.pub > authorized_keys2
user@stella:~/.ssh> ssh stella  # try the new setup, and agree to any question