cluster.adoc

Basic cluster usage

Connect to the cluster

In order to connect to the cluster type the following command, replacing ngsXX with your username:

ssh -Y ngsXX@ngs-login.linux.crg.es

The -Y option allows graphical output (X11 forwarding).

Basic commands

qsub -q <queue> <script>	submit a batch job to a specific queue
qstat	monitor the status of submitted jobs
qstat -j <job_id>	display detailed information of a specific job
qdel <job_id>	delete a submitted job

The job_id is an important number that identifies your job in the cluster. It’s necessary for managing and controlling the job.

A simple example of job submission and deletion:

$ qsub -q course sleeper.sh

Your job 393672 ("sleeper.sh") has been submitted

$ qstat

job-ID     prior   name       user      state submit/start at   queue         jclass      slots ja-task-ID
----------------------------------------------------------------------------------------------------------
  393672   0.00000 sleeper.sh ngsXX  qw    11/09/2015 11:18:01                               1

$ qdel 393672

ngsXX has deleted job 393672

Note	See http://www.linux.crg.es for the complete CRG cluster documentation