Running Jobs on HPC

Overview

Teaching: 15 min
Exercises: 0 min

Questions

• How do I submit jobs to the cluster?

• How do I request an interactive terminal?

Objectives

• Learn how to submit and run jobs on the clusters

So, now you know how to login to the cluster, how to check the status of the queue, and have an understanding of the directory structure and how to use the common software applications. Now how do we actually use the cluster and the associated queue system to run our analysis?

The qsub command

The Queue Submission (qsub) command is how you request that your job be scheduled by the queue manager.

Interactive Mode: The qsub -I command can be used to request an interactive terminal, similar to that you’ve already been getting familair with throughout the day. From the submission node (helix.jax.org), let’s try it out.

Exercise:

SSH to helix.jax.org and run the command

qsub -I -q short

The -q short option specifies which queue your request will be placed into. Your request will be processed by the queue manager. Once the queue manager processes your request, you’ll be given a shell with minimal resources on one of the nodes of the cluster. Once you’re done, type the exit command to return to the submission node.

The true power of high performance computing systems is not in their ability to grant access to interactive resources, but is in their ability to allow users to submit shell scripts to the queue for processing without the -I option.

Users have to request resources from the queue so it knows how and where to schedule their jobs.

Non-interactive Mode:

Important qsub options

• -l nodes=1:ppn=2 - Request a certain number of nodes and processors on that node for your application.
• -l walltime=48:00:00 - Request a the resources for a certain amount of time. Note: The default walltime is 1 hour, so by not specifying a walltime, all your jobs, regardless of whether they complete or not, will be terminated after an hour.
• -q short - Request your jobs run in a certain queue. By default, all jobs that do not specify a queue will be placed in the batch queue.

The qsub command can be used to submit your scripts to process to the cluster as follows:

qsub -l nodes=1:ppn=2 -l walltime=48:00:00 -q batch your_script.sh

Excerise

Submit one of the scripts you previously submitted created to the queue using the above format.

Key Points