Introduction to High-Performance Computing: Cheatsheets for Queuing System Quick Reference

High Performance Computing (HPC) typically involves connecting to very large computing systems elsewhere in the world.

These other systems can be used to do work that would either be impossible or much slower on smaller systems.

The standard method of interacting with such systems is via a command line interface called bash which runs on the remote server.

You first have to log in to your personal user account on the server.

An HPC system is a set of networked machines.

HPC systems typically provides login nodes and a set of worker nodes.

The resources found on independent (worker) nodes can vary in volume and type (amount of RAM, processor architecture, availability of network mounted file systems, etc.).

Files saved on one node are available on all nodes.

The scheduler handles how compute resources are shared between users.

Everything you do should be run through the scheduler.

A job is just a shell script.

If in doubt, request slightly more resources than you will need.

Load software with module load softwareName

Unload software with module purge

The module system handles software versioning and package conflicts for you automatically.

You can edit your .bashrc file to automatically load a software package.

wget downloads a file from the internet.

scp transfer files to and from your computer.

You can use an SFTP client like FileZilla to transfer files through a GUI.

To use resources effectively, you need to understand the performance of your jobs.

Be careful how you use the login node.

Your data on the system is your responsibility.

Plan and test large data transfers.

It is often best to convert many files to a single archive file before transferring.

Again, don’t run stuff on the login node.

Don’t be a bad person and run stuff on the login node.