Introduction to High-Performance Computing: Glossary

Learn about CPUs, cores, and cache, and compare your machine with an HPC cluster

Identify how an HPC cluster could benefit your research.

Open On-demand allow you to create interactive sessions using Jupyter and RStudio

Open On-demand includes a basic text editor, file manager and the ability to visualize plots in JPEG, PDF and PNG

Open On-demand interacts with the queue system to monitor and control jobs running on the cluster.

The basic commands you must know are echo, cat, date, pwd, cd, mkdir, touch, cp, mv, rm. You will use these commands very often.

For editing files from the terminal there are several editor available

nano is an easy to use editor with commands that are shown on the bottom, good for beginners.

emacs is a full featured editor that relies on multiple key combinations to control its operation.

vi/vim is installed by default on every Linux system, it works by changing between ‘modes’

Use module avail to know all the modules on the cluster.

Use module load <module_name> to load the module that you need.

You can preload modules for each login by adding the load line on your $HOME/.bashrc

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 more resources than you will need.

It is a good idea to keep aliases to common torque commands for easy execution.

tmux allows you to keep terminal sessions on the cluster that persist in case of network disconnection.

Singularity containers give you control on the software you want on a machine, helping you with reproducible executions.

Singularity containers give you control on the software you want on a machine, helping you with reproducible executions.

Version control systems were created to keep track of changes in a set of files.

They work better with text files

Compile code in several languages and using OpenMP and MPI

Shell scripting brings the ability to control the workflow of commands that you use on the terminal

Shell scripting is important when you need more complex runs or for post-processing