Introduction to High-Performance Computing

High-performance computing (HPC) clusters offer researchers an opportunity to perform work that would be impossible with ordinary computers. In this three-hour hands-on workshop, you will learn the basics of supercomputers and how to use them: finding and loading scientific software, performing calculations in batch jobs or interactive sessions, storing and managing data, and using resources efficiently and responsibly.

Note

  • This is the draft HPC Carpentry release, with modifications for use on the Plato HPC cluster at the University of Saskatchewan. Comments and feedback are welcome.

Prerequisites

  • Introduction to the Linux command line or equivalent skills
  • Attendees must bring a laptop with SSH capabilities: a terminal and SSH client for Linux, MacOS, other UNIX systems, or up-to-date Windows 10; MobaXterm or PUTTY for older Windows. We can help attendees prepare their laptop on request.
  • Campus wifi users must be connected to the uofs-secure access point.
  • Remote users must be connected to the network through the USask VPN.
  • See the Setup page for details.

Schedule

Setup Download files required for the lesson
00:00 1. Why use a Cluster? Why would I be interested in High Performance Computing (HPC)?
What can I expect to learn from this course?
00:20 2. Working on a remote HPC system What is an HPC system?
How does an HPC system work?
How do I log on to a remote HPC system?
00:55 3. Scheduling jobs What is a scheduler and why are they used?
How do I launch a program to run on any one node in the cluster?
How do I capture the output of a program that is run on a node in the cluster?
02:10 4. Accessing software How do we load and unload software packages?
02:55 5. Transferring files How do I upload/download files to the cluster?
03:35 6. Running a parallel job How do we execute a task in parallel?
03:50 7. Using resources effectively How do we monitor our jobs?
How can I get my jobs scheduled more easily?
04:15 8. Using shared resources responsibly How can I be a responsible user?
How can I protect my data?
How can I best get large amounts of data off an HPC system?
04:35 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.