Summary and Schedule

This is a new lesson built with The Carpentries Workbench.

Lesson content is heavily based on the HPC intro lesson in the Carpentries Incubator.

	Setup Instructions	Download files required for the lesson
Duration: 00h 00m	1. What is an HPC cluster?	What is an HPC cluster? When would you use HPC instead of a laptop? How does HPC allocate resources to your job?
Duration: 00h 20m	2. Connecting to an HPC system	How do I connect to an HPC cluster?
Duration: 01h 00m	3. The job scheduler	What is a job scheduler? How do I run a program on HPC? How do I check on a submitted job or cancel it?
Duration: 01h 45m	4. Transferring files	How do I transfer files to and from an HPC cluster?
Duration: 02h 20m	5. Accessing software via module files	How do I access different versions of software packages?
Duration: 02h 55m	6. Parallel jobs	How do I use multiple cores for my HPC job? How much faster is it to use more cores?
Duration: 03h 40m	7. High Throughput Computing	What is High Throughput Computing? How can I run lots of similar tasks at the same time? What types of task are suitable for a job array?
Duration: 04h 10m	Finish

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

Software Setup

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Discussion

Details

This course uses a UNIX shell to run commands both on your laptop and on the HPC cluster.

The shell is a program that enables us to send commands to the computer and receive output. It is also referred to as the terminal or command line.

Some computers include a default Unix Shell program. The steps below describe some methods for identifying and opening a Unix Shell program if you already have one installed.

There are also options for downloading a Unix Shell program if you don’t already have one.

Windows

Computers with Windows operating systems do not automatically have a Unix Shell program installed.

In this lesson, we encourage you to use an emulator included in Git for Windows, which gives you access to both Bash shell commands and Git.

Once installed, you can open a terminal by running the program Git Bash from the Windows start menu.

MacOS

On macOS, the default Unix Shell is accessible by running the Terminal program from the /Application/Utilities folder in Finder.

To open Terminal, try one or both of the following:

• In Finder, select the Go menu, then select Utilities. Locate Terminal in the Utilities folder and open it.
• Use the Mac ‘Spotlight’ computer search function. Search for: Terminal and press Return.

Linux

On most versions of Linux, the default Unix Shell is accessible by running Terminal (Gnome) or Konsole (KDE), which can be found via the applications menu or the search bar.

Accounts on the HPC cluster

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Your instructor will provide you with a username and password to log in to the cluster. How to log in to the cluster is covered in episode 2

Callout

The training cluster vs a real HPC cluster

The cluster that we will use for this training is a simplified system for the purposes of learning how to interact with a job scheduler. The take home message is that this system has way fewer resources than a typical HPC system.

Some of the key differences include:

• there is only one login node
• there is only one compute node
• the nodes only have 4 cores and 16GB RAM
• there are only a small number of software modules
• there is just one SLURM partition

Some of these terms will be unfamiliar to you, but will be explained in the introduction.