May 11-12, 2021

1:00 pm - 4:30 pm

Instructors: Ed Bennett, Michele Mesiti

Helpers: Vladimir Khodygo, Ben Thorpe

General Information

High-Performance Computing refers to the spectrum of computational facilities that give more power than you can fit in a typical desktop machine. This hands-on workshop will cover the techniques you need to effectively make use of High-Performance Computing resources in your research, including the Unix shell, and interacting with the job scheduler used on HPC systems.

Who: The course is aimed at graduate students and other researchers at Swansea University with an interest in making use of High Performance Computing. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Zoom; link circulated by email. Get directions with OpenStreetMap or Google Maps.

When: May 11-12, 2021. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email e.j.bennett@swansea.ac.uk for more information.

Please be sure to complete these surveys before and after the workshop.



13:00 Automating tasks with the Unix shell
14:45 Break
15:00 Automating tasks with the Unix shell (continued)
16:30 END


13:00 Interacting with HPC
14:45 Break
15:00 Interacting with HPC (continued)
16:30 END

We will use ReCoN, the Swansea University Research Computing Network, for chatting, taking notes, and sharing URLs and bits of code.


The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...

Interacting with HPC

  • Connecting and copying files
  • Submitting jobs
  • Checking the status of jobs
  • Loading software modules
  • Running many copies of an application


To participate in a workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.


Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. Select “Use the nano editor by default” and click on “Next”.
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Select "Use Windows' default console window" and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.


The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.


The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Supercomputing Wales

In this workshop we will use the Supercomputing Wales facilities to learn to use High-Performance Computing. For this, you will need an account on the Supercomputing Wales facilities.
  1. Visit My Supercomputing Wales
  2. Sign in with your Swansea University email and password
  3. Fill in the form requesting a Supercomputing Wales account. Your aaccount request will be processed by an administrator.
  4. Once you receive an email indicating that your account has been created, then revisit My Supercomputing Wales, and log in again if necessary.
  5. Click the "Reset SCW Password" button, and enter a password that you will use to access the Supercomputing Wales hardware. (This does not have to be the same as your Swansea University password.) Click Submit.
  6. Under "Join a project", enter scw1389 as the project code for this training session, and click "Join".


We will use FileZilla to transfer files to and from the Supercomputing Wales facilities.


  1. Open https://filezilla-project.org/download.php?platform=win64 with your web browser.
  2. Download and run the installer. You only need FileZilla, not FileZilla Pro.
  3. Follow the on-screen instructions. Note that while the installer may try to convince you to install additional software, you do not need to agree to this; if you do not agree to the additional license agreement, FileZilla will still install.
  4. FileZilla has been known to trigger some antivirus and anti-malware applications. You can also use WinSCP, which functions in the same way.


  1. Open https://filezilla-project.org/download.php?platform=osx with your web browser.
  2. Download and open the Client bundle. You only need FileZilla, not FileZilla Pro.
  3. Copy the FileZilla app to your Applications folder.


  1. Search for and install FileZilla in your distribution's package manager.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

  • Two monitors: If you have two monitors, plan to have your terminal up on one monitor and the video conferencing software on the other.
  • Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
  • Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.
This blog post includes detailed information on how to set up your screen to follow along during the workshop.