UCL Introduction to HPC (Onsite)

UCL

Feb 13-15, 2024

09:30 - 13:00 GMT (13th and 14th Feb), 09:30 - 17:00 GMT (15th Feb)

Instructors: Samantha Ahern, Day 1, Heather Kelly, Camilla Harris and Daniel Chau - Days 2 & 3

Helpers: Stephen Thompson, Day 1, Kai Yu, Day 3

General Information

Where: Room 4, 188 Tottenham Court Road, London. Get directions with OpenStreetMap or Google Maps.

When: Feb 13-15, 2024. 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).

Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:

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 arc.teaching@ucl.ac.uk for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Who can attend?: This workshop is open to researchers, staff and students at UCL. You will need an account on UCL's High Performance Computing cluster "Myriad" in order to complete the course.

Booking: Book via Ticket Tailor: Workshop: Introduction to Higher Performance Computing at UCL Please use your UCL email address when booking.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Schedule

Day 1, Tuesday 13th 09:30 - 13:00

Before Complete setup instructions
09:30 Optional Help with setup and installation
10:00 Welcome and course information
10:15 Introduction to Unix Shell
10:55 Break
11:05 Introduction to Unix Shell cont'd
11:55 Break
12:05 Introduction to Unix Shell cont'd
12:55 Wrap-Up
13:00 END

Day 2, Wednesday 14th 09:30 - 13:00

09:30 Optional Help with issues from Day 1
10:00 Introduction to High-Performance Computing
10:55 Break
11:05 Introduction to High-Performance Computing (Continued)
11:55 Break
12:05 Introduction to High-Performance Computing (Continued)
12:55 Wrap-Up
13:00 END

Day 3, Thursday 15th 09:30 - 17:00

09:30 Optional Help with issues from Day 2
10:00 Introduction to High-Performance Computing (Continued)
10:55 Break
11:05 Introduction to High-Performance Computing (Continued)
11:55 Break
12:05 Introduction to High-Performance Computing (Continued)
13:00 Lunch
14:00 Introduction to High-Performance Computing (Continued)
14:55 Break
15:05 Hands-on exercise
16:30 Wrap-Up
17:00 END

Syllabus

The Unix Shell

  • Introducing the Shell
  • Navigating Files and Directories
  • Working with Files and Directories
  • Pipes and Filters
  • Loops
  • Shell scripts
  • Finding Things

Introduction to High-Performance Computing

  • Working on a remote HPC system
  • Scheduling jobs
  • Accessing software
  • Transferring files
  • Using resources effectively
  • Using shared resources responsibly

Setup

To participate in a workshop, you will need access to software as described below. You must apply for access to Myriad in advance of the course via the web form at the following link: Research Computing account services. Please fill in the request as soon as you register as it can take a couple of days for accounts to be activated. 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 tasks more quickly.

  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. From the dropdown menu, "Choosing the default editor used by Git", select "Use the Nano editor by default" (NOTE: you will need to scroll up to find it) and click on "Next".
    3. On the page that says "Adjusting the name of the initial branch in new repositories", ensure that "Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
    4. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
    5. Select "Use bundled OpenSSH".
    6. Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
    7. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    8. Ensure that "Use Windows' default console window" is selected and click on "Next".
    9. Ensure that "Default (fast-forward or merge) is selected and click "Next"
    10. Ensure that "Git Credential Manager" is selected and click on "Next".
    11. Ensure that "Enable file system caching" is selected and click on "Next".
    12. Click on "Install".
    13. Click on "Finish" or "Next".
  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.

Video Tutorial

The default shell in Mac OS X Ventura and newer versions is Zsh, but Bash is available in all versions, 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.

To see if your default shell is Bash type echo $SHELL in Terminal and press the Return key. If the message printed does not end with '/bash' then your default is something else, you can change your current shell to Bash by typing bash and then pressing Return. To check your current shell type echo $0 and press Return.

To change your default shell to Bash type chsh -s /bin/bash and press the Return key, then reboot for the change to take effect. To change your default back to Zsh, type chsh -s /bin/zsh, press the Return key and reboot. To check available shells, type cat /etc/shells.

Video Tutorial

The default shell is usually Bash and there is usually no need to install anything.

To see if your default shell is Bash type echo $SHELL in Terminal and press the Return key. If the message printed does not end with '/bash' then your default is something else, you can change your current shell to Bash by typing bash and then pressing Return. To check your current shell type echo $0 and press Return.

To change your default shell to Bash type chsh -s /bin/bash and press the Return key, then reboot for the change to take effect. To change your default back to Zsh, type chsh -s /bin/zsh, press the Return key and reboot. To check available shells, type cat /etc/shells.