HPC Carpentry Workshop

UCL

Online

Nov 22nd - 24th, 2021

09:30 - 13:00

Instructors: Ian Kirker, Krishnakumar Gopalakrishnan, Tuomas Koskela

Helpers: Ian Kirker, Krishnakumar Gopalakrishnan, Sarah Jaffa, Heather Kelly, Tom Couch, Jamie Quinn

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: Nov 22nd - 24th, 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).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email s.jaffa@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.

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.

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1

Before Follow setup instruction and complete pre-workshop survey
09:30 (Optional) Help with setup issues
10:00 Introduction to using the shell in a High-Performance Computing context
10:55 Morning break
11:05 Introduction to using the shell in a High-Performance Computing context (Continued)
11:55 2nd Morning break
12:05 Introduction to using the shell in a High-Performance Computing context (Continued)
12:55 Wrap-up
13:00 END

Day 2

10:00 Introduction to using the shell in a High-Performance Computing context (Continued)
10:55 Morning break
11:05 Introduction to High-Performance Computing
11:55 2nd Morning break
12:05 Introduction to High-Performance Computing (Continued)
12:55 Wrap-up
13:00 END

Day 3

10:00 Introduction to High-Performance Computing (Continued)
10:55 Morning break
11:05 Introduction to High-Performance Computing (Continued)
11:55 2nd Morning break
12:05 Hands-on Exercise
12:55 Wrap-up
12:58 Post-workshop Survey
13:00 END

Syllabus

The Unix Shell

  • Why Use a Cluster?
  • Connecting to the remote HPC system
  • Moving around and looking at things
  • Writing and reading files
  • Wildcards and pipes
  • Scripts, variables, and loops

Introduction to High-Performance Computing

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

Setup

To participate in a Software Carpentry 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.

HPC account

You must apply for access to Myriad in advance of the course via the web form at the following link: Research Computing account services

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 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. Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
    6. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    7. Ensure that "Use Windows' default console window" is selected and click on "Next".
    8. Ensure that "Default (fast-forward or merge) is selected and click "Next"
    9. Ensure that "Git Credential Manager Core" is selected and click on "Next".
    10. Ensure that "Enable file system caching" is selected and click on "Next".
    11. Click on "Install".
    12. 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 some versions of macOS is Bash, and 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 and you can run Bash by typing bash

If you want to change your default shell, see this Apple Support article and follow the instructions on "How to change your default shell".

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 a terminal and press the Enter key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.

SSH

All students should have an SSH client installed. SSH is a tool that allows us to connect to and use a remote computer as our own. Please follow the directions below to install an SSH client for your system.

Windows: Install MobaXterm from http://mobaxterm.mobatek.net. You will want to get the Home edition (Installer edition).

macOS: Although macOS comes with SSH pre-installed, you will need to install XQuartz to enable graphical support. Note that you must restart your computer to complete the installation.

Linux: Linux users do not need to install anything, you should be set!

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Video Tutorial

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.