ARCHER2 HPC Carpentry

EPCC, The University of Edinburgh

Online

Jun 29-30, 2020

10:00 - 16:00 BST

Instructors: David Henty, Juan Herrera

Helpers: Holly Judge, Julien Sindt

General Information

This course introduces accessing remote advanced computing facilities via the command line and High Performance Computing (HPC). After completing this course, participants will:

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

When: Jun 29-30, 2020. 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 support@archer2.ac.uk for more information.

Code of Conduct

Everyone who participates in ARCHER2 activities is required to conform to the ARCHER2 Code of Conduct. This document also outlines how to report an incident if needed.

Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

Schedule

The workshop starts at 10:00 on Monday 29th of June, but we will be online a short while before, so if you have any issues with the setup, please join the Collaborate session from 09:00 BST onwards.

Monday, 29th June

09:00 Help with ARCHER login accounts
10:00 HPC Shell
11:00 Morning break
11:15 HPC Shell (Continued)
12:15 Lunch break
13:15 HPC Shell (Continued)
14:15 Afternoon break
14:30 HPC Shell (Continued)
15:30 Wrap-up
16:00 END

Tuesday, 30th June

   
10:00 HPC Intro
11:00 Morning break
11:15 HPC Intro (Continued)
12:15 Lunch break
13:15 HPC Intro (Continued)
14:15 Afternoon break
14:30 HPC Intro (Continued)
15:30 Wrap-up and Feedback survey
16:00 END

Syllabus

HPC Shell (course materials)

  • 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
  • Key points, cheatsheets and glossary

HPC Intro (course materials)

  • Why Use a Cluster?
  • Working on a remote HPC system
  • Scheduling jobs
  • Accessing software
  • Transferring files
  • Using resources effectively
  • Using shared resources responsibly
  • Key points, cheatsheets and glossary

Setup

To participate in a HPC 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.

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. From the dropdown menu select "Use the nano editor by default" and click on "Next".
    3. 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.)
    4. Ensure that "Use the native Windows Secure Channel library" is selected and click on "Next".
    5. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    6. Ensure that "Use Windows' default console window" is selected and click on "Next".
    7. Ensure that "Enable file system caching" and "Enable Git Credential Manager" are selected and click on "Next".
    8. Click on "Install".
    9. 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 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 enter/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".

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/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.

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.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

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.

Others editors that you can use are BBEdit or Sublime Text.

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

Others editors that you can use are Gedit, Kate or Sublime Text.