University of Alberta

September 25 & 26, 2018

9am - 4pm

Instructors: John Simpson, Kamil Marchinkowksi, Chris Want

Helpers: Erming Pei

General Information

HPC Carpentry is a new workshop in the beta development phase for inclusion in The Carpentries. In is designed to teach how to interact with a compute cluster. The first lesson, HPC Shell, is a general introduction to the bash command line with specific reference to working on remote system. The second lesson, HPC Intro, focuses on submitting work on a typical HPC cluster through the scheduler. The third lesson, HPC Beyond, is a alpha protoype focusing on parallelization and optomization. Each lesson takes roughly a half day.

Workshops are intended to be fully interactive and taught in the “Software Carpentry” format: instruction is done live, with learners coding along with workshop instructors. Frequent excercises and test problems have been added to ensure students have a chance to try things on their own. No prior computing experience is required or expected.

Where: CCIS L1-150. Get directions with OpenStreetMap or Google Maps.

When: September 25 & 26, 2018. 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 Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. 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 john.simpson@ualberta.ca for more information.

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Schedule

The workshop is split into three modules, as follows:

  1. HPC Shell, Tuesday 1pm-3:50pm
  2. HPC Intro, Wednesday 9am-11:50am
  3. HPC Beyond, Wednesday 1pm-3:50pm

Click the links in the list above for a list of specific content. HPC Beyond is so new that we don't have any pages available for it yet.

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

Setup

To participate in HPC Carpentry you will need an up-to-date web browser and access to the software described below.

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.

Windows

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.

macOS

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.

Linux

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.

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, try typing the escape key, followed by :q! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

Windows

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.

macOS

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 Text Wrangler or Sublime Text.

Linux

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.