Introduction to High Performance Computing

June 7, 2019

9:00 am - 3:00 pm

Instructors: David McKenzie, Aaron McDivitt, Jason Macklin

Helpers:

General Information

This workshop is an introduction to high performance computing using the Jackson Laboratory’s computing cluster.

The goal of this lesson is to teach novice programmers to use powerful tools and computing resources, and to engage in best practices for using these resources. The emphasis of this workshop is to give attendees a strong foundation in the fundamentals of the bash shell, and to teach best practices for scientific computing.

This workshop is only open to Jackson Laboratory employees.

Where: Holt Conference Room, The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr, Farmington CT. Get directions with OpenStreetMap or Google Maps.

When: June 7, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). They should have a few specific software packages installed (listed below).

Code of Conduct: Everyone who participates is required to conform to the 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 susan.mcclatchy@jax.org or jason.macklin@jax.org for more information.

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1

Before Pre-workshop survey
09:00 Welcome and introductions
09:15 Introducing the Shell
09:20 Navigating Files and Directories
10:00 Working With Files and Directories
10:30 Coffee
10:45 Working With Files and Directories (continued)
11:05 Pipes and Filters
12:00 Lunch break
13:00 Introduction to JAX High Performance Computing
14:45 Post-workshop survey
15:00 END

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

Syllabus

The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Reference...

Setup

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.

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.

High Performance Computing Cluster

JAX provides access to high performance computing (HPC) through two computing clusters: 1) Cadillac, which serves Bar Harbor; and 2) Helix, which serves Farmington.

Cluster Access

Ask the JAX IT Service Desk to give you an account for Cadillac (Bar Harbor) or Helix (Farmington).