High Performance Computing

The Jackson Laboratory

Online

June 23, 2021

9:00 am - 12:00 pm

Instructors: Jason Macklin, Richard Yanicky, David McKenzie, Aaron McDivitt

Helpers: Sandeep Namburi

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General Information

This workshop introduces high performance computing using the Jackson Laboratory’s computing cluster. The goal 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 teach best practices for scientific computing in high performance computing environments. By the end of this workshop, participants will be able to:

connect to a cluster
write simple shell scripts
submit and manage jobs on a cluster using a scheduler
transfer files
use software through environment modules

Who: The course is aimed at graduate students and other researchers at the Jackson Laboratory. For IT security reasons, external participants will not be admitted. Knowledge of basic UNIX shell commands is a prerequisite for this training.

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

When: June 23, 2021. Add to your Google Calendar.

Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). 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 jason.macklin@jax.org or susan.mcclatchy@jax.org for more information.

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

Surveys

Please be sure to complete this survey after the workshop.

Post-workshop Survey

Schedule

Wednesday June 23

09:00	Workshop overview and introductions
09:15	Logging in and commands available to the user
09:20	SBATCH options/script
9:25	Batch jobs
9:35	Interactive jobs
9:45	Profiling
10:30	Morning break
10:45	Basic job arrays
11:00	Moving data around (Globus)
11:55	Wrap-up
12:00	END

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.

Install the videoconferencing client

Please ask the JAX IT help desk to download and install the Webex client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Webex video conference client open. In order to see both at once, we recommend using one of the following set up options:

Two monitors: If you have two monitors, plan to have the tool you are learing up on one monitor and the video conferencing software on the other.
Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Download and install MobaXterm or PuTTY.
If your "HOME" environment variable is not set (or you don't know what this is):

Open command prompt (Open Start Menu then type cmd and press [Enter])
Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
Press [Enter], you should see SUCCESS: Specified value was saved.
Quit command prompt by typing exit then pressing [Enter]

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.

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.