Online
Apr 1, 2021
9:00 am - 12:00 pm
Instructors: Jason Macklin, Richard Yanicky, David McKenzie, Aaron McDivitt
Helpers: Matt Bradley
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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:
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: Apr 1, 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.
Please be sure to complete this survey after the workshop.
| 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 |
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.
If you haven't used Webex before, ask the JAX IT Help Desk to download and install the Webex client for your computer.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
cmd and press [Enter])setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.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.