Online
Mar 8, 2022
9:00 am - 12:00 pm
Instructors: Jason Macklin, Kurt Showmaker, Aaron McDivitt, Richard Yanicky, Lucie Hutchins, David McKenzie
Helpers:
Some adblockers block the registration window. If you do not see the registration box below, please check your adblocker settings.
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:
• Use the UNIX command line to connect to a cluster. • Submit and manage jobs on a cluster using a scheduler, transfer files, and use software through environment modules.
Prerequisites: If you have used the UNIX command line (the “shell”) to operate a computer, you’re ready for this workshop.
This course is intended for Jackson Laboratory researchers only. For IT security reasons, external participants will not be admitted.
Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.
When: Mar 8, 2022. 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).
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 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 |
| 09:05 | BASH |
| 09:25 | Intro to HPC/Cyberinfrastructure |
| 9:45 | Batch & Interactive Jobs |
| 10:05 | Break |
| 10:20 | Intro to HPC Profiling |
| 10:40 | Moving Data Around |
| 11:00 | Slurm Arrays |
| 11:20 | END |
To participate in a workshop, you will need access to software as 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.
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.