HPC for Instructional Use

Request a consultation if assistance is needed in planning the HPC related course materials, or see the items below to inform lesson plans.

Requesting access for instructional use

Managing access, storage, and software - By Example

Consider a biology class that is listed in Registration and Records as BIO 427.

Instructors are responsible for ensuring proper use of the HPC by the class.

All users are required to learn the basics for using Henry2. Folks who are completely new to HPC will have quite a bit to learn, but students, instructors, and teaching assistants who have used other systems also need to review the basics. Henry2 is very different from other centers, and misunderstandings about this often lead to repeated violations of the AUP.

Usage may be monitored by doing the following.
  1. On the top nav bar of the HPC website under Resources, click on Manage Existing Project, or use the direct link to OIT Research Services. Click the green button Manage HPC Project.
  2. Under Projects that you own, click the eye icon.
  3. HPC usage for the Project is shown for the past 90 days. CPU is in CPU hours.
  4. Screenshots for checking usage

Instructional material for teaching the basics of HPC

HPC's full recommendation is that instructors request that all students complete the HPC Beginner Workshop. Students recieve a certificate of completion, and we recommend that the student should forward that certificate of completion as a class assignment. The Workshop is fully online and asynchronous, and takes anywhere from 1.5 to 5 hours depending on the user's current familiarity with Linux and the command line. Alternatively, instructors might request students to take the HPC Quiz and send proof of successful completion. The HPC Quiz is 10 questions that specifically call attention to the Acceptable Use Policy.

For some classes, HPC is only necessary to run a very specific, well defined task or set of tasks. In that case, an instructor may want minimize time spent on general HPC training. That is fine if the instructor provides their own teaching plans on using the HPC, including providing the batch script and list of commands. Instructors have had success with taking a look at the format of the HPC Beginner Workshop, and selecting a subset of the links and videos to include with their lesson plans. For example, an instructor might only include the HPC video tutorials for logging in, basic Linux, and the Acceptable Use Policy. Then, if the instructor has all of the materials available on the HPC, they can provide custom instructions for students to log in, cd to /share, copy and then run the class batch script.

Examples of HPC instructional materials

Metagenomics on the HPC: QIIME2 example

  • BIT 477/577: Metagenomics QIIME Analysis - Example of creating custom HPC instructions specific to a class.
  • BIT 477/577: QIIME2 Moving Pictures Tutorial - Example of providing guidance on how to modify existing tutorials for HPC use.
  • Supplemental HPC training request: WRF example

  • MEA 716: Tips for analysis on Henry2 - written for MEA716, 1/26/2020, but useful for any class. Includes where to login/run, disk space management, what NOT to do on the HPC system, and considerations for creating an optimal batch submission script for MPI WRF jobs.
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