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Software Package/Environment Management Workshop

On October 3-4, 2024, the SCINet Office will be leading a 2-day workshop on Software Package/Environment Management.

In this workshop, we will cover best practices for managing software packages and computing environments on SCINet’s supercomputers. This will be a hands-on workshop that will provide you with the practical knowledge and skills you need to spend less time worrying about package management and more time focusing on your research!

Here is a daily breakdown of the topics:

  • Day 1, October 3, 1:00 PM - 4:30 PM ET: Introduction, Python & conda
  • Day 2, October 4, 1:00 PM - 4:00 PM ET: R

To register for the Software Package and Environment Management Workshop, please fill out this form.

Pre-Workshop Instructions:

To help minimize technical issues and delays at the start of the workshop, please try the following four tests prior to the workshop.

  • Logging on to Atlas Open OnDemand (OOD): Please confirm you can successfully log in to Atlas OOD with your SCINet account (see instructions here). If you are successful, you will be able to see the Atlas OOD home page.
  • Atlas Shell Access: When on Atlas OOD, click on the top navigation bar: “Clusters” > “Atlas Shell Access”. A new tab will appear that looks like a shell terminal (e.g., like PowerShell). Please confirm you do not receive any error messages or requests to re-authenticate and that the final line looks like “[firstname.lastname@atlas-login-1 ~]$”.
  • JupyterLab Server: Back on the main Atlas OOD tab, click on the top or side navigation bar: “Interactive Apps” > “JupyterLab Server”.
    • Fill the input fields with the following (input fields not listed below can be left at their default values):
      • Partition: atlas
      • Number of hours: 1
      • Number of nodes: 1
      • Number of tasks: 1
      • Additional Slurm Parameters: (leave empty)
    • Click the “Launch” button.
    • Wait a moment for the job card to update from “Queued” to “Running”.
    • Please confirm that clicking on the “Connect to JupyterLab Server” button opens a new tab with the JupyterLab Server interface.
  • RStudio Server: Back on the main Atlas OOD tab, click on the top or side navigation bar: “Interactive Apps” > “RStudio Server”. Repeat the same steps as for JupyterLab Server to confirm you can launch an RStudio Server session.

Tutorial Setup Instructions

Steps to prepare for the tutorial session each day:

  1. Login to Atlas Open OnDemand at https://atlas-ood.hpc.msstate.edu/. For more information on login procedures for web-based SCINet access, see the SCINet access user guide.

  2. Open a command-line session by clicking on “Clusters” -> “Atlas Shell Access” on the top menu. This will open a new tab with a command-line session on Atlas’ login node.

  3. Request resources on a compute node by running the following command.

     srun --reservation=workshop -A scinet_workshop1 -t 05:00:00 -n 1 --mem 8G --pty bash

  4. Create a workshop working directory by running the following commands. Note: you do not have to edit the commands with your username as it will be determined by the $USER variable.

     mkdir -p /90daydata/shared/$USER/
 cd /90daydata/shared/$USER/