Setup & Explore the Codebase

[smarru]

The notebook works locally, but we need a reproducible setup for the ICE cluster and documentation of the code structure.

Goals

• Resolve dependencies and confirm reproducible runs.
• Run the provided notebook in HPC environment.
• Document which modules (general utils, arc diagram utils, 3D utils) handle which parts of the workflow.

Expected Outputs

• Notes or wiki entry: “How to run attention-viz-demo on ICE cluster.”
• Report/diagram of code structure (what calls what).

Discussion Prompt

• What challenges did you hit when running on ICE?
• Can we containerize or provide environment.yml improvements?

[Elliptic461]

I am interested in working on this issue. I believe that we could create a reproducible environment by using a environment.yml or a container. Maybe also write a short guide to document the code structure.

[smarru]

@KevinYinGithub can you keep capturing your work on this issue in a PR or here on this issue thread?

[Elliptic461]

@KevinYinGithub can you keep capturing your work on this issue in a PR or here on this issue thread?
Sure, I can capture my work on this issue using PR.

[Dfromond]

I am interested on working on this issue. I have prior experience working with HPC environments and documenting the setup process. I would like to include an architectural model, similar to my work with PACE's accounting model.

[kbecker35]

I am interested in working on this issue. I plan to work on creating documentation that will be digestible to any user who wants to understand attention-viz (what is attention-viz, why is it important, how does attention-viz digest openfold). I will open a PR and write files organized by topic... the end goal will be to take all of the info and create a wiki website