Update GROMACS.md #738
Update GROMACS.md #738
Conversation
add some example scripts. Disclaimer: Unverified. I have no idea how to run gromacs Signed-off-by: Cal <35017184+CallumWalley@users.noreply.github.com>
![gemini-code-assist[bot]](https://avatars.githubusercontent.com/in/956858?s=60&v=4){kind=small}
There was a problem hiding this comment.
Summary of Changes
Hello @CallumWalley, I'm Gemini Code Assist1! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!
This pull request primarily enhances the GROMACS.md documentation by introducing practical example SLURM scripts. These examples aim to guide users on how to run GROMACS simulations in different configurations, specifically serial and shared memory setups. Additionally, it includes unverified examples for GPU and multi-node execution, which are currently commented out. The PR also refines existing text for clarity and adds a recommendation regarding checkpointing for long-running jobs.
Highlights
- New GROMACS Example Scripts: Added a dedicated "Examples" section to the GROMACS documentation, providing SLURM scripts for serial and shared memory execution.
- Unverified GPU and Multi-Node Examples: Included commented-out SLURM scripts for running GROMACS on GPUs and across multiple nodes, pending verification.
- Documentation Refinements: Minor text and formatting improvements were made, including a recommendation for using checkpointing in long-running GROMACS jobs.
Using Gemini Code Assist
The full guide for Gemini Code Assist can be found on our documentation page, here are some quick tips.
Invoking Gemini
You can request assistance from Gemini at any point in your pull request via creating an issue comment (i.e. comment on the pull request page) using either /gemini <command> or @gemini-code-assist <command>. Below is a summary of the supported commands.
| Feature | Command | Description |
|---|---|---|
| Code Review | /gemini review |
Performs a code review for the current pull request in its current state. |
| Pull Request Summary | /gemini summary |
Provides a summary of the current pull request in its current state. |
| Comment | @gemini-code-assist | Responds in comments when explicitly tagged, both in issue comments and review comments. |
| Help | /gemini help |
Displays a list of available commands. |
Customization
To customize Gemini Code Assist for GitHub experience, repository maintainers can create a configuration file and/or provide a custom code review style guide (such as PEP-8 for Python) by creating and adding files to a .gemini/ folder in the base of the repository. Detailed instructions can be found here.
Limitations & Feedback
Gemini Code Assist may make mistakes. Please leave feedback on any instances where its feedback is incorrect or counter productive. You can react with 👍 and 👎 on @gemini-code-assist comments. If you're interested in giving your feedback about your experience with Gemini Code Assist for Github and other Google products, sign up here.
You can also get AI-powered code generation, chat, as well as code reviews directly in the IDE at no cost with the Gemini Code Assist IDE Extension.
A doc's new code, a script's fresh start, For GROMACS runs, a guiding art. Though unverified, a helpful hand, To aid the user, across the land.
Footnotes
-
Review the Privacy Notices, Generative AI Prohibited Use Policy, Terms of Service, and learn how to configure Gemini Code Assist in GitHub here. Gemini can make mistakes, so double check it and use code with caution. ↩
|
Test deployment available at https://callumwalley.github.io/mkdocs-demo-deploy/nesi/support-docs/gromacs-examples See all deployed demo sites |
|
Sorry for jumping in, but,
|
| Unless your problem is so large | ||
| that it does not fit on one whole compute node you are probably best | ||
| off not using `gmx-mpi`. The GROMACS documentation says on this: |
There was a problem hiding this comment.
Nitpicking: it would be challenging not to fit a simulation to one node, GROMACS has rather low memory usage. But with the 128+ cores per node (per https://docs.nesi.org.nz/General/FAQs/Mahuika_HPC3_Differences/#cpu-cores-per-node), it could indeed be that one node gives good enough performance for many usecases.
There was a problem hiding this comment.
@al42and Thank you for your feedback! Super helpful as I don't have time to get antiquated with GROMACS at the moment.
I removed some stuff, tried to simplify the message.
Remove some duplication. Uncommented mpi and gpu examples (still untested though). Clarified GROMACS is not an acronym. Signed-off-by: Cal <35017184+CallumWalley@users.noreply.github.com>
add some example scripts. and formatting fixes.
Disclaimer: Unverified. I have no idea how to run gromacs