COSIMA Working Group Meeting Minutes

COSIMA Working Group
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By popular demand, today’s COSIMA meeting was recorded.

You can find the recording of Taimoor’s presentation here:

I also realised that I hadn’t uploaded the recording of Wilton’s talk from February. You can find it here:

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Thanks! Is there a recording of Andy Hoggs talk from last week?

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No sorry. I ran out of bandwidth to record and upload every talk, so now I’m just doing it on an adhoc basis if people ask for a recording of a specific talk.

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@dougiesquire’s slides Squire_ACCESS_BGC.pdf (1.3 MB) from today’s discussion about BGC in ACCESS-OM3.

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Thanks @anton for running today’s training session on the ACCESS-NRI’s intake catalogue.

You can find more information and links to the resources here: ACCESS-NRI Intake Catalog Resources

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I had a request to record @olerieke’s talk last week. You can find the video here: https://youtu.be/nYMlVdbcTA0

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Notes from the first session of “Decoding MOM6”

Presented at the COSIMA meeting on 4 Dec 2025

General info on decoding MOM6 sessions

  • The early sessions of these “Decoding MOM6” segments will talk through the tools that might be useful to navigate the MOM6 code
  • The later sessions will dive deeper into the code itself

How to use github’s search functionality to find code: MOM6 as an example.

Presenter: @dougiesquire

Searching the MOM6 code repository in the ACCESS-NRI GitHub org.
Contains all of the MOM6 Fortran code used in ACCESS-OM3

Quick summary of GitHub search functionality

Pros:

  • Easy and convenient
  • Allows you to see how parts of the model work

Cons:

  • Can only search on the default branch of the repo.
  • GitHub doesn’t actually index everything.

More detailed notes

  • Why use the GitHub search bar?
    • See how a specific piece of code is written - how is it implemented in MOM6? Need to search through the code
  • Dougie’s screen: Looking at MOM6 fork on ACCESS-NRI GitHub org
    • Can click on search at top or click “/“ to start a search
    • Eg search global
      • Will return all files in this repo with “Global” (not case sensitive by default)
      • Get the summary of the files, and can click to expand more lines of code
      • Can click on the line itself and it will take you to that line in the file
    • Can search on multiple terms
      • Eg Global Mean - searches all files with global or mean
      • Eg “Global Mean” - search for specific phrase
      • Eg “Global mean ocean salinity” - can search directly for this diagnostic
        • Finds where it’s registered, and can backtrack to find the code
    • Can search on patterns (regex) rather than words
      • Eg search Global but only at specific path: Global path:src/core
    • Fast, powerful, easy to use
    • Can share searches with people (can’t do this if you are, eg, using “grep” on Gadi terminal)
  • Gotchas
    • Can only search on default branch
    • GitHub doesn’t index everything, and opaque which code is indexed
      • Eg doesn’t index vendor code, but not clear what that means
      • If you search something and it seems weird that nothing is found, then this might be the main issue

Questions from the audience

  • Q: Can it organize the search in order of the subroutines called?
    • MOM6 docs does include schematics on subroutines that are called from specific file
      • But may not be generated anymore, so may be out of date
  • Q: Can searches be case sensitive?
    • Yes, you can use regex: /(?-i)Global/
    • By default they aren’t case sensitive
  • Q: What is regex?
    • Language for pattern matching
    • Stands for regular expression
    • Lots of resources online
      • Just be sure to use the correct version of regex, as there are different types
    • Can click “Search syntax tips” - link at bottom of search popup in GitHub - provides quick help for lots of common regex uses
  • Q: OM3 configurations are all on a branch - does that mean we’ve eliminated the ability to search through OM3 configurations?
    • Yes, we can’t search OM3 configurations at the moment using this tool, because there is almost nothing on the default branch. This is definitely a limitation.
    • Some parameter documentation has been moved to main branch specifically to be able to search on them
    • There are other ways to search through other branches, but no examples were given
    • Lots of people would like GitHub to add functionality to search on a branch other than the default, but not the case currently

More resources

Understanding GitHub Code Search syntax

NOTE: These notes have been added to the Decoding OM3 website (the version above is currently in a PR). Going forward, we’ll plan to add notes for future sessions only on that website, unless there’s interest in keeping them posted here instead.

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