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. 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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