update regional mom6 notebook to work with regional mom6 v1.0.1

[mmr0]

1. Updated to use regional-mom6 v1.0.1.
2. Changed the ACCESS-OM2 model experiment used to produce the boundary forcing as well as the time period, to be consistent with the regional model setup instructions here

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[mmr0]

@navidcy

[navidcy]

Great! Thanks!

It's a good opportunity to force myself install the environment on xp65 to review this. @mmr0 could you point me to the instructions to do so?

[mmr0]

Thanks @navidcy. Some info here:

https://forum.access-hive.org.au/t/access-nri-analysis3-conda-environments-new-release-announcement/4377

When using Australian Research Environment (ARE), add gdata/xp65 to “Storage”, /g/data/xp65/public/modules/ to “Module directories” (under “Advanced options”), and add conda/analysis3 to “Modules”. Additionally, users can switch kernels inside their ARE JupyterLab instance to select the appropriate environment.

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navidcy commented on 2025-06-10T03:24:38Z
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Line #1.    client = Client(threads_per_worker = 7)

why change this to 7?

mmr0 commented on 2025-06-10T03:54:40Z
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This is a hangover from my larger domain where I needed more memory (per worker) to run `setup_initial_condition'. So, 7 is not a special number. It might be more useful to revert to 1 but add a comment. Here's the relevant thread:

COSIMA/regional-mom6#215 (comment)

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navidcy commented on 2025-06-10T03:24:39Z
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Line #1.    #expt_name = "tassie-access-om2-forced"

why commented out code? doesn't add anything

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navidcy commented on 2025-06-10T03:24:39Z
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Line #7.    # longitude_extent = [131, 158]

we don't need commented out code; just have one domain here

there is no need to keep history of what was "the original domain" and then "the post-original domain" and what not; this is just an example it's not the reference case that all researchers are using

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navidcy commented on 2025-06-10T03:24:40Z
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What are all those xarray warnings? They seem scary? Should we deal with this? @anton-seaice, @dougiesquire do you have an opinion?

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navidcy commented on 2025-06-10T03:24:41Z
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Line #5.    #experiment = catalog["01deg_jra55v13_ryf9091"]

remove commented out code

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navidcy commented on 2025-06-10T03:24:42Z
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where's the plot?

ashjbarnes commented on 2025-06-13T03:44:52Z
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Yeah when we're happy we should re-execute the whole notebook, then clear the output from the top cell so we have the plots, but not 1241521 messages from dask

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navidcy commented on 2025-06-10T03:24:42Z
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is this step required?

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navidcy commented on 2025-06-10T03:24:43Z
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Line #6.        #minimum_layers=1

why is this commented out?

if it's not needed then let's delete it

commented out code doesn't mean anything...

mmr0 commented on 2025-06-10T03:56:28Z
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It throws an error with the new version. @ashjbarnes should it be replaced with something or can I just delete?

[navidcy]

I haven't run it yet, but I posted few comments just from glancing the PR -- thanks!

[mmr0]

This is a hangover from my larger domain where I needed more memory (per worker) to run `setup_initial_condition'. So, 7 is not a special number. It might be more useful to revert to 1 but add a comment. Here's the relevant thread:

COSIMA/regional-mom6#215 (comment)

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[mmr0]

It throws an error with the new version. @ashjbarnes should it be replaced with something or can I just delete?

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[ashjbarnes]

It throws an error with the new version. @ashjbarnes should it be replaced with something or can I just delete?

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Yeah the functions have been changed so that 'minimum layers' is replaced with 'minimum depth', and this is implemented at the initialisation of the experiment rather than at the bathymetry step now.

The ACCESS-OM2 forced notebook should be identical to the demo in the package where possible, as this demo notebook is part of the github testing so will always work with latest version

https://github.com/COSIMA/regional-mom6/blob/main/demos/reanalysis-forced.ipynb

[ashjbarnes]

Yeah when we're happy we should re-execute the whole notebook, then clear the output from the top cell so we have the plots, but not 1241521 messages from dask

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[ashjbarnes]

This looks good, thanks @mmr0 ! I'm happy to approve the PR when

1. Commented out code deleted as pointed out by Navid
2. The notebook has been executed to populate the plot Navid noted are missing
3. Outputs that we don't need has been cleared, e.g. the dask worker stuff after the first cell and some of the walls of text that rmom6 prints out after regridding and writing the config files

I wouldn't worry about handling the errors that @navidcy mentioned for the purposes of this PR, but good to keep note of them in case we need to action them later