Helping new users run ACCESS-OM2 from an existing control run

COSIMA Ocean
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Hi,

I have been helping a new user, Mike Eabry, get started with running ACCESS-OM2. Specifically, he wants to rerun a small section of the ACCESS-OM2-025 OMIP-2 control run (025deg_jra55_iaf_omip2_cycle6, described at ACCESS-OM2 Control Experiments) and then eventually run a perturbation.

Originally, he followed the tutorial at Run ACCESS-OM - ACCESS-Hive Docs to get started. It was useful, but it does not describe how to restart from an existing run and so he immediately ran into problems. To get it working we had to revert to my old methods (git clone instead of payu clone, linking restarts/outputs by hand into the archive etc…). This is probably not the best since they are outdated and not NRI supported.

So my suggestion is that the Hive docs instructions include information on how to restart from (and use the configs from) an existing run. To me, this is the most common use case that a new user is going to encounter. I feel like it is pretty unlikely that a new user wants to start a new run from scratch (initial conditions), and so the current direct audience for the tutorial is pretty narrow. Happy to hear alternative thoughts though, as I’m sure a lot more has been done in this space since I was last involved.

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Thanks for raising the profile of this issue Ryan. We have actually discussed this before, and from memory we decided to add a warning/redirection at the top of that ACCESS-NRI docs page to direct people wanting to run from old configs/restarts to Tutorials · COSIMA/access-om2 Wiki · GitHub instead. @cbull or someone at ACCESS-NRI, can we add this warning?

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Thanks @adele157 !

I have also just found @Aidan’s post at Running Model Experiments with payu and git which covers similar material. However, this is again using a different method. Specifically, there he links to the payu docs and the line payu checkout -b perturb --restart path/to/restart to restart from a specific restart, whereas the github tutorial recommends linking/copying the output/restart into your archive directly as I’ve always done. Both will work, but it would probably better to be consistent across the various tutorials.

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Hi @rmholmes, mike (not on the forum?) and @adele157

Thanks for highlighting. I agree it would be helpful to add restart instructions onto the hive docs – it is an ongoing challenge keeping multiple doc’s up to date – I’m cc’ing @atteggiani to hopefully help us with the hive docs side / add a link.

@anton gave a discussion on this at last week’s COSIMA meeting (I don’t know if you were able to make it?). His notes and slides are here. Specifically see slide 12:

payu clone –-new-branch <new-branch> --restart <folder_path> <URL> <my-folder>

e.g.:

payu clone --new-branch my_iaf_extension --restart /g/data/ik11/outputs/accessom2/1deg_era5_iaf/restart040 https://github.com/COSIMA/1deg_era5_iaf my_iaf_experiment

So this is the new preferred way of operating afaik. Regarding updating the wiki, @rmholmes – I think you mean this step?

copy (or link) the required restart and output directories from the previous experiment (say, restart123 and output123) into the newly created archive directory (you will need the output directory due to this bug Restarting access-om2 requires outputNNN/ice/cice_in.nml · Issue #193 · payu-org/payu · GitHub)

Correct? @aekiss, would you like to update that? (I suppose this bug got fixed?)

Please mention to Mike that we’re running a session on
“How to run an ACCESS-OM2 model” on 21/03/2025. Feedback on topics we should cover are welcome.

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The advantage of using the --restart method is that it inserts a restart: /path/to/restart/folder option in the config.yaml.

This means the restart location is captured directly in the git history of the config.yaml and the configuration can be re-used as-is by anyone who clones the experiment configuration.

Symlinks also aren’t portable and they’re deleted by the scratch clean-up or a payu sweep --clean and need to be re-linked.

I agree it isn’t great having contradictory information, but also note that is a COSIMA repo, not ACCESS-NRI. Updating it is an option, but it is an overhead to maintain more than one source of information, and confusing to users to know where to look.

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Thank you @rmholmes for pointing this out and @adele157, @cbull and @Aidan for providing further information.

I think, for a user, knowing how to (re)start a run from an existing run is very important and this piece of information should definitely be included within the Hive Docs.

I opened this related issue on the Hive Docs repo, detailing some ideas for the inclusion of this information.

Please have a look and feel free to comment with your suggestions.

Thank you!

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Wonderful @atteggiani, thanks for progressing this. I’ve made a comment on the issue – reach out if anything is unclear. In any case, getting something into the hive docs would be great.

Not sure it’s possible but does the hive docs have the potential to do this kind of thing?

Alternative workflow: restart OM2 off a restart...

#add --restart <folder_path> when cloning
payu clone –-new-branch –restart <folder_path>

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That can be done.
However, I replied with another option, which is on the same line as yours.

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Note @rmholmes and @adele157, this is about to be updated, so feedback is still possible on @atteggiani PR.

Unfortunately, it’s not very graceful but the best we have for the moment.

Thanks @atteggiani!

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