Changes related to 0.4.0 build release

[anton-seaice]

1. Summary:

Config tidyups and improvements to go along with the cosima 0.4.0 access-om3 release.

Changes by commit, in order:

General tidyup:
2. Add LICENSE file
3. Remove note in MOM_override per COSIMA/access-om3#251
4. Re-order MOM_input per COSIMA/access-om3#200
5. Add WIND_STAGGER to MOM_input per COSIMA/access-om3#258
6. Remove unused components from nuopc.runconfig
New build related:
7. Use new deployment (2025.01.0) per COSIMA/access-om3#209
8. Update field dictionary from CESM
9. add_gusts parameter added upstream
10. Turn off restart pointers per COSIMA/access-om3#237
11. Use netcdf4 (parallel) per COSIMA/access-om3#81
12. Use .d and .m in CICE history output filenames per COSIMA/access-om3#201
13. use 'stop_option = end' as default restart write time Turn off extra cice restarts per COSIMA/access-om3#175
Changing to using mom supergrid in CICE:
15. Use mom_supergrid file per COSIMA/access-om3#116
16. set earths radius in MOM to the UM value

3. Dependencies (e.g. on payu, model or om3-scripts)

This change requires:

• access-om3 2025.01.0 deployment / cosima 0.4.0 release.
• payu 1.1.6

It is backwards compatible with om3-scripts, but some scripts can be removed after this change (e.g. cice restart files can now be symlinks 1 2)

4. Ad-hoc Testing

I ran ad-hoc test (payu run -n 2) to check the model restarts.

5. CI Testing

There are several runs below of the CI testing - this shows results did not change ocean.stats output.

6. Reproducibility

The hash for restart files changes for all components with the new build. The hash for mom & cice & the coupler restart files changes with the move to mom supergrid.

7. Documentation

https://github.com/ACCESS-NRI/access-om3-configs/blob/main/doc/MOM_input should be updated if this is merged

8. Formatting

Changes in MOM_input now follow the order of docs/MOM_parameter_short.doc

9. Merge Strategy

Merge commit

[anton-seaice]

!test repro

(Old build - tidied config)

[github-actions]

❌ !test Command Failed ❌ The command given could not be parsed correctly. Usage: !test TYPE [commit] See https://github.com/ACCESS-NRI/access-om3-configs/actions/runs/13063815293

[anton-seaice]

!test repro

[github-actions]

❌ The Bitwise Reproducibility Check Failed ❌

When comparing:

• dev-1deg_jra55do_ryf-iss209 (checksums created using commit f9bd1cf), against
• dev-1deg_jra55do_ryf (checksums in commit 38c039f)

Further information

The experiment can be found on Gadi at /scratch/tm70/repro-ci/experiments/access-om3-configs/f9bd1cf52eb9a155d0a3ea78592e37fd5c30e486, and the test results at https://github.com/ACCESS-NRI/access-om3-configs/runs/36452678213.

The checksums generated by this !test command are found in the testing/checksum directory of https://github.com/ACCESS-NRI/access-om3-configs/actions/runs/13063827808/artifacts/2514228158.

The checksums compared against are found here https://github.com/ACCESS-NRI/access-om3-configs/tree/38c039f4b87e6394ff54adde1986686195bb12e3/testing/checksum

[anton-seaice]

I updated the CI to payu 1.1.6

[anton-seaice]

!test repro

[github-actions]

✅ The Bitwise Reproducibility Check Succeeded ✅

When comparing:

• dev-1deg_jra55do_ryf-iss209 (checksums created using commit f9bd1cf), against
• dev-1deg_jra55do_ryf (checksums in commit 38c039f)

Further information

The experiment can be found on Gadi at /scratch/tm70/repro-ci/experiments/access-om3-configs/f9bd1cf52eb9a155d0a3ea78592e37fd5c30e486, and the test results at https://github.com/ACCESS-NRI/access-om3-configs/runs/36459364300.

The checksums generated by this !test command are found in the testing/checksum directory of https://github.com/ACCESS-NRI/access-om3-configs/actions/runs/13066335556/artifacts/2514904392.

The checksums compared against are found here https://github.com/ACCESS-NRI/access-om3-configs/tree/38c039f4b87e6394ff54adde1986686195bb12e3/testing/checksum

[anton-seaice]

Changes up to this comment are using the old binary.

[anton-seaice]

!test repro

[github-actions]

✅ The Bitwise Reproducibility Check Succeeded ✅

When comparing:

• dev-1deg_jra55do_ryf-iss209 (checksums created using commit db3e538), against
• dev-1deg_jra55do_ryf (checksums in commit 38c039f)

Further information

The experiment can be found on Gadi at /scratch/tm70/repro-ci/experiments/access-om3-configs/db3e5384b6aefd2e292e11e2b99670b428c63a91, and the test results at https://github.com/ACCESS-NRI/access-om3-configs/runs/36560475988.

The checksums generated by this !test command are found in the testing/checksum directory of https://github.com/ACCESS-NRI/access-om3-configs/actions/runs/13105780077/artifacts/2524652405.

The checksums compared against are found here https://github.com/ACCESS-NRI/access-om3-configs/tree/38c039f4b87e6394ff54adde1986686195bb12e3/testing/checksum

[anton-seaice]

The previous test shows no change in results. I've changed cice to use the mom supergrid now, that may change the answers !

[anton-seaice]

!test repro

[github-actions]

✅ The Bitwise Reproducibility Check Succeeded ✅

When comparing:

• dev-1deg_jra55do_ryf-iss209 (checksums created using commit 9d3a779), against
• dev-1deg_jra55do_ryf (checksums in commit 38c039f)

Further information

The experiment can be found on Gadi at /scratch/tm70/repro-ci/experiments/access-om3-configs/9d3a779fc0158f6bdb36a31c990e0dfa77f06d32, and the test results at https://github.com/ACCESS-NRI/access-om3-configs/runs/36560757019.

The checksums generated by this !test command are found in the testing/checksum directory of https://github.com/ACCESS-NRI/access-om3-configs/actions/runs/13105902368/artifacts/2524677912.

The checksums compared against are found here https://github.com/ACCESS-NRI/access-om3-configs/tree/38c039f4b87e6394ff54adde1986686195bb12e3/testing/checksum

[anton-seaice]

@dougiesquire - this is ready for review. @minghangli-uni and @aekiss you might find this interesting

[dougiesquire]

Thanks @anton-seaice. A couple of questions.

I haven't really looked at the pio configuration changes in nuopc.runconfig in any detail. Let me know if it would be helpful if I did.

[anton-seaice]

I haven't really looked at the pio configuration changes in nuopc.runconfig in any detail. Let me know if it would be helpful if I did.

I think they are safe, they should mean:

Use netcdf4 instead instead of netcdf classic
Use 1 processor, which is PE1 as PE0 is busy with being master_task

The mediator is set to use 4 tasks as it can produce lots of output, but none is on by default

[anton-seaice]

!test repro

[github-actions]

✅ The Bitwise Reproducibility Check Succeeded ✅

When comparing:

• dev-1deg_jra55do_ryf-iss209 (checksums created using commit 1566f53), against
• dev-1deg_jra55do_ryf (checksums in commit 3f930d5)

Further information

The experiment can be found on Gadi at /scratch/tm70/repro-ci/experiments/access-om3-configs/1566f53e09d7d05781c9ecfc65155a4a7a80ae6c, and the test results at https://github.com/ACCESS-NRI/access-om3-configs/runs/36820037986.

The checksums generated by this !test command are found in the testing/checksum directory of https://github.com/ACCESS-NRI/access-om3-configs/actions/runs/13189652327/artifacts/2550952931.

The checksums compared against are found here https://github.com/ACCESS-NRI/access-om3-configs/tree/3f930d5ce3dccc48df986b221226e496ff45e17c/testing/checksum

[anton-seaice]

This is ready for re-review. I added the change the Earths radius in MOM. @dougiesquire

[dougiesquire]

Thanks @anton-seaice. LGTM, though I do have one question

[anton-seaice]

!cherry-pick a35956d da28a54 c64bb84 e38a615 4f510d5 0d0d2f5 44c2743 7501a8e 509054f da8b31e 295455a 0137228 4ff72ff 1566f53 4dbb6b8 into dev-1deg_jra55do_ryf_wombatlite

[github-actions]

Automatic Git cherry-picking of commit(s) a35956d da28a54 c64bb84 e38a615 4f510d5 0d0d2f5 44c2743 7501a8e 509054f da8b31e 295455a 0137228 4ff72ff 1566f53 4dbb6b8 into dev-1deg_jra55do_ryf_wombatlite failed. This usually happens when cherry-picking results in a conflic or an empty commit. To manually cherry-pick the commits and open a pull request, please follow these instructions:

1. Create new branch from target branch:

git checkout dev-1deg_jra55do_ryf_wombatlite
git pull
git checkout -b cherry_pick_from_pr161_into_dev-1deg_jra55do_ryf_wombatlite

2. Cherry-pick commits:

git cherry-pick a35956d59c35ce8f1c97227162a4e22f9d7411c2 da28a5488f19e82041600e9d9fa2be39a961744c c64bb84e664f2a15e757b4e331b4e9c800f2efa5 e38a61582e603fe7f25856a42db8110c4400aaed 4f510d58c2ee1a25b8751a67d7284eff234a47d0 0d0d2f55051a116b4b7cac5eeaba5a84c32a023c 44c27438f9974956ecfd4664d625c25727d98302 7501a8e7c4368d18d564b62e574f9f514cf507d2 509054f879765a811e24b4d173d0b7f8affaaa76 da8b31e175967f2bea7951c5627d742ad1e367de 295455aff1022952a9c3fea93bf82776f77f21ec 01372288a10a15caf8d39644977efcc83b76c29e 4ff72ff2a654914921a4bdb36de25e405fdf9080 1566f53e09d7d05781c9ecfc65155a4a7a80ae6c 4dbb6b8ee945ec42b130436fd7f75ce0710a21e0

3. Fix any conflicts and/or empty commits by following the instructions provided by Git.
4. Push the new branch:

git push --set-upstream origin cherry_pick_from_pr161_into_dev-1deg_jra55do_ryf_wombatlite

5. Open a new pull request on github making sure the target branch is set to dev-1deg_jra55do_ryf_wombatlite.