ACCESS-ROM3 setup instructions

[mmr0 (Madi Rosevear)]

Hi Helen - I’ve had this (nonfatal) error too but haven’t yet had a chance to dig into it. Perhaps relatedly, I don’t think I can pick up from a restart. Have you been able to restart?

[dougiesquire (Dougie Squire, ACCESS-NRI Ocean/Sea-Ice Modelling Team)]

@Paul.Gregory

I tried using payu with the xp65 modules.

$ module use /g/data/xp65/public/modules
$ module load conda/analysis3

Then load payu

$ module use /g/data/vk83/prerelease/modules
$ module load payu/dev

But this generates a PE error.

FATAL from PE     0: time_interp_external 2: time 734872 (20130105.000050 is after range of list 734868-734872(20130101.000000 - 201301
05.000000),file=INPUT/forcing_obc_segment_001.nc,field=u_segment_001

in mom_cap.F90

My guess is that this isn’t related to Payu. But, it’s quite hard to help debug your issues without seeing your Payu configuration. Can you push your config to Github (apologies if you have already and I missed it)?

To work around the non-fatal issues described in this post, I’d try for now just commenting out the entire userscripts section in the config.yaml.

[Aidan (Aidan Heerdegen, ACCESS-NRI Release Team Lead)]

@Paul.Gregory

I tried using payu with the xp65 modules.

payu is also distributed as a `conda environment.

Its generally isn’t recommended to try and use two conda environments at the same time.

Why is this necessary?

[Paul.Gregory]

Yes I forgot that payu contains its own conda

I’ve uploaded my working config (using @mmr0 's 4x4 decomposition running on 16 CPUs) to :

GitHub - Rush74/access-om3-configs: Configuration setup for access-om3

[helen (Helen Macdonald)]

Hi all – the general agreement is that this thread is getting unwieldy, and we would like to split the errors up into separate topics. We now have a space for starting new regional-mom threads here. It is a new space for regional and coastal ocean modelling in general so is very basic stencil at the moment but we will grow it a bit to add more in the coming weeks.

I will start a new one for the CICE error.

@mmr0 the CICE error didn’t used to affect restarts can you please start a new thread for your restart issue. Is there an error message that can be shared?

@Paul.Gregory, can you please start a new thread for your current error

Any other ongoing issues that I have missed?

[helen (Helen Macdonald)]

@helen

I will start a new one for the CICE error.

This is here

[helen (Helen Macdonald)]

@Paul.Gregory @mmr0 @PSpence @Lizzie: just a heads-up that this has now been moved to ancoms/regional-mom

[anton (Anton Steketee, ACCESS-NRI Oceans Team)]

@dougiesquire

Yeah this an issue that is fixed in more recent versions of access-nri-intake - see Ship schema with package · Issue #185 · ACCESS-NRI/access-nri-intake-catalog · GitHub.

The version in hh5 environment is quite old now. Using the xp65 environment should fix the issue. I can provide more details on Tuesday if someone doesn’t do so first.

This should be resolved now through

use xp65 instead of hh5 for new versions

which has been pulled to

/g/data/vk83/apps/om3-scripts and will be picked up automatically (as that path is common to all om3 configs).

[Lizzie (elizabeth ellison)]

I have been getting an error

(File "/g/data/vk83/apps/payu/1.1.5/lib/python3.10/site-packages/payu/models/cesm_cmeps.py", line 165, in setup
    ntasks = int(self.runconfig.get("PELAYOUT_attributes", f"{realm}_ntasks"))
TypeError: int() argument must be a string, a bytes-like object or a real number, not 'NoneType'")

in my setup and eventually noticed in these instructions is says
module use /g/data/vk83/modules
module load payu/1.1.5
but in the config.yaml file I am using (from GitHub - ACCESS-NRI/access-om3-configs: ACCESS-OM3 MOM6-CICE6 configurations) it actually says “payu_minimum_version: 1.1.6”.
Did this change recently because I had no problems with this before!

[helen (Helen Macdonald)]

Thanks @Lizzie - good catch! Yes, it was a recent change. I was able to replicate your error using payu/1.1.5 and fix it by using payu/1.1.6

Can I please get you to check that it runs for you if you swap:

module use /g/data/vk83/modules
module load payu/1.1.5

to

module use /g/data/vk83/modules
module load payu/1.1.6

I will update the instructions.

(edited to make it payu/1.1.6)

[anton (Anton Steketee, ACCESS-NRI Oceans Team)]

@Lizzie

Did this change recently because I had no problems with this before!

Yes - this changed with Remove unused components · ACCESS-NRI/access-om3-configs@4f510d5 · GitHub

As Helen is saying - use payu/1.1.6

[Lizzie (elizabeth ellison)]

Yep, I forgot to say loading in payu 1.1.6 fixed it for me! Thank you

[Paul.Gregory]

Hi @Lizzie

If you’re able to successfully run this example (a 140 x 249 grid over Tasmania with a 10x10 layout) can you upload your configuration to GitHub so I can try it?

Thanks.

[Lizzie (elizabeth ellison)]

Hi Paul
This ran for me (a few weeks ago!)

GitHub - elizabeth-ellison/example-access-rom3

I was using a different version of the regional mom6 package, so I had more in the MOM override file than the input file compared to Helen’s instructions.

[Paul.Gregory]

Thanks. I’ll have a look at it.

[mmr0 (Madi Rosevear)]

@helen

Download your other configuration files from an ACCESS_OM3 run

Hi Helen, can you confirm which branch we should use here?

The instructions say payu clone -b expt -B dev-1deg_jra55do_iaf https://github.com/ACCESS-NRI/access-om3-configs/ access-rom3

But that branch doesn’t exist. Is dev-MC_100km_jra_iaf the best/equivalent choice?

[helen (Helen Macdonald)]

Thanks @mmr0 - yes, please use that one. We have recently changed the branch names and you are correct that this is the equivilent. I will update the instructions.

[helen (Helen Macdonald)]

Note all that @mmr0 has reported troubles running the notebook using the latest analysis3 environment. Check this thread for updates and workarounds on the issue.

[mmr0 (Madi Rosevear)]

Hi - having just gotten this running again after a long time spent in the weeds, I suggest:

1. Using the latest version of regional-mom6 and this notebook (currently my own fork, but hopefully will be merged into the cosima recipes) and the conda environment analysis3-25.05 to generate the input files
2. Following the above instructions

The only “broken” instruction is about the diag_table which must have changed since the instructions were written. Perhaps we can put a file that’s well-suited to a regional config somewhere @helen ?

ping @Paul.Gregory @Lizzie