Payu collate dies for mitgcm with "module not found"

COSIMA
,
1

Description of request:

I’m finding that the mitgcm payu collate crashes with the payu sourced from vk83 (see error below). There was no issue with the same operation for the old hh5 version. Note that payu run etc works fine, it just dies on collate with module not found. Ideas?

Environment:

What executed:

The .e for payu collate is the following:
Traceback (most recent call last):
File “/g/data/vk83/apps/base_conda/envs/payu-1.2.0/bin/payu-collate”, line 10, in
sys.exit(runscript())
File “/g/data/vk83/apps/base_conda/envs/payu-1.2.0/lib/python3.10/site-packages/payu/subcommands/collate_cmd.py”, line 111, in runscript
expt.collate()
File “/g/data/vk83/apps/base_conda/envs/payu-1.2.0/lib/python3.10/site-packages/payu/experiment.py”, line 973, in collate
model.collate()
File “/g/data/vk83/apps/base_conda/envs/payu-1.2.0/lib/python3.10/site-packages/payu/models/mitgcm.py”, line 281, in collate
from mnctools import mnctools as mnc
ModuleNotFoundError: No module named ‘mnctools’

Actual results:

Expected results:

Additional info:

2

Thanks for reporting this. It is because the conda environment we deploy to support payu doesn’t have mnctools:

I’ll look into what is required to add it and get back to you.

4

@CallumJShakespeare I have added mnctools to the payu/dev environment.

You can access it like so:

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

I have tested it and mnctools is available:

$ module use /g/data/vk83/prerelease/modules
$ module load payu
Loading payu/dev-20251111T000211Z-46fb4ac
  Loading requirement: singularity
$ python -c 'from mnctools import mnctools as mnc'
$

Can you try using payu/dev and confirm it fixes your problem and let me know?

When it’s confirmed this solves your issue I’ll update the payu/1.2.0 release conda environment with the same fix.

5

Hi @Aidan Thanks! Can confirm this has fixed the issue!

6

Great.

I have updated the payu/1.2.0 environment (which is the default) to include mnctools, so it should now work as well.

$ module load payu
Loading payu/1.2.0
  Loading requirement: singularity
$ python -c 'from mnctools import mnctools as mnc'
$

If this solves your issue can you mark it as the solution?

Thanks.