Once the laboratory has been created and the experiment has been configured, as an optional step you can check that the paths have been correctly specified by running:
This creates the temporary work directory and is done automatically when the model is run. If there any errors in the configuration, such as incorrect or missing paths, these can be fixed. payu will not run the model if there is an existing work directory, so this must be removed (see Cleaning up).
The setup command will also generate manifest files in the manifest directory. The manifest files track the executable, input and restart files used in each run. When running at NCI the manifest file must be present as it is scanned for storage points in order to correctly specify the argument to the -l storage= option when submitting a PBS job.
Takeaway: always run payu setup on the login node when you set up a new experiment, to check the paths are correct and update the manifest files, which means when you submit a run payu will add the correct storage flags to your PBS job.
If either of these responses solves your issue, feel free to mark it as the solution, which will help others if they have a similar issue find the correct solution, and close the topic if you think it has been resolved.
@ars599 I’m not sure if it’s useful for you but for this paper I ran a bunch of different vertical resolution runs (kds50, kds75, kds100, kds135 and gfdl50) in the 1-degree ACCESS-OM2 on Gadi. The configurations are on different branches of my 1deg_jra55_ryf repository, e.g. kds75 and kds135. They might save you having to update your old vayu configurations?