Payu: a workflow manager for some ACCESS models

ACCESS-NRI Releases
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12

22/05/2026

:rocket: Release: 1.3.1

https://github.com/payu-org/payu/releases/tag/1.3.1

Getting Started

This version of payu is now available on gadi:

module use /g/data/vk83/modules
module load payu/1.3.1

Updates

For a full list of pull requests that includes additional bug fixes, please see Payu Github 1.3.1 release.

Notes

1. A clearer instruction of payu status

The documentation for payu status has been updated with instructions on how to continuously monitor jobs. To refresh status automatically, you can use watch, for example:

watch -n 30 payu status

refreshes every 30 seconds. Alternatively, a simple loop can be used:

while true; do payu status; sleep 30; done

This keeps a history of status in the terminal and is useful for tracking job progress over time. Note that payu status reads information from job files rather than calling qstat each time it runs, allowing refreshes with minimal impact on the scheduler.

2. Optional auxiliary input directory support for ACCESS-OM3

Payu now automatically copies an optional directory called

auxilary_input

from the control directory into the work directory during setup.
This is intended for extra input files that are not included via the standard input: directive but are instead tracked and versioned by git (see issue #727 for details). Ideally these extra input files would be small text files, not large binary files. The auxiliary_input directory is not intended to replace specifying inputs in config.yaml, but to make experiment setup more flexible and still reproducible.

3. Improvements on payu clone

Following community feedback, the colour palette in payu clone adapts user’s terminal theme for better readability.

Now we can view the flowchart in payu by entering a question mark (?) during the prompts, in addition to the documentation.

4. Tracking collation process and file mapping

payu status now displays both run and collation job information.
For example:

========================================
Run: 0
  ------------- Run Info -------------
  Job ID:            10000.gadi-pbs
  Run ID:            aebsc
  Stage:             archive
  Total Queue Time:  0h 0m 41s
  Model Finish Time: 1950-02-01T00:00:00
  ::
  Job File:          /xxx/.../1deg_jra_ryf-setupTest-hash/payu_jobs/0/run/10000.gadi-pbs.json
  ------------- Collate Info -------------
  Job ID:            20000.gadi-pbs
  Stage:             exited
  Total Queue Time:  0h 0m 30s
  Exit Status:       0 (Success)
  Output Log:        /home/xxx/1deg_jra55_ry_c.o20000
  Error Log:         /home/xxx/1deg_jra_ryf/1deg_jra55_ry_c.e20000
  Job File:          /scratch/$PROJECT/$USER/access-om2/archive/1deg_jra_ryf-setupTest-uuid/payu_jobs/0/collate/20000.gadi-pbs.json
========================================

Collate job files include a collate_mapping dictionary, recording the mapping between uncollated tiles and their corresponding collated files. This is important information for provenance and reproducibility.

For example:

"collate_mapping": {
    "restart012": {
        "hash_collated_file_1": ["hash_uncollated_tiles_1a", ...],
        "hash_collated_file_2": ["hash_uncollated_tiles_2a", ...], ...
             }
 }

Support

Replies to this topic are disabled.

If you have specific questions about this release follow the guidelines for requesting help from ACCESS-NRI.

If you have questions about payu create a topic in a category that best matches the model you are using, or in the Technical category and tag it with payu. If you require assistance follow the guidelines for requesting help from ACCESS-NRI.

Credits

Developments was by @Qianhui_Chen, @jo-basevi, @anton.

Reviewers included @jo-basevi, @Aidan, @dougiesquire, @anton, @atteggiani.