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Minor changes to text for better readability/correctness.
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atteggiani committed Aug 26, 2024
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16 changes: 9 additions & 7 deletions docs/models/run-a-model/run-access-esm.md
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Expand Up @@ -48,7 +48,7 @@ Before running {{ model }}, you need to fulfil general prerequisites outlined in

<terminal-window>
<terminal-line data="input">payu --version</terminal-line>
<terminal-line lineDelay="1000">1.1.3</terminal-line>
<terminal-line lineDelay="1000">1.1.5</terminal-line>
</terminal-window>

!!! warning
Expand Down Expand Up @@ -308,7 +308,7 @@ One of the most common changes is to adjust the duration of the model run.<br> {

The length of an {{model}} run is controlled by the `runtime` settings in the `config.yaml` file:

```
```yml
runtime:
years: 1
months: 0
Expand Down Expand Up @@ -356,7 +356,7 @@ Now some practical examples:
### Running for less than one year {: id="shorter-runs"}
When debugging changes to a model, it is common to reduce the run length to minimise resource consumption and return faster feedback on changes. In order to run the model for a single month, the `runtime` can be changed to

```
```yml
runtime:
years: 0
months: 1
Expand Down Expand Up @@ -419,7 +419,8 @@ sync:
To enable syncing, change `enable` to `True`, and set `path` to a location on `/g/data`, where _payu_ will copy output and restart folders.

!!! Warning
The {{model}} configurations include a postprocessing [postcript](#postscripts) which converts atmospheric outputs to NetCDF format. This runs in a separate PBS job and this prevents the output and restart files of the most recent run from being automatically synced. When a series of runs completes and the final post-processing is completed, run `payu sync` in the control directory to sync the final outputs and restarts.
The {{model}} configurations include a [postprocessing script](#postscripts) which converts atmospheric outputs to NetCDF format. This script runs in a separate PBS job and prevents the output and restart files of the most recent run from being automatically synced.<br>
After a series of runs and the final post-processing is completed, manually execute `payu sync` in the control directory to sync the final output and restart files.

### Saving model restarts

Expand Down Expand Up @@ -595,13 +596,14 @@ Run scripts or subcommands at various stages of a _payu_ submission. The above e
For more information about specific `userscripts` fields, check the relevant section of [_payu_ Configuration Settings documentation](https://payu.readthedocs.io/en/latest/config.html#postprocessing).


#### Postscripts {: id="postscripts"}
Postprocessing scripts that need to be run after _payu_ has completed all steps that might alter the output directory can be run as postscripts. These run in separate PBS jobs than the main model simulation.
#### Postscripts
Postprocessing scripts that run after _payu_ has completed all steps. Scripts that might alter the output directory, for example, can be run as postscripts. These run in PBS jobs separate from the main model simulation.

```yaml
postscript: -v PAYU_CURRENT_OUTPUT_DIR,PROJECT -lstorage=${PBS_NCI_STORAGE} ./scripts/NetCDF-conversion/UM_conversion_job.sh
```
All {{ model }} configurations include the above NetCDF conversion postscript, which converts the atmosphere model's fields file format output to NetCDF in order to aid analysis and reduce storage requirements. By default, the conversion script will delete the fields files upon successful completion, leaving only the NetCDF output. This automatic deletion can be disabled by commenting out the `--delete-ff` command line flag from the conversion job submission script `./scripts/NetCDF-conversion/UM_conversion_job.sh`. That is, changing

All {{ model }} configurations include the NetCDF conversion postscript mentioned above. This script converts the [UM](/models/model_components/atmosphere#unified-model-um)'s fields file format output to NetCDF in order to facilitate analysis and reduce storage requirements. By default, the conversion script will delete the fields files upon successful completion, leaving only the NetCDF output. This automatic deletion can be disabled by commenting out the `--delete-ff` command line flag from the conversion job submission script `./scripts/NetCDF-conversion/UM_conversion_job.sh`. That is, changing

```bash
esm1p5_convert_nc $PAYU_CURRENT_OUTPUT_DIR --delete-ff
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