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Updated by revising Anton's suggestions.
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Updated by revising Anton's suggestions.
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atteggiani committed Jul 15, 2024
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13 changes: 8 additions & 5 deletions docs/models/run-a-model/run-access-om.md
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Expand Up @@ -127,7 +127,7 @@ _Payu_ also creates symbolic links in the _control_ directory pointing to the `a
This design allows multiple self-resubmitting experiments that share common executables and input data to be run simultaneously.

!!! admonition warning
The _laboratory_ directory might get deleted if not accessed for several days. To know more about how to preserve your experiment refer to [Syncing output data](#syncing-output-data).
Files on the `/scratch` drive, such as the _laboratory_ directory, might get deleted if not accessed for several days and the `/scratch` drive is limited in space. For these reasons, all model runs which are to be kept should be moved to `/g/data/` by enabling the _sync_ step in _payu_. To know more refer to [Syncing output data](#syncing-output-data).

### Run configuration

Expand Down Expand Up @@ -376,7 +376,7 @@ project: ol01
### Syncing output data

The _laboratory_ directory is typically under the `/scratch` storage on _Gadi_, where [files are regularly deleted once they have been unaccessed for a period of time](https://opus.nci.org.au/pages/viewpage.action?pageId=156434436). For this reason climate model outputs need to be moved to a location with longer term storage.<br>
On _Gadi_, this is typically under a project code on `/g/data`.
On _Gadi_, this is typically in a folder under a project code on `/g/data`.

_Payu_ has built-in support to sync outputs, restarts and a copy of the _control_ directory git history to another location.<br>
This feature is controlled by the following section in the `config.yaml` file:
Expand All @@ -390,7 +390,10 @@ sync:
- '*.nc.*'
- 'iceh.????-??-??.nc'
```
To enable output syncing, change `enable` to `True`, and set `path` to a location on `/g/data`.
To enable syncing, change `enable` to `True`, and set `path` to a location on `/g/data`, where _payu_ will copy output and restart folders. A sensible `path` could be: `/g/data/$PROJECT/$USER/experiment_name/`.

!!! admonition tip
The {{model}} default configurations include a [userscript](#userscripts) in the _sync_ step that concatenates daily history/diagnostic output from the Sea-Ice model (CICE5) into monthly files. This speeds up access and saves storage space, but will only run if _sync_ is enabled.

### Saving model restarts

Expand Down Expand Up @@ -535,8 +538,8 @@ A dictionary to run scripts or subcommands at various stages of a _payu_ submiss

- `error` gets called if the model does not run correctly and returns an error code.
- `run` gets called after the model execution, but prior to model output archive.
- `sync` gets called at the start of the sync pbs job.

- `sync` gets called at the start of the sync pbs job. For more information refer to [Syncing output data](#syncing-output-data).
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).

#### Miscellaneous
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