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README.md: Add archive message, fix formatting #21

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36 changes: 21 additions & 15 deletions README.md
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# ACCESS-OM2: ACCESS Ocean-Sea Ice Model with WOMBAT Biogeochemistry

# ACCESS-OM2-BGC: ACCESS Ocean-Sea Ice Model with WOMBAT Biogeochemistry

> [!IMPORTANT]
> This repository is archived, as the biogeochemistry functionality is now available in [`ACCESS-NRI/ACCESS-OM2`](https://github.com/ACCESS-NRI/ACCESS-OM2) as a runtime configuration through the use of generic tracers. Future updates to ACCESS-OM2 with BGC will be in the linked repository.
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Just reiterating my comments on Zulip:

There hasn't yet been a release of ACCESS-OM2 with support for generic tracer WOMBAT. I don't think we want to archive this and direct people to ACCESS-OM2 until there has.

We're just working through some details of the build process of ACCESS-OM2 with generic tracers. Hopefully this will be done soon and then we can archive this.

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Fair enough! Maybe I'm just feeling overzealous


## About the model
ACCESS-OM2-BGC is a global coupled ocean - sea ice model with WOMBAT biogeochemistrydeveloped by [COSIMA](http://www.cosima.org.au).

ACCESS-OM2-BGC is a global coupled ocean - sea ice model with WOMBAT biogeochemistry developed by [COSIMA](http://www.cosima.org.au).

ACCESS-OM2-BGC consists of the [MOM 5](https://github.com/ACCESS-NRI/MOM5) ocean model with WOMBAT Biogeochemistry, [CICE 5](https://github.com/ACCESS-NRI/cice5) sea ice model, and a file-based atmosphere called [YATM](https://github.com/ACCESS-NRI/libaccessom2) coupled together using [OASIS3-MCT v2.0](https://github.com/ACCESS-NRI/oasis3-mct). ACCESS-OM2-BGC builds on the ACCESS-OM ([Bi et al., 2013](http://www.bom.gov.au/jshess/docs/2013/bi2_hres.pdf)) and AusCOM ([Roberts et al., 2007](https://50years.acs.org.au/content/dam/acs/50-years/journals/jrpit/JRPIT39.2.137.pdf); [Bi and Marsland, 2010](https://www.cawcr.gov.au/technical-reports/CTR_027.pdf)) models originally developed at [CSIRO](http://www.csiro.au).

The model code, configurations and performance were described in [Kiss et al. (2020)](https://doi.org/10.5194/gmd-13-401-2020), with further details in the draft [ACCESS-OM2 technical report](https://github.com/COSIMA/ACCESS-OM2-1-025-010deg-report). The current code and configurations differ from this version in a number of ways (biogeochemistry, updated forcing, improvements and bug fixes), as described by [Solodoch et al. (2022)](https://doi.org/10.1029/2021GL097211), [Hayashida et al. (2023)](https://dx.doi.org/10.1029/2023JC019697), [Menviel et al. (2023)](https://doi.org/10.5194/egusphere-2023-390) and [Wang et al. (2023)](https://doi.org/10.5194/gmd-2023-123).

## Support

[ACCESS-NRI](https://www.access-nri.org.au) has assumed responsibility for supporting ACCESS-OM2-BGC for the Australian Research Community. As part of this support ACCESS-NRI has developed a new build and deployment system for ACCESS-OM2-BGC to align with plans for supporting a range of Earth System Models.

Any questions about ACCESS-NRI releases of ACCESS-OM2-BGC should be done through the [ACCESS-Hive Forum](https://forum.access-hive.org.au/). See the [ACCESS Help and Support topic](https://forum.access-hive.org.au/t/access-help-and-support/908) for details on how to do this.
Expand All @@ -20,32 +23,35 @@ ACCESS-NRI is using [spack](https://spack.io), a build from source package manag

Spack automatically builds all the components and their dependencies, producing model component executables. Spack already contains support for compiling thousands of common software packages. Spack packages for the components in ACCESS-OM2-BGC are defined in the [spack packages repository](https://github.com/ACCESS-NRI/spack_packages/).

ACCESS-OM2-BGC is built and deployed automatically to `gadi` on NCI (see below). However it is possible to use spack to compile the model using the `spack.yaml` environment file in this repository. To do so follow the [instructions on the ACCESS Forum for configuring spack on `gadi`](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545).
ACCESS-OM2-BGC is built and deployed automatically to `gadi` on NCI (see below). However it is possible to use spack to compile the model using the `spack.yaml` environment file in this repository. To do so follow the [instructions on the ACCESS Forum for configuring spack on `gadi`](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545).

Then clone this repository and run the following commands on `gadi`:
```

```bash
spack env create access-om2-bgc spack.yaml
spack env activate access-om2-bgc
spack install
```

to create a spack environment called `access-om2-bgc` and build all the ACCESS-OM2-BGC components, the locations of which can be found using `spack find --paths`.

In contrast, the [COSIMA ACCESS-OM2 repository](https://github.com/COSIMA/access-om2) uses [submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules) to bring all the code dependencies into a single repository and build all the models together.
In contrast, the [COSIMA ACCESS-OM2 repository](https://github.com/COSIMA/access-om2) uses [submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules) to bring all the code dependencies into a single repository and build all the models together.

### Deployment
ACCESS-OM2-BGC is deployed automatically when a new version of the [`spack.yaml`](https://github.com/ACCESS-NRI/ACCESS-OM2-BGC/blob/main/spack.yaml) file is committed to this repository and tagged with a new version. All the ACCESS-OM2-BGC components are built using `spack` on `gadi` and installed under the [`vk83`](https://my.nci.org.au/mancini/project/vk83) project in `/g/data/vk83`. It is necessary to be a member of [`vk83`](https://my.nci.org.au/mancini/project/vk83) project to use ACCESS-NRI deployments of ACCESS-OM2-BGC.

ACCESS-OM2-BGC is deployed automatically when a new version of the [`spack.yaml`](https://github.com/ACCESS-NRI/ACCESS-OM2-BGC/blob/main/spack.yaml) file is committed to this repository and tagged with a new version. All the ACCESS-OM2-BGC components are built using `spack` on `gadi` and installed under the [`vk83`](https://my.nci.org.au/mancini/project/vk83) project in `/g/data/vk83`. It is necessary to be a member of [`vk83`](https://my.nci.org.au/mancini/project/vk83) project to use ACCESS-NRI deployments of ACCESS-OM2-BGC.

The deployment process also creates a GitHub release with the same tag. All releases are available under the [Releases page](https://github.com/ACCESS-NRI/ACCESS-OM2-BGC/releases). Each release has a changelog and meta-data with detailed information about the build and deployment, including:

- paths on `gadi` to all executables built in the deployment process (`spack.location`)
- a `spack.lock` file, which is a complete build provenance document, listing all the components that were built and their dependencies, versions, compiler version, build flags and build architecture
- the environment `spack.yaml` file used for deployment

Additionally the deployment creates environment modulefiles, the [standard method for deploying software on `gadi`](https://opus.nci.org.au/display/Help/Environment+Modules). To view available ACCESS-OM2-BGC versions:
```

```bash
module use /g/data/vk83/apps/spack/0.20/release/modules/linux-rocky8-x86_64
module avail access-om2-bgc
```

For users of ACCESS-OM2-BGC model configurations released by ACCESS-NRI the exact location of the ACCESS-OM2-BGC model executables is not required. Model configurations will be updated with new model components when necessary.