access-nri/access-om2-bgc

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

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

About the model

ACCESS-OM2-BGC is a global coupled ocean - sea ice model with WOMBAT biogeochemistrydeveloped by COSIMA.

ACCESS-OM2-BGC consists of the MOM 5 ocean model with WOMBAT Biogeochemistry, CICE 5 sea ice model, and a file-based atmosphere called YATM coupled together using OASIS3-MCT v2.0. ACCESS-OM2-BGC builds on the ACCESS-OM (Bi et al., 2013) and AusCOM (Roberts et al., 2007; Bi and Marsland, 2010) models originally developed at CSIRO.

The model code, configurations and performance were described in Kiss et al. (2020), with further details in the draft ACCESS-OM2 technical 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), Hayashida et al. (2023), Menviel et al. (2023) and Wang et al. (2023).

Support

ACCESS-NRI 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. See the ACCESS Help and Support topic for details on how to do this.

Build

ACCESS-NRI is using spack, a build from source package manager designed for use with high performance computing. This repository contains a spack environment definition file (spack.yaml) that defines all the essential components of the ACCESS-OM2-BGC model, including exact versions.

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.

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.

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

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 uses 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 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 project in /g/data/vk83. It is necessary to be a member of 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. 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. To view available ACCESS-OM2-BGC versions:

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.

access-om2-bgc's Issues

Update `CI/CD` to simplified version

Due to this PR: ACCESS-NRI/build-cd#47, we can simplify the CI/CD workflow similarly to ACCESS-NRI/ACCESS-OM2#59.

Update the CI/CD to the new version.

Modify `spack.modules.default.tcl.exclude_implicits: true` -> `hide_implicits: true`

See ACCESS-NRI/ACCESS-OM2#60

Investigation: ACCESS-OM2-BGC Versioning

Some questions that came up on slack regarding the spack.yaml of this repository:

• Should the name of the spec be access-om2 like the existing https://github.com/ACCESS-NRI/access-om2 repo? Could lead to clashes in the vk83 spack environment. See

  ACCESS-OM2-BGC/spack.yaml

  Lines 10 to 11 in af942a8

  	specs:
  	- [email protected]

  . I'm not too sure about remediation actions for this one (@harshula ?) but it might require the creation of a new package in spack-packages? Also note that a change to the package name will mean the removal of the -bgc bit here:

  ACCESS-OM2-BGC/spack.yaml

  Line 59 in af942a8

  access-om2: '{name}-bgc/2023.11.23'

• Should the versions of access-om2 and access-om2-bgc be in lockstep? Currently, both have the version @git.2023.11.23. Would an update to one of the models require an update to the other, or will they drift out of sync? If it's the latter, we should start access-om2-bgc at @git.2024.03.0.

And just for my own understanding:

• What is the type syntax here?

  ACCESS-OM2-BGC/spack.yaml

  Line 16 in af942a8

  require: '@git.2023.11.09 type=ACCESS-OM-BGC'

Tagging @aidanheerdegen as well

2024.03.1 and 2024.06.0 releases are broken

access-om2-bgc 2024.03.1 and access-om2-bgc 2024.06.0 are built with hdf5 1.14.3 which contains a bug that prevents ACCESS-OM2-BGC from running.

The issue is fixed in hdf5 1.14.4, but this version is not yet available in the spack package.

What's the right way forward here? Revert to hdf5 1.14.2 for now?

Note, this issue also affects one ACCESS-OM2 release - see ACCESS-NRI/ACCESS-OM2#74

Tasks

• Remove access-om2-bgc 2024.03.1 as a Release (but keep the tag for transparency)
• Remove access-om2-bgc 2024.06.0 as a Release (but keep the tag for transparency)
• Create the (first!) backport/2024.03 branch, which is where the 2024.03.* (namely, 2024.03.2) tags will live, since there is a 2024.06.0 in front in the history.
• Link PR for 2024.03.2 that addresses the above
• Link PR for 2024.06.1 that addresses the above (can be main branch)

New release with WOMBAT coupling bug fix

There is a bug in MOM5 in the coupling of BGC fields between the sea-ice and WOMBAT - see here. This has been fixed in this PR. A few in the community are keen to test the impact of the fix.

Once the above PR is merged, we should update the ACCESS-NRI fork of MOM5 and do a new release of ACCESS-OM2-BGC that includes the fix.

Update dependencies and compiler version in line with ACCESS-OM2

See the recent updates to ACCESS-OM2: ACCESS-NRI/ACCESS-OM2#73