Running MOM5

Running an ocean simulation using MOM5 requires three steps:

  1. Designing an experiment, including its numerical grids and forcing fields
  2. Configuring MOM's numerical settings and physical parameterisations
  3. Executing MOM and generating numerical output

This section focusses on the final step of model execution, as well as a cursory discussion of model configuration. It assumes that you have been provided with a pre-configured experiment, such as one of the MOM5 examples.

In general, model design and configuration is a complex process which can require a broad range of expertise. For more detailed discussions about experiment design, consult the MOM5 documentation and ocean modelling literature.

Running MOM

Before beginning, make sure that you have an experiment ready for MOM simulation, as well as a compiled MOM5 executable. Whilst there are other ways of running MOM5, the recommended (and supported) way is to use | payu, an experiment running program.

Loading payu

Payu is available as a system wide loadable software module.

module load payu

should load the most recent version. You can check which versions are available like so:

module avail payu

And which is currently loaded:

module list

Configuring your workspace

Payu places the experiment configuration in a separate directory tree to the large input and output files. This is a deliberate design decision so that the smaller model configuration files can be in the user's home directory. This means they are backed up in case of catastrophic disk failure, and can be restored.

Create a directory for your model experiment configurations:

mkdir -p experiments/mom
cd experiments/mom

The easiest way to obtain the necessary configuration files is to copy an existing experiment. Preferably one that is as close as possible to the experimental configuration you wish to use.

If the experiment you wish to copy has the automatic experiment logging feature turned on, then it can be as simple as

git clone /path/to/experiment/config

or if it is available as a repository on a server:

git clone url

For example, this will clone a standard 1/4 degree MOM-SIS configuration into a directory named gfdl_nyf_18080.

git clone

To clone into a different directory name, specify a new name. For example, the following will clone the same configuration into a directory gfdl_nyf_1080_mycopy

git clone gfdl_nyf_1080_mycopy