AtlantisCmd Package Installation

AtlantisCmd is a Python package that provides the atlantis command-line tool for managing runs of the CSIRO Atlantis ecosystem model. It is an extension of the SalishSeaCast/NEMO-Cmd package customized for working with the Atlantis ecosystem model.

These instructions assume that you have installed the Pixi package and environments manager (installation instructions).

Installation of AtlantisCmd is a 2 step process:

  1. Clone the SS-Atlantis/AtlantisCmd repository from GitHub

  2. Use Pixi to install Python and the packages needed to run AtlantisCmd

The following sections assume that the base directory for your Atlantis work is /ocean/$USER/Atlantis/.

Once you have completed the installation, please see atlantis Sub-Commands for information about how to use the atlantis command, and Run Description File Structure for information about how to construct the run description YAML files that it uses.

For doing development, testing, and documentation of the AtlantisCmd package, please see the AtlantisCmd Package Development section.

Clone Repository

Clone the repository from GitHub with:

$ cd /ocean/$USER/Atlantis/
$ git clone git@github.com:SS-Atlantis/AtlantisCmd.git

Note

The git clone command above assumes that you are connecting to GitHub using SSH. If it fails, please follow the instructions in our Secure Remote Access docs to set up your SSH keys and Copy Your Public ssh Key to GitHub.

Install Python and Dependency Packages

Use Pixi to create an isolated environment for AtlantisCmd to avoid conflicts with other Python packages installed on your system. That environment will have all of the Python packages necessary to use the atlantis command that is provided by the AtlantisCmd package.

$ cd AtlantisCmd
$ pixi install

When you are in the AtlantisCmd/ directory (or a sub-directory) you can run the atlantis command with with the pixi run command. Example:

$ pixi run atlantis help

A common use-case is to execute the atlantis run command in the directory containing your run description YAML file. To accomplish that, we have to tell Pixi where to find the AtlantisCmd/ directory so that it can use the correct environment. We do that by using the -m or --manifest option of pixi run. Example:

$ cd /ocean/$USER/Atlantis/SSAM_Runs/
$ pixi run -m /ocean/$USER/Atlantis/AtlantisCmd salishsea run atlantis_highres_d0.yaml \
    /ocean/$USER/Atlantis/highres-d0_5b_2019-01-20_depth_PC/