DAR1

Built off of Gael Forget's MITgcmTools! (https://github.com/gaelforget/MITgcmTools.jl)

DAR1 Documentation

• tutorials
• case studies

Documentation for the darwin3 MITgcm fortran model can be found here

Overview of program structure

DAR1 is a tool for designing and running experiments simulating the marine microbiome within a single cube of water. The biogeochemical forcing is powered by the MIT Darwin Model, and DAR1 provides a Julia interface to build, configure, and run experiments with a simple, streamlined workflow. DAR1 is composed of two main parts:

• DAR1 - Julia interface for organizing experiments and setting up parameters for model runs
  • MITgcm_path variable should point to darwin3
• darwin3 - MITgcm source code set up to include all things Darwin
  • DAR1_config - folder for the base configuration files for DAR1, which lives in the darwin3/verification/ folder. (DAR1_config github)

DAR1 can be run in one of two ways.

1. In a docker container using the DAR1_docker image, where all dependencies are handled for you
2. On your local machine, where you have to set up the environment, download dependencies, etc
   • this is more time consuming, and I strongly recommend using the docker image
   • instructions for local setup are below

Setting up with docker

(1) Download and install docker desktop.

• Run the docker application, which will start up the docker "daemon"
• The docker daemon must be running in order to download the DAR1 image

(2) Get the DAR1_docker image.

• using the command line, run

  docker pull birdy1123/DAR1_docker

• If you go to the "Images" tab in the docker desktop UI, you should see "birdy1123/DAR1_docker"

(3) Run a container based on the DAR1_docker image

• using the command line, run

  docker run -it birdy1123/DAR1_docker

• this runs the container in interactive mode (-i) with terminal access (-t)

• you should see the prompt change to root@some-number:/DAR1_docker#

  • if the container is already running, you can connect to it with docker exec -it [CONTAINER_ID] bash
  • Note: connecting with bash rather than sh gives you more a powerful terminal (i.e. with tab completion)

You're now ready for the beginner tutorial!

Setting up on local machine

See instructions in the documentation: https://barbara42.github.io/Dar_One/build/getting_started/#Setting-up-on-local-machine

Contributing

We have three main branches: main, test, and dev.

All other branches are feature branches. Once a feature has been implemented, tested, and documented you can make a pull request to merge it into the dev branch.

main is the most stable version of the code. This branch is used for the docker image.