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Colin Thackray wrote the Python interface to pass information between the MITgcm and GEOS-Chem.
Code credit: Colin Thackray (MIT) and Helen Amos (Harvard)
Tested for the following model versions
- MITgcm ECCOv4 (lat-lon-cap grid configuration) PCB simulation
- GEOS-Chem v9-01-03 PCB simulation
Prerequisites for running the coupler
- An account on Odyssey or Svante
- Space on a file/storage server
- A copy of GEOS-Chem that compiles and runs standalone (i.e., not as part of the coupler)
- A copy of the MITgcm that compiles and runs standalone (i.e., not as part of the coupler)
- A GitHub account
- Python
- MATLAB
- gcmfaces package
Step 1: Download the coupler
Put the coupler on a file/storage server. The coupler will run GEOS-Chem and MITgcm together, generating large output files from both models. If you run it from your home directory, you will quickly hit your storage quota. On Svante, I put the coupler on file server #2: /net/fs02/d2/geos_harvard/helen/coupler/.
Open up a terminal and login to your head node (i.e., login node). For example, this is how I log into Svante
ssh -Y geos_harvard@svante.mit.edu
Go to the location on the file server where you want to put the coupler. For example, this is where I want my coupler on Svante
cd /net/fs02/d2/geos_harvard/helen/
Clone a copy of the coupler from Colin's GitHub page
git clone https://github.com/thackray/coupler.git
Step 2: Initial set up
After cloning a copy of the coupler, type this series of commands into the terminal to set up your coupler. You should be logged into the head node.
cd /your_directory/coupler/
ssh -Y <username>@svante2.mit.edu (ssh to a file server, here's how on Svante)
python setup.py
exit (go back to head node)
csh
chmod 755 startup.sh
./startup.sh
exit
ssh -Y username@svante2.mit.edu (ssh to a file server)
python example.py