FABMOS-BFM

Python scripts to perform global ocean offline simulations with BFM.

INSTALLING

First clone this repository and enter the new folder

git clone --recursive https://github.com/inogs/FABMOS-BFM.git
cd FABMOS-BFM

Use new branch of fabmos

cd fabmos
git checkout new_pygetm

To be sure to use the last version of the BFM checkout the master branch of the FABM and BFM repository

cd extern/fabm
git checkout master
cd extern/ogs
git checkout iron

Back to fabmos

cd ../../../../

Create a conda environment with the necessary packages

conda env create -f environment.yml
conda activate fabmos

On HPC machines some errors in installing the package pygetm in fabmos environment can occur. The package can be installed with the following specifications.

conda install pygetm -c bolding-bruggeman -c conda-forge --override-channels

Install FABMOS

pip install .

In case of errors in compilation phase, consider to add the following setup.cfg file in fabmos folder containing the following two lines:

[build_ext]
cmake_opts=-DFABM_USE_CONTIGUOUS=OFF

then launch

pip install .

RUN SIMULATIONS

To run a simulation a transport matrix is needed for the circulation. Several matrices are available at Samar Khatiwala. Download one in the testcases directory and unzip it.

For example the MITgcm 2.8° global configuration

cd testcases
wget http://kelvin.earth.ox.ac.uk/spk/Research/TMM/TransportMatrixConfigs/MITgcm_2.8deg.tar
tar xopf MITgcm_2.8deg.tar

Use the directory of the transport matrix as working directory to launch simulations

cd MITgcm_2.8deg

Link a configuration file from the BFM repository

ln -s ../../fabmos/extern/fabm/extern/ogs/fabm_iron.yaml fabm.yaml

Link the python script to run the simulation

ln -s ../BFM.py

Launch the simulation

python BFM.py