*Authors: Romain Caneill, Fabien Roquet, Gurvan Madec, Jonas Nycander
Sources for the paper Caneill, R., Roquet, F., Madec, G., and Nycander, J. (2022). The polar transition from alpha to beta regions set by a surface buoyancy flux inversion., published by the Journal of Physical Oceanography.
DOI: https://doi.org/10.1175/JPO-D-21-0295.1
URL: https://journals.ametsoc.org/view/journals/phoc/52/8/JPO-D-21-0295.1.xml
This repository along with the zenodo data zip can be used to reproduce all the analyzes of the study. All the study, from the model runs to their output analyze, is entirely reproducible from a few commands.
Released on Zenodo
- BASIN/
This folder contains the sources for the NEMO configuration used in this study - configuration/
Some configuration files for the analyzes - data/
Location for the raw and processed data - figures/
Location for the figures - lib_position_transition_zone/
Python library containing some functions for the data processing - rules/
Snakemake rules - scripts/
Python scripts for the data processing and analyzes - Pipfile*
Environment files for python's pipenv - setupy.py
Installation script for lib_position_transition_zone - Snakefile
Main file used by Snakemake
The analyze is based on python scripts. The main used libraries are xarray, xgcm, cf-xarray, xnemogcm, dask, and matplotlib.
Snakemake is used as workflow management tool. The mentality is that snakemake will process every intermediate step needed to achieve the rule it is asked to compute, more to read on the official documentation.
The svg images present in figures/paper_DAG and figures/paper_RULEGRAPH represent the
directed acyclic graph or rule graph for each figure of the paper. These file are
generated by snakemake (which means that you can regenerate them as any other figure),
but we include them here. They can be used to see all the steps needed to compute each
figure of the paper, in case you would like to look at the code behind.
git clone https://github.com/rcaneill/caneill-et-al-JPO-nemo-transition-zone
cd caneill-et-al-JPO-nemo-transition-zone
Or use the release from zenodo:
If you haven't already installed pipenv:
pip3 install --user pipenv
And then (in the base directory):
pipenv install
pipenv shell # launches a shell inside the environment
We use apptainer as container manager. Please install apptainer.
apptainer build container.sif .container/apptainer.def
# And then open a shell in the container
apptainer shell container.sif
Be careful, use this method only if you trust me (Romain Caneill). I signed the container with my open GPG key.
# Download the containter from the github release
wget https://github.com/rcaneill/caneill-et-al-JPO-nemo-transition-zone/releases/download/v1.0/container.sif
# Verify the container
apptainer verify container.sif
# open a shell in the container
apptainer shell container.sif
You first need to download the raw data from zenodo, and unzip the content into the folder data/raw.
These data are the output files of all the NEMO runs used in this study.
You need to have zip and unzip installed (e.g. on a debian like linux
sudo apt install zip unzip, not needed if you use the container).
You can use the download_and_extract_data_from_zenodo.sh script:
./download_and_extract_data_from_zenodo.sh
As mentionned, the analyzes are organized by the use of snakemake. One can think of it as a python friendly GNU make equivalent.
All the next steps are assuming either that you are in the pipenv shell, or the apptainer shell.
A first good step is to reproduce the figures used in the paper:
snakemake --cores 8 paper_all_fig
You can adapt the number of cores depending on you computer. With 8 cores in a modern laptop this takes few minutes to run.
It is then possible to generate other figures, like e.g. the MOC in another configuration:
snakemake --cores 8 figures/EXP_main/EXP_rn_lambda1_0.06_rn_a0_0.145/moc.pdf
To generate all the figures at once (about 5 minutes to run for one experiment):
snakemake --cores 8 figures/plot_all.done
You can also generate the figures giving the figure number from the paper, e.g.:
snakemake --cores 8 figures/paper_by_number/figure_1.pdf
The rules are described in the files located in rules/, and each rule uses a python script located in scripts/. The names are self-describing.
Follow the BASIN/README.md instructions.
e.g. rsync -avz user@supercomputer:/path/to/nemo/NEMOGCM/tests/BASIN_compiled_v0.1.0/EXP_* data/raw/
Use snakemake to run the analyze by asking it to produce the desired figures.