Installation

Quick guide

There are a few steps that should be carried out prior to the installation of exorad.

  1. Download and familiarise with MITgcm

  2. Get permission to the exorad repository

  3. Clone the exorad repository and move inside the repo.

  4. run install_exorad.sh to link exorad into MITgcm

  5. Install anaconda

  6. create a virtual environment for exorad conda create -n exorad

  7. Install exorad_opac

  8. Download and set the opacity sources for petitRADTRANS into this environment

Install exorad

MITgcm

To install exorad you will first need to install MITgcm. Follow the instructions in MITgcm to download the code and to understand how MITgcm works.

Note

This guide does not cover how to install or use MITgcm. Please read the MITgcm documentation carefully.

Once you downloaded MITgcm it is important to set the MITGCM_ROOTDIR environmental variable:

export MITGCM_ROOTDIR=<path to MITgcm>

You can do so by appending the above line to your .zshrc / .bashrc / .bash_profile file.

MITgcm is still developed. To go to a version that is known to work with expeRT do the following (inside the MITgcm directory):

git checkout 8b41e6235cdfefca3b75a9c4c8cc300edbe9af64

exorad

Note

This guide only covers expeRT/MITgcm (Schneider et al. 2022)

Note

Please contact Aaron Schneider to get access to expeRT/MITgcm.

The first installation step is to clone expeRT/MITgcm (into any directory of your choice):

git clone https://github.com/exorad/exorad.git

Note

Most users prefer to clone private repositories via ssh.

You can then do

git clone git@github.com:exorad/exorad.git

Link exorad to the MITgcm directory using the supplied install_exorad.sh script.

cd <directory of exorad repo>
bash install_exorad.sh

The script comes with an option to prettify the exorad code (using findent). More information on how to use the script can be found using the -h argument.

Install python packages (6-9)

expeRT/MITgcm uses petitRADTRANS to create the opacity input files.

Note

This guide bases on anaconda. Other python installations are possible as well.

Install anaconda. Once installed, create a virtual environment for expeRT/MITgcm and petitRADTRANS:

conda create -n exorad pip numpy python=3

Note

We recommend to install a few more packages (do this instead of the above):

conda env create -n exorad -f https://raw.githubusercontent.com/exorad/gcm_toolkit/main/ci/environment-3.10.yml
conda activate exorad
conda install -c conda-forge jupyterlab cartopy -y
pip install gcm-toolkit

This will automatically install gcm_toolkit and a few other useful packages for postprocessing of the data.

Activate the environment using

conda activate exorad

Install petitRADTRANS and the preprocessing package of expeRT/MITgcm using

cd <directory of exorad repo>
pip install -e exorad_opac

The installation of exorad_opac will automatically trigger the installation of petitRADTRANS. The last step is then to install the opacity sources for petitRADTRANS.

Important

instructions for the installation of the opacity sources can be found here.