Installation

pyNublado manages the creation of input scripts for Cloudy runs, their execution, and parsing of the resulting outputs. This installation guide gives two options to install and use CLOUDY & pyNublado: Installing them directly or using Docker.

Using Docker

For information about Docker a good reference is their documentation https://www.docker.com/.

  1. First build the image using the Dockerfile provided:

    sudo docker build . --tag="pynublado:latest"

  2. Once built we can then run our application on the Docker container.

    sudo docker run -v $PWD/data:/root/pyNublado/data -it --rm  "pynublado:latest" hpc.py --N_sample=<N_sample> --N_cpus=<N_cpus>

Installing CLOUDY & pyNublado

Requirements

  • Python 3.7 or newer

  • Your favourite C++ compiler to build Cloudy

Installing CLOUDY

Instructions from the Cloudy wiki:

  • Download the latest Cloudy version

    wget https://data.nublado.org/cloudy_releases/c17/c17.03.tar.gz --no-check-certificate

  • Unpack the files

    tar xvfz c17.03.tar.gz

  • Move the extracted Cloudy folder to where you want it to live, e.g. your home directory

    mv c17.03 ~/c17.03

  • Navigate to the source folder

    cd ~/c17.03/source

  • Build the executable

    make

Once installed, you can test whether the installation was successful:

  • Run the executable

    ~/c17.03/source/cloudy.exe

  • Type “test” then press Enter twice

  • Cloudy should print some output, which ends with “Cloudy exited OK”

Installing pyNublado

  1. Clone the repository

    git clone https://github.com/raulorteg/pyNublado

  2. Install all dependencies, either via pip or conda

pip

  • Create virtual environment:

    • Update pip python -m pip install pip --upgrade

    • Install virtualenv using pip python -m pip install virtualenv

    • Create Virtual environment virtualenv pynublado

    • Activate Virtual environment (Mac OS/Linux: source pynublado/bin/activate, Windows: pynublado\Scripts\activate)

    • Note: to deactivate environmet run deactivate

  • Install requirements on the Virtual environment python -m pip install -r requirements.txt

conda

In an existing Anaconda (or Miniconda) environment the requirements can be installed like so:

  • conda config --add channels conda-forge

  • conda install --yes --file requirements_conda.txt