Using Docker - Geodels/eSCAPE GitHub Wiki
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eSCAPE Docker image contains all the requirements and dependencies necessary to use the code and can be run on parallel on local computers.
This is the preferred and recommended way for running eSCAPE simulation on local machines. 👍
Content
To use/test eSCAPE quickly, it is recommended to use the Geodels escape-docker image that is shipped with all the required libraries.
https://hub.docker.com/u/geodels/
Below is a step by step guide on how to get eSCAPE via Docker on your local machine.
eSCAPE tutorials are based on Jupyter Notebook App. This server-client application allows editing and running notebook documents via a web browser. It can be executed on a local desktop requiring no internet access or installed on a remote server and accessed through the internet.
To look at what are Jupyter Notebooks visit jupyter-notebook-beginner-guide
First, you will only need to download the free Docker application by clicking on the link and choosing the right one for your operating system.
You will now need to open Docker. On Windows go to "All programs" and search for Docker in the list. If you are using a Mac open the "Spotlight Search" (arrow #1 in the figure below) and look for Docker (#2), open it (#3). Once Docker is open you will get the Docker App icon on the right hand side of the top bar (#4). On Windows it will appear as other Programs and a list of options will be visible from the main menu directly.
It is possible to adjust the settings/preferences of Docker application by going in the "Preferences" menu (arrow #1 in the top figure). On Mac, a window will pop-up and you can allocate the number of processors (arrow #2) and memory (#3) that will be use by the software. This step is similar for Windows operating system.
You are now ready to fire-up Kitematic (arrow #4 in the top figure).
Using Docker App as shown above or by looking for it directly in "All Programs" on Windows machine, open Kitematic. Kitematic is an open source project built to simplify and streamline using Docker on a Mac or Windows PC. Kitematic automates the Docker installation and setup process and provides an intuitive graphical user interface (GUI) for running Docker containers.
During the opening process the application might ask for a Docker Hub account and you will skip this step as it is not required for our tutorials.
Once the initialisation process finishes (it could take several minutes the first time), a window will pop-up similar to the one below:
We will now start the Jupyter container containing the eSCAPE tutorials by searching for Geodels. To do so, search of this container as shown in the figure below and click on the create button (arrow #2). When you will create the container for the first time, this operation will take several minutes.
Now that the container has been installed, we will link the container to a specific folder also called a volume on the machine.
This operation allows you to use native text editors on your local environment and protects any work you do from loss deleting a Docker container will not delete the files in mounted volumes (unlike files hosted locally by the container itself).
To set up the volume, click on each of the "wheel" icon as shown in the figure below.
From the pop-up window (see figure below) look for the directory where you want the local data to be store on your local development machine. It will also allow you to easely create, modify or delete files/directory directly from your machine.
You are now ready to open the Jupyter environment using the icon shown below. It will open the lab notebooks in a web browser.
The Jupyter Notebook is officially supported for the following browsers:
- Chrome
- Safari
- Firefox
When you launch Jupyter notebook the first page that you encounter is the Notebooks Dashboard. This page is your home directory and shows a file tree view of the folders and files installed on the container (as shown in figure below). share is the folder connected to your local architecture and the place where you will store your eSCAPE models to prevent any loss.
Once you’ve selected a Notebook file (.ipynb extension), the Notebook will open in the Notebook Editor.