TutorialSetup.md

Setup tutorial for Multiscale Migration Prediction

This document describes what you need to do to set up all the software required for Multiscale Migration Prediction application.

Prerequisites

To perform this tutorial, you will require

• Linux environment
• Python3
• Python libraries
  • numpy (see https://www.numpy.org)
  • pandas (see https://pandas.pydata.org)
  • matplotlib (see https://matplotlib.org)
  • PyYaml (see https://pyyaml.org)
  • Fabric3 (see http://www.fabfile.org)
• The following software packages:
  • FLEE
  • Flare
  • FabSim3
  • The FabFlee plugin

Below you can find installation instructions for each of these packages.

Installing FLEE

To install FLEE on your local workstation, you need to clone the FLEE repository (see http://www.github.com/djgroen/flee):

git clone https://github.com/djgroen/flee.git

We will assume that you will install FLEE in a directory called (FLEE Home), e.g. ~/flee/

Installing Flare

To install Flare on your local workstation, you need to clone the Flare repository (see http://www.github.com/djgroen/flare-release):

git clone https://github.com/djgroen/flare-release.git

We will assume that you will install Flare in a directory called (Flare Home), e.g. ~/flare-release/.

Installing FabSim3

To install FabSim3, you need to install dependencies and clone the FabSim3 repository.
For detailed installation instructions, see https://github.com/djgroen/FabSim3/blob/master/INSTALL.md

git clone https://github.com/djgroen/FabSim3.git

We will assume that you will install FabSim3 in a directory called (FabSim3 Home), e.g. ~/FabSim3/.

NOTE: Please make sure both machines.yml and machines_user.yml are configured correctly based on the installation guide.

Installing the FabFlee plugin

Once you have installed FabSim3, you can install FabFlee by typing:

fabsim localhost install_plugin:FabFlee

The FabFlee plugin will appear in ~/FabSim3/plugins/FabFlee.

2. Configuration

Once you have installed the required dependencies, you will need to take a few small configuration steps:

1. Go to (FabSim Home)/deploy
2. Open machines_user.yml
3. Under the section default:, please add the following lines:
   a. flee_location: (FLEE Home)
   NOTE: Please replace (FLEE Home) with your actual install directory.
   b. flare_location: (Flare Home)
   NOTE: Please replace (Flare Home) with your actual install directory.

3. Main tutorial

Once you have completed these tasks, you can do the main tutorial at https://github.com/djgroen/FabFlee/blob/master/doc/Tutorial.md