Install EMOD on Linux#

To install EMOD on Linux computers, follow the steps below. You will install the pre-built Eradication binary for Linux and all supporting software needed to run simulations locally. Optionally, you can install Python virtual environments, software to plot the output of simulations, and EMOD input files for various regions.

The Eradication binary for Linux is tested and supported on a CentOS 7.1 virtual machine on Azure. It has also been successfully built and run on Ubuntu, SUSE, and Arch, but has not been tested and is not supported on those Linux distributions.

Install EMOD using a script#

The setup script installs most prerequisite software, including Python and the Python packages dateutil, six, pyparsing, NumPy, and matplotlib. Other prerequisites, such as Boost 1.77.0 and Microsoft MPI v10, are declared by the script as required. Because the installation instructions for these packages will vary based on the particular Linux distribution you are running, installation instructions are not included here.

Note

IDM does not provide support or guarantees for any third-party software, even software that we recommend you install. Send feedback if you encounter any issues, but any support must come from the makers of those software packages and their user communities.

The script provides the option to install input files that describe the demographics, migration patterns, and climate of many different locations across the world.

Before you begin, you must have the following:

  • sudo privileges to install packages

  • 15 GB free in your home directory (if you install the EMOD source code and input files)

  • An Internet connection

  1. On GitHub on the EMOD releases page, download and run the PrepareLinuxEnvironment.sh script.

    Respond to the prompts for information while the script is running.

    1. Set the EMOD_ROOT environment variable to the path to the EMOD source path:

      EMOD_ROOT=~/IDM/EMOD

    2. Include Scripts and . in the path:

      export PATH=$PATH:.:$EMOD_ROOT/Scripts

    3. If you want to run simulations in the same session that you updated EMOD_ROOT and the Scripts path, reload the .bashrc file using source .bashrc.

  1. Download the Eradication binary for Linux for CentOS 7.1 (not Eradication.exe for Windows). See on EMOD releases on GitHub. Save to a local drive, such as the desktop.

(Optional) Install Python virtual environments#

Python virtual environments enable you to isolate your Python environments from one another and give you the option to run multiple versions of Python on the same computer. When using a virtual environment, you can indicate the version of Python you want to use and the packages you want to install, which will remain separate from other Python environments. You may use virtualenv, but venv is recommended and included with Python 3.3+.

  1. Navigate to the location where you want to create the virtual environment directory and enter the following to create a environment called “idm”, or other desired name:

    python -m venv idm

  2. To activate the virtual environment, enter the following:

    source idm/bin/activate

  3. Verify that the command prompt displays “idm” at the beginning, which indicates that you are in the idm virtual environment. For example:

    (idm) my-computer:idm

  4. To verify you are using Python 3.9 64-bit, enter the following:

    python --version

  5. When you are done working in this virtual environment, deactivate the environment. The environment will be saved and you can reactivate it at any time. To deactivate it, enter the following:

    deactivate

(Optional) Install plotting software#

None of the following plotting software is required to run simulations with EMOD, but they are useful for creating graphs from and evaluating the model output. In addition, EMOD provides many Python scripts for analyzing data.

R#

R is a free software environment for statistical computing and graphics.