Install EMOD on CentOS on Azure

Follow the steps below to install EMOD on CentOS 7.1 on Azure environments. This installs the pre- built Eradication binary and all software needed to run simulations. The setup script installs most prerequisite software, including Python and the Python packages dateutil, six, pyparsing, NumPy, and matplotlib. Other prerequisites, such as Boost 1.61.0 and Microsoft MPI v8, are declared by the script as required. Because the installation instructions will vary based on the particular distribution you are running, instruction information is not included here.

Note

If you want to download and modify the EMOD source code and build the Eradication binary yourself, see EMOD source code installation.

The Eradication binary is tested and supported on a CentOS 7.1 on Azure virtual machine. 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.

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 of installing the EMOD source code and input data files provided by IDM, but these steps will install a pre-built version of the Eradication binary. For information on building the Eradication binary from source code, see EMOD source code installation.

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 data files)
  • An Internet connection
  1. Download and run the PrepareLinuxEnvironment.sh script on EMOD releases on GitHub.

    Respond to the prompts for information while the script is running. If you choose not to download the EMOD source and input data files, do the following. This example assumes that a directory named IDM is in your home directory and contains the subdirectories EMOD, containing the EMOD source code, and EMOD_InputData, containing the input data files directory.

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

      EMOD_ROOT=~/IDM/EMOD
      
    2. Put Scripts and . in the path:

      export PATH=$PATH:.:$EMOD_ROOT/Scripts
      
    3. Create a symlink from the EMOD directory to InputDataFiles:

      ln -s /home/general/IDM/EMOD-InputData $EMOD_ROOT/InputData
      
    4. If you run simulations using in the same session that you updated EMOD_ROOT and the Scripts path, reload the .bashrc file using source .bashrc.

  2. Download the Eradication binary for CentOS 7.1 on Azure. See on EMOD releases on GitHub.

(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.

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.

R

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

MATLAB

MATLAB is a high-level language and interactive environment for numerical computation, visualization, and programming. The MATLAB Statistics and Machine Learning Toolbox™ provides functions and applications to describe, analyze and model data using statistics and machine learning algorithms.

  1. Go to http://www.mathworks.com/products/matlab/ and install MATLAB R2015a.
  2. If desired, go to https://www.mathworks.com/products/statistics.html and install the MATLAB Statistics and Machine Learning Toolbox™ R2015a.