Install EMOD on Windows

Follow the steps below to install EMOD on computers running Windows 10, Windows Server 12, and Windows HPC Server 12 (64-bit). This installs the pre-built Eradication.exe and all software necessary to run simulations.

Note

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

The EMOD executable (Eradication.exe) is tested using Windows 10, Windows Server 12, and Windows HPC Server 12 (64-bit). Windows HPC Server is used for testing remote simulations on a high-performance computing (HPC) cluster and the other Windows operating systems are used to test local simulations.

  1. Install the Microsoft HPC Pack 2012 Client Utilities Redistributable Package (64-bit). See http://www.microsoft.com/en-us/download/details.aspx?id=36044 for instructions.

  2. Install the Microsoft MPI v8. See https://www.microsoft.com/en-us/download/details.aspx?id=54607 for instructions, being sure to run the MSMpiSetup.exe file.

  3. Install the Microsoft Visual C++ 2015 Redistributable (64-bit). See https://www.microsoft.com/en-us/download/details.aspx?id=53840 for instructions.

  4. Download the EMOD executable (Eradication.exe) (not the Eradication binary for CentOS on Azure). See EMOD releases on GitHub. Save to a local drive, such as the desktop.

Warning

Double-clicking Eradication.exe will not run the EMOD software. EMOD must be run from the command line or a script. See Running a simulation for more information.

(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.

Python and Python packages

Python is required to install many of the software packages described below.

  1. In a web browser, go to https://www.python.org/downloads/ to install Python 3.6.

  2. Download one of the x86-64 bit installers (you may use the executable installer or the web-based installer.)

  3. Double-click the executable file and in the installer window check the Add Python 3.6 to PATH checkbox and click Customize installation.

    _images/PythonInstaller.png

  4. On the Optional Features window, leave all default values selected and click Next. The Python package manager, pip, is used to install other Python packages.

  5. On the Advanced Options window, we recommend that you customize the installation location to “C:Python36”.

    _images/PythonAdvanced.png

    You may install Python in another location, but the Python plotting scripts included in the EMODScenarios folder assume that Python is installed directly under the C: drive. If you install it elsewhere, you may need to edit those scripts when using the scenarios to learn about EMOD functionality.

  6. Click Install. When installation is complete, click Close.

  7. To verify installation, open a Command Prompt window and type the following:

    python --version

  8. If you need to keep Python 2.7 installed alongside Python 3.6, we recommend that you install virtualenv and virtualenvwrapper, tools used to create and work in isolated Python environments. See Pipenv & Virtual Environments for installation instructions.

NumPy

We recommended that you download some of the NumPy Python package from http://www.lfd.uci.edu/~gohlke/pythonlibs, a page compiled by Christoph Gohlke, University of California, Irvine. The libraries there include linear algebra packages that are not included by default with the standard Windows packages. They are compiled Windows binaries, including the 64-bit versions required by EMOD. The naming convention used lists the Python version after “cp”, for example “cp36-cp36m”, and the Windows bit version after “win”, for example “win_amd64”.

The NumPy package adds support for large, multi-dimensional arrays and matrices to Python.

  1. Go to http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy and select the WHL file for NumPy 1.14.5 (64-bit) that is compatible with Python 3.6.

  2. Save the file to your Python installation directory.

  3. Open a Command Prompt window and navigate to the Python installation directory, then enter the following, substituting the name of the specific NumPy WHL file you downloaded:

    pip install numpy-1.x.x+mkl-cp36-cp36m-win_amd64.whl

Python packages

The Python packages dateutil, six, and pyparsing provide text parsing and datetime functionality.

Note

Be sure NumPy is installed before you install Matplotlib.

  1. Open a Command Prompt window.

  2. Enter the following commands:

    pip install python-dateutil
pip install pyparsing
pip install matplotlib

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.

Download input files

IDM provides input files that describe the demographics, migration patterns, and climate of many different locations across the world. You can download these files from the EMOD-InputData repository, which uses large file storage (LFS) to manage the binaries and large JSON (JavaScript Object Notation) files. A standard Git clone of the repository will only retrieve the metadata for these files managed with LFS. To retrieve the actual data, follow the steps below.

  1. Install the Git LFS plugin, if it is not already installed.

    • For Windows users, download the plugin from https://git-lfs.github.com.

    • For CentOS on Azure users, the plugin is included with the PrepareLinuxEnvironment.sh script.

  2. Using a Git client or Command Prompt window, clone the input data repository to retrieve the metadata:

    git clone https://github.com/InstituteforDiseaseModeling/EMOD-InputData.git

  3. Navigate to the directory where you downloaded the metadata for the input data files.

  4. Cache the actual data on your local machine:

    git lfs fetch

  5. Replace the metadata in the files with the actual contents:

    git lfs checkout