Install CentOS on Azure prerequisites for EMOD source code¶

This section describes the software packages or utilities must be installed on computers running CentOS 7.1 on Azure to build the Eradication binary from source code and run regression tests.

If additional software is needed for the prerequisite software due to your specific environment, the installer for the prerequisite software should provide instructions. For example, if Microsoft MPI v8 requires additional Visual C++ redistributable packages, the installer will display that information.

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.

Install prerequisites for running simulations¶

The following software packages are required to run simulations using the Eradication binary. If you already installed the pre-built Eradication.exe using the instructions in EMOD installation, you can skip this section.

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

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.

Install prerequisites for compiling from source code¶

For CentOS 7.1 on Azure, all prerequisites for building the Eradication binary are installed by the setup script described above. However, if you originally installed EMOD without including the source code and input data files that are optional for running simulations using a pre-built Eradication binary, rerun the script and install those.

Install prerequisites for running regression tests¶

The setup script includes most plotting software required for running regression tests, where graphs of model output are created both before and after source code changes are made to see if those changes created a discrepancy in the regression test output. For more information, see Regression testing. You may want to install R or MATLAB, but both are optional.

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”.

(Optional) R¶

The IDM test team uses R 3.2.0 (64-bit) for regression testing, but it is considered optional.

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

Go to https://www.r-project.org/ and install R 3.2.0 (64-bit).

(Optional) MATLAB¶

The IDM test team uses MATLAB R2015a and the MATLAB Statistics and Machine Learning Toolbox™ R2015a for regression testing, but they are both considered optional.

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.

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