There are a number of ways to run an EMOD simulation, whether locally or on a remote HPC cluster. The simplest way is to run a simulation at the command line, however that limits you to running one local simulation at a time. Because the EMOD model is stochastic, you must run many simulations before you can interpret the outcome. You may want to use a scripting language like Python or MATLAB or an application like mpiexec to run multiple simulations at once.
In addition, if you are modifying the EMOD source code to add functionality to the model, you can run simulations in Visual Studio as part of debugging. This process is described in Run debug simulations in Visual Studio.
No matter how you choose to run simulations, you must have a built copy of the EMOD executable (Eradication.exe) or Eradication binary, either downloaded directly from GitHub or built from the EMOD source code. See EMOD installation. In addition, you must know the paths to the configuration file and input data files and where you want to store the output files. You will pass this information as arguments to Eradication.exe.
Although there are many ways you can structure the files needed to run a simulation, we recommend the following to keep your files organized and simplify the file paths set in the configuration file or passed as arguments to Eradication.exe.
Place the configuration and campaign files needed for a simulation in the same directory. This is also known as the working directory.
However, if you are using overlay files, you may want the default configuration or campaign file in a separate directory so they can be used with different overlay files for other simulations.
Place all input data files for a given region in the same directory.
Place output for a simulation in a subdirectory of the directory containing configuration and campaign files.
It is not important where you install Eradication.exe or the Eradication binary.