Input data files¶
The input data files determine the demographics, migration, climate, and other relatively
fixed information about the population within each geographic node. For example, the number of
individuals, geographic data, climate, demographics, and migration data. These files are specified
using the -I argument when running EMOD from the command line. Input data files are in
contrast to the population, geographic, and migration parameters in the configuration file
that control simulation-wide qualities, such as enabling air migration across all nodes in the
simulation.
Generally, input data files are optional. The Institute for Disease Modeling (IDM) provides collections of input data files for many different locations in the world for download on GitHub. For instructions, see EMOD installation. Some input files were prepared using CIESIN Gridded Population of the World (GPW) population distribution and a corresponding spatial resolution grid (for example, 2.5 arc minutes) to define the initial population and extent of the nodes for country-wide input files. Therefore, the naming convention for this files usually leads with the geographic location, followed by the spatial resolution, and input file type.
The demographics files use JSON (JavaScript Object Notation). The other input data files use both a JSON file for metadata and an associated binary file that contains the actual data. Except for the demographics file, you will typically use these input data files in their default state. See Input data files for the configuration parameters that specify input data files to use.
All input files include the parameter IdReference in the metadata, which is used to generate the NodeID associated with each node in a simulation. The values for IdReference and NodeID must be the same across all input data files used in a simulation. See Demographics parameters for more information about NodeID generation.
Demographics¶
Demographics files contain information on the demographics of the population in a geographical region to simulate. For example, the number of individuals and the distribution for age, gender, immunity, risk, and mortality.
These files can include many user-defined parameter values to set individual and node characteristics and will likely require modification.
You do have the option to run a simulation without a demographics file if you set Enable_Demographics_Builtin to 1 in the configuration file. However, this option is primarily used for software testing. It will not provide meaningful simulation data as it does not represent the population of a real geographic location.
Migration¶
Migration files describe the rate of migration of individuals out of a geographic node. There are four types of migration files that can be used by EMOD: local migration, regional migration, air migration, and sea migration.
For all types, migration data is contained in a set of two files, a JSON metadata file with header information and a binary data file with the actual migration data. Both files are required to include migration in a simulation. The basic file structure is identical for all types, with the only exception being the number of columns per row allowed to each type.
Climate¶
There are two general types of climate files usable by EMOD: climate files generated through actual data, referred to as “climate by data,” and climate files generated from the Koppen classification system, referred to as “climate by Koppen.”
For both types, climate data is contained in a set of two files, a JSON metadata file with header information and a binary file that contains the actual climate data. Both files are required to include climate in a simulation.
Load-balancing¶
When running a simulation on a multi-core HPC cluster, you can include a load-balancing file to control how the computing load is distributed across the cluster. The load balancing file is a binary file that allocates the simulation of each geographic node to cores in the cluster. If no file is submitted, EMOD allocates nodes to cores according to a checkerboard pattern.