Simulator

Workspace

By default, Stride is installed in ./target/installed/ inside the project directory though this can be modified using the CMakeLocalConfig.txt file (example is given in ./src/main/resources/make). Compilation and installation of the software will create the following files and directories: (illustrated in Figure [fig:workspace]):

Binaries in directory <project_dir>/bin

  • stride: executable.
  • gtester: regression tests for the sequential code.
  • wrapper\_sim.py: Python simulation wrapper

Configuration files (xml and json) in directory <project_dir>/config

  • run\_default.xml: default configuration file for Stride to perform a Nassau simulation.
  • run\_miami\_weekend.xml: configuration file for Stride to perform Miami simulations with uniform social contact rates in the community clusters.
  • wrapper_miami.json: default configuration file for the wrapper_sim binary to perform Miami simulations with different attack rates.
  • ...

Data files (csv) in directory <project_dir>/data

  • belgium\_commuting: Belgian commuting data for the active populations. The fraction of residents from “city_depart” that are employed in “city_arrival”. Details are provided for all cities and for 13 major cities.
  • belgium\_population: Relative Belgian population per city. Details are provided for all cities and for 13 major cities.
  • contact\_matrix_average: Social contact rates, given the cluster type. Community clusters have average (week/weekend) rates.
  • contact\_matrix_week: Social contact rates, given the cluster type. Community clusters have week rates.
  • contact\_matrix_week: Social contact rates, given the cluster type. Primary Community cluster has weekend rates, Secondary Community has week rates.
  • disease\_xxx: Disease characteristics (incubation and infectious period) for xxx.
  • holidays\_xxx: Holiday characteristics for xxx.
  • pop\_xxx: Synthetic population data extracted from the 2010 U.S. Synthetic Population Database (Version 1) from RTI International for xxx [Int14], [Whe14].
  • ref\_2011: Reference data from EUROSTAT on the Belgian population of 2011. Population ages and household sizes.
  • ref\_fl2010\_xxx: Reference data on social contacts for Belgium, 2011.

Documentation files in directory ./target/installed/doc

  • Reference manual
  • User manual

Run the simulator

From the workspace directory, the simulator can be started with default configuration using the command . Settings can be passed to the simulator using one or more command line arguments:

  • -c or --config: The configuration file.
  • -r or --r0: To obtain the basic reproduction number, no tertiary infections.
  • -m or --mode: The simulation run mode (defaults to Extend mode).
  • -f or --frequency: The checkpointing frequency.
  • -h or --hdf5: The hdf5 file used by checkpointing.
  • -o or --hdf5output: Output file for checkpointing over h argument if specified.
  • -t or --timestamp: The timestep from which Replay mode is replayed.

Python Wrapper

A Python wrapper is provided to perform multiple runs with the C++ executable. The wrapper is designed to be used with .json configuration files and examples are provided with the source code. For example:

./bin/wrapper_sim –config ./config/wrapper_default.json

will start the simulator with each configuration in the file. It is important to note the input notation: values given inside brackets can be extended (e.g., "rng_seeds"=[1,2,3]) but single values can only be replaced by one other value (e.g., "days": 100).