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Created by Julien Pireaud

This file is to guide you through compile VarroaPop simulator on Linux / macOS

Compilation

Run setup.py to prepare the Linux folder to be ready to build

For C++ dependency management we use Hunter package manager.

To compile in release:

  1. create a directory FOO
  2. move in FOO directory
  3. execute python ../setup.py to generate appropriate CMakeLists.txt file for datamodel
  4. prepare cmake folder cmake -DCMAKE_BUILD_TYPE=Release ..
  5. cd to parent of FOO directory
  6. call cmake --build FOO --target VarroaPop -- -j <number of threads>
  7. call program ./FOO/VarroaPop -h

To time an execution you can use:

  • On Linux: time ./<build>/VarroaPop -d VarroaPop/files/ -v exe/default.vrp -o output/vp_output_linux.txt -i input/vp_linux.txt -f
  • On Windows (PowerShell): Measure-Command {start-process Release\VarroaPop.exe -argumentlist "exe\default.vrp /b /or output\vp_output_win.txt /i input\vp_input.txt" -wait}

Run Simulations

The options that we keep for now are:

  • -f to force overwriting existing files
  • -v simplified.vrp minimal VRP file
  • -i rcp85-input.txt
  • --binaryWeatherFileFormat Rcp85 specifies the binary format of the weather file Observed|Modeled|Rcp85|Rcp45
  • -w data_46.03125_-118.34375 weather file
  • -o output.txt output file
  • --forageDayNoTemp --hourlyTemperaturesEstimation --adultsAgingBasedOnForageInc --adultsAgingBasedOnLaidEggs --applyLifespanReduction=false --inOutEvents options to properly run the simulations with the selected aging model

Helper scrips

  • run-simulations.py will run simulations for omak, wenatchee, walla-walla with historical and future weather simulations. Make sure the path to executable in the script is correct.
  • scripts/plots.py sample script which aim to automate plots generation, this is out of date but is a good source of inspiration
  • scripts/simulations.py sample script to call VarroaPop simulations with different sets of options

Weather format supported

  • ObservedHistorical (1/1/1979 - 12/31/2016)
  • ModeledHistorical (1/1/1950 - 12/31/2005)
  • Rcp85 starting (1/1/2006 - 12/31/2099)
  • Rcp45 starting (1/1/2006 - 12/31/2099)

Changes made to the original VarroaPop codebase

Changes to existing codebase

  • Adult
    • Changed current age from being an Integer to a Float number. Currently the m_CurrentAge attribute is not used, but it would be useful if we want to use it and age Adults with a portion of a day;
    • Added missing attributes initialisation in constructors.
  • Bee
    • Added missing attributes initialisation in constructor.
  • Colony
    • Added a CAdultList::Add method to be able to add new Adults to the first box card without making other Adults age;
    • Added InOutEvent structure to add addtional output data on what's moved from one aging structure to the other;
    • Changed Foragers aging structure with --foragerAgingBasedOnHourlyTemperatureEstimate.
    • Changed Adult aging structure with --adultsAgingBasedOnLaidEggs option.
  • Queen
    • Extracted L daylight hours based component of the egg laying equation in CQueen::ComputeL method.
  • VarroaPopSession
    • Enhanced output formating by extracting parameter specification and adding delimiter afterwards.
  • WeatherEvents
    • Added ability to load binary data from WSU grid weather data;
    • Added a common utility function UpdateForageAttributeForEvent to set m_ForageDay and m_ForageInc with the same logic for all types of input weather data;
    • Added functionnality to CEvent GetTemp, GetMaxTemp, GetMinTemp, IsForageDay and GetForageInc methods to behave correctly in the case we activated the CColdStorageSimulator;
    • Fixed bad interpretation of Rainfall and Windspeed for WSU grid weather files;
    • Made Windspeed and Rainfall threasholds customizable.

Addition to existing codebase

  • GlobalOptions
    • Singleton object used to set global parameters used to control behavior of simulation.
  • ColdStorageSimulator
    • Singleton object used to simulate cold storage.
  • WeatherGridData
    • Class used to load different WSU weather grid data files.

Locations

  • Walla Walla: 46.03125,-118.34375
  • Richland: 46.28125, -119.34375
  • Wenatchee: 47.40625, -120.34375
  • Omak: 48.40625, -119.53125

Roadmap

  • Refactor to remove dependency on port code to make the VarroaPop library solely based on standard library (using Poco libraries as a base framework)
  • Enhance Binary serialization feedback to reject invalid files (check if eof is reached in >> operators)
  • Introduce endianess support to the binary serialization
  • Add a logger to have several logging levels INFO/WARNING/ERROR so that it can be easily disabled