Randomize iteration order

Author: Lukas Breitwieser
In this tutorial we show how to randomize the order that BioDynaMo uses in each iteration to process the agents.

Let's start by setting up BioDynaMo notebooks.

%jsroot on
gROOT->LoadMacro("${BDMSYS}/etc/rootlogon.C");

INFO: Created simulation object 'simulation' with UniqueName='simulation'.

Let's create two helper functions:

• AddAgents to add four agents to the simulation
• print_uid which prints the uid of the given agent

void AddAgents(ResourceManager* rm) {
    for (int i = 0; i < 4; ++i) {
        rm->AddAgent(new SphericalAgent());
    }
}
auto print_uid = [](Agent* a) { 
  std::cout << a->GetUid() << std::endl;
};

We define an experiment which

1. takes a simulation object as input
2. adds four agents
3. calls print_uid for each agent
4. print a separator so we can distinguish the output of the two different time steps
5. advances to the next time step
6. calls print_uid for each agent again

void Experiment(Simulation* sim) {
    auto* rm = sim->GetResourceManager();
    AddAgents(rm);
    
    rm->ForEachAgent(print_uid);
    rm->EndOfIteration();
    std::cout << "-----------------" << std::endl;
    rm->ForEachAgent(print_uid);
}

The default behavior of BioDynaMo is to iterate over the agents in the order they were added (not taking multi-threading and load balancing into account). Therefore, we expect to see the same order twice.

Experiment(&simulation)

0-0
1-0
2-0
3-0
-----------------
0-0
1-0
2-0
3-0

BioDynaMo also provides a wrapper called RandomizedRm, which, as the name suggests, randomizes the iteration order after each iteration. It just takes two lines to add this functionality to the simulation.

Simulation simulation("my-sim");
auto* rand_rm = new RandomizedRm<ResourceManager>();
simulation.SetResourceManager(rand_rm);

Let's run our experiment again. This time with the simulation which has a randomized resource manager. We expect two different orders.

Experiment(&simulation)

0-0
1-0
2-0
3-0
-----------------
2-0
3-0
0-0
1-0