Runner

run(T::AbstractTrial[; force_recompile::Bool=false, prune_options::PruneOptions=PruneOptions()])`

Run the given simulation, monad, sampling, or trial.

Call the appropriate functions to run the simulations and return the number of successful simulations. Also print out messages to the console to inform the user about the progress and results of the simulations.

Arguments

• T::AbstractTrial: The trial, sampling, monad, or simulation to run.
• force_recompile::Bool=false: If true, forces a recompilation of all files by removing all .o files in the PhysiCell directory.
• prune_options::PruneOptions=PruneOptions(): Options for pruning simulations.

runAbstractTrial(T::AbstractTrial; force_recompile::Bool=false, prune_options::PruneOptions=PruneOptions())

Deprecated alias for run, but only with this particular signature. Does not work on Cmd objects as Base.run is built for. Also, does not work with running sensitivity samplings.

simulationIDs(output::PCMMOutput)

Get the simulation IDs from the output of the PhysiCellModelManager.jl run.

PCMMOutput{T<:AbstractTrial}

A struct to hold the output of the PhysiCellModelManager.jl run, including the AbstractTrial object, the number of scheduled simulations, and the number of successful simulations.

Fields

• trial::T: The trial, sampling, monad, or simulation that was run.
• n_scheduled::Int: The number of simulations that were scheduled to run.
• n_success::Int: The number of simulations that were successfully completed.

SimulationProcess

A struct to hold the simulation process and its associated monad ID. Users should not need to interact with this struct directly.

Fields

• simulation::Simulation: The simulation object.
• monad_id::Int: The ID of the associated monad.
• process::Union{Nothing,Base.Process}: The process associated with the simulation. If the simulation process fails, e.g. if the command cannot be constructed, this will be nothing.

collectSimulationTasks(T::AbstractTrial[; force_recompile::Bool=false])

Collect the simulation tasks for the given trial, sampling, monad, or simulation.

Arguments

• T::AbstractTrial: The trial, sampling, monad, or simulation to collect tasks for.

Keyword Arguments

• force_recompile::Bool=false: If true, forces a recompilation of all files by removing all .o files in the PhysiCell directory.
• do_full_setup::Bool=true: If true, performs a full setup of the simulation, including compiling code and preparing input files. Only used for AbstractMonad objects.

prepCmdForWrap(cmd::Cmd)

Prepare the command for wrapping in the sbatch command. This is a helper function to remove the backticks from the command string.

prepareHPCCommand(cmd::Cmd, simulation_id::Int)

Prepare the command to run a simulation on an HPC system using sbatch. This function adds the necessary flags to the command and returns it as a Cmd object.

prepareSimulationCommand(simulation::Simulation, monad_id::Int, do_full_setup::Bool, force_recompile::Bool)

Internal function to prepare the command to run a simulation, including preparing input files and compiling the custom code if necessary.

processSimulationTask(simulation_task, prune_options)

Process the given simulation task and return whether it was successful.

resolveSimulation(simulation_process::SimulationProcess, prune_options::PruneOptions)

Resolve the simulation process by checking its exit code and updating the database accordingly.

simulationFailedToRun(simulation::Simulation, monad_id::Int)

Set the status code of the simulation to "Failed" and erase the simulation ID from the simulations.csv file for the monad it belongs to.

trialID(output::PCMMOutput)

Get the ID of the trial from the output of the PhysiCellModelManager.jl run.

trialType(output::PCMMOutput)

Get the type of the trial from the output of the PhysiCellModelManager.jl run.