A search through two parameters can be generated using the following command
python src/routines/generate_parameter_space_search.py --numberTrials 100 --dims 1000,1000 --savepath workspace/experiments/phase_diagram_no_mutations_phi_0.25 --mutation 0.000 --selection 0.0 --intensity 10 --radius 10 --density 0.25 --overwrite --parameters selection,intensity --intervals_1 0,0.01,0.1 --intervals_2 0,0.5,6 --model src/base/ --environments 20 --standing_variation To execute a simulation through a single parameter search:
A single simulation across one variable can be perfomed using
sbatch src/scripts/slurm_main.sh --model src/base/ --initial_type alt --numberTrials 500 --dims 500,500 --mutation 0.01 --intensity 4 --density 0 --selection 0.1 --radius 5 --savepath workspace/simulation_data/stable_density --parameter selection --intervals 0,0.025,0.5 --env_type uniform --flags standing_variation
A list of simulation options and their descriptions can be found using
python src/processing/generate_parameter_space_search.py --help
Source code used to generate article figures are contained in the figures/ directory. Analysis is performed by providing a list of directories (input variable) containing the simluation data from generate_parameter_space_search.py. If all data are saved in, for example, workarea/experiments/, the figure scripts will automatically scan and collect all simulation data and proceed with the analysis. Commands used to generate the datasets are located in the datasets.md file. These commmands will source the parameter space search routine to submit many jobs to the slurm queue. The output location is given by --savepath option, and are named based on which figure they're used to generate.
Additionally, individual simulations can be executed using main.jl; a list of command-line options can be displayed using
julia src/base/main.jl --help
This code requires both Julia (v1.10.4) and python (v3.11.5) to be installed. Our Julia environment is contained in the Manifest.toml and Project.toml files. Our Python environment is provided in requirements.txt and in environment.yml.
Julia package dependencies can be downloaded and installed for the current project using the Project.toml file through the following command:
julia --project=. -e 'using Pkg; Pkg.instantiate()'
If using the Conda package manager for python, the python dependencies can be installed using
conda create --name <env_name> --file requirements.txt
While the script generate_parameter_space_search.py to generate simulations works best with the slurm workload manager installed, the script will check for an existing slurm installion and will fallback to executing sequentially via bash if no slurm installation is found.