Chapter 3 Compilation instructions

Instructions for compiling and running the software used in this study on your local machine. All experiments were run on Mac or Linux-based operating systems.

You will need a C++ compiler that supports at least C++17. We used g++13 for all local compilations.

You will also need Python to run graph generation and analysis. Python dependencies are listed in the requirements.txt at the root of this repository.

Statistical analyses and data visualizations were conducted using R.

Experiments in our simplified model used the MABE2 software, and experiments with digital organisms (self-replicating computer programs) used a modified version of the Avida software platform.

3.1 Instructions

First, clone the alife-2025-env-conn repository (https://github.com/amlalejini/alife-2025-env-conn.git) to your machine. Then, initialize and update git submodule inside the repository. From inside the repository on your machine, run:

git submodule update --init --recursive

This will download and update the following dependencies:

  • avida-empirical (commit hash: 266f95f8fcb452655330dab55caa9f1408b49ffa): A modified implementation of the Avida software that supports the capacity to configure environmental connectivity.
  • evo_spatial_discoveries (commit hash: 2c384e93df231125bae83fc6c38d8dc8c64eb6ee): Contains configurations for MABE2 experiments.
  • MABE2 (commit hash: 4f8eb86f997ee89f6d0e0b1144c5be162f4d8d1b): MABE = “Modular agent-based evolver”, which is a software platform deigned to empower developers to easily build and customize software for evolutionary computation or artificial life. We used this platform to implement our non-avida experiments.
  • network_correlation (commit hash: 9d9a07f7436c3569d10eb3b03c6b30e1238c74ef): Third-party python implementations of various graph statistics and analyses.

To compile Avida, navigate into the third-party/avida-empirical/ directory and run ./build_avida/. The compiled executable will be created in the third-party/avida-empirical/cbuild/work/ directory.

To compile MABE2, navigate into the third-party/MABE2/build directory and run make native. The compiled executable will be created in the third-party/MABE2/build directory.

Configuration files used Avida experiments can be found in the experiments/ directory (within the hpc/config subdirectory for any given experiment). Configuration files used for MABE2 experiments can be found in third-party/evo_spatial_discoveries/experiments/.