Chapter 3 Compile and run experiments locally

Here, we provide a brief guide to compiling and running our experiments using our Docker image.

Please file an issue on GitHub if something is unclear or does not work.

3.1 Docker

You can use the Dockerfile in our repository to build a docker image locally, or you can pull the latest docker image from DockerHub using

docker pull amlalejini/evolutionary-consequences-of-plasticity

This will pull down a docker image with:

• all of the requisite dependencies installed/downloaded
• all experiment source code
• the minimal set of raw data needed to compile the supplemental material
• a build of our supplemental material (which will also run all of our analyses)

To run the container interactively:

docker run -it --entrypoint bash amlalejini/evolutionary-consequences-of-plasticity

You can exit the container at any point with ctrl-d.

Inside the container, you should be able to navigate to /opt/evolutionary-consequences-of-plasticity:

cd /opt/evolutionary-consequences-of-plasticity

To run Avida, you’ll need to cd into the avida directory and run ./build_avida.

All of the Avida configuration files necessary for re-running our experiments can be found here: https://github.com/amlalejini/evolutionary-consequences-of-plasticity/tree/master/experiments.

For example, the configuration files for our evolutionary change experiment are here: https://github.com/amlalejini/evolutionary-consequences-of-plasticity/tree/master/experiments/2021-02-08-evo-dynamics/hpcc/config.