sPEGG

sPEGG is a simulator and framework for studying eco-evolutionary dynamics. Using forward-time population genetics, sPEGG allows researchers to study the interplay between ecological and evolutionary processes in multispecies metacommunities.

sPEGG harnesses the massive parallelization potential of relatively economical General-Purpose Graphics Processing units (GPGPUs) installed on modern desktops. Depending on the complexity of the ecological and evolutionary components of your model, sPEGG can provide performance gains on your desktop comparable to gains obtainable on a small-to-medium sized cluster.

Version 0.5

sPEGG continues to be under active development. Should you have any comments or if there are aspects of the usage that are unclear, please feel free to note any issues you might have, to help make sPEGG more useful 😄.

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Currently, sPEGG has only been tested on Linux (debian-based distributions to be specific). If you encounter platform-specific commands that need to be added while porting sPEGG to other operating systems, please create an issue and I will update the documentation. Or, if you can get it to work reliably, consider becoming a contributor!

## Pre-requisites

• Linux OS

• The latest NVIDIA CUDA for your distro; appropriate drivers and the required thrust library should come with this.

• gcc

• libconfig

• ConfigFile(included)

• CUDA-enabled GPU (generally this will require compute capability >= 2.0)

In addition, the CPU version requires

• GNU Scientific Library

Please see here for some [possible issues](Documentation/Tutorial.md#setup_issues) you may run into when setting up **sPEGG**.

Once you have everything in place, you can run your first sPEGG simulation!

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Quick-start example: Simulating genetic drift

We'll use the code for the simulation that is created from the tutorial to simulate genetic drift in two demes of 10000 individuals each across 100000 generations on the GPU.

Open a terminal (ctrl+Alt+T in recent ubuntu versions) and navigate to your project directory.

$ cd </path/to/My_sPEGG_project>

Using git, clone sPEGG's git repository

$ git clone --recursive https://github.com/kewok/spegg/

Enter the main code base for sPEGG

$ cd spegg

in your terminal.

Now, simply type

$ make

in the terminal. Depending on your system, this might take awhile.

Now, navigate into the directory:

$ cd Examples/Tutorial_Simulation

and type

$ make

in the terminal. If everything has been installed correctly, this will create an executable (a.out). You can run it as:

$ ./a.out

However, the genetic drift simulator you downloaded is only configured to run for a single generation. Open the file Simulation.conf using a text editor (e.g., gedit) and change this line:

n_timesteps = 1

to something like:

n_timesteps = 10000

Now launch the sPEGG simulation by running this executable you created from the terminal via

$ ./a.out 

If all went well, you should have output that looks something like:

The average genotypes at locus 1 for the two demes are:
-0.596273 0.99806 

The exact numbers may very well differ, however depending on your hardware.

This just gives you a flavor for running a sPEGG simulation. If you are interested in simulating more biologically relevant models, have a look at the other examples described (here). To configure and run those models, you'll want to modify the deme_config.txt and environment_config.txt files as well.

For those of you who'd like to build your own sPEGG model, have a look at our more in-depth Tutorial.

License

sPEGG is released under the terms of the GNU Public License v3.0. Please refer to the LICENSE file. © Kenichi Okamoto, 2016.