Sibernetic is a fluid mechanics simulator developed for simulations of C. elegans in the OpenWorm project developed for the OpenWorm project by Andrey Palyanov, Sergey Khayrulin and Mike Vella as part of the OpenWorm team.

This fork is an effort to clean it up and improve the performance.

Unlike the original, this version of the code will currently run only on Linux. No support for OSX or Windows is planned until the code is understood, refactored and commented.

Sibernetic is primarily written in C++ and OpenCL, it also provides a Python API.

Compiling / running

Linux

Install OpenCL on Ubuntu. We suggest you initially go with AMD OpenCL drivers as we have found these to be the most stable and complete.

You'll also need a variety of libraries. In ubuntu, install the dependencies with:

sudo apt-get install g++ python-dev freeglut3-dev nvidia-opencl-dev libglu1-mesa-dev libglew-dev python-numpy

Next, navigate to the build folder and run:

make clean
make all

You should see an output which looks something like this:

Building file: ../src/PyramidalSimulation.cpp
Invoking: GCC C++ Compiler

Then navigate to the top-level folder in the hierarchy (e.g Smoothed-Particle-Hydrodynamics) and set your PYTHONPATH:

export PYTHONPATH=$PYTHONPATH:'./src'

Finally, to run, run the command:

./release/sph