Pick a suitable platform-specific subdirectory in the compile directory and use it either directly or make a copy to modify. The file make_head.mk holds all build settings. Run make and the resulting executable will be placed in bin.
There are example simulations ready to run in the examples directory.
There are some Python tools that can help with preparing and post-processing a PINY simulation. They include command line utilities as well as a Python package. To use these, set your paths by sourcing the env.sh file in the python directory. For shells other than bash, set the required environment variables "by hand". For repeated use, it is probably a good idea to place these settings in your shell's RC file.
The tools require the numpy library.
Additionally, if you want to use the optional Python interface to PINY itself, you also need to have Cython. First, in one of the compile subdirectories, do make libpiny to link a shared library. Then, do make in the python directory to build the interface.
Funding for the development of PINY_MD has come from a variety of sources, most recently, from grants from the National Science Foundation CHE-1301314 and CHE-1566085