Tutorial on using Cython

This basic tutorial will show how to do a simple iterative wave propagation in python and then speed it us using cython and C++ and OpenMP.

Algorithm

The basic algorithm takes the pressure in one cell of the matrix and then calculates the velocity in the four adjacent cells (up,down,left,right) based on the pressure difference in those four cells. After the velocities are calculated the pressure at the points is re-calculated knowing that some of the pressure has moved by the velocity. The pressure at the center oscillates with a sinusoidal frequency for some number of steps.

for each step:
  presure_at_center = initial_P * sin(omega * step)
  for x in size_x:
    for y in size_y
      velocity_u[x][y] += pressure[x][y] - pressure[x - 1][y]
      velocity_d[x][y] += pressure[x][y] - pressure[x][y + 1]
      velocity_l[x][y] += pressure[x][y] - pressure[x + 1][y]
      velocity_r[x][y] += pressure[x][y] - pressure[x][y - 1]
    for x in size_x:
      for y in size_y
        pressure[x][y] -= sum(velocities)

Building and using cython modules

In each folder there are setup.py and CMake build scripts to build the example.

To build using setup.py:

python setup.py build_ext --inplace

To build using CMake:

mkdir build
cd build
cmake ..
make

To use module the shared library which is built (wave_propogation.cpython-{PYVER}-{PLATROM}.so) it should either be in your current directory, or in a directory accessible by your $PYTHON_PATH. It can also be in a sub folder such as build by using .'s in place of /.

Using the Templates

There are two templates available to start your cython project from, either using setup.py or cmake as the build platfom. Put your code into a pyx file in the folder, change the name in the setup.py or CMakeLists.txt and use it yourself. For an existing python project you want to speedup use the setup.py template. For a C/C++/Fortran project start with the cmake template.

Credits

Basic wave propagation algorithm found in https://github.com/Alexander3/wave-propagation.