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Writing C in Cython

For the last two years, I’ve done almost all of my work in Cython. And I don’t mean, I write Python, and then “Cythonize” it, with various type-declarations etc. I just, write Cython.

I use “raw” C structs and arrays, and occasionally C++ vectors, with a thin wrapper around malloc/free that I wrote myself. The code is almost always exactly as fast as C/C++, because it really is just C/C++ with some syntactic sugar — but with Python “right there”, should I need/want it.

This is basically the inverse of the old promise that languages like Python came with: that you would write your whole application in Python, optimise the “hot spots” with C, and voila! C speed, Python convenience, and money in the bank.

This was always much nicer in theory than practice. In practice, your data structures have a huge influence on both the efficiency of your code, and how annoying it is to write. Arrays are a pain and fast; lists are blissfully convenient, and very slow. Python loops and function calls are also quite slow, so the part you have to write in C tends to wriggle its way up the stack, until it’s almost your whole application.

Today a post came up on HN, on writing C extensions for Python. The author wrote both a pure Python implementation, and a C implementation, using the Numpy C API. This seemed a good opportunity to demonstrate the difference, so I wrote a Cython implementation for comparison:

import random
from cymem.cymem cimport Pool
from libc.math cimport sqrt
cimport cython
cdef struct Point:
double x
double y
cdef class World:
cdef Pool mem
cdef int N
cdef double* m
cdef Point* r
cdef Point* v
cdef Point* F
cdef readonly double dt
def __init__(self, N, threads=1, m_min=1, m_max=30.0, r_max=50.0, v_max=4.0, dt=1e-3):
self.mem = Pool()
self.N = N
self.m = <double*>self.mem.alloc(N, sizeof(double))
self.r = <Point*>self.mem.alloc(N, sizeof(Point))
self.v = <Point*>self.mem.alloc(N, sizeof(Point))
self.F = <Point*>self.mem.alloc(N, sizeof(Point))
for i in range(N):
self.m[i] = random.uniform(m_min, m_max)
self.r[i].x = random.uniform(-r_max, r_max)
self.r[i].y = random.uniform(-r_max, r_max)
self.v[i].x = random.uniform(-v_max, v_max)
self.v[i].y = random.uniform(-v_max, v_max)
self.F[i].x = 0
self.F[i].y = 0
self.dt = dt
def compute_F(World w):
"""Compute the force on each body in the world, w."""
cdef int i, j
cdef double s3, tmp
cdef Point s
cdef Point F
for i in range(w.N):
# Set all forces to zero.
w.F[i].x = 0
w.F[i].y = 0
for j in range(i+1, w.N):
s.x = w.r[j].x - w.r[i].x
s.y = w.r[j].y - w.r[i].y
s3 = sqrt(s.x * s.x + s.y * s.y)
s3 *= s3 * s3;
tmp = w.m[i] * w.m[j] / s3
F.x = tmp * s.x
F.y = tmp * s.y
w.F[i].x += F.x
w.F[i].y += F.y
w.F[j].x -= F.x
w.F[j].y -= F.y
def evolve(World w, int steps):
"""Evolve the world, w, through the given number of steps."""
cdef int _, i
for _ in range(steps):
for i in range(w.N):
w.v[i].x += w.F[i].x * w.dt / w.m[i]
w.v[i].y += w.F[i].y * w.dt / w.m[i]
w.r[i].x += w.v[i].x * w.dt
w.r[i].y += w.v[i].y * w.dt

The Cython version took about 30 minutes to write, and it runs just as fast as the C code — because, why wouldn’t it? It is C code, really, with just some syntactic sugar. And you don’t even have to learn or think about a foreign, complicated C API… You just, write C. Or C++ — although that’s a little more awkward. Both the Cython version and the C version are about 70x faster than the pure Python version, which uses Numpy arrays.

One difference from C: I wrote a little wrapper around malloc/free, cymem. All it does is remember the addresses it served, and when the Pool is garbage collected, it frees the memory it allocated. I’ve had no trouble with memory leaks since I started using this.

The “intermediate” way of writing Cython, using typed memory-views, allows you to use the Numpy multi-dimensional array features. However, to me it feels more complicated, and the applications I tend to write involve very sparse arrays — where, once again, I want to define my own data structures.


I found a Russian translation of this post here. I don’t know how accurate it is.