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Created June 16, 2016 23:17
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Optimizing with Cython Introduction\n",
"-------------------------------------"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Make a large set of random integers"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"from array import array\n",
"from random import randint\n",
"a = array('i', (randint(-1000, 1000) for _ in xrange(10000000)))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Simple way to sum with a `for` loop"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"def sum_py(a):\n",
" s = 0\n",
" for x in a: s += x\n",
" return s"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Time the baseline simple sum methods"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"1 loops, best of 3: 373 ms per loop\n",
"10 loops, best of 3: 100 ms per loop\n"
]
}
],
"source": [
"%timeit sum_py(a)\n",
"%timeit sum(a)"
]
},
{
"cell_type": "markdown",
"metadata": {
"collapsed": true
},
"source": [
"**Compile with Cython**"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"# needs to be run once every time the kernel is started\n",
"%load_ext cython"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%%cython\n",
"def sum_cy(a):\n",
" s = 0\n",
" for x in a: s += x\n",
" return s"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"10 loops, best of 3: 100 ms per loop\n",
"1 loops, best of 3: 233 ms per loop\n"
]
}
],
"source": [
"%timeit sum(a)\n",
"%timeit sum_cy(a)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**Static Typing**"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%%cython\n",
"def sum_cy_st(a):\n",
" cdef int x, s = 0\n",
" for x in a: s += x\n",
" return s"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"10 loops, best of 3: 101 ms per loop\n",
"10 loops, best of 3: 104 ms per loop\n"
]
}
],
"source": [
"%timeit sum(a)\n",
"%timeit sum_cy_st(a)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**Colorized Annotations**"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false
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"source": [
"%%cython --annotate\n",
"from cpython cimport array\n",
"def sum_cy_tm(int[:] a):\n",
" cdef int x, s = 0\n",
" for x in a:\n",
" s += x\n",
" return s"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
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},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"10 loops, best of 3: 101 ms per loop\n",
"1 loops, best of 3: 2.31 s per loop\n"
]
}
],
"source": [
"%timeit sum(a)\n",
"%timeit sum_cy_tm(a)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"With C-like looping"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
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"source": [
"%%cython --annotate\n",
"from cpython cimport array\n",
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" cdef int i, n = a.shape[0], s = 0\n",
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"metadata": {
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{
"name": "stdout",
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"text": [
"10 loops, best of 3: 101 ms per loop\n",
"100 loops, best of 3: 9.8 ms per loop\n"
]
}
],
"source": [
"%timeit sum(a)\n",
"%timeit sum_cy_tm(a)"
]
},
{
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"source": [
"**Compile Optimizations**"
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"%%cython --annotate\n",
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"\n",
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{
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{
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"text": [
"10 loops, best of 3: 102 ms per loop\n",
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]
}
],
"source": [
"%timeit sum(a)\n",
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]
},
{
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"text": [
"10 loops, best of 3: 101 ms per loop\n",
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}
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"**Multithreading**"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"%%cython\n",
"cimport cython\n",
"from cpython cimport array\n",
"\n",
"@cython.boundscheck(False)\n",
"@cython.wraparound(False)\n",
"def __sum_gil(int[::1] a, int[:] out):\n",
" cdef int i, n = a.shape[0], s = 0\n",
" for i in range(n): s += a[i]\n",
" out[0] = s\n",
" \n",
"def sum_par(int[::1] a):\n",
" cdef int[::1] A1 = a[0 : a.shape[0]//2]\n",
" cdef int[::1] A2 = a[a.shape[0]//2 : a.shape[0]]\n",
" cdef int[:] out = array.array('i', (0,0))\n",
" from threading import Thread\n",
" T1 = Thread(target=__sum_gil, args=(A1, out[0:1]))\n",
" T2 = Thread(target=__sum_gil, args=(A2, out[1:2]))\n",
" T1.start(); T2.start()\n",
" T1.join(); T2.join()\n",
" return out[0] + out[1]"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"10 loops, best of 3: 101 ms per loop\n",
"100 loops, best of 3: 4.44 ms per loop\n"
]
}
],
"source": [
"%timeit sum(a)\n",
"%timeit sum_par(a)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"With release of the GIL "
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"%%cython\n",
"cimport cython\n",
"from cpython cimport array\n",
"\n",
"@cython.boundscheck(False)\n",
"@cython.wraparound(False)\n",
"def __sum_gil(int[::1] a, int[:] out):\n",
" cdef int i, n = a.shape[0], s = 0\n",
" with nogil:\n",
" for i in range(n): s += a[i]\n",
" out[0] = s\n",
" \n",
"def sum_par(int[::1] a):\n",
" cdef int[::1] A1 = a[0 : a.shape[0]//2]\n",
" cdef int[::1] A2 = a[a.shape[0]//2 : a.shape[0]]\n",
" cdef int[:] out = array.array('i', (0,0))\n",
" from threading import Thread\n",
" T1 = Thread(target=__sum_gil, args=(A1, out[0:1]))\n",
" T2 = Thread(target=__sum_gil, args=(A2, out[1:2]))\n",
" T1.start(); T2.start()\n",
" T1.join(); T2.join()\n",
" return out[0] + out[1]"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"10 loops, best of 3: 101 ms per loop\n",
"100 loops, best of 3: 2.47 ms per loop\n"
]
}
],
"source": [
"%timeit sum(a)\n",
"%timeit sum_par(a)"
]
},
{
"cell_type": "markdown",
"metadata": {
"collapsed": true
},
"source": [
"**Interfacing with C Code**\n",
"\n",
"Need sum.h with `int sum_c(int* a, int n);` and sum.c with the following:\n",
" #include \"sum.h\"\n",
" int sum_c(int* a, int n) {\n",
" int i, s = 0;\n",
" for (i = 0; i < n; ++i) { s += a[i]; }\n",
" return s;\n",
" }\n",
" \n",
"Also, the following needs to be updated where `-I` is the path to where the above is saved."
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {
"collapsed": false,
"scrolled": false
},
"outputs": [],
"source": [
"%%cython -I C:/Python27/notebooks\n",
"#distutils: sources=sum.c\n",
"\n",
"cimport cython\n",
"from cpython cimport array\n",
"\n",
"cdef extern from \"sum.h\" nogil:\n",
" cdef int sum_c(int* a, int n)\n",
" \n",
"@cython.boundscheck(False)\n",
"@cython.wraparound(False)\n",
"def sum_cy_c(int[::1] a):\n",
" cdef int out\n",
" with nogil: out = sum_c(&a[0], a.shape[0])\n",
" return out"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"100 loops, best of 3: 3.54 ms per loop\n",
"100 loops, best of 3: 3.56 ms per loop\n"
]
}
],
"source": [
"%timeit sum_cy_cc(a)\n",
"%timeit sum_cy_c(a)"
]
},
{
"cell_type": "markdown",
"metadata": {
"collapsed": true
},
"source": [
"**Numpy Equivilent**"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"1 loops, best of 3: 859 ms per loop\n",
"100 loops, best of 3: 4.34 ms per loop\n",
"100 loops, best of 3: 3.53 ms per loop\n"
]
}
],
"source": [
"import numpy as np\n",
"#np_a = np.random.randint(-1000, 1000, size=10000000)\n",
"np_a = np.array(a)\n",
"%timeit sum(np_a)\n",
"%timeit np_a.sum()\n",
"%timeit sum_cy_cc(a)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**Check they all sum properly**"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"(2140693,\n",
" 2140693,\n",
" 2140693,\n",
" 2140693,\n",
" 2140693,\n",
" 2140693,\n",
" 2140693,\n",
" 2140693,\n",
" 2140693,\n",
" 2140693)"
]
},
"execution_count": 25,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"(sum_py(a), sum_cy(a), sum(a), sum_cy_st(a), sum_cy_tm(a), sum_cy_co(a),\n",
" sum_cy_cc(a), sum_par(a), sum_cy_c(a), np_a.sum())"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.10"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
#include "sum.h"
int sum_c(int* a, int n)
{
int i, s = 0;
for (i = 0; i < n; ++i) { s += a[i]; }
return s;
}
int sum_c(int* a, int n);
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