Fastest way to list all primes below N in python

Question

This is the best algorithm I could come up with after struggling with a couple of Project Euler's questions.

def get_primes(n):
    numbers = set(range(n, 1, -1))
    primes = []
    while numbers:
        p = numbers.pop()
        primes.append(p)
        numbers.difference_update(set(range(p*2, n+1, p)))
    return primes

>>> timeit.Timer(stmt='get_primes.get_primes(1000000)', setup='import   get_primes').timeit(1)
1.1499958793645562

Can it be made even faster?

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EDIT: This code has a flaw: Since numbers is an unordered set, there is no guarantee that numbers.pop() will remove the lowest number from the set. Nevertheless, it works (at least for me) for some input numbers:

>>> sum(get_primes(2000000))
142913828922L
#That's the correct sum of all numbers below 2 million
>>> 529 in get_primes(1000)
False
>>> 529 in get_primes(530)
True

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EDIT: The rank so far (pure python, no external sources, all primes below 1 million):

1. Sundaram's Sieve implementation by myself: 327ms
2. Daniel's Sieve: 435ms
3. Alex's recipe from Cookbok: 710ms

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EDIT: ~unutbu is leading the race.

Answer 1

There's a pretty neat sample from the Python Cookbook here -- the fastest version proposed on that URL is:

import itertools
def erat2( ):
    D = {  }
    yield 2
    for q in itertools.islice(itertools.count(3), 0, None, 2):
        p = D.pop(q, None)
        if p is None:
            D[q*q] = q
            yield q
        else:
            x = p + q
            while x in D or not (x&1):
                x += p
            D[x] = p

so that would give

get_primes_erat(n):
  return list(itertools.takewhile(lambda p: p<n, erat2()))

Measuring at the shell prompt (as I prefer to do) with this code in pri.py, I observe:

$ python2.5 -mtimeit -s'import pri' 'pri.get_primes(1000000)'
10 loops, best of 3: 1.69 sec per loop
$ python2.5 -mtimeit -s'import pri' 'pri.get_primes_erat(1000000)'
10 loops, best of 3: 673 msec per loop

so it looks like the Cookbook solution is over twice as fast.

Answer 2

What size of primes do you want? There are some very fast statistical algorithms out there (eg Miller-Rabin), but their overheads mean they turn out slower unless dealing with very big (over 2^64) numbers..

Answer 3

In general if you need fast number computation python is not the best choice. Today there are a lot of faster (and complex) algorithm. For example on my computer I got 2.2 second for your code, with Mathematica I got 0.088005.

First of all: do you need set?

Answer 4

The easiest optimization to implement is that if you want to check whether n is prime, you only have to check to see if n is divisible by a number up to square_root(n). Is this for Project Euler?

Answer 5

The algorithm is fast, but it has a serious flaw:

>>> sorted(get_primes(530))
[2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73,
79, 83, 89, 97, 101, 103, 107, 109, 113, 127, 131, 137, 139, 149, 151, 157, 163,
167, 173, 179, 181, 191, 193, 197, 199, 211, 223, 227, 229, 233, 239, 241, 251,
257, 263, 269, 271, 277, 281, 283, 293, 307, 311, 313, 317, 331, 337, 347, 349,
353, 359, 367, 373, 379, 383, 389, 397, 401, 409, 419, 421, 431, 433, 439, 443,
449, 457, 461, 463, 467, 479, 487, 491, 499, 503, 509, 521, 523, 527, 529]
>>> 17*31
527
>>> 23*23
529

You assume that numbers.pop() would return the smallest number in the set, but this is not guaranteed at all. Sets are unordered and pop() removes and returns an arbitrary element, so it cannot be used to select the next prime from the remaining numbers.

Answer 6

For the fastest code, the numpy solution is the best. For purely academic reasons, though, I'm posting my pure python version, which is a bit less than 50% faster than the cookbook version posted above. Since I make the entire list in memory, you need enough space to hold everything, but it seems to scale fairly well.

def daniel_sieve_2(maxNumber):
    """
    Given a number, returns all numbers less than or equal to
    that number which are prime.
    """
    allNumbers = range(3, maxNumber+1, 2)
    for mIndex, number in enumerate(xrange(3, maxNumber+1, 2)):
        if allNumbers[mIndex] == 0:
            continue
        # now set all multiples to 0
        for index in xrange(mIndex+number, (maxNumber-3)/2+1, number):
            allNumbers[index] = 0
    return [2] + filter(lambda n: n!=0, allNumbers)

And the results:

>>>mine = timeit.Timer("daniel_sieve_2(1000000)",
...                    "from sieves import daniel_sieve_2")
>>>prev = timeit.Timer("get_primes_erat(1000000)",
...                    "from sieves import get_primes_erat")
>>>print "Mine: {0:0.4f} ms".format(min(mine.repeat(3, 1))*1000)
Mine: 428.9446 ms
>>>print "Previous Best {0:0.4f} ms".format(min(prev.repeat(3, 1))*1000)
Previous Best 621.3581 ms

Answer 7

For truly fastest solution with sufficiently large N would be to download a pre-calculated list of primes, store it as a tuple and do something like:

for pos,i in enumerate(primes):
    if i > N:
        print primes[:pos]

If N > primes[-1] only then calculate more primes and save the new list in your code, so next time it is equally as fast.

Always think outside the box.

Answer 8

Using Sundaram's Sieve, I think I broke pure-Python's record:

def sundaram3(max_n):
    numbers = range(3, max_n+1, 2)
    half = (max_n)//2
    initial = 4

    for step in xrange(3, max_n+1, 2):
        for i in xrange(initial, half, step):
            numbers[i-1] = 0
        initial += 2*(step+1)

        if initial > half:
            return [2] + filter(None, numbers)

Comparasion:

C:\USERS>python -m timeit -n10 -s "import get_primes" "get_primes.get_primes_erat(1000000)"
10 loops, best of 3: 710 msec per loop

C:\USERS>python -m timeit -n10 -s "import get_primes" "get_primes.daniel_sieve_2(1000000)"
10 loops, best of 3: 435 msec per loop

C:\USERS>python -m timeit -n10 -s "import get_primes" "get_primes.sundaram3(1000000)"
10 loops, best of 3: 327 msec per loop

Answer 9

A deterministic implementation of Miller-Rabin's Primality test on the assumption that N < 9,080,191

import sys
import random

def miller_rabin_pass(a, n):
    d = n - 1
    s = 0
    while d % 2 == 0:
        d >>= 1
        s += 1

    a_to_power = pow(a, d, n)
    if a_to_power == 1:
        return True
    for i in xrange(s-1):
        if a_to_power == n - 1:
            return True
        a_to_power = (a_to_power * a_to_power) % n
    return a_to_power == n - 1


def miller_rabin(n):
    for a in [2, 3, 37, 73]:
      if not miller_rabin_pass(a, n):
        return False
    return True


n = int(sys.argv[1])
primes = [2]
for p in range(3,n,2):
  if miller_rabin(p):
    primes.append(p)
print len(primes)

According to the article on Wikipedia (http://en.wikipedia.org/wiki/Miller–Rabin_primality_test) testing N < 9,080,191 for a = 2,3,37, and 73 is enough to decide whether N is composite or not.

And I adapted the source code from the probabilistic implementation of original Miller-Rabin's test found here: http://en.literateprograms.org/Miller-Rabin_primality_test_(Python)

Answer 10

If you have control over N, the very fastest way to list all primes is to precompute them. Seriously. Precomputing is a way overlooked optimization.

Answer 11

Here's the code I normally use to generate primes in Python:

$ python -mtimeit -s'import sieve' 'sieve.sieve(1000000)' 
10 loops, best of 3: 445 msec per loop
$ cat sieve.py
from math import sqrt

def sieve(size):
 prime=[True]*size
 rng=xrange
 limit=int(sqrt(size))

 for i in rng(3,limit+1,+2):
  if prime[i]:
   prime[i*i::+i]=[False]*len(prime[i*i::+i])

 return [2]+[i for i in rng(3,size,+2) if prime[i]]

if __name__=='__main__':
 print sieve(100)

It can't compete with the faster solutions posted here, but at least it is pure python.

Thanks for posting this question. I really learnt a lot today.

Answer 12

My guess is that the fastest of all ways is to hard code the primes in your code.

So why not just write a slow script that generates another source file that has all numbers hardwired in it, and then import that source file when you run your actual program.

Of course, this works only if you know the upper bound of N at compile time, but thus is the case for (almost) all project Euler problems.

 

PS: I might be wrong though iff parsing the source with hard-wired primes is slower than computing them in the first place, but as far I know Python runs from compiled .pyc files so reading a binary array with all primes up to N should be bloody fast in that case.

Answer 13

Related question(dealing with primes generators & including benchmarks):
Speed up bitstring/bit operations in Python?

Faster & more memory-wise pure Python code:

def primes(n):
    """ Returns  a list of primes < n """
    sieve = [True] * n
    for i in xrange(3,int(n**0.5)+1,2):
        if sieve[i]:
            sieve[i*i::2*i]=[False]*((n-i*i-1)/(2*i)+1)
    return [2] + [i for i in xrange(3,n,2) if sieve[i]]

or starting with half sieve

def primes1(n):
    """ Returns  a list of primes < n """
    sieve = [True] * (n/2)
    for i in xrange(3,int(n**0.5)+1,2):
        if sieve[i/2]:
            sieve[i*i/2::i] = [False] * ((n-i*i-1)/(2*i)+1)
    return [2] + [2*i+1 for i in xrange(1,n/2) if sieve[i]]

Faster & more memory-wise numpy code:

import numpy
def primesfrom3to(n):
    """ Returns a array of primes, 3 <= p < n """
    sieve = numpy.ones(n/2, dtype=numpy.bool)
    for i in xrange(3,int(n**0.5)+1,2):
        if sieve[i/2]:
            sieve[i*i/2::i] = False
    return 2*numpy.nonzero(sieve)[0][1::]+1

a faster variation starting with a third of a sieve:

import numpy
def primesfrom2to(n):
    """ Input n>=6, Returns a array of primes, 2 <= p < n """
    sieve = numpy.ones(n/3 + (n%6==2), dtype=numpy.bool)
    for i in xrange(1,int(n**0.5)/3+1):
        if sieve[i]:
            k=3*i+1|1
            sieve[       k*k/3     ::2*k] = False
            sieve[k*(k-2*(i&1)+4)/3::2*k] = False
    return numpy.r_[2,3,((3*numpy.nonzero(sieve)[0][1:]+1)|1)]

A (hard-to-code) pure-python version of the above code would be:

def primes2(n):
    """ Input n>=6, Returns a list of primes, 2 <= p < n """
    n, correction = n-n%6+6, 2-(n%6>1)
    sieve = [True] * (n/3)
    for i in xrange(1,int(n**0.5)/3+1):
      if sieve[i]:
        k=3*i+1|1
        sieve[      k*k/3      ::2*k] = [False] * ((n/6-k*k/6-1)/k+1)
        sieve[k*(k-2*(i&1)+4)/3::2*k] = [False] * ((n/6-k*(k-2*(i&1)+4)/6-1)/k+1)
    return [2,3] + [3*i+1|1 for i in xrange(1,n/3-correction) if sieve[i]]

Unfortunately pure-python don't adopt the simpler and faster numpy way of doing Assignment, and calling len() inside the loop as in [False]*len(sieve[((k*k)/3)::2*k]) is too slow. So i had to improvise to correct input (& avoid more math) and do some extreme (& painful) math-magic.
Personally i think it is a shame that numpy (which is so widely used) is not part of python standard library(2 years after python 3 release & no numpy compatibility), and that the improvements in syntax and speed seem to be completely overlooked by python developers.

Answer 14

Sorry to bother but erat2() has a serious flaw in the algorithm.

While searching for the next composite, we need to test odd numbers only. q,p both are odd; then q+p is even and doesn't need to be tested, but q+2*p is always odd. This eliminates the "if even" test in the while loop condition and saves about 30% of the runtime.

While we're at it: instead of the elegant 'D.pop(q,None)' get and delete method use 'if q in D: p=D[q],del D[q]' which is twice as fast! At least on my machine (P3-1Ghz). So I suggest this implementation of this clever algorithm:

def erat3( ):
    from itertools import islice, count

    # q is the running integer that's checked for primeness.
    # yield 2 and no other even number thereafter
    yield 2
    D = {}
    # no need to mark D[4] as we will test odd numbers only
    for q in islice(count(3),0,None,2):
        if q in D:                  #  is composite
            p = D[q]
            del D[q]
            # q is composite. p=D[q] is the first prime that
            # divides it. Since we've reached q, we no longer
            # need it in the map, but we'll mark the next
            # multiple of its witnesses to prepare for larger
            # numbers.
            x = q + p+p        # next odd(!) multiple
            while x in D:      # skip composites
                x += p+p
            D[x] = p
        else:                  # is prime
            # q is a new prime.
            # Yield it and mark its first multiple that isn't
            # already marked in previous iterations.
            D[q*q] = q
            yield q

Answer 15

A slightly different implementation of a half sieve using Numpy:

http://rebrained.com/?p=458

import math
import numpy
def prime6(upto):
    primes=numpy.arange(3,upto+1,2)
    isprime=numpy.ones((upto-1)/2,dtype=bool)
    for factor in primes[:int(math.sqrt(upto))]:
        if isprime[(factor-2)/2]: isprime[(factor*3-2)/2:(upto-1)/2:factor]=0
    return numpy.insert(primes[isprime],0,2)

Can someone compare this with the other timings? On my machine it seems pretty comparable to the other Numpy half-sieve.

Answer 16

The fastest method I've tried so far is based on the Python cookbook erat2 function:

import itertools as it
def erat2a( ):
    D = {  }
    yield 2
    for q in it.islice(it.count(3), 0, None, 2):
        p = D.pop(q, None)
        if p is None:
            D[q*q] = q
            yield q
        else:
            x = q + 2*p
            while x in D:
                x += 2*p
            D[x] = p

See this answer for an explanation of the speeding-up.