Permutation in Numpy
#perm.py def perm(k): # Compute the list of all permutations of k if len(k) <= 1: return [k] r = [] for i in range(len(k)): s = k[:i] + k[i+1:] p = perm(s) for x in p: r.append(k[i:i+1] + x) return r Does anyone know if there is a builtin function in Numpy (or Numarray) that does the above task faster (computes the list of all permutations of a list, k)? Or is there a way to make the above function run faster using Numpy? I'm asking because I need to create a very large list which contains all permutations of range(12), in which case there would be 12! permutations. I created a file test.py: #!/usr/bin/env python from perm import perm print perm(range(12)) And ran the program: $ ./test.py >> list.txt The program ran for about 90 minutes and was still running on my machine (667 MHz PowerPC G4, 512 MB SDRAM) until I quit the process as I was getting nervous (and impatient). I would highly appreciate anyone's suggestions. Many thanks, Kye
On Sun, Jul 25, 2004 at 07:24:49AM 0400, HeeSeng Kye wrote:
#perm.py def perm(k): # Compute the list of all permutations of k if len(k) <= 1: return [k] r = [] for i in range(len(k)): s = k[:i] + k[i+1:] p = perm(s) for x in p: r.append(k[i:i+1] + x) return r
Does anyone know if there is a builtin function in Numpy (or Numarray) that does the above task faster (computes the list of all permutations of a list, k)? Or is there a way to make the above function run faster using Numpy?
I'm asking because I need to create a very large list which contains all permutations of range(12), in which case there would be 12! permutations. I created a file test.py:
Do you really need a *list* of all those permutations? Think about it: 12! is about 0.5 billion, which is about as much RAM as your machine has. Each permutation is going to be a list taking 20 bytes of overhead plus 4 bytes per entry, so 68 bytes per permutation. You need 32 GB of RAM to store that. You probably want to just be able to access them in order, so a generator is a better bet. That way, you're only storing the current permutation instead of all of them. Something like def perm(k): k = tuple(k) lk = len(k) if lk <= 1: yield k else: for i in range(lk): s = k[:i] + k[i+1:] t = (k[i],) for x in perm(s): yield t + x Then: for p in perm(range(12): print p (I'm using tuples instead of lists as that gives a better performance here.) For n = 9, your code takes 9.4 s on my machine. The above take 3 s, and will scale with n (n=12 should take 3s * 10*11*12= 1.1 h). Your original code won't scale with n, as more and more time will be taken up reallocated the list of permutations. We can get fancier and unroll it a bit more: def perm(k): k = tuple(k) lk = len(k) if lk <= 1: yield k elif lk == 2: yield k yield (k[1], k[0]) elif lk == 3: k0, k1, k2 = k yield k yield (k0, k2, k1) yield (k1, k0, k2) yield (k1, k2, k0) yield (k2, k0, k1) yield (k2, k1, k0) else: for i in range(lk): s = k[:i] + k[i+1:] t = (k[i],) for x in perm(s): yield t + x This takes 1.3 s for n = 9 on my machine. Hope this helps.  >\/< /\ David M. Cooke http://arbutus.physics.mcmaster.ca/dmc/ cookedm@physics.mcmaster.ca
Thank you so much for your suggestion! You are right that I only need to access permutations of 12 in order, so your suggestion of using generator is perfect. In fact, I only need to access first half of permutations of 12 that begin on 0 (12! / 12 / 2, about 20 million), so the last code you offered would really speed things up. Thanks again. Best, Kye On Jul 28, 2004, at 7:05 PM, David M. Cooke wrote:
On Sun, Jul 25, 2004 at 07:24:49AM 0400, HeeSeng Kye wrote:
#perm.py def perm(k): # Compute the list of all permutations of k if len(k) <= 1: return [k] r = [] for i in range(len(k)): s = k[:i] + k[i+1:] p = perm(s) for x in p: r.append(k[i:i+1] + x) return r
Does anyone know if there is a builtin function in Numpy (or Numarray) that does the above task faster (computes the list of all permutations of a list, k)? Or is there a way to make the above function run faster using Numpy?
I'm asking because I need to create a very large list which contains all permutations of range(12), in which case there would be 12! permutations. I created a file test.py:
Do you really need a *list* of all those permutations? Think about it: 12! is about 0.5 billion, which is about as much RAM as your machine has. Each permutation is going to be a list taking 20 bytes of overhead plus 4 bytes per entry, so 68 bytes per permutation. You need 32 GB of RAM to store that.
You probably want to just be able to access them in order, so a generator is a better bet. That way, you're only storing the current permutation instead of all of them. Something like
def perm(k): k = tuple(k) lk = len(k) if lk <= 1: yield k else: for i in range(lk): s = k[:i] + k[i+1:] t = (k[i],) for x in perm(s): yield t + x
Then:
for p in perm(range(12): print p
(I'm using tuples instead of lists as that gives a better performance here.)
For n = 9, your code takes 9.4 s on my machine. The above take 3 s, and will scale with n (n=12 should take 3s * 10*11*12= 1.1 h). Your original code won't scale with n, as more and more time will be taken up reallocated the list of permutations.
We can get fancier and unroll it a bit more: def perm(k): k = tuple(k) lk = len(k) if lk <= 1: yield k elif lk == 2: yield k yield (k[1], k[0]) elif lk == 3: k0, k1, k2 = k yield k yield (k0, k2, k1) yield (k1, k0, k2) yield (k1, k2, k0) yield (k2, k0, k1) yield (k2, k1, k0) else: for i in range(lk): s = k[:i] + k[i+1:] t = (k[i],) for x in perm(s): yield t + x
This takes 1.3 s for n = 9 on my machine.
Hope this helps.
 >\/< / \ David M. Cooke http://arbutus.physics.mcmaster.ca/dmc/ cookedm@physics.mcmaster.ca
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David M. Cooke

HeeSeng Kye