Subject: Re: [Haskell-cafe] hamming distance allocation
Am Montag 19 April 2010 01:03:14 schrieb Arnoldo Muller:
Hello all:
I want to generate some hamming distance statistics about a set of strings. As explained in another e-mail in this list, I used the following code to call the functions: (exampl holds the list of strings of size w) filter (\x -> x /= 0) $ map (uncurry hammingX) [(xs, ys) | xs <- exampl, ys <- exampl]
I have two hamming functions: -- hamming distance for variable length strings hamming :: String -> String -> Int hamming x y = hamming' x y 0 where hamming' [] _ !c = c hamming' _ [] !c = c hamming' (x:xs) (y:ys) !c | x == y = hamming' xs ys c | otherwise = hamming' xs ys (c + 1)
-- function posted in this mailing list hamming2 :: String -> String -> Int hamming2 xs ys = length (filter not (zipWith (==) xs ys))
I am executing these functions millions of times and the bottleneck of my program is in them as explained by running in profiling mode with +RTS -K400M -p -RTS
The costlier function is the hamming distance COST CENTRE MODULE %time %alloc
hamming Distances 66.6 41.9
It says that it is performing 41% of the allocations. In the case of hamming2 the allocations go as far as 52%.
Allocations are cheap, so that's not necessarily a problem. More important is, what's the maximum residency and how much is copied during GC? Are you compiling with -O2 ?
I could understand that there are allocations in "hamming2" because we are creating pairs, but in the case of "hamming" there should be no allocation.
Why not? I don't know how GHC counts allocations, but everytime you go from (x:xs) to xs, you need a new pointer to the tail. If that counts as allocation, hamming must allocate a lot, too.
Is it really necessary to use Strings? I think a packed type, e.g. Vector or ByteString, would be much more efficient here. Of course this is only likely to be a benefit if you can move away from String entirely. I suspect that "hamming2" would perform better then. John