Finally, I have made it ;)Trick was in more threads . For some reason if I run 64 (sweet spot) threads program runsfaster both with -threaded and without ;)Other trick is that I don't convert to uppercase (shaves second) rather pack nucleotidein 64 bit int.Program runs 30% faster multithreaded (scales better) than current entry, and consumes 50% less memory,and is shorter.If someone can see some improvement please post, otherwise I will contribute this program. {-# Language BangPatterns #-}---- The Computer Language Benchmarks Game-- http://benchmarksgame.alioth.debian.org/---- Contributed by Branimir Maksimovic--import Data.Bitsimport Data.Charimport Data.Intimport Data.Listimport Data.IORefimport Data.Array.Unboxedimport Data.Array.Baseimport qualified Data.HashTable.IO as Himport Data.Hashableimport qualified Data.ByteString.Char8 as Simport Control.Concurrentimport Text.Printf main = do s <- S.getContents let (_,subs) = S.breakSubstring (S.pack ">THREE") s content = (S.filter ((/=) '\n') . S.dropWhile ((/=) '\n')) subs mapM_ (execute content) actions data Actions = I Int | S Stringactions = [I 1,I 2, S "GGT",S "GGTA",S "GGTATT",S "GGTATTTTAATT",S "GGTATTTTAATTTATAGT"]execute content (I i) = writeFrequencies content iexecute content (S s) = writeCount content s writeFrequencies :: S.ByteString -> Int -> IO ()writeFrequencies input size = do ht <- tcalculate input size lst <- H.foldM (\lst (k,v)->do v' <- readIORef v return $ insertBy (\(_,x) (_,y)->y `compare` x) (k,v') lst) [] ht let sum = fromIntegral ((S.length input) + 1 - size) mapM_ (\(k,v)-> do printf "%s %.3f\n" (toString k) ((100 * (fromIntegral v)/sum)::Double)) lst putChar '\n' writeCount :: S.ByteString -> String -> IO ()writeCount input string = do let size = length string ht <- tcalculate input size let k = T (toNum (S.pack string) 0 size) size res <- H.lookup ht k case res of Nothing -> putStrLn $ string ++ " not found..." Just v -> do r <- readIORef v printf "%d\t%s\n" r string tcalculate :: S.ByteString -> Int -> IO HMtcalculate input size = do let l = [0..63] actions = map (\i -> (calculate input i size (length l))) l vars <- mapM (\action -> do var <- newEmptyMVar forkIO $ do answer <- action putMVar var answer return var) actions result <- newTable :: IO HM results <- mapM takeMVar vars mapM_ (\ht -> H.foldM (\lst (k,v) -> do res <- H.lookup lst k case res of Nothing -> do r1 <- readIORef v r2 <- newIORef r1 H.insert lst k r2 Just v1 -> do r1 <- readIORef v1 r2 <- readIORef v writeIORef v1 (r1+r2) return lst) result ht) results return result calculate :: S.ByteString -> Int -> Int -> Int -> IO HM calculate input beg size incr = do !ht <- newTable :: IO HM let calculate' i | i >= ((S.length input)+1 - size) = return ht | otherwise = do res <- H.lookup ht k case res of Nothing -> do !r <- newIORef 1 H.insert ht k r Just v -> do !r <- readIORef v writeIORef v (r+1) calculate' (i+incr) where k = T (toNum input i size) size calculate' beg toNum :: S.ByteString -> Int -> Int -> Int64toNum s beg size = toNum' 0 size where toNum' v 0 = v toNum' v i = toNum' ((v `shiftL` 2) .|. (toNumA `unsafeAt` (ord (S.index s (beg+i-1))))) (i-1) toString :: T -> StringtoString (T v s) = toString' v s where toString' v 0 = [] toString' v i = case v.&.3 of 0 -> 'A' 1 -> 'C' 2 -> 'T' 3 -> 'G' : toString' (v `shiftR` 2) (i-1) toNumA :: UArray Int Int64toNumA = array (0,255) [(ord 'a',0),(ord 'c',1),(ord 't',2),(ord 'g',3), (ord 'A',0),(ord 'C',1),(ord 'T',2),(ord 'G',3)] data T = T !Int64 !Intinstance Eq T where (T a _) == (T b _) = a == binstance Hashable T where hashWithSalt _ (T a _) = fromIntegral a type HM = H.BasicHashTable T (IORef Int)newTable = H.new Date: Sun, 24 Mar 2013 20:12:57 +0100 Subject: Re: [Haskell-cafe] my take at knucleotide From: greg@gregorycollins.net To: bmaxa@hotmail.com CC: haskell-cafe@haskell.org What happens to performance if you compile and link with "cabal install --constraint='hashable < 1.2'" ? G _______________________________________________ Haskell-Cafe mailing list Haskell-Cafe@haskell.org http://www.haskell.org/mailman/listinfo/haskell-cafe