[Haskell-cafe] my take at knucleotide

[Branimir Maksimovic]

Hi, I have tried to implement knucleotide benchmark program this time:http://benchmarksgame.alioth.debian.org/u64q/performance.php?test=knucleotide
Implementation is shorter (uses hashtable from hashtables package),but two time slower then current Haskell entry ( which is too low levelfor my taste :)).What is interesting is that if I try to place Int64 as a key tohash table, performance is even slower.Strange that dropping and taking from bytestring would befaster than packing string in 64 bit int and directly indexing.
If someone can see something that can bring performance on parwith current haskell entry , I would post it , otherwise no point,except that program is shorter and not low level.
{-# Language BangPatterns #-}---- The Computer Language Benchmarks Game-- http://benchmarksgame.alioth.debian.org/---- Contributed by Branimir Maksimovic--import Data.Charimport Data.Listimport Data.IORefimport qualified Data.HashTable.IO as Himport qualified Data.ByteString.Char8 as Simport Control.Concurrentimport Text.Printf
main = do    s <- S.getContents    let content = (S.map toUpper . S.concat . tail .                  dropWhile (\l->not $ S.isPrefixOf (S.pack ">THREE") l) .                  S.lines) s    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 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"             (S.unpack k) ((100 * (fromIntegral v)/sum)::Double)) lst    putChar '\n'
writeCount input string = do    let size = length string    ht <- tcalculate input size    res <- H.lookup ht (S.pack string)    case res of         Nothing -> putStrLn $ string ++ " not found..."        Just v -> do            r <- readIORef v            printf "%d\t%s\n" r (string::String)
tcalculate input size = do    let         l = [0..7]        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    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 input beg size incr = do    ht <- newTable    let        calculate' :: S.ByteString -> Int -> IO HashTable        calculate' str 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' (S.drop incr str) (i+incr)                where k = S.take size str    calculate' (S.drop beg input) beg
type HashTable = H.BasicHashTable S.ByteString (IORef Int) newTable :: IO HashTablenewTable = H.new
 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.haskell.org/pipermail/haskell-cafe/attachments/20130324/da20ad8e/attachment.htm>