What happens to performance if you compile and link with "cabal install
--constraint='hashable < 1.2'" ?
G
On Sun, Mar 24, 2013 at 4:08 PM, Branimir Maksimovic
Hi, I have tried to implement knucleotide benchmark program this time:
http://benchmarksgame.alioth.debian.org/u64q/performance.php?test=knucleotid...
Implementation is shorter (uses hashtable from hashtables package), but two time slower then current Haskell entry ( which is too low level for my taste :)). What is interesting is that if I try to place Int64 as a key to hash table, performance is even slower. Strange that dropping and taking from bytestring would be faster than packing string in 64 bit int and directly indexing.
If someone can see something that can bring performance on par with 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.Char import Data.List import Data.IORef import qualified Data.HashTable.IO as H import qualified Data.ByteString.Char8 as S import Control.Concurrent import 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 String actions = [I 1,I 2, S "GGT",S "GGTA",S "GGTATT",S "GGTATTTTAATT",S "GGTATTTTAATTTATAGT"] execute content (I i) = writeFrequencies content i execute 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 HashTable newTable = H.new
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Gregory Collins