Revision as of 18:04, 21 September 2008
Old submission is:
This is almost identical to the old code, with a parallel map used to perform the first phase of the benchmark (counting matches of each variant). I had trouble compiling the original with Text.Regex.Posix so I used Text.Regex.PCRE (which is probably faster, are hackage packages fair game?). I see a speedup from 46 seconds to 33 seconds when running this case -N2 vs the original case (with PCRE) unthreaded.
I see some weirdness in the shootout page's numbers. They list haskell running at 70 seconds (with Posix regex) and Python running as 25 seconds. I have a comparable system (roughly), and when I run the Python test case I get 46 seconds (nearly identical to the Haskell PCRE case). This probably means their machine has better memory bandwidth and that moving to PCRE is a big win (I believe python uses PCRE), but I'm not sure.
-- The Computer Language Benchmarks Game -- http://shootout.alioth.debian.org/ -- Contributed by: Sergei Matusevich 2007 import Control.Parallel.Strategies import List import Text.Regex.PCRE -- requires regex-pcre-builtin import qualified Data.ByteString.Char8 as B variants = [ "agggtaaa|tttaccct", "[cgt]gggtaaa|tttaccc[acg]", "a[act]ggtaaa|tttacc[agt]t", "ag[act]gtaaa|tttac[agt]ct", "agg[act]taaa|ttta[agt]cct", "aggg[acg]aaa|ttt[cgt]ccct", "agggt[cgt]aa|tt[acg]accct", "agggta[cgt]a|t[acg]taccct", "agggtaa[cgt]|[acg]ttaccct" ] main = do file <- B.getContents let [s1,s2,s3] = map (B.concat . tail) $ groupBy notHeader $ B.split '\n' file showVars r = r ++ ' ' : show ((s2 =~ r :: Int) + (s3 =~ r :: Int)) mapM_ putStrLn $ parMap rnf showVars variants putChar '\n' print (B.length file) print (B.length s1 + B.length s2 + B.length s3) print (B.length s1 + B.length s3 + length (B.unpack s2 >>= substCh)) where notHeader _ s = B.null s || B.head s /= '>' substCh 'B' = "(c|g|t)" substCh 'D' = "(a|g|t)" substCh 'H' = "(a|c|t)" substCh 'K' = "(g|t)" substCh 'M' = "(a|c)" substCh 'N' = "(a|c|g|t)" substCh 'R' = "(a|g)" substCh 'S' = "(c|g)" substCh 'V' = "(a|c|g)" substCh 'W' = "(a|t)" substCh 'Y' = "(c|t)" substCh etc = [etc]