Benchmarks Game/Parallel/RegexDNA
< Benchmarks Game | Parallel
Jump to navigation
Jump to search
Regex-DNA
Old submission is:
Running:
- ghc --make -O2 -fglasgow-exts -package regex-posix -optc-O3 -threaded regexdna3.hs
- ./regexdna3 +RTS -N2 < big.txt
Code:
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]
The changes should be directly applicable to the non-PCRE version as well. Just change the import to use the Posix library. Here are the parallelizing changes:
--- regexdna2.hs 2008-09-22 07:56:49.000000000 -1000
+++ regexdna3.hs 2008-09-21 07:50:32.000000000 -1000
@@ -2,6 +2,7 @@
-- 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
@@ -20,7 +21,8 @@
main = do
file <- B.getContents
let [s1,s2,s3] = map (B.concat . tail) $ groupBy notHeader $ B.split '\n' file
- mapM_ (printVars s2 s3) variants
+ 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)
@@ -38,8 +40,4 @@
substCh 'W' = "(a|t)"
substCh 'Y' = "(c|t)"
substCh etc = [etc]
- printVars s2 s3 r = do
- putStr r
- putChar ' '
- print ((s2 =~ r :: Int) + (s3 =~ r :: Int))
I submitted this
by Stephen Blackheath
Not pretty, but fast and legal, and by no means the final word on the matter!
{-# LANGUAGE ForeignFunctionInterface, BangPatterns #-}
{-# OPTIONS_GHC -O2 #-}
-- The Computer Language Benchmarks Game
-- http://shootout.alioth.debian.org/
--
-- contributed by Sergei Matusevich 2007
-- modified by Tim Newsham
-- modified by Stephen Blackheath 2009, v1.0
-----------------------------------------
-- Requires the regex-pcre cabal package.
--
-- Instructions for installing it, assuming ghc version 6.10.1 already
-- installed, tested on Ubuntu 8.10:
--
-- 1. Make sure these OS packages are installed:
-- libgmp3-dev
-- zlib1g-dev
-- libcurl4-gnutls-dev
-- libpcre3-dev
--
-- 2. get cabal-install package from
-- http://hackage.haskell.org/packages/archive/cabal-install/0.6.0/cabal-install-0.6.0.tar.gz
--
-- 3. Unpack cabal-install, cd into directory, and type
-- sudo sh ./bootstap.sh
--
-- 4. Type
-- sudo $HOME/.cabal/bin/cabal update
-- sudo $HOME/.cabal/bin/cabal install regex-pcre
-----------------------------------------
-- Compile command: ghc -o regex regex.hs -threaded --make
-- Run command: ./regex +RTS -N4 (quad core)
-- ./regex (single core)
import Control.Concurrent
import Control.Parallel
import Control.Parallel.Strategies
import Control.Monad
import Foreign.Storable
import Foreign.Marshal.Alloc
import Foreign.Marshal.Array
import Foreign.Ptr
import Foreign.ForeignPtr
import Foreign.C.Types
import Text.Regex.PCRE -- requires haskell-regex-pcre-builtin
import qualified Data.ByteString as B
import qualified Data.ByteString.Internal as BI
import System.IO.Unsafe
import Data.Array
import Debug.Trace
import Data.List
import Data.Word
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" ]
subs = [
("B", "(c|g|t)"),
("D", "(a|g|t)"),
("H", "(a|c|t)"),
("K", "(g|t)"),
("M", "(a|c)"),
("N", "(a|c|g|t)"),
("R", "(a|g)"),
("S", "(c|g)"),
("V", "(a|c|g)"),
("W", "(a|t)"),
("Y", "(c|t)")]
main = do
file <- B.getContents
let [s1,s2,s3] = map (B.concat . tail) $
groupBy notHeader $ B.split (BI.c2w '\n') file
showVars r = r ++ ' ' : show ((s2 =~ r :: Int) + (s3 =~ r :: Int))
results = map showVars variants ++ [
"",
show $ B.length file,
show $ B.length s1 + B.length s2 + B.length s3]
r2 = flip map (zip [1..] results) $ \(idx, a) ->
trace ("start "++show idx) () `seq` (a `using` rnf) `seq` trace ("end "++show idx) () `seq` a
-- Ensure that the data blocks are fully evaluated before we start
-- executing things in parallel, since they all depend on them
return $! (s1 `par` s2 `par` s3) `seq` s1 `seq` s2 `seq` s3
mapM_ putStrLn $ parList rnf results `seq` results
let chunks = fragment 5000 s2 -- break into chunks to parallelize, which
-- is possible as our regexes are 1 char long
chunks' <- parallel $ map substituteAll chunks -- do regex substitutions
print $ B.length s1 + B.length s3 + B.length (B.concat chunks')
where notHeader _ s = B.null s || B.head s /= (BI.c2w '>')
-- Drop in replacement for sequence
parallel :: [IO a] -> IO [a]
parallel actions = do
vars <- forM actions $ \action -> do
var <- newEmptyMVar
forkIO $ do
answer <- action
return $! answer
putMVar var answer
return var
forM vars takeMVar
fragment :: Int -> B.ByteString -> [B.ByteString]
fragment chunkSize bs =
let (start, rem) = B.splitAt chunkSize bs
in if B.null rem
then [start]
else start : fragment chunkSize rem
-- Precompile regexes
subRegexes :: [(Regex, B.ByteString)]
subRegexes = flip map subs $ \(pattern, sub) ->
(makeRegex pattern :: Regex, B.pack (map BI.c2w sub))
substituteAll :: B.ByteString -> IO B.ByteString
substituteAll !txt = do
let BI.PS srcFP srcOff srcLen = txt
withForeignPtr srcFP $ \src0 -> do
let src = src0 `plusPtr` srcOff
-- Capacity of -1 guarantees that a new buffer will be allocated
(dst, dstLen, _) <- foldM substitute_ (src, srcLen, -1) subRegexes
dstFP <- newForeignPtr finalizerFree dst
return $ BI.PS dstFP 0 dstLen
foreign import ccall unsafe "string.h memmove" memmove
:: Ptr Word8 -> Ptr Word8 -> CSize -> IO (Ptr Word8)
-- A function that does nothing
foreign import ccall unsafe "static unistd.h &getpid" c_null_finalizer
:: FunPtr (Ptr Word8 -> IO ())
-- Do a single regex substitution, returning the modified string
substitute_ :: (Ptr Word8, Int, Int) -> (Regex, B.ByteString) -> IO (Ptr Word8, Int, Int)
substitute_ (src, srcLen, srcCap) (regex, sub) = do
-- Make a new string given the input string, regex match positions, and
-- string to substitute
-- Turn the source buffer into a byte string to pass to 'match'
srcFP <- newForeignPtr c_null_finalizer src
let srcBS = BI.PS srcFP 0 srcLen
am :: Array Int (MatchOffset, MatchLength)
AllMatches am = match regex srcBS
(start, end) = bounds am
matches = end + 1
BI.PS subFP subOff subLen = sub
newLength = srcLen + matches * (subLen - 1)
withForeignPtr subFP $ \sub0 -> do
let sub = sub0 `plusPtr` subOff
(dst, dstCap) <-
if newLength > srcCap
then do
let dstCap = if srcCap < 0
then srcLen * 2
else srcCap * 2
dst <- mallocBytes dstCap
return (dst, dstCap)
else
return (src, srcCap)
let copy :: Int -> Int -> Int -> IO ()
copy idx sOff dOff | idx < 0 = do
let chunkLen = sOff
when (dst /= src) $
BI.memcpy dst src (fromIntegral chunkLen)
copy idx sOff dOff = do
let (matchOff, _) = am ! idx
sOff' = matchOff + 1
chunkLen = sOff - sOff'
dOff' = dOff - chunkLen
memmove (dst `plusPtr` dOff') (src `plusPtr` sOff')
(fromIntegral chunkLen)
let dOff'' = dOff' - subLen
sOff'' = sOff' - 1
BI.memcpy (dst `plusPtr` dOff'') sub
(fromIntegral subLen)
copy (idx-1) sOff'' dOff''
copy end srcLen newLength
when (dst /= src && srcCap >= 0) $ free src
return (dst, newLength, dstCap)