MdxBhmt
Reputation: 1310
Why my program use so much memory?
For just a 25mb file the memory usage is constant at 792mb! I thought it had to do with my usage from list, but moving certain parts of the code for vector (the arrays where fft is applied, for example) didn't change how much memory being used at all!
{-# LANGUAGE OverloadedStrings,BangPatterns #-}
import qualified Data.Attoparsec.Char8 as Ap
import Data.Attoparsec
import Control.Monad
import Control.Applicative
--import Control.DeepSeq (force)
import System.IO
import System.Environment
import Data.List (zipWith4,unzip4,zip4,foldl')
import Data.Bits
import Data.Complex
import Data.String (fromString)
import Data.ByteString.Internal
import qualified Data.ByteString.Char8 as B
import qualified Data.ByteString.Lazy.Char8 as Bl
import qualified Data.Vector.Unboxed as Vu
import qualified Statistics.Transform as St
{-
I run a test on a collection of data from a file
[(1,t),(2,t),(3,t),(4,t),(5,t)]
- - -
| - - -
| | - - -
| | |
[y++t, n, y++t]
To do that, I use splitN to create a list of list
[[(1,t),(2,t),(3,t)],[(2,t),(3,t),(4,t)],[(3,t),(4,t),(5,t)]]
Map a serie of functions to determine a value for each inner collection,
and return when an event happened.
-}
data FourD b a = FourD a a a b
instance Functor (FourD c) where
fmap f (FourD x y z d) = FourD (f x) (f y) (f z) d
mgrav_per_bit = [ 18, 36, 71, 143, 286, 571, 1142 ]
--Converting raw data to mg
aToG :: Int -> Double
aToG a = fromIntegral . sign $ uresult
where
twocomp = if a>128
then 256-a
else a
uresult = sum $ zipWith (*) mgrav_per_bit (map (fromEnum . testBit twocomp) [0..7])
sign = if a > 128
then negate
else id
--Data is (int,int,int,time)
--Converted to (St.CD^3,Bytestring) in place of maping afterwards.
parseAcc :: Parser (FourD B.ByteString St.CD)
parseAcc = do Ap.char '('
x <- fmap ((:+0) . aToG) Ap.decimal
Ap.char ','
y <- fmap ((:+0) . aToG) Ap.decimal
Ap.char ','
z <- fmap ((:+0) . aToG) Ap.decimal
Ap.char ','
time <- takeTill (== 41)
Ap.char ')'
return $! FourD x y z time
--applies parseAcc to many lines, fails at the end of file (Need to add a newline)
parseFile = many $ parseAcc <* (Ap.endOfInput <|> Ap.endOfLine)
readExpr input = case parse parseFile input of
Done b val -> val
Partial p -> undefined
Fail a b c -> undefined
unType (FourD x y d z) = (x ,y ,d ,z)
-- Breaks a list of FourD into smaller lists, apply f and g to those lists, then filter the result based if an even happened or not
amap :: (Num c, Ord c) => ([a] -> [c]) -> ([d] -> [ByteString]) -> [FourD d a] -> [Bl.ByteString]
amap f g = (uncurry4 (zipWith4 (filterAcc))). map4 f g . unzip4 . map (unType)
where map4 f g (a,b,c,d) = (f a,f b,f c,g d)
uncurry4 f (a,b,c,d) = f a b c d
-- before i had map filterAcc,outside amap. Tried to fuse everything to eliminate intermediaries
-- An event is detected if x > 50
filterAcc x y z t = if x > 50
then (Bl.pack . B.unpack) $ "yes: " `B.append` t
else ""
-- split [St.CD] in [(Vector St.CD)], apply fft to each, and compress to a single value.
-- Core of the application
fftAcross :: [St.CD] -> [Int]
fftAcross = map (floor . noiseEnergy . St.fft) . splitN 32
-- how the value is determined (sum of all magnitudes but the first one)
noiseEnergy :: (RealFloat a, Vu.Unbox a) => Vu.Vector (Complex a) -> a
noiseEnergy x = (Vu.foldl' (\b a-> b+(magnitude a)) 0 (Vu.drop 1 x))/32
-- how the values are split in (Vector St.CD), if lenght > 32, takes 32, otherwhise I'm done
splitN :: Vu.Unbox a => Int -> [a] -> [Vu.Vector a]
splitN n x = helper x
where
helper x = if atLeast n x
then (Vu.take n (Vu.fromList x)) : (helper (drop 1 x) )
else []
-- Replacing the test by atLeast in place of a counter (that compared to length x,calculated once) reduced the behaviour that memory usage was constant.
-- this is replicated so the behaviour of splitN happens on the time part of FourD, Can't use the same since there is no Vector Bytestring instance
splitN2 n x = helper x
where
helper x = if atLeast n x
then (head x) : (helper (drop 1 x))
else []
atLeast :: Int -> [a] -> Bool
atLeast 0 _ = True
atLeast _ [] = False
atLeast n (_:ys) = atLeast (n-1) ys
main = do
filename <- liftM head getArgs
filehandle <- openFile "results.txt" WriteMode
contents <- liftM readExpr $ B.readFile filename
Bl.hPutStr (filehandle) . Bl.unlines . splitAndApplyAndFilter $ contents where
splitAndApplyAndFilter = amap fftAcross (splitN2 32)
Edit: after some refactoring, fusing some maps, reducing length, I managed to get this working at 400~ with a 25mb input file. Still, on a 100mb, it takes 1.5gb.
The program is intended to determine if a certain event happened ina point of time, for that it requries a collection of values (im using 32 atm), runs a fft in it, sum those values and see if passes a threshold. If yes, print the time to a file.
http://db.tt/fT8kXPKz for a 25mb testfile
Upvotes: 5
Views: 485
Answers (1)
MdxBhmt
Reputation: 1310
I found the solution due a topic in reddit about the same problem! Parsing with Haskell and Attoparsec
The great majority of my problem was caused by the fact attoparsec is strict and haskell data are rather large (so a 100mb text file can be actually much more in run time)
The other half was that profiling doubles the memory use, and I didn't account for that.
After changing the parser to be lazy, my program uses 120mb in place of 800mb (when input size is 116mb), so sucess!
In case this interest someone, here is the relevant piece of code change:
readExpr input = case parse (parseAcc<*(Ap.endOfLine<*Ap.endOfInput<|>Ap.endOfLine)) input of
Done b val -> val : readExpr b
Partial e -> []
Fail _ _ c -> error c
The full code:
{-# LANGUAGE OverloadedStrings,BangPatterns #-}
import qualified Data.Attoparsec.Char8 as Ap
import Data.Attoparsec
import Control.Monad
import Control.Applicative
--import Control.DeepSeq (force)
import System.IO
import System.Environment
import Data.List (zipWith4,unzip4,zip4,foldl')
import Data.Bits
import Data.Complex
import Data.String (fromString)
import Data.ByteString.Internal
import qualified Data.ByteString.Char8 as B
import qualified Data.ByteString.Lazy.Char8 as Bl
import qualified Data.Vector.Unboxed as Vu
import qualified Statistics.Transform as St
{-
I run a test on a collection of data from a file
[(1,t),(2,t),(3,t),(4,t),(5,t)]
- - -
| - - -
| | - - -
| | |
[y++t, n, y++t]
To do that, I use splitN to create a list of list
[[(1,t),(2,t),(3,t)],[(2,t),(3,t),(4,t)],[(3,t),(4,t),(5,t)]]
Map a serie of functions to determine a value for each inner collection,
and return when an event happened.
-}
data FourD b a = FourD a a a b
instance Functor (FourD c) where
fmap f (FourD x y z d) = FourD (f x) (f y) (f z) d
mgrav_per_bit = [ 18, 36, 71, 143, 286, 571, 1142 ]
--Converting raw data to mg
aToG :: Int -> Double
aToG a = fromIntegral . sign $ uresult
where
twocomp
| a>128 = 256-a
| otherwise = a
uresult = sum $ zipWith (*) mgrav_per_bit (map (fromEnum . testBit twocomp) [0..7])
sign
| a > 128 = negate
| otherwise = id
--Data is (int,int,int,time)
--Converted to (St.CD^3,Bytestring) in place of maping afterwards.
parseAcc :: Parser (FourD B.ByteString St.CD)
parseAcc = do Ap.char '('
x <- fmap ((:+0) . aToG) Ap.decimal -- Parse, transform to mg, convert to complex
Ap.char ','
y <- fmap ((:+0) . aToG) Ap.decimal
Ap.char ','
z <- fmap ((:+0) . aToG) Ap.decimal
Ap.char ','
time <- takeTill (== 41)
Ap.char ')'
return $! FourD x y z time
--applies parseAcc to many lines, fails at the end of file (Need to add a newline)
parseFile = many $ parseAcc <* (Ap.endOfInput <|> Ap.endOfLine)
readExpr input = case parse (parseAcc<*(Ap.endOfLine<*Ap.endOfInput<|>Ap.endOfLine)) input of
Done b val -> val : readExpr b
Partial e -> []
Fail _ _ c -> error c
unType (FourD x y d z) = (x ,y ,d ,z)
-- Breaks a list of FourD into smaller lists, apply f and g to those lists, then filter the result based if an even happened or not
amap :: (Num c, Ord c) => ([a] -> [c]) -> ([d] -> [ByteString]) -> [FourD d a] -> [ByteString]
amap f g = (uncurry4 (zipWith4 (filterAcc))). map4 f g . unzip4 . map (unType)
where map4 f g (a,b,c,d) = (f a,f b,f c,g d)
uncurry4 f (a,b,c,d) = f a b c d
-- before i had map filterAcc,outside amap. Tried to fuse everything to eliminate intermediaries
-- An event is detected if x > 50
filterAcc x y z t
| x > 50 = t
| otherwise = ""
-- split [St.CD] in [(Vector St.CD)], apply fft to each, and compress to a single value.
-- Core of the application
fftAcross :: [St.CD] -> [Int]
fftAcross = map (floor . noiseEnergy . St.fft) . splitN 32
-- how the value is determined (sum of all magnitudes but the first one)
noiseEnergy :: (RealFloat a, Vu.Unbox a) => Vu.Vector (Complex a) -> a
noiseEnergy x = (Vu.foldl' (\b a-> b+(magnitude a)) 0 (Vu.drop 1 x))/32
-- how the values are split in (Vector St.CD), if lenght > 32, takes 32, otherwhise I'm done
splitN :: Vu.Unbox a => Int -> [a] -> [Vu.Vector a]
splitN n x = helper x
where
helper x
| atLeast n x = (Vu.take n (Vu.fromList x)) : (helper (drop 1 x) )
| otherwise = []
-- Replacing the test by atLeast in place of a counter (that compared to length x,calculated once) reduced the behaviour that memory usage was constant.
-- this is replicated so the behaviour of splitN happens on the time part of FourD, Can't use the same since there is no Vector Bytestring instance
splitN2 n x = helper x
where
helper x
| atLeast n x = (head x) : (helper (drop 1 x))
| otherwise = []
atLeast :: Int -> [a] -> Bool
atLeast 0 _ = True
atLeast _ [] = False
atLeast n (_:ys) = atLeast (n-1) ys
intervalFinder :: [ByteString]->[B.ByteString]
intervalFinder x = helper x ""
where
helper (x:xs) ""
| x /= "" = ("Start Time: " `B.append` x `B.append` "\n"):(helper xs x)
| otherwise = helper xs ""
helper (x:xs) y
| x == "" = ( "End Time: "`B.append` y `B.append` "\n\n" ):(helper xs "")
| otherwise = helper xs x
helper _ _ = []
main = do
filename <- liftM head getArgs
filehandle <- openFile "results.txt" WriteMode
contents <- liftM readExpr $ B.readFile filename
Bl.hPutStr (filehandle) . Bl.fromChunks . intervalFinder . splitAndApplyAndFilter $ contents
hClose filehandle
where
splitAndApplyAndFilter = amap fftAcross (splitN2 32)
--contents <- liftM ((map ( readExpr )) . B.lines) $ B.readFile filename
{- *Main> let g = liftM ((amap fftAcross (splitN2 32)) . readExpr) $ B.readFile "te
stpattern2.txt"
-}
-- B.hPutStrLn (filehandle) . B.unlines . map (B.pack . show ) . amap (map (floor .quare) . (filter (/=[])) . map ( (drop 1) . (map (/32)) . fft ) . splitN 32) . map ( fmap(fromIntegral . aToG)) . map readExpr $ contents
Upvotes: 3
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