堆在Haskell溢出
Gla*_*kon 5 heap haskell overflow strict lazy-evaluation
我Heap exhausted在一个足够大的数据集上运行以下简短的Haskell程序时收到消息.例如,程序在20 Mb输入文件上失败(堆溢出),大约900k行.堆大小设置(通过-with-rtsopts)为1 Gb.如果longestCommonSubstrB被定义为更简单的东西,它运行正常,例如commonPrefix.我需要处理大约100 Mb的文件.
我使用以下命令行编译程序(GHC 7.8.3):
ghc -Wall -O2 -prof -fprof-auto "-with-rtsopts=-M512M -p -s -h -i0.1" SampleB.hs
我希望任何帮助使这个东西在合理的空间(按输入文件大小的顺序)运行,但我特别欣赏找到瓶颈所在的思维过程以及在何处以及如何强制严格.
我的猜测是,以某种方式强制longestCommonSubstrB功能严格评估会解决问题,但我不知道该怎么做.
{-# LANGUAGE BangPatterns #-}
module Main where
import System.Environment (getArgs)
import qualified Data.ByteString.Lazy.Char8 as B
import Data.List (maximumBy, sort)
import Data.Function (on)
import Data.Char (isSpace)
-- | Returns a list of lexicon items, i.e. [[w1,w2,w3]]
readLexicon :: FilePath -> IO [[B.ByteString]]
readLexicon filename = do
text <- B.readFile filename
return $ map (B.split '\t' . stripR) . B.lines $ text
where
stripR = B.reverse . B.dropWhile isSpace . B.reverse
transformOne :: [B.ByteString] -> B.ByteString
transformOne (w1:w2:w3:[]) =
B.intercalate (B.pack "|") [w1, longestCommonSubstrB w2 w1, w3]
transformOne a = error $ "transformOne: unexpected tuple " ++ show a
longestCommonSubstrB :: B.ByteString -> B.ByteString -> B.ByteString
longestCommonSubstrB xs ys = maximumBy (compare `on` B.length) . concat $
[f xs' ys | xs' <- B.tails xs] ++
[f xs ys' | ys' <- tail $ B.tails ys]
where f xs' ys' = scanl g B.empty $ B.zip xs' ys'
g z (x, y) = if x == y
then z `B.snoc` x
else B.empty
main :: IO ()
main = do
(input:output:_) <- getArgs
lexicon <- readLexicon input
let flattened = B.unlines . sort . map transformOne $ lexicon
B.writeFile output flattened
这是测试数据集的配置文件输出(100k行,堆大小设置为1 GB,即generateSample.exe 100000生成的文件大小为2.38 MB):
随时间变化的堆配置文件:
执行统计:
3,505,737,588 bytes allocated in the heap
785,283,180 bytes copied during GC
62,390,372 bytes maximum residency (44 sample(s))
216,592 bytes maximum slop
96 MB total memory in use (0 MB lost due to fragmentation)
Tot time (elapsed) Avg pause Max pause
Gen 0 6697 colls, 0 par 1.05s 1.03s 0.0002s 0.0013s
Gen 1 44 colls, 0 par 4.14s 3.99s 0.0906s 0.1935s
INIT time 0.00s ( 0.00s elapsed)
MUT time 7.80s ( 9.17s elapsed)
GC time 3.75s ( 3.67s elapsed)
RP time 0.00s ( 0.00s elapsed)
PROF time 1.44s ( 1.35s elapsed)
EXIT time 0.02s ( 0.00s elapsed)
Total time 13.02s ( 12.85s elapsed)
%GC time 28.8% (28.6% elapsed)
Alloc rate 449,633,678 bytes per MUT second
Productivity 60.1% of total user, 60.9% of total elapsed
时间和分配情况分析报告:
SampleB.exe +RTS -M1G -p -s -h -i0.1 -RTS sample.txt sample_out.txt
total time = 3.97 secs (3967 ticks @ 1000 us, 1 processor)
total alloc = 2,321,595,564 bytes (excludes profiling overheads)
COST CENTRE MODULE %time %alloc
longestCommonSubstrB Main 43.3 33.1
longestCommonSubstrB.f Main 21.5 43.6
main.flattened Main 17.5 5.1
main Main 6.6 5.8
longestCommonSubstrB.g Main 5.0 5.8
readLexicon Main 2.5 2.8
transformOne Main 1.8 1.7
readLexicon.stripR Main 1.8 1.9
individual inherited
COST CENTRE MODULE no. entries %time %alloc %time %alloc
MAIN MAIN 45 0 0.1 0.0 100.0 100.0
main Main 91 0 6.6 5.8 99.9 100.0
main.flattened Main 93 1 17.5 5.1 89.1 89.4
transformOne Main 95 100000 1.8 1.7 71.6 84.3
longestCommonSubstrB Main 100 100000 43.3 33.1 69.8 82.5
longestCommonSubstrB.f Main 101 1400000 21.5 43.6 26.5 49.5
longestCommonSubstrB.g Main 104 4200000 5.0 5.8 5.0 5.8
readLexicon Main 92 1 2.5 2.8 4.2 4.8
readLexicon.stripR Main 98 0 1.8 1.9 1.8 1.9
CAF GHC.IO.Encoding.CodePage 80 0 0.0 0.0 0.0 0.0
CAF GHC.IO.Encoding 74 0 0.0 0.0 0.0 0.0
CAF GHC.IO.FD 70 0 0.0 0.0 0.0 0.0
CAF GHC.IO.Handle.FD 66 0 0.0 0.0 0.0 0.0
CAF System.Environment 65 0 0.0 0.0 0.0 0.0
CAF Data.ByteString.Lazy.Char8 54 0 0.0 0.0 0.0 0.0
CAF Main 52 0 0.0 0.0 0.0 0.0
transformOne Main 99 0 0.0 0.0 0.0 0.0
readLexicon Main 96 0 0.0 0.0 0.0 0.0
readLexicon.stripR Main 97 1 0.0 0.0 0.0 0.0
main Main 90 1 0.0 0.0 0.0 0.0
更新:以下程序可用于生成样本数据.它需要一个参数,即生成的数据集中的行数.生成的数据将保存到sample.txt文件中.当我用它生成900k行数据集(通过运行generateSample.exe 900000)时,生成的数据集使上述程序失败并发生堆溢出(堆大小设置为1 GB).生成的数据集大约为20 MB.
module Main where
import System.Environment (getArgs)
import Data.List (intercalate, permutations)
generate :: Int -> [(String,String,String)]
generate n = take n $ zip3 (f "banana") (f "ruanaba") (f "kikiriki")
where
f = cycle . permutations
main :: IO ()
main = do
(n:_) <- getArgs
let flattened = unlines . map f $ generate (read n :: Int)
writeFile "sample.txt" flattened
where
f (w1,w2,w3) = intercalate "\t" [w1, w2, w3]
在我看来，你已经实现了一个朴素的最长公共子串，其空间复杂度非常糟糕（至少 O(n^2)）。严格与此无关。
您将需要实现动态编程算法。您可能会在string-similarity包或Diff包内部的lcs函数中找到灵感。