Parallel Haskell with HXT - haskell

I'm trying to get performance increases in a program I have that parses XML. The program can parse multiple XML files so I thought that I could make this run in parallel, but all my attempts have resulted in lower performance!
For XML parsing, I am using HXT.
I have a run function defined like this:
run printTasks xs = pExec xs >>= return . concat >>= doPrint printTasks 1
'pExec' is given a list of file names and is defined as:
pExec xs = do
ex <- mapM exec xs
as <- ex `usingIO` parList rdeepseq
return as
where 'exec' is defined as:
exec = runX . process
threadscope shows only one thread e ver being used (until the very end).
Can anyone explain why I have failed so miserably to parallelise this code?
In case it helps:
exec :: FilePath -> [CV_scene]
pExec :: [FilePath] -> IO [[CV_scene]]
data CV_scene = Scene [CV_layer] Time deriving (Show)
data CV_layer = Layer [DirtyRects] SourceCrop deriving (Show)
data Rect = Rect Int Int Int Int deriving (Show)-- Left Top Width Height
instance NFData CV_scene where
rnf = foldScene reduceScene
where reduceScene l t = rnf (seq t l)
instance NFData CV_layer where
rnf = foldLayer reduceLayer
where reduceLayer d s = rnf (seq s d)
instance NFData Rect where
rnf = foldRect reduceRect
where reduceRect l t w h = rnf [l,t,w,h]
type SourceCrop = Rect
type DirtyRect = Rect
type Time = Int64
Thanks in advance for your help!

First, it looks like you mislabeled the signature of exec, which should probably be:
exec :: FilePath -> IO [CV_scene]
Now for the important part. I've commented inline on what I think you think is going on.
pExec xs = do
-- A. Parse the file found at each location via exec.
ex <- mapM exec xs
-- B. Force the lazy parsing in parallel.
as <- ex `usingIO` parList rdeepseq
return as
Note that line A does not happen in paralell, which you might think is okay since it will just set up the parsing thunks which are forced in parallel in B. This is a fair assumption, and a clever use of laziness, but the results pull that into question for me.
I suspect that the implementation of exec forces most of the parsing before line B is even reached so that the deep seq doesn't do much. That fits pretty well with my experince parsing and the profiling supports that explanation.
Without the ability to test your code, I can only make the following suggestions. First try separating the parsing of the file from the IO and put the parsing in the parallel execution strategy. In that case lines A and B become something like:
ex <- mapM readFile xs
as <- ex `usingIO` parList (rdeepseq . exec')
with exec' the portion of exec after the file is read from disk.
exec' :: FilePath -> [CVScene]
Also, you may not even need rdeepSeq after this change.
As an alternative, you can do the IO and parsing in parallel using Software Transactional Memory. STM approaches are normally used for separate IO threads which act more like services, rather than pure computations. But if for some reason you cant get the strategies based approach to work, this might be worth a try.
import Control.Concurrent.STM.TChan --(from stm package)
import Control.Concurrent(forkIO)
pExec'' :: [FilePath] -> IO [[CVSene]]
pExec'' xs = do
-- A. create [(Filename,TChan [CVScene])]
tcx <- mapM (\x -> (x,) <$> newTChanIO) xs
-- B. do the reading/parsing in separate threads
mapM_ (forkIO . exec'') tcx
-- C. Collect the results
cvs <- mapM (atomically . readTChan . snd) tcx
exec'' :: [(FilePath,TChan [CVScene])] -> IO ()
exec'' (x,tch) = do
--D. The original exec function
cv <- exec x
--E. Put on the channel fifo buffer
atomically $ writeTChan tch cv
Good luck!

Related

Lazy evaluation of IO actions

I'm trying to write code in source -> transform -> sink style, for example:
let (|>) = flip ($)
repeat 1 |> take 5 |> sum |> print
But would like to do that using IO. I have this impression that my source can be an infinite list of IO actions, and each one gets evaluated once it is needed downstream. Something like this:
-- prints the number of lines entered before "quit" is entered
[getLine..] >>= takeWhile (/= "quit") >>= length >>= print
I think this is possible with the streaming libraries, but can it be done along the lines of what I'm proposing?
Using the repeatM, takeWhile and length_ functions from the streaming library:
import Streaming
import qualified Streaming.Prelude as S
count :: IO ()
count = do r <- S.length_ . S.takeWhile (/= "quit") . S.repeatM $ getLine
print r
This seems to be in that spirit:
let (|>) = flip ($)
let (.>) = flip (.)
getContents >>= lines .> takeWhile (/= "quit") .> length .> print
The issue here is that Monad is not the right abstraction for this, and attempting to do something like this results in a situation where referential transparency is broken.
Firstly, we can do a lazy IO read like so:
module Main where
import System.IO.Unsafe (unsafePerformIO)
import Control.Monad(forM_)
lazyIOSequence :: [IO a] -> IO [a]
lazyIOSequence = pure . go where
go :: [IO a] -> [a]
go (l:ls) = (unsafePerformIO l):(go ls)
main :: IO ()
main = do
l <- lazyIOSequence (repeat getLine)
forM_ l putStrLn
This when run will perform cat. It will read lines and output them. Everything works fine.
But consider changing the main function to this:
main :: IO ()
main = do
l <- lazyIOSequence (map (putStrLn . show) [1..])
putStrLn "Hello World"
This outputs Hello World only, as we didn't need to evaluate any of l. But now consider replacing the last line like the following:
main :: IO ()
main = do
x <- lazyIOSequence (map (putStrLn . show) [1..])
seq (head x) putStrLn "Hello World"
Same program, but the output is now:
1
Hello World
This is bad, we've changed the results of a program just by evaluating a value. This is not supposed to happen in Haskell, when you evaluate something it should just evaluate it, not change the outside world.
So if you restrict your IO actions to something like reading from a file nothing else is reading from, then you might be able to sensibly lazily evaluate things, because when you read from it in relation to all the other IO actions your program is taking doesn't matter. But you don't want to allow this for IO in general, because skipping actions or performing them in a different order can matter (and above, certainly does). Even in the reading a file lazily case, if something else in your program writes to the file, then whether you evaluate that list before or after the write action will affect the output of your program, which again, breaks referential transparency (because evaluation order shouldn't matter).
So for a restricted subset of IO actions, you can sensibly define Functor, Applicative and Monad on a stream type to work in a lazy way, but doing so in the IO Monad in general is a minefield and often just plain incorrect. Instead you want a specialised streaming type, and indeed Conduit defines Functor, Applicative and Monad on a lot of it's types so you can still use all your favourite functions.

Haskell Turtle get out of Shell Monad

could you please help me with Turtle library.
I want to write simple program, that calculates disk space usage.
Here is the code:
getFileSize :: FilePath -> IO Size
getFileSize f = do
status <- stat f
return $ fileSize status
main = sh $ do
let sizes = fmap getFileSize $ find (suffix ".hs") "."
so now I have sizes bind of type Shell (IO Size). But I can't just sum it, with sum fold, cause there is IO Size in there. If it was something like [IO Size] I could pull IO monad out of there by using sequence to transform it to IO [Size]. But I can't do this with Shell monad since it is not Traversable. So I wrote something like this
import qualified Control.Foldl as F
main = sh $ do
let sizes = fmap getFileSize $ find (suffix ".hs") "."
lst <- fold sizes F.list
let cont = sequence lst
sz <- liftIO $ cont
liftIO $ putStrLn (show (sum sz))
First I folded Shell (IO Size) to [IO Size] and then to IO [Size] to sum list afterwards.
But I wonder if there is more canonical or elegant solution to this, because here I created two lists to accomplish my task. And I throught that Shell monad is for manipulating entities in constant space. Maybe there is some fold to make IO (Shell Size) from Shell (IO Size)?
Thanks.
You have an IO action, and you really want a Shell action. The usual way to handle that is with the liftIO method, which is available because Shell is an instance of MonadIO.
file <- find (suffix ".hs") "."
size <- liftIO $ getFileSize file
or even
size <- liftIO . getFileSize =<< find (suffix ".hs") "."
Fortunately, the Turtle package itself offers some size functions you can use directly with MonadIO instances like Shell in Turtle.Prelude so you don't need to use liftIO yourself.
Now you actually have to sum these up, but you can do that with fold and sum.
I would recommend that you avoid breaking open the Shell type itself. That should be reserved for adding totally new functionality to the API. That certainly isn't necessary in this case.
Actually I've managed to get rid of IO here by using helper transformation
sio :: Shell (IO a) -> Shell a
sio s = Shell (\(FoldShell step begin done) ->
let step' x a = do
a' <- a
step x a'
in
_foldShell s (FoldShell step' begin done))
But now I wonder is there any simpler solution to this task...

Is it recommended to use recursive IO actions in the tail recursive form?

Consider the two following variations:
myReadListTailRecursive :: IO [String]
myReadListTailRecursive = go []
where
go :: [String] -> IO [String]
go l = do {
inp <- getLine;
if (inp == "") then
return l;
else go (inp:l);
}
myReadListOrdinary :: IO [String]
myReadListOrdinary = do
inp <- getLine
if inp == "" then
return []
else
do
moreInps <- myReadListOrdinary
return (inp:moreInps)
In ordinary programming languages, one would know that the tail recursive variant is a better choice.
However, going through this answer, it is apparent that haskell's implementation of recursion is not similar to that of using the recursion stack repeatedly.
But because in this case the program in question involves actions, and a strict monad, I am not sure if the same reasoning applies. In fact, I think in the IO case, the tail recursive form is indeed better. I am not sure how to correctly reason about this.
EDIT: David Young pointed out that the outermost call here is to (>>=). Even in that case, does one of these styles have an advantage over the other?
FWIW, I'd go for existing monadic combinators and focus on readability/consiseness. Using unfoldM :: Monad m => m (Maybe a) -> m [a]:
import Control.Monad (liftM, mfilter)
import Control.Monad.Loops (unfoldM)
myReadListTailRecursive :: IO [String]
myReadListTailRecursive = unfoldM go
where
go :: IO (Maybe String)
go = do
line <- getLine
return $ case line of
"" -> Nothing
s -> Just s
Or using MonadPlus instance of Maybe, with mfilter :: MonadPlus m => (a -> Bool) -> m a -> m a:
myReadListTailRecursive :: IO [String]
myReadListTailRecursive = unfoldM (liftM (mfilter (/= "") . Just) getLine)
Another, more versatile option, might be to use LoopT.
That’s really not how I would write it, but it’s clear enough what you’re doing. (By the way, if you want to be able to efficiently insert arbitrary output from any function in the chain, without using monads, you might try a Data.ByteString.Builder.)
Your first implementation is very similar to a left fold, and your second very similar to a right fold or map. (You might try actually writing them as such!) The second one has several advantages for I/O. One of the most important, for handling input and output, is that it can be interactive.
You’ll notice that the first builds the entire list from the outside in: in order to determine what the first element of the list is, the program needs to compute the entire structure to get to the innermost thunk, which is return l. The program generates the entire data structure first, then starts to process it. That’s useful when you’re reducing a list, because tail-recursive functions and strict left folds are efficient.
With the second, the outermost thunk contains the head and tail of the list, so you can grab the tail, then call the thunk to generate the second list. This can work with infinite lists, and it can produce and return partial results.
Here’s a contrived example: a program that reads in one integer per line and prints the sums so far.
main :: IO ()
main = interact( display . compute 0 . parse . lines )
where parse :: [String] -> [Int]
parse [] = []
parse (x:xs) = (read x):(parse xs)
compute :: Int -> [Int] -> [Int]
compute _ [] = []
compute accum (x:xs) = let accum' = accum + x
in accum':(compute accum' xs)
display = unlines . map show
If you run this interactively, you’ll get something like:
$ 1
1
$ 2
3
$ 3
6
$ 4
10
But you could also write compute tail-recursively, with an accumulating parameter:
main :: IO ()
main = interact( display . compute [] . parse . lines )
where parse :: [String] -> [Int]
parse = map read
compute :: [Int] -> [Int] -> [Int]
compute xs [] = reverse xs
compute [] (y:ys) = compute [y] ys
compute (x:xs) (y:ys) = compute (x+y:x:xs) ys
display = unlines . map show
This is an artificial example, but strict left folds are a common pattern. If, however, you write either compute or parse with an accumulating parameter, this is what you get when you try to run interactively, and hit EOF (control-D on Unix, control-Z on Windows) after the number 4:
$ 1
$ 2
$ 3
$ 4
1
3
6
10
This left-folded version needs to compute the entire data structure before it can read any of it. That can’t ever work on an infinite list (When would you reach the base case? How would you even reverse an infinite list if you did?) and an application that can’t respond to user input until it quits is a deal-breaker.
On the other hand, the tail-recursive version can be strict in its accumulating parameter, and will run more efficiently, especially when it’s not being consumed immediately. It doesn’t need to keep any thunks or context around other than its parameters, and it can even re-use the same stack frame. A strict accumulating function, such as Data.List.foldl', is a great choice whenver you’re reducing a list to a value, not building an eagerly-evaluated list of output. Functions such as sum, product or any can’t return any useful intermediate value. They inherently have to finish the computation first, then return the final result.

Reduce memory usage of a Haskell program

I have a following program in Haskell:
processDate :: String -> IO ()
processDate date = do
...
let newFlattenedPropertiesWithPrice = filter (notYetInserted date existingProperties) flattenedPropertiesWithPrice
geocodedProperties <- propertiesWithGeocoding newFlattenedPropertiesWithPrice
propertiesWithGeocoding :: [ParsedProperty] -> IO [(ParsedProperty, Maybe LatLng)]
propertiesWithGeocoding properties = do
let addresses = fmap location properties
let batchAddresses = chunksOf 100 addresses
batchGeocodedLocations <- mapM geocodeAddresses batchAddresses
let geocodedLocations = fromJust $ concat <$> sequence batchGeocodedLocations
return (zip properties geocodedLocations)
geocodeAddresses :: [String] -> IO (Maybe [Maybe LatLng])
geocodeAddresses addresses = do
mapQuestKey <- getEnv "MAP_QUEST_KEY"
geocodeResponse <- openURL $ mapQuestUrl mapQuestKey addresses
return $ geocodeResponseToResults geocodeResponse
geocodeResponseToResults :: String -> Maybe [Maybe LatLng]
geocodeResponseToResults inputResponse =
latLangs
where
decodedResponse :: Maybe GeocodingResponse
decodedResponse = decodeGeocodingResponse inputResponse
latLangs = fmap (fmap geocodingResultToLatLng . results) decodedResponse
decodeGeocodingResponse :: String -> Maybe GeocodingResponse
decodeGeocodingResponse inputResponse = Data.Aeson.decode (fromString inputResponse) :: Maybe GeocodingResponse
It reads a list of properties (homes and apartments) from html files, parses them, geocodes the addresses and saves the results into sqlite db.
Everything works fine except for a very high memory usage (around 800M).
By commenting code out I have pinpointed the problem to be the geocoding step.
I send 100 addresses at a time to MapQuest api (https://developer.mapquest.com/documentation/geocoding-api/batch/get/).
The response for 100 addresses is quite massive so it might be one of the culprits, but 800M? I feel like it holds to all of the results until the end which drives the memory usage so high.
After commenting out the geocoding part of the program memory usage is around 30M which is fine.
You can get the full version which reproduces the issue here: https://github.com/Leonti/haskell-memory-so
I'm quite a newbie in Haskell, so not sure how I can optimize it.
Any ideas?
Cheers!
It might be worth recording that this turned out to be a simple streaming problem arising from use of mapM and sequence, which with replicateM and traverse and other things that make you "extract a list from IO" always raise accumulation worries. So a little detour by a streaming library was needed. So in the repo it was necessary just to replace
processDate :: String -> IO ()
processDate date = do
allFiles <- listFiles date
allProperties <- mapM fileToProperties allFiles
let flattenedPropertiesWithPrice = filter hasPrice $ concat allProperties
geocodedProperties <- propertiesWithGeocoding flattenedPropertiesWithPrice
print geocodedProperties
propertiesWithGeocoding :: [ParsedProperty] -> IO [(ParsedProperty, Maybe LatLng)]
propertiesWithGeocoding properties = do
let batchProperties = chunksOf 100 properties
batchGeocodedLocations <- mapM geocodeAddresses batchProperties
let geocodedLocations = fromJust $ concat <$> sequence batchGeocodedLocations
return geocodedLocations
with something like this
import Streaming
import qualified Streaming.Prelude as S
processDate :: String -> IO ()
processDate date = do
allFiles <- listFiles date -- we accept an unstreamed list
S.print $ propertiesWithGeocoding -- this was the main pain point see below
$ S.filter hasPrice
$ S.concat
$ S.mapM fileToProperties -- this mapM doesn't accumulate
$ S.each allFiles -- the list is converted to a stream
propertiesWithGeocoding
:: Stream (Of ParsedProperty) IO r
-> Stream (Of (ParsedProperty, Maybe LatLng)) IO r
propertiesWithGeocoding properties =
S.concat $ S.concat
$ S.mapM geocodeAddresses -- this mapM doesn't accumulate results from mapquest
$ S.mapped S.toList -- convert segments to haskell lists
$ chunksOf 100 properties -- this is the streaming `chunksOf`
-- concat here flattens a stream of lists of as into a stream of as
-- and a stream of maybe as into a stream of as
Then the memory use looks like so, each peak corresponding to a trip to Mapquest promply followed by a little processing and a print, whereupon ghc forgets all about it and moves on:
Of course this could be done with pipes or conduit. But here we just need a little bit of simple mapM / sequence/ traverse / replicateM avoidance and streaming is perhaps simplest for this sort of quick local refactoring. Note that this list is quite short so the thought 'but short lists are cool with mapM/traverse/etc !" can be quite spectacularly false. Why not just get rid of them? Whenever you are about to write list mapM f it is a good idea to consider S.mapM f . S.each (or conduit or pipes equivalent) . You will now have a stream and can recover a list with S.toList or an equivalent, but it is likely that, as in this case, you will find you don't need a reified accumulated list but can e.g. use some streaming process like printing to file or stdout or writing things to a database, after making whatever list like manipulations are needed (here we use eg. streaming filter and also concat to flatten streamed lists and as a sort of catMaybe).

How do I avoid memory problems when writing to file using the Writer monad?

I am building some moderately large DIMACS files, however with the method used below the memory usage is rather large compared to the size of the files generated, and on some of the larger files I need to generate I run in to out of memory problems.
import Control.Monad.State.Strict
import Control.Monad.Writer.Strict
import qualified Data.ByteString.Lazy.Char8 as B
import Control.Monad
import qualified Text.Show.ByteString as BS
import Data.List
main = printDIMACS "test.cnf" test
test = do
xs <- freshs 100000
forM_ (zip xs (tail xs))
(\(x,y) -> addAll [[negate x, negate y],[x,y]])
type Var = Int
type Clause = [Var]
data DIMACSS = DS{
nextFresh :: Int,
numClauses :: Int
} deriving (Show)
type DIMACSM a = StateT DIMACSS (Writer B.ByteString) a
freshs :: Int -> DIMACSM [Var]
freshs i = do
next <- gets nextFresh
let toRet = [next..next+i-1]
modify (\s -> s{nextFresh = next+i})
return toRet
fresh :: DIMACSM Int
fresh = do
i <- gets nextFresh
modify (\s -> s{nextFresh = i+1})
return i
addAll :: [Clause] -> DIMACSM ()
addAll c = do
tell
(B.concat .
intersperse (B.pack " 0\n") .
map (B.unwords . map BS.show) $ c)
tell (B.pack " 0\n")
modify (\s -> s{numClauses = numClauses s + length c})
add h = addAll [h]
printDIMACS :: FilePath -> DIMACSM a -> IO ()
printDIMACS file f = do
writeFile file ""
appendFile file (concat ["p cnf ", show i, " ", show j, "\n"])
B.appendFile file b
where
(s,b) = runWriter (execStateT f (DS 1 0))
i = nextFresh s - 1
j = numClauses s
I would like to keep the monadic building of clauses since it is very handy, but I need to overcome the memory problem. How do I optimize the above program so that it doesn't use too much memory?
If you want good memory behavior, you need to make sure that you write out the clauses as you generate them, instead of collecting them in memory and dumping them as such, either using lazyness or a more explicit approach such as conduits, enumerators, pipes or the like.
The main obstacle to that approach is that the DIMACS format expects the number of clauses and variables in the header. This prevents the naive implementation from being sufficiently lazy. There are two possibilities:
The pragmatic one is to write the clauses first to a temporary location. After that the numbers are known, so you write them to the real file and append the contents of the temporary file.
The prettier approach is possible if the generation of clauses has no side effects (besides the effects offered by your DIMACSM monad) and is sufficiently fast: Run it twice, first throwing away the clauses and just calculating the numbers, print the header line, run the generator again; now printing the clauses.
(This is from my experience with implementing SAT-Britney, where I took the second approach, because it fitted better with other requirements in that context.)
Also, in your code, addAll is not lazy enough: The list c needs to be retained even after writing (in the MonadWriter sense) the clauses. This is another space leak. I suggest you implement add as the primitive operation and then addAll = mapM_ add.
As explained in Joachim Breitner's answer the problem was that DIMACSM was not lazy enough, both because the strict versions of the monads was used and because the number of variables and clauses are needed before the ByteString can be written to the file. The solution is to use the lazy versions of the Monads and execute them twice. It turns out that it is also necessary to have WriterT be the outer monad:
import Control.Monad.State
import Control.Monad.Writer
...
type DIMACSM a = WriterT B.ByteString (State DIMACSS) a
...
printDIMACS :: FilePath -> DIMACSM a -> IO ()
printDIMACS file f = do
writeFile file ""
appendFile file (concat ["p cnf ", show i, " ", show j, "\n"])
B.appendFile file b
where
s = execState (execWriterT f) (DS 1 0)
b = evalState (execWriterT f) (DS 1 0)
i = nextFresh s - 1
j = numClauses s

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