Haskell: Optimising Graph processing algorithm - algorithm

Question

This is a follow up to this post, with code now based on Structuring Depth-First Search Algorithms in Haskell to do depth first search, by King and Launchbury in the 1990s. That paper suggests a generate and prune strategy, but uses a mutable array with a State Monad (with some grammar that I suspect has since been deprecated). The authors hint that a set could be used for remembering nodes visited, as the cost of an additional O(log n). I tried to implement with a set (we have better machines now than they did in the 1990s!), to use modern State Monad syntax, and to use Vectors rather than arrays (as I read that that is normally better).
As before, my code runs on small data sets, but fails to return on the 5m edge graph I need to analyse, and I'm looking for hints only as to the weakness operating at scale. What I do know is that the code operates comfortably within memory, so that is not the problem, but have I inadvertently slipped to O(n2)? (By contrast, the official implementation of this paper in the Data.Graph library (which I have lately also borrowed some code from) uses a mutable Array but fails on the big data set with a ... Stack Overflow!!!)
So now I have a Vector data store with IntSet State that does not complete and an Array with ST Monad Array 'official' one that crashes! Haskell should be able to do better than this?
import Data.Vector (Vector)
import qualified Data.IntSet as IS
import qualified Data.Vector as V
import qualified Data.ByteString.Char8 as BS
import Control.Monad.State
type Vertex = Int
type Table a = Vector a
type Graph = Table [Vertex]
type Edge = (Vertex, Vertex)
data Tree a = Node a (Forest a) deriving (Show,Eq)
type Forest a = [Tree a]
-- ghc -O2 -threaded --make
-- +RTS -Nx
generate :: Graph -> Vertex -> Tree Vertex
generate g v = Node v $ map (generate g) (g V.! v)
chop :: Forest Vertex -> State IS.IntSet (Forest Vertex)
chop [] = return []
chop (Node x ts:us) = do
visited <- contains x
if visited then
chop us
else do
include x
x1 <- chop ts
x2 <- chop us
return (Node x x1:x2)
prune :: Forest Vertex -> State IS.IntSet (Forest Vertex)
prune vs = chop vs
main = do
--edges <- V.fromList `fmap` getEdges "testdata.txt"
edges <- V.fromList `fmap` getEdges "SCC.txt"
let
-- calculate size of five largest SCC
maxIndex = fst $ V.last edges
gr = buildG maxIndex edges
sccRes = scc gr
big5 = take 5 sccRes
big5' = map (\l -> length $ postorder l) big5
putStrLn $ show $ big5'
contains :: Vertex -> State IS.IntSet Bool
contains v = state $ \visited -> (v `IS.member` visited, visited)
include :: Vertex -> State IS.IntSet ()
include v = state $ \visited -> ((), IS.insert v visited)
getEdges :: String -> IO [Edge]
getEdges path = do
lines <- (map BS.words . BS.lines) `fmap` BS.readFile path
let pairs = (map . map) (maybe (error "can't read Int") fst . BS.readInt) lines
return [(a, b) | [a, b] <- pairs]
vertices :: Graph -> [Vertex]
vertices gr = [1.. (V.length gr - 1)]
edges :: Graph -> [Edge]
edges g = [(u,v) | u <- vertices g, v <- g V.! u]
-- accumulate :: (a -> b -> a) -> Vector a-> Vector (Int, b)--> Vector a
-- accumulating function f
-- initial vector (of length m)
-- vector of index/value pairs (of length n)
buildG :: Int -> Table Edge -> Graph
buildG maxIndex edges = graph' where
graph = V.replicate (maxIndex + 1) []
--graph' = V.accumulate (\existing new -> new:existing) graph edges
-- flip f takes its (first) two arguments in the reverse order of f
graph' = V.accumulate (flip (:)) graph edges
mapT :: Ord a => (Vertex -> a -> b) -> Table a -> Table b
mapT = V.imap
outDegree :: Graph -> Table Int
outDegree g = mapT numEdges g
where numEdges v es = length es
indegree :: Graph -> Table Int
indegree g = outDegree $ transposeG g
transposeG :: Graph -> Graph
transposeG g = buildG (V.length g - 1) (reverseE g)
reverseE :: Graph -> Table Edge
reverseE g = V.fromList [(w, v) | (v,w) <- edges g]
-- --------------------------------------------------------------
postorder :: Tree a -> [a]
postorder (Node a ts) = postorderF ts ++ [a]
postorderF :: Forest a -> [a]
postorderF ts = concat (map postorder ts)
postOrd :: Graph -> [Vertex]
postOrd g = postorderF (dff g)
dfs :: Graph -> [Vertex] -> Forest Vertex
dfs g vs = map (generate g) vs
dfs' :: Graph -> [Vertex] -> Forest Vertex
dfs' g vs = fst $ runState (prune d) $ IS.fromList []
where d = dfs g vs
dff :: Graph -> Forest Vertex
dff g = dfs' g $ reverse (vertices g)
scc :: Graph -> Forest Vertex
scc g = dfs' g $ reverse $ postOrd (transposeG g)

Answer 1

Some small possible improvements:
Change
type Edge = (Vertex, Vertex)
to
data Edge = Edge {-# UNPACK #-} !Vertex {-# UNPACK #-} !Vertex
to reuse the memory usage for each edge from 7 words to 3 words and to improve cache locality. Reducing memory pressure almost always also improves runtime. As #jberryman mentioned could use an unboxed vector for Table Edge (then you don't need the above custom data type).
generate :: Graph -> Vertex -> Tree Vertex
generate g v = Node v $ map (generate g) (g V.! v)
If you're sure that the index is in bounds, you could use the unsafe indexing function from vector instead of .!.
contains :: Vertex -> State IS.IntSet Bool
contains v = state $ \visited -> (v `IS.member` visited, visited)
Use a combination of get and put $! instead.
include :: Vertex -> State IS.IntSet ()
include v = state $ \visited -> ((), IS.insert v visited)
Use modify' instead.
You're using quite a lot of lists in your program. Linked lists aren't the most memory/cache efficient data structures. See if you can convert your code to use more vectors.