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4 3 559 9 5 +283 4 2 506 1 14 +284 11 4 432 7 5 +285 4 3 323 9 16 +286 10 2 605 3 2 +287 4 3 317 5 14 +288 7 1 350 8 1 +289 2 4 700 3 3 +290 13 2 1480 1 19 +291 4 4 443 6 1 +292 16 1 149 5 4 +293 6 1 845 4 5 +294 6 4 2364 5 19 +295 4 1 354 4 8 +296 6 0 745 1 0 +297 6 3 433 9 3 +298 3 1 899 7 15 +299 2 1 193 7 3 diff --git a/sampledataSmall.adj b/sampledataSmall.adj new file mode 100644 index 0000000..6589938 --- /dev/null +++ b/sampledataSmall.adj @@ -0,0 +1,6 @@ +010111 +101100 +010100 +111011 +100100 +100100 diff --git a/sampledataSmall.adj.atr b/sampledataSmall.adj.atr new file mode 100644 index 0000000..566665a --- /dev/null +++ b/sampledataSmall.adj.atr @@ -0,0 +1,6 @@ +0.5 0 -1 +1 1 -1 +1 0.5 -1 +1 1 -0.5 +0.5 0 0 +-1 0 2 diff --git a/src/DCB/DCB.hs b/src/DCB/DCB.hs index b2bc6e1..1b917b6 100644 --- a/src/DCB/DCB.hs +++ b/src/DCB/DCB.hs @@ -20,20 +20,23 @@ import Util import DCB.Structures import DCB.IO -import Prelude hiding ((++)) -import qualified Prelude as P ((++)) +import Prelude hiding ((++)) +import qualified Prelude as P ((++)) import Control.Monad.Par -import Data.Array.Repa ((:.) (..), Array, (!), (*^), (++), (+^), - (-^), (/^)) -import qualified Data.Array.Repa as A +import Control.Parallel.Strategies +import Control.Monad.Identity +import Control.DeepSeq +import Data.Array.Repa ((:.) (..), Array, (!), (*^), (++), (+^), + (-^), (/^)) +import qualified Data.Array.Repa as A import Data.Array.Repa.Index import Data.Either import Data.Int -import qualified Data.List as L +import qualified Data.List as L import Data.Maybe -import qualified Data.Vector.Unboxed as V -import Debug.Trace +import qualified Data.Vector.Unboxed as V +--import Debug.Trace import qualified Data.ByteString.Char8 as B @@ -62,12 +65,21 @@ testDivergence = A.fromListUnboxed (ix1 5) [3.0, 0.0, 300.0, 2.0, 10.0] testDensity = 0.7::Density; testReq = 3 ::Int +force :: (A.Shape sh, V.Unbox e) => Array A.D sh e -> Array A.U sh e +force a = runIdentity (A.computeP a) + +--ignore A.U-Array in deepseq - already unboxed.. +instance (A.Shape sh, V.Unbox e) => NFData (Array A.U sh e) where + rnf a = () + {-# INLINE rnf #-} --TODO: Do we have to filter? step :: [Graph] -> Adj -> Attr -> Density -> MaxDivergence -> Int -> [Graph] step gs@((ind,_,_):_) a b c d e = --trace ("step from " P.++ show (A.extent ind) ) $ filterLayer $ concat $ map (expand a b c d e ) gs + +|| (parBuffer 75 rdeepseq) + -- | calculates all possible additions to one Graph, yielding a list of valid expansions @@ -90,13 +102,14 @@ preprocess :: Adj -- ^ original adjacency matrix -> (Adj, [Graph]) preprocess adj attr div req = let - (Z:.nNodes:._) = A.extent adj - results = map (initGraph attr div req) [(i, j) | i <- [0..(nNodes-1)], j <- [(i+1)..(nNodes-1)], adj!(ix2 i j) /= 0] - finalGraphs = lefts results - mask = A.fromUnboxed (A.extent adj) $V.replicate (nNodes*nNodes) False V.// + ! (Z:.nNodes:._) = A.extent adj + ! results = map (initGraph attr div req) [(i, j) | i <- [0..(nNodes-1)], j <- [(i+1)..(nNodes-1)], adj!(ix2 i j) /= 0] + +|| (parBuffer 25 rdeepseq) + ! finalGraphs = lefts results + ! mask = A.fromUnboxed (A.extent adj) $V.replicate (nNodes*nNodes) False V.// ((map (\(i,j) -> (i*nNodes + (mod j nNodes), True)) $rights results) P.++ (map (\(i,j) -> (j*nNodes + (mod i nNodes), True)) $rights results)) - adj' = A.computeS $A.fromFunction (A.extent adj) (\sh -> if mask!sh then 0 else adj!sh) + ! adj' = runIdentity $ A.computeUnboxedP $A.fromFunction (A.extent adj) (\sh -> if mask!sh then 0 else adj!sh) in (adj', finalGraphs) -- | Initializes a seed 'Graph' if it fulfills the constraints, returns the input nodes @@ -108,7 +121,7 @@ initGraph :: Attr -- ^ table of all node’s attributes -> Either Graph (Int, Int) initGraph attr div req (i, j) = let - constr = constraintInit attr div req i j + ! constr = constraintInit attr div req i j in case constr of Nothing -> Right (i, j) Just c -> Left (A.fromListUnboxed (ix1 2) [i,j], c, 1) @@ -119,20 +132,23 @@ constraintInit :: Attr -> MaxDivergence -> Int -- ^ required number of consisten -> Int -- ^ first node to test -> Int -- ^ second node to test first node against -> Maybe Constraints -constraintInit attr div req i j = +constraintInit ! attr ! div req i j = let - (Z:._:.nAttr) = A.extent attr + ! (Z:._:.nAttr) = A.extent attr fConstr (Z:.a:.c) = let - col = A.slice attr (A.Any:.a) + ! col = A.slice attr (A.Any:.a) in case c of 0 -> min (attr!(ix2 i a)) (attr!(ix2 j a)) 1 -> max (attr!(ix2 i a)) (attr!(ix2 j a)) - constr = A.computeS $A.fromFunction (ix2 nAttr 2) fConstr - fulfill = A.zipWith (\thediv dist -> if abs dist <= thediv then 1 else 0) div - $A.foldS (-) 0 constr - nrHit = A.foldAllS (+) (0::Int) $A.map fromIntegral fulfill - in if nrHit >= req then Just (A.computeS fulfill, constr) else Nothing + (constr, fulfill, nrHit) = runIdentity $ + do + ! constr <- return $ A.computeUnboxedS $A.fromFunction (ix2 nAttr 2) fConstr + ! fulfill <- return $ A.computeUnboxedS $ A.zipWith (\thediv dist -> if abs dist <= thediv then 1 else 0) div + $A.foldS (-) 0 constr + ! nrHit <- return $ A.foldAllS (+) (0::Int) $A.map fromIntegral fulfill + return (constr, fulfill, nrHit) + in if nrHit >= req then Just (fulfill, constr) else Nothing -- | removes all duplicate graphs filterLayer :: [Graph] -> [Graph] @@ -151,16 +167,16 @@ constraint :: Attr -> MaxDivergence -> Int -- ^ required number of consistent at constraint attr div req (ind, (fulfill, constr), _) newNode = let --TODO: UGLY hack... this has to be somewhere .. -.- - posInf = read "Infinity" :: Double - negInf = read "-Infinity" :: Double + ! posInf = read "Infinity" :: Double + ! negInf = read "-Infinity" :: Double -- convert into Vector of new Indices after appending new node-index - totalInd = A.toUnboxed $ A.computeUnboxedS $ ind ++ A.fromListUnboxed (ix1 1) [newNode] + ! totalInd = A.toUnboxed $ A.computeUnboxedS $ ind ++ A.fromListUnboxed (ix1 1) [newNode] updateConstr :: (DIM2 -> Double) -> DIM2 -> Double updateConstr f sh@(Z:.i:.c) = let - slice = A.slice attr (A.Any :. i) - mins = A.traverse slice id (\g sh'@(Z :. j)-> if V.any (==j) totalInd then (g sh') else posInf) - maxs = A.traverse slice id (\g sh'@(Z :. j)-> if V.any (==j) totalInd then (g sh') else negInf) + ! slice = A.slice attr (A.Any :. i) + ! mins = A.traverse slice id (\g sh'@(Z :. j)-> if V.any (==j) totalInd then (g sh') else posInf) + ! maxs = A.traverse slice id (\g sh'@(Z :. j)-> if V.any (==j) totalInd then (g sh') else negInf) in -- trace (show i P.++ show (A.toList slice) P.++ show c P.++ "\n " P.++ show (A.foldAllS (max) negInf $ maxs)) $ @@ -175,7 +191,7 @@ constraint attr div req (ind, (fulfill, constr), _) newNode = $A.zipWith (\thediv dist -> abs dist <= thediv) div $A.foldS (-) 0 constrNew ! nrHit = A.foldAllS (+) (0::Int) $A.map fromIntegral fulfillNew in if nrHit >= req then Just {-$ trace ("returning const-matrix for "P.++ show (A.toList ind) P.++"\n" P.++ (B.unpack $ outputArray constrNew))-} - (A.computeS fulfillNew, constrNew) else Nothing + (A.computeUnboxedS fulfillNew, constrNew) else Nothing -- updates the density of a graph extended by a single node updateDensity :: Adj -- ^ global adjacency matrix of all nodes @@ -225,8 +241,8 @@ addPoint :: Adj -- ^ global adjacency matrix of all nodes -> Maybe Graph addPoint adj attr d div req g@(nodes, _, dens) n = let - constr = constraint attr div req g n - densNew = updateDensity adj nodes n dens + (! constr,! densNew) = (constraint attr div req g n,updateDensity adj nodes n dens) + -- +|| (parTuple2 rdeepseq rdeepseq) in case constr of Nothing -> Nothing @@ -234,7 +250,7 @@ addPoint adj attr d div req g@(nodes, _, dens) n = --trace (B.unpack $ outputArray constr) $ case densNew >= d of True -> Just {-$ trace ("submitting graph:\n================\n " P.++ (B.unpack $ outputGraph [(A.computeS $nodes ++ A.fromListUnboxed (ix1 1) [n], c, densNew)])) -} - (A.computeS $nodes ++ A.fromListUnboxed (ix1 1) [n], c, densNew) + (A.computeUnboxedS $nodes ++ A.fromListUnboxed (ix1 1) [n], c, densNew) False -> Nothing reduceDim :: (A.Shape sh, Integral a) => (sh :. a) -> sh @@ -242,7 +258,7 @@ reduceDim (a :. b) = a --A.shapeOfList $ tail $ A.listOfShape a -- | yields all valid addititons (=neighbours) to a Graph addablePoints :: Adj -> Graph -> Vector A.U Bool -addablePoints adj (ind,_,_) = A.computeS $ +addablePoints adj (ind,_,_) = A.computeUnboxedS $ (A.traverse adj reduceDim diff --git a/src/Main.hs b/src/Main.hs index 0c61b67..f0a4611 100644 --- a/src/Main.hs +++ b/src/Main.hs @@ -42,7 +42,7 @@ import qualified Data.Stream as S import qualified Data.Text as T import Data.Text.Encoding import qualified Data.Vector.Unboxed as V -import Debug.Trace +--import Debug.Trace import System.Environment import System.Exit (exitFailure, exitSuccess) import Test.QuickCheck.All (quickCheckAll) @@ -120,20 +120,21 @@ emptyLine a doCalculation adj attr = let dens = 0.75 - omega = (A.fromListUnboxed (ix1 3) [0.5,0.5,0.5]) + omega = (A.fromListUnboxed (ix1 6) [0,5,3,300,5,10]) delta = 2 (adj_, graph_) = preprocess adj attr {--0.8--} omega delta in B.concat $ [ - outputArray $ trace ("After: "++ show (sumAllS adj_)++"\n") adj_, + --outputArray $ --trace ("After: "++ show (sumAllS adj_)++"\n") + -- adj_, outputGraph $ L.sort $ doAll graph_ adj_ attr dens omega delta --- outputGraph $ L.sort $ (step graph_ adj attr dens omega delta) --- ++ (step (step graph_ adj attr dens omega delta) adj attr dens omega delta) ] where + -- don't print out seeds doAll [] _ _ _ _ _ = [] doAll gs a b c d e = doAll' (step gs a b c d e) a b c d e + -- but everything in the following recursive calls doAll' [] _ _ _ _ _ = [] doAll' gs a b c d e = gs ++ doAll' (step gs a b c d e) a b c d e @@ -172,7 +173,7 @@ checkError a -- | convinience debug-function. Needs to be -- changed to return () to disable Debug. -debug a = putStrLn a +debug a = return () --putStrLn a -- | The main-function to bootstrap our application @@ -226,5 +227,230 @@ main = do ----- CALCULATE & OUTPUT - debug $ "Before: " ++ show (sumAllS graph) + --debug $ "Before: " ++ show (sumAllS graph) B.putStr $ doCalculation graph attr + + + + +{---TIMINGS + +SINGLE CORE +=========== + ./hgraph +RTS -s >result + 197,751,229,488 bytes allocated in the heap + 290,034,880 bytes copied during GC + 11,061,600 bytes maximum residency (10 sample(s)) + 1,513,488 bytes maximum slop + 33 MB total memory in use (0 MB lost due to fragmentation) + + Tot time (elapsed) Avg pause Max pause + Gen 0 381500 colls, 0 par 2.24s 2.20s 0.0000s 0.0005s + Gen 1 10 colls, 0 par 0.05s 0.05s 0.0054s 0.0154s + + TASKS: 3 (1 bound, 2 peak workers (2 total), using -N1) + + SPARKS: 6266 (0 converted, 0 overflowed, 0 dud, 15 GC'd, 6251 fizzled) + + INIT time 0.00s ( 0.00s elapsed) + MUT time 74.11s ( 74.11s elapsed) + GC time 2.30s ( 2.25s elapsed) + EXIT time 0.00s ( 0.00s elapsed) + Total time 76.42s ( 76.36s elapsed) + + Alloc rate 2,668,183,845 bytes per MUT second + + Productivity 97.0% of total user, 97.1% of total elapsed + +gc_alloc_block_sync: 0 +whitehole_spin: 0 +gen[0].sync: 0 +gen[1].sync: 0 + +4 CORES: +======== +./hgraph +RTS -s -N4 >result + 197,754,645,560 bytes allocated in the heap + 293,083,624 bytes copied during GC + 11,061,264 bytes maximum residency (10 sample(s)) + 1,555,576 bytes maximum slop + 34 MB total memory in use (0 MB lost due to fragmentation) + + Tot time (elapsed) Avg pause Max pause + Gen 0 380952 colls, 380952 par 15.25s 3.92s 0.0000s 0.0255s + Gen 1 10 colls, 9 par 0.22s 0.06s 0.0056s 0.0181s + + Parallel GC work balance: 1.68% (serial 0%, perfect 100%) + + TASKS: 6 (1 bound, 5 peak workers (5 total), using -N4) + + SPARKS: 6266 (6228 converted, 0 overflowed, 0 dud, 30 GC'd, 8 fizzled) + + INIT time 0.00s ( 0.00s elapsed) + MUT time 105.25s ( 86.11s elapsed) + GC time 15.47s ( 3.98s elapsed) + EXIT time 0.00s ( 0.00s elapsed) + Total time 120.73s ( 90.09s elapsed) + + Alloc rate 1,878,861,647 bytes per MUT second + + Productivity 87.2% of total user, 116.8% of total elapsed + +gc_alloc_block_sync: 661438 +whitehole_spin: 0 +gen[0].sync: 655 +gen[1].sync: 1347 + + +parallel preprocessing (Adj, Seeds) +================================== +./hgraph +RTS -s -N4 >result +Building hgraph-0.0.1... +Preprocessing executable 'hgraph' for hgraph-0.0.1... +[4 of 5] Compiling DCB.DCB ( src/DCB/DCB.hs, dist/build/hgraph/hgraph-tmp/DCB/DCB.o ) +Linking dist/build/hgraph/hgraph ... + 197,755,802,848 bytes allocated in the heap + 289,986,840 bytes copied during GC + 11,071,880 bytes maximum residency (10 sample(s)) + 1,566,376 bytes maximum slop + 34 MB total memory in use (0 MB lost due to fragmentation) + + Tot time (elapsed) Avg pause Max pause + Gen 0 380919 colls, 380919 par 15.73s 3.93s 0.0000s 0.0112s + Gen 1 10 colls, 9 par 0.28s 0.07s 0.0073s 0.0335s + + Parallel GC work balance: 1.69% (serial 0%, perfect 100%) + + TASKS: 6 (1 bound, 5 peak workers (5 total), using -N4) + + SPARKS: 7895 (7825 converted, 0 overflowed, 0 dud, 50 GC'd, 20 fizzled) + + INIT time 0.00s ( 0.00s elapsed) + MUT time 98.47s ( 81.37s elapsed) + GC time 16.01s ( 4.00s elapsed) + EXIT time 0.00s ( 0.00s elapsed) + Total time 114.49s ( 85.37s elapsed) + + Alloc rate 2,008,240,220 bytes per MUT second + + Productivity 86.0% of total user, 115.3% of total elapsed + +gc_alloc_block_sync: 757575 +whitehole_spin: 0 +gen[0].sync: 592 +gen[1].sync: 510 + +parallel processing (primitive, too many sparks fizzled) - Speedup: 76.36/51.51 = 1.48 +======================================================== +./hgraph +RTS -s -N4 >result +Building hgraph-0.0.1... +Preprocessing executable 'hgraph' for hgraph-0.0.1... +[4 of 5] Compiling DCB.DCB ( src/DCB/DCB.hs, dist/build/hgraph/hgraph-tmp/DCB/DCB.o ) +[5 of 5] Compiling Main ( src/Main.hs, dist/build/hgraph/hgraph-tmp/Main.o ) +Linking dist/build/hgraph/hgraph ... + 205,324,862,344 bytes allocated in the heap + 224,224,264 bytes copied during GC + 11,157,008 bytes maximum residency (9 sample(s)) + 1,559,568 bytes maximum slop + 35 MB total memory in use (0 MB lost due to fragmentation) + + Tot time (elapsed) Avg pause Max pause + Gen 0 123063 colls, 123063 par 6.77s 1.67s 0.0000s 0.0074s + Gen 1 9 colls, 8 par 0.21s 0.06s 0.0061s 0.0190s + + Parallel GC work balance: 8.15% (serial 0%, perfect 100%) + + TASKS: 6 (1 bound, 5 peak workers (5 total), using -N4) + + SPARKS: 1714681 (861196 converted, 0 overflowed, 0 dud, 78 GC'd, 853407 fizzled) + + INIT time 0.00s ( 0.00s elapsed) + MUT time 145.46s ( 49.78s elapsed) + GC time 6.99s ( 1.73s elapsed) + EXIT time 0.00s ( 0.00s elapsed) + Total time 152.45s ( 51.51s elapsed) + + Alloc rate 1,411,565,587 bytes per MUT second + + Productivity 95.4% of total user, 282.4% of total elapsed + +gc_alloc_block_sync: 378641 +whitehole_spin: 0 +gen[0].sync: 572 +gen[1].sync: 609 + + +parallel processing (monad-par, repa-stuff seqential) - Speedup: 76.36/34,05 = 2.243 +===================================================== + +./hgraph +RTS -N4 -s > result.txt + 204,368,634,080 bytes allocated in the heap + 306,058,720 bytes copied during GC + 11,108,872 bytes maximum residency (10 sample(s)) + 1,597,088 bytes maximum slop + 35 MB total memory in use (0 MB lost due to fragmentation) + + Tot time (elapsed) Avg pause Max pause + Gen 0 108838 colls, 108838 par 9.21s 2.29s 0.0000s 0.0020s + Gen 1 10 colls, 9 par 0.32s 0.08s 0.0083s 0.0245s + + Parallel GC work balance: 29.41% (serial 0%, perfect 100%) + + TASKS: 6 (1 bound, 5 peak workers (5 total), using -N4) + + SPARKS: 15737 (14412 converted, 0 overflowed, 0 dud, 1251 GC'd, 74 fizzled) + + INIT time 0.00s ( 0.00s elapsed) + MUT time 124.37s ( 31.67s elapsed) + GC time 9.53s ( 2.37s elapsed) + EXIT time 0.00s ( 0.00s elapsed) + Total time 133.91s ( 34.05s elapsed) + + Alloc rate 1,643,242,747 bytes per MUT second + + Productivity 92.9% of total user, 365.3% of total elapsed + +gc_alloc_block_sync: 531144 +whitehole_spin: 0 +gen[0].sync: 758 +gen[1].sync: 17 + + +ADDITIONAL OVERHEAD (running on 1 Core with parallel stuff): Slowdown: 76.36/123.39 = 0.62885 +============================================================ + +./hgraph +RTS -N1 -s > result.txt + 204,364,490,096 bytes allocated in the heap + 291,824,120 bytes copied during GC + 10,081,664 bytes maximum residency (11 sample(s)) + 1,545,536 bytes maximum slop + 30 MB total memory in use (0 MB lost due to fragmentation) + + Tot time (elapsed) Avg pause Max pause + Gen 0 393965 colls, 0 par 6.77s 6.72s 0.0000s 0.0017s + Gen 1 11 colls, 0 par 0.09s 0.09s 0.0079s 0.0217s + + TASKS: 3 (1 bound, 2 peak workers (2 total), using -N1) + + SPARKS: 15737 (0 converted, 0 overflowed, 0 dud, 166 GC'd, 15571 fizzled) + + INIT time 0.00s ( 0.00s elapsed) + MUT time 116.53s (116.52s elapsed) + GC time 6.85s ( 6.80s elapsed) + EXIT time 0.00s ( 0.00s elapsed) + Total time 123.39s (123.32s elapsed) + + Alloc rate 1,753,707,727 bytes per MUT second + + Productivity 94.4% of total user, 94.5% of total elapsed + +gc_alloc_block_sync: 0 +whitehole_spin: 0 +gen[0].sync: 0 +gen[1].sync: 0 + + +REAL SPEEDUP AGAINST OVERHEAD-VARIANT: 129.39/34.05 = 3.8 +========================================================= + +-} \ No newline at end of file