made parallel
some performance-data in main.hs. Changes can be viewed in git. TODO: - Find out why there is overhed of >50%
This commit is contained in:
parent
9abbf0f508
commit
1ec8de8ee2
@ -21,7 +21,8 @@ executable hgraph
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repa >=3.2,
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repa >=3.2,
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text -any,
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text -any,
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transformers >=0.3.0,
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transformers >=0.3.0,
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vector >=0.10.9
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vector >=0.10.9,
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mtl >=2.1 && <3
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main-is: Main.hs
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main-is: Main.hs
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buildable: True
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buildable: True
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hs-source-dirs: src
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hs-source-dirs: src
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@ -1,6 +0,0 @@
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010111
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101100
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010100
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111011
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100100
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100100
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1
sampledata.adj
Symbolic link
1
sampledata.adj
Symbolic link
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sampledata512.adj
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@ -1,6 +0,0 @@
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0.5 0 -1
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1 1 -1
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1 0.5 -1
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1 1 -0.5
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0.5 0 0
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-1 0 2
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1
sampledata.adj.atr
Symbolic link
1
sampledata.adj.atr
Symbolic link
@ -0,0 +1 @@
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sampledata512.adj.atr
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100
sampledata100.adj
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sampledata100.adj
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100
sampledata100.adj.atr
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100
sampledata100.adj.atr
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91 6 2 478 4 9
|
||||||
|
92 29 4 450 3 11
|
||||||
|
93 3 3 1014 0 6
|
||||||
|
94 2 1 2701 1 16
|
||||||
|
95 2 1 332 1 17
|
||||||
|
96 1 1 646 0 11
|
||||||
|
97 2 4 574 7 2
|
||||||
|
98 3 3 742 3 4
|
||||||
|
99 6 3 473 7 15
|
||||||
|
100 32 3 969 5 10
|
||||||
|
101 8 1 178 4 8
|
||||||
|
102 14 0 295 7 17
|
||||||
|
103 3 3 288 0 4
|
||||||
|
104 3 3 1356 9 0
|
||||||
|
105 9 1 1009 5 0
|
||||||
|
106 3 0 1374 4 4
|
||||||
|
107 3 0 186 5 11
|
||||||
|
108 4 4 359 3 3
|
||||||
|
109 5 0 767 9 4
|
||||||
|
110 9 3 556 5 1
|
||||||
|
111 3 0 976 9 8
|
||||||
|
112 3 0 415 9 7
|
||||||
|
113 5 2 207 2 2
|
||||||
|
114 4 2 454 3 6
|
||||||
|
115 4 3 399 9 3
|
||||||
|
116 4 3 95 7 5
|
||||||
|
117 2 3 673 6 2
|
||||||
|
118 11 3 770 1 19
|
||||||
|
119 101 3 536 6 11
|
||||||
|
120 8 1 528 3 2
|
||||||
|
121 4 0 524 3 12
|
||||||
|
122 3 3 1544 4 6
|
||||||
|
123 3 3 304 4 16
|
||||||
|
124 8 2 595 1 2
|
||||||
|
125 3 4 391 1 16
|
||||||
|
126 11 2 781 8 12
|
||||||
|
127 3 4 1333 0 14
|
||||||
|
128 3 0 1112 5 2
|
||||||
|
129 6 4 1441 9 17
|
||||||
|
130 48 3 245 5 10
|
||||||
|
131 3 1 561 1 14
|
||||||
|
132 21 1 360 7 8
|
||||||
|
133 7 4 403 0 12
|
||||||
|
134 4 3 496 4 5
|
||||||
|
135 9 3 537 7 9
|
||||||
|
136 4 0 377 5 15
|
||||||
|
137 6 3 496 4 1
|
||||||
|
138 6 3 206 8 10
|
||||||
|
139 4 0 92 2 11
|
||||||
|
140 12 1 377 4 13
|
||||||
|
141 5 3 817 5 12
|
||||||
|
142 3 4 393 7 8
|
||||||
|
143 3 2 1038 3 14
|
||||||
|
144 6 4 360 4 10
|
||||||
|
145 3 3 429 4 18
|
||||||
|
146 3 3 757 3 0
|
||||||
|
147 3 3 143 0 12
|
||||||
|
148 3 0 413 1 0
|
||||||
|
149 18 3 391 7 3
|
||||||
|
150 19 2 439 7 0
|
||||||
|
151 9 0 100 9 1
|
||||||
|
152 4 1 785 7 19
|
||||||
|
153 3 2 313 8 9
|
||||||
|
154 3 0 743 5 10
|
||||||
|
155 6 0 217 9 6
|
||||||
|
156 4 1 505 4 4
|
||||||
|
157 5 0 292 6 6
|
||||||
|
158 3 0 1591 6 5
|
||||||
|
159 3 1 673 4 12
|
||||||
|
160 5 2 758 1 1
|
||||||
|
161 6 0 738 9 18
|
||||||
|
162 2 1 1585 8 3
|
||||||
|
163 1 4 184 8 1
|
||||||
|
164 4 1 400 1 18
|
||||||
|
165 6 4 1106 5 7
|
||||||
|
166 5 0 331 4 5
|
||||||
|
167 4 3 656 3 1
|
||||||
|
168 3 0 529 5 1
|
||||||
|
169 4 3 446 4 15
|
||||||
|
170 5 4 381 6 10
|
||||||
|
171 4 0 444 3 13
|
||||||
|
172 10 1 2414 0 0
|
||||||
|
173 3 3 330 6 9
|
||||||
|
174 13 2 676 6 10
|
||||||
|
175 3 2 361 7 11
|
||||||
|
176 4 3 283 8 2
|
||||||
|
177 7 2 735 8 9
|
||||||
|
178 2 2 295 8 10
|
||||||
|
179 25 1 193 0 15
|
||||||
|
180 1 2 405 6 3
|
||||||
|
181 11 0 592 1 15
|
||||||
|
182 6 2 1275 6 7
|
||||||
|
183 3 0 476 6 12
|
||||||
|
184 3 3 1154 8 16
|
||||||
|
185 3 2 327 6 14
|
||||||
|
186 2 1 197 4 19
|
||||||
|
187 3 1 897 8 5
|
||||||
|
188 3 0 334 7 11
|
||||||
|
189 7 0 870 5 19
|
||||||
|
190 8 3 1863 5 7
|
||||||
|
191 5 2 976 7 19
|
||||||
|
192 4 1 150 6 6
|
||||||
|
193 3 4 482 5 16
|
||||||
|
194 3 1 430 4 4
|
||||||
|
195 3 4 586 2 14
|
||||||
|
196 3 2 2471 1 15
|
||||||
|
197 35 2 433 1 14
|
||||||
|
198 4 3 787 3 15
|
||||||
|
199 4 4 655 9 0
|
||||||
|
200 3 2 355 4 13
|
||||||
|
201 4 4 544 0 2
|
||||||
|
202 3 3 526 6 1
|
||||||
|
203 3 1 350 4 10
|
||||||
|
204 5 2 641 6 9
|
||||||
|
205 8 0 341 6 19
|
||||||
|
206 3 1 465 7 17
|
||||||
|
207 3 2 629 9 3
|
||||||
|
208 2 0 1279 4 11
|
||||||
|
209 12 3 557 2 5
|
||||||
|
210 2 2 689 5 1
|
||||||
|
211 3 0 1159 8 13
|
||||||
|
212 3 3 986 9 0
|
||||||
|
213 3 1 847 3 8
|
||||||
|
214 3 1 1076 8 18
|
||||||
|
215 5 2 901 2 6
|
||||||
|
216 7 4 1367 6 12
|
||||||
|
217 4 1 1271 9 6
|
||||||
|
218 3 4 196 5 3
|
||||||
|
219 6 0 477 5 19
|
||||||
|
220 3 1 592 0 2
|
||||||
|
221 4 2 737 0 4
|
||||||
|
222 3 0 179 8 6
|
||||||
|
223 3 0 412 3 14
|
||||||
|
224 5 0 726 2 12
|
||||||
|
225 3 1 473 3 11
|
||||||
|
226 3 2 470 5 11
|
||||||
|
227 6 0 794 4 3
|
||||||
|
228 13 4 271 5 3
|
||||||
|
229 6 2 189 0 7
|
||||||
|
230 4 1 94 5 4
|
||||||
|
231 9 4 553 4 17
|
||||||
|
232 4 0 411 0 1
|
||||||
|
233 19 4 467 0 13
|
||||||
|
234 3 3 552 0 19
|
||||||
|
235 3 3 946 2 1
|
||||||
|
236 3 3 1105 3 18
|
||||||
|
237 8 2 1770 4 3
|
||||||
|
238 10 3 583 0 4
|
||||||
|
239 5 3 596 2 13
|
||||||
|
240 55 4 593 9 1
|
||||||
|
241 16 1 379 3 3
|
||||||
|
242 3 2 316 3 2
|
||||||
|
243 4 0 309 9 14
|
||||||
|
244 3 2 1192 9 5
|
||||||
|
245 3 2 555 4 15
|
||||||
|
246 2 3 2138 6 4
|
||||||
|
247 44 1 1047 0 12
|
||||||
|
248 3 3 606 0 2
|
||||||
|
249 3 4 293 7 19
|
||||||
|
250 3 1 577 0 15
|
||||||
|
251 4 0 1647 5 8
|
||||||
|
252 3 0 440 0 3
|
||||||
|
253 3 2 1562 6 19
|
||||||
|
254 3 3 1130 2 1
|
||||||
|
255 4 0 281 8 19
|
||||||
|
256 3 2 1304 7 17
|
||||||
|
257 3 1 225 3 7
|
||||||
|
258 9 1 1074 0 17
|
||||||
|
259 4 0 817 0 12
|
||||||
|
260 7 4 768 8 14
|
||||||
|
261 5 1 489 8 6
|
||||||
|
262 3 1 418 1 2
|
||||||
|
263 35 3 672 1 17
|
||||||
|
264 3 1 181 2 19
|
||||||
|
265 4 3 651 7 9
|
||||||
|
266 7 2 425 2 9
|
||||||
|
267 3 0 594 1 16
|
||||||
|
268 3 4 52 8 16
|
||||||
|
269 3 4 444 7 10
|
||||||
|
270 3 0 416 4 9
|
||||||
|
271 24 3 239 7 7
|
||||||
|
272 11 4 246 9 7
|
||||||
|
273 3 4 529 8 4
|
||||||
|
274 3 3 789 9 18
|
||||||
|
275 3 3 279 1 12
|
||||||
|
276 4 2 834 0 2
|
||||||
|
277 4 2 676 1 8
|
||||||
|
278 8 1 2871 4 0
|
||||||
|
279 4 1 796 0 18
|
||||||
|
280 3 3 631 5 18
|
||||||
|
281 2 4 198 9 8
|
||||||
|
282 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
|
6
sampledataSmall.adj
Normal file
6
sampledataSmall.adj
Normal file
@ -0,0 +1,6 @@
|
|||||||
|
010111
|
||||||
|
101100
|
||||||
|
010100
|
||||||
|
111011
|
||||||
|
100100
|
||||||
|
100100
|
6
sampledataSmall.adj.atr
Normal file
6
sampledataSmall.adj.atr
Normal file
@ -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
|
@ -20,20 +20,23 @@ import Util
|
|||||||
import DCB.Structures
|
import DCB.Structures
|
||||||
import DCB.IO
|
import DCB.IO
|
||||||
|
|
||||||
import Prelude hiding ((++))
|
import Prelude hiding ((++))
|
||||||
import qualified Prelude as P ((++))
|
import qualified Prelude as P ((++))
|
||||||
|
|
||||||
import Control.Monad.Par
|
import Control.Monad.Par
|
||||||
import Data.Array.Repa ((:.) (..), Array, (!), (*^), (++), (+^),
|
import Control.Parallel.Strategies
|
||||||
(-^), (/^))
|
import Control.Monad.Identity
|
||||||
import qualified Data.Array.Repa as A
|
import Control.DeepSeq
|
||||||
|
import Data.Array.Repa ((:.) (..), Array, (!), (*^), (++), (+^),
|
||||||
|
(-^), (/^))
|
||||||
|
import qualified Data.Array.Repa as A
|
||||||
import Data.Array.Repa.Index
|
import Data.Array.Repa.Index
|
||||||
import Data.Either
|
import Data.Either
|
||||||
import Data.Int
|
import Data.Int
|
||||||
import qualified Data.List as L
|
import qualified Data.List as L
|
||||||
import Data.Maybe
|
import Data.Maybe
|
||||||
import qualified Data.Vector.Unboxed as V
|
import qualified Data.Vector.Unboxed as V
|
||||||
import Debug.Trace
|
--import Debug.Trace
|
||||||
import qualified Data.ByteString.Char8 as B
|
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;
|
testDensity = 0.7::Density;
|
||||||
testReq = 3 ::Int
|
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?
|
--TODO: Do we have to filter?
|
||||||
|
|
||||||
step :: [Graph] -> Adj -> Attr -> Density -> MaxDivergence -> Int -> [Graph]
|
step :: [Graph] -> Adj -> Attr -> Density -> MaxDivergence -> Int -> [Graph]
|
||||||
step gs@((ind,_,_):_) a b c d e = --trace ("step from " P.++ show (A.extent ind) ) $
|
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
|
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
|
-- | calculates all possible additions to one Graph, yielding a list of valid expansions
|
||||||
@ -90,13 +102,14 @@ preprocess :: Adj -- ^ original adjacency matrix
|
|||||||
-> (Adj, [Graph])
|
-> (Adj, [Graph])
|
||||||
preprocess adj attr div req =
|
preprocess adj attr div req =
|
||||||
let
|
let
|
||||||
(Z:.nNodes:._) = A.extent adj
|
! (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]
|
! 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
|
+|| (parBuffer 25 rdeepseq)
|
||||||
mask = A.fromUnboxed (A.extent adj) $V.replicate (nNodes*nNodes) False V.//
|
! 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)
|
((map (\(i,j) -> (i*nNodes + (mod j nNodes), True)) $rights results)
|
||||||
P.++ (map (\(i,j) -> (j*nNodes + (mod i 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)
|
in (adj', finalGraphs)
|
||||||
|
|
||||||
-- | Initializes a seed 'Graph' if it fulfills the constraints, returns the input nodes
|
-- | 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)
|
-> Either Graph (Int, Int)
|
||||||
initGraph attr div req (i, j) =
|
initGraph attr div req (i, j) =
|
||||||
let
|
let
|
||||||
constr = constraintInit attr div req i j
|
! constr = constraintInit attr div req i j
|
||||||
in case constr of
|
in case constr of
|
||||||
Nothing -> Right (i, j)
|
Nothing -> Right (i, j)
|
||||||
Just c -> Left (A.fromListUnboxed (ix1 2) [i,j], c, 1)
|
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 -- ^ first node to test
|
||||||
-> Int -- ^ second node to test first node against
|
-> Int -- ^ second node to test first node against
|
||||||
-> Maybe Constraints
|
-> Maybe Constraints
|
||||||
constraintInit attr div req i j =
|
constraintInit ! attr ! div req i j =
|
||||||
let
|
let
|
||||||
(Z:._:.nAttr) = A.extent attr
|
! (Z:._:.nAttr) = A.extent attr
|
||||||
fConstr (Z:.a:.c) =
|
fConstr (Z:.a:.c) =
|
||||||
let
|
let
|
||||||
col = A.slice attr (A.Any:.a)
|
! col = A.slice attr (A.Any:.a)
|
||||||
in case c of
|
in case c of
|
||||||
0 -> min (attr!(ix2 i a)) (attr!(ix2 j a))
|
0 -> min (attr!(ix2 i a)) (attr!(ix2 j a))
|
||||||
1 -> max (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
|
(constr, fulfill, nrHit) = runIdentity $
|
||||||
fulfill = A.zipWith (\thediv dist -> if abs dist <= thediv then 1 else 0) div
|
do
|
||||||
$A.foldS (-) 0 constr
|
! constr <- return $ A.computeUnboxedS $A.fromFunction (ix2 nAttr 2) fConstr
|
||||||
nrHit = A.foldAllS (+) (0::Int) $A.map fromIntegral fulfill
|
! fulfill <- return $ A.computeUnboxedS $ A.zipWith (\thediv dist -> if abs dist <= thediv then 1 else 0) div
|
||||||
in if nrHit >= req then Just (A.computeS fulfill, constr) else Nothing
|
$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
|
-- | removes all duplicate graphs
|
||||||
filterLayer :: [Graph] -> [Graph]
|
filterLayer :: [Graph] -> [Graph]
|
||||||
@ -151,16 +167,16 @@ constraint :: Attr -> MaxDivergence -> Int -- ^ required number of consistent at
|
|||||||
constraint attr div req (ind, (fulfill, constr), _) newNode =
|
constraint attr div req (ind, (fulfill, constr), _) newNode =
|
||||||
let
|
let
|
||||||
--TODO: UGLY hack... this has to be somewhere .. -.-
|
--TODO: UGLY hack... this has to be somewhere .. -.-
|
||||||
posInf = read "Infinity" :: Double
|
! posInf = read "Infinity" :: Double
|
||||||
negInf = read "-Infinity" :: Double
|
! negInf = read "-Infinity" :: Double
|
||||||
-- convert into Vector of new Indices after appending new node-index
|
-- 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 :: (DIM2 -> Double) -> DIM2 -> Double
|
||||||
updateConstr f sh@(Z:.i:.c) =
|
updateConstr f sh@(Z:.i:.c) =
|
||||||
let
|
let
|
||||||
slice = A.slice attr (A.Any :. i)
|
! 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)
|
! 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)
|
! maxs = A.traverse slice id (\g sh'@(Z :. j)-> if V.any (==j) totalInd then (g sh') else negInf)
|
||||||
|
|
||||||
in
|
in
|
||||||
-- trace (show i P.++ show (A.toList slice) P.++ show c P.++ "\n " P.++ show (A.foldAllS (max) negInf $ maxs)) $
|
-- 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
|
$A.zipWith (\thediv dist -> abs dist <= thediv) div $A.foldS (-) 0 constrNew
|
||||||
! nrHit = A.foldAllS (+) (0::Int) $A.map fromIntegral fulfillNew
|
! 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))-}
|
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
|
-- updates the density of a graph extended by a single node
|
||||||
updateDensity :: Adj -- ^ global adjacency matrix of all nodes
|
updateDensity :: Adj -- ^ global adjacency matrix of all nodes
|
||||||
@ -225,8 +241,8 @@ addPoint :: Adj -- ^ global adjacency matrix of all nodes
|
|||||||
-> Maybe Graph
|
-> Maybe Graph
|
||||||
addPoint adj attr d div req g@(nodes, _, dens) n =
|
addPoint adj attr d div req g@(nodes, _, dens) n =
|
||||||
let
|
let
|
||||||
constr = constraint attr div req g n
|
(! constr,! densNew) = (constraint attr div req g n,updateDensity adj nodes n dens)
|
||||||
densNew = updateDensity adj nodes n dens
|
-- +|| (parTuple2 rdeepseq rdeepseq)
|
||||||
in
|
in
|
||||||
case constr of
|
case constr of
|
||||||
Nothing -> Nothing
|
Nothing -> Nothing
|
||||||
@ -234,7 +250,7 @@ addPoint adj attr d div req g@(nodes, _, dens) n =
|
|||||||
--trace (B.unpack $ outputArray constr) $
|
--trace (B.unpack $ outputArray constr) $
|
||||||
case densNew >= d of
|
case densNew >= d of
|
||||||
True -> Just {-$ trace ("submitting graph:\n================\n " P.++ (B.unpack $ outputGraph [(A.computeS $nodes ++ A.fromListUnboxed (ix1 1) [n], c, densNew)])) -}
|
True -> Just {-$ 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
|
False -> Nothing
|
||||||
|
|
||||||
reduceDim :: (A.Shape sh, Integral a) => (sh :. a) -> sh
|
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
|
-- | yields all valid addititons (=neighbours) to a Graph
|
||||||
addablePoints :: Adj -> Graph -> Vector A.U Bool
|
addablePoints :: Adj -> Graph -> Vector A.U Bool
|
||||||
addablePoints adj (ind,_,_) = A.computeS $
|
addablePoints adj (ind,_,_) = A.computeUnboxedS $
|
||||||
(A.traverse
|
(A.traverse
|
||||||
adj
|
adj
|
||||||
reduceDim
|
reduceDim
|
||||||
|
240
src/Main.hs
240
src/Main.hs
@ -42,7 +42,7 @@ import qualified Data.Stream as S
|
|||||||
import qualified Data.Text as T
|
import qualified Data.Text as T
|
||||||
import Data.Text.Encoding
|
import Data.Text.Encoding
|
||||||
import qualified Data.Vector.Unboxed as V
|
import qualified Data.Vector.Unboxed as V
|
||||||
import Debug.Trace
|
--import Debug.Trace
|
||||||
import System.Environment
|
import System.Environment
|
||||||
import System.Exit (exitFailure, exitSuccess)
|
import System.Exit (exitFailure, exitSuccess)
|
||||||
import Test.QuickCheck.All (quickCheckAll)
|
import Test.QuickCheck.All (quickCheckAll)
|
||||||
@ -120,20 +120,21 @@ emptyLine a
|
|||||||
doCalculation adj attr =
|
doCalculation adj attr =
|
||||||
let
|
let
|
||||||
dens = 0.75
|
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
|
delta = 2
|
||||||
(adj_, graph_) = preprocess adj attr {--0.8--} omega delta
|
(adj_, graph_) = preprocess adj attr {--0.8--} omega delta
|
||||||
in
|
in
|
||||||
B.concat $
|
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 $ 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
|
where
|
||||||
|
-- don't print out seeds
|
||||||
doAll [] _ _ _ _ _ = []
|
doAll [] _ _ _ _ _ = []
|
||||||
doAll gs a b c d e = doAll' (step gs a b c d e) a b c d e
|
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' [] _ _ _ _ _ = []
|
||||||
doAll' gs a b c d e = gs ++ doAll' (step gs a b c d e) a b c d e
|
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
|
-- | convinience debug-function. Needs to be
|
||||||
-- changed to return () to disable Debug.
|
-- changed to return () to disable Debug.
|
||||||
debug a = putStrLn a
|
debug a = return () --putStrLn a
|
||||||
|
|
||||||
|
|
||||||
-- | The main-function to bootstrap our application
|
-- | The main-function to bootstrap our application
|
||||||
@ -226,5 +227,230 @@ main = do
|
|||||||
|
|
||||||
----- CALCULATE & OUTPUT
|
----- CALCULATE & OUTPUT
|
||||||
|
|
||||||
debug $ "Before: " ++ show (sumAllS graph)
|
--debug $ "Before: " ++ show (sumAllS graph)
|
||||||
B.putStr $ doCalculation graph attr
|
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
|
||||||
|
=========================================================
|
||||||
|
|
||||||
|
-}
|
Loading…
Reference in New Issue
Block a user