add parallelism

package.yaml

@@ -103,6 +103,7 @@ library:
   - contravariant
   - crawlerPubMed
   - data-time-segment
+  - deepseq
   - directory
   - duckling
   - exceptions
@@ -138,6 +139,7 @@ library:
   - natural-transformation
   - opaleye
   - pandoc
+  - parallel
   - parsec
   - patches-class
   - patches-map

src/Gargantext/Viz/Phylo.hs

@@ -22,7 +22,7 @@ one 8, e54847.
 
 -}
 
-{-# LANGUAGE DeriveGeneric     #-}
+{-# LANGUAGE DeriveGeneric, DeriveAnyClass #-}
 {-# LANGUAGE NoImplicitPrelude #-}
 {-# LANGUAGE TemplateHaskell   #-}
 {-# LANGUAGE MultiParamTypeClasses #-}
@@ -44,6 +44,8 @@ import Gargantext.Core.Utils.Prefix (unPrefix)
 import Gargantext.Text.Context (TermList)
 import Gargantext.Prelude
 
+import Control.DeepSeq
+
 --------------------
 -- | PhyloParam | --
 --------------------
@@ -161,7 +163,9 @@ data PhyloGroup =
                 , _phylo_groupLevelParents  :: [Pointer]
                 , _phylo_groupLevelChilds   :: [Pointer]
                 }
-                deriving (Generic, Show, Eq, Ord)
+                deriving (Generic, NFData, Show, Eq, Ord)
+
+-- instance NFData PhyloGroup
 
 
 -- | Level : A level of aggregation (-1 = Txt, 0 = Ngrams, 1 = Fis, [2..] = Cluster)

src/Gargantext/Viz/Phylo/Aggregates/Cluster.hs

@@ -13,11 +13,13 @@ Portability : POSIX
 {-# LANGUAGE NoImplicitPrelude #-}
 {-# LANGUAGE FlexibleContexts  #-}
 {-# LANGUAGE OverloadedStrings #-}
+{-# LANGUAGE TemplateHaskell #-}
 
 module Gargantext.Viz.Phylo.Aggregates.Cluster
   where
 
-import Data.List        (null,tail,concat,sort,intersect)
+import Control.Parallel.Strategies
+import Data.List        (null,concat,sort,intersect,(++))
 import Data.Map         (Map)
 import Data.Tuple       (fst)
 import Gargantext.Prelude
@@ -44,15 +46,17 @@ getCandidates gs = filter (\(g,g') -> (not . null) $ intersect (getGroupNgrams g
 graphToClusters :: Cluster -> GroupGraph -> [PhyloCluster]
 graphToClusters clust (nodes,edges) = case clust of
       Louvain (LouvainParams _)      -> undefined
-      RelatedComponents (RCParams _) -> relatedComp 0 (head' "graphToClusters" nodes) (tail nodes,edges) [] []
+      RelatedComponents (RCParams _) -> relatedComp $ ((map (\((g,g'),_) -> [g,g']) edges) ++ (map (\g -> [g]) nodes))
       _                              -> panic "[ERR][Viz.Phylo.Aggregates.Cluster.graphToClusters] not implemented"
 
 
 -- | To transform a list of PhyloGroups into a Graph of Proximity
 groupsToGraph :: Double -> Proximity -> [PhyloGroup] -> ([GroupNode],[GroupEdge])
 groupsToGraph nbDocs prox gs = case prox of 
-      WeightedLogJaccard (WLJParams _ sens) -> (gs, map (\(x,y) -> ((x,y), weightedLogJaccard sens nbDocs (getGroupCooc x) (getGroupCooc y) (getGroupNgrams x) (getGroupNgrams y)))
-                                                  $ getCandidates gs)
+      WeightedLogJaccard (WLJParams _ sens) -> (gs, let candidates  = map (\(x,y) -> ((x,y), weightedLogJaccard sens nbDocs (getGroupCooc x) (getGroupCooc y) (getGroupNgrams x) (getGroupNgrams y)))
+                                                                    $ getCandidates gs
+                                                        candidates' = candidates `using` parList rdeepseq
+                                                    in  candidates' )
       Hamming (HammingParams _)             -> (gs, map (\(x,y) -> ((x,y), hamming (getGroupCooc x) (getGroupCooc y))) $ getCandidates gs)
       _                                     -> undefined     
 
@@ -80,7 +84,9 @@ phyloToClusters lvl clus p = Map.fromList
     --------------------------------------
     graphs :: [([GroupNode],[GroupEdge])]
     graphs = traceGraph lvl (getThreshold prox)
-            $ map (\prd -> groupsToGraph (periodsToNbDocs [prd] p) prox (getGroupsWithFilters lvl prd p)) periods 
+           $ let gs  = map (\prd -> groupsToGraph (periodsToNbDocs [prd] p) prox (getGroupsWithFilters lvl prd p)) periods
+                 gs' = gs `using` parList rdeepseq
+             in  gs'
     --------------------------------------
     prox :: Proximity
     prox = getProximity clus
@@ -115,7 +121,3 @@ traceGraphFiltered lvl g = trace ( "----\nClustering in Phylo" <> show (lvl) <>
                                                          <> show (percentile 90 (VS.fromList lst)) <> " (90%)\n") g
   where 
     lst = sort $ map snd $ concat $ map snd g 
-
-
--- traceSim :: PhyloGroup -> PhyloGroup  -> Phylo -> Double -> Double
--- traceSim g g' p sim = trace (show (getGroupText g p) <> " [vs] " <>  show (getGroupText g' p) <> " = " <> show (sim) <> "\n") sim

src/Gargantext/Viz/Phylo/BranchMaker.hs

@@ -17,6 +17,7 @@ Portability : POSIX
 module Gargantext.Viz.Phylo.BranchMaker
   where
 
+import Control.Parallel.Strategies
 import Control.Lens     hiding (both, Level)
 import Data.List        (concat,nub,(++),tail,sortOn,take,reverse,sort,null,intersect,union)
 import Data.Map         (Map)
@@ -82,13 +83,14 @@ findSimBranches frame thr nth p (id,gs) bs
     pks = getGroupsPeaks gs nth p
     --------------------------------------
 
+
 findBestPointer :: Phylo -> Proximity -> [PhyloGroup] -> [PhyloGroup] -> [(PhyloGroupId,Pointer)]
-findBestPointer p prox gs gs' = take 1
-                              $ reverse 
-                              $ sortOn (snd . snd) 
-                              $ concat
-                              $ map (\g -> let pts = findBestCandidates' prox gs' g p
+findBestPointer p prox gs gs' =
+  let candidates  = map (\g -> let pts = findBestCandidates' prox gs' g p
                                in map (\pt -> (getGroupId g,pt)) pts) gs
+      candidates' = candidates `using` parList rdeepseq
+  in take 1 $ reverse $ sortOn (snd . snd) $ concat candidates' 
+
 
 makeBranchLinks :: Phylo -> Proximity -> (PhyloBranchId,[PhyloGroup]) -> [(PhyloBranchId,[PhyloGroup])] -> [(PhyloGroupId,Pointer)] -> [(PhyloGroupId,Pointer)]
 makeBranchLinks p prox (id,gs) bs pts
@@ -126,34 +128,22 @@ linkPhyloBranches lvl prox p = setPhyloBranches lvl
 
 
 -- | To transform a PhyloGraph into a list of PhyloBranches by using the relatedComp clustering
-graphToBranches :: Level -> GroupGraph -> Phylo -> [(Int,PhyloGroupId)]
-graphToBranches _lvl (nodes,edges) _p = concat
+graphToBranches :: [PhyloGroup] -> Phylo -> [(Int,PhyloGroupId)]
+graphToBranches groups p = concat
                          $ map (\(idx,gs) -> map (\g -> (idx,getGroupId g)) gs)
                          $ zip [1..]
-                                    $ relatedComp 0 (head' "branchMaker" nodes) (tail nodes,edges) [] []
-
-
-
--- | To build a graph using the parents and childs pointers
-makeGraph :: [PhyloGroup] -> Phylo -> GroupGraph
-makeGraph gs p = (gs,edges)
-  where 
-    edges :: [GroupEdge]
-    edges = (nub . concat) 
-          $ map (\g -> (map (\g' -> ((g',g),1)) $ getGroupParents g p)
-                       ++
-                       (map (\g' -> ((g,g'),1)) $ getGroupChilds g p)) gs
+                         $ relatedComp
+                         $ map (\g -> nub $ [g] ++ (getGroupParents g p) ++ (getGroupChilds g p)) groups
 
 
 -- | To set all the PhyloBranches for a given Level in a Phylo
 setPhyloBranches :: Level -> Phylo -> Phylo
-setPhyloBranches lvl p = alterGroupWithLevel (\g -> let bIdx = (fst $ head' "branchMaker" $ filter (\b -> snd b == getGroupId g) bs)
+setPhyloBranches lvl p = alterGroupWithLevel (\g -> 
+  let bIdx = (fst $ head' "branchMaker" 
+                  $ filter (\b -> snd b == getGroupId g) branches)
   in  over (phylo_groupBranchId) (\_ -> Just (lvl,bIdx)) g) lvl p
   where 
     --------------------------------------
-    bs :: [(Int,PhyloGroupId)]
-    bs = graphToBranches lvl graph p
-    --------------------------------------
-    graph :: GroupGraph
-    graph = makeGraph (getGroupsWithLevel lvl p) p
+    branches :: [(Int,PhyloGroupId)]
+    branches = graphToBranches (getGroupsWithLevel lvl p) p
     --------------------------------------

src/Gargantext/Viz/Phylo/Example.hs

@@ -105,7 +105,7 @@ queryEx = "title=Cesar et Cleôpatre"
 
 phyloQueryBuild :: PhyloQueryBuild
 phyloQueryBuild = PhyloQueryBuild "Cesar et Cleôpatre" "An example of Phylomemy (french without accent)"
-             5 3 defaultFis [] [] (WeightedLogJaccard $ WLJParams 0.1 20) 5 0.5 4 2 (RelatedComponents $ RCParams $ WeightedLogJaccard $ WLJParams 0.3 0) 
+             5 3 defaultFis [] [] (WeightedLogJaccard $ WLJParams 0.6 20) 5 0.5 4 2 (RelatedComponents $ RCParams $ WeightedLogJaccard $ WLJParams 0.4 0) 
 
 
 

src/Gargantext/Viz/Phylo/LevelMaker.hs

@@ -19,6 +19,7 @@ Portability : POSIX
 module Gargantext.Viz.Phylo.LevelMaker
   where
 
+import Control.Parallel.Strategies
 import Control.Lens                 hiding (both, Level)
 import Data.List                    ((++), sort, concat, nub, zip, last)
 import Data.Map                     (Map, (!), empty, singleton)
@@ -61,7 +62,10 @@ instance PhyloLevelMaker PhyloCluster
       | otherwise = panic ("[ERR][Viz.Phylo.Example.addPhyloLevel] No process declared for adding Clusters at level < 2")
     --------------------------------------
     -- | Level -> (Date,Date) -> [Cluster] -> Map (Date,Date) [Cluster] -> Phylo -> [PhyloGroup]
-    toPhyloGroups lvl (d,d') l m p = map (\(idx,cluster) -> clusterToGroup (d,d') lvl idx "" cluster m p) $ zip [1..] l
+    toPhyloGroups lvl (d,d') l m p = 
+      let clusters  = map (\(idx,cluster) -> clusterToGroup (d,d') lvl idx "" cluster m p) $ zip [1..] l
+          clusters' = clusters `using` parList rdeepseq
+      in  clusters'
     --------------------------------------
 
 
@@ -74,7 +78,10 @@ instance PhyloLevelMaker PhyloFis
       | otherwise = panic ("[ERR][Viz.Phylo.Example.addPhyloLevel] No process declared for adding Fis at level <> 1")
     --------------------------------------
     -- | Level -> (Date,Date) -> [Fis] -> Map (Date,Date) [Fis] -> Phylo -> [PhyloGroup]
-    toPhyloGroups lvl (d,d') l _ p = map (\(idx,fis) -> cliqueToGroup (d,d') lvl idx "" fis p) $ zip [1..] l
+    toPhyloGroups lvl (d,d') l _ p =
+      let groups  = map (\(idx,fis) -> cliqueToGroup (d,d') lvl idx "" fis p) $ zip [1..] l
+          groups' = groups `using` parList rdeepseq
+      in  groups' 
     --------------------------------------
 
 
@@ -87,8 +94,7 @@ instance PhyloLevelMaker Document
       | otherwise = panic ("[ERR][Viz.Phylo.Example.addPhyloLevel] No process declared for adding Documents at level <> 0")
     --------------------------------------
     -- | Level -> (Date,Date) -> [Document] -> Map (Date,Date) [Fis] -> Phylo -> [PhyloGroup]
-    toPhyloGroups lvl (d,d') l _m p = map (\(idx,ngram) -> ngramsToGroup (d,d') lvl idx ngram [ngram] p)
-                                          $ zip [1..]
+    toPhyloGroups lvl (d,d') l _m p = map (\ngram -> ngramsToGroup (d,d') lvl (getIdxInRoots ngram p) ngram [ngram] p)
                                           $ (nub . concat)
                                           $ map text l
     --------------------------------------
@@ -100,11 +106,13 @@ clusterToGroup prd lvl idx lbl groups _m p =
     PhyloGroup ((prd, lvl), idx) lbl ngrams empty 
       Nothing
       (getMiniCooc (listToFullCombi ngrams) (periodsToYears [prd]) (getPhyloCooc p))
-      [] [] [] childs
+      ascLink desLink [] childs
       where
         --------------------------------------
         childs :: [Pointer]
         childs = map (\g -> (getGroupId g, 1)) groups
+        ascLink = concat $ map getGroupPeriodParents groups 
+        desLink = concat $ map getGroupPeriodChilds  groups        
         --------------------------------------
         ngrams :: [Int]
         ngrams = (sort . nub . concat) $ map getGroupNgrams groups
@@ -116,7 +124,7 @@ cliqueToGroup :: PhyloPeriodId -> Level -> Int -> Text -> PhyloFis -> Phylo -> P
 cliqueToGroup prd lvl idx lbl fis p =
     PhyloGroup ((prd, lvl), idx) lbl ngrams (singleton "support" (fromIntegral $ getSupport fis)) Nothing
     (getMiniCooc (listToFullCombi ngrams) (periodsToYears [prd]) (getPhyloCooc p))
-    [] [] [] []
+    [] [] [] childs
       where
         --------------------------------------
         ngrams :: [Int]
@@ -124,6 +132,9 @@ cliqueToGroup prd lvl idx lbl fis p =
                       $ Set.toList
                       $ getClique fis
         --------------------------------------
+        childs :: [Pointer]
+        childs = map (\n -> (((prd, lvl - 1), n),1)) ngrams
+        --------------------------------------
 
 
 -- | To transform a list of Ngrams into a PhyloGroup
@@ -152,6 +163,7 @@ toNthLevel lvlMax prox clus p
                   $ traceBranches (lvl + 1)
                   $ setPhyloBranches (lvl + 1)
                   $ transposePeriodLinks (lvl + 1)
+                  $ tracePhyloN (lvl + 1)
                   $ setLevelLinks (lvl, lvl + 1)
                   $ addPhyloLevel (lvl + 1)
                     (clusters) p
@@ -169,15 +181,15 @@ toNthLevel lvlMax prox clus p
 toPhylo1 :: Cluster -> Proximity -> Map (Date, Date) [Document] -> Phylo -> Phylo
 toPhylo1 clus prox d p = case clus of
   Fis (FisParams k s t) -> traceReBranches 1 
-                       $ linkPhyloBranches 1 prox
+                       -- $ linkPhyloBranches 1 prox
                        $ traceBranches 1 
                        $ setPhyloBranches 1
                        $ traceTempoMatching Descendant 1
                        $ interTempoMatching Descendant 1 prox
                        $ traceTempoMatching Ascendant 1
                        $ interTempoMatching Ascendant 1 prox
+                       $ tracePhylo1
                        $ setLevelLinks (0,1)
-                       $ setLevelLinks (1,0)
                        $ addPhyloLevel 1 phyloFis phylo'
     where
       --------------------------------------
@@ -212,7 +224,7 @@ instance PhyloMaker [(Date, Text)]
         phylo1 = toPhylo1 (getContextualUnit q) (getInterTemporalMatching q) phyloDocs phylo0
         --------------------------------------
         phylo0 :: Phylo
-        phylo0 = toPhylo0 phyloDocs phyloBase
+        phylo0 = tracePhylo0 $ toPhylo0 phyloDocs phyloBase
         --------------------------------------
         phyloDocs :: Map (Date, Date) [Document]
         phyloDocs = corpusToDocs c phyloBase
@@ -251,7 +263,7 @@ instance PhyloMaker [Document]
         phylo1 = toPhylo1 (getContextualUnit q) (getInterTemporalMatching q) phyloDocs phylo0
         --------------------------------------
         phylo0 :: Phylo
-        phylo0 = toPhylo0 phyloDocs phyloBase
+        phylo0 = tracePhylo0 $ toPhylo0 phyloDocs phyloBase
         --------------------------------------
         phyloDocs :: Map (Date, Date) [Document]
         phyloDocs = corpusToDocs c phyloBase
@@ -286,13 +298,16 @@ instance PhyloMaker [Document]
 
 
 tracePhylo0 :: Phylo -> Phylo 
-tracePhylo0 p = trace ("\n---------------\n--| Phylo 0 |--\n---------------\n\n") p
+tracePhylo0 p = trace ("\n---------------\n--| Phylo 0 |--\n---------------\n\n"
+                      <> show (length $ getGroupsWithLevel 0 p) <> " groups created \n") p
 
 tracePhylo1 :: Phylo -> Phylo 
-tracePhylo1 p = trace ("\n---------------\n--| Phylo 1 |--\n---------------\n\n") p
+tracePhylo1 p = trace ("\n---------------\n--| Phylo 1 |--\n---------------\n\n"
+                      <> show (length $ getGroupsWithLevel 1 p) <> " groups created \n") p
 
 tracePhyloN :: Level -> Phylo -> Phylo
-tracePhyloN lvl p = trace ("\n---------------\n--| Phylo " <> show (lvl) <> " |--\n---------------\n\n") p
+tracePhyloN lvl p = trace ("\n---------------\n--| Phylo " <> show (lvl) <> " |--\n---------------\n\n"
+                      <> show (length $ getGroupsWithLevel lvl p) <> " groups created \n") p
 
 
 tracePhyloBase :: Phylo -> Phylo

src/Gargantext/Viz/Phylo/Metrics/Clustering.hs

@@ -18,36 +18,20 @@ module Gargantext.Viz.Phylo.Metrics.Clustering
   where
 
 import Data.Graph.Clustering.Louvain.CplusPlus
-import Data.List        (last,concat,null,nub,(++),init,tail,elemIndex,groupBy,(!!))
+import Data.List        (concat,null,nub,(++),elemIndex,groupBy,(!!), (\\), union, intersect)
 import Data.Map         (fromList,mapKeys)
 import Gargantext.Prelude
 import Gargantext.Viz.Phylo
-import Gargantext.Viz.Phylo.Tools
-
--- | To apply the related components method to a PhyloGraph
--- curr = the current PhyloGroup 
--- (nodes,edges) = the initial PhyloGraph minus the current PhyloGroup
--- next = the next PhyloGroups to be added in the cluster  
--- memo = the memory of the allready created clusters
-relatedComp :: Int -> PhyloGroup -> GroupGraph -> [PhyloGroup] -> [[PhyloGroup]] -> [[PhyloGroup]]
-relatedComp idx curr (nodes,edges) next memo
-  | null nodes' && null next' = memo'
-  | (not . null) next'        = relatedComp  idx      (head' "relatedComp1" next' ) (nodes'     ,edges) (tail next') memo'
-  | otherwise                 = relatedComp (idx + 1) (head' "relatedComp2" nodes') (tail nodes',edges) []           memo'
-  where
-    --------------------------------------
-    memo' :: [[PhyloGroup]]
-    memo' 
-      | null memo                  = [[curr]]
-      | idx == ((length memo) - 1) = (init memo) ++ [(last memo) ++ [curr]]
-      | otherwise                  = memo ++ [[curr]]
-    --------------------------------------
-    next' :: [PhyloGroup]
-    next' = filter (\x -> not $ elem x $ concat memo) $ nub $ next ++ (getNeighbours False curr edges)
-    --------------------------------------
-    nodes' :: [PhyloGroup]
-    nodes' = filter (\x -> not $ elem x next') nodes
-    --------------------------------------
+
+relatedComp :: [[PhyloGroup]] -> [[PhyloGroup]]
+relatedComp graphs = foldl' (\mem groups -> 
+  if (null mem)
+  then mem ++ [groups]
+  else 
+    let related = filter (\groups' -> (not . null) $ intersect groups groups') mem
+    in if (null related)
+       then mem ++ [groups]
+       else (mem \\ related) ++ [union groups (nub $ concat related)] ) [] graphs
 
 
 louvain :: ([GroupNode],[GroupEdge]) -> IO [[PhyloGroup]]

src/Gargantext/Viz/Phylo/Tools.hs

@@ -110,6 +110,13 @@ listToDirectedCombi :: Eq a => [a] -> [(a,a)]
 listToDirectedCombi l = [(x,y) | x <- l, y <- l, x /= y]
 
 
+listToEqualCombi :: Eq a => [a] -> [(a,a)]
+listToEqualCombi l = [(x,y) | x <- l, y <- l, x == y]
+
+listToPairs :: Eq a => [a] -> [(a,a)]
+listToPairs l = (listToEqualCombi l) ++ (listToUnDirectedCombi l)
+
+
 -- | To get all combinations of a list and apply a function to the resulting list of pairs
 listToDirectedCombiWith :: Eq a => forall b. (a -> b) -> [a] -> [(b,b)]
 listToDirectedCombiWith f l = [(f x,f y) | x <- l, y <- l, x /= y]
@@ -195,6 +202,9 @@ getPhyloDescription p = _q_phyloTitle $ _phyloParam_query $ getPhyloParams p
 getPhyloMatchingFrame :: Phylo -> Int
 getPhyloMatchingFrame p = _q_interTemporalMatchingFrame $ _phyloParam_query $ getPhyloParams p
 
+getPhyloProximity :: Phylo -> Proximity
+getPhyloProximity p = _q_interTemporalMatching $ _phyloParam_query $ getPhyloParams p
+
 getPhyloReBranchThr :: Phylo -> Double
 getPhyloReBranchThr p = _q_reBranchThr $ _phyloParam_query $ getPhyloParams p
 

stack.yaml

@@ -35,6 +35,7 @@ extra-deps:
 - KMP-0.1.0.2
 - accelerate-1.2.0.0
 - aeson-lens-0.5.0.0
+- deepseq-th-0.1.0.4
 - duckling-0.1.3.0
 - full-text-search-0.2.1.4
 - fullstop-0.1.4