improve performance

app/Main.hs

@@ -16,8 +16,6 @@ import Prelude (String)
 import Protolude
 import qualified Data.IntMap                       as Dict
 import qualified Data.List as List
-import qualified Eigen.Matrix as Matrix
-import qualified Eigen.SparseMatrix as SMatrix
 import qualified Prelude as Prelude
 import qualified Data.Graph.Inductive.PatriciaTree as DGIP
 
@@ -31,9 +29,11 @@ setupEnv _    = getUnlabGraph Random
 main :: IO ()
 main = do
   fp <- getArgs
-
-  withArgs [] $
-    defaultMain
-      [ env (snd <$> setupEnv fp) $ \ ~g ->
-        bench "bench" (nf (\ x -> withG x (parts . clusteringOptim 3 Conf)) g)
-      ]
+  setupEnv fp >>= \(_, ~g) ->
+    evaluate $ withG g (clusteringOptim 3 Conf)
+  return ()
+  -- withArgs [] $
+  --   defaultMain
+  --     [ env (snd <$> setupEnv fp) $ \ ~g ->
+  --       bench "bench" (nf (\ x -> withG x (parts . clusteringOptim 3 Conf)) g)
+  --     ]

gargantext-graph.cabal

 cabal-version: 1.12
 
--- This file has been generated from package.yaml by hpack version 0.33.0.
+-- This file has been generated from package.yaml by hpack version 0.34.4.
 --
 -- see: https://github.com/sol/hpack
 --
@@ -9,8 +9,8 @@ cabal-version: 1.12
 name:           gargantext-graph
 version:        0.1.0.0
 description:    Please see the README on GitHub at <https://github.com/githubuser/gargantext-graph#readme>
-homepage:       https://github.com/https://gitlab.iscpif.fr/gargantext/gargantext-graph#readme
-bug-reports:    https://github.com/https://gitlab.iscpif.fr/gargantext/gargantext-graph/issues
+homepage:       https://github.com/gargantext/gargantext-graph#readme
+bug-reports:    https://github.com/gargantext/gargantext-graph/issues
 author:         Alexandre Delanoë
 maintainer:     alexandre+dev@delanoe.org
 copyright:      2021 CNRS / Alexandre Delanoë
@@ -23,12 +23,12 @@ extra-source-files:
 
 source-repository head
   type: git
-  location: https://github.com/https://gitlab.iscpif.fr/gargantext/gargantext-graph
+  location: https://github.com/gargantext/gargantext-graph
 
 library
   exposed-modules:
       Data.Array.Accelerate.Utils
-      Data.Eigen.Coeff
+      -- Data.Eigen.Coeff
       Graph.BAC.Clustering
       Graph.BAC.Proxemy
       Graph.BAC.ProxemyOptim
@@ -45,7 +45,10 @@ library
       Paths_gargantext_graph
   hs-source-dirs:
       src
-  default-extensions: DataKinds FlexibleInstances OverloadedStrings
+  default-extensions:
+      DataKinds
+      FlexibleInstances
+      OverloadedStrings
   build-depends:
       accelerate
     , accelerate-arithmetic
@@ -55,14 +58,16 @@ library
     , cassava
     , cereal
     , containers
-    , eigen
+    -- , eigen
     , fgl
     , haskell-igraph >=0.6.0
+    , hmatrix
     , lens
     , pretty-simple
     , protolude
     , reflection
-    , singletons
+    , singletons == 2.7
+    , sparse-linear
     , string-conversions
     , text
     , vector
@@ -86,7 +91,7 @@ executable gargantext-graph-exe
     , cereal
     , containers
     , criterion
-    , eigen
+    -- , eigen
     , fgl
     , gargantext-graph
     , haskell-igraph >=0.6.0
@@ -107,7 +112,10 @@ test-suite gargantext-graph-test
       Paths_gargantext_graph
   hs-source-dirs:
       test
-  default-extensions: DataKinds FlexibleInstances OverloadedStrings
+  default-extensions:
+      DataKinds
+      FlexibleInstances
+      OverloadedStrings
   ghc-options: -threaded -rtsopts -with-rtsopts=-N
   build-depends:
       QuickCheck
@@ -119,7 +127,7 @@ test-suite gargantext-graph-test
     , cassava
     , cereal
     , containers
-    , eigen
+    -- , eigen
     , fgl
     , gargantext-graph
     , haskell-igraph >=0.6.0

package.yaml

 name:                gargantext-graph
 version:             0.1.0.0
-github:              "https://gitlab.iscpif.fr/gargantext/gargantext-graph"
+github:              gargantext/gargantext-graph
 license:             AGPL
 author:              "Alexandre Delanoë"
 maintainer:          "alexandre+dev@delanoe.org"

src/Graph/Tools/CSV.hs

@@ -22,7 +22,6 @@ import Data.Vector hiding (map, uniq)
 import Prelude (read)
 import Protolude
 import Graph.Types
-import qualified Eigen.SparseMatrix as SMatrix
 import qualified Data.Map                          as Map
 import qualified Data.ByteString.Lazy              as BL
 import qualified Data.Graph.Inductive              as DGI

src/Graph/Tools/Import.hs

+{-# LANGUAGE TypeApplications #-}
 {-| Module      : Graph.Tools
 Description :
 Copyright   : (c) CNRS, Alexandre Delanoë
@@ -25,7 +26,7 @@ import Graph.Types
 import Graph.Tools.Random
 import Graph.Tools.CSV
 import Graph.FGL
-import qualified Eigen.SparseMatrix as SMatrix
+import qualified Data.Matrix.Sparse.Static         as SMatrix
 import qualified Data.IntMap                       as Dict
 import qualified Data.Map                          as Map
 import qualified Data.ByteString.Lazy              as BL
@@ -44,7 +45,7 @@ data GraphData = LightGraph    { lightGraph :: Graph () () }
 
 
 getGraph :: GetGraph -> IO GraphData
-getGraph Random = randomAdjacency
+getGraph Random = randomAdjacency @100
                 >>= \m -> pure $ LightGraph
                                $ mkGraphUfromEdges
                                $ List.map (\(x,y,_) -> (x,y))

src/Graph/Tools/Random.hs

@@ -6,7 +6,6 @@ Maintainer  : alexandre+dev@delanoe.org
 Stability   : experimental
 Portability : POSIX
 
-
 -}
 
 {-# LANGUAGE ConstraintKinds #-}
@@ -22,18 +21,21 @@ import Data.Vector hiding (map, uniq)
 import Prelude (read)
 import Protolude
 import Graph.Types
-import qualified Eigen.SparseMatrix                as SMatrix
-import qualified Eigen.Matrix                      as DMatrix
+-- import qualified Eigen.SparseMatrix                as SMatrix
+-- import qualified Eigen.Matrix                      as DMatrix
 import qualified Data.Graph.Inductive.PatriciaTree as DGIP
 import qualified Data.Set                          as Set
 import qualified Data.Vector                       as Vector
 
+import qualified Data.Matrix.Sparse.Static    as SMatrix
+import qualified Numeric.LinearAlgebra.Static as DMatrix
+
 -- Random Matrix
 -- | Random Matrix && Graph
 -- TODO random matrix of any size for the tests
 
-randomMatrix :: IO (MatrixD 100)
-randomMatrix = DMatrix.random
+randomMatrix :: KnownNat n => IO (MatrixD n)
+randomMatrix = DMatrix.rand
 
 {-
 matrix2graph :: forall   n
@@ -44,10 +46,12 @@ matrix2graph m = withG (mkGraphUfromEdges $ map (\(x,y,_) -> (x,y)) $ SMatrix.to
                        identity
 -}
 
-randomAdjacency :: IO (MatrixS 100)
+randomAdjacency :: KnownNat n => IO (MatrixS n)
 randomAdjacency = do
   m1 <- randomMatrix
   m2 <- randomMatrix
-  pure $ SMatrix.fromMatrix
-       $ DMatrix.imap (\i j v -> if i < j && v > 0.9 then 1 else 0)
+  pure $ SMatrix.sparsify (\(i, j) v -> if i < j && v > 0.9 then Just 1 else Nothing)
        $ DMatrix.mul m1 m2
+  -- pure $ SMatrix.fromMatrix
+  --      $ DMatrix.imapL (\(i, j) v -> if i < j && v > 0.9 then 1 else 0)
+  --      $ DMatrix.mul m1 m2

src/Graph/Types.hs

@@ -15,8 +15,12 @@ module Graph.Types where
 
 import qualified Data.Graph.Inductive.PatriciaTree as DGIP
 import Data.IntMap (IntMap)
-import qualified Eigen.Matrix as DenseMatrix
-import Eigen.SparseMatrix (SparseMatrix)
+-- import qualified Eigen.Matrix as DenseMatrix
+-- import Eigen.SparseMatrix (SparseMatrix)
+
+import qualified Data.Matrix.Sparse.Static    as Sparse
+import qualified Data.Vector.Unboxed          as VU
+import qualified Numeric.LinearAlgebra.Static as Dense
 
 -- | Main Types use in this libray
 
@@ -26,8 +30,5 @@ type Dict = IntMap
 type Graph a b = DGIP.Gr a b
 
 -- | Type for Matrix computation optimizations (with Eigen)
-type MatrixD          n = DenseMatrix.Matrix n n Double
-type MatrixS          n = SparseMatrix n n Double
-
-
-
+type MatrixD          n = Dense.L n n
+type MatrixS          n = Sparse.Matrix n n Double

stack.yaml

@@ -44,8 +44,16 @@ extra-deps:
   commit: f5c0e0071ec7b6532f9a9cd3eb33d14f340fbcc9
 - git: https://gitlab.iscpif.fr/anoe/accelerate-utility.git
   commit: 83ada76e78ac10d9559af8ed6bd4064ec81308e4
+- git: https://github.com/alpmestan/sparse-linear.git
+  commit: 785f12c99615907b207f5499dd3b70a486a0249b
+  subdirs:
+    - sparse-linear
+- git: https://github.com/alpmestan/hmatrix.git
+  commit: 39155c60c97ba8cd5c8ab9c202b428fec42faa3c
+  subdirs:
+    - packages/base
 - accelerate-arithmetic-1.0.0.1@sha256:555639232aa5cad411e89247b27871d09352b987a754230a288c690b6de6d888,2096
-- eigen-3.3.7.0@sha256:7c24a86426b238e02ba0ac2179cc44997518b443a13828ed7a791fe49a6dffa5,82060
+# - eigen-3.3.7.0@sha256:7c24a86426b238e02ba0ac2179cc44997518b443a13828ed7a791fe49a6dffa5,82060
 
 
 # Override default flag values for local packages and extra-deps
@@ -64,7 +72,6 @@ extra-deps:
 # Override the architecture used by stack, especially useful on Windows
 # arch: i386
 # arch: x86_64
-#
 # Extra directories used by stack for building
 # extra-include-dirs: [/path/to/dir]
 # extra-lib-dirs: [/path/to/dir]