Add basic benchmarks

bench/Main.hs

 {-# LANGUAGE TypeApplications  #-}
+{-# LANGUAGE OverloadedStrings #-}
 
 module Main where
 
@@ -9,9 +10,14 @@ import Gargantext.Core.Viz.Phylo.API.Tools (readPhylo)
 import Gargantext.Core.Viz.Phylo.PhyloMaker (toPhylo)
 import Gargantext.Core.Viz.Phylo.PhyloTools
 import Gargantext.Prelude.Crypto.Auth (createPasswordHash)
+import qualified Gargantext.Core.LinearAlgebra as LA
+import qualified Gargantext.Core.Methods.Similarities.Accelerate.Distributional as Accelerate
 
 import Test.Tasty.Bench
 import Paths_gargantext
+import qualified Data.Array.Accelerate as A
+import qualified Data.Massiv.Array as Massiv
+import qualified Data.Array.Accelerate.Interpreter as Naive
 
 phyloConfig :: PhyloConfig
 phyloConfig = PhyloConfig {
@@ -37,6 +43,28 @@ phyloConfig = PhyloConfig {
   , exportFilter = [ByBranchSize {_branch_size = 3.0}]
   }
 
+testMatrix :: A.Matrix Int
+testMatrix = A.fromList (A.Z A.:. 14 A.:. 14) $
+  [  30,  36, -36, -16,   0,   7,  34,  -7,   5,  -4,   0,  21,   6, -35,
+      0, -31,  20, -15, -22,  -7, -22, -37, -29, -29,  23, -31, -29, -23,
+    -24, -29,  19,  -6,  16,   7,  15, -27, -27, -30,  -9, -33,  18, -23,
+      7, -36,  12,  26, -17,  -3,  -2, -15,  -4,  26,  24,   9,  -4,   4,
+     32,  28,  -2, -10,  34,  -3,  20,  -9, -22,  20, -26,  34,  18, -21,
+      7, -12,  12,  -2,  36,  10,  34, -37,  13,  -9, -28,  34,  33, -18,
+     -4, -32,  -1,  29,  29, -28,  24,  28,  35,  19,   8, -18,  25, -35,
+    -14,  -4, -24,  -1,   7,  34, -37, -28, -12, -32,  -5, -23,  27,  33,
+    -36, -28,  21, -29,  -2, -26,  -4, -31, -26, -21,  33, -11, -33,  20,
+     25,  14,   5,  -7,   5,  24,  37,   1,  -3,  23,  25, -16,  17,   5,
+    -35,  36,  -2,  -2,   1, -14,  34, -30, -10,  12,  25,  21,   0,  34,
+     17,  -1,  20, -19,  15,  20,  -5, -30, -35, -13,   5,  17, -10, -19,
+    -34, -11, -18,  26, -29, -28,   0,   3,  23,  -6,  36,   4,  16,  28,
+     13, -37, -16,   2,   7, -13,  21, -10, -33, -33, -26, -19,  -1,  29]
+{-# INLINE testMatrix #-}
+
+testMassivMatrix :: Massiv.Matrix Massiv.D Int
+testMassivMatrix = LA.accelerate2MassivMatrix testMatrix
+{-# INLINE testMassivMatrix #-}
+
 main :: IO ()
 main = do
   _issue290Phylo     <- force . setConfig phyloConfig <$> (readPhylo =<< getDataFileName "bench-data/phylo/issue-290.json")
@@ -51,5 +79,10 @@ main = do
       , bgroup "Phylo" [
           bench "toPhylo (small)" $ nf toPhylo issue290PhyloSmall
       ]
+      , bgroup "distributional" [
+          bench "Accelerate (Naive)" $ nf (Accelerate.distributionalWith @Double Naive.run) testMatrix
+      ,   bench "Accelerate (LLVM)"  $ nf Accelerate.distributional testMatrix
+      ,   bench "Massiv " $ nf (Massiv.computeAs Massiv.U . LA.distributional @Double) testMassivMatrix
+      ]
       ]
     ]

gargantext.cabal

@@ -902,6 +902,10 @@ benchmark garg-bench
       Paths_gargantext
   build-depends: base
                , bytestring ^>= 0.11.5.3
+               , accelerate
+               , accelerate-llvm
+               , massiv
+               , deepseq
                , gargantext
                , gargantext-prelude
                , tasty-bench

src/Gargantext/Core/LinearAlgebra.hs

 {-# LANGUAGE DerivingStrategies #-}
 {-# LANGUAGE ScopedTypeVariables #-}
+{-# LANGUAGE TypeApplications #-}
 {-|
 Module      : Gargantext.Core.LinearAlgebra
 Description : Linear Algebra utility functions
@@ -19,6 +20,11 @@ module Gargantext.Core.LinearAlgebra (
   -- * Functions
   , createIndices
 
+  -- * Convertion functions
+  , accelerate2MassivMatrix
+  , massiv2AccelerateMatrix
+  , massiv2AccelerateVector
+
   -- * Operations on matrixes
   , (.*)
   , diag
@@ -26,15 +32,18 @@ module Gargantext.Core.LinearAlgebra (
   , distributional
   ) where
 
+import Data.Array.Accelerate qualified as Acc
 import Data.Bimap (Bimap)
 import Data.Bimap qualified as Bimap
+import Data.List.Split qualified as Split
 import Data.Map.Strict (Map)
 import Data.Map.Strict qualified as M
+import Data.Massiv.Array (D, Matrix, Vector, Array, Ix3)
+import Data.Massiv.Array qualified as A
 import Data.Set qualified as S
 import Data.Set (Set)
 import Prelude
-import Data.Massiv.Array qualified as A
-import Data.Massiv.Array (D, Matrix, Vector, Array, Ix3)
+import Protolude.Safe (headMay)
 
 newtype Index = Index { _Index :: Int }
   deriving newtype (Eq, Show, Ord, Num, Enum)
@@ -48,6 +57,28 @@ createIndices = set2indices . map2set
     set2indices :: Ord t => Set t -> Bimap Index t
     set2indices s = foldr (uncurry Bimap.insert) Bimap.empty (zip [0..] $ S.toList s)
 
+-- | Converts an accelerate matrix into a Massiv matrix.
+accelerate2MassivMatrix :: (A.Unbox a, Acc.Elt a) => Acc.Matrix a -> Matrix D a
+accelerate2MassivMatrix m =
+  let (Acc.Z Acc.:. _r Acc.:. c) = Acc.arrayShape m
+  in A.delay $ A.fromLists' @A.U A.Par $ Split.chunksOf c (Acc.toList m)
+
+-- | Converts a massiv matrix into an accelerate matrix.
+massiv2AccelerateMatrix :: (Acc.Elt a, A.Source r a) => Matrix r a -> Acc.Matrix a
+massiv2AccelerateMatrix m =
+  let m' = A.toLists2 m
+      r  = Prelude.length m'
+      c  = maybe 0 Prelude.length (headMay m')
+  in Acc.fromList (Acc.Z Acc.:. r Acc.:. c) (mconcat m')
+
+-- | Converts a massiv vector into an accelerate one.
+massiv2AccelerateVector :: (A.Source r a, Acc.Elt a) => A.Vector r a -> Acc.Vector a
+massiv2AccelerateVector m =
+  let m' = A.toList m
+      r  = Prelude.length m'
+  in Acc.fromList (Acc.Z Acc.:. r) m'
+
+
 -- | Computes the diagnonal matrix of the input one.
 diag :: Num e => Matrix D e -> Vector D e
 diag matrix =

test/Test/Core/LinearAlgebra.hs

@@ -97,24 +97,6 @@ testMatrix_02 = SquareMatrix $ fromList (Z :. 7 :. 7) $
      13, -37, -16,   2,   7, -13,  21]
 
 
-accelerate2MassivMatrix :: (Massiv.Unbox a, Elt a) => Matrix a -> Massiv.Matrix Massiv.D a
-accelerate2MassivMatrix m =
-  let (Z :. _r :. c) = A.arrayShape m
-  in Massiv.delay $ Massiv.fromLists' @Massiv.U Massiv.Par $ Split.chunksOf c (A.toList m)
-
-massiv2AccelerateMatrix :: (Elt a, Massiv.Source r a) => Massiv.Matrix r a -> Matrix a
-massiv2AccelerateMatrix m =
-  let m' = Massiv.toLists2 m
-      r  = Prelude.length m'
-      c  = maybe 0 Prelude.length (headMay m')
-  in A.fromList (Z :. r :. c) (mconcat m')
-
-massiv2AccelerateVector :: (Massiv.Source r a, Elt a) => Massiv.Vector r a -> Vector a
-massiv2AccelerateVector m =
-  let m' = Massiv.toList m
-      r  = Prelude.length m'
-  in A.fromList (Z :. r) m'
-
 --
 -- Main test runner
 --