Drop accelerate-llvm dependency

This also changes the cabal.project to not pull the accelerate-llvm or
the llvm-hs dependencies.

bin/update-project-dependencies

@@ -18,8 +18,8 @@ fi
 # with the `sha256sum` result calculated on the `cabal.project` and
 # `cabal.project.freeze`. This ensures the files stay deterministic so that CI
 # cache can kick in.
-expected_cabal_project_hash="ac293a4c66092996bc85fbf14ef34b7cce3ed5b0612ceb9e1a5f395059631e0b"
-expected_cabal_project_freeze_hash="32310c4d4e7b4679dcb90dcfcd0d6d1b175dbf885a77ffddca16d422998a521c"
+expected_cabal_project_hash="ecf81ae67d3b7adbaf579187cc06592ed2cb0db625d16f69de8f16fa1bd3a2a1"
+expected_cabal_project_freeze_hash="50f40d4fc0190b8e8645e2de3c3d40ddb3664339e7995f52f883d925685a9a49"
 
 
 cabal --store-dir=$STORE_DIR v2-build --dry-run

cabal.project

@@ -5,6 +5,7 @@ index-state: 2024-09-12T03:02:26Z
 
 with-compiler: ghc-9.4.8
 optimization: 2
+benchmarks: False
 
 packages:
     ./
@@ -14,13 +15,6 @@ source-repository-package
     location: https://github.com/AccelerateHS/accelerate.git
     tag: 334d05519436bb7f20f9926ec76418f5b8afa359
 
-source-repository-package
-    type: git
-    location: https://github.com/AccelerateHS/accelerate-llvm.git
-    tag: 2b5d69448557e89002c0179ea1aaf59bb757a6e3
-    subdir: accelerate-llvm-native/
-            accelerate-llvm/
-
 -- Patch for "Allow NOT to backtrack"
 source-repository-package
     type: git
@@ -32,13 +26,6 @@ source-repository-package
     location: https://gitlab.iscpif.fr/gargantext/opaleye-textsearch.git
     tag: 04b5c9044fef44393b66bffa258ca0b0f59c1087
 
-source-repository-package
-    type: git
-    location: https://github.com/adinapoli/llvm-hs.git
-    tag: 7533a9ccd3bfe77141745f6b61039a26aaf5c83b
-    subdir: llvm-hs
-            llvm-hs-pure
-
 source-repository-package
     type: git
     location: https://github.com/alpmestan/accelerate-arithmetic.git

cabal.project.freeze

@@ -26,8 +26,6 @@ constraints: any.Boolean ==0.2.4,
              any.accelerate ==1.3.0.0,
              accelerate +bounds-checks -debug -internal-checks -nofib -unsafe-checks,
              any.accelerate-arithmetic ==1.0.0.1,
-             any.accelerate-llvm ==1.3.0.0,
-             any.accelerate-llvm-native ==1.3.0.0,
              any.accelerate-utility ==1.0.0.1,
              any.adjunctions ==4.4.2,
              any.aeson ==2.1.2.1,
@@ -308,9 +306,6 @@ constraints: any.Boolean ==0.2.4,
              any.linear ==1.23,
              linear -herbie +template-haskell,
              any.list-t ==1.0.5.7,
-             any.llvm-hs ==12.0.0,
-             llvm-hs -debug -llvm-with-rtti +shared-llvm,
-             any.llvm-hs-pure ==12.0.0,
              any.lockfree-queue ==0.2.4,
              any.logict ==0.8.1.0,
              any.loop ==0.3.0,

gargantext.cabal

@@ -100,6 +100,10 @@ flag no-phylo-debug-logs
   default: False
   manual: True
 
+flag enable-benchmarks
+  default: False
+  manual: True
+
 library
   import:
     defaults
@@ -493,7 +497,6 @@ library
     , MonadRandom ^>= 0.6
     , QuickCheck ^>= 2.14.2
     , accelerate ^>= 1.3.0.0
-    , accelerate-llvm-native ^>= 1.3.0.0
     , aeson ^>= 2.1.2.1
     , ansi-terminal
     , array ^>= 0.5.4.0
@@ -712,7 +715,6 @@ common testDependencies
       base >=4.7 && <5
     , QuickCheck ^>= 2.14.2
     , accelerate >= 1.3.0.0
-    , accelerate-llvm-native
     , aeson ^>= 2.1.2.1
     , aeson-qq
     , async ^>= 2.2.4

src/Gargantext/Core/Methods/Similarities.hs

@@ -20,10 +20,11 @@ import Data.Swagger
 import Data.Text (Text)
 import GHC.Generics (Generic)
 import Gargantext.Core.Methods.Similarities.Accelerate.Conditional (measureConditional')
-import Gargantext.Core.Methods.Similarities.Accelerate.Distributional (logDistributional2)
+import Gargantext.Core.LinearAlgebra.Operations (accelerate2MassivMatrix, massiv2AccelerateMatrix)
+import Gargantext.Core.LinearAlgebra.Distributional (logDistributional2)
 -- import Gargantext.Core.Text.Metrics.Count (coocOn)
 -- import Gargantext.Core.Viz.Graph.Index
-import Gargantext.Prelude (Ord, Eq, Int, Double, Show, map)
+import Gargantext.Prelude (Ord, Eq, Int, Double, Show, map, ($), (.))
 import Prelude (Enum, Bounded, minBound, maxBound)
 import Test.QuickCheck (elements)
 import Test.QuickCheck.Arbitrary
@@ -36,7 +37,7 @@ data Similarity = Conditional | Distributional
 
 measure :: Similarity -> Matrix Int -> Matrix Double
 measure Conditional    x = measureConditional' x
-measure Distributional x = logDistributional2 x
+measure Distributional x = massiv2AccelerateMatrix . logDistributional2 . accelerate2MassivMatrix $ x
 
 ------------------------------------------------------------------------
 withMetric :: GraphMetric -> Similarity

src/Gargantext/Core/Methods/Similarities/Accelerate/Distributional.hs

@@ -103,8 +103,7 @@ module Gargantext.Core.Methods.Similarities.Accelerate.Distributional
 -- import qualified Data.Foldable as P (foldl1)
 -- import Debug.Trace (trace)
 import Data.Array.Accelerate as A
--- import Data.Array.Accelerate.Interpreter (run)
-import Data.Array.Accelerate.LLVM.Native qualified as LLVM -- TODO: try runQ?
+import Data.Array.Accelerate.Interpreter qualified as Naive
 import Gargantext.Core.Methods.Matrix.Accelerate.Utils
 
 import qualified Prelude
@@ -146,7 +145,7 @@ import qualified Prelude
 -- /IMPORTANT/: As this function computes the diagonal matrix in order to carry on the computation
 -- the input has to be a square matrix, or this function will fail at runtime.
 distributional :: Matrix Int -> Matrix Double
-distributional = distributionalWith LLVM.run
+distributional = distributionalWith Naive.run
 
 distributionalWith :: (Elt e, FromIntegral Int e, Eq e, Prelude.Fractional (Exp e), Ord e)
                    => (forall a. Arrays a => Acc a -> a)
@@ -183,7 +182,7 @@ distributionalWith interpret m' = interpret $ result
     result = termDivNan z_1 z_2
 
 logDistributional2 :: Matrix Int -> Matrix Double
-logDistributional2 m = logDistributional2With LLVM.run m
+logDistributional2 m = logDistributional2With Naive.run m
 
 logDistributional2With :: ( Elt e
                           , Prelude.Num (Exp e)

stack.yaml

@@ -67,6 +67,7 @@
 - "linear-1.23"
 - "logict-0.8.1.0"
 - "lzma-0.0.1.1"
+- "massiv-test-1.1.0.0"
 - "math-functions-0.3.4.4"
 - "megaparsec-9.6.1"
 - "microlens-th-0.4.3.15"
@@ -440,6 +441,7 @@ flags:
   formatting:
     "no-double-conversion": false
   gargantext:
+    "enable-benchmarks": false
     "no-phylo-debug-logs": true
     "test-crypto": false
   graphviz:
@@ -509,6 +511,8 @@ flags:
     "shared-llvm": true
   lzma:
     pkgconfig: true
+  massiv:
+    "unsafe-checks": false
   "math-functions":
     "system-erf": true
     "system-expm1": true
@@ -557,6 +561,9 @@ flags:
   prettyprinter:
     buildreadme: false
     text: true
+  "quickcheck-classes-base":
+    "binary-laws": true
+    "unary-laws": true
   "quickcheck-instances":
     "bytestring-builder": false
   reflection:

test/Test/Core/LinearAlgebra.hs

@@ -124,8 +124,6 @@ testMatrix_04 = SquareMatrix $ fromList (Z :. 8 :. 8) $
 -- Main test runner
 --
 
--- | Needed as the LLVM and Naive backend generates some double with a long exponent which
--- won't compare verbatim.
 tests :: TestTree
 tests = testGroup "LinearAlgebra" [
       testProperty "createIndices roundtrip" (compareImplementations (LA.createIndices @Int @Int) Legacy.createIndices mapCreateIndices)