elynx-tree-0.7.0.1: bench/Bench.hs
{-# LANGUAGE BangPatterns #-}
-- |
-- Module : Bench
-- Description : Various benchmarks
-- Copyright : 2021 Dominik Schrempf
-- License : GPL-3.0-or-later
--
-- Maintainer : dominik.schrempf@gmail.com
-- Stability : unstable
-- Portability : portable
--
-- Creation date: Mon Dec 16 13:33:27 2019.
module Main where
import Control.Parallel.Strategies
import Criterion.Main
import Data.Bifunctor
import Data.Foldable
import ELynx.Tools.InputOutput
import ELynx.Tree
import ELynx.Tree.Simulate.PointProcess
import Length
import Lens
import System.Random.Stateful
import Tree
treeFileMany :: FilePath
treeFileMany = "data/Many.trees"
getManyTrees :: IO (Forest Phylo Name)
getManyTrees = parseFileWith (someNewick Standard) treeFileMany
hugeTree :: IO (Tree Length Int)
hugeTree = newIOGenM (mkStdGen 0) >>= simulateReconstructedTree 50000 Random 1.0 0.9
sinN :: Int -> Length -> Length
sinN n x = iterate sin x !! n
func :: Length -> Length
func = sinN 200
hugeTreeCalcPar :: Int -> Tree Length Int -> Tree Length Int
hugeTreeCalcPar n t = first func t `using` parTree n
main :: IO ()
main = do
!ts <- getManyTrees
!ht <- first getLength <$> hugeTree
let !pht = lengthToPhyloTree ht
!ht' = flipLabels ht
mr1 = hugeTreeCalcPar 0 ht
mr2 = hugeTreeCalcPar 1 ht
if mr1 == mr2
then putStrLn "Map OK."
else do
print mr1
print mr2
error "Map wrong."
let fr1 = (foldl' (+) 0 . branches) ht
fr2 = parBranchFoldMap 3 id (+) ht
if 1e-8 > abs (fr1 - fr2)
then putStrLn "Fold OK."
else do
print fr1
print fr2
error "Fold wrong."
defaultMain
[ bgroup "bipartition" [bench "manyTrees" $ nf (map bipartitions) ts],
bgroup
"map strategies"
[ bench "sequential" $ nf (hugeTreeCalcPar 0) ht,
bench "parallel 3" $ nf (hugeTreeCalcPar 3) ht
],
bgroup
"fold strategies"
[ bench "sequential" $ nf (parBranchFoldMap 0 func (+)) ht,
bench "parallel 3" $ nf (parBranchFoldMap 3 func (+)) ht
],
-- Unsafe operations are fast, safe operations are roughly 50 percent slower.
bgroup
"length"
[ bench "length sum foldl' safe" $ nf lengthSumFoldl' [0 .. 10000000],
bench "length sum foldl' unsafe" $ nf lengthSumFoldl'Unsafe [0 .. 10000000],
bench "length sum foldl' num instance" $ nf lengthSumFoldl'NumInstance [0 .. 10000000],
bench "double sum foldl'" $ nf doubleSumFoldl' [0 .. 10000000],
bench "double sum" $ nf doubleSum [0 .. 10000000]
],
-- Lenses are fast.
bgroup
"lens"
[ bench "sum with getter" $ nf sumWithGetter [0 .. 1000000 :: Length],
bench "sum with accessor function" $ nf sumWithAccessorFunction [0 .. 1000000 :: Length],
bench "sum with setter and getter" $ nf sumWithSetter [0 .. 1000000 :: Length],
bench "sum with modify and accessor functions" $ nf sumWithModifyFunction [0 .. 1000000 :: Length]
],
bgroup
"[mono|bi][functor|foldable|traversable]"
[ bench "normal fmap tree" $ nf fmapNormalFunctor ht',
bench "mono fmap tree" $ nf fmapFunctor ht,
bench "bi fmap tree" $ nf fmapBifunctor ht,
bench "mono fold tree" $ nf totalBranchLengthFoldable ht,
bench "bi fold tree" $ nf totalBranchLengthBifoldable ht,
bench "mono traverse tree" $ nf toLengthTreeTraversable pht,
bench "bi traverse tree" $ nf toLengthTreeBitraversable pht
]
]
-- Results 2020 Nov 2, commit aee6818.
-- benchmarking bipartition/manyTrees
-- time 9.631 ms (9.583 ms .. 9.721 ms)
-- 0.998 R² (0.995 R² .. 1.000 R²)
-- mean 9.723 ms (9.670 ms .. 9.879 ms)
-- std dev 220.5 μs (87.68 μs .. 421.0 μs)
-- benchmarking map strategies/sequential
-- time 851.4 ms (666.8 ms .. 1.025 s)
-- 0.994 R² (0.978 R² .. 1.000 R²)
-- mean 735.3 ms (676.0 ms .. 766.2 ms)
-- std dev 66.42 ms (55.94 ms .. 69.47 ms)
-- variance introduced by outliers: 22% (moderately inflated)
-- benchmarking map strategies/parallel 3
-- time 362.1 ms (348.5 ms .. 377.0 ms)
-- 1.000 R² (0.999 R² .. 1.000 R²)
-- mean 354.6 ms (348.1 ms .. 358.2 ms)
-- std dev 4.959 ms (1.499 ms .. 6.727 ms)
-- variance introduced by outliers: 19% (moderately inflated)
-- benchmarking fold strategies/sequential
-- time 762.0 ms (682.7 ms .. 913.8 ms)
-- 0.995 R² (0.992 R² .. 1.000 R²)
-- mean 676.3 ms (647.5 ms .. 720.1 ms)
-- std dev 42.34 ms (11.72 ms .. 57.27 ms)
-- variance introduced by outliers: 19% (moderately inflated)
-- benchmarking fold strategies/parallel 3
-- time 413.4 ms (330.2 ms .. 536.7 ms)
-- 0.990 R² (0.972 R² .. 1.000 R²)
-- mean 368.3 ms (345.6 ms .. 394.6 ms)
-- std dev 25.80 ms (7.999 ms .. 35.08 ms)
-- variance introduced by outliers: 20% (moderately inflated)
-- benchmarking length/length sum foldl' safe
-- time 123.4 ms (117.8 ms .. 136.4 ms)
-- 0.993 R² (0.986 R² .. 1.000 R²)
-- mean 120.3 ms (118.1 ms .. 124.8 ms)
-- std dev 4.572 ms (2.556 ms .. 6.511 ms)
-- variance introduced by outliers: 11% (moderately inflated)
-- benchmarking length/length sum foldl' unsafe
-- time 82.04 ms (77.92 ms .. 86.95 ms)
-- 0.994 R² (0.988 R² .. 0.999 R²)
-- mean 88.56 ms (85.87 ms .. 92.70 ms)
-- std dev 6.079 ms (4.635 ms .. 7.548 ms)
-- variance introduced by outliers: 19% (moderately inflated)
-- benchmarking length/length sum foldl' num instance
-- time 102.4 ms (89.16 ms .. 124.8 ms)
-- 0.964 R² (0.896 R² .. 0.994 R²)
-- mean 98.94 ms (91.15 ms .. 106.4 ms)
-- std dev 11.90 ms (8.779 ms .. 15.29 ms)
-- variance introduced by outliers: 32% (moderately inflated)
-- benchmarking length/double sum foldl'
-- time 83.87 ms (71.82 ms .. 104.0 ms)
-- 0.954 R² (0.878 R² .. 0.996 R²)
-- mean 103.1 ms (95.66 ms .. 112.2 ms)
-- std dev 14.21 ms (10.77 ms .. 17.84 ms)
-- variance introduced by outliers: 43% (moderately inflated)
-- benchmarking length/double sum
-- time 102.6 ms (88.13 ms .. 116.0 ms)
-- 0.970 R² (0.938 R² .. 0.997 R²)
-- mean 94.08 ms (89.94 ms .. 100.9 ms)
-- std dev 8.071 ms (5.233 ms .. 10.58 ms)
-- variance introduced by outliers: 21% (moderately inflated)
-- benchmarking lens/sum with getter
-- time 4.320 ms (4.303 ms .. 4.352 ms)
-- 1.000 R² (0.999 R² .. 1.000 R²)
-- mean 4.328 ms (4.320 ms .. 4.346 ms)
-- std dev 38.06 μs (18.94 μs .. 58.05 μs)
-- benchmarking lens/sum with accessor function
-- time 4.314 ms (4.073 ms .. 4.509 ms)
-- 0.912 R² (0.795 R² .. 0.986 R²)
-- mean 4.795 ms (4.546 ms .. 5.264 ms)
-- std dev 1.056 ms (562.7 μs .. 1.691 ms)
-- variance introduced by outliers: 90% (severely inflated)
-- benchmarking lens/sum with setter and getter
-- time 16.34 ms (14.93 ms .. 18.00 ms)
-- 0.955 R² (0.913 R² .. 0.983 R²)
-- mean 17.06 ms (16.30 ms .. 18.25 ms)
-- std dev 2.137 ms (1.656 ms .. 2.794 ms)
-- variance introduced by outliers: 59% (severely inflated)
-- benchmarking lens/sum with modify and accessor functions
-- time 14.87 ms (14.11 ms .. 15.68 ms)
-- 0.977 R² (0.946 R² .. 0.993 R²)
-- mean 15.54 ms (15.15 ms .. 16.23 ms)
-- std dev 1.319 ms (882.4 μs .. 2.030 ms)
-- variance introduced by outliers: 40% (moderately inflated)
-- Mono vs bi.
--
-- The Bifoldable instance is much slower.
--
-- The Bifunctor instance is as fast as the normal Functor instance.
--
-- The Bitraversable instance is fine, although slightly slower.
-- benchmarking [mono|bi][functor|foldable|traversable]/normal fmap tree
-- time 30.57 ms (29.87 ms .. 31.16 ms)
-- 0.999 R² (0.998 R² .. 1.000 R²)
-- mean 29.84 ms (29.66 ms .. 30.23 ms)
-- std dev 528.5 μs (358.8 μs .. 725.0 μs)
-- benchmarking [mono|bi][functor|foldable|traversable]/mono fmap tree
-- time 28.98 ms (28.54 ms .. 29.36 ms)
-- 0.999 R² (0.999 R² .. 1.000 R²)
-- mean 28.73 ms (28.44 ms .. 29.40 ms)
-- std dev 901.2 μs (411.2 μs .. 1.583 ms)
-- variance introduced by outliers: 10% (moderately inflated)
-- benchmarking [mono|bi][functor|foldable|traversable]/bi fmap tree
-- time 29.53 ms (28.27 ms .. 31.23 ms)
-- 0.993 R² (0.984 R² .. 1.000 R²)
-- mean 28.93 ms (28.57 ms .. 29.55 ms)
-- std dev 1.103 ms (436.8 μs .. 1.577 ms)
-- variance introduced by outliers: 10% (moderately inflated)
-- benchmarking [mono|bi][functor|foldable|traversable]/mono fold tree
-- time 81.88 ms (80.24 ms .. 83.03 ms)
-- 0.999 R² (0.996 R² .. 1.000 R²)
-- mean 83.68 ms (82.70 ms .. 85.33 ms)
-- std dev 2.207 ms (581.3 μs .. 2.915 ms)
-- benchmarking [mono|bi][functor|foldable|traversable]/bi fold tree
-- time 124.1 ms (120.7 ms .. 129.4 ms)
-- 0.999 R² (0.996 R² .. 1.000 R²)
-- mean 123.9 ms (121.8 ms .. 127.5 ms)
-- std dev 4.128 ms (2.139 ms .. 6.374 ms)
-- variance introduced by outliers: 11% (moderately inflated)
-- benchmarking [mono|bi][functor|foldable|traversable]/mono traverse tree
-- time 118.5 ms (115.2 ms .. 122.6 ms)
-- 0.999 R² (0.995 R² .. 1.000 R²)
-- mean 122.2 ms (120.4 ms .. 126.8 ms)
-- std dev 4.086 ms (1.704 ms .. 5.961 ms)
-- variance introduced by outliers: 11% (moderately inflated)
-- benchmarking [mono|bi][functor|foldable|traversable]/bi traverse tree
-- time 122.6 ms (116.8 ms .. 127.2 ms)
-- 0.999 R² (0.997 R² .. 1.000 R²)
-- mean 121.3 ms (120.2 ms .. 123.0 ms)
-- std dev 2.377 ms (1.043 ms .. 3.289 ms)
-- variance introduced by outliers: 11% (moderately inflated)