parallelizing BallTree construction

Author: SebastianAment

.github/workflows/CI.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.0'
+          - '1.3'
           - '1'
           - 'nightly'
         os:

Project.toml

@@ -1,15 +1,16 @@
 name = "NearestNeighbors"
 uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
-version = "0.4.10"
+version = "0.5.0"
 
 [deps]
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
 Distances = "0.9, 0.10"
 StaticArrays = "0.9, 0.10, 0.11, 0.12, 1.0"
-julia = "1.0"
+julia = "1.3"
 
 [extras]
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"

src/NearestNeighbors.jl

@@ -5,7 +5,7 @@ import Distances: Metric, result_type, eval_reduce, eval_end, eval_op, eval_star
 
 using StaticArrays
 import Base.show
-using Base.Threads: @threads
+using Base.Threads
 
 export NNTree, BruteTree, KDTree, BallTree, DataFreeTree
 export knn, nn, inrange # TODOs? , allpairs, distmat, npairs

src/ball_tree.jl

@@ -12,17 +12,6 @@ struct BallTree{V <: AbstractVector,N,T,M <: Metric} <: NNTree{V,M}
     reordered::Bool                       # If the data has been reordered
 end
 
-# When we create the bounding spheres we need some temporary arrays.
-# We create a type to hold them to not allocate these arrays at every
-# function call and to reduce the number of parameters in the tree builder.
-struct ArrayBuffers{N,T <: AbstractFloat}
-    center::MVector{N,T}
-end
-
-function ArrayBuffers(::Type{Val{N}}, ::Type{T}) where {N, T}
-    ArrayBuffers(zeros(MVector{N,T}))
-end
-
 """
     BallTree(data [, metric = Euclidean(), leafsize = 10]) -> balltree
 
@@ -33,14 +22,14 @@ function BallTree(data::AbstractVector{V},
                   leafsize::Int = 10,
                   reorder::Bool = true,
                   storedata::Bool = true,
+                  parallel::Bool = true,
                   reorderbuffer::Vector{V} = Vector{V}()) where {V <: AbstractArray, M <: Metric}
     reorder = !isempty(reorderbuffer) || (storedata ? reorder : false)
 
     tree_data = TreeData(data, leafsize)
     n_d = length(V)
     n_p = length(data)
 
-    array_buffs = ArrayBuffers(Val{length(V)}, get_T(eltype(V)))
     indices = collect(1:n_p)
 
     # Bottom up creation of hyper spheres so need spheres even for leafs)
@@ -70,7 +59,8 @@ function BallTree(data::AbstractVector{V},
     if n_p > 0
         # Call the recursive BallTree builder
         build_BallTree(1, data, data_reordered, hyper_spheres, metric, indices, indices_reordered,
-                       1,  length(data), tree_data, array_buffs, reorder)
+                       1, length(data), tree_data, reorder, Val(parallel))
+
     end
 
     if reorder
@@ -86,6 +76,7 @@ function BallTree(data::AbstractVecOrMat{T},
                   leafsize::Int = 10,
                   storedata::Bool = true,
                   reorder::Bool = true,
+                  parallel::Bool = true,
                   reorderbuffer::Matrix{T} = Matrix{T}(undef, 0, 0)) where {T <: AbstractFloat, M <: Metric}
     dim = size(data, 1)
     npoints = size(data, 2)
@@ -96,7 +87,7 @@ function BallTree(data::AbstractVecOrMat{T},
         reorderbuffer_points = copy_svec(T, reorderbuffer, Val(dim))
     end
     BallTree(points, metric, leafsize = leafsize, storedata = storedata, reorder = reorder,
-            reorderbuffer = reorderbuffer_points)
+            parallel = parallel, reorderbuffer = reorderbuffer_points)
 end
 
 # Recursive function to build the tree.
@@ -110,16 +101,16 @@ function build_BallTree(index::Int,
                         low::Int,
                         high::Int,
                         tree_data::TreeData,
-                        array_buffs::ArrayBuffers{N,T},
-                        reorder::Bool) where {V <: AbstractVector, N, T}
+                        reorder::Bool,
+                        parallel::Val{false}) where {V <: AbstractVector, N, T}
 
     n_points = high - low + 1 # Points left
     if n_points <= tree_data.leafsize
         if reorder
             reorder_data!(data_reordered, data, index, indices, indices_reordered, tree_data)
         end
         # Create bounding sphere of points in leaf node by brute force
-        hyper_spheres[index] = create_bsphere(data, metric, indices, low, high, array_buffs)
+        hyper_spheres[index] = create_bsphere(data, metric, indices, low, high)
         return
     end
 
@@ -132,22 +123,74 @@ function build_BallTree(index::Int,
 
     # Sort the data at the mid_idx boundary using the split_dim
     # to compare
-    select_spec!(indices, mid_idx, low, high, data, split_dim)
+    select_spec!(indices, mid_idx, low, high, data, split_dim) # culprit? technically, low and high should be disjoint for different threads
 
     build_BallTree(getleft(index), data, data_reordered, hyper_spheres, metric,
-                   indices, indices_reordered, low, mid_idx - 1,
-                   tree_data, array_buffs, reorder)
+                 indices, indices_reordered, low, mid_idx - 1,
+                 tree_data, reorder, parallel)
 
     build_BallTree(getright(index), data, data_reordered, hyper_spheres, metric,
-                  indices, indices_reordered, mid_idx, high,
-                  tree_data, array_buffs, reorder)
+                indices, indices_reordered, mid_idx, high,
+                tree_data, reorder, parallel)
 
     # Finally create bounding hyper sphere from the two children's hyper spheres
     hyper_spheres[index]  =  create_bsphere(metric, hyper_spheres[getleft(index)],
-                                            hyper_spheres[getright(index)],
-                                            array_buffs)
+                                            hyper_spheres[getright(index)])
+    return
 end
 
+# Parallelized recursive function to build the tree.
+function build_BallTree(index::Int,
+                        data::Vector{V},
+                        data_reordered::Vector{V},
+                        hyper_spheres::Vector{HyperSphere{N,T}},
+                        metric::Metric,
+                        indices::Vector{Int},
+                        indices_reordered::Vector{Int},
+                        low::Int,
+                        high::Int,
+                        tree_data::TreeData,
+                        reorder::Bool,
+                        parallel::Val{true}) where {V <: AbstractVector, N, T}
+
+    n_points = high - low + 1 # Points left
+    if n_points <= tree_data.leafsize
+        if reorder
+            reorder_data!(data_reordered, data, index, indices, indices_reordered, tree_data)
+        end
+        # Create bounding sphere of points in leaf node by brute force
+        hyper_spheres[index] = create_bsphere(data, metric, indices, low, high)
+        return
+    end
+
+    # Find split such that one of the sub trees has 2^p points
+    # and the left sub tree has more points
+    mid_idx = find_split(low, tree_data.leafsize, n_points)
+
+    # Brute force to find the dimension with the largest spread
+    split_dim = find_largest_spread(data, indices, low, high)
+
+    # Sort the data at the mid_idx boundary using the split_dim
+    # to compare
+    select_spec!(indices, mid_idx, low, high, data, split_dim) # culprit? technically, low and high should be disjoint for different threads
+
+    @sync begin
+        @spawn build_BallTree(getleft(index), data, data_reordered, hyper_spheres, metric,
+                       indices, indices_reordered, low, mid_idx - 1,
+                       tree_data, reorder, parallel)
+
+        @spawn build_BallTree(getright(index), data, data_reordered, hyper_spheres, metric,
+                      indices, indices_reordered, mid_idx, high,
+                      tree_data, reorder, parallel)
+    end
+
+    # Finally create bounding hyper sphere from the two children's hyper spheres
+    hyper_spheres[index]  =  create_bsphere(metric, hyper_spheres[getleft(index)],
+                                            hyper_spheres[getright(index)])
+    return
+end
+
+
 function _knn(tree::BallTree,
               point::AbstractVector,
               best_idxs::AbstractVector{Int},

src/hyperspheres.jl

@@ -7,6 +7,8 @@ end
 
 HyperSphere(center::SVector{N,T1}, r::T2) where {N, T1, T2} = HyperSphere(center, convert(T1, r))
 
+Base.:(==)(A::HyperSphere, B::HyperSphere) = A.center == B.center && A.r == B.r
+
 @inline function intersects(m::M,
                             s1::HyperSphere{N,T},
                             s2::HyperSphere{N,T}) where {T <: AbstractFloat, N, M <: Metric}
@@ -19,55 +21,22 @@ end
     evaluate(m, s1.center, s2.center) + s1.r <= s2.r
 end
 
-@inline function interpolate(::M,
-                             c1::V,
-                             c2::V,
-                             x,
-                             d,
-                             ab) where {V <: AbstractVector, M <: NormMetric}
-    alpha = x / d
-    @assert length(c1) == length(c2)
-    @inbounds for i in eachindex(ab.center)
-        ab.center[i] = (1 - alpha) .* c1[i] + alpha .* c2[i]
-    end
-    return ab.center, true
-end
-
-@inline function interpolate(::M,
-                             c1::V,
-                             ::V,
-                             ::Any,
-                             ::Any,
-                             ::Any) where {V <: AbstractVector, M <: Metric}
-    return c1, false
-end
-
-function create_bsphere(data::AbstractVector{V}, metric::Metric, indices::Vector{Int}, low, high, ab) where {V}
-    n_dim = size(data, 1)
-    n_points = high - low + 1
-    # First find center of all points
-    fill!(ab.center, 0.0)
-    for i in low:high
-        for j in 1:length(ab.center)
-            ab.center[j] += data[indices[i]][j]
-        end
-    end
-    ab.center .*= 1 / n_points
-
+# versions with no array buffer - still not allocating in sequential BallTree construction
+using Statistics: mean
+function create_bsphere(data::AbstractVector{V}, metric::Metric, indices::Vector{Int}, low, high) where {V}
+    # find center
+    center = mean(@views(data[indices[low:high]]))
     # Then find r
     r = zero(get_T(eltype(V)))
     for i in low:high
-        r = max(r, evaluate(metric, data[indices[i]], ab.center))
+        r = max(r, evaluate(metric, data[indices[i]], center))
     end
     r += eps(get_T(eltype(V)))
-    return HyperSphere(SVector{length(V),eltype(V)}(ab.center), r)
+    return HyperSphere(SVector{length(V),eltype(V)}(center), r)
 end
 
 # Creates a bounding sphere from two other spheres
-function create_bsphere(m::Metric,
-                        s1::HyperSphere{N,T},
-                        s2::HyperSphere{N,T},
-                        ab) where {N, T <: AbstractFloat}
+function create_bsphere(m::Metric, s1::HyperSphere{N,T}, s2::HyperSphere{N,T}) where {N, T <: AbstractFloat}
     if encloses(m, s1, s2)
         return HyperSphere(s2.center, s2.r)
     elseif encloses(m, s2, s1)
@@ -79,7 +48,7 @@ function create_bsphere(m::Metric,
     # neither s1 nor s2 contains the other)
     dist = evaluate(m, s1.center, s2.center)
     x = 0.5 * (s2.r - s1.r + dist)
-    center, is_exact_center = interpolate(m, s1.center, s2.center, x, dist, ab)
+    center, is_exact_center = interpolate(m, s1.center, s2.center, x, dist)
     if is_exact_center
         rad = 0.5 * (s2.r + s1.r + dist)
     else
@@ -88,3 +57,14 @@ function create_bsphere(m::Metric,
 
     return HyperSphere(SVector{N,T}(center), rad)
 end
+
+@inline function interpolate(::M, c1::V, c2::V, x, d) where {V <: AbstractVector, M <: NormMetric}
+    length(c1) == length(c2) || throw(DimensionMismatch("interpolate arguments have length $(length(c1)) and $(length(c2))"))
+    alpha = x / d
+    center = (1 - alpha) * c1 + alpha * c2
+    return center, true
+end
+
+@inline function interpolate(::M, c1::V, ::V, ::Any, ::Any) where {V <: AbstractVector, M <: Metric}
+    return c1, false
+end

test/runtests.jl

@@ -6,13 +6,12 @@ using LinearAlgebra
 
 using Distances: Distances, Metric, evaluate, PeriodicEuclidean
 struct CustomMetric1 <: Metric end
-Distances.evaluate(::CustomMetric1, a::AbstractVector, b::AbstractVector) = maximum(abs.(a .- b))
+Distances.evaluate(::CustomMetric1, a::AbstractVector, b::AbstractVector) = maximum(abs, (a .- b))
 function NearestNeighbors.interpolate(::CustomMetric1,
                                       a::V,
                                       b::V,
                                       x,
-                                      d,
-                                      ab) where {V <: AbstractVector}
+                                      d) where {V <: AbstractVector}
     idx = (abs.(b .- a) .>= d - x)
     c = copy(Array(a))
     c[idx] = (1 - x / d) * a[idx] + (x / d) * b[idx]

test/test_monkey.jl

@@ -1,9 +1,8 @@
 import NearestNeighbors.MinkowskiMetric
 # This contains a bunch of random tests that should hopefully detect if
 # some edge case has been missed in the real tests
-
-
 @testset "metric $metric" for metric in fullmetrics
+    nrep = 30
     @testset "tree type $TreeType" for TreeType in trees_with_brute
         @testset "element type $T" for T in (Float32, Float64)
             @testset "knn monkey" begin
@@ -14,7 +13,7 @@ import NearestNeighbors.MinkowskiMetric
                 elseif TreeType == BallTree && isa(metric, Hamming)
                     continue
                 end
-                for i in 1:30
+                for i in 1:nrep
                     dim_data = rand(1:4)
                     size_data = rand(1000:1300)
                     data = rand(T, dim_data, size_data)
@@ -28,7 +27,7 @@ import NearestNeighbors.MinkowskiMetric
                 end
 
                 # Compares vs Brute Force
-                for i in 1:30
+                for i in 1:nrep
                     dim_data = rand(1:5)
                     size_data = rand(100:151)
                     data = rand(T, dim_data, size_data)
@@ -45,7 +44,7 @@ import NearestNeighbors.MinkowskiMetric
 
             @testset "inrange monkey" begin
                 # Test against brute force
-                for i in 1:30
+                for i in 1:nrep
                     dim_data = rand(1:6)
                     size_data = rand(20:250)
                     data = rand(T, dim_data, size_data)
@@ -62,17 +61,30 @@ import NearestNeighbors.MinkowskiMetric
             end
 
             @testset "coupled monkey" begin
-                for i in 1:50
+                for i in 1:nrep
                     dim_data = rand(1:5)
                     size_data = rand(100:1000)
                     data = randn(T, dim_data, size_data)
-                    tree = TreeType(data, metric; leafsize = rand(1:8))
+
+                    lf = rand(1:8)
+                    tree = TreeType(data, metric; leafsize = lf)
+
+                    if TreeType == BallTree # this caught a race-condition in an early version of the parallel BallTree code
+                        tree2 = TreeType(data, metric; leafsize = lf, parallel = false)
+                        @test tree.data == tree2.data
+                        @test tree.hyper_spheres[1] == tree2.hyper_spheres[1]
+                        @test tree.indices == tree2.indices
+                        @test tree.metric == tree2.metric
+                        @test tree.tree_data == tree2.tree_data
+                        @test tree.reordered == tree2.reordered
+                    end
+
                     point = randn(dim_data)
                     idxs_ball = Int[]
                     r = 0.1
                     while length(idxs_ball) < 10
                         r *= 2.0
-                        idxs_ball = inrange(tree,  point, r, true)
+                        idxs_ball = inrange(tree, point, r, true)
                     end
                     idxs_knn, dists = knn(tree, point, length(idxs_ball))