NearestNeighbors.jl - Can I formulate this in a way which makes it allocate less?

General Usage
1

Hello!

I am using a library called NearestNeighbors to calculate neighbouring points. A simple script below shows the general idea of what I want to do:

using NearestNeighbors
using StaticArrays


function help_me_allocate_less()
    nCoords  = 3000
    coordsSA = [SVector{3,Float64}(rand(),rand(),rand()) for i in 1:nCoords]
    R = 0.2
    balltree = BallTree(coordsSA,reorder = false)
    idxs = inrange(balltree,coordsSA, R, false)

    for t = 1:100
        if mod(t,8) == 0
            balltree = BallTree(coordsSA,reorder = false)
            idxs = inrange(balltree, coordsSA, R, false)
        end
        coordsSA = [SVector{3,Float64}(rand(),rand(),rand()) for i in 1:nCoords]
    end
end

@time help_me_allocate_less()

And when I run this:

 @time help_me_allocate_less()
  0.270642 seconds (261.25 k allocations: 73.013 MiB, 10.49% gc time)

Would it be possible in some way to “replace” balltree and idxs “in place” such that it does not allocate that much?

Kind regards

2

Why do you need to recreate balltree in each loop iteration, in your example you are not modifying the inputs ro BallTree?

1 Like
3

Sorry, the example was a bit too simple. I have to update the balltree since “coordsSA” is changing.

I updated the example to reflect that now, thanks!