How to better initialize a dictionary containing multidimensional array?

General Usage Performance
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1

Hi everyone, I want to create a Dict() object where the keys are NTuple{6, Int} and the corresponding values are rank-6 arrays. I found the following function to create such Dict object with 64 items are much slower than I expected:

function test_time()
a = Dict()
for k in Iterators.product([0:1, 0:1, 0:1, 0:1, 0:1, 0:1]…)
a[k] = Array{Float64}(undef, 16, 16, 16, 16, 16, 16)
end
return a
end

julia> @btime test_time();
1.371 s (497 allocations: 8.00 GiB)

In the function above, I add 64 key-value pairs sequentially. But a single array initialization only cost little time :

julia> @btime Array{Float64}(undef, 16, 16, 16, 16, 16, 16);
1.681 μs (2 allocations: 128.00 MiB)

And 1.371 s / 64 is much larger than 1.681 μs.

Can anybody help me with the problem, or provide better practices ?

Thanks in advance !

2

Instead of using Dict{Any, Any} you can create the Dict with the proper types:

function test_time_new()
a = Dict{NTuple{6, Int64},Array{Float64}}()
for k in Iterators.product([0:1, 0:1, 0:1, 0:1, 0:1, 0:1]...)
a[k] = Array{Float64}(undef, 16, 16, 16, 16, 16, 16)
end
return a
end

julia> @btime test_time();
  372.200 μs (564 allocations: 8.00 GiB)

julia> @btime test_time_new();
  256.400 μs (447 allocations: 8.00 GiB)

But I suspect that you may be able to overthink your data representation to gain much more performance.

3

Further type restriction might help for down-stream tasks:

a = Dict{NTuple{6, Int64}, Array{Float64, 6}}()
                                       #^^^
4 
function test_time_new2()
a = Dict{NTuple{6, Int64},Array{Float64, 6}}()
for k in Iterators.product([0:1, 0:1, 0:1, 0:1, 0:1, 0:1]...)
a[k] = Array{Float64}(undef, 16, 16, 16, 16, 16, 16)
end
return a
end

julia> @btime test_time();
  268.700 μs (564 allocations: 8.00 GiB)

julia> @btime test_time_new();
  259.400 μs (447 allocations: 8.00 GiB)

julia> @btime test_time_new2();
  257.900 μs (447 allocations: 8.00 GiB)

My first timings were wrong, the function are too volatile to window switches and mouse movings…

5

Thanks for your comments, your timing results are much more reasonable compared with mine, Is this a Julia version problem ? My version is 1.10.2

6

I observe similar timings on my laptop. Is there a chance that you don’t have enough available memory and your OS has to resort to the swap space? That might slow down the allocations.

7

I am not quite sure but it seems to be a version problem. I switch to Julia 1.7.2 on the same machine and the timing results looks good as @oheil. How can different versions result in such a huge difference if it is so :upside_down_face:

8

This is possible in general, but I lack the skill to connect your code to the former changes in versions.

My Julia version is 1.11.5

9

Looking at the timing differences at OPs and mine (plenty of RAM) this seems to be reasonable.

10

Can you explain what you want to do downstream with this dictionary?

11

I see the same slow behavior on a machine with plenty of RAM (48 GB) and Julia 1.11.5.

julia> @b test_time()
315.842 ms (204 allocs: 8.000 GiB, 99.55% gc time, without a warmup)

julia> @b Array{Float64}(undef, 2^6, 16, 16, 16, 16, 16, 16)  # allocate all in one step
168.777 μs (3 allocs: 8.000 GiB, 81.04% gc time)

julia> @b begin GC.enable(false); test_time(); GC.enable(true) end
232.363 μs (204 allocs: 8.000 GiB)

Most of the time is spent on garbage collection. I wonder why.