The code you provided is still not self-contained, it isn’t a ‘minimal working example’ or MWE. Can you provide some example data for spikes?
Also, when developing and testing code, I suggest that you make smaller data sets. Waiting for minutes just to see if your code works seems like a waste of time.
function sum_spikes(spikes)
ϵ = 0.9
ee_counter = [sum(i->s<=i<s+ϵ, spikes) for s in range(0,3,5000000)]
pdf = ee_counter ./ sum(spikes)
end
spikes = randn(3098)
@btime sum_spikes($spikes) # 3.237 s (4 allocations: 76.29 MiB)