It takes 3s in Julia:
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)