rewrite of some benchmark

bench/pkg/euclidean_distance_repressilator.jl

@@ -21,37 +21,33 @@ b_vectorize = @benchmark begin
     σ = simulate($(repressilator)) 
     euclidean_distance(σ, :P1, tml_obs, y_obs)
 end
+#=
 @btime begin
     σ = simulate($(repressilator)) 
     euclidean_distance(σ, :P1, tml_obs, y_obs)
 end
+=#
 @show minimum(b_vectorize), mean(b_vectorize), maximum(b_vectorize)
 
 println("Automaton with 1 loc")
 aut1 = create_euclidean_distance_automaton(repressilator, tml_obs, y_obs, :P1)
 sync1 = repressilator * aut1
 b_sim_aut1 = @benchmark (σ = simulate($(sync1)))
-@btime (σ = simulate($(sync1)))
+#@btime (σ = simulate($(sync1)))
 @show minimum(b_sim_aut1), mean(b_sim_aut1), maximum(b_sim_aut1)
 b_vol_sim_aut1 = @benchmark (σ = volatile_simulate($(sync1)))
-@btime (σ = volatile_simulate($(sync1)))
+#@btime (σ = volatile_simulate($(sync1)))
 @show minimum(b_vol_sim_aut1), mean(b_vol_sim_aut1), maximum(b_vol_sim_aut1)
 
 println("ABC reject automaton with 1 loc")
 aut1_abc = create_abc_euclidean_distance_automaton(repressilator, tml_obs, y_obs, :P1)
 aut1_abc.ϵ = Inf
 sync1_abc = repressilator * aut1_abc
-println("After creating sync model")
-@show aut1_abc.ϵ
 b_sim_aut1_abc = @benchmark (σ = simulate($(sync1_abc)))
-@btime (σ = simulate($(sync1_abc)))
-println("After bench simulate sync model")
-@show aut1_abc.ϵ
+#@btime (σ = simulate($(sync1_abc)))
 @show minimum(b_sim_aut1_abc), mean(b_sim_aut1_abc), maximum(b_sim_aut1_abc)
 b_vol_sim_aut1_abc = @benchmark (σ = volatile_simulate($(sync1_abc)))
-@btime (σ = volatile_simulate($(sync1_abc)))
-println("After bench volatile_simulate sync model")
-@show aut1_abc.ϵ
+#@btime (σ = volatile_simulate($(sync1_abc)))
 @show minimum(b_vol_sim_aut1_abc), mean(b_vol_sim_aut1_abc), maximum(b_vol_sim_aut1_abc)
 
 #=
@@ -65,9 +61,9 @@ println("Automaton with nbr_obs loc")
 aut2 = create_euclidean_distance_automaton_2(repressilator, tml_obs, y_obs, :P1)
 sync2 = repressilator * aut2
 b_sim_aut2 = @benchmark (σ = simulate($(sync2)))
-@btime (σ = simulate($(sync2)))
+#@btime (σ = simulate($(sync2)))
 @show minimum(b_sim_aut2), mean(b_sim_aut2), maximum(b_sim_aut2)
 b_vol_sim_aut2 = @benchmark (σ = volatile_simulate($(sync2)))
-@btime (σ = volatile_simulate($(sync2)))
+#@btime (σ = volatile_simulate($(sync2)))
 @show minimum(b_vol_sim_aut2), mean(b_vol_sim_aut2), maximum(b_vol_sim_aut2)
 

bench/pkg/sim_repressilator.jl

@@ -5,14 +5,26 @@ using MarkovProcesses
 import LinearAlgebra: dot
 import Distributions: Uniform
 
-load_automaton("euclidean_distance_automaton")
 load_model("repressilator")
-tb = 210.0
-tml_obs = 0:10.0:210.0
+observe_all!(repressilator)
+N_periods, ref_mean_tp = 8, 20.0
 set_param!(repressilator, [:α, :β, :n, :α0], [200.0, 2.0, 2.0, 0.0])
-set_time_bound!(repressilator, tb)
+set_time_bound!(repressilator, (N_periods)*ref_mean_tp)
 
 b_sim = @benchmark σ = simulate($(repressilator)) 
-@btime σ = simulate($(repressilator)) 
+@show mean(b_sim)
 @show mean(b_sim).time, mean(b_sim).memory
 
+load_automaton("period_automaton")
+L, H = 20.0, 100.0
+A_per = create_period_automaton(repressilator, L, H, N_periods, :P1; ref_mean_tp = ref_mean_tp, error_func = :max_mean_var_relative_error)
+sync_repressilator = repressilator * A_per
+
+b_period = @benchmark σ = simulate($(sync_repressilator)) 
+@show mean(b_period)
+@show mean(b_period).time, mean(b_period).memory
+
+b_vol_period = @benchmark σ = volatile_simulate($(sync_repressilator)) 
+@show mean(b_vol_period)
+@show mean(b_vol_period).time, mean(b_vol_period).memory
+