Update benchmark code (#293)

Author: sunxd3

benchmark/juliabugs.jl

@@ -85,6 +85,20 @@ function benchmark_JuliaBUGS_model_with_Mooncake(model::JuliaBUGS.BUGSModel)
     return BenchmarkResult(:juliabugs, dim, density_time, density_and_gradient_time)
 end
 
+# function benchmark_JuliaBUGS_model_with_ReverseDiff(model::JuliaBUGS.BUGSModel)
+#     model = JuliaBUGS.set_evaluation_mode(model, JuliaBUGS.UseGraph())
+#     ad_model = LogDensityProblemsAD.ADgradient(:ReverseDiff, model; compile=Val(true))
+#     dim = LogDensityProblems.dimension(model)
+#     params_values = JuliaBUGS.getparams(model)
+#     density_time = Chairmarks.@be LogDensityProblemsAD.logdensity($model, $params_values)
+#     density_and_gradient_time = Chairmarks.@be LogDensityProblemsAD.logdensity_and_gradient(
+#         $ad_model, $params_values
+#     )
+#     return BenchmarkResult(
+#         :juliabugs_reverse_diff, dim, density_time, density_and_gradient_time
+#     )
+# end
+
 # function benchmark_JuliaBUGS_model_with_Enzyme(model::JuliaBUGS.BUGSModel)
 #     f(params, model) = LogDensityProblems.logdensity(model, params)
 #     backend = AutoEnzyme()

benchmark/nimble/nimble.r

@@ -225,7 +225,7 @@ for (example in names(benchmark_results)) {
     result <- benchmark_results[[example]]
 
     if (!is.null(result$non_compiled_log_joint)) {
-        cat("Non-compiled log joint time (microseconds):\n")
+        cat("Non-compiled log joint time (milliseconds):\n")
         print(summary(result$non_compiled_log_joint))
     }
 
@@ -252,7 +252,7 @@ for (example in names(benchmark_results_vol2)) {
     result <- benchmark_results_vol2[[example]]
 
     if (!is.null(result$non_compiled_log_joint)) {
-        cat("Non-compiled log joint time (microseconds):\n")
+        cat("Non-compiled log joint time (milliseconds):\n")
         print(summary(result$non_compiled_log_joint))
     }
 

benchmark/run_benchmarks.jl

@@ -4,6 +4,33 @@ examples_to_benchmark = [
     :rats, :pumps, :bones, :oxford, :epil, :lsat, :schools, :beetles, :air
 ]
 
+examples_to_benchmark_full = [
+    :rats,
+    :pumps,
+    :seeds,
+    :surgical_realistic,
+    :magnesium,
+    :salm,
+    :equiv,
+    :dyes,
+    :stacks,
+    :epil,
+    :blockers,
+    :oxford,
+    :lsat,
+    :bones,
+    :mice,
+    :kidney,
+    :leuk,
+    :leukfr,
+    :dugongs,
+    :air,
+    :birats,
+    :schools,
+    :beetles,
+    :alligators,
+]
+
 stan_results = benchmark_Stan_models(examples_to_benchmark)
 
 juliabugs_models = [
@@ -17,19 +44,8 @@ for (model_name, model) in zip(examples_to_benchmark, juliabugs_models)
     juliabugs_results[model_name] = benchmark_JuliaBUGS_model_with_Mooncake(model)
 end
 
-# juliabugs_enzyme_results = OrderedDict{Symbol,BenchmarkResult}()
-# for (model_name, model) in zip(examples_to_benchmark, juliabugs_models)
-#     @info "Benchmarking $model_name with Enzyme"
-#     try
-#         juliabugs_enzyme_results[model_name] = benchmark_JuliaBUGS_model_with_Enzyme(model)
-#     catch e
-#         @warn "Error benchmarking $model_name with Enzyme: $e"
-#     end
-# end
-
 println("### Stan results:")
 _print_results_table(stan_results; backend=Val(:markdown))
+
 println("### JuliaBUGS Mooncake results:")
 _print_results_table(juliabugs_results; backend=Val(:markdown))
-# println("### JuliaBUGS Enzyme results:")
-# _print_results_table(juliabugs_enzyme_results; backend=Val(:markdown))

benchmark/stan.jl

@@ -3,7 +3,7 @@
 const stan_models_path_info = (
     rats=(1, :rats, :rats),
     pumps=(1, :pump, :pump),
-    # dogs=(1, :dogs, :dogs),
+    dogs=(1, :dogs, :dogs),
     seeds=(1, :seeds, :seeds),
     surgical_realistic=(1, :surgical, :surgical),
     magnesium=(1, :magnesium, :magnesium),
@@ -26,6 +26,12 @@ const stan_models_path_info = (
     schools=(2, :schools, :schools),
     beetles=(2, :beetles, :beetles_logit),
     alligators=(2, :alli, :alli2),
+    endo=(2, :endo, :endo2),
+    stagnant=(2, :stagnant, :stagnant),
+    biopsies=(2, :biopsies, :biopsies),
+    eyes=(2, :eyes, :eyes),
+    hearts=(2, :hearts, :hearts),
+    cervix=(2, :cervix, :cervix2),
 )
 
 const stan_examples_folder = joinpath(@__DIR__, "stan/bugs_examples/")