Benchmark timings for mkin on various systems

Johannes Ranke

2020-05-27

Source: vignettes/web_only/benchmarks.Rmd

Systems

Each system is characterized by its CPU type, the operating system type and the mkin version.

cpu_model <- benchmarkme::get_cpu()$model_name
operating_system <- Sys.info()[["sysname"]]
mkin_version <- as.character(packageVersion("mkin"))
system_string <- paste0(operating_system, ", ", cpu_model, ", mkin version ", mkin_version)
load("~/git/mkin/vignettes/web_only/mkin_benchmarks.rda")
mkin_benchmarks[system_string, c("CPU", "OS", "mkin")] <- c(cpu_model, operating_system, mkin_version)

if (mkin_version > "0.9.48.1") {
  mmkin_bench <- function(models, datasets, error_model = "const") mmkin(models, datasets, error_model = error_model, cores = 1, quiet = TRUE)
} else {
  mmkin_bench <- function(models, datasets, error_model = NULL) mmkin(models, datasets, reweight.method = error_model, cores = 1, quiet = TRUE)
}
FOCUS_C <- FOCUS_2006_C
FOCUS_D <- subset(FOCUS_2006_D, value != 0)
# Parent only
t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_C, FOCUS_D)))[["elapsed"]]
t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_C, FOCUS_D), error_model = "tc"))[["elapsed"]]
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
## iteration limit reached without convergence (10)
# One metabolite
SFO_SFO <- mkinmod(
  parent = mkinsub("SFO", "m1"),
  m1 = mkinsub("SFO"))
## Successfully compiled differential equation model from auto-generated C code.
FOMC_SFO <- mkinmod(
  parent = mkinsub("FOMC", "m1"),
  m1 = mkinsub("SFO"))
## Successfully compiled differential equation model from auto-generated C code.
DFOP_SFO <- mkinmod(
  parent = mkinsub("FOMC", "m1"),
  m1 = mkinsub("SFO"))
## Successfully compiled differential equation model from auto-generated C code.
t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[["elapsed"]]
t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D), error_model = "tc"))[["elapsed"]]
t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D), error_model = "obs"))[["elapsed"]]

# Two metabolites, synthetic data
m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
                           M1 = mkinsub("SFO", "M2"),
                           M2 = mkinsub("SFO"),
                           use_of_ff = "max", quiet = TRUE)

m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
                           M1 = mkinsub("SFO"),
                           M2 = mkinsub("SFO"),
                           use_of_ff = "max", quiet = TRUE)

SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data

DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data

t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))["elapsed"]
t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))["elapsed"]

t8 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = "tc"))["elapsed"]
t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "tc"))["elapsed"]

t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = "obs"))["elapsed"]
t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "obs"))["elapsed"]

mkin_benchmarks[system_string, paste0("t", 1:11)] <- c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
mkin_benchmarks[, -c(1:3)]
##                                                                        t1
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.610
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2 1.679
##                                                                         t2
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2  3.613
##                                                                        t3
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2 1.366
##                                                                         t4
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  8.461
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2  6.545
##                                                                        t5    t6
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 2.623
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 2.542
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 2.723
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 2.643
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002 2.635
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2 2.709 0.752
##                                                                        t7    t8
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 7.525
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 4.632
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 4.862
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374  7.02
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259 4.737
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2 1.214 1.455
##                                                                         t9
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  8.171
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  7.618
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  7.763
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2  4.196
##                                                                       t10
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2 1.996
##                                                                        t11
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  5.636
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.574
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.365
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  5.626
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2    3.1
save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")