From 6178249bbb5e9de7cb7f34287ee7de28a68fed6c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 10 Aug 2022 15:38:17 +0200 Subject: Change dev branch used for docs, update static docs --- docs/dev/articles/web_only/benchmarks.html | 555 +++++++++++++++++++++++------ 1 file changed, 437 insertions(+), 118 deletions(-) (limited to 'docs/dev/articles/web_only/benchmarks.html') diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html index a6d52649..3dbf2881 100644 --- a/docs/dev/articles/web_only/benchmarks.html +++ b/docs/dev/articles/web_only/benchmarks.html @@ -20,6 +20,8 @@ + +
+

Benchmark timings for mkin

-

Johannes Ranke

+

Johannes Ranke

-

Last change 13 May 2020 (rebuilt 2021-02-15)

+

Last change 14 July 2022 (rebuilt 2022-08-10)

- Source: vignettes/web_only/benchmarks.rmd + Source: vignettes/web_only/benchmarks.rmd
-

Each system is characterized by its CPU type, the operating system type and the mkin version. Currently only values for one system are available. A compiler was available, so if no analytical solution was available, compiled ODE models are used.

-
-

-Test cases

-

Parent only:

+

Each system is characterized by the operating system type, the CPU type, the mkin version, and, as in June 2022 the current R version lead to worse performance, the R version. A compiler was available, so if no analytical solution was available, compiled ODE models are used.

+

Every fit is only performed once, so the accuracy of the benchmarks is limited.

+

The following wrapper function for mmkin is used because the way the error model is specified was changed in mkin version 0.9.49.1.

-FOCUS_C <- FOCUS_2006_C
-FOCUS_D <- subset(FOCUS_2006_D, value != 0)
-parent_datasets <- list(FOCUS_C, FOCUS_D)
-
-t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), parent_datasets))[["elapsed"]]
-t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), parent_datasets,
-    error_model = "tc"))[["elapsed"]]
-

One metabolite:

+if (packageVersion("mkin") > "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) + } +}
+
+

Test cases +

+

Parent only:

-SFO_SFO <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
-FOMC_SFO <- mkinmod(
-  parent = mkinsub("FOMC", "m1"),
-  m1 = mkinsub("SFO"))
-DFOP_SFO <- mkinmod(
-  parent = mkinsub("FOMC", "m1"),
-  m1 = mkinsub("SFO"))
-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:

+FOCUS_C <- FOCUS_2006_C +FOCUS_D <- subset(FOCUS_2006_D, value != 0) +parent_datasets <- list(FOCUS_C, FOCUS_D) + + +t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), parent_datasets))[["elapsed"]] +t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), parent_datasets, + error_model = "tc"))[["elapsed"]]
+

One metabolite:

-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"]]
+SFO_SFO <- mkinmod( + parent = mkinsub("SFO", "m1"), + m1 = mkinsub("SFO")) +FOMC_SFO <- mkinmod( + parent = mkinsub("FOMC", "m1"), + m1 = mkinsub("SFO")) +DFOP_SFO <- mkinmod( + parent = mkinsub("FOMC", "m1"), + m1 = mkinsub("SFO")) +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:

-mkin_benchmarks[system_string, paste0("t", 1:11)] <-
-  c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
-save(mkin_benchmarks, file = "~/git/mkin/vignettes/web_only/mkin_benchmarks.rda")
+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"]]
-
-

-Results

-

Currently, we only have benchmark information on one system, therefore only the mkin version is shown with the results below. Timings are in seconds, shorter is better. All results were obtained by serial, i.e. not using multiple computing cores.

-

Benchmarks for all available error models are shown.

-
-

-Parent only

+
+

Results +

+

Benchmarks for all available error models are shown. They are intended for improving mkin, not for comparing CPUs or operating systems. All trademarks belong to their respective owners.

+
+

Parent only +

Constant variance (t1) and two-component error model (t2) for four models fitted to two datasets, i.e. eight fits for each test.

- - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
mkin versiont1 [s]t2 [s]OSCPURmkint1t2
LinuxRyzen 7 1700NA 0.9.48.1 3.610 11.019
LinuxRyzen 7 1700NA 0.9.49.1 8.184 22.889
LinuxRyzen 7 1700NA 0.9.49.2 7.064 12.558
LinuxRyzen 7 1700NA 0.9.49.3 7.296 21.239
LinuxRyzen 7 1700NA 0.9.49.4 5.936 20.545
LinuxRyzen 7 1700NA 0.9.50.2 1.714 3.971
LinuxRyzen 7 1700NA 0.9.50.3 1.752 4.156
LinuxRyzen 7 1700NA 0.9.50.4 1.786 3.729
LinuxRyzen 7 1700NA 1.0.31.7223.4191.8813.504
1.0.3.90002.7703.458LinuxRyzen 7 1700NA1.0.41.8673.450
LinuxRyzen 7 17004.1.31.1.01.7913.289
LinuxRyzen 7 17004.2.11.1.01.8423.453
Linuxi7-4710MQ4.2.11.1.01.9594.116
Linuxi7-4710MQ4.1.31.1.01.8773.906
Linuxi7-4710MQ4.2.11.1.11.6443.172
LinuxRyzen 7 17004.2.11.1.11.7703.377
LinuxRyzen 7 17004.2.11.1.21.9403.619
-
-

-One metabolite

+
+

One metabolite +

Constant variance (t3), two-component error model (t4), and variance by variable (t5) for three models fitted to one dataset, i.e. three fits for each test.

- - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
mkin versiont3 [s]t4 [s]t5 [s]OSCPURmkint3t4t5
LinuxRyzen 7 1700NA 0.9.48.1 3.764 14.347 9.495
LinuxRyzen 7 1700NA 0.9.49.1 4.649 13.789 6.395
LinuxRyzen 7 1700NA 0.9.49.2 4.786 8.461 5.675
LinuxRyzen 7 1700NA 0.9.49.3 4.510 13.805 7.386
LinuxRyzen 7 1700NA 0.9.49.4 4.446 15.335 6.002
LinuxRyzen 7 1700NA 0.9.50.2 1.402 6.174 2.764
LinuxRyzen 7 1700NA 0.9.50.3 1.430 6.615 2.878
LinuxRyzen 7 1700NA 0.9.50.4 1.397 7.251 2.810
LinuxRyzen 7 1700NA 1.0.31.4026.3432.8021.4306.3442.798
1.0.3.90001.4056.4172.824LinuxRyzen 7 1700NA1.0.41.4156.3642.820
LinuxRyzen 7 17004.1.31.1.01.3106.2792.681
LinuxRyzen 7 17004.2.11.1.03.80221.2478.461
Linuxi7-4710MQ4.2.11.1.03.33419.5217.565
Linuxi7-4710MQ4.1.31.1.01.5788.0583.339
Linuxi7-4710MQ4.2.11.1.11.2305.8392.444
LinuxRyzen 7 17004.2.11.1.11.3085.7582.558
LinuxRyzen 7 17004.2.11.1.21.4906.0352.799
-
-

-Two metabolites

+
+

Two metabolites +

Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.

- - - - - - - + + + + + + + + + + + + + @@ -341,6 +545,9 @@ + + + @@ -350,6 +557,9 @@ + + + @@ -359,6 +569,9 @@ + + + @@ -368,6 +581,9 @@ + + + @@ -377,6 +593,9 @@ + + + @@ -386,6 +605,9 @@ + + + @@ -395,6 +617,9 @@ + + + @@ -404,22 +629,112 @@ + + + - - - - - - + + + + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + + +
mkin versiont6 [s]t7 [s]t8 [s]t9 [s]t10 [s]t11 [s]OSCPURmkint6t7t8t9t10t11
LinuxRyzen 7 1700NA 0.9.48.1 2.623 4.58731.267
LinuxRyzen 7 1700NA 0.9.49.1 2.542 4.1285.636
LinuxRyzen 7 1700NA 0.9.49.2 2.723 4.4785.574
LinuxRyzen 7 1700NA 0.9.49.3 2.643 4.3747.365
LinuxRyzen 7 1700NA 0.9.49.4 2.635 4.2595.626
LinuxRyzen 7 1700NA 0.9.50.2 0.777 1.2362.987
LinuxRyzen 7 1700NA 0.9.50.3 0.858 1.2643.073
LinuxRyzen 7 1700NA 0.9.50.4 0.783 1.2823.105
LinuxRyzen 7 1700NA 1.0.30.7711.2511.4643.0741.9402.8310.7631.2441.4573.0541.9232.839
1.0.3.90000.7721.263LinuxRyzen 7 1700NA1.0.40.7851.2521.4663.0911.9362.826
LinuxRyzen 7 17004.1.31.1.00.7441.2271.2883.5531.8952.738
LinuxRyzen 7 17004.2.11.1.03.0184.1655.03610.8446.6239.722
Linuxi7-4710MQ4.2.11.1.02.5223.7924.14311.2685.9358.728
Linuxi7-4710MQ4.1.31.1.00.9071.5351.5894.5442.3023.463
Linuxi7-4710MQ4.2.11.1.10.6781.0951.1493.2471.6582.472
LinuxRyzen 7 17004.2.11.1.10.6961.1241.3212.7861.7442.566
LinuxRyzen 7 17004.2.11.1.20.8571.295 1.4833.1011.9582.8432.9891.9192.766
@@ -438,11 +753,13 @@ @@ -451,5 +768,7 @@ + + -- cgit v1.2.1