diff options
Diffstat (limited to 'vignettes/web_only/benchmarks.rmd')
| -rw-r--r-- | vignettes/web_only/benchmarks.rmd | 53 |
1 files changed, 39 insertions, 14 deletions
diff --git a/vignettes/web_only/benchmarks.rmd b/vignettes/web_only/benchmarks.rmd index 9697f96b..9ac87631 100644 --- a/vignettes/web_only/benchmarks.rmd +++ b/vignettes/web_only/benchmarks.rmd @@ -1,7 +1,7 @@ --- title: "Benchmark timings for mkin" author: "Johannes Ranke" -date: Last change 13 May 2020 (rebuilt `r Sys.Date()`) +date: Last change 30 June 2022 (rebuilt `r Sys.Date()`) output: html_document: toc: true @@ -19,19 +19,40 @@ opts_chunk$set(tidy = FALSE, cache = FALSE) library("mkin") ``` -Each system is characterized by its CPU type, the operating system type and the -mkin version. Currently only values for one system are available. A compiler -was available, so if no analytical solution was available, compiled ODE models are -used. +Each system is characterized by the operating system type, the CPU type, the +mkin version, and, as in June 2022 the current R version lead to worse +performance, the R version. A compiler was available, so if no analytical +solution was available, compiled ODE models are used. + +Every fit is only performed once, so the accuracy of the benchmarks is limited. ```{r include = FALSE} cpu_model <- benchmarkme::get_cpu()$model_name +# Abbreviate CPU identifiers +cpu_model <- gsub("AMD ", "", cpu_model) +cpu_model <- gsub("Intel\\(R\\) Core\\(TM\\) ", "", cpu_model) +cpu_model <- gsub(" Eight-Core Processor", "", cpu_model) +cpu_model <- gsub(" CPU @ 2.50GHz", "", cpu_model) + 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) +R_version <- paste0(R.version$major, ".", R.version$minor) +system_string <- paste0(operating_system, ", ", cpu_model, ", mkin ", mkin_version, ", R ", R_version) + +benchmark_path = normalizePath("~/git/mkin/vignettes/web_only/mkin_benchmarks.rda") +load(benchmark_path) + +# Used for reformatting the data on 2022-06-30 +# mkin_benchmarks[, "R"] <- NA +# mkin_benchmarks <- mkin_benchmarks[c(2, 1, 15, 3, 4:14)] +# mkin_benchmarks[, "CPU"] <- gsub("AMD.*", "Ryzen 7 1700", mkin_benchmarks[, "CPU"]) +# mkin_benchmarks[, "CPU"] <- gsub("Intel.*", "i7-4710MQ", mkin_benchmarks[, "CPU"]) +# rownames(mkin_benchmarks) <- gsub("AMD Ryzen 7 1700 Eight-Core Processor", "Ryzen 7 1700", rownames(mkin_benchmarks)) +# rownames(mkin_benchmarks) <- gsub("Intel\\(R\\) Core\\(TM\\) i7-4710MQ CPU @ 2.50GHz", "i7-4710MQ", rownames(mkin_benchmarks)) +# rownames(mkin_benchmarks) <- gsub(" version", "", rownames(mkin_benchmarks)) + +mkin_benchmarks[system_string, c("CPU", "OS", "mkin", "R")] <- + c(cpu_model, operating_system, mkin_version, R_version) if (mkin_version > "0.9.48.1") { mmkin_bench <- function(models, datasets, error_model = "const") { @@ -111,12 +132,16 @@ t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), ```{r results} 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") +save(mkin_benchmarks, file = benchmark_path) +# Hide rownames from kable for results section +rownames(mkin_benchmarks) <- NULL ``` ## Results -Benchmarks for all available error models are shown. +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 @@ -124,7 +149,7 @@ Constant variance (t1) and two-component error model (t2) for four models fitted to two datasets, i.e. eight fits for each test. ```{r, echo = FALSE} -kable(mkin_benchmarks[, 4:5]) +kable(mkin_benchmarks[, c(1:4, 5:6)]) ``` ### One metabolite @@ -133,7 +158,7 @@ Constant variance (t3), two-component error model (t4), and variance by variable for three models fitted to one dataset, i.e. three fits for each test. ```{r, echo = FALSE} -kable(mkin_benchmarks[, 6:8]) +kable(mkin_benchmarks[, c(1:4, 7:9)]) ``` ### Two metabolites @@ -143,5 +168,5 @@ variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test. ```{r, echo = FALSE} -kable(mkin_benchmarks[, 9:14]) +kable(mkin_benchmarks[, c(1:4, 10:15)]) ``` |