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Diffstat (limited to 'vignettes/web_only/benchmarks.html')
| -rw-r--r-- | vignettes/web_only/benchmarks.html | 243 |
1 files changed, 112 insertions, 131 deletions
diff --git a/vignettes/web_only/benchmarks.html b/vignettes/web_only/benchmarks.html index 054b4afc..c80a7e44 100644 --- a/vignettes/web_only/benchmarks.html +++ b/vignettes/web_only/benchmarks.html @@ -1,17 +1,17 @@ <!DOCTYPE html> -<html xmlns="http://www.w3.org/1999/xhtml"> +<html> <head> <meta charset="utf-8" /> -<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <meta name="generator" content="pandoc" /> +<meta http-equiv="X-UA-Compatible" content="IE=EDGE" /> <meta name="author" content="Johannes Ranke" /> -<meta name="date" content="2019-05-02" /> +<meta name="date" content="2020-05-10" /> <title>Benchmark timings for mkin on various systems</title> @@ -69,8 +69,6 @@ overflow: auto; margin-left: 2%; position: fixed; border: 1px solid #ccc; -webkit-border-radius: 6px; -moz-border-radius: 6px; border-radius: 6px; } @@ -98,10 +96,15 @@ font-size: 12px; .tocify-subheader .tocify-subheader { text-indent: 30px; } - .tocify-subheader .tocify-subheader .tocify-subheader { text-indent: 40px; } +.tocify-subheader .tocify-subheader .tocify-subheader .tocify-subheader { +text-indent: 50px; +} +.tocify-subheader .tocify-subheader .tocify-subheader .tocify-subheader .tocify-subheader { +text-indent: 60px; +} .tocify .tocify-item > a, .tocify .nav-list .nav-header { margin: 0px; @@ -504,13 +507,13 @@ float: none; item.append($("<a/>", { - "text": self.text() + "html": self.html() })); } else { - item.text(self.text()); + item.html(self.html()); } @@ -1285,7 +1288,7 @@ window.initializeCodeFolding = function(show) { // create a collapsable div to wrap the code in var div = $('<div class="collapse r-code-collapse"></div>'); - if (show) + if (show || $(this)[0].classList.contains('fold-show')) div.addClass('in'); var id = 'rcode-643E0F36' + currentIndex++; div.attr('id', id); @@ -1401,7 +1404,6 @@ code { } img { max-width:100%; - height: auto; } .tabbed-pane { padding-top: 12px; @@ -1463,6 +1465,7 @@ summary { border: none; display: inline-block; border-radius: 4px; + background-color: transparent; } .tabset-dropdown > .nav-tabs.nav-tabs-open > li { @@ -1475,56 +1478,12 @@ summary { } </style> -<script> -$(document).ready(function () { - window.buildTabsets("TOC"); -}); - -$(document).ready(function () { - $('.tabset-dropdown > .nav-tabs > li').click(function () { - $(this).parent().toggleClass('nav-tabs-open') - }); -}); -</script> - <!-- code folding --> <style type="text/css"> .code-folding-btn { margin-bottom: 4px; } </style> -<script> -$(document).ready(function () { - window.initializeCodeFolding("show" === "show"); -}); -</script> - - - -<script> -$(document).ready(function () { - // move toc-ignore selectors from section div to header - $('div.section.toc-ignore') - .removeClass('toc-ignore') - .children('h1,h2,h3,h4,h5').addClass('toc-ignore'); - // establish options - var options = { - selectors: "h1,h2,h3", - theme: "bootstrap3", - context: '.toc-content', - hashGenerator: function (text) { - return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase(); - }, - ignoreSelector: ".toc-ignore", - scrollTo: 0 - }; - options.showAndHide = true; - options.smoothScroll = true; - - // tocify - var toc = $("#TOC").tocify(options).data("toc-tocify"); -}); -</script> <style type="text/css"> @@ -1538,6 +1497,12 @@ $(document).ready(function () { } } +@media print { +.toc-content { + /* see https://github.com/w3c/csswg-drafts/issues/4434 */ + float: right; +} +} .toc-content { padding-left: 30px; @@ -1573,8 +1538,6 @@ div.tocify { .tocify-subheader .tocify-item { font-size: 0.90em; - padding-left: 25px; - text-indent: 0; } .tocify .list-group-item { @@ -1620,7 +1583,7 @@ div.tocify { <h1 class="title toc-ignore">Benchmark timings for mkin on various systems</h1> <h4 class="author">Johannes Ranke</h4> -<h4 class="date">2019-05-02</h4> +<h4 class="date">2020-05-10</h4> </div> @@ -1640,11 +1603,16 @@ if (mkin_version > "0.9.48.1") { } else { mmkin_bench <- function(models, datasets, error_model = NULL) mmkin(models, datasets, reweight.method = error_model, cores = 1, quiet = TRUE) }</code></pre> -<pre class="r"><code># Parent only -t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D)))[["elapsed"]] -t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D), error_model = "tc"))[["elapsed"]]</code></pre> +<pre class="r"><code>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"]]</code></pre> <pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge: -## false convergence (8)</code></pre> +## iteration limit reached without convergence (10) + +## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge: +## iteration limit reached without convergence (10)</code></pre> <pre class="r"><code># One metabolite SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), @@ -1658,25 +1626,11 @@ SFO_SFO <- mkinmod( parent = mkinsub("FOMC", "m1"), m1 = mkinsub("SFO"))</code></pre> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<pre class="r"><code>t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D)))[["elapsed"]]</code></pre> -<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data</code></pre> -<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data - -## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data</code></pre> -<pre class="r"><code>t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(subset(FOCUS_2006_D, value != 0)), error_model = "tc"))[["elapsed"]] -t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D), error_model = "obs"))[["elapsed"]]</code></pre> -<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data - -## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data - -## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data</code></pre> -<pre class="r"><code># Two metabolites, synthetic data +<pre class="r"><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"), @@ -1701,91 +1655,70 @@ t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_ 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</code></pre> -<pre><code>## CPU -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 AMD Ryzen 7 1700 Eight-Core Processor -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 AMD Ryzen 7 1700 Eight-Core Processor -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 AMD Ryzen 7 1700 Eight-Core Processor -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 AMD Ryzen 7 1700 Eight-Core Processor -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 AMD Ryzen 7 1700 Eight-Core Processor -## OS -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 Linux -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 Linux -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 Linux -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 Linux -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 Linux -## mkin -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 0.9.48.1 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 0.9.49.1 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 0.9.49.2 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 0.9.49.3 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 0.9.49.4 -## t1 +mkin_benchmarks[, -c(1:3)]</code></pre> +<pre><code>## 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 6.023 +## 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 1.658 ## 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 20.409 +## 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 3.820 ## 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 4.283 +## 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 3.424 ## 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 14.531 -## t5 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.744 -## t6 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.518 -## t7 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.211 -## t8 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.02 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.557 +## 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 18.375 +## 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 7.480 2.188 +## 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 3.69 3.87 ## 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 7.739 +## 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 8.872 ## 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 3.413 +## 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 6.257 ## 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 5.588</code></pre> +## 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 9.289</code></pre> <pre class="r"><code>save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")</code></pre> </div> @@ -1809,6 +1742,54 @@ $(document).ready(function () { </script> +<!-- tabsets --> + +<script> +$(document).ready(function () { + window.buildTabsets("TOC"); +}); + +$(document).ready(function () { + $('.tabset-dropdown > .nav-tabs > 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