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diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index d2e1d87d..e02b9cf3 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -1,10 +1,10 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Performance benefit by using compiled model definitions in mkin. mkin</title><!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<!-- Generated by pkgdown: do not edit by hand --><html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Performance benefit by using compiled model definitions in mkin • mkin</title><!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"><script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--></head><body> - <div class="container"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container template-vignette"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> @@ -30,6 +30,7 @@ </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header><div class="row"> <div class="col-md-9"> @@ -37,13 +38,14 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-10-06</h4> + <h4 class="date">2016-10-26</h4> </div> +<div class="contents"> <div id="benchmark-for-a-model-that-can-also-be-solved-with-eigenvalues" class="section level2"> -<h2>Benchmark for a model that can also be solved with Eigenvalues</h2> +<h2 class="hasAnchor"><html><body><a href="#benchmark-for-a-model-that-can-also-be-solved-with-eigenvalues" class="anchor"> </a></body></html>Benchmark for a model that can also be solved with Eigenvalues</h2> <p>This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The <code><a href="../reference/mkinmod.html">mkinmod()</a></code> function checks for presence of the gcc compiler using</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">Sys.which</span>(<span class="st">"gcc"</span>)</code></pre></div> <pre><code>## gcc @@ -73,25 +75,25 @@ mb<span class="fl">.1</span> <-<span class="st"> </span><span class="kw">micr <span class="kw">print</span>(mb<span class="fl">.1</span>)</code></pre></div> <pre><code>## Unit: milliseconds ## expr min lq mean median uq -## deSolve, not compiled 6365.2773 6407.1609 6467.4083 6449.0446 6518.4738 -## Eigenvalue based 872.0339 912.6754 926.7178 953.3169 954.0597 -## deSolve, compiled 730.1252 740.7149 751.8881 751.3045 762.7695 +## deSolve, not compiled 6298.7342 6308.6792 6343.9668 6318.6243 6366.5831 +## Eigenvalue based 871.7379 880.7757 903.5267 889.8135 919.4211 +## deSolve, compiled 724.9025 730.6729 732.9837 736.4432 737.0243 ## max neval cld -## 6587.9031 3 b -## 954.8026 3 a -## 774.2345 3 a</code></pre> +## 6414.5420 3 c +## 949.0287 3 b +## 737.6054 3 a</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.1</span>)</code></pre></div> <p><img src="compiled_models_files/figure-html/benchmark_SFO_SFO-1.png" width="672"></p> <p>We see that using the compiled model is by a factor of 8.6 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rownames</span>(smb<span class="fl">.1</span>) <-<span class="st"> </span>smb<span class="fl">.1</span>$expr smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="fl">.1</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div> <pre><code>## median -## deSolve, not compiled 8.583796 -## Eigenvalue based 1.268882 +## deSolve, not compiled 8.579920 +## Eigenvalue based 1.208258 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> -<h2>Benchmark for a model that can not be solved with Eigenvalues</h2> +<h2 class="hasAnchor"><html><body><a href="#benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="anchor"> </a></body></html>Benchmark for a model that can not be solved with Eigenvalues</h2> <p>This evaluation is also taken from the example section of mkinfit.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>( <span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>), @@ -108,28 +110,29 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span> <-<span class="st"> </span><span class="kw">summary</span>(mb<span class="fl">.2</span>) <span class="kw">print</span>(mb<span class="fl">.2</span>)</code></pre></div> <pre><code>## Unit: seconds -## expr min lq mean median uq -## deSolve, not compiled 13.464194 13.498471 13.52712 13.532748 13.558577 -## deSolve, compiled 1.328628 1.342168 1.35224 1.355707 1.364046 +## expr min lq mean median uq +## deSolve, not compiled 13.265212 13.330161 13.412053 13.395109 13.485473 +## deSolve, compiled 1.322466 1.326851 1.364827 1.331236 1.386007 ## max neval cld -## 13.584407 3 b -## 1.372385 3 a</code></pre> +## 13.575837 3 b +## 1.440779 3 a</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span>[<span class="st">"median"</span>]/smb<span class="fl">.2</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div> <pre><code>## median ## 1 NA ## 2 NA</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.2</span>)</code></pre></div> <p><img src="compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png" width="672"></p> -<p>Here we get a performance benefit of a factor of 10 using the version of the differential equation model compiled from C code!</p> +<p>Here we get a performance benefit of a factor of 10.1 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.44.9000 on</p> <pre><code>## R version 3.3.1 (2016-06-21) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 8 (jessie)</code></pre> <pre><code>## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</code></pre> </div> +</div> </div> - <div class="col-md-3 hidden-xs"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"><li><a href="#benchmark-for-a-model-that-can-also-be-solved-with-eigenvalues">Benchmark for a model that can also be solved with Eigenvalues</a></li> @@ -140,7 +143,14 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" </div> - <footer><p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. 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