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| -rw-r--r-- | docs/articles/compiled_models.html | 62 |
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diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index d5d29a1a..9f0b5708 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -8,8 +8,11 @@ <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://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Performance benefit by using compiled model definitions in mkin"> +<meta property="og:description" content=""> +<meta name="twitter:card" content="summary"> +<!-- mathjax --><script src="https://mathjax.rstudio.com/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]--> @@ -77,7 +80,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-01-16</h4> + <h4 class="date">2018-03-01</h4> </div> @@ -97,73 +100,66 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.</p> -<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">if (<span class="kw">require</span>(rbenchmark)) { +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) { b<span class="fl">.1</span> <-<span class="st"> </span><span class="kw">benchmark</span>( - <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_2006_D, + <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), - <span class="st">"Eigenvalue based"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_2006_D, + <span class="st">"Eigenvalue based"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">solution_type =</span> <span class="st">"eigen"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), - <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_2006_D, + <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), <span class="dt">replications =</span> <span class="dv">3</span>) <span class="kw">print</span>(b<span class="fl">.1</span>) factor_SFO_SFO <-<span class="st"> </span><span class="kw">round</span>(b<span class="fl">.1</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>]) -} else { +} <span class="cf">else</span> { factor_SFO_SFO <-<span class="st"> </span><span class="ot">NA</span> <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>) }</code></pre></div> <pre><code>## Lade nötiges Paket: rbenchmark</code></pre> -<pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 1.940 1.000 1.940 0 -## 1 deSolve, not compiled 3 13.865 7.147 13.864 0 -## 2 Eigenvalue based 3 2.427 1.251 2.428 0 -## user.child sys.child -## 3 0 0 -## 1 0 0 -## 2 0 0</code></pre> -<p>We see that using the compiled model is by a factor of around 7 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> +<pre><code>## Warning in library(package, lib.loc = lib.loc, character.only = TRUE, +## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'</code></pre> +<pre><code>## [1] "R package benchmark is not available"</code></pre> +<p>We see that using the compiled model is by a factor of around NA 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> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> <h2 class="hasAnchor"> <a href="#model-that-can-not-be-solved-with-eigenvalues" class="anchor"></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">if (<span class="kw">require</span>(rbenchmark)) { +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) { 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>), <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>)) b<span class="fl">.2</span> <-<span class="st"> </span><span class="kw">benchmark</span>( - <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_2006_D, + <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), - <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_2006_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), + <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), <span class="dt">replications =</span> <span class="dv">3</span>) <span class="kw">print</span>(b<span class="fl">.2</span>) factor_FOMC_SFO <-<span class="st"> </span><span class="kw">round</span>(b<span class="fl">.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>]) -} else { +} <span class="cf">else</span> { factor_FOMC_SFO <-<span class="st"> </span><span class="ot">NA</span> <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>) }</code></pre></div> -<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 3.432 1.000 3.428 0 -## 1 deSolve, not compiled 3 28.844 8.404 28.840 0 -## user.child sys.child -## 2 0 0 -## 1 0 0</code></pre> -<p>Here we get a performance benefit of a factor of 8 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 0.9.47.1 on</p> +<pre><code>## Lade nötiges Paket: rbenchmark</code></pre> +<pre><code>## Warning in library(package, lib.loc = lib.loc, character.only = TRUE, +## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'</code></pre> +<pre><code>## [1] "R package benchmark is not available"</code></pre> +<p>Here we get a performance benefit of a factor of NA using the version of the differential equation model compiled from C code!</p> +<p>This vignette was built with mkin 0.9.46.3 on</p> <pre><code>## R version 3.4.3 (2017-11-30) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 9 (stretch)</code></pre> -<pre><code>## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</code></pre> +<pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre> </div> </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div id="tocnav"> - <h2>Contents</h2> + <h2 class="hasAnchor"> +<a href="#tocnav" class="anchor"></a>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#model-that-can-also-be-solved-with-eigenvalues">Model that can also be solved with Eigenvalues</a></li> <li><a href="#model-that-can-not-be-solved-with-eigenvalues">Model that can not be solved with Eigenvalues</a></li> @@ -179,7 +175,7 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> |