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diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html new file mode 100644 index 00000000..1eeb78c6 --- /dev/null +++ b/docs/articles/compiled_models.html @@ -0,0 +1,146 @@ +<!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]> +<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"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header><div class="row"> + <div class="col-md-9"> + <div class="page-header toc-ignore"> + <h1>Performance benefit by using compiled model definitions in mkin</h1> + <h4 class="author">Johannes Ranke</h4> + + <h4 class="date">2016-10-06</h4> + </div> + + + +<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> +<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 +## "/usr/bin/gcc"</code></pre> +<p>First, we build a simple degradation model for a parent compound with one metabolite.</p> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">"mkin"</span>) +SFO_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">"SFO"</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>))</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 microbenchmark package.</p> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">"microbenchmark"</span>) +<span class="kw">library</span>(<span class="st">"ggplot2"</span>) +mb<span class="fl">.1</span> <-<span class="st"> </span><span class="kw">microbenchmark</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="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="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="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), + <span class="dt">times =</span> <span class="dv">3</span>, <span class="dt">control =</span> <span class="kw">list</span>(<span class="dt">warmup =</span> <span class="dv">0</span>))</code></pre></div> +<pre><code>## Warning in microbenchmark(`deSolve, not compiled` = mkinfit(SFO_SFO, +## FOCUS_2006_D, : Could not measure overhead. Your clock might lack +## precision.</code></pre> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.1</span> <-<span class="st"> </span><span class="kw">summary</span>(mb<span class="fl">.1</span>) +<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 6407.0333 6420.1971 6434.6510 6433.3609 6448.4598 +## Eigenvalue based 887.4338 891.8401 906.9270 896.2463 916.6735 +## deSolve, compiled 720.2433 727.8793 733.2019 735.5152 739.6812 +## max neval cld +## 6463.5587 3 c +## 937.1007 3 b +## 743.8472 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 8.7 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> +<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 8.746741 +## Eigenvalue based 1.218529 +## 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> +<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>), + <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> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">mb<span class="fl">.2</span> <-<span class="st"> </span><span class="kw">microbenchmark</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="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="dt">times =</span> <span class="dv">3</span>, <span class="dt">control =</span> <span class="kw">list</span>(<span class="dt">warmup =</span> <span class="dv">0</span>))</code></pre></div> +<pre><code>## Warning in microbenchmark(`deSolve, not compiled` = mkinfit(FOMC_SFO, +## FOCUS_2006_D, : Could not measure overhead. Your clock might lack +## precision.</code></pre> +<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 13.501761 13.52142 13.697021 13.541086 13.794651 +## deSolve, compiled 1.359921 1.35996 1.366796 1.359999 1.370233 +## max neval cld +## 14.048217 3 b +## 1.380468 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>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 class="col-md-3 hidden-xs"> + <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> + <li><a href="#benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues">Benchmark for a model that can not be solved with Eigenvalues</a></li> + </ul></div> + </div> + +</div> + + + <footer><p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. 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