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<!-- 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]>
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      <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 &lt;-<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> &lt;-<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> &lt;-<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 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
##        max neval cld
##  6587.9031     3   b
##   954.8026     3  a 
##   774.2345     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>) &lt;-<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, 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 &lt;-<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> &lt;-<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> &lt;-<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
##        max neval cld
##  13.584407     3   b
##   1.372385     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>
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  <div class="col-md-3 hidden-xs">
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      <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>

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