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      <h1>Performance benefit by using compiled model definitions in mkin</h1>
                        <h4 class="author">Johannes Ranke</h4>
            
            <h4 class="date">2018-03-21</h4>
          </div>

    
    
<div class="contents">
<div id="model-that-can-also-be-solved-with-eigenvalues" class="section level2">
<h2 class="hasAnchor">
<a href="#model-that-can-also-be-solved-with-eigenvalues" class="anchor"></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>, <span class="dt">quietly =</span> <span class="ot">TRUE</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 benchmark package.</p>
<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> &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></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_<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_<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_<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 &lt;-<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>])
} <span class="cf">else</span> {
  factor_SFO_SFO &lt;-<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   2.155    1.000     2.152        0
## 1 deSolve, not compiled            3  15.124    7.018    15.109        0
## 2      Eigenvalue based            3   2.576    1.195     2.574        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>
</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"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) {
  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>))

  b<span class="fl">.2</span> &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></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_<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_<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 &lt;-<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>])
} <span class="cf">else</span> {
  factor_FOMC_SFO &lt;-<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   3.419    1.000     3.415        0
## 1 deSolve, not compiled            3  31.159    9.113    31.130        0
##   user.child sys.child
## 2          0         0
## 1          0         0</code></pre>
<p>Here we get a performance benefit of a factor of 9 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 3.4.4 (2018-03-15)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 9 (stretch)</code></pre>
<pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre>
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<li><a href="#model-that-can-also-be-solved-with-eigenvalues">Model that can also be solved with Eigenvalues</a></li>
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