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<h1>Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author">Johannes Ranke</h4>
<h4 class="date">2016-12-08</h4>
</div>
<div class="contents">
<div id="model-that-can-also-be-solved-with-eigenvalues" class="section level2">
<h2 class="hasAnchor"><html><body><a href="#model-that-can-also-be-solved-with-eigenvalues" class="anchor"> </a></body></html>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>)</code></pre></div>
<pre><code>## Loading required package: minpack.lm</code></pre>
<pre><code>## Loading required package: rootSolve</code></pre>
<pre><code>## Loading required package: inline</code></pre>
<pre><code>## Loading required package: methods</code></pre>
<pre><code>## Loading required package: parallel</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">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 5006.3815 5014.4629 5112.7115 5022.5443 5165.8765
## Eigenvalue based 840.3027 874.3549 892.0593 908.4071 917.9376
## deSolve, compiled 706.9909 712.8031 723.4380 718.6154 731.6615
## max neval cld
## 5309.2087 3 b
## 927.4680 3 a
## 744.7077 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 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 6.989197
## Eigenvalue based 1.264108
## deSolve, compiled 1.000000</code></pre>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
<h2 class="hasAnchor"><html><body><a href="#model-that-can-not-be-solved-with-eigenvalues" class="anchor"> </a></body></html>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 11.015990 11.17783 11.24827 11.339674 11.364403
## deSolve, compiled 1.285264 1.29794 1.32988 1.310616 1.352189
## max neval cld
## 11.389132 3 b
## 1.393762 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 8.7 using the version of the differential equation model compiled from C code!</p>
<p>This vignette was built with mkin 0.9.45 on</p>
<pre><code>## R version 3.3.2 (2016-10-31)
## 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>
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<h2>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>
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