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<title>Performance benefit by using compiled model definitions in mkin</title>
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<h1 class="title toc-ignore">Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author"><em>Johannes Ranke</em></h4>
<h4 class="date"><em>2017-07-21</em></h4>
<div id="model-that-can-also-be-solved-with-eigenvalues" class="section level2">
<h2>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>mkinmod()</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: parallel</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">SFO_SFO <-<span class="st"> </span><span class="kw">mkinmod</span>(
<span class="dt">parent =</span> <span class="kw">mkinsub</span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),
<span class="dt">m1 =</span> <span class="kw">mkinsub</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)) {
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">mkinfit</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">mkinfit</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">mkinfit</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">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 {
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>## Loading required package: rbenchmark</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
## 3 deSolve, compiled 3 2.101 1.000 2.100 0.000
## 1 deSolve, not compiled 3 25.685 12.225 25.600 0.088
## 2 Eigenvalue based 3 2.729 1.299 2.728 0.000
## 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 12 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>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)) {
FOMC_SFO <-<span class="st"> </span><span class="kw">mkinmod</span>(
<span class="dt">parent =</span> <span class="kw">mkinsub</span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),
<span class="dt">m1 =</span> <span class="kw">mkinsub</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">mkinfit</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">mkinfit</span>(FOMC_SFO, FOCUS_2006_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 {
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 3.590 1.000 3.592 0.000
## 1 deSolve, not compiled 3 51.219 14.267 51.028 0.192
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
<p>Here we get a performance benefit of a factor of 14 using the version of the differential equation model compiled from C code!</p>
<p>This vignette was built with mkin 0.9.45.2 on</p>
<pre><code>## R version 3.4.1 (2017-06-30)
## 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>
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