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authorJohannes Ranke <jranke@uni-bremen.de>2018-09-14 16:57:17 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2018-09-14 17:00:08 +0200
commit70d158c4dd919f4f77bc12f8ace333d29d249b79 (patch)
treeab0dd14d85a0c1506262bb6866e2cc49c2400389 /docs/articles/web_only/compiled_models.html
parentd52e522a9abea09fae1189b066e2a2e1dbb9cb34 (diff)
Remove two vignettes from the package but not from docs
- Rebuild static documentation - Adapt test to new approach to two component error model where the model is inadequate
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+ <h1>Performance benefit by using compiled model definitions in mkin</h1>
+ <h4 class="author">Johannes Ranke</h4>
+
+ <h4 class="date">2018-09-14</h4>
+
+
+ <div class="hidden name"><code>compiled_models.Rmd</code></div>
+
+ </div>
+
+
+
+<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" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">Sys.which</span>(<span class="st">"gcc"</span>)</a></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" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw">library</span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a>
+<a class="sourceLine" id="cb3-2" data-line-number="2">SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a>
+<a class="sourceLine" id="cb3-3" data-line-number="3"> <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>),</a>
+<a class="sourceLine" id="cb3-4" data-line-number="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></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" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) {</a>
+<a class="sourceLine" id="cb5-2" data-line-number="2"> 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>(</a>
+<a class="sourceLine" id="cb5-3" data-line-number="3"> <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,</a>
+<a class="sourceLine" id="cb5-4" data-line-number="4"> <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>,</a>
+<a class="sourceLine" id="cb5-5" data-line-number="5"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
+<a class="sourceLine" id="cb5-6" data-line-number="6"> <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,</a>
+<a class="sourceLine" id="cb5-7" data-line-number="7"> <span class="dt">solution_type =</span> <span class="st">"eigen"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
+<a class="sourceLine" id="cb5-8" data-line-number="8"> <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,</a>
+<a class="sourceLine" id="cb5-9" data-line-number="9"> <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
+<a class="sourceLine" id="cb5-10" data-line-number="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a>
+<a class="sourceLine" id="cb5-11" data-line-number="11"> <span class="kw">print</span>(b<span class="fl">.1</span>)</a>
+<a class="sourceLine" id="cb5-12" data-line-number="12"> 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>])</a>
+<a class="sourceLine" id="cb5-13" data-line-number="13">} <span class="cf">else</span> {</a>
+<a class="sourceLine" id="cb5-14" data-line-number="14"> factor_SFO_SFO &lt;-<span class="st"> </span><span class="ot">NA</span></a>
+<a class="sourceLine" id="cb5-15" data-line-number="15"> <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>)</a>
+<a class="sourceLine" id="cb5-16" data-line-number="16">}</a></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 2.120 1.000 2.118 0.000
+## 1 deSolve, not compiled 3 17.195 8.111 17.187 0.000
+## 2 Eigenvalue based 3 2.589 1.221 2.582 0.004
+## 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 8 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" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) {</a>
+<a class="sourceLine" id="cb8-2" data-line-number="2"> FOMC_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a>
+<a class="sourceLine" id="cb8-3" data-line-number="3"> <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>),</a>
+<a class="sourceLine" id="cb8-4" data-line-number="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>))</a>
+<a class="sourceLine" id="cb8-5" data-line-number="5"></a>
+<a class="sourceLine" id="cb8-6" data-line-number="6"> 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>(</a>
+<a class="sourceLine" id="cb8-7" data-line-number="7"> <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,</a>
+<a class="sourceLine" id="cb8-8" data-line-number="8"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
+<a class="sourceLine" id="cb8-9" data-line-number="9"> <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>),</a>
+<a class="sourceLine" id="cb8-10" data-line-number="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a>
+<a class="sourceLine" id="cb8-11" data-line-number="11"> <span class="kw">print</span>(b<span class="fl">.2</span>)</a>
+<a class="sourceLine" id="cb8-12" data-line-number="12"> 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>])</a>
+<a class="sourceLine" id="cb8-13" data-line-number="13">} <span class="cf">else</span> {</a>
+<a class="sourceLine" id="cb8-14" data-line-number="14"> factor_FOMC_SFO &lt;-<span class="st"> </span><span class="ot">NA</span></a>
+<a class="sourceLine" id="cb8-15" data-line-number="15"> <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>)</a>
+<a class="sourceLine" id="cb8-16" data-line-number="16">}</a></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 3.761 1.000 3.758 0.000
+## 1 deSolve, not compiled 3 36.462 9.695 36.441 0.004
+## user.child sys.child
+## 2 0 0
+## 1 0 0</code></pre>
+<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 0.9.47.5 on</p>
+<pre><code>## R version 3.5.1 (2018-07-02)
+## 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>
+</div>
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+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <div id="tocnav">
+ <h2 class="hasAnchor">
+<a href="#tocnav" class="anchor"></a>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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