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<h1 data-toc-skip>Performance benefit by using compiled model
definitions in mkin</h1>
<h4 data-toc-skip class="author">Johannes
Ranke</h4>
<h4 data-toc-skip class="date">2023-10-30</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/compiled_models.rmd" class="external-link"><code>vignettes/web_only/compiled_models.rmd</code></a></small>
<div class="hidden name"><code>compiled_models.rmd</code></div>
</div>
<div class="section level2">
<h2 id="how-to-benefit-from-compiled-models">How to benefit from compiled models<a class="anchor" aria-label="anchor" href="#how-to-benefit-from-compiled-models"></a>
</h2>
<p>When using an mkin version equal to or greater than 0.9-36 and a C
compiler is available, you will see a message that the model is being
compiled from autogenerated C code when defining a model using mkinmod.
Starting from version 0.9.49.9, the <code><a href="../../reference/mkinmod.html">mkinmod()</a></code> function
checks for presence of a compiler using</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu">pkgbuild</span><span class="fu">::</span><span class="fu"><a href="https://pkgbuild.r-lib.org/reference/has_compiler.html" class="external-link">has_compiler</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>In previous versions, it used <code>Sys.which("gcc")</code> for this
check.</p>
<p>On Linux, you need to have the essential build tools like make and
gcc or clang installed. On Debian based linux distributions, these will
be pulled in by installing the build-essential package.</p>
<p>On MacOS, which I do not use personally, I have had reports that a
compiler is available by default.</p>
<p>On Windows, you need to install Rtools and have the path to its bin
directory in your PATH variable. You do not need to modify the PATH
variable when installing Rtools. Instead, I would recommend to put the
line</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/Sys.setenv.html" class="external-link">Sys.setenv</a></span><span class="op">(</span>PATH <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"C:/Rtools/bin"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"PATH"</span><span class="op">)</span>, sep<span class="op">=</span><span class="st">";"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<p>into your .Rprofile startup file. This is just a text file with some
R code that is executed when your R session starts. It has to be named
.Rprofile and has to be located in your home directory, which will
generally be your Documents folder. You can check the location of the
home directory used by R by issuing</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"HOME"</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="comparison-with-other-solution-methods">Comparison with other solution methods<a class="anchor" aria-label="anchor" href="#comparison-with-other-solution-methods"></a>
</h2>
<p>First, we build a simple degradation model for a parent compound with
one metabolite, and we remove zero values from the dataset.</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="st"><a href="https://pkgdown.jrwb.de/mkin/">"mkin"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span>
<span> parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span>
<span> m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></span></code></pre></div>
<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. In the output of
below code, the warnings about zero being removed from the FOCUS D
dataset are suppressed. Since mkin version 0.9.49.11, an analytical
solution is also implemented, which is included in the tests below.</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
<span> <span class="va">b.1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span>
<span> <span class="st">"deSolve, not compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>,</span>
<span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>,</span>
<span> use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> <span class="st">"Eigenvalue based"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>,</span>
<span> solution_type <span class="op">=</span> <span class="st">"eigen"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> <span class="st">"deSolve, compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>,</span>
<span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> <span class="st">"analytical"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>,</span>
<span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>,</span>
<span> use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>,</span>
<span> columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"replications"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span><span class="op">)</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">b.1</span><span class="op">)</span></span>
<span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span></span>
<span><span class="op">}</span></span></code></pre></div>
<pre><code><span><span class="co">## test replications relative elapsed</span></span>
<span><span class="co">## 4 analytical 1 1.000 0.213</span></span>
<span><span class="co">## 3 deSolve, compiled 1 1.418 0.302</span></span>
<span><span class="co">## 2 Eigenvalue based 1 2.000 0.426</span></span>
<span><span class="co">## 1 deSolve, not compiled 1 23.535 5.013</span></span></code></pre>
<p>We see that using the compiled model is by more than a factor of 10
faster than using deSolve without compiled code.</p>
</div>
<div class="section level2">
<h2 id="model-without-analytical-solution">Model without analytical solution<a class="anchor" aria-label="anchor" href="#model-without-analytical-solution"></a>
</h2>
<p>This evaluation is also taken from the example section of mkinfit. No
analytical solution is available for this system, and now Eigenvalue
based solution is possible, so only deSolve using with or without
compiled code is available.</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
<span> <span class="va">FOMC_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span>
<span> parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span>
<span> m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span> <span class="va">b.2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span>
<span> <span class="st">"deSolve, not compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>,</span>
<span> use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> <span class="st">"deSolve, compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>,</span>
<span> columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"replications"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span><span class="op">)</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">b.2</span><span class="op">)</span></span>
<span> <span class="va">factor_FOMC_SFO</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">b.2</span><span class="op">[</span><span class="st">"1"</span>, <span class="st">"relative"</span><span class="op">]</span><span class="op">)</span></span>
<span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span>
<span> <span class="va">factor_FOMC_SFO</span> <span class="op"><-</span> <span class="cn">NA</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"R package benchmark is not available"</span><span class="op">)</span></span>
<span><span class="op">}</span></span></code></pre></div>
<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
<pre><code><span><span class="co">## test replications relative elapsed</span></span>
<span><span class="co">## 2 deSolve, compiled 1 1.000 0.492</span></span>
<span><span class="co">## 1 deSolve, not compiled 1 20.398 10.036</span></span></code></pre>
<p>Here we get a performance benefit of a factor of 20 using the version
of the differential equation model compiled from C code!</p>
<p>This vignette was built with mkin 1.2.6 on</p>
<pre><code><span><span class="co">## R version 4.3.1 (2023-06-16)</span></span>
<span><span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span></span>
<span><span class="co">## Running under: Ubuntu 22.04.3 LTS</span></span></code></pre>
<pre><code><span><span class="co">## CPU model: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</span></span></code></pre>
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