Initialize dev docsHEAD dev

author: Johannes Ranke <johannes.ranke@jrwb.de> 2025-02-14 09:15:20 +0100
committer: Johannes Ranke <johannes.ranke@jrwb.de> 2025-02-14 09:15:20 +0100
commit: 91a5834dd701211f929fd25419dc34561ce3b4e7 (patch)
tree: 860862d680fea23581d08b2948c5ac3e922a8447 /docs/dev/articles/web_only/compiled_models.html
parent: b0f08271d1dae8ffaf57f557c27eba1314ece1d5 (diff)
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+    <li><a class="dropdown-item" href="../../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li>
+    <li><a class="dropdown-item" href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li>
+    <li><a class="dropdown-item" href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li>
+    <li><a class="dropdown-item" href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li>
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+    <li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li>
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+      <h1>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">2025-02-14</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="d-none 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">&lt;-</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">&lt;-</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">&lt;-</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   0.102</span></span>
+<span><span class="co">## 3     deSolve, compiled            1    1.324   0.135</span></span>
+<span><span class="co">## 2      Eigenvalue based            1    1.706   0.174</span></span>
+<span><span class="co">## 1 deSolve, not compiled            1   22.627   2.308</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">&lt;-</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">&lt;-</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">&lt;-</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">&lt;-</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   0.170</span></span>
+<span><span class="co">## 1 deSolve, not compiled            1   23.865   4.057</span></span></code></pre>
+<p>Here we get a performance benefit of a factor of 24 using the version
+of the differential equation model compiled from C code!</p>
+<p>This vignette was built with mkin 1.2.10 on</p>
+<pre><code><span><span class="co">## R version 4.4.2 (2024-10-31)</span></span>
+<span><span class="co">## Platform: x86_64-pc-linux-gnu</span></span>
+<span><span class="co">## Running under: Debian GNU/Linux 12 (bookworm)</span></span></code></pre>
+<pre><code><span><span class="co">## CPU model: AMD Ryzen 9 7950X 16-Core Processor</span></span></code></pre>
+</div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside>
+</div>
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+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Johannes Ranke.</p>
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author	Johannes Ranke <johannes.ranke@jrwb.de>	2025-02-14 09:15:20 +0100
committer	Johannes Ranke <johannes.ranke@jrwb.de>	2025-02-14 09:15:20 +0100
commit	91a5834dd701211f929fd25419dc34561ce3b4e7 (patch)
tree	860862d680fea23581d08b2948c5ac3e922a8447 /docs/dev/articles/web_only/compiled_models.html
parent	b0f08271d1dae8ffaf57f557c27eba1314ece1d5 (diff)