diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2018-09-14 16:57:17 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-09-14 17:00:08 +0200 |
| commit | 70d158c4dd919f4f77bc12f8ace333d29d249b79 (patch) | |
| tree | ab0dd14d85a0c1506262bb6866e2cc49c2400389 /vignettes/compiled_models.html | |
| parent | d52e522a9abea09fae1189b066e2a2e1dbb9cb34 (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
Diffstat (limited to 'vignettes/compiled_models.html')
| -rw-r--r-- | vignettes/compiled_models.html | 164 |
1 files changed, 0 insertions, 164 deletions
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rel="stylesheet" type="text/css" /> - -</head> - -<body> - - - - -<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>2018-07-17</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>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>) -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"><span class="cf">if</span> (<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_<span class="dv">2006</span>_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_<span class="dv">2006</span>_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_<span class="dv">2006</span>_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>]) -} <span class="cf">else</span> { - 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 2.116 1.000 2.115 0 -## 1 deSolve, not compiled 3 16.563 7.828 16.555 0 -## 2 Eigenvalue based 3 2.599 1.228 2.597 0 -## 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>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"><span class="cf">if</span> (<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_<span class="dv">2006</span>_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_<span class="dv">2006</span>_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>]) -} <span class="cf">else</span> { - 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 3.809 1.000 3.806 0 -## 1 deSolve, not compiled 3 35.885 9.421 35.866 0 -## user.child sys.child -## 2 0 0 -## 1 0 0</code></pre> -<p>Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 0.9.47.1 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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