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Diffstat (limited to 'docs/dev/articles/web_only/compiled_models.html')
| -rw-r--r-- | docs/dev/articles/web_only/compiled_models.html | 28 |
1 files changed, 14 insertions, 14 deletions
diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html index 3d1c7fcd..a444f4bc 100644 --- a/docs/dev/articles/web_only/compiled_models.html +++ b/docs/dev/articles/web_only/compiled_models.html @@ -102,7 +102,7 @@ <h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-11-19</h4> + <h4 class="date">2020-11-30</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/compiled_models.rmd"><code>vignettes/web_only/compiled_models.rmd</code></a></small> <div class="hidden name"><code>compiled_models.rmd</code></div> @@ -134,9 +134,9 @@ <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">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 class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span> - parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, - m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> + 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>, + 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></code></pre></div> +<pre><code>## Temporary DLL for differentials generated and loaded</code></pre> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/subset.html">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></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> @@ -160,10 +160,10 @@ <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span> <span class="op">}</span></code></pre></div> <pre><code>## test replications relative elapsed -## 4 analytical 1 1.000 0.186 -## 3 deSolve, compiled 1 1.742 0.324 -## 2 Eigenvalue based 1 2.048 0.381 -## 1 deSolve, not compiled 1 42.532 7.911</code></pre> +## 4 analytical 1 1.000 0.187 +## 3 deSolve, compiled 1 1.807 0.338 +## 2 Eigenvalue based 1 2.032 0.380 +## 1 deSolve, not compiled 1 43.048 8.050</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 id="model-without-analytical-solution" class="section level2"> @@ -173,8 +173,8 @@ <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</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> - parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>, - m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span><span class="op">(</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</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>, + 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 class="va">b.2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html">benchmark</a></span><span class="op">(</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>, @@ -188,11 +188,11 @@ <span class="va">factor_FOMC_SFO</span> <span class="op"><-</span> <span class="cn">NA</span> <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="st">"R package benchmark is not available"</span><span class="op">)</span> <span class="op">}</span></code></pre></div> -<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<pre><code>## Temporary DLL for differentials generated and loaded</code></pre> <pre><code>## test replications relative elapsed -## 2 deSolve, compiled 1 1.000 0.465 -## 1 deSolve, not compiled 1 30.852 14.346</code></pre> -<p>Here we get a performance benefit of a factor of 31 using the version of the differential equation model compiled from C code!</p> +## 2 deSolve, compiled 1 1.000 0.483 +## 1 deSolve, not compiled 1 29.969 14.475</code></pre> +<p>Here we get a performance benefit of a factor of 30 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.50.4 on</p> <pre><code>## R version 4.0.3 (2020-10-10) ## Platform: x86_64-pc-linux-gnu (64-bit) |