diff options
Diffstat (limited to 'docs/articles/web_only/compiled_models.html')
| -rw-r--r-- | docs/articles/web_only/compiled_models.html | 30 |
1 files changed, 12 insertions, 18 deletions
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 35ea6f27..330c25c6 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -43,7 +43,7 @@ <a href="../../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -105,7 +105,7 @@ <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">2022-03-02</h4> + <h4 data-toc-skip class="date">2022-05-18</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> @@ -141,11 +141,11 @@ 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><span class="co">## Temporary DLL for differentials generated and loaded</span></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" 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></code></pre></div> +<code class="sourceCode R"><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></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 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 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 class="va">b.1</span> <span class="op"><-</span> <span class="fu">benchmark</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">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</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>, @@ -162,11 +162,7 @@ <span class="op">}</span> <span class="kw">else</span> <span class="op">{</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 class="op">}</span></code></pre></div> -<pre><code><span class="co">## test replications relative elapsed</span> -<span class="co">## 4 analytical 1 1.000 0.216</span> -<span class="co">## 3 deSolve, compiled 1 1.708 0.369</span> -<span class="co">## 2 Eigenvalue based 1 1.866 0.403</span> -<span class="co">## 1 deSolve, not compiled 1 34.009 7.346</span></code></pre> +<pre><code><span class="co">## [1] "R package rbenchmark is not available"</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"> @@ -179,7 +175,7 @@ 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" class="external-link">benchmark</a></span><span class="op">(</span> + <span class="va">b.2</span> <span class="op"><-</span> <span class="fu">benchmark</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>, 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 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>, @@ -191,16 +187,14 @@ <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" 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 class="op">}</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> -<pre><code><span class="co">## test replications relative elapsed</span> -<span class="co">## 2 deSolve, compiled 1 1.000 0.533</span> -<span class="co">## 1 deSolve, not compiled 1 25.146 13.403</span></code></pre> -<p>Here we get a performance benefit of a factor of 25 using the version of the differential equation model compiled from C code!</p> +<pre><code><span class="co">## Loading required package: rbenchmark</span></code></pre> +<pre><code><span class="co">## [1] "R package benchmark is not available"</span></code></pre> +<p>Here we get a performance benefit of a factor of NA using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 1.1.0 on</p> -<pre><code><span class="co">## R version 4.1.2 (2021-11-01)</span> +<pre><code><span class="co">## R version 4.2.0 (2022-04-22)</span> <span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span> <span class="co">## Running under: Debian GNU/Linux 11 (bullseye)</span></code></pre> -<pre><code><span class="co">## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</span></code></pre> +<pre><code><span class="co">## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</span></code></pre> </div> </div> @@ -221,7 +215,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer> |