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1 files changed, 84 insertions, 132 deletions
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</li> </ul> -<ul class="nav navbar-nav navbar-right"> -<li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../../search.json" id="search-input" placeholder="Search for" autocomplete="off"> +</form> + + <ul class="navbar-nav"> +<li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> </ul> </div> -<!--/.nav-collapse --> + + </div> -<!--/.container --> -</div> -<!--/.navbar --> +</nav><div class="container template-article"> + + - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Performance benefit by using compiled model -definitions in mkin</h1> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><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">2023-10-30</h4> + <h4 data-toc-skip class="date">2023-11-16</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 class="d-none name"><code>compiled_models.rmd</code></div> </div> @@ -216,10 +175,10 @@ solution is also implemented, which is included in the tests below.</p> <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> +<span><span class="co">## 4 analytical 1 1.000 0.109</span></span> +<span><span class="co">## 3 deSolve, compiled 1 1.284 0.140</span></span> +<span><span class="co">## 2 Eigenvalue based 1 1.670 0.182</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 21.927 2.390</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> @@ -250,44 +209,37 @@ compiled code is available.</p> <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 +<span><span class="co">## 2 deSolve, compiled 1 1.000 0.181</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 23.646 4.280</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 1.2.6 on</p> -<pre><code><span><span class="co">## R version 4.3.1 (2023-06-16)</span></span> +<pre><code><span><span class="co">## R version 4.3.2 (2023-10-31)</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> -</div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> +<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"><h2>On this page</h2> + </nav></aside> </div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p> <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p> <p>Site built 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