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Diffstat (limited to 'docs/articles/compiled_models.html')
| -rw-r--r-- | docs/articles/compiled_models.html | 43 |
1 files changed, 23 insertions, 20 deletions
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index e02b9cf3..5a04168e 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -16,13 +16,16 @@ </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin"> + <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> </a> @@ -38,7 +41,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-10-26</h4> + <h4 class="date">2016-11-03</h4> </div> @@ -75,21 +78,21 @@ mb<span class="fl">.1</span> <-<span class="st"> </span><span class="kw">micr <span class="kw">print</span>(mb<span class="fl">.1</span>)</code></pre></div> <pre><code>## Unit: milliseconds ## expr min lq mean median uq -## deSolve, not compiled 6298.7342 6308.6792 6343.9668 6318.6243 6366.5831 -## Eigenvalue based 871.7379 880.7757 903.5267 889.8135 919.4211 -## deSolve, compiled 724.9025 730.6729 732.9837 736.4432 737.0243 +## deSolve, not compiled 6306.4527 6340.7895 6403.5937 6375.1264 6452.1643 +## Eigenvalue based 918.0808 929.7217 948.9742 941.3626 964.4210 +## deSolve, compiled 736.1337 753.6016 773.5605 771.0696 792.2739 ## max neval cld -## 6414.5420 3 c -## 949.0287 3 b -## 737.6054 3 a</code></pre> +## 6529.2022 3 b +## 987.4793 3 a +## 813.4783 3 a</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.1</span>)</code></pre></div> <p><img src="compiled_models_files/figure-html/benchmark_SFO_SFO-1.png" width="672"></p> -<p>We see that using the compiled model is by a factor of 8.6 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> +<p>We see that using the compiled model is by a factor of 8.3 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 class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rownames</span>(smb<span class="fl">.1</span>) <-<span class="st"> </span>smb<span class="fl">.1</span>$expr smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="fl">.1</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div> <pre><code>## median -## deSolve, not compiled 8.579920 -## Eigenvalue based 1.208258 +## deSolve, not compiled 8.267900 +## Eigenvalue based 1.220853 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -111,20 +114,20 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" <span class="kw">print</span>(mb<span class="fl">.2</span>)</code></pre></div> <pre><code>## Unit: seconds ## expr min lq mean median uq -## deSolve, not compiled 13.265212 13.330161 13.412053 13.395109 13.485473 -## deSolve, compiled 1.322466 1.326851 1.364827 1.331236 1.386007 +## deSolve, not compiled 13.604720 13.667244 13.689764 13.729768 13.732286 +## deSolve, compiled 1.305077 1.311124 1.328943 1.317172 1.340876 ## max neval cld -## 13.575837 3 b -## 1.440779 3 a</code></pre> +## 13.734804 3 b +## 1.364579 3 a</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span>[<span class="st">"median"</span>]/smb<span class="fl">.2</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div> <pre><code>## median ## 1 NA ## 2 NA</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.2</span>)</code></pre></div> <p><img src="compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png" width="672"></p> -<p>Here we get a performance benefit of a factor of 10.1 using the version of the differential equation model compiled from C code!</p> +<p>Here we get a performance benefit of a factor of 10.4 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.44.9000 on</p> -<pre><code>## R version 3.3.1 (2016-06-21) +<pre><code>## R version 3.3.2 (2016-10-31) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 8 (jessie)</code></pre> <pre><code>## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</code></pre> @@ -144,7 +147,7 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" <footer><div class="copyright"> - <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> |