diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2018-03-09 23:14:39 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-03-09 23:14:39 +0100 |
| commit | 0b677308e3ffbf742880f05cc54da469f3ecc854 (patch) | |
| tree | 26dab561d6f5a31923b28b5fdf6c1859727dfe7f /vignettes | |
| parent | 5aec8e34680e05671347f7577ae36c9ad8e37063 (diff) | |
Another rebuild of the static docs
Now with rbenchmark installed, to get results for the compiled_models
vignette
Diffstat (limited to 'vignettes')
| -rw-r--r-- | vignettes/compiled_models.html | 38 |
1 files changed, 19 insertions, 19 deletions
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index 8aaa70d6..d8c5b19b 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -12,7 +12,7 @@ <meta name="author" content="Johannes Ranke" /> -<meta name="date" content="2018-01-14" /> +<meta name="date" content="2018-03-09" /> <title>Performance benefit by using compiled model definitions in mkin</title> @@ -70,7 +70,7 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf <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>2018-01-14</em></h4> +<h4 class="date"><em>2018-03-09</em></h4> @@ -87,27 +87,27 @@ SFO_SFO <-<span class="st"> </span><span class="kw">mkinmod</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">if (<span class="kw">require</span>(rbenchmark)) { +<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_2006_D, + <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_2006_D, + <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_2006_D, + <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>]) -} else { +} <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 2.005 1.000 2.000 0.004 -## 1 deSolve, not compiled 3 14.202 7.083 14.196 0.000 -## 2 Eigenvalue based 3 2.427 1.210 2.428 0.000 +## 3 deSolve, compiled 3 1.980 1.000 1.979 0 +## 1 deSolve, not compiled 3 13.926 7.033 13.914 0 +## 2 Eigenvalue based 3 2.362 1.193 2.360 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -117,35 +117,35 @@ SFO_SFO <-<span class="st"> </span><span class="kw">mkinmod</span>( <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">if (<span class="kw">require</span>(rbenchmark)) { +<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_2006_D, + <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_2006_D, <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>]) -} else { +} <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 3.489 1.000 3.488 0 -## 1 deSolve, not compiled 3 28.906 8.285 28.904 0 +## 2 deSolve, compiled 3 3.437 1.000 3.433 0 +## 1 deSolve, not compiled 3 30.406 8.847 30.380 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> -<p>Here we get a performance benefit of a factor of 8 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> +<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 0.9.46.3 on</p> <pre><code>## R version 3.4.3 (2017-11-30) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 9 (stretch)</code></pre> -<pre><code>## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</code></pre> +<pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre> </div> |