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authorJohannes Ranke <jranke@uni-bremen.de>2018-03-01 14:32:46 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2018-03-01 14:32:46 +0100
commit6653ff2507f45eae909f491a9af3f1eb5358a600 (patch)
tree03a43f9cf86cc1d675eba1c6f9c5e31da9c2acdd /docs/articles/compiled_models.html
parenta767013f407f7495492af6a1ceba4cf2b8aae839 (diff)
Static documentation rebuilt using current pkgdown::build_site()
Diffstat (limited to 'docs/articles/compiled_models.html')
-rw-r--r--docs/articles/compiled_models.html62
1 files changed, 29 insertions, 33 deletions
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index d5d29a1a..9f0b5708 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -8,8 +8,11 @@
<title>Performance benefit by using compiled model definitions in mkin • mkin</title>
<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
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+<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Performance benefit by using compiled model definitions in mkin">
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@@ -77,7 +80,7 @@
<h1>Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-01-16</h4>
+ <h4 class="date">2018-03-01</h4>
</div>
@@ -97,73 +100,66 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mki
<span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></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> &lt;-<span class="st"> </span><span class="kw">benchmark</span>(
- <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_2006_D,
+ <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></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"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_2006_D,
+ <span class="st">"Eigenvalue based"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></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"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_2006_D,
+ <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></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 &lt;-<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 &lt;-<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>## Lade nötiges Paket: rbenchmark</code></pre>
-<pre><code>## test replications elapsed relative user.self sys.self
-## 3 deSolve, compiled 3 1.940 1.000 1.940 0
-## 1 deSolve, not compiled 3 13.865 7.147 13.864 0
-## 2 Eigenvalue based 3 2.427 1.251 2.428 0
-## user.child sys.child
-## 3 0 0
-## 1 0 0
-## 2 0 0</code></pre>
-<p>We see that using the compiled model is by a factor of around 7 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>
+<pre><code>## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
+## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'</code></pre>
+<pre><code>## [1] "R package benchmark is not available"</code></pre>
+<p>We see that using the compiled model is by a factor of around NA 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>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
<h2 class="hasAnchor">
<a href="#model-that-can-not-be-solved-with-eigenvalues" class="anchor"></a>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 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(
<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),
<span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>))
b<span class="fl">.2</span> &lt;-<span class="st"> </span><span class="kw">benchmark</span>(
- <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_2006_D,
+ <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></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"><a href="../reference/mkinfit.html">mkinfit</a></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"><a href="../reference/mkinfit.html">mkinfit</a></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 &lt;-<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 &lt;-<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 3.432 1.000 3.428 0
-## 1 deSolve, not compiled 3 28.844 8.404 28.840 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>
+<pre><code>## Lade nötiges Paket: rbenchmark</code></pre>
+<pre><code>## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
+## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'</code></pre>
+<pre><code>## [1] "R package benchmark is not available"</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 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>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<div id="tocnav">
- <h2>Contents</h2>
+ <h2 class="hasAnchor">
+<a href="#tocnav" class="anchor"></a>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#model-that-can-also-be-solved-with-eigenvalues">Model that can also be solved with Eigenvalues</a></li>
<li><a href="#model-that-can-not-be-solved-with-eigenvalues">Model that can not be solved with Eigenvalues</a></li>
@@ -179,7 +175,7 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mki
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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