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<h1 data-toc-skip>Benchmark timings for mkin</h1>
<h4 class="author">Johannes Ranke</h4>
<h4 class="date">2020-05-13</h4>
<small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/benchmarks.rmd"><code>vignettes/web_only/benchmarks.rmd</code></a></small>
<div class="hidden name"><code>benchmarks.rmd</code></div>
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<p>Each system is characterized by its CPU type, the operating system type and the mkin version. Currently only values for one system are available. A compiler was available, so if no analytical solution was available, compiled ODE models are used.</p>
<div id="test-cases" class="section level2">
<h2 class="hasAnchor">
<a href="#test-cases" class="anchor"></a>Test cases</h2>
<p>Parent only:</p>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="no">FOCUS_C</span> <span class="kw"><-</span> <span class="no">FOCUS_2006_C</span>
<span class="no">FOCUS_D</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html">subset</a></span>(<span class="no">FOCUS_2006_D</span>, <span class="no">value</span> <span class="kw">!=</span> <span class="fl">0</span>)
<span class="no">parent_datasets</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_C</span>, <span class="no">FOCUS_D</span>)
<span class="no">t1</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="no">parent_datasets</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
<span class="no">t2</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="no">parent_datasets</span>,
<span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]</pre></body></html></div>
<p>One metabolite:</p>
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(
<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),
<span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))
<span class="no">FOMC_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(
<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),
<span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))
<span class="no">DFOP_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(
<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),
<span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))
<span class="no">t3</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOMC_SFO</span>, <span class="no">DFOP_SFO</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_D</span>)))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
<span class="no">t4</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOMC_SFO</span>, <span class="no">DFOP_SFO</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_D</span>),
<span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
<span class="no">t5</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOMC_SFO</span>, <span class="no">DFOP_SFO</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_D</span>),
<span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]</pre></body></html></div>
<p>Two metabolites, synthetic data:</p>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">m_synth_SFO_lin</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),
<span class="kw">M1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),
<span class="kw">M2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),
<span class="kw">use_of_ff</span> <span class="kw">=</span> <span class="st">"max"</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
<span class="no">m_synth_DFOP_par</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"M1"</span>, <span class="st">"M2"</span>)),
<span class="kw">M1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),
<span class="kw">M2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),
<span class="kw">use_of_ff</span> <span class="kw">=</span> <span class="st">"max"</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
<span class="no">SFO_lin_a</span> <span class="kw"><-</span> <span class="no">synthetic_data_for_UBA_2014</span><span class="kw">[[</span><span class="fl">1</span>]]$<span class="no">data</span>
<span class="no">DFOP_par_c</span> <span class="kw"><-</span> <span class="no">synthetic_data_for_UBA_2014</span><span class="kw">[[</span><span class="fl">12</span>]]$<span class="no">data</span>
<span class="no">t6</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>)))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
<span class="no">t7</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>)))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
<span class="no">t8</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>),
<span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
<span class="no">t9</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>),
<span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
<span class="no">t10</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>),
<span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
<span class="no">t11</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>),
<span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]</pre></body></html></div>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="no">mkin_benchmarks</span>[<span class="no">system_string</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="st">"t"</span>, <span class="fl">1</span>:<span class="fl">11</span>)] <span class="kw"><-</span>
<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">t1</span>, <span class="no">t2</span>, <span class="no">t3</span>, <span class="no">t4</span>, <span class="no">t5</span>, <span class="no">t6</span>, <span class="no">t7</span>, <span class="no">t8</span>, <span class="no">t9</span>, <span class="no">t10</span>, <span class="no">t11</span>)
<span class="fu"><a href="https://rdrr.io/r/base/save.html">save</a></span>(<span class="no">mkin_benchmarks</span>, <span class="kw">file</span> <span class="kw">=</span> <span class="st">"~/git/mkin/vignettes/web_only/mkin_benchmarks.rda"</span>)</pre></body></html></div>
</div>
<div id="results" class="section level2">
<h2 class="hasAnchor">
<a href="#results" class="anchor"></a>Results</h2>
<p>Currently, we only have benchmark information on one system, therefore only the mkin version is shown with the results below. Timings are in seconds, shorter is better. All results were obtained by serial, i.e. not using multiple computing cores.</p>
<p>Benchmarks for all available error models are shown.</p>
<div id="parent-only" class="section level3">
<h3 class="hasAnchor">
<a href="#parent-only" class="anchor"></a>Parent only</h3>
<p>Constant variance (t1) and two-component error model (t2) for four models fitted to two datasets, i.e. eight fits for each test.</p>
<table class="table">
<thead><tr class="header">
<th align="left">mkin version</th>
<th align="right">t1 [s]</th>
<th align="right">t2 [s]</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">0.9.48.1</td>
<td align="right">3.610</td>
<td align="right">11.019</td>
</tr>
<tr class="even">
<td align="left">0.9.49.1</td>
<td align="right">8.184</td>
<td align="right">22.889</td>
</tr>
<tr class="odd">
<td align="left">0.9.49.2</td>
<td align="right">7.064</td>
<td align="right">12.558</td>
</tr>
<tr class="even">
<td align="left">0.9.49.3</td>
<td align="right">7.296</td>
<td align="right">21.239</td>
</tr>
<tr class="odd">
<td align="left">0.9.49.4</td>
<td align="right">5.936</td>
<td align="right">20.545</td>
</tr>
<tr class="even">
<td align="left">0.9.50.2</td>
<td align="right">1.704</td>
<td align="right">3.909</td>
</tr>
</tbody>
</table>
</div>
<div id="one-metabolite" class="section level3">
<h3 class="hasAnchor">
<a href="#one-metabolite" class="anchor"></a>One metabolite</h3>
<p>Constant variance (t3), two-component error model (t4), and variance by variable (t5) for three models fitted to one dataset, i.e. three fits for each test.</p>
<table class="table">
<thead><tr class="header">
<th align="left">mkin version</th>
<th align="right">t3 [s]</th>
<th align="right">t4 [s]</th>
<th align="right">t5 [s]</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">0.9.48.1</td>
<td align="right">3.764</td>
<td align="right">14.347</td>
<td align="right">9.495</td>
</tr>
<tr class="even">
<td align="left">0.9.49.1</td>
<td align="right">4.649</td>
<td align="right">13.789</td>
<td align="right">6.395</td>
</tr>
<tr class="odd">
<td align="left">0.9.49.2</td>
<td align="right">4.786</td>
<td align="right">8.461</td>
<td align="right">5.675</td>
</tr>
<tr class="even">
<td align="left">0.9.49.3</td>
<td align="right">4.510</td>
<td align="right">13.805</td>
<td align="right">7.386</td>
</tr>
<tr class="odd">
<td align="left">0.9.49.4</td>
<td align="right">4.446</td>
<td align="right">15.335</td>
<td align="right">6.002</td>
</tr>
<tr class="even">
<td align="left">0.9.50.2</td>
<td align="right">1.370</td>
<td align="right">6.147</td>
<td align="right">2.747</td>
</tr>
</tbody>
</table>
</div>
<div id="two-metabolites" class="section level3">
<h3 class="hasAnchor">
<a href="#two-metabolites" class="anchor"></a>Two metabolites</h3>
<p>Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.</p>
<table class="table">
<thead><tr class="header">
<th align="left">mkin version</th>
<th align="right">t6 [s]</th>
<th align="right">t7 [s]</th>
<th align="right">t8 [s]</th>
<th align="right">t9 [s]</th>
<th align="right">t10 [s]</th>
<th align="right">t11 [s]</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">0.9.48.1</td>
<td align="right">2.623</td>
<td align="right">4.587</td>
<td align="right">7.525</td>
<td align="right">16.621</td>
<td align="right">8.576</td>
<td align="right">31.267</td>
</tr>
<tr class="even">
<td align="left">0.9.49.1</td>
<td align="right">2.542</td>
<td align="right">4.128</td>
<td align="right">4.632</td>
<td align="right">8.171</td>
<td align="right">3.676</td>
<td align="right">5.636</td>
</tr>
<tr class="odd">
<td align="left">0.9.49.2</td>
<td align="right">2.723</td>
<td align="right">4.478</td>
<td align="right">4.862</td>
<td align="right">7.618</td>
<td align="right">3.579</td>
<td align="right">5.574</td>
</tr>
<tr class="even">
<td align="left">0.9.49.3</td>
<td align="right">2.643</td>
<td align="right">4.374</td>
<td align="right">7.020</td>
<td align="right">11.124</td>
<td align="right">5.388</td>
<td align="right">7.365</td>
</tr>
<tr class="odd">
<td align="left">0.9.49.4</td>
<td align="right">2.635</td>
<td align="right">4.259</td>
<td align="right">4.737</td>
<td align="right">7.763</td>
<td align="right">3.427</td>
<td align="right">5.626</td>
</tr>
<tr class="even">
<td align="left">0.9.50.2</td>
<td align="right">0.761</td>
<td align="right">1.213</td>
<td align="right">1.287</td>
<td align="right">2.886</td>
<td align="right">2.054</td>
<td align="right">2.984</td>
</tr>
</tbody>
</table>
</div>
</div>
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<nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
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