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<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Parallelize Remake-Style Workflows with Makefiles • parallelRemake</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"><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
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<div id="parallelremake" class="section level1">
<div class="page-header"><h1 class="hasAnchor"><a href="#parallelremake" class="anchor"> </a>parallelRemake</h1></div>
<p>The <code>parallelRemake</code> package is a helper add-on for <a href="https://github.com/richfitz/remake"><code>remake</code></a>, a <a href="https://www.gnu.org/software/make/">Makefile</a>-like reproducible build system for R. If you haven’t done so already, go learn <a href="https://github.com/richfitz/remake"><code>remake</code></a>! Also learn <a href="https://www.gnu.org/software/make/">GNU make</a>, and then recall that <code>make -j 4</code> runs a <a href="https://www.gnu.org/software/make/">Makefile</a> while distributing the rules over four parallel processes. This mode of parallelism is the whole point of <code>parallelRemake</code>. With <code>parallelRemake</code>, you can write an overarching <a href="https://www.gnu.org/software/make/">Makefile</a> for a <a href="https://github.com/richfitz/remake"><code>remake</code></a> project to run <a href="https://github.com/richfitz/remake"><code>remake</code></a> targets in parallel. This distributed parallelism is extremely helpful for large clusters that use the <a href="http://slurm.schedmd.com/">Slurm job scheduler</a>, for example, as explained in <a href="http://plindenbaum.blogspot.com/2014/09/parallelizing-gnu-make-4-in-slurm.html">this post</a>.</p>
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<div id="installation" class="section level1">
<h1 class="hasAnchor">
<a href="#installation" class="anchor"> </a>Installation</h1>
<p>To install the development version, get the <a href="https://cran.r-project.org/web/packages/devtools/">devtools</a> package and run</p>
<pre><code>devtools::install_github("wlandau/parallelRemake", build = TRUE)</code></pre>
<p>If you specify a tag, you can install a GitHub release.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">devtools::<span class="kw">install_github</span>(<span class="st">"wlandau/parallelRemake@v0.0.2"</span>, <span class="dt">build =</span> <span class="ot">TRUE</span>)</code></pre></div>
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<h1 class="hasAnchor">
<a href="#rtools-for-windows-users" class="anchor"> </a>Rtools for Windows users</h1>
<p>The example and tests sometimes use <code>system("make")</code> and similar commands. So if you’re using the Windows operating system, you will need to install the <a href="https://github.com/stan-dev/rstan/wiki/Install-Rtools-for-Windows"><code>Rtools</code></a> package.</p>
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<a href="#tutorial" class="anchor"> </a>Tutorial</h1>
<p>The <a href="https://github.com/wlandau/parallelRemake/blob/master/vignettes/parallelRemake.Rmd">online package vignette</a> has a complete tutorial. You can load the compiled version from an R session.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">vignette</span>(<span class="st">"parallelRemake"</span>)</code></pre></div>
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<h1 class="hasAnchor">
<a href="#help-and-troubleshooting" class="anchor"> </a>Help and troubleshooting</h1>
<p>Use the <code><a href="reference/help_parallelRemake.html">help_parallelRemake()</a></code> function to obtain a collection of helpful links. For troubleshooting, please refer to <a href="https://github.com/wlandau/parallelRemake/blob/master/TROUBLESHOOTING.md">TROUBLESHOOTING.md</a> on the <a href="https://github.com/wlandau/parallelRemake">GitHub page</a> for instructions.</p>
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<div id="acknowledgements" class="section level1">
<h1 class="hasAnchor">
<a href="#acknowledgements" class="anchor"> </a>Acknowledgements</h1>
<p>This package stands on the shoulders of <a href="https://richfitz.github.io/">Rich FitzJohn</a>’s <a href="https://github.com/richfitz/remake"><code>remake</code></a> package. Also thanks to <a href="http://danielfalster.com/">Daniel Falster</a> for <a href="https://github.com/richfitz/remake/issues/84">the idea</a> that made <code>parallelRemake</code> practical and clean.</p>
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<h2>Links</h2><ul class="list-unstyled"><li>Report a bug at <br><a href="https://github.com/wlandau/parallelRemake/issues">https://​github.com/​wlandau/​parallelRemake/​issues</a></li>
</ul><h2>License</h2>
<p>GPL (>=3)</p>
<h2>Developers</h2><ul class="list-unstyled"><li>William Michael Landau <br><small class="roles"> Author, maintainer, copyright holder </small> </li>
<li><a href="authors.html">All authors...</a></li>
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