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0_run_analyses_on_cluster.html
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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<title>Run Analyses On Cluster</title>
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<body>
<div class="container-fluid main-container">
<div class="row">
<div class="col-md-2" style="border-top:solid #E2A674 20px"></div>
<div class="col-md-2 rpqa" style="border-top:solid #9F3B2B 20px"></div>
<div class="col-md-4" style="background:black;text-align:center"><a href="index.html" style="color:white"><i class="glyphicon glyphicon-th-list"></i> Back to index</a></div>
<div class="col-md-2 hist_sweden" style="border-top:solid #21523B 20px"></div>
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</div>
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<div class="container-fluid main-container">
<div id="cluster-scripts" class="section level1">
<h1>Cluster scripts</h1>
<div id="automatically-generate-job-commands-for-the-cluster" class="section level2">
<h2>Automatically generate job commands for the cluster</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">pops =<span class="st"> </span><span class="kw">c</span>(<span class="st">"krmh"</span>, <span class="st">"rpqa"</span>, <span class="st">"ddb"</span>, <span class="st">"swed"</span>)
scripts =<span class="st"> </span><span class="kw">list.files</span>(<span class="st">"cluster"</span>, <span class="dt">pattern =</span> <span class="st">"^[me][0-9]"</span>)
type =<span class="st"> </span><span class="kw">str_match</span>(scripts, <span class="st">"^([a-z][0-9]+)"</span>)[, <span class="dv">2</span>]
job =<span class="st"> </span><span class="kw">c</span>(<span class="kw">rep</span>(<span class="st">'bsub -q mpi -W 48:00 -n 6 -R span[hosts=1] Rscript "/usr/users/rarslan/updated_data/cluster/'</span>,<span class="dv">3</span>),
<span class="st">'bsub -q mpi-long -W 120:00 -n 6,20 -R span[hosts=1] Rscript "/usr/users/rarslan/updated_data/cluster/'</span>)
uptobyear =<span class="st"> </span><span class="kw">c</span>(<span class="dv">1835</span>, <span class="dv">1740</span>, <span class="dv">1850</span>, <span class="dv">1960</span>)
for (s in <span class="kw">seq_along</span>(scripts)) {
for (p in <span class="kw">seq_along</span>(pops)) {
if (!<span class="st"> </span><span class="kw">file.exists</span>( <span class="kw">paste0</span>(<span class="st">"coefs/"</span>, pops[p], <span class="st">"/"</span>, stringr::<span class="kw">str_sub</span>(scripts[s], <span class="dv">1</span>, -<span class="dv">3</span>), <span class="st">".rds"</span> ))) {
byear =<span class="st"> </span>uptobyear[p]
pop =<span class="st"> </span>pops[p]
if(pop ==<span class="st"> "swed"</span> &&<span class="st"> </span>type[s] %in%<span class="st"> </span><span class="kw">c</span>(<span class="st">"e1"</span>, <span class="st">"e2"</span>) ) {
pop =<span class="st"> "swed_subset_survival"</span>
byear =<span class="st"> </span><span class="dv">2000</span>
if(type[s] ==<span class="st"> "e2"</span>) byear =<span class="st"> </span><span class="dv">1990</span>
}
<span class="kw">cat</span>(job[p], scripts[s],<span class="st">'" '</span>, pop, <span class="st">" "</span>, byear, <span class="st">"</span><span class="ch">\n</span><span class="st">"</span>, <span class="dt">sep =</span> <span class="st">""</span>)
}
}
}</code></pre></div>
</div>
</div>
<div id="cluster-scripts-1" class="section level1">
<h1>Cluster scripts</h1>
<div id="automatically-generate-job-commands-for-the-cluster-1" class="section level2">
<h2>Automatically generate job commands for the cluster</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">pops =<span class="st"> </span><span class="kw">c</span>(<span class="st">"krmh"</span>, <span class="st">"rpqa"</span>, <span class="st">"ddb"</span>, <span class="st">"swed_subset_children"</span>)
scripts =<span class="st"> </span><span class="kw">list.files</span>(<span class="st">"cluster"</span>, <span class="dt">pattern =</span> <span class="st">"^[srg][0-9]"</span>)
job =<span class="st"> </span><span class="kw">c</span>(<span class="kw">rep</span>(<span class="st">'bsub -q mpi -W 48:00 -n 6 -R span[hosts=1] Rscript "/usr/users/rarslan/updated_data/cluster/'</span>,<span class="dv">4</span>))
uptobyear =<span class="st"> </span><span class="kw">c</span>(<span class="dv">1835</span>, <span class="dv">1740</span>, <span class="dv">1850</span>, <span class="dv">1960</span>)
for (s in <span class="kw">seq_along</span>(scripts)) {
for (p in <span class="kw">seq_along</span>(pops)) {
pop =<span class="st"> </span>pops[p]
if (pop ==<span class="st"> "swed_subset_children"</span>) {
pop =<span class="st"> "swed"</span>
}
if (!<span class="st"> </span><span class="kw">file.exists</span>( <span class="kw">paste0</span>(<span class="st">"coefs/"</span>, pop, <span class="st">"/"</span>, stringr::<span class="kw">str_sub</span>(scripts[s], <span class="dv">1</span>, -<span class="dv">3</span>), <span class="st">".rds"</span> ))) {
<span class="kw">cat</span>(job[p], scripts[s],<span class="st">'" '</span>, pops[p], <span class="st">" "</span>, uptobyear[p], <span class="st">"</span><span class="ch">\n</span><span class="st">"</span>, <span class="dt">sep =</span> <span class="st">""</span>)
}
}
}</code></pre></div>
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