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	<title><![CDATA[BOL: SLURM basics !]]></title>
	<link>https://bioinformaticsonline.com/pages/view/27321/slurm-basics?</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/27321/slurm-basics</guid>
	<pubDate>Fri, 13 May 2016 04:42:24 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/27321/slurm-basics</link>
	<title><![CDATA[SLURM basics !]]></title>
	<description><![CDATA[<p><a href="http://bioinformaticsonline.com/bookmarks/view/27238/slurm" target="_blank">SLURM</a> is a queue management system and stands for Simple Linux Utility for Resource Management. SLURM was developed at the Lawrence Livermore National Lab and currently runs some of the largest compute clusters in the world.</p><p>SLURM is similar in many ways to most other queue systems. You write a batch script then submit it to the queue manager. The queue manager then schedules your job to run on the queue (or partition in SLURM parlance) that you designate. Below we will provide an outline of how to submit jobs to SLURM, how SLURM decides when to schedule your job and how to monitor progress.</p><p>SLURM has a number of valuable features compared to other job management systems:</p><ul>
<li><em>Kill and Requeue</em> SLURM&rsquo;s ability to kill and requeue is superior to that of other systems. It waits for jobs to be cleared before scheduling the high priority job. It also does kill and requeue on memory rather than just on core count.</li>
<li><em>Memory</em> Memory requests are sacrosanct in SLURM. Thus the amount of memory you request at run time is guaranteed to be there. No one can infringe on that memory space and you cannot exceed the amount of memory that you request.</li>
<li><em>Accounting Tools</em> SLURM has a back end database which stores historical information about the cluster. This information can be queried by the users who are curious about how much resources they have used.</li>
</ul><p><strong>Summary of SLURM commands</strong></p><p>The table below shows a summary of SLURM commands. These commands are described in more detail below along with links to the SLURM doc site.</p><table>
<tbody>
<tr><th>&nbsp;</th><th>SLURM</th><th>SLURM Example</th></tr>
<tr>
<td>Submit a batch serial job</td>
<td><a href="http://slurm.schedmd.com/sbatch.html">sbatch</a></td>
<td><code>sbatch runscript.sh</code></td>
</tr>
<tr>
<td>Run a script interatively</td>
<td><a href="http://slurm.schedmd.com/srun.html">srun</a></td>
<td><code>srun --pty -p interact -t 10 --mem 1000 /bin/bash /bin/hostname</code></td>
</tr>
<tr>
<td>Kill a job</td>
<td><a href="http://slurm.schedmd.com/scancel.html">scancel</a></td>
<td><code>scancel 999999</code></td>
</tr>
<tr>
<td>View status of queues</td>
<td><a href="http://slurm.schedmd.com/squeue.html">squeue</a></td>
<td><code>squeue -u akitzmiller</code></td>
</tr>
<tr>
<td>Check current job by id</td>
<td><a href="http://slurm.schedmd.com/squeue.html">sacct</a></td>
<td><code>sacct -j 999999</code></td>
</tr>
</tbody>
</table>]]></description>
	<dc:creator>Radha Agarkar</dc:creator>
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	<guid isPermaLink='true'>https://bioinformaticsonline.com/pages/view/27321/slurm-basics#item-annotation-2422</guid>
	<pubDate>Fri, 20 May 2016 20:32:00 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/27321/slurm-basics#item-annotation-2422</link>
	<title><![CDATA[Comment by Abhi]]></title>
	<description><![CDATA[<p>In addition to that, I found this weppage also useful&nbsp;http://www.hpc2n.umu.se/node/877</p>]]></description>
	<dc:creator>Abhi</dc:creator>
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