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Accessing Jupyterhub and launching a session
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<a href="https://gitea.psi.ch/hpce/gitea-pages/_edit/master/docs/merlin7/04-Jupyterhub/jupyterhub.md" title="Edit this page" class="md-content__button md-icon" rel="edit">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M10 20H6V4h7v5h5v3.1l2-2V8l-6-6H6c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h4zm10.2-7c.1 0 .3.1.4.2l1.3 1.3c.2.2.2.6 0 .8l-1 1-2.1-2.1 1-1c.1-.1.2-.2.4-.2m0 3.9L14.1 23H12v-2.1l6.1-6.1z"></path></svg>
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<h1 id="jupyterhub-on-merlin7">Jupyterhub on Merlin7<a class="headerlink" href="#jupyterhub-on-merlin7" title="Permanent link"></a></h1>
<p>Jupyterhub provides <a href="https://jupyter.org/">jupyter notebooks</a> that are launched on
cluster nodes of merlin and can be accessed through a web portal.</p>
<h2 id="accessing-jupyterhub-and-launching-a-session">Accessing Jupyterhub and launching a session<a class="headerlink" href="#accessing-jupyterhub-and-launching-a-session" title="Permanent link"></a></h2>
<p>The service is available inside of PSI (or through a VPN connection) at</p>
<p><strong><a href="https://merlin7-jupyter01.psi.ch:8000/hub/">https://merlin7-jupyter01.psi.ch:8000/hub/</a></strong></p>
<ol>
<li><strong>Login</strong>: You will be presented with a <strong>Login</strong> web page for
authenticating with your PSI account.</li>
<li><strong>Spawn job</strong>: The <strong>Spawner Options</strong> page allows you to
specify the properties (Slurm partition, running time,...) of
the batch jobs that will be running your jupyter notebook. Once
you click on the <code>Spawn</code> button, your job will be sent to the
Slurm batch system. If the cluster is not currently overloaded
and the resources you requested are available, your job will
usually start within 30 seconds.</li>
</ol>
<h3 id="recommended-partitions">Recommended partitions<a class="headerlink" href="#recommended-partitions" title="Permanent link"></a></h3>
<p>Running on the <code>merlin7</code> cluster and using the <code>interactive</code> partition would
in general guarantee fast access to resources. Keep in mind, that this partition
has a limit of 12 hours.</p>
<h2 id="requesting-additional-resources">Requesting additional resources<a class="headerlink" href="#requesting-additional-resources" title="Permanent link"></a></h2>
<p>The <strong>Spawner Options</strong> page covers the most common options. These are used to
create a submission script for the jupyterhub job and submit it to the slurm
queue. Additional customization can be implemented using the <em>'Optional user
defined line to be added to the batch launcher script'</em> option. This line is
added to the submission script at the end of other <code>#SBATCH</code> lines. Parameters can
be passed to SLURM by starting the line with <code>#SBATCH</code>, like in <a href="../../03-Slurm-General-Documentation/slurm-examples/">Running Slurm
Scripts</a>. Some ideas:</p>
<p><strong>Request additional memory</strong></p>
<div class="language-text highlight"><span class="filename">Text Only</span><pre><span></span><code><span id="__span-0-1"><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>#SBATCH --mem=100G
</span></code></pre></div>
<p><strong>Request multiple GPUs</strong> (gpu partition only)</p>
<div class="language-text highlight"><span class="filename">Text Only</span><pre><span></span><code><span id="__span-1-1"><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>#SBATCH --gpus=2
</span></code></pre></div>
<p><strong>Log additional information</strong></p>
<div class="language-text highlight"><span class="filename">Text Only</span><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>hostname; date; echo $USER
</span></code></pre></div>
<p>Output is found in <code>~/jupyterhub_batchspawner_&lt;jobid&gt;.log</code>.</p>
<h2 id="contact">Contact<a class="headerlink" href="#contact" title="Permanent link"></a></h2>
<p>In case of problems or requests, please either submit a <strong><a href="https://psi.service-now.com/psisp">PSI Service
Now</a></strong> incident containing <em>"Merlin
Jupyterhub"</em> as part of the subject, or contact us by mail through
<a href="mailto:merlin-admins@lists.psi.ch">merlin-admins@lists.psi.ch</a>.</p>
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