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<h1 id="merlin6-storage">Merlin6 Storage<a class="headerlink" href="#merlin6-storage" title="Permanent link"></a></h1>
<h2 id="introduction">Introduction<a class="headerlink" href="#introduction" title="Permanent link"></a></h2>
<p>This document describes the different directories of the Merlin6 cluster.</p>
<h3 id="user-and-project-data">User and project data<a class="headerlink" href="#user-and-project-data" title="Permanent link"></a></h3>
<ul>
<li>
<p><strong><em>Users are responsible for backing up their own data</em></strong>. Is recommended to backup the data on third party independent systems (i.e. LTS, Archive, AFS, SwitchDrive, Windows Shares, etc.).</p>
<ul>
<li><strong><code>/psi/home</code></strong>, as this contains a small amount of data, is the only directory where we can provide daily snapshots for one week. This can be found in the following directory <strong><code>/psi/home/.snapshot/</code></strong></li>
</ul>
</li>
<li>
<p><strong><em>When a user leaves PSI, she or her supervisor/team are responsible to backup and move the data out from the cluster</em></strong>: every few months, the storage space will be recycled for those old users who do not have an existing and valid PSI account.</p>
</li>
</ul>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>When a user leaves PSI and his account has been removed, her storage space in Merlin may be recycled.
Hence, <strong>when a user leaves PSI</strong>, she, her supervisor or team <strong>must ensure that the data is backed up to an external storage</strong></p>
</div>
<h3 id="checking-user-quota">Checking user quota<a class="headerlink" href="#checking-user-quota" title="Permanent link"></a></h3>
<p>For each directory, we provide a way for checking quotas (when required). However, a single command <code>merlin_quotas</code>
is provided. This is useful to show with a single command all quotas for your filesystems (including AFS, which is not mentioned here).</p>
<p>To check your quotas, please run:</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-0-1"><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>merlin_quotas
</span></code></pre></div>
<h2 id="merlin6-directories">Merlin6 directories<a class="headerlink" href="#merlin6-directories" title="Permanent link"></a></h2>
<p>Merlin6 offers the following directory classes for users:</p>
<ul>
<li>
<p><code>/psi/home/&lt;username&gt;</code>: Private user <strong>home</strong> directory</p>
</li>
<li>
<p><code>/data/user/&lt;username&gt;</code>: Private user <strong>data</strong> directory</p>
</li>
<li>
<p><code>/data/project/general/&lt;projectname&gt;</code>: Shared <strong>Project</strong> directory</p>
<ul>
<li>For BIO experiments, a dedicated <code>/data/project/bio/$projectname</code> exists.</li>
</ul>
</li>
<li>
<p><code>/scratch</code>: Local <em>scratch</em> disk (only visible by the node running a job).</p>
</li>
<li><code>/shared-scratch</code>: Shared <em>scratch</em> disk (visible from all nodes).</li>
<li><code>/export</code>: Export directory for data transfer, visible from <code>ra-merlin-01.psi.ch</code>, <code>ra-merlin-02.psi.ch</code> and Merlin login nodes.<ul>
<li>Refer to <strong><a href="../transfer-data/">Transferring Data</a></strong> for more information about the export area and data transfer service.</li>
</ul>
</li>
</ul>
<div class="admonition tip">
<p class="admonition-title">Tip</p>
<p>In GPFS there is a concept called <strong>GraceTime</strong>. Filesystems have a block
(amount of data) and file (number of files) quota. This quota contains a soft
and hard limits. Once the soft limit is reached, users can keep writing up to
their hard limit quota during the <strong>grace period</strong>. Once <strong>GraceTime</strong> or hard
limit are reached, users will be unable to write and will need remove data
below the soft limit (or ask for a quota increase when this is possible, see
below table).</p>
</div>
<p>Properties of the directory classes:</p>
<table>
<thead>
<tr>
<th>Directory</th>
<th>Block Quota [Soft:Hard]</th>
<th>Block Quota [Soft:Hard]</th>
<th style="text-align: center;">GraceTime</th>
<th style="text-align: left;">Quota Change Policy: Block</th>
<th style="text-align: left;">Quota Change Policy: Files</th>
<th>Backup</th>
<th style="text-align: left;">Backup Policy</th>
</tr>
</thead>
<tbody>
<tr>
<td>/psi/home/$username</td>
<td>USR [10GB:11GB]</td>
<td><em>Undef</em></td>
<td style="text-align: center;">N/A</td>
<td style="text-align: left;">Up to x2 when strongly justified.</td>
<td style="text-align: left;">N/A</td>
<td>yes</td>
<td style="text-align: left;">Daily snapshots for 1 week</td>
</tr>
<tr>
<td>/data/user/$username</td>
<td>USR [1TB:1.074TB]</td>
<td>USR [1M:1.1M]</td>
<td style="text-align: center;">7d</td>
<td style="text-align: left;">Inmutable. Need a project.</td>
<td style="text-align: left;">Changeable when justified.</td>
<td>no</td>
<td style="text-align: left;">Users responsible for backup</td>
</tr>
<tr>
<td>/data/project/general/$projectname</td>
<td>GRP [1TB:1.074TB]</td>
<td>GRP [1M:1.1M]</td>
<td style="text-align: center;">7d</td>
<td style="text-align: left;">Subject to project requirements.</td>
<td style="text-align: left;">Subject to project requirements.</td>
<td>no</td>
<td style="text-align: left;">Project responsible for backup</td>
</tr>
<tr>
<td>/scratch</td>
<td><em>Undef</em></td>
<td><em>Undef</em></td>
<td style="text-align: center;">N/A</td>
<td style="text-align: left;">N/A</td>
<td style="text-align: left;">N/A</td>
<td>no</td>
<td style="text-align: left;">N/A</td>
</tr>
<tr>
<td>/shared-scratch</td>
<td>USR [512GB:2TB]</td>
<td>USR [2M:2.5M]</td>
<td style="text-align: center;">7d</td>
<td style="text-align: left;">Up to x2 when strongly justified.</td>
<td style="text-align: left;">Changeable when justified.</td>
<td>no</td>
<td style="text-align: left;">N/A</td>
</tr>
<tr>
<td>/export</td>
<td>USR [10MB:20TB]</td>
<td>USR [512K:5M]</td>
<td style="text-align: center;">10d</td>
<td style="text-align: left;">Soft can be temporary increased.</td>
<td style="text-align: left;">Changeable when justified.</td>
<td>no</td>
<td style="text-align: left;">N/A</td>
</tr>
</tbody>
</table>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>The use of <strong>scratch</strong> and <strong>export</strong> areas as an extension of the quota
<em>is forbidden</em>. <strong>scratch</strong> and <strong>export</strong> areas <em>must not contain</em> final
data.</p>
<p><strong><em>Auto cleanup policies</em></strong> in the <strong>scratch</strong> and <strong>export</strong> areas are applied.</p>
</div>
<h3 id="user-home-directory">User home directory<a class="headerlink" href="#user-home-directory" title="Permanent link"></a></h3>
<p>This is the default directory users will land when login in to any Merlin6 machine.
It is intended for your scripts, documents, software development, and other files which
you want to have backuped. Do not use it for data or HPC I/O-hungry tasks.</p>
<p>This directory is mounted in the login and computing nodes under the path:</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-1-1"><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>/psi/home/<span class="nv">$username</span>
</span></code></pre></div>
<p>Home directories are part of the PSI NFS Central Home storage provided by AIT and
are managed by the Merlin6 administrators.</p>
<p>Users can check their quota by running the following command:</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>quota<span class="w"> </span>-s
</span></code></pre></div>
<h4 id="home-directory-policy">Home directory policy<a class="headerlink" href="#home-directory-policy" title="Permanent link"></a></h4>
<ul>
<li>Read <strong><a href="../../quick-start-guide/code-of-conduct/">Important: Code of Conduct</a></strong> for more information about Merlin6 policies.</li>
<li>
<p>Is <strong>forbidden</strong> to use the home directories for IO intensive tasks</p>
<ul>
<li>Use <code>/scratch</code>, <code>/shared-scratch</code>, <code>/data/user</code> or <code>/data/project</code> for this purpose.</li>
</ul>
</li>
<li>
<p>Users can retrieve up to 1 week of their lost data thanks to the automatic <strong>daily snapshots for 1 week</strong>.
Snapshots can be accessed at this path:</p>
</li>
</ul>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-3-1"><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>/psi/home/.snapshop/<span class="nv">$username</span>
</span></code></pre></div>
<h3 id="user-data-directory">User data directory<a class="headerlink" href="#user-data-directory" title="Permanent link"></a></h3>
<p>The user data directory is intended for <em>fast IO access</em> and keeping large amounts of private data.
This directory is mounted in the login and computing nodes under the directory</p>
<p>```bash
/data/user/$username
</p><div class="language-text highlight"><span class="filename">Text Only</span><pre><span></span><code><span id="__span-4-1"><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>Users can check their quota by running the following command:
</span><span id="__span-4-2"><a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>
</span><span id="__span-4-3"><a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>```bash
</span><span id="__span-4-4"><a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a>mmlsquota -u &lt;username&gt; --block-size auto merlin-user
</span></code></pre></div><p></p>
<h4 id="user-data-directory-policy">User data directory policy<a class="headerlink" href="#user-data-directory-policy" title="Permanent link"></a></h4>
<ul>
<li>Read <strong><a href="../../quick-start-guide/code-of-conduct/">Important: Code of Conduct</a></strong> for more information about Merlin6 policies.</li>
<li>
<p>Is <strong>forbidden</strong> to use the data directories as <code>scratch</code> area during a job runtime.</p>
<ul>
<li>Use <code>/scratch</code>, <code>/shared-scratch</code> for this purpose.</li>
</ul>
</li>
<li>
<p>No backup policy is applied for user data directories: users are responsible for backing up their data.</p>
</li>
</ul>
<h3 id="project-data-directory">Project data directory<a class="headerlink" href="#project-data-directory" title="Permanent link"></a></h3>
<p>This storage is intended for <em>fast IO access</em> and keeping large amounts of a project's data, where the data also can be
shared by all members of the project (the project's corresponding unix group). We recommend to keep most data in
project related storage spaces, since it allows users to coordinate. Also, project spaces have more flexible policies
regarding extending the available storage space.</p>
<p>Experiments can request a project space as described in <strong><a href="../../quick-start-guide/requesting-projects/">[Accessing Merlin -&gt; Requesting a Project]</a></strong></p>
<p>Once created, the project data directory will be mounted in the login and computing nodes under the dirctory:</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-5-1"><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>/data/project/general/<span class="nv">$projectname</span>
</span></code></pre></div>
<p>Project quotas are defined on a per <em>group</em> basis. Users can check the project quota by running the following command:</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-6-1"><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>mmlsquota<span class="w"> </span>-j<span class="w"> </span><span class="nv">$projectname</span><span class="w"> </span>--block-size<span class="w"> </span>auto<span class="w"> </span>-C<span class="w"> </span>merlin.psi.ch<span class="w"> </span>merlin-proj
</span></code></pre></div>
<h4 id="project-directory-policy">Project Directory policy<a class="headerlink" href="#project-directory-policy" title="Permanent link"></a></h4>
<ul>
<li>Read <strong><a href="../../quick-start-guide/code-of-conduct/">Important: Code of Conduct</a></strong> for more information about Merlin6 policies.</li>
<li>It is <strong>forbidden</strong> to use the data directories as <code>scratch</code> area during a job's runtime, i.e. for high throughput I/O for a job's temporary files. Please Use <code>/scratch</code>, <code>/shared-scratch</code> for this purpose.</li>
<li>No backups: users are responsible for managing the backups of their data directories.</li>
</ul>
<h3 id="scratch-directories">Scratch directories<a class="headerlink" href="#scratch-directories" title="Permanent link"></a></h3>
<p>There are two different types of scratch storage: <strong>local</strong> (<code>/scratch</code>) and <strong>shared</strong> (<code>/shared-scratch</code>).</p>
<p><strong>local</strong> scratch should be used for all jobs that do not require the scratch files to be accessible from multiple nodes, which is trivially
true for all jobs running on a single node.
<strong>shared</strong> scratch is intended for files that need to be accessible by multiple nodes, e.g. by a MPI-job where tasks are spread out over the cluster
and all tasks need to do I/O on the same temporary files.</p>
<p><strong>local</strong> scratch in Merlin6 computing nodes provides a huge number of IOPS thanks to the NVMe technology. <strong>Shared</strong> scratch is implemented using a distributed parallel filesystem (GPFS) resulting in a higher latency, since it involves remote storage resources and more complex I/O coordination.</p>
<p><code>/shared-scratch</code> is only mounted in the <em>Merlin6</em> computing nodes (i.e. not on the login nodes), and its current size is 50TB. This can be increased in the future.</p>
<p>The properties of the available scratch storage spaces are given in the following table</p>
<table>
<thead>
<tr>
<th>Cluster</th>
<th>Service</th>
<th>Scratch</th>
<th>Scratch Mountpoint</th>
<th>Shared Scratch</th>
<th>Shared Scratch Mountpoint</th>
<th>Comments</th>
</tr>
</thead>
<tbody>
<tr>
<td>merlin6</td>
<td>login node</td>
<td>100GB / SAS</td>
<td><code>/scratch</code></td>
<td>50TB / GPFS</td>
<td><code>/shared-scratch</code></td>
<td><code>merlin-l-0[1,2]</code></td>
</tr>
<tr>
<td>merlin6</td>
<td>computing node</td>
<td>1.3TB / NVMe</td>
<td><code>/scratch</code></td>
<td>50TB / GPFS</td>
<td><code>/shared-scratch</code></td>
<td><code>merlin-c-[001-024,101-124,201-224]</code></td>
</tr>
<tr>
<td>merlin6</td>
<td>login node</td>
<td>2.0TB / NVMe</td>
<td><code>/scratch</code></td>
<td>50TB / GPFS</td>
<td><code>/shared-scratch</code></td>
<td><code>merlin-l-00[1,2]</code></td>
</tr>
</tbody>
</table>
<h4 id="scratch-directories-policy">Scratch directories policy<a class="headerlink" href="#scratch-directories-policy" title="Permanent link"></a></h4>
<ul>
<li>Read <strong><a href="../../quick-start-guide/code-of-conduct/">Important: Code of Conduct</a></strong> for more information about Merlin6 policies.</li>
<li>By default, <em>always</em> use <strong>local</strong> first and only use <strong>shared</strong> if your specific use case requires it.</li>
<li>Temporary files <em>must be deleted at the end of the job by the user</em>.<ul>
<li>Remaining files will be deleted by the system if detected.</li>
<li>Files not accessed within 28 days will be automatically cleaned up by the system.</li>
<li>If for some reason the scratch areas get full, admins have the rights to cleanup the oldest data.</li>
</ul>
</li>
</ul>
<h3 id="export-directory">Export directory<a class="headerlink" href="#export-directory" title="Permanent link"></a></h3>
<p>Export directory is exclusively intended for transferring data from outside PSI to Merlin and viceversa. Is a temporary directoy with an auto-cleanup policy.
Please read <strong><a href="../transfer-data/">Transferring Data</a></strong> for more information about it.</p>
<h4 id="export-directory-policy">Export directory policy<a class="headerlink" href="#export-directory-policy" title="Permanent link"></a></h4>
<ul>
<li>Temporary files <em>must be deleted at the end of the job by the user</em>.<ul>
<li>Remaining files will be deleted by the system if detected.</li>
<li>Files not accessed within 28 days will be automatically cleaned up by the system.</li>
<li>If for some reason the export area gets full, admins have the rights to cleanup the oldest data</li>
</ul>
</li>
</ul>
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