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<h1 id="merlin7-storage">Merlin7 Storage<a class="headerlink" href="#merlin7-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 Merlin7 cluster.</p>
<h3 id="backup-and-data-policies">Backup and data policies<a class="headerlink" href="#backup-and-data-policies" title="Permanent link"></a></h3>
<ul>
<li><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.).</li>
<li><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.</li>
</ul>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>When a user leaves PSI and their account is removed, their storage space in
Merlin may be recycled. Hence, <strong>when a user leaves PSI</strong>, they, their
supervisor or team <strong>must ensure that the data is backed up to an external
storage</strong>!</p>
</div>
<h3 id="how-to-check-quotas">How to check quotas<a class="headerlink" href="#how-to-check-quotas" title="Permanent link"></a></h3>
<p>Some of the Merlin7 directories have quotas applied. A way for checking the quotas is provided with the <code>merlin_quotas</code> command.
This command is useful to show all quotas for the different user storage directories and partitions (including AFS). To check your quotas, please run:</p>
<div class="language-console highlight"><span class="filename">Bash Session</span><pre><span></span><code><span id="__span-0-1"><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="gp">$ </span>merlin_quotas
</span><span id="__span-0-2"><a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="go">Path SpaceUsed SpaceQuota Space % FilesUsed FilesQuota Files %</span>
</span><span id="__span-0-3"><a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a><span class="go">-------------- --------- ---------- ------- --------- ---------- -------</span>
</span><span id="__span-0-4"><a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a><span class="go">/data/user 30.26G 1T 03% 367296 2097152 18%</span>
</span><span id="__span-0-5"><a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a><span class="go"> └─ &lt;USERNAME&gt;</span>
</span><span id="__span-0-6"><a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a><span class="go">/afs/psi.ch 3.4G 9.5G 36% 0 0 0%</span>
</span><span id="__span-0-7"><a id="__codelineno-0-7" name="__codelineno-0-7" href="#__codelineno-0-7"></a><span class="go"> └─ user/&lt;USERDIR&gt;</span>
</span><span id="__span-0-8"><a id="__codelineno-0-8" name="__codelineno-0-8" href="#__codelineno-0-8"></a><span class="go">/data/scratch 688.9M 2T 00% 368471 0 00%</span>
</span><span id="__span-0-9"><a id="__codelineno-0-9" name="__codelineno-0-9" href="#__codelineno-0-9"></a><span class="go"> └─ shared</span>
</span><span id="__span-0-10"><a id="__codelineno-0-10" name="__codelineno-0-10" href="#__codelineno-0-10"></a><span class="go">/data/project 3.373T 11T 31% 425644 2097152 20%</span>
</span><span id="__span-0-11"><a id="__codelineno-0-11" name="__codelineno-0-11" href="#__codelineno-0-11"></a><span class="go"> └─ bio/shared</span>
</span><span id="__span-0-12"><a id="__codelineno-0-12" name="__codelineno-0-12" href="#__codelineno-0-12"></a><span class="go">/data/project 4.142T 11T 38% 579596 2097152 28%</span>
</span><span id="__span-0-13"><a id="__codelineno-0-13" name="__codelineno-0-13" href="#__codelineno-0-13"></a><span class="go"> └─ bio/hpce</span>
</span></code></pre></div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>On first use you will see a message about some configuration being
generated, this is expected. Don't be surprised that it takes some time.
After this using <code>merlin_quotas</code> should be faster.</p>
</div>
<p>The output shows the quotas set and how much you are using of the quota, for each filesystem that has this set. Notice that some users will have
one or more <code>/data/project/...</code> directories showing, depending on whether you are part of a specific PSI research group or project.</p>
<p>The general quota constraints for the different directories are shown in the <a href="#dir_classes">table below</a>. Further details on how to use <code>merlin_quotas</code>
can be found on the <a href="../merlin_tools/">Tools page</a>.</p>
<div class="admonition tip">
<p class="admonition-title">Tip</p>
<p>If you're interesting, you can retrieve the Lustre-based quota information
directly by calling <code>lfs quota -h -p $(( 100000000 + $(id -u $USER) ))
/data</code> directly. Using the <code>merlin_quotas</code> command is more convenient and
shows all your relevant filesystem quotas.</p>
</div>
<h2 id="merlin7-directories">Merlin7 directories<a class="headerlink" href="#merlin7-directories" title="Permanent link"></a></h2>
<p>Merlin7 offers the following directory classes for users:</p>
<ul>
<li><code>/data/user/&lt;username&gt;</code>: Private user <strong>home</strong> directory</li>
<li><code>/data/project/general</code>: project directory for Merlin</li>
<li><code>/data/project/bio/$projectname</code>: project directory for BIO</li>
<li><code>/data/project/mu3e/$projectname</code>: project directory for Mu3e</li>
<li><code>/data/project/meg/$projectname</code>: project directory for Mu3e</li>
<li><code>/scratch</code>: Local <em>scratch</em> disk (only visible by the node running a job).</li>
<li><code>/data/scratch/shared</code>: Shared <em>scratch</em> disk (visible from all nodes).</li>
</ul>
<div class="admonition tip">
<p class="admonition-title">Tip</p>
<p>In Lustre there is a concept called <strong>grace time</strong>. Filesystems have a
block (amount of data) and inode (number of files) quota. These quotas
contain 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 the <strong>grace time</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><a name="dir_classes"></a>Properties of the directory classes:</p>
<table>
<thead>
<tr>
<th>Directory</th>
<th>Block Quota [Soft:Hard]</th>
<th>Inode 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: Inodes</th>
<th>Backup</th>
</tr>
</thead>
<tbody>
<tr>
<td>/data/user/$username</td>
<td>PRJ [1TB:1.074TB]</td>
<td>PRJ [2M:2.1M]</td>
<td style="text-align: center;">7d</td>
<td style="text-align: left;">Immutable. Need a project.</td>
<td style="text-align: left;">Changeable when justified.</td>
<td>no</td>
</tr>
<tr>
<td>/data/project/bio/$projectname</td>
<td>PRJ [1TB:1.074TB]</td>
<td>PRJ [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>
</tr>
<tr>
<td>/data/project/general/$projectname</td>
<td>PRJ [1TB:1.074TB]</td>
<td>PRJ [1M:1.1M]</td>
<td style="text-align: center;">7d</td>
<td style="text-align: left;">Subject to project requirements.</td>
<td style="text-align: left;">Subject to project requirements.</td>
<td>no</td>
</tr>
<tr>
<td>/data/scratch/shared</td>
<td>USR [512GB:2TB]</td>
<td></td>
<td style="text-align: center;">7d</td>
<td style="text-align: left;">Up to x2 when strongly justified.</td>
<td style="text-align: left;">Changeable when justified.</td>
<td>no</td>
</tr>
<tr>
<td>/scratch</td>
<td><em>Undef</em></td>
<td><em>Undef</em></td>
<td style="text-align: center;">N/A</td>
<td style="text-align: left;">N/A</td>
<td style="text-align: left;">N/A</td>
<td>no</td>
</tr>
</tbody>
</table>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>The use of <code>/scratch</code> and <code>/data/scratch/shared</code> areas as an extension of
the quota <em>is forbidden</em>. The <code>/scratch</code> and <code>/data/scratch/shared</code> areas
<strong><em>must not contain</em></strong> final data. Keep in mind that <strong><em>auto cleanup
policies</em></strong> in the <code>/scratch</code> and <code>/data/scratch/shared</code> areas are applied.</p>
</div>
<h3 id="user-home-directory">User home directory<a class="headerlink" href="#user-home-directory" title="Permanent link"></a></h3>
<p>This is the default directory users will land when login in to any Merlin7 machine.
It is intended for your scripts, documents, software development and data. Do not use it for I/O-hungry tasks.</p>
<p>The home directories are mounted in the login and computing nodes under the directory</p>
<p>```bash
/data/user/$username
</p><div class="language-text highlight"><span class="filename">Text Only</span><pre><span></span><code><span id="__span-1-1"><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>Directory policies:
</span><span id="__span-1-2"><a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>
</span><span id="__span-1-3"><a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>* Read **[Important: Code of Conduct](../01-Quick-Start-Guide/code-of-conduct.md)** for more information about Merlin7 policies.
</span><span id="__span-1-4"><a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>* Is **forbidden** to use the home directories for IO-intensive tasks, instead use one of the **[scratch](storage.md#scratch-directories)** areas instead!
</span><span id="__span-1-5"><a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>* No backup policy is applied for the user home directories: **users are responsible for backing up their data**.
</span><span id="__span-1-6"><a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a>
</span><span id="__span-1-7"><a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a>Home directory quotas are defined in a per Lustre project basis. The quota can be checked using the `merlin_quotas` command described
</span><span id="__span-1-8"><a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a>[above](storage.md#how-to-check-quotas).
</span><span id="__span-1-9"><a id="__codelineno-1-9" name="__codelineno-1-9" href="#__codelineno-1-9"></a>
</span><span id="__span-1-10"><a id="__codelineno-1-10" name="__codelineno-1-10" href="#__codelineno-1-10"></a>### Project data directory
</span><span id="__span-1-11"><a id="__codelineno-1-11" name="__codelineno-1-11" href="#__codelineno-1-11"></a>
</span><span id="__span-1-12"><a id="__codelineno-1-12" name="__codelineno-1-12" href="#__codelineno-1-12"></a>This storage is intended for keeping large amounts of a project's data, where the data also can be
</span><span id="__span-1-13"><a id="__codelineno-1-13" name="__codelineno-1-13" href="#__codelineno-1-13"></a>shared by all members of the project (the project's corresponding UNIX group). We recommend to keep most data in
</span><span id="__span-1-14"><a id="__codelineno-1-14" name="__codelineno-1-14" href="#__codelineno-1-14"></a>project related storage spaces, since it allows users to coordinate. Also, project spaces have more flexible policies
</span><span id="__span-1-15"><a id="__codelineno-1-15" name="__codelineno-1-15" href="#__codelineno-1-15"></a>regarding extending the available storage space.
</span><span id="__span-1-16"><a id="__codelineno-1-16" name="__codelineno-1-16" href="#__codelineno-1-16"></a>
</span><span id="__span-1-17"><a id="__codelineno-1-17" name="__codelineno-1-17" href="#__codelineno-1-17"></a>Scientists can request a Merlin project space as described in **[[Accessing Merlin -&gt; Requesting a Project]](../01-Quick-Start-Guide/requesting-projects.md)**.
</span><span id="__span-1-18"><a id="__codelineno-1-18" name="__codelineno-1-18" href="#__codelineno-1-18"></a>By default, Merlin can offer **general** project space, centrally covered, as long as it does not exceed 10TB (otherwise, it has to be justified).
</span><span id="__span-1-19"><a id="__codelineno-1-19" name="__codelineno-1-19" href="#__codelineno-1-19"></a>General Merlin projects might need to be reviewed after one year of their creation.
</span><span id="__span-1-20"><a id="__codelineno-1-20" name="__codelineno-1-20" href="#__codelineno-1-20"></a>
</span><span id="__span-1-21"><a id="__codelineno-1-21" name="__codelineno-1-21" href="#__codelineno-1-21"></a>Once a Merlin project is created, the directory will be mounted in the login and computing nodes under the directory:
</span><span id="__span-1-22"><a id="__codelineno-1-22" name="__codelineno-1-22" href="#__codelineno-1-22"></a>
</span><span id="__span-1-23"><a id="__codelineno-1-23" name="__codelineno-1-23" href="#__codelineno-1-23"></a>```bash
</span><span id="__span-1-24"><a id="__codelineno-1-24" name="__codelineno-1-24" href="#__codelineno-1-24"></a>/data/project/general/$projectname
</span></code></pre></div><p></p>
<p>Project quotas are defined in a per Lustre project basis. Users can check the project quota by running the following command:</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>lfs<span class="w"> </span>quota<span class="w"> </span>-h<span class="w"> </span>-p<span class="w"> </span><span class="nv">$projectid</span><span class="w"> </span>/data
</span></code></pre></div>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>Checking <strong>quotas</strong> for the Merlin projects is not yet possible. In the
future, a list of <code>projectid</code> will be provided, so users can check their
quotas.</p>
</div>
<p>Directory policies:</p>
<ul>
<li>Read <strong><a href="../../01-Quick-Start-Guide/code-of-conduct/">Important: Code of Conduct</a></strong> for more information about Merlin7 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.<ul>
<li>Please Use <code>/scratch</code>, <code>/data/scratch/shared</code> for this purpose.</li>
</ul>
</li>
<li>No backups: users are responsible for managing the backups of their data directories.</li>
</ul>
<h4 id="dedicated-project-directories">Dedicated project directories<a class="headerlink" href="#dedicated-project-directories" title="Permanent link"></a></h4>
<p>Some departments or divisions have bigger storage space requirements on Merlin7. At present, <code>bio</code>, <code>mu3e</code> and <code>meg</code> are the main ones.
These are mounted under the following paths:</p>
<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>/data/project/bio
</span><span id="__span-3-2"><a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>/data/project/mu3e
</span><span id="__span-3-3"><a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>/data/project/meg
</span></code></pre></div>
<p>They follow the same rules as the general projects, except that they have assigned more space.</p>
<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>/data/scratch/shared</code>).</p>
<ul>
<li><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. Mount path:</li>
</ul>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-4-1"><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>/scratch
</span></code></pre></div>
<ul>
<li><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.</li>
</ul>
<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/scratch/shared
</span></code></pre></div>
<p>Scratch directories policies:</p>
<ul>
<li>Read <strong><a href="../../01-Quick-Start-Guide/code-of-conduct/">Important: Code of Conduct</a></strong> for more information about Merlin7 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>
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