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<h1 id="transferring-data">Transferring Data<a class="headerlink" href="#transferring-data" title="Permanent link"></a></h1>
<h2 id="overview">Overview<a class="headerlink" href="#overview" title="Permanent link"></a></h2>
<p>Most methods allow data to be either transmitted or received, so it may make sense to
initiate the transfer from either merlin or the other system, depending on the network
visibility.</p>
<ul>
<li>Merlin login nodes are visible from the PSI network, so direct data transfer
(rsync/WinSCP) is generally preferable. This can be initiated from either endpoint.</li>
<li>Merlin login nodes can access the internet using a limited set of protocols:<ul>
<li>SSH-based protocols using port 22 (rsync-over-ssh, sftp, WinSCP, etc)</li>
<li>HTTP-based protocols using ports 80 or 445 (https, WebDav, etc)</li>
<li>Protocols using other ports require admin configuration and may only work with
specific hosts (ftp, rsync daemons, etc)</li>
</ul>
</li>
<li>Systems on the internet can access the <a href="https://www.psi.ch/en/photon-science-data-services/data-transfer">PSI Data Transfer</a> service
<code>datatransfer.psi.ch</code>, using ssh-based protocols and <a href="https://www.globus.org/">Globus</a></li>
</ul>
<h2 id="direct-transfer-via-merlin6-login-nodes">Direct transfer via Merlin6 login nodes<a class="headerlink" href="#direct-transfer-via-merlin6-login-nodes" title="Permanent link"></a></h2>
<p>The following methods transfer data directly via the <a href="../../quick-start-guide/accessing-interactive-nodes/">login
nodes</a>. They are suitable
for use from within the PSI network.</p>
<h3 id="rsync">Rsync<a class="headerlink" href="#rsync" title="Permanent link"></a></h3>
<p>Rsync is the preferred method to transfer data from Linux/MacOS. It allows
transfers to be easily resumed if they get interrupted. The general syntax is:</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>rsync<span class="w"> </span>-avAHXS<span class="w"> </span>&lt;src&gt;<span class="w"> </span>&lt;dst&gt;
</span></code></pre></div>
<p>For example, to transfer files from your local computer to a merlin project
directory:</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>rsync<span class="w"> </span>-avAHXS<span class="w"> </span>~/localdata<span class="w"> </span>user@merlin-l-01.psi.ch:/data/project/general/myproject/
</span></code></pre></div>
<p>You can resume interrupted transfers by simply rerunning the command. Previously
transferred files will be skipped.</p>
<h3 id="winscp">WinSCP<a class="headerlink" href="#winscp" title="Permanent link"></a></h3>
<p>The WinSCP tool can be used for remote file transfer on Windows. It is available
from the Software Kiosk on PSI machines. Add <code>merlin-l-01.psi.ch</code> as a host and
connect with your PSI credentials. You can then drag-and-drop files between your
local computer and merlin.</p>
<h3 id="switchfilesender">SWITCHfilesender<a class="headerlink" href="#switchfilesender" title="Permanent link"></a></h3>
<p><strong><a href="https://filesender.switch.ch/filesender2/?s=upload">SWITCHfilesender</a></strong> is an installation of the FileSender project (filesender.org) which is a web based application that allows authenticated users to securely and easily send arbitrarily large files to other users.</p>
<p>Authentication of users is provided through SimpleSAMLphp, supporting SAML2, LDAP and RADIUS and more. Users without an account can be sent an upload voucher by an authenticated user. FileSender is developed to the requirements of the higher education and research community.</p>
<p>The purpose of the software is to send a large file to someone, have that file available for download for a certain number of downloads and/or a certain amount of time, and after that automatically delete the file. The software is not intended as a permanent file publishing platform.</p>
<p><strong><a href="https://filesender.switch.ch/filesender2/?s=upload">SWITCHfilesender</a></strong> is fully integrated with PSI, therefore, PSI employees can log in by using their PSI account (through Authentication and Authorization Infrastructure / AAI, by selecting PSI as the institution to be used for log in).</p>
<h2 id="psi-data-transfer">PSI Data Transfer<a class="headerlink" href="#psi-data-transfer" title="Permanent link"></a></h2>
<p>From August 2024, Merlin is connected to the <strong><a href="https://www.psi.ch/en/photon-science-data-services/data-transfer">PSI Data
Transfer</a></strong>
service, <code>datatransfer.psi.ch</code>. This is a central service managed by the
<strong><a href="https://linux.psi.ch/index.html">Linux team</a></strong>. However, any problems or
questions related to it can be directly <a href="../../support/index.md">reported</a> to the
Merlin administrators, which will forward the request if necessary.</p>
<p>The PSI Data Transfer servers supports the following protocols:</p>
<ul>
<li>Data Transfer - SSH (scp / rsync)</li>
<li>Data Transfer - Globus</li>
</ul>
<p>Notice that <code>datatransfer.psi.ch</code> does not allow SSH login, only <code>rsync</code>, <code>scp</code> and <a href="https://www.globus.org/">Globus</a> access is allowed.</p>
<p>The following filesystems are mounted:</p>
<ul>
<li><code>/merlin/export</code> which points to the <code>/export</code> directory in Merlin.</li>
<li><code>/merlin/data/experiment/mu3e</code> which points to the <code>/data/experiment/mu3e</code> directories in Merlin.<ul>
<li>Mu3e sub-directories are mounted in RW (read-write), except for <code>data</code> (read-only mounted)</li>
</ul>
</li>
<li><code>/merlin/data/project/general</code> which points to the <code>/data/project/general</code> directories in Merlin.<ul>
<li>Owners of Merlin projects should request explicit access to it.</li>
<li>Currently, only <code>CSCS</code> is available for transferring files between PizDaint/Alps and Merlin</li>
</ul>
</li>
<li><code>/merlin/data/project/bio</code> which points to the <code>/data/project/bio</code> directories in Merlin.</li>
<li><code>/merlin/data/user</code> which points to the <code>/data/user</code> directories in Merlin.</li>
</ul>
<p>Access to the PSI Data Transfer uses <strong><em>Multi factor authentication</em></strong> (MFA).
Therefore, having the Microsoft Authenticator App is required as explained <a href="https://www.psi.ch/en/computing/change-to-mfa">here</a>.</p>
<div class="admonition tip">
<p class="admonition-title">Official Documentation</p>
<p>Please follow the <a href="https://www.psi.ch/en/photon-science-data-services/data-transfer">Official PSI Data Transfer</a> documentation for further instructions.</p>
</div>
<h3 id="directories">Directories<a class="headerlink" href="#directories" title="Permanent link"></a></h3>
<h4 id="merlindatauser">/merlin/data/user<a class="headerlink" href="#merlindatauser" title="Permanent link"></a></h4>
<p>User data directories are mounted in RW.</p>
<div class="admonition warning">
<p class="admonition-title">Secure Permissions</p>
<p>Please, <strong>ensure proper secured permissions</strong> in your <code>/data/user</code>
directory. By default, when directory is created, the system applies the
most restrictive permissions. However, this does not prevent users for
changing permissions if they wish. At this point, users become responsible
of those changes.</p>
</div>
<h4 id="merlinexport">/merlin/export<a class="headerlink" href="#merlinexport" title="Permanent link"></a></h4>
<p>Transferring big amounts of data from outside PSI to Merlin is always possible through <code>/export</code>.</p>
<div class="admonition tip">
<p class="admonition-title">Export Directory Access</p>
<p>The <code>/export</code> directory can be used by any Merlin user. This is configured
in Read/Write mode. If you need access, please, contact the Merlin
administrators.</p>
</div>
<div class="admonition warning">
<p class="admonition-title">Export Usage Policy</p>
<p>The use <strong>export</strong> as an extension of the quota <em>is forbidden</em>. Auto
cleanup policies in the <strong>export</strong> area apply for files older than 28 days.</p>
</div>
<h5 id="exporting-data-from-merlin">Exporting data from Merlin<a class="headerlink" href="#exporting-data-from-merlin" title="Permanent link"></a></h5>
<p>For exporting data from Merlin to outside PSI by using <code>/export</code>, one has to:</p>
<ul>
<li>From a Merlin login node, copy your data from any directory (i.e. <code>/data/project</code>, <code>/data/user</code>, <code>/scratch</code>) to
<code>/export</code>. Ensure to properly secure your directories and files with proper permissions.</li>
<li>Once data is copied, from <strong><code>datatransfer.psi.ch</code></strong>, copy the data from <code>/merlin/export</code> to outside PSI</li>
</ul>
<h5 id="importing-data-to-merlin">Importing data to Merlin<a class="headerlink" href="#importing-data-to-merlin" title="Permanent link"></a></h5>
<p>For importing data from outside PSI to Merlin by using <code>/export</code>, one has to:</p>
<ul>
<li>From <strong><code>datatransfer.psi.ch</code></strong>, copy the data from outside PSI to <code>/merlin/export</code>.</li>
</ul>
<p>Ensure to properly secure your directories and files with proper permissions.</p>
<ul>
<li>Once data is copied, from a Merlin login node, copy your data from <code>/export</code> to any directory (i.e. <code>/data/project</code>, <code>/data/user</code>, <code>/scratch</code>).</li>
</ul>
<h4 id="request-access-to-your-project-directory">Request access to your project directory<a class="headerlink" href="#request-access-to-your-project-directory" title="Permanent link"></a></h4>
<p>Optionally, instead of using <code>/export</code>, Merlin project owners can request Read/Write or Read/Only access to their project directory.</p>
<div class="admonition tip">
<p class="admonition-title">Project Access</p>
<p>Merlin projects can request direct access. This can be configured in Read/Write or Read/Only modes. If your project needs access, please, contact the Merlin administrators.</p>
</div>
<h2 id="connecting-to-merlin6-from-outside-psi">Connecting to Merlin6 from outside PSI<a class="headerlink" href="#connecting-to-merlin6-from-outside-psi" title="Permanent link"></a></h2>
<p>Merlin6 is fully accessible from within the PSI network. To connect from outside you can use:</p>
<ul>
<li><a href="https://www.psi.ch/en/computing/vpn">VPN</a> (<a href="https://intranet.psi.ch/BIO/ComputingVPN">alternate instructions</a>)</li>
<li><a href="https://www.psi.ch/en/computing/ssh-hop">SSH hopx</a><ul>
<li>Please avoid transferring big amount data through <strong>hopx</strong></li>
</ul>
</li>
<li><a href="../nomachine/">No Machine</a><ul>
<li>Remote Interactive Access through <a href="https://www.psi.ch/en/photon-science-data-services/remote-interactive-access"><strong>'rem-acc.psi.ch'</strong></a></li>
<li>Please avoid transferring big amount of data through <strong>NoMachine</strong></li>
</ul>
</li>
</ul>
<h2 id="connecting-from-merlin6-to-outside-file-shares">Connecting from Merlin6 to outside file shares<a class="headerlink" href="#connecting-from-merlin6-to-outside-file-shares" title="Permanent link"></a></h2>
<h3 id="merlin_rmount-command"><code>merlin_rmount</code> command<a class="headerlink" href="#merlin_rmount-command" title="Permanent link"></a></h3>
<p>Merlin provides a command for mounting remote file systems, called <code>merlin_rmount</code>. This
provides a helpful wrapper over the Gnome storage utilities, and provides support for a wide range of remote file formats, including
* SMB/CIFS (Windows shared folders)
* WebDav
* AFP
* FTP, SFTP
* <a href="https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/8/html/using_the_desktop_environment_in_rhel_8/managing-storage-volumes-in-gnome_using-the-desktop-environment-in-rhel-8#gvfs-back-ends_managing-storage-volumes-in-gnome">others</a></p>
<p><a href="../../software-support/merlin-rmount/">More instruction on using <code>merlin_rmount</code></a></p>
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