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<meta name="description" content=" Bind Paths / File Sharing Previous Next Singularity ‘swaps’ out the currently running root operating system on the host for what is inside the container, and in doing so none of the host file systems are accessible anymore. As a workaround for this, Singularity will bind those paths back in via two primary methods: system defined bind points and conditional user defined bind points.To mount a bind path inside the container, a bind point must be defined within the container. The bind point is a target location entity to which the actual directory or file can be bound to. This means that if you want to bind to a point within the container such as /global, that directory must already exist within the container.It is however possible that the system administrator has enabled a Singularity feature called overlay in the /etc/singularity/singularity.conf file. This will cause the bind points to be created on an as needed basis in an overlay file system so that the underlying container is not modified. But because the overlay feature is not always used, it maybe necessary for container standards to exist to ensure portability from host to host.If a bind path is requested, and the bind point does not exist within the container, a warning message will be displayed, and Singularity will continue trying to mount file system. For example:$ singularity shell /tmp/Centos7-ompi.img WARNING: Non existant bind point (directory) in container: '/global'Singularity: Invoking an interactive shell within container...Singularity.Centos7-ompi.img> Even though /global did not exist inside the container, the shell command printed a warning but continued on. If we enable enable overlay = yes in the /etc/singularity/singularity.conf you will find that we no longer get the error and /global is created and accessible as expected:$ singularity shell /tmp/Centos7-ompi.img Singularity: Invoking an interactive shell within container...Singularity.Centos7-ompi.img> System defined bind pointsThe system administrator has the ability to define what bind points will be included automatically inside each container. The bind paths are locations on the host’s root file system which should also be visible within the container. Some of the bind paths are automatically derived (e.g. a user’s home directory) and some are statically defined (e.g. bind path = in /etc/singularity/singularity.conf).User defined bind pointsIf the system administrator has enabled user control of binds (via user bind control = yes in /etc/singularity/singularity.conf), you will be able to request your own bind points within your container.Further, if the administrator has enabled the use of file system overlay (via enable overlay = yes in /etc/singularity/singularity.conf), you can bind host system directories to directories that do not exist within the container. Singularity will dynamically create the necessary bind points in your container on demand. This feature may not be supported on older host systems.Here’s an example of using the --bind option and binding /tmp to /scratch (which may not already exist within the container if file system overlay is enabled):$ singularity shell -B /tmp:/scratch /tmp/Centos7-ompi.img Singularity: Invoking an interactive shell within container...Singularity.Centos7-ompi.img> ls /scratchssh-7vywtVeOez systemd-private-cd84c81dda754fe4a7a593647d5a5765-ntpd.service-12nMO4 Previous Next Edit me Site last generated: Jul 26, 2017 ">
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<p>Singularity ‘swaps’ out the currently running root operating system on the host for what is inside the container, and in doing so none of the host file systems are accessible anymore. As a workaround for this, Singularity will <em>bind</em> those paths back in via two primary methods: system defined bind points and conditional user defined bind points.</p>
<p>To <em>mount</em> a bind path inside the container, a <strong><em>bind point</em></strong> must be defined within the container. The bind point is a target location entity to which the actual directory or file can be bound to. This means that if you want to bind to a point within the container such as <code class="highlighter-rouge">/global</code>, that directory must already exist within the container.</p>
<p>It is however possible that the system administrator has enabled a Singularity feature called <em>overlay</em> in the <code class="highlighter-rouge">/etc/singularity/singularity.conf</code> file. This will cause the bind points to be created on an as needed basis in an overlay file system so that the underlying container is not modified. But because the <em>overlay</em> feature is not always used, it maybe necessary for container standards to exist to ensure portability from host to host.</p>
<p>If a bind path is requested, and the bind point does not exist within the container, a warning message will be displayed, and Singularity will continue trying to mount file system. For example:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>singularity shell /tmp/Centos7-ompi.img
WARNING: Non existant <span class="nb">bind </span>point <span class="o">(</span>directory<span class="o">)</span> <span class="k">in </span>container: <span class="s1">'/global'</span>
Singularity: Invoking an interactive shell within container...
<span class="gp">Singularity.Centos7-ompi.img> </span>
</code></pre>
</div>
<p>Even though <code class="highlighter-rouge">/global</code> did not exist inside the container, the shell command printed a warning but continued on. If we enable <code class="highlighter-rouge">enable overlay = yes</code> in the <code class="highlighter-rouge">/etc/singularity/singularity.conf</code> you will find that we no longer get the error and <code class="highlighter-rouge">/global</code> is created and accessible as expected:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>singularity shell /tmp/Centos7-ompi.img
Singularity: Invoking an interactive shell within container...
<span class="gp">Singularity.Centos7-ompi.img> </span>
</code></pre>
</div>
<h4 id="system-defined-bind-points">System defined bind points</h4>
<p>The system administrator has the ability to define what bind points will be included automatically inside each container. The bind paths are locations on the host’s root file system which should also be visible within the container. Some of the bind paths are automatically derived (e.g. a user’s home directory) and some are statically defined (e.g. <code class="highlighter-rouge">bind path = </code> in <code class="highlighter-rouge">/etc/singularity/singularity.conf</code>).</p>
<h4 id="user-defined-bind-points">User defined bind points</h4>
<p>If the system administrator has enabled user control of binds (via <code class="highlighter-rouge">user bind control = yes</code> in <code class="highlighter-rouge">/etc/singularity/singularity.conf</code>), you will be able to request your own bind points within your container.</p>
<p>Further, if the administrator has enabled the use of file system overlay (via <code class="highlighter-rouge">enable overlay = yes</code> in <code class="highlighter-rouge">/etc/singularity/singularity.conf</code>), you can bind host system directories to directories that do not exist within the container. Singularity will dynamically create the necessary bind points in your container on demand. This feature may not be supported on older host systems.</p>
<p>Here’s an example of using the <code class="highlighter-rouge">--bind</code> option and binding <code class="highlighter-rouge">/tmp</code> to <code class="highlighter-rouge">/scratch</code> (which may not already exist within the container if file system overlay is enabled):</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>singularity shell -B /tmp:/scratch /tmp/Centos7-ompi.img
Singularity: Invoking an interactive shell within container...
<span class="gp">Singularity.Centos7-ompi.img> </span>ls /scratch
ssh-7vywtVeOez systemd-private-cd84c81dda754fe4a7a593647d5a5765-ntpd.service-12nMO4
</code></pre>
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