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<meta name="description" content=" Singularity Run UsageIt’s common to want your container to “do a thing.” Singularity run allows you to define a custom action to be taken when a container is either run or executed directly by file name. Specifically, you might want it to execute a command, or run an executable that gives access to many different functions for the user. First, how do we run a container? We can do that in one of two ways - the commands below are identical:singularity run centos7.img./centos7.imgIn both cases, we are executing the container’s “runscript,” which is the executable /singularity at the root of the image, which is either an actual file (version 2.2 and earlier) or a link to one (2.3 and later). For example, looking at a 2.3 image, I can see the runscript via the path to the link:singularity exec centos7.img cat /singularity#!/bin/shexec /bin/bash "$@"or to the actual file in the container’s metadata folder, /.singularity.dsingularity exec centos7.img cat /.singularity.d/runscript#!/bin/shexec /bin/bash "$@"The usage is as follows:$ singularity runUSAGE: singularity (options) run [container image] (options)Notice how the runscript has bash followed by `$@`? This is good practice to include in a runscript, as any arguments passed by the user will be given to the container. Thus, I could send a command to the container for bash to run:```bashecho "echo motorobot" >> /home/vanessa/Desktop/runme.shsingularity run centos7.img runme.shmotorbotDefining the RunscriptWhen using the “run” command, the order of operations for runscripts works as follows: A user defined runscript in the %runscript section of a bootstrap takes preference over all If the user has not defined a runscript and is importing a Docker container, the Docker ENTRYPOINT is used. If a user has not defined a runscript and adds IncludeCmd: yes to the bootstrap file, the CMD is used over the ENTRYPOINT If the user has not defined a runscript and the Docker container doesn’t have an ENTRYPOINT, we look for CMD, even if the user hasn’t asked for it. If the user has not deifned a runscript, and there is no ENTRYPOINT or CMD (or we aren’t importing Docker at all) then we default to /bin/bashHere is how you would define the runscript section when you bootstrap an image:Bootstrap: dockerFrom: ubuntu:latest%runscriptexec /usr/bin/python "$@"`and of course python should be installed as /usr/bin/python. The addition of $@ ensures that arguments are passed along from the user. If you want your container to run absolutely any command given to it, and you want to use run instead of exec, you could also just do:Bootstrap: dockerFrom: ubuntu:latest%runscriptexec "$@"`Generally, it is advised to provide a runscript that tells your user how to use the container, and gives access to the important executables. A user should be able to find your container, and execute it without an arguments, and get the equivalent of --help. Depending on your language of choice, you can do this in multiple ways. Previous Next Edit me Site last generated: Jul 26, 2017 ">
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<h1 class="post-title-main">Singularity Run</h1>
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<h2 id="usage">Usage</h2>
<p>It’s common to want your container to “do a thing.” Singularity <code class="highlighter-rouge">run</code> allows you to define a custom action to be taken when a container is either <code class="highlighter-rouge">run</code> or executed directly by file name. Specifically, you might want it to execute a command, or run an executable that gives access to many different functions for the user. First, how do we run a container? We can do that in one of two ways - the commands below are identical:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>singularity run centos7.img
./centos7.img
</code></pre>
</div>
<p>In both cases, we are executing the container’s “runscript,” which is the executable <code class="highlighter-rouge">/singularity</code> at the root of the image, which is either an actual file (version 2.2 and earlier) or a link to one (2.3 and later). For example, looking at a 2.3 image, I can see the runscript via the path to the link:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>singularity <span class="nb">exec </span>centos7.img cat /singularity
<span class="c">#!/bin/sh</span>
<span class="nb">exec</span> /bin/bash <span class="s2">"</span><span class="nv">$@</span><span class="s2">"</span>
</code></pre>
</div>
<p>or to the actual file in the container’s metadata folder, <code class="highlighter-rouge">/.singularity.d</code></p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>singularity <span class="nb">exec </span>centos7.img cat /.singularity.d/runscript
<span class="c">#!/bin/sh</span>
<span class="nb">exec</span> /bin/bash <span class="s2">"</span><span class="nv">$@</span><span class="s2">"</span>
</code></pre>
</div>
<p>The usage is as follows:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>singularity run
USAGE: singularity <span class="o">(</span>options<span class="o">)</span> run <span class="o">[</span>container image] <span class="o">(</span>options<span class="o">)</span>
Notice how the runscript has bash followed by <span class="sb">`</span><span class="nv">$@</span><span class="sb">`</span>? This is good practice to include <span class="k">in </span>a runscript, as any arguments passed by the user will be given to the container. Thus, I could send a <span class="nb">command </span>to the container <span class="k">for </span>bash to run:
<span class="sb">```</span>bash
<span class="nb">echo</span> <span class="s2">"echo motorobot"</span> >> /home/vanessa/Desktop/runme.sh
singularity run centos7.img runme.sh
motorbot
</code></pre>
</div>
<h3 id="defining-the-runscript">Defining the Runscript</h3>
<p>When using the “run” command, the order of operations for runscripts works as follows:</p>
<ol>
<li>A user defined runscript in the <code class="highlighter-rouge">%runscript</code> section of a bootstrap takes preference over all</li>
<li>If the user has not defined a runscript and is importing a Docker container, the Docker <code class="highlighter-rouge">ENTRYPOINT</code> is used.</li>
<li>If a user has not defined a runscript and adds <code class="highlighter-rouge">IncludeCmd: yes</code> to the bootstrap file, the <code class="highlighter-rouge">CMD</code> is used over the <code class="highlighter-rouge">ENTRYPOINT</code></li>
<li>If the user has not defined a runscript and the Docker container doesn’t have an <code class="highlighter-rouge">ENTRYPOINT</code>, we look for <code class="highlighter-rouge">CMD</code>, even if the user hasn’t asked for it.</li>
<li>If the user has not deifned a runscript, and there is no <code class="highlighter-rouge">ENTRYPOINT</code> or <code class="highlighter-rouge">CMD</code> (or we aren’t importing Docker at all) then we default to <code class="highlighter-rouge">/bin/bash</code></li>
</ol>
<p>Here is how you would define the runscript section when you <a href="/bootstrap-image">bootstrap</a> an image:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>Bootstrap: docker
From: ubuntu:latest
%runscript
<span class="nb">exec</span> /usr/bin/python <span class="s2">"</span><span class="nv">$@</span><span class="s2">"</span><span class="sb">`</span>
</code></pre>
</div>
<p>and of course python should be installed as /usr/bin/python. The addition of <code class="highlighter-rouge">$@</code> ensures that arguments are passed along from the user. If you want your container to run absolutely any command given to it, and you want to use run instead of exec, you could also just do:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>Bootstrap: docker
From: ubuntu:latest
%runscript
<span class="nb">exec</span> <span class="s2">"</span><span class="nv">$@</span><span class="s2">"</span><span class="sb">`</span>
</code></pre>
</div>
<p>Generally, it is advised to provide a runscript that tells your user how to use the container, and gives access to the important executables. A user should be able to find your container, and execute it without an arguments, and get the equivalent of <code class="highlighter-rouge">--help</code>. Depending on your language of choice, you can do this in multiple ways.</p>
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