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<meta name="description" content=" Singularity Run Previous Next UsageSingularity run allows you to define a custom action to be taken when a container is either run or executed directly by file name. The action is defined by a Singularity “runscript” which is an executable file (script or binary) located within the container physically at ‘/singularity’.The usage is as follows:$ singularity runUSAGE: singularity (options) run [container image] (options)The command that you want to exec will follow the container image along with any additional arguments will all be passed directly to the program being executed within the container.You can also execute the container directly, and it will automatically pass the execution process to the Singularity runscript along with any arguments.ExamplesAs we have defined within the %runscript in bootstrap, we can execute a script, workflow, or a given command using the run Singularity container interface command. In the above examples, we specified the run script to exec /usr/bin/python "$@" which will call Python and pass along any arguments we have supply.For example:$ singularity run /tmp/Centos7-ompi.img --versionPython 2.7.5$ singularity run /tmp/Centos7-ompi.img hello.py Hello World: The Python version is 2.7.5$ singularity run /tmp/Centos7-ompi.img Python 2.7.5 (default, Nov 20 2015, 02:00:19) [GCC 4.8.5 20150623 (Red Hat 4.8.5-4)] on linux2Type "help", "copyright", "credits" or "license" for more information.>>> Executing a container directlyAdditionally, the run interface gets called when the container file is executed directly (yes, the container is set as executable!):$ ls -l /tmp/Centos7-ompi.img -rwxr-xr-x. 1 root root 2147483679 Oct 9 05:31 /tmp/Centos7-ompi.img$ /tmp/Centos7-ompi.img hello.py Hello World: The Python version is 2.7.5This means you could even rename this container to something related to the runscript (perhaps “centos7-python.exe”) and have users call that directly instead of the system python program. 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>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. The action is defined by a Singularity “runscript” which is an executable file (script or binary) located within the container physically at ‘/singularity’.</p>
<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>
The <span class="nb">command </span>that you want to <span class="nb">exec </span>will follow the container image along with any additional arguments will all be passed directly to the program being executed within the container.
You can also execute the container directly, and it will automatically pass the execution process to the Singularity runscript along with any arguments.
</code></pre>
</div>
<h3 id="examples">Examples</h3>
<p>As we have defined within the <code class="highlighter-rouge">%runscript</code> in <a href="/bootstrap-image">bootstrap</a>, we can execute a script, workflow, or a given command using the <code class="highlighter-rouge">run</code> Singularity container interface command. In the above examples, we specified the run script to <code class="highlighter-rouge">exec /usr/bin/python "$@"</code> which will call Python and pass along any arguments we have supply.</p>
<p>For example:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>singularity run /tmp/Centos7-ompi.img --version
Python 2.7.5
<span class="gp">$ </span>singularity run /tmp/Centos7-ompi.img hello.py
Hello World: The Python version is 2.7.5
<span class="gp">$ </span>singularity run /tmp/Centos7-ompi.img
Python 2.7.5 <span class="o">(</span>default, Nov 20 2015, 02:00:19<span class="o">)</span>
<span class="o">[</span>GCC 4.8.5 20150623 <span class="o">(</span>Red Hat 4.8.5-4<span class="o">)]</span> on linux2
Type <span class="s2">"help"</span>, <span class="s2">"copyright"</span>, <span class="s2">"credits"</span> or <span class="s2">"license"</span> <span class="k">for </span>more information.
<span class="gp">>>> </span>
</code></pre>
</div>
<h2 id="executing-a-container-directly">Executing a container directly</h2>
<p>Additionally, the <code class="highlighter-rouge">run</code> interface gets called when the container file is executed directly (yes, the container is set as executable!):</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>ls -l /tmp/Centos7-ompi.img
-rwxr-xr-x. 1 root root 2147483679 Oct 9 05:31 /tmp/Centos7-ompi.img
<span class="gp">$ </span>/tmp/Centos7-ompi.img hello.py
Hello World: The Python version is 2.7.5
</code></pre>
</div>
<p>This means you could even rename this container to something related to the runscript (perhaps “<em>centos7-python.exe</em>”) and have users call that directly instead of the system python program.</p>
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