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<meta name="description" content=" Singularity Shell Previous Next UsageThe shell Singularity sub-command will automatically spawn a shell within a container. The default and the only requirement of any Singularity container is that /bin/sh must be present, and thus /bin/sh is also used as the default shell.The usage is as follows:$ singularity shellUSAGE: singularity (options) shell [container image] (options)Additionally any arguments passed to the Singularity command (after the container name) will be passed to the called shell within the container.OptionsThe shell sub-command allows you to set or change the default shell which is used by using the --shell argument. As of Singularity version 2.2, you can also use the environment variable SINGULARITY_SHELL which will use that as your shell entry point into the container.Notes about dot filesSome shells (e.g. /bin/bash) will automatically try to execute the user’s dot files and system login scripts. This carries with it several caveats that must be noted: Singularity automatically tries to set the prompt (PS1 environment variable) to something related to the container, but many cases the dot files override this and reset the prompt. Custom commands inside a user’s dot file maybe parsed and executed when the container is called (a common example of this is environment modules) and that may lead to errors or unexpected behaviors when spawning a shell inside a container. For these reasons (and if you experience issues like this) you may want to consider also telling the shell inside the container not to parse dot files and login scripts. Read the documentation on your desired shell (for Bash check into --norc and --noprofile).Examples$ singularity shell container.img Singularity/container.img> echo $SHELL/bin/shSingularity/container.img> exit$ $ echo world > hello$ singularity shell /tmp/Centos7-ompi.img Singularity: Invoking an interactive shell within container...Singularity.Centos7-ompi.img> pwd/home/gmk/demoSingularity.Centos7-ompi.img> lshelloSingularity.Centos7-ompi.img> cat hello worldSingularity.Centos7-ompi.img> exitYou can see from the above example, we were able to have access to our current working directory. That is because one of the default bind paths that is included and enabled by default in Singularity is the binding of the user’s home directory. In this example, you can see that we created a file called hello in the current directory and after we entered the Singularity container we landed in the same directory and thus hello is accessible to us here as we would expect.Help$ singularity shell container.img --helpGNU bash, version 4.3.30(1)-release-(x86_64-pc-linux-gnu)Usage: /bin/sh [GNU long option] [option] ... /bin/sh [GNU long option] [option] script-file ...GNU long options: --debug --debugger --dump-po-strings --dump-strings --help --init-file --login --noediting --noprofile --norc --posix --rcfile --restricted --verbose --versionShell options: -ilrsD or -c command or -O shopt_option (invocation only) -abefhkmnptuvxBCHP or -o optionType `/bin/sh -c "help set"' for more information about shell options.Type `/bin/sh -c help' for more information about shell built in commands.Use the `bashbug' command to report bugs.$ And thus we should be able to do:$ singularity shell container.img -c "echo hello world"hello world$ Previous Next Edit me Site last generated: Jul 26, 2017 ">
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<h1 class="post-title-main">Singularity Shell</h1>
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<div id="toc"></div>
<h2 id="usage">Usage</h2>
<p>The <code class="highlighter-rouge">shell</code> Singularity sub-command will automatically spawn a shell within a container. The default and the only requirement of any Singularity container is that /bin/sh must be present, and thus /bin/sh is also used as the default shell.</p>
<p>The usage is as follows:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>singularity shell
USAGE: singularity <span class="o">(</span>options<span class="o">)</span> shell <span class="o">[</span>container image] <span class="o">(</span>options<span class="o">)</span>
</code></pre>
</div>
<p>Additionally any arguments passed to the Singularity command (after the container name) will be passed to the called shell within the container.</p>
<h2 id="options">Options</h2>
<p>The shell sub-command allows you to set or change the default shell which is used by using the <code class="highlighter-rouge">--shell</code> argument. As of Singularity version 2.2, you can also use the environment variable SINGULARITY_SHELL which will use that as your shell entry point into the container.</p>
<h3 id="notes-about-dot-files">Notes about dot files</h3>
<p>Some shells (e.g. /bin/bash) will automatically try to execute the user’s dot files and system login scripts. This carries with it several caveats that must be noted:</p>
<ul>
<li>Singularity automatically tries to set the prompt (PS1 environment variable) to something related to the container, but many cases the dot files override this and reset the prompt.</li>
<li>Custom commands inside a user’s dot file maybe parsed and executed when the container is called (a common example of this is environment modules) and that may lead to errors or unexpected behaviors when spawning a shell inside a container.</li>
<li>For these reasons (and if you experience issues like this) you may want to consider also telling the shell inside the container not to parse dot files and login scripts. Read the documentation on your desired shell (for Bash check into <code class="highlighter-rouge">--norc</code> and <code class="highlighter-rouge">--noprofile</code>).</li>
</ul>
<h2 id="examples">Examples</h2>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>singularity shell container.img
<span class="gp">Singularity/container.img> </span><span class="nb">echo</span> <span class="nv">$SHELL</span>
/bin/sh
<span class="gp">Singularity/container.img> </span><span class="nb">exit</span>
<span class="gp">$ </span>
</code></pre>
</div>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span><span class="nb">echo </span>world > hello
<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><span class="nb">pwd</span>
/home/gmk/demo
<span class="gp">Singularity.Centos7-ompi.img> </span>ls
hello
<span class="gp">Singularity.Centos7-ompi.img> </span>cat hello
world
<span class="gp">Singularity.Centos7-ompi.img> </span><span class="nb">exit</span>
</code></pre>
</div>
<p>You can see from the above example, we were able to have access to our current working directory. That is because one of the default bind paths that is included and enabled by default in Singularity is the binding of the user’s home directory. In this example, you can see that we created a file called <code class="highlighter-rouge">hello</code> in the current directory and after we entered the Singularity container we landed in the same directory and thus <code class="highlighter-rouge">hello</code> is accessible to us here as we would expect.</p>
<h2 id="help">Help</h2>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>singularity shell container.img --help
GNU bash, version 4.3.30<span class="o">(</span>1<span class="o">)</span>-release-<span class="o">(</span>x86_64-pc-linux-gnu<span class="o">)</span>
Usage: /bin/sh <span class="o">[</span>GNU long option] <span class="o">[</span>option] ...
/bin/sh <span class="o">[</span>GNU long option] <span class="o">[</span>option] script-file ...
GNU long options:
--debug
--debugger
--dump-po-strings
--dump-strings
--help
--init-file
--login
--noediting
--noprofile
--norc
--posix
--rcfile
--restricted
--verbose
--version
Shell options:
-ilrsD or -c <span class="nb">command </span>or -O shopt_option <span class="o">(</span>invocation only<span class="o">)</span>
-abefhkmnptuvxBCHP or -o option
Type <span class="sb">`</span>/bin/sh -c <span class="s2">"help set"</span><span class="s1">' for more information about shell options.
Type `/bin/sh -c help'</span> <span class="k">for </span>more information about shell built <span class="k">in </span>commands.
Use the <span class="sb">`</span>bashbug<span class="s1">' command to report bugs.
$
</span></code></pre>
</div>
<p>And thus we should be able to do:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>singularity shell container.img -c <span class="s2">"echo hello world"</span>
hello world
<span class="gp">$ </span>
</code></pre>
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