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<meta name="description" content=" Image Environment Directory accessBy default Singularity tries to create a seamless user experience between the host and the container. To do this, Singularity makes various locations accessible within the container automatically. For example, the user’s home directory is always bound into the container as is /tmp and /var/tmp. Additionally your current working directory (cwd/pwd) is also bound into the container iff it is not an operating system directory or already accessible via another mount. For almost all cases, this will work flawlessly as follows:$ pwd/home/gmk/demo$ singularity shell container.img Singularity/container.img> pwd/home/gmk/demoSingularity/container.img> ls -l debian.def -rw-rw-r--. 1 gmk gmk 125 May 28 10:35 debian.defSingularity/container.img> exit$ For directory binds to function properly, there must be an existing target endpoint within the container (just like a mount point). This means that if your home directory exists in a non-standard base directory like “/foobar/username” then the base directory “/foobar” must already exist within the container.Singularity will not create these base directories! You must enter the container with the --writable option being set, and create the directory manually.Current Working DirectorySingularity will try to replicate your current working directory within the container. Sometimes this is straight forward and possible, other times it is not (e.g. if the base dir of your current working directory does not exist). In that case, Singularity will retain the file descriptor to your current directory and change you back to it. If you do a ‘pwd’ within the container, you may see some weird things. For example:$ pwd/foobar$ ls -ltotal 0-rw-r--r--. 1 root root 0 Jun 1 11:32 mooooo$ singularity shell ~/demo/container.img WARNING: CWD bind directory not present: /foobarSingularity/container.img> pwd(unreachable)/foobarSingularity/container.img> ls -ltotal 0-rw-r--r--. 1 root root 0 Jun 1 18:32 moooooSingularity/container.img> exit$ But notice how even though the directory location is not resolvable, the directory contents are available.Standard IO and pipesSingularity automatically sends and receives all standard IO from the host to the applications within the container to facilitate expected behavior from the interaction between the host and the container. For example:$ cat debian.def | singularity exec container.img grep 'MirrorURL'MirrorURL "http://ftp.us.debian.org/debian/"$ Making changes to the container (writable)By default, containers are accessed as read only. This is both to enable parallel container execution (e.g. MPI). To enter a container using exec, run, or shell you must pass the --writable flag in order to open the image as read/writable.Containing the containerBy providing the argument --contain to exec, run or shell you will find that shared directories are no longer shared. For example, the user’s home directory is writable, but it is non-persistent between non-overlapping runs. Previous Next Edit me Site last generated: Jul 26, 2017 ">
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<h2 id="directory-access">Directory access</h2>
<p>By default Singularity tries to create a seamless user experience between the host and the container. To do this, Singularity makes various locations accessible within the container automatically. For example, the user’s home directory is always bound into the container as is /tmp and /var/tmp. Additionally your current working directory (cwd/pwd) is also bound into the container iff it is not an operating system directory or already accessible via another mount. For almost all cases, this will work flawlessly as follows:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span><span class="nb">pwd</span>
/home/gmk/demo
<span class="gp">$ </span>singularity shell container.img
<span class="gp">Singularity/container.img> </span><span class="nb">pwd</span>
/home/gmk/demo
<span class="gp">Singularity/container.img> </span>ls -l debian.def
-rw-rw-r--. 1 gmk gmk 125 May 28 10:35 debian.def
<span class="gp">Singularity/container.img> </span><span class="nb">exit</span>
<span class="gp">$ </span>
</code></pre>
</div>
<p>For directory binds to function properly, there must be an existing target endpoint within the container (just like a mount point). This means that if your home directory exists in a non-standard base directory like “/foobar/username” then the base directory “/foobar” must already exist within the container.</p>
<p>Singularity will not create these base directories! You must enter the container with the <code class="highlighter-rouge">--writable</code> option being set, and create the directory manually.</p>
<h3 id="current-working-directory">Current Working Directory</h3>
<p>Singularity will try to replicate your current working directory within the container. Sometimes this is straight forward and possible, other times it is not (e.g. if the base dir of your current working directory does not exist). In that case, Singularity will retain the file descriptor to your current directory and change you back to it. If you do a ‘pwd’ within the container, you may see some weird things. For example:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span><span class="nb">pwd</span>
/foobar
<span class="gp">$ </span>ls -l
total 0
-rw-r--r--. 1 root root 0 Jun 1 11:32 mooooo
<span class="gp">$ </span>singularity shell ~/demo/container.img
WARNING: CWD <span class="nb">bind </span>directory not present: /foobar
<span class="gp">Singularity/container.img> </span><span class="nb">pwd</span>
<span class="o">(</span>unreachable<span class="o">)</span>/foobar
<span class="gp">Singularity/container.img> </span>ls -l
total 0
-rw-r--r--. 1 root root 0 Jun 1 18:32 mooooo
<span class="gp">Singularity/container.img> </span><span class="nb">exit</span>
<span class="gp">$ </span>
</code></pre>
</div>
<p>But notice how even though the directory location is not resolvable, the directory contents are available.</p>
<h2 id="standard-io-and-pipes">Standard IO and pipes</h2>
<p>Singularity automatically sends and receives all standard IO from the host to the applications within the container to facilitate expected behavior from the interaction between the host and the container. For example:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>cat debian.def | singularity <span class="nb">exec </span>container.img grep <span class="s1">'MirrorURL'</span>
MirrorURL <span class="s2">"http://ftp.us.debian.org/debian/"</span>
<span class="gp">$ </span>
Making changes to the container <span class="o">(</span>writable<span class="o">)</span>
By default, containers are accessed as <span class="nb">read </span>only. This is both to <span class="nb">enable </span>parallel container execution <span class="o">(</span>e.g. MPI<span class="o">)</span>. To enter a container using <span class="nb">exec</span>, run, or shell you must pass the --writable flag <span class="k">in </span>order to open the image as <span class="nb">read</span>/writable.
</code></pre>
</div>
<h2 id="containing-the-container">Containing the container</h2>
<p>By providing the argument <code class="highlighter-rouge">--contain</code> to <code class="highlighter-rouge">exec</code>, <code class="highlighter-rouge">run</code> or <code class="highlighter-rouge">shell</code> you will find that shared directories are no longer shared. For example, the user’s home directory is writable, but it is non-persistent between non-overlapping runs.</p>
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