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<meta name="description" content=" Changing Existing Containers Previous Next Making Changes to an Existing ContainerIt is possible that you may need to make changes to a container after it has been bootstrapped. For that, let’s repeat the Singularity mantra “A user inside a Singularity container is the same user as outside the container”. This means if you want to make changes to your container, you must be root inside your container, which means you must first become root outside your container. Additionally you will need to tell Singularity that you wish to mount the container as --writable so you can change the contents. Let’s examine the following example:$ singularity shell /tmp/Centos7-ompi.img Singularity: Invoking an interactive shell within container...Singularity.Centos7-ompi.img> which lssh: which: command not foundLet’s use this opportunity to install an additional package into this container:$ sudo singularity exec --writable /tmp/Centos7-ompi.img yum install whichLoaded plugins: fastestmirrorLoading mirror speeds from cached hostfile * base: mirror.hostduplex.com * extras: mirrors.centos.webair.com * updates: linux.mirrors.es.netResolving Dependencies--> Running transaction check---> Package which.x86_64 0:2.20-7.el7 will be installed--> Finished Dependency ResolutionDependencies Resolved==================================================================================================== Package Arch Version Repository Size====================================================================================================Installing: which x86_64 2.20-7.el7 base 41 kTransaction Summary====================================================================================================Install 1 PackageTotal download size: 41 kInstalled size: 75 kIs this ok [y/d/N]: yDownloading packages:which-2.20-7.el7.x86_64.rpm | 41 kB 00:00:00 Running transaction checkRunning transaction testTransaction test succeededRunning transaction Installing : which-2.20-7.el7.x86_64 1/1 Verifying : which-2.20-7.el7.x86_64 1/1 Installed: which.x86_64 0:2.20-7.el7 Complete!We could have also used the shell container interface command to do this.$ sudo singularity shell --writable /tmp/Centos7-ompi.imgSingularity: Invoking an interactive shell within container...Singularity.Centos7-ompi.img> yum install viLoaded plugins: fastestmirrorLoading mirror speeds from cached hostfile * base: mirror.hostduplex.com * extras: mirrors.centos.webair.com * updates: linux.mirrors.es.netResolving Dependencies--> Running transaction check---> Package vim-minimal.x86_64 2:7.4.160-1.el7 will be installed--> Finished Dependency ResolutionDependencies Resolved==================================================================================================== Package Arch Version Repository Size====================================================================================================Installing: vim-minimal x86_64 2:7.4.160-1.el7 base 436 kTransaction Summary====================================================================================================Install 1 PackageTotal download size: 436 kInstalled size: 896 kIs this ok [y/d/N]: yDownloading packages:vim-minimal-7.4.160-1.el7.x86_64.rpm | 436 kB 00:00:00 Running transaction checkRunning transaction testTransaction test succeededRunning transaction Installing : 2:vim-minimal-7.4.160-1.el7.x86_64 1/1 Verifying : 2:vim-minimal-7.4.160-1.el7.x86_64 1/1 Installed: vim-minimal.x86_64 2:7.4.160-1.el7 Complete!Singularity.Centos7-ompi.img> exit Previous Next Edit me Site last generated: Jul 26, 2017 ">
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<h2 id="making-changes-to-an-existing-container">Making Changes to an Existing Container</h2>
<p>It is possible that you may need to make changes to a container after it has been bootstrapped. For that, let’s repeat the Singularity mantra “<em>A user inside a Singularity container is the same user as outside the container</em>”. This means if you want to make changes to your container, you must be root inside your container, which means you must first become root outside your container. Additionally you will need to tell Singularity that you wish to mount the container as <code class="highlighter-rouge">--writable</code> so you can change the contents. Let’s examine the following example:</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>which ls
sh: which: <span class="nb">command </span>not found
</code></pre>
</div>
<p>Let’s use this opportunity to install an additional package into this container:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>sudo singularity <span class="nb">exec</span> --writable /tmp/Centos7-ompi.img yum install which
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
<span class="k">*</span> base: mirror.hostduplex.com
<span class="k">*</span> extras: mirrors.centos.webair.com
<span class="k">*</span> updates: linux.mirrors.es.net
Resolving Dependencies
<span class="gp">--> </span>Running transaction check
<span class="gp">---> </span>Package which.x86_64 0:2.20-7.el7 will be installed
<span class="gp">--> </span>Finished Dependency Resolution
Dependencies Resolved
<span class="o">====================================================================================================</span>
Package Arch Version Repository Size
<span class="o">====================================================================================================</span>
Installing:
which x86_64 2.20-7.el7 base 41 k
Transaction Summary
<span class="o">====================================================================================================</span>
Install 1 Package
Total download size: 41 k
Installed size: 75 k
Is this ok <span class="o">[</span>y/d/N]: y
Downloading packages:
which-2.20-7.el7.x86_64.rpm | 41 kB 00:00:00
Running transaction check
Running transaction <span class="nb">test
</span>Transaction <span class="nb">test </span>succeeded
Running transaction
Installing : which-2.20-7.el7.x86_64 1/1
Verifying : which-2.20-7.el7.x86_64 1/1
Installed:
which.x86_64 0:2.20-7.el7
Complete!
</code></pre>
</div>
<p>We could have also used the <code class="highlighter-rouge">shell</code> container interface command to do this.</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>sudo singularity shell --writable /tmp/Centos7-ompi.img
Singularity: Invoking an interactive shell within container...
<span class="gp">Singularity.Centos7-ompi.img> </span>yum install vi
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
<span class="k">*</span> base: mirror.hostduplex.com
<span class="k">*</span> extras: mirrors.centos.webair.com
<span class="k">*</span> updates: linux.mirrors.es.net
Resolving Dependencies
<span class="gp">--> </span>Running transaction check
<span class="gp">---> </span>Package vim-minimal.x86_64 2:7.4.160-1.el7 will be installed
<span class="gp">--> </span>Finished Dependency Resolution
Dependencies Resolved
<span class="o">====================================================================================================</span>
Package Arch Version Repository Size
<span class="o">====================================================================================================</span>
Installing:
vim-minimal x86_64 2:7.4.160-1.el7 base 436 k
Transaction Summary
<span class="o">====================================================================================================</span>
Install 1 Package
Total download size: 436 k
Installed size: 896 k
Is this ok <span class="o">[</span>y/d/N]: y
Downloading packages:
vim-minimal-7.4.160-1.el7.x86_64.rpm | 436 kB 00:00:00
Running transaction check
Running transaction <span class="nb">test
</span>Transaction <span class="nb">test </span>succeeded
Running transaction
Installing : 2:vim-minimal-7.4.160-1.el7.x86_64 1/1
Verifying : 2:vim-minimal-7.4.160-1.el7.x86_64 1/1
Installed:
vim-minimal.x86_64 2:7.4.160-1.el7
Complete!
<span class="gp">Singularity.Centos7-ompi.img> </span><span class="nb">exit</span>
</code></pre>
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