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<meta name="description" content=" Changing Existing Containers 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”. If you want to make changes to your container, you must mount the container as --writable so you can change the contents. Note that standard Linux ownership and permission rules pertain to files within the container, so the --writable option does not guarantee you can do things like install new software. This might be a bit confusing if you copy a container from one computer to another. If your pids are different on the two computers you will lose the ability to edit files you previous had write access to. In these instances, it might be best to modify your container as root and so you would first need to become root outside of the container. Let’s examine the following example:Installing Additional SoftwareWe strongly recommend that you add additional software installation to your bootstrap, and re-create the image. However if you must, you can use shell and exec with --writable to issue additional commands.$ 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 ResolutionuDependencies 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> exitResizing ImagesYou can expand your container to make it bigger after it’s been created! You don’t need sudo. You can specify a --size to expand by, or use the default of 768MiB: singularity expand ubuntu.img Initializing Singularity image subsystemOpening image file: ubuntu.imgExpanding image by 768MiBBinding image to loopChecking file systeme2fsck 1.42.13 (17-May-2015)Pass 1: Checking inodes, blocks, and sizesPass 2: Checking directory structurePass 3: Checking directory connectivityPass 4: Checking reference countsPass 5: Checking group summary information/dev/loop0: 11/49152 files (0.0% non-contiguous), 7387/196608 blocksResizing file systemresize2fs 1.42.13 (17-May-2015)Resizing the filesystem on /dev/loop0 to 393216 (4k) blocks.The filesystem on /dev/loop0 is now 393216 (4k) blocks long. Previous Next Edit me Site last generated: Jul 26, 2017 ">
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<h1 id="making-changes-to-an-existing-container">Making Changes to an Existing Container</h1>
<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>”. If you want to make changes to your container, you must mount the container as <code class="highlighter-rouge">--writable</code> so you can change the contents. Note that standard Linux ownership and permission rules pertain to files within the container, so the <code class="highlighter-rouge">--writable</code> option does not guarantee you can do things like install new software. This might be a bit confusing if you copy a container from one computer to another. If your pids are different on the two computers you will lose the ability to edit files you previous had write access to. In these instances, it might be best to modify your container as root and so you would first need to become root outside of the container. Let’s examine the following example:</p>
<h2 id="installing-additional-software">Installing Additional Software</h2>
<p>We strongly recommend that you add additional software installation to your bootstrap, and re-create the image. However if you must, you can use <code class="highlighter-rouge">shell</code> and <code class="highlighter-rouge">exec</code> with <code class="highlighter-rouge">--writable</code> to issue additional commands.</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
u
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>
</div>
<h2 id="resizing-images">Resizing Images</h2>
<p>You can expand your container to make it bigger after it’s been created! You don’t need sudo. You can specify a <code class="highlighter-rouge">--size</code> to expand by, or use the default of 768MiB:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code> singularity expand ubuntu.img
Initializing Singularity image subsystem
Opening image file: ubuntu.img
Expanding image by 768MiB
Binding image to loop
Checking file system
e2fsck 1.42.13 <span class="o">(</span>17-May-2015<span class="o">)</span>
Pass 1: Checking inodes, blocks, and sizes
Pass 2: Checking directory structure
Pass 3: Checking directory connectivity
Pass 4: Checking reference counts
Pass 5: Checking group summary information
/dev/loop0: 11/49152 files <span class="o">(</span>0.0% non-contiguous<span class="o">)</span>, 7387/196608 blocks
Resizing file system
resize2fs 1.42.13 <span class="o">(</span>17-May-2015<span class="o">)</span>
Resizing the filesystem on /dev/loop0 to 393216 <span class="o">(</span>4k<span class="o">)</span> blocks.
The filesystem on /dev/loop0 is now 393216 <span class="o">(</span>4k<span class="o">)</span> blocks long.
</code></pre>
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