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<!DOCTYPE html>
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<meta name="description" content=" Quick Start Installation Quick Startgit clone https://github.com/singularityware/singularity.gitcd singularity./autogen.sh./configure --prefix=/usr/localmakesudo make installCommand Quick StartMake a containersingularity create centos7.imgInitializing Singularity image subsystemOpening image file: centos7.imgCreating 768MiB imageBinding image to loopCreating file system within imageImage is done: centos7.imgDump docker layers into it! Nope, you don’t need sudo.singularity import centos7.img docker://centos:7Cache folder set to /home/vanessa/.singularity/dockerImporting: base Singularity environmentImporting: /home/vanessa/.singularity/docker/sha256:785fe1d06b2d42874d3e18fb0747ad8c9ed83d04e7641279a4d5ae353f27eff9.tar.gzImporting: /home/vanessa/.singularity/docker/sha256:a90ac515821d5b70fe202c201485396ba95305348f9f7f52813e2873d3c72eee.tar.gzShell into containersingularity shell centos7.imgSingularity: Invoking an interactive shell within container...# I am the same user inside as outside!Singularity centos7.img:~/Desktop> whoamivanessaSingularity centos7.img:~/Desktop> iduid=1000(vanessa) gid=1000(vanessa) groups=1000(vanessa),4(adm),24,27,30(tape),46,113,128,999(input)Want to keep the container’s environment contained, meaning no sharing of host environment?singularity shell --contain centos7.imgWriting in the containerBy default, containers run in read only. While we discourage making tweaks on the fly to containers (you should properly define all edits to the container in a boostrap specification file, shown later) you can add --writable to any command to write inside the container. Let’s make a directory. This command must be done with sudo.sudo singularity shell --writable centos7.imgSingularity centos7.img:/root> mkdir /dataSingularity centos7.img:/root> touch /data/noodles.txtexitExecuting CommandsSingularity exec will send a custom command for the container to run, anything that you like! Unlike docker exec, the container doesn’t have to be actively running. So, to list the /data folder we just bound, we could do the following:# Did the directory persist?singularity exec centos7.img ls /datanoodles.txtWorking with FilesFiles on the host can be reachable from within the containerecho "Hello World" > /home/vanessa/Desktop/hello-kitty.txtsingularity exec centos7.img cat /home/vanessa/Desktop/hello-kitty.txtHello WorldBy default, most configurations will mount /tmp and the home directories by default. On a research cluster, you probably want to access locations with big datasets, and then write results too. For this, you will want to bind a folder to the container. Here, we are binding my Desktop to the data folder, and listing the contents to show it worked. We use the command -B or --bind to do this.$ singularity exec --bind /home/vanessa/Desktop:/data centos7.img ls /datacentos7.img researchapps-matlab-sherlock-master.imghello-kitty.txt singularity-recipe-demo.mp4party_dinosaur.gifBootstrap RecipesFor a reproducible container, the recommended practice is to build by way of a bootstrap file. This also makes it easy to add files, environment variables, and install custom software, and still start from your bootstrap of source (e.g., Docker). Here is what a basic bootstrap file looks like for Singularity 2.3:Bootstrap: DockerFrom: ubuntu:latest%runscriptexec echo "The runscript is the containers default runtime command!"%files/home/vanessa/Desktop/hello-kitty.txt /data/hello-kitty.txt/home/vanessa/Desktop/party_dinosaur.gif /tmp/the-party-dino.gif%environmentVARIABLE MEATBALLVALUE%labelsAUTHOR [email protected]%postapt-get update && apt-get install python3 git wgetmkdir /dataecho "The post section is where you can install, and configure your container." Previous Next Edit me Site last generated: Jul 26, 2017 ">
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<h2 id="installation-quick-start">Installation Quick Start</h2>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>git clone https://github.com/singularityware/singularity.git
<span class="nb">cd </span>singularity
./autogen.sh
./configure --prefix<span class="o">=</span>/usr/local
make
sudo make install
</code></pre>
</div>
<h2 id="command-quick-start">Command Quick Start</h2>
<h3 id="make-a-container">Make a container</h3>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>singularity create centos7.img
Initializing Singularity image subsystem
Opening image file: centos7.img
Creating 768MiB image
Binding image to loop
Creating file system within image
Image is <span class="k">done</span>: centos7.img
</code></pre>
</div>
<p>Dump docker layers into it! Nope, you don’t need sudo.</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>singularity import centos7.img docker://centos:7
Cache folder <span class="nb">set </span>to /home/vanessa/.singularity/docker
Importing: base Singularity environment
Importing: /home/vanessa/.singularity/docker/sha256:785fe1d06b2d42874d3e18fb0747ad8c9ed83d04e7641279a4d5ae353f27eff9.tar.gz
Importing: /home/vanessa/.singularity/docker/sha256:a90ac515821d5b70fe202c201485396ba95305348f9f7f52813e2873d3c72eee.tar.gz
</code></pre>
</div>
<h3 id="shell-into-container">Shell into container</h3>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>singularity shell centos7.img
Singularity: Invoking an interactive shell within container...
<span class="c"># I am the same user inside as outside!</span>
Singularity centos7.img:~/Desktop> whoami
vanessa
Singularity centos7.img:~/Desktop> id
<span class="nv">uid</span><span class="o">=</span>1000<span class="o">(</span>vanessa<span class="o">)</span> <span class="nv">gid</span><span class="o">=</span>1000<span class="o">(</span>vanessa<span class="o">)</span> <span class="nv">groups</span><span class="o">=</span>1000<span class="o">(</span>vanessa<span class="o">)</span>,4<span class="o">(</span>adm<span class="o">)</span>,24,27,30<span class="o">(</span>tape<span class="o">)</span>,46,113,128,999<span class="o">(</span>input<span class="o">)</span>
</code></pre>
</div>
<p>Want to keep the container’s environment contained, meaning no sharing of host environment?</p>
<div class="highlighter-rouge"><pre class="highlight"><code>singularity shell --contain centos7.img
</code></pre>
</div>
<h3 id="writing-in-the-container">Writing in the container</h3>
<p>By default, containers run in read only. While we discourage making tweaks on the fly to containers (you should properly define all edits to the container in a boostrap specification file, shown later) you can add <code class="highlighter-rouge">--writable</code> to any command to write inside the container. Let’s make a directory. This command must be done with sudo.</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>sudo singularity shell --writable centos7.img
Singularity centos7.img:/root> mkdir /data
Singularity centos7.img:/root> touch /data/noodles.txt
<span class="nb">exit</span>
</code></pre>
</div>
<h3 id="executing-commands">Executing Commands</h3>
<p>Singularity <code class="highlighter-rouge">exec</code> will send a custom command for the container to run, anything that you like! Unlike docker exec, the container doesn’t have to be actively running. So, to list the <code class="highlighter-rouge">/data</code> folder we just bound, we could do the following:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="c"># Did the directory persist?</span>
singularity <span class="nb">exec </span>centos7.img ls /data
noodles.txt
</code></pre>
</div>
<h3 id="working-with-files">Working with Files</h3>
<p>Files on the host can be reachable from within the container</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="nb">echo</span> <span class="s2">"Hello World"</span> > /home/vanessa/Desktop/hello-kitty.txt
singularity <span class="nb">exec </span>centos7.img cat /home/vanessa/Desktop/hello-kitty.txt
Hello World
</code></pre>
</div>
<p>By default, most configurations will mount <code class="highlighter-rouge">/tmp</code> and the home directories by default. On a research cluster, you probably want to access locations with big datasets, and then write results too. For this, you will want to bind a folder to the container. Here, we are binding my Desktop to the data folder, and listing the contents to show it worked. We use the command <code class="highlighter-rouge">-B</code> or <code class="highlighter-rouge">--bind</code> to do this.</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span>singularity <span class="nb">exec</span> --bind /home/vanessa/Desktop:/data centos7.img ls /data
centos7.img researchapps-matlab-sherlock-master.img
hello-kitty.txt singularity-recipe-demo.mp4
party_dinosaur.gif
</code></pre>
</div>
<h3 id="bootstrap-recipes">Bootstrap Recipes</h3>
<p>For a reproducible container, the recommended practice is to build by way of a bootstrap file. This also makes it easy to add files, environment variables, and install custom software, and still start from your bootstrap of source (e.g., Docker). Here is what a basic bootstrap file looks like for Singularity 2.3:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>Bootstrap: Docker
From: ubuntu:latest
%runscript
<span class="nb">exec echo</span> <span class="s2">"The runscript is the containers default runtime command!"</span>
%files
/home/vanessa/Desktop/hello-kitty.txt /data/hello-kitty.txt
/home/vanessa/Desktop/party_dinosaur.gif /tmp/the-party-dino.gif
%environment
VARIABLE MEATBALLVALUE
%labels
AUTHOR [email protected]
%post
apt-get update <span class="o">&&</span> apt-get install python3 git wget
mkdir /data
<span class="nb">echo</span> <span class="s2">"The post section is where you can install, and configure your container."</span>
</code></pre>
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