How to use Singularity!
This is an introductory workshop on Singularity. It was originally taught by David Godlove at the NIH HPC, but the content has since been adapted to a general audience. For more information about the topics covered here, see the following:
- Singularity Home
- Singularity on GitHub
- Singularity on Google Groups
- Singularity at the NIH HPC
- Docker documentation
- Singularity Hub
- Docker Hub
A container allows you to stick an application and all of its dependencies into a single package. This makes your application portable, shareable, and reproducible.
Containers foster portability and reproducibility because they package ALL of an applications dependencies... including its own tiny operating system!
This means your application won't break when you port it to a new environment. Your app brings its environment with it.
Here are some examples of things you can do with containers:
- Package an analysis pipeline so that it runs on your laptop, in the cloud, and in a high performance computing (HPC) environment to produce the same result.
- Publish a paper and include a link to a container with all of the data and software that you used so that others can easily reproduce your results.
- Install and run an application that requires a complicated stack of dependencies with a few keystrokes.
- Create a pipeline or complex workflow where each individual program is meant to run on a different operating system.
Containers and VMs are both types of virtualization. But it's important to understand the differences between the two and know when to use each.
Virtual Machines install every last bit of an operating system (OS) right down to the core software that allows the OS to control the hardware (called the kernel). This means that VMs:
- Are complete in the sense that you can use a VM to interact with your computer via a different OS.
- Are extremely flexible. For instance you an install a Windows VM on a Mac using software like VirtualBox.
- Are slow and resource hungry. Every time you start a VM it has to bring up an entirely new OS.
Containers share a kernel with the host OS. This means that Containers:
- Are less flexible than VMs. For example, a Linux container must be run on a Linux host OS. (Although you can mix and match distributions.) In practice, containers are only extensively developed on Linux.
- Are much faster and lighter weight than VMs. A container may be just a few MB.
- Start and stop quickly and are suitable for running single apps.
Because of their differences, VMs and containers serve different purposes and should be favored under different circumstances.
- VMs are good for long running interactive sessions where you may want to use several different applications. (Checking email on Outlook and using Microsoft Word and Excel).
- Containers are better suited to running one or two applications non-interactively in their own custom environments.
Docker is currently the most widely used container software. It has several strengths and weaknesses that make it a good choice for some projects but not for others.
philosophy
Docker is built for running multiple containers on a single system and it allows containers to share common software features for efficiency. It also seeks to fully isolate each container from all other containers and from the host system.
Docker assumes that you will be a root user. Or that it will be OK for you to elevate your privileges if you are not a root user.
strengths
- Mature software with a large user community
- Docker Hub!
- A place to build and host your containers
- Fully integrated into core Docker
- Over 100,000 pre-built containers
- Provides an ecosystem for container orchestration
- Rich feature set
weaknesses
- Difficult to learn
- Hidden innards
- Complex container model (layers)
- Not architected with security in mind
- Not built for HPC (but good for cloud)
Docker shines for DevOPs teams providing cloud-hosted micro-services to users.
Singularity is a relatively new container software originally developed by Greg Kurtzer while at Lawrence Berkley National labs. It was developed with security, scientific software, and HPC systems in mind.
philosophy
Singularity assumes (more or less) that each application will have its own container. It does not seek to fully isolate containers from one another or the host system. Singularity assumes that you will have a build system where you are the root user, but that you will also have a production system where you may or may not be the root user.
strengths
- Easy to learn and use (relatively speaking)
- Approved for HPC (installed on some of the biggest HPC systems in the world)
- Can convert Docker containers to Singularity and run containers directly from Docker Hub
- Singularity Hub!
- A place to build and host your containers similar to Docker Hub
weaknesses
- Younger and less mature than Docker
- Smaller user community (as of now)
- Under active development (must keep up with new changes)
Singularity shines for scientific software running in an HPC environent. We will use it for the remainder of the class.
Here we will install the latest tagged release from GitHub. If you prefer to install a different version or to install Singularity in a different location, see these Singularity docs.
We're going to compile Singularity from source code. First we'll need to make sure we have some development tools installed so that we can do that. On Ubuntu, run these commands to make sure you have all the necessary packages installed.
$ sudo apt-get update
$ sudo apt-get -y install python build-essential debootstrap
On CentOS, these commmands should get you up to speed.
$ sudo yum update
$ sudo yum groupinstall 'Development Tools'
$ sudo yum install wget epel-release
$ sudo yum install debootstrap.noarch
Next we'll download a compressed archive of the source code (using the the wget command). Then we'll extract the source code from the archive (with the tar command).
$ wget https://github.com/singularityware/singularity/releases/download/2.4/singularity-2.4.tar.gz
$ tar xvf singularity-2.4.tar.gz
Finally it's time to build and install!
$ cd singularity-2.4
$ ./configure --prefix=/usr/local
$ make
$ sudo make install
If you want support for tab completion of Singularity commands, you need to source the appropriate file and add it to the bash completion directory in /etc so that it will be sourced automatically when you start another shell.
$ . etc/bash_completion.d/singularity
$ sudo cp etc/bash_completion.d/singularity /etc/bash_completion.d/
If everything went according to plan, you now have a working installation of Singularity. You can test your installation like so:
$ singularity run docker://godlovedc/lolcow
You should see something like the following.
Docker image path: index.docker.io/godlovedc/lolcow:latest
Cache folder set to /home/ubuntu/.singularity/docker
[6/6] |===================================| 100.0%
Creating container runtime...
_______________________________________
/ Excellent day for putting Slinkies on \
\ an escalator. /
---------------------------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
Your cow will likely say something different (and be more colorful), but as long as you see a cow your installation is working properly.
This command downloads and runs a container from Docker Hub. During the next hour we will learn how to build a similar container from scratch.
In the second hour we will build the preceding container from scratch.
Simply typing singularity will give you an summary of all the commands you can use. Typing singularity help <command> will give you more detailed information about running an individual command.
To build a singularity container, you must use the build command. The build command installs an OS, sets up your container's environment and installs the apps you need. To use the build command, we need a recipe file (also called a definition file). A Singularity recipe file is a set of instructions telling Singularity what software to install in the container.
The Singularity source code contains several example definition files in the /examples subdirectory. Let's copy the ubuntu example to our home directory and inspect it.
$ mkdir ../lolcow
$ cp examples/ubuntu/Singularity ../lolcow/
$ cd ../lolcow
$ nano Singularity
It should look something like this:
BootStrap: debootstrap
OSVersion: trusty
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%runscript
echo "This is what happens when you run the container..."
%post
echo "Hello from inside the container"
sed -i 's/$/ universe/' /etc/apt/sources.list
apt-get -y --force-yes install vim
See the Singularity docs for an explanation of each of these sections.
Now let's use this recipe file as a starting point to build our lolcow.img container. Note that the build command requires sudo privileges, when used in combination with a recipe file.
$ sudo singularity build --sandbox lolcow Singularity
The --sandbox option in the command above tells Singularity that we want to build a special type of container for development purposes.
Singularity can build containers in several different file formats. The default is to build a squashfs image. The squashfs format is compressed and immutable making it a good choice for reproducible, production-grade containers.
But if you want to shell into a container and tinker with it (like we will do here), you should build a sandbox (which is really just a directory). This is great when you are still developing your container and don't yet know what should be included in the recipe file.
When your build finishes, you will have a basic Ubuntu container saved in a local directory called lolcow.
Now let's enter our new container and look around.
$ singularity shell lolcow
Depending on the environment on your host system you may see your prompt change. Let's look at what OS is running inside the container.
Singularity lolcow:~> cat /etc/os-release
NAME="Ubuntu"
VERSION="14.04, Trusty Tahr"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 14.04 LTS"
VERSION_ID="14.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/"
BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"
No matter what OS is running on your host, your container is running Ubuntu 14.04!
Let's try a few more commands:
Singularity lolcow:~> whoami
dave
Singularity lolcow:~> hostname
hal-9000
This is one of the core features of Singularity that makes it so attractive from a security standpoint. The user remains the same inside and outside of the container.
Let's try installing some software. I used the programs fortune, cowsay, and lolcat to produce the container that we saw in the first demo.
Singularity lolcow:~> sudo apt-get update && sudo apt-get -y install fortune cowsay lolcat
bash: sudo: command not found
Whoops!
Singularity complains that it can't find the sudo command. But even if you try to install sudo or change to root using su, you will find it impossible to elevate your privileges within the container.
Once again, this is an important concept in Singularity. If you enter a container without root privileges, you are unable to obtain root privileges within the container. This insurance against privilege escalation is the reason that you will find Singularity installed in so many HPC environments.
Let's exit the container and re-enter as root.
Singularity lolcow:~> exit
$ sudo singularity shell --writable lolcow
Now we are the root user inside the container. Note also the addition of the --writable option. This option allows us to modify the container. The changes will actually be saved into the container and will persist across uses.
Let's try installing some software again.
Singularity lolcow:~> apt-get update && apt-get -y install fortune cowsay lolcat
Now you should see the programs successfully installed. Let's try running the demo in this new container.
Singularity lolcow:~> fortune | cowsay | lolcat
bash: lolcat: command not found
bash: cowsay: command not found
bash: fortune: command not found
Drat! It looks like the programs were not added to our $PATH. Let's add them and try again.
Singularity lolcow:~> export PATH=/usr/games:$PATH
Singularity lolcow:~> fortune | cowsay | lolcat
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
________________________________________
/ Keep emotionally active. Cater to your \
\ favorite neurosis. /
----------------------------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
We're making progress, but we are now receiving a warning from perl. However, before we tackle that, let's think some more about the $PATH variable.
We changed our path in this session, but those changes will disappear as soon as we exit the container just like they will when you exit any other shell. To make the changes permanent we should add them to the definition file and re-bootstrap the container. We'll do that in a minute.
Now back to our perl warning. Perl is complaining that the locale is not set properly. Basically, perl wants to know where you are and what sort of language encoding it should use. Should you encounter this warning you can probably fix it with the locale-gen command or by setting LC_ALL=C. Here we'll just set the environment variable.
Singularity lolcow:~> export LC_ALL=C
Singularity lolcow:~> fortune | cowsay | lolcat
_________________________________________
/ FORTUNE PROVIDES QUESTIONS FOR THE \
| GREAT ANSWERS: #19 A: To be or not to |
\ be. Q: What is the square root of 4b^2? /
-----------------------------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
Great! Things are working properly now.
Although it is fine to shell into your Singularity container and make changes while you are debugging, you ultimately want all of these changes to be reflected in your recipe file. Otherwise if you need to reproduce it from scratch you will forget all of the changes you made.
Let's update our definition file with the changes we made to this container.
Singularity lolcow:~> exit
$ nano Singularity
Here is what our updated definition file should look like.
BootStrap: debootstrap
OSVersion: trusty
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%runscript
echo "This is what happens when you run the container..."
%post
echo "Hello from inside the container"
sed -i 's/$/ universe/' /etc/apt/sources.list
apt-get update
apt-get -y install fortune cowsay lolcat
apt-get clean
%environment
export PATH=/usr/games:$PATH
export LC_ALL=C
Let's rebuild the container with the new definition file.
$ sudo singularity build lolcow.simg Singularity
Note that we changed the name of the container. By omitting the --sandbox option, we are building our container in the standard Singularity squashfs file format. We are denoting the file format with the (optional) .simg extension. A squashfs file is compressed and immutable making it a good choice for a production environment.
Singularity stores a lot of useful metadata. For instance, if you want to see the recipe file that was used to create the container you can use the inspect command like so:
$ singularity inspect --deffile lolcow.simg
BootStrap: debootstrap
OSVersion: trusty
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%runscript
echo "This is what happens when you run the container..."
%post
echo "Hello from inside the container"
sed -i 's/$/ universe/' /etc/apt/sources.list
apt-get update
apt-get -y install vim fortune cowsay lolcat
%environment
export PATH=/usr/games:$PATH
export LC_ALL=C
Singularity does not try to isolate your container completely from the host system. This allows you to do some interesting things.
Using the exec command, we can run commands within the container from the host system.
$ singularity exec lolcow.simg cowsay 'How did you get out of the container?'
_______________________________________
< How did you get out of the container? >
---------------------------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
In this example, singularity entered the container, ran the cowsay command, displayed the standard output on our host system terminal, and then exited.
You can also use pipes and redirection to blur the lines between the container and the host system.
$ singularity exec lolcow.simg cowsay moo > cowsaid
$ cat cowsaid
_____
< moo >
-----
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
We created a file called cowsaid in the current working directory with the output of a command that was executed within the container.
We can also pipe things into the container.
$ cat cowsaid | singularity exec lolcow.simg cowsay -n
______________________________
/ _____ \
| < moo > |
| ----- |
| \ ^__^ |
| \ (oo)\_______ |
| (__)\ )\/\ |
| ||----w | |
\ || || /
------------------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
We've created a meta-cow (a cow that talks about cows). 😜
In the third hour we are going to consider an extended example describing a containerized application that takes a file as input, analyzes the data in the file, and produces another file as output. This is obviously a very common situation.
Let's imagine that we want to use the cowsay program in our lolcow.simg to "analyze data". We should give our container an input file, it should reformat it (in the form of a cow speaking), and it should dump the output into another file.
Here's an example. First I'll make some "data"
$ echo "The grass is always greener over the septic tank" > input
Now I'll "analyze" the "data"
$ cat input | singularity exec lolcow.simg cowsay > output
The "analyzed data" is saved in a file called output.
$ cat output
______________________________________
/ The grass is always greener over the \
\ septic tank /
--------------------------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
This works... but the syntax is ugly and difficult to remember.
Singularity supports a neat trick for making a container function as though it were an executable. We need to create a runscript inside the container. It turns out that our Singularity recipe file already contains a runscript. It causes our container to print a helpful message.
$ ./lolcow.simg
This is what happens when you run the container...
Let's rewrite this runscript in the definition file and rebuild our container so that it does something more useful.
BootStrap: debootstrap
OSVersion: trusty
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%runscript
infile=
outfile=
usage() {
>&2 echo "Usage:"
>&2 echo "$SINGULARITY_NAME -i <infile> -o <outfile> [ -- <cowsay options> ]"
exit 1
}
while getopts i:o: argument
do
case $argument in
i)
infile="$OPTARG"
;;
o)
outfile="$OPTARG"
;;
?)
usage
;;
esac
done
shift "$((OPTIND - 1))"
if [ -z "$infile" ] || [ -z "$outfile" ]
then
usage
fi
cat "$infile" | cowsay "$@" > "$outfile"
%post
echo "Hello from inside the container"
sed -i 's/$/ universe/' /etc/apt/sources.list
apt-get update
apt-get -y install fortune cowsay lolcat
apt-get clean
%environment
export PATH=/usr/games:$PATH
export LC_ALL=C
Now we must rebuild out container to install the new runscript.
$ sudo singularity build --force lolcow.simg Singularity
Note the --force option which ensures our previous container is completely overwritten.
After rebuilding our container, we can call the lolcow.simg as though it were an executable, give it input and output file names, and optionally give additional arguments to go directly to the cowsay program.
$ ./lolcow.simg
Usage:
lolcow.simg -i <infile> -o <outfile> [ -- <cowsay options> ]
$ ./lolcow.simg -i input -o output2
$ cat output2
______________________________________
/ The grass is always greener over the \
\ septic tank /
--------------------------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
It's possible to create and modify files on the host system from within the container. In fact, that's exactly what we did in the previous example when we created output files in our home directory.
Let's be more explicit. Consider this example.
$ singularity shell lolcow.simg
Singularity lolcow.simg:~> echo wutini > ~/jawa.txt
Singularity lolcow.simg:~> cat ~/jawa.txt
wutini
Singularity lolcow.simg:~> exit
$ cat ~/jawa.txt
wutini
Here we shelled into a container and created a file with some text in our home directory. Even after we exited the container, the file still existed. How did this work?
There are several special directories that Singularity bind mounts into your container by default. These include:
$HOME/tmp/proc/sys/dev
You can specify other directories to bind using the --bind option or the environmental variable $SINGULARITY_BINDPATH
Let's say we want to use our cowsay.img container to "analyze data" and save results in a different directory. For this example, we first need to create a new directory with some data on our host system.
$ sudo mkdir /data
$ sudo chown $USER:$USER /data
$ echo 'I am your father' > /data/vader.txt
We also need a directory within our container where we can bind mount the host system /data directory. We could create another directory in the %post section of our recipe file and rebuild the container, but our container already has a directory called /mnt that we can use for this example.
Now let's see how bind mounts work. First, let's list the contents of /mnt within the container without bind mounting /data to it.
$ singularity exec lolcow.simg ls -l /mnt
total 0
The /mnt directory within the container is empty. Now let's repeat the same command but using the --bind option to bind mount /data into the container.
$ singularity exec --bind /data:/mnt lolcow.simg ls -l /mnt
total 4
-rw-rw-r-- 1 ubuntu ubuntu 17 Jun 7 20:57 vader.txt
Now the /mnt directory in the container is bind mounted to the /data directory on the host system and we can see its contents.
Now what about our earlier example in which we used a runscript to run a our container as though it were an executable? The singularity run command accepts the --bind option and can execute our runscript like so.
$ singularity run --bind /data:/mnt lolcow.simg -i /mnt/vader.txt -o /mnt/output3
$ cat /data/output3
__________________
< I am your father >
------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
But that's a cumbersome command. Instead, we could set the variable $SINGULARITY_BINDPATH and then use our container as before.
$ export SINGULARITY_BINDPATH=/data:/mnt
$ ./lolcow.simg -i /mnt/output3 -o /mnt/metacow2 -- -n
$ ls -l /data/
total 12
-rw-rw-r-- 1 ubuntu ubuntu 809 Jun 7 21:07 metacow2
-rw-rw-r-- 1 ubuntu ubuntu 184 Jun 7 21:06 output3
-rw-rw-r-- 1 ubuntu ubuntu 17 Jun 7 20:57 vader.txt
$ cat /data/metacow2
______________________________
/ __________________ \
| < I am your father > |
| ------------------ |
| \ ^__^ |
| \ (oo)\_______ |
| (__)\ )\/\ |
| ||----w | |
\ || || /
------------------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
For a lot more info on how to bind mount host directories to your container, check out the NIH HPC Binding external directories section.
We've spent a lot of time on building and using your own containers so that you understand how Singularity works. But there's an easier way! Docker Hub hosts over 100,000 pre-built, ready-to-use containers. And singularity makes it easy to use them.
When we first installed Singularity we tested the installation by running a container from Docker Hub like so.
$ singularity run docker://godlovedc/lolcow
Instead of running this container from Docker Hub, we could also just copy it to our local system with the build command.
$ sudo singularity build lolcow-from-docker.simg docker://godlovedc/lolcow
You can build and host your own images on Docker Hub, (using Docker) or you can download and run images that others have built.
$ singularity shell docker://tensorflow/tensorflow
Singularity tensorflow:~> python
>>> import tensorflow as tf
>>> quit()
Singularity tensorflow:~> exit
You can also build, download, and run containers from Singularity Hub
$ singularity run shub://GodloveD/lolcow
You can even use images on Docker Hub and Singularity Hub as a starting point for your own images. Singularity recipe files allow you to specifiy a Docker Hub or Singularity Hub registry to bootstrap from
and you can use the %post section to modify the container to your liking.
For example, to start from a Docker Hub image of Ubuntu in your recipe, you could do something like this:
BootStrap: docker
From: ubuntu
%runscript
echo "This is what happens when you run the container..."
%post
echo "Hello from inside the container"
echo "Install additional software here"
Or to start from a Singularity Hub version of BusyBox you could do something like this:
BootStrap: shub
From: GodloveD/busybox
%runscript
echo "This is what happens when you run the container..."
%post
echo "Hello from inside the container"
echo "Install additional software here"
Both Docker Hub and Singularity Hub link to your GitHub account. New container builds are automatically triggered every time you push changes to a Docker file or a Singularity recipe file in a linked repository.
As we demonstrated earlier, pipes and redirects work as expected between a container and host system. If you need to pipe the output of one command in your container to another command in your container things are slightly more complicated.
$ singularity exec lolcow.img sh -c "fortune | cowsay | lolcat"
You can use Singularity containers to display graphics through common protocols. To do this, you need to install the proper graphics stack within the Singularity container. For instance if you want to display X11 graphics you must install xorg within your container. In an Ubuntu container the command would look like this.
$ apt-get install xorg
In Singularity v2.3+ the experimental --nv option will look for NVIDIA libraries on the host system and automatically bind mount them to the container so that GPUs work seamlessly.
Network ports on the host system are accessible from within the container and work seamlessly. For example, you could install ipython within a container, start a jupyter notebook instance, and then connect to that instance using a browser running outside of the container on the host system or from another host.
Some programs need root privileges to run. These often include services or daemons that start via the init.d or system.d systems and run in the background. For instance, sshd the ssh daemon that listens on port 22 and allows another user to connect to your computer requires root privileges. You will not be able to run it in a container unless you start the container as root.
Other programs may set the SUID bit or capabilities to run as root or with elevated privileges without your knowledge. For instance, the well-known ping program actually runs with elevated privileges (and needs to since it sets up a raw network socket). This program will not run in a container unless you are root in the container.