Quick Start
This guide is intended for running Apptainer on a computer where you will install Apptainer yourself.
If you need to request an installation on your shared resource, see the requesting an installation section for information to send to your system administrator.
For any additional help or support contact the Apptainer Community: https://apptainer.org/help
Quick Installation
You will need a Linux system to run Apptainer natively and it’s easiest to install if you have root access.
To install from source, follow the instructions in the INSTALL.md on github. Other installation options, including installing from a pre-built RPM, building an RPM or Debian package, installing Apptainer without root privileges, and using Apptainer on Mac and Windows machines are discussed in the installation section of the admin guide.
Overview of the Apptainer Interface
Apptainer’s command line interface allows you to build and interact with containers transparently. You can run programs inside a container as if they were running on your host system. You can easily redirect IO, use pipes, pass arguments, and access files, sockets, and ports on the host system from within a container.
The help command gives an overview of Apptainer options and
subcommands as follows:
$ apptainer help
Linux container platform optimized for High Performance Computing (HPC) and
Enterprise Performance Computing (EPC)
Usage:
apptainer [global options...]
Description:
Apptainer containers provide an application virtualization layer enabling
mobility of compute via both application and environment portability. With
Apptainer one is capable of building a root file system that runs on any
other Linux system where Apptainer is installed.
Options:
-d, --debug print debugging information (highest verbosity)
-h, --help help for apptainer
--nocolor print without color output (default False)
-q, --quiet suppress normal output
-s, --silent only print errors
-v, --verbose print additional information
Available Commands:
build Build an Apptainer image
cache Manage the local cache
capability Manage Linux capabilities for users and groups
exec Run a command within a container
help Help about any command
inspect Show metadata for an image
instance Manage containers running as services
key Manage OpenPGP keys
oci Manage OCI containers
plugin Manage apptainer plugins
pull Pull an image from a URI
push Upload image to the provided URI
remote Manage apptainer remote endpoints
run Run the user-defined default command within a container
run-help Show the user-defined help for an image
search Search a Container Library for images
shell Run a shell within a container
sif siftool is a program for Singularity Image Format (SIF) file manipulation
sign Attach a cryptographic signature to an image
test Run the user-defined tests within a container
verify Verify cryptographic signatures attached to an image
version Show the version for Apptainer
Examples:
$ apptainer help <command> [<subcommand>]
$ apptainer help build
$ apptainer help instance start
For additional help or support, please visit https://www.apptainer.org/docs/
Information about subcommand can also be viewed with the help
command.
$ apptainer help verify
Verify cryptographic signatures attached to an image
Usage:
apptainer verify [verify options...] <image path>
Description:
The verify command allows a user to verify cryptographic signatures on SIF
container files. There may be multiple signatures for data objects and
multiple data objects signed. By default the command searches for the primary
partition signature. If found, a list of all verification blocks applied on
the primary partition is gathered so that data integrity (hashing) and
signature verification is done for all those blocks.
Options:
-a, --all verify all objects
-g, --group-id uint32 verify objects with the specified group ID
-h, --help help for verify
-j, --json output json
--legacy-insecure enable verification of (insecure) legacy signatures
-l, --local only verify with local keys
-i, --sif-id uint32 verify object with the specified ID
-u, --url string key server URL (default "https://keys.openpgp.org")
Examples:
$ apptainer verify container.sif
For additional help or support, please visit https://www.apptainer.org/docs/
Apptainer uses positional syntax (i.e. the order of commands and
options matters). Global options affecting the behavior of all commands
follow the main apptainer command. Then sub commands are followed
by their options and arguments.
For example, to pass the --debug option to the main apptainer
command and run Apptainer with debugging messages on:
$ apptainer --debug run docker://alpine
To pass the --containall option to the run command and run a
Apptainer image in an isolated manner:
$ apptainer run --containall docker://alpine
Apptainer has the concept of command groups. For
instance, to list Linux capabilities for a particular user, you would
use the list command in the capability command group like so:
$ apptainer capability list dave
Container authors might also write help docs specific to a container or
for an internal module called an app. If those help docs exist for a
particular container, you can view them like so.
$ apptainer inspect --helpfile container.sif # See the container's help, if provided
$ apptainer inspect --helpfile --app=foo foo.sif # See the help for foo, if provided
Downloading images
You can use the pull and build commands to download images from an external resource like an OCI registry.
You can use pull with the docker:// uri to reference OCI
images served from an OCI registry. In this case pull does not just
download an image file. OCI images are stored in layers, so pull
must also combine those layers into a usable Apptainer file.
$ apptainer pull docker://alpine
You can also use the build command to download pre-built images from
an external resource. When using build you must specify a name for
your container like so:
$ apptainer build alpine.sif docker://alpine
Unlike pull, build will convert your image to the latest
Apptainer image format after downloading it. build is like a
“Swiss Army knife” for container creation. In addition to downloading
images, you can use build to create images from other images or from
scratch using a definition file. You can also
use build to convert an image between the container formats
supported by Apptainer. To see a comparison of Apptainer
definition file with Dockerfile, please see: this section.
Interact with images
You can interact with images in several ways, each of which can accept image URIs in addition to a local image path.
For demonstration, we will use a lolcow_latest.sif image that can be
pulled from ghcr.io:
$ apptainer pull docker://ghcr.io/apptainer/lolcow
Shell
The shell command allows you to spawn a new shell within your container and interact with it as though it were a small virtual machine.
$ apptainer shell lolcow_latest.sif
Apptainer lolcow_latest.sif:~>
The change in prompt indicates that you have entered the container (though you should not rely on that to determine whether you are in container or not).
Once inside of an Apptainer container, you are the same user as you are on the host system.
Apptainer lolcow_latest.sif:~> whoami
david
Apptainer lolcow_latest.sif:~> id
uid=1000(david) gid=1000(david) groups=1000(david),65534(nfsnobody)
shell also works with the docker://, oras://, library://, and
shub:// URIs. This creates an ephemeral container that disappears
when the shell is exited.
$ apptainer shell docker://ghcr.io/apptainer/lolcow
Executing Commands
The exec
command allows you to execute a custom command within a container by
specifying the image file. For instance, to execute the cowsay
program within the lolcow_latest.sif container:
$ apptainer exec lolcow_latest.sif cowsay moo
_____
< moo >
-----
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
exec also works with the docker://, oras://, library://, and
shub:// URIs. This creates an ephemeral container that executes a
command and disappears.
$ apptainer exec docker://ghcr.io/apptainer/lolcow cowsay "Fresh from the internet"
_________________________
< Fresh from the internet >
-------------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
Running a container
Apptainer containers contain runscripts. These are user defined scripts that define the actions a container should perform when someone runs it. The runscript can be triggered with the run command, or simply by calling the container as though it were an executable.
$ apptainer run lolcow_latest.sif
______________________________
< Mon Aug 16 13:01:55 CDT 2021 >
------------------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
$ ./lolcow_latest.sif
______________________________
< Mon Aug 16 13:12:50 CDT 2021 >
------------------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
run also works with the docker://, oras://, library://, and
shub:// URIs. This creates an ephemeral container that runs and then
disappears.
$ apptainer run docker://ghcr.io/apptainer/lolcow
______________________________
< Mon Aug 16 13:12:33 CDT 2021 >
------------------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
Arguments to run
You can pass arguments to the runscript of a container, if it accepts
them. For example, the default runscript of the docker://alpine
container passes any arguments to a shell. We can ask the container
to run echo command in this shell:
$ apptainer run docker://alpine echo "hello"
hello
Because Apptainer runscripts are evaluated shell scripts arguments can behave slightly differently than in Docker/OCI runtimes, if they contain shell code that may be evaluated. To replicate Docker/OCI behaviour you may need additional escaping or quoting of arguments.
$ docker run -it --rm alpine echo "\$HOSTNAME"
$HOSTNAME
$ apptainer run docker://alpine echo "\$HOSTNAME"
p700
$ apptainer run docker://alpine echo "\\\$HOSTNAME"
$HOSTNAME
The exec command replicates the Docker/OCI behavior as it calls
the specified executable directly.
Working with Files
Files on the host are reachable from within the container.
$ echo "Hello from inside the container" > $HOME/hostfile.txt
$ apptainer exec lolcow_latest.sif cat $HOME/hostfile.txt
Hello from inside the container
This example works because hostfile.txt exists in the user’s home
directory. By default Apptainer bind mounts /home/$USER,
/tmp, and $PWD into your container at runtime.
You can specify additional directories to bind mount into your container
with the --bind option. In this example, the data directory on
the host system is bind mounted to the /mnt directory inside the
container.
$ echo "Drink milk (and never eat hamburgers)." > /data/cow_advice.txt
$ apptainer exec --bind /data:/mnt lolcow_latest.sif cat /mnt/cow_advice.txt
Drink milk (and never eat hamburgers).
Pipes and redirects also work with Apptainer commands just like they do with normal Linux commands.
$ cat /data/cow_advice.txt | apptainer exec lolcow_latest.sif cowsay
________________________________________
< Drink milk (and never eat hamburgers). >
----------------------------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
Build images from scratch
Apptainer produces immutable images in the Singularity Image File (SIF) format. This ensures reproducible and verifiable images and allows for many extra benefits such as the ability to sign and verify your containers.
However, during testing and debugging you may want an image format that
is writable. This way you can shell into the image and install
software and dependencies until you are satisfied that your container
will fulfill your needs. For these scenarios, Apptainer also
supports the sandbox format (which is really just a directory).
Sandbox Directories
To build into a sandbox (container in a directory) use the build
--sandbox command and option:
$ apptainer build --sandbox ubuntu/ docker://ubuntu
This command creates a directory called ubuntu/ with an entire
Ubuntu Operating System and some Apptainer metadata in your current
working directory.
You can use commands like shell, exec , and run with this
directory just as you would with an Apptainer image. If you pass the
--writable option when you use your container you can also write
files within the sandbox directory (provided you have the permissions to
do so).
$ apptainer exec --writable ubuntu touch /foo
$ apptainer exec ubuntu/ ls /foo
/foo
Converting images from one format to another
The build command allows you to build a container from an existing
container. This means that you can use it to convert a container from
one format to another. For instance, if you have already created a
sandbox (directory) and want to convert it to the default immutable
image format (squashfs) you can do so:
$ apptainer build new-sif sandbox
Doing so may break reproducibility if you have altered your sandbox outside of the context of a definition file, so you are advised to exercise care.
Apptainer Definition Files
For a reproducible, verifiable and production-quality container you should build a SIF file using an Apptainer definition file. This also makes it easy to add files, environment variables, and install custom software. You can start with base images from Docker Hub and use images directly from official repositories such as Ubuntu, Debian, CentOS, Arch, and BusyBox.
A definition file has a header and a body. The header determines the base container to begin with, and the body is further divided into sections that perform things like software installation, environment setup, and copying files into the container from host system, etc.
Here is an example of a definition file:
BootStrap: docker
From: ubuntu:20.04
%post
apt-get -y update
apt-get -y install cowsay lolcat
%environment
export LC_ALL=C
export PATH=/usr/games:$PATH
%runscript
date | cowsay | lolcat
%labels
Author Alice
To build a container from this definition file (assuming it is a file named lolcow.def), you would call build like so:
$ apptainer build lolcow.sif lolcow.def
In this example, the header tells Apptainer to use a base Ubuntu 16.04 image from the default OCI registry.
The
%postsection executes within the container at build time after the base OS has been installed. The%postsection is therefore the place to perform installations of new applications.The
%environmentsection defines some environment variables that will be available to the container at runtime.The
%runscriptsection defines actions for the container to take when it is executed.And finally, the
%labelssection allows for custom metadata to be added to the container.
This is a very small example of the things that you can do with a definition file. You can also use an existing container on your host system as a base.
This quickstart document just scratches the surface of all of the things you can do with Apptainer!
If you need additional help or support, see https://apptainer.org/help.