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 requesting an installation for information to send to your system administrator.
For any additional help or support contact the Apptainer Community: https://apptainer.org/support
Installation
You will need a Linux system to run Apptainer. Root access is not required if user namespaces are available.
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.
If you have an existing version of Apptainer installed from source, which you wish to upgrade or remove / uninstall, also see 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 I/O, 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:
--build-config use configuration needed for building containers
-c, --config string specify a configuration file (for root or
unprivileged installation only) (default
"/etc/apptainer/apptainer.conf")
-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
--version version for apptainer
Available Commands:
build Build an Apptainer image
cache Manage the local cache
capability Manage Linux capabilities for users and groups
checkpoint Manage container checkpoint state (experimental)
completion Generate the autocompletion script for the specified shell
config Manage various apptainer configuration (root user only)
delete Deletes requested image from the library
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
keyserver Manage apptainer keyservers
oci Manage OCI containers
overlay Manage an EXT3 writable overlay image
plugin Manage Apptainer plugins
pull Pull an image from a URI
push Upload image to the provided URI
registry Manage authentication to OCI/Docker registries
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 Manipulate Singularity Image Format (SIF) images
sign Add digital signature(s) to an image
test Run the user-defined tests within a container
verify Verify digital signature(s) within 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://apptainer.org/help/
Information about individual subcommands can also be viewed by using the
help command:
$ apptainer help verify
Verify digital signature(s) within an image
Usage:
apptainer verify [verify options...] <image path>
Description:
The verify command allows a user to verify one or more digital signatures
within a SIF image.
Key material can be provided via PEM-encoded file, or via the PGP keyring. To
manage the PGP keyring, see 'apptainer help key'.
Options:
-a, --all verify all objects
--certificate string path to the certificate
--certificate-intermediates string path to pool of intermediate
certificates
--certificate-roots string path to pool of root certificates
-g, --group-id uint32 verify objects with the
specified group ID
-h, --help help for verify
-j, --json output json
--key string path to the public key file
--legacy-insecure enable verification of
(insecure) legacy signatures
-l, --local only verify with local key(s)
in keyring
--ocsp-verify enable online revocation check
for certificates
-i, --sif-id uint32 verify object with the specified ID
-u, --url string specify a URL for a key server
Examples:
Verify with a public key:
$ apptainer verify --key public.pem container.sif
Verify with PGP:
$ apptainer verify container.sif
For additional help or support, please visit https://apptainer.org/help/
Apptainer uses positional syntax (i.e., the order of commands and options
matters). Global options affecting the behavior of all commands follow
immediately after the main apptainer command. Then come subcommands,
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, as
follows:
$ apptainer capability list myuser
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 as follows:
$ apptainer inspect --helpfile container.sif # See the container's help, if provided
$ apptainer inspect --helpfile --app=foo foo.sif # See the help for the app 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 image.
$ 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 the Apptainer
definition file with Dockerfile, please see this section.
Interacting with images
You can interact with images in several ways, each of which can accept image URIs in addition to local image paths.
As an example, the following command will pull a lolcow_latest.sif image
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 virtual machine.
$ apptainer shell lolcow_latest.sif
Apptainer>
The change in prompt indicates that you have entered the container (though you should not rely on prompt forms to determine whether you are in a container or not).
Once inside of an Apptainer container, you are the same user as you are on the host system.
Apptainer> whoami
david
Apptainer> id
uid=1000(david) gid=1000(david) groups=1000(david),65534(nfsnobody)
shell also works with the docker://, oras://, and library://
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://, and library://
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 may 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://, and library://
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 as follows:
$ 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 expressions that have special meaning to the shell. Here is an illustrative example:
$ docker run -it --rm alpine echo "\$HOSTNAME"
$HOSTNAME
$ apptainer run docker://alpine echo "\$HOSTNAME"
p700
$ apptainer run docker://alpine echo "\\\$HOSTNAME"
$HOSTNAME
To replicate Docker/OCI behavior, you may need additional escaping or quoting of arguments.
Unlike the run command, the exec command does behave in the same
manner as Docker/OCI, because it calls the specified executable directly:
$ apptainer exec docker://alpine echo "\$HOSTNAME"
$HOSTNAME
$ apptainer exec docker://alpine echo "\\\$HOSTNAME"
\$HOSTNAME
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 $HOME/hostfile.txt
Hello from inside the container
This example works because hostfile.txt exists in the user’s home directory
($HOME). By default, Apptainer bind mounts $HOME, the current
working directory, and additional system locations from the host into the
container.
You can specify additional directories to bind mount into your container
with the --bind option. In the following 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 |
|| ||
Building 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 new 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 Singularity Image Format, you can do so as follows:
$ apptainer build new.sif sandbox
Note, however, that this approach may break reproducibility, in the event that 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, it is recommended that you 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, Fedora, 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 tasks such as software installation, environment setup, and copying files into the container from host system.
Here is an example of a definition file:
BootStrap: docker
From: ubuntu:22.04
%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 as follows:
$ apptainer build lolcow.sif lolcow.def
In this example, the header tells Apptainer to use a base Ubuntu 22.04 image from the Container Library. The other sections in this definition file are as follows:
The
%postsection is executed within the container at build time, after the base OS has been installed. The%postsection is therefore the place to perform installations of new libraries and applications.The
%environmentsection defines environment variables that will be available to the container at runtime.The
%runscriptsection defines actions for the container to take when it is executed. (These commands will therefore not be run at build time.)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. Definition files also support “templating”: the ability to pass values from the command-line, or from a definitions file, that will replace placeholders in the definition file at build time.
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.