Installing Apptainer

This section will guide you through the process of installing Apptainer 1.1.3 via several different methods. (For instructions on installing earlier versions of Apptainer please see earlier versions of the docs.)

Installation on Linux

Apptainer can be installed on any modern Linux distribution, on bare-metal or inside a Virtual Machine. It can even often be run nested inside another Apptainer container or inside some other container system.

System Requirements

Apptainer requires ~150MiB disk space once compiled and installed.

There are no specific CPU or memory requirements at runtime, though at least 2GB of RAM is recommended when building from source.

Full functionality of Apptainer requires that the kernel supports:

  • Unprivileged user namespaces - (minimum kernel >=3.8, >=4.18 or 3.10.0-1127 on RHEL7 recommended) Required to run containers without root or setuid privilege. The recommended versions are required for unprivileged SIF file mounts.

  • OverlayFS mounts - (minimum kernel >=3.18, >=5.11 recommended) Required for full flexibility in bind mounts to containers in suid mode, and to support persistent overlays for writable containers in suid mode. Kernel 5.11 enables support for persistent overlay unprivileged, but otherwise fuse-overlayfs will be used for that.

Instructions to install without or with setuid privileges are below. Please make sure you are familiar with the discussion on Setuid & User Namespaces in the Security section of the user guide, and the User Namespace Requirements in this guide.

Non-standard ldconfig / Nix & Guix Environments

If Apptainer is installed under a package manager such as Nix or Guix, but on top of a standard Linux distribution (e.g. RHEL or Debian), it may be unable to correctly find the libraries for --nv and --rocm GPU support. This issue occurs as the package manager supplies an alternative ldconfig, which does not identify GPU libraries installed from host packages.

To allow Apptainer to locate the host (i.e. RHEL / Debian) GPU libraries correctly, set binary path in apptainer.conf to point to the directory of the host’s ldconfig before the $PATH: which is replaced by the user’s PATH. I.E., /sbin should be before any Nix or Guix related path or the user’s PATH.

Filesystem support / limitations

Apptainer supports most filesystems, but there are some limitations when installing Apptainer on, or running containers from, common parallel / network filesystems. In general:

  • We recommend installing Apptainer on local disk on each compute node.

  • If Apptainer is installed to a network location, a --localstatedir should be provided on each node, and Apptainer configured to use it.

  • The --localstatedir filesystem should support overlay mounts.

  • TMPDIR / APPTAINER_TMPDIR should be on a local filesystem wherever possible.

Note

Set the --localstatedir location by by providing --localstatedir my/dir as an option when you configure your Apptainer build with ./mconfig.

Disk usage at the --localstatedir location is negligible (<1MiB). The directory is used as a location to mount the container root filesystem, overlays, bind mounts etc. that construct the runtime view of a container. You will not see these mounts from a host shell, as they are made in a separate mount namespace.

Overlay support

Some features of Apptainer, such as the --writable-tmpfs and --overlay options, try to use the Linux overlay filesystem driver to construct a container root filesystem that combines files from different locations. Not all filesystems can be used with the overlay driver, so when containers are run from these filesystems some Apptainer features may not be available.

If the overlay kernel driver does not work, but the setuid flow is not being used and unprivileged user namespaces are available, then Apptainer will use the fuse-overlayfs command if it can be found. That works with additional filesystem types than the overlay kernel driver does not work with, and also works in cases where older kernels do not support using the overlay driver unprivileged.

Overlay support has two aspects, referenced below:

  • lowerdir support for a filesystem allows a directory on that filesystem to act as the ‘base’ of a container. A filesystem must support overlay lowerdir for you be able to run an Apptainer sandbox container on it, while using functionality such as --writable-tmpfs / --overlay.

  • upperdir support for a filesystem allows a directory on that filesystem to be merged on top of a lowerdir to construct a container. If you use the --overlay option to overlay a directory onto a container, then the filesystem holding the overlay directory must support upperdir.

Fakeroot with uid/gid mapping on Network filesystems

When Apptainer is run using the fakeroot option and mappings are available in /etc/subuid and /etc/subgid then uids / gids inside the container are mapped to different host uids / gids.

Most local filesystems (ext4/xfs etc.) have no problem with this uid/gid mapping. Most network filesystems (NFS/Lustre/GPFS etc.), however, only support a single uid for each user. When additional user ids are attempted to be used the fileserver will deny many operations, with ‘permission denied’ errors. This is currently a generic problem for rootless container runtimes.

This is only a problem when sandbox images are stored on the network filesystems. For that case it is probably better to use one of the other fakeroot modes that Apptainer supports. Alternatively, use SIF images instead of sandbox images because they don’t have the problem.

Apptainer cache / atomic rename

Apptainer will cache SIF container images generated from remote sources, and any OCI/docker layers used to create them. The cache is created at $HOME/.apptainer/cache by default. The location of the cache can be changed by setting the APPTAINER_CACHEDIR environment variable.

The directory used for APPTAINER_CACHEDIR should be:

  • A unique location for each user. Permissions are set on the cache so that private images cached for one user are not exposed to another. This means that APPTAINER_CACHEDIR cannot be shared.

  • Located on a filesystem with sufficient space for the number and size of container images anticipated.

  • Located on a filesystem that supports atomic rename, if possible.

The Apptainer cache is concurrency safe. Parallel runs of Apptainer that would create overlapping cache entries will not conflict, as long as the filesystem used by APPTAINER_CACHEDIR supports atomic rename operations.

Support for atomic rename operations is expected on local POSIX filesystems, but varies for network / parallel filesystems and may be affected by topology and configuration. For example, Lustre supports atomic rename of files only on a single MDT. Rename on NFS is only atomic to a single client, not across systems accessing the same NFS share.

If you are not certain that your $HOME or APPTAINER_CACHEDIR filesystems support atomic rename, do not run apptainer in parallel using remote container URLs. Instead use apptainer pull to create a local SIF image, and then run this SIF image in a parallel step. An alternative is to use the --disable-cache option, but this will result in each Apptainer instance independently fetching the container from the remote source, into a temporary location.

NFS

NFS filesystems support overlay mounts as a lowerdir only, and do not support user-namespace (sub)uid/gid mapping.

  • Containers run from SIF files located on an NFS filesystem do not have restrictions.

  • In setuid mode, you cannot use --overlay mynfsdir/ to overlay a directory onto a container when the overlay (upperdir) directory is on an NFS filesystem. In non-setuid mode and fuse-overlayfs it is allowed but will be read-only.

  • When using --fakeroot and /etc/subuid mappings to build or run a container, your TMPDIR / APPTAINER_TMPDIR should not be set to an NFS location.

  • You should not run a sandbox container with --fakeroot and /etc/subuid mappings from an NFS location.

Lustre / GPFS

Lustre and GPFS do not have sufficient upperdir or lowerdir overlay support for certain Apptainer features, and do not support user-namespace (sub)uid/gid mapping.

  • In setuid mode, you cannot use --overlay or --writable-tmpfs with a sandbox container that is located on a Lustre or GPFS filesystem. SIF containers on Lustre / GPFS will work correctly with these options. It works with fuse-overlayfs in non-setuid mode.

  • In setuid mode, you cannot use --overlay to overlay a directory onto a container, when the overlay (upperdir) directory is on a Lustre or GPFS filesystem. In non-setuid mode and fuse-overlayfs it is allowed but will be read-only.

  • When using --fakeroot and /etc/subuid mappings to build or run a container, your TMPDIR/APPTAINER_TMPDIR should not be a Lustre or GPFS location.

  • You should not run a sandbox container with --fakeroot and /etc/subuid mappings from a Lustre or GPFS location.

FUSE-based filesystems

The kernel overlay driver does not allow the upperdir to be a FUSE-based filesystem, so in setuid mode that is disallowed. It does work in non-setuid mode with fuse-overlayfs.

Install from Pre-built packages

Prebuilt packages are available for released versions of Apptainer on a variety of host operating systems.

Install RPM from EPEL or Fedora

Multiple architectures of RPMs are available for Red Hat Enterprise Linux and Fedora.

First, on Red Hat Enterprise Linux derived systems enable the EPEL repositories like this:

$ sudo yum install -y epel-release

Then to install a non-setuid installation of Apptainer do:

$ sudo yum install -y apptainer

or for a setuid installation do:

$ sudo yum install -y apptainer-suid

Install from GitHub release RPMs

Alternatively, x86_64 RPMs are available on GitHub immediately after each Apptainer release and they can be installed directly from there. For the non-setuid installation:

$ sudo yum install -y https://github.com/apptainer/apptainer/releases/download/v1.1.3/apptainer-1.1.3-1.x86_64.rpm

For the setuid installation do above command first and then this one:

$ sudo yum install -y https://github.com/apptainer/apptainer/releases/download/v1.1.3/apptainer-suid-1.1.3-1.x86_64.rpm

Install Debian/Ubuntu packages

Pre-built Debian/Ubuntu packages are only available on GitHub and only for the amd64 architecture. For the non-setuid installation use these commands:

$ sudo apt-get update
$ sudo apt-get install -y wget
$ cd /tmp
$ wget https://github.com/apptainer/apptainer/releases/download/v1.1.3/apptainer_1.1.3_amd64.deb
$ sudo apt-get install -y ./apptainer_1.1.3_amd64.deb

For the setuid installation do above commands first and then these:

$ wget https://github.com/apptainer/apptainer/releases/download/v1.1.3/apptainer-suid_1.1.3_amd64.deb
$ sudo dpkg -i ./apptainer-suid_1.1.3_amd64.deb

Install from Source

To install from source, follow the instructions in INSTALL.md on GitHub.

Relocatable Installation

An unprivileged (non-setuid) Apptainer installation built from source is relocatable. As long as the structure inside the installation directory (--prefix) is maintained, it can be moved to a different location and Apptainer will continue to run normally.

Relocation of a setuid installation is not supported, as restricted location / ownership of configuration files is important to security.

Source bash completion file

If you installed from source, then to enjoy bash shell completion with Apptainer commands and options, source the bash completion file (assuming the default installation prefix):

$ . /usr/local/share/bash-completion/completions/apptainer

Add this command to your ~/.bashrc file so that bash completion continues to work in new shells. (Adjust the path if you installed Apptainer to a different location.)

Build an RPM

If you use RHEL, CentOS or SUSE, building and installing an Apptainer RPM allows your Apptainer installation be more easily managed, upgraded and removed.

The instructions on how to build the RPM from source are in a INSTALL.md section on GitHub.

Build a Debian package

Packaging for Debian and Ubuntu can also be built from source. The instructions on how to do that are in a separate file DEBIAN_PACKAGE.md on GitHub.

Testing & Checking the Build Configuration

After installation you can perform a basic test of Apptainer functionality by executing a simple alpine container:

$ apptainer exec docker://alpine cat /etc/alpine-release
3.9.2

See the user guide for more information about how to use Apptainer.

apptainer buildcfg

Running apptainer buildcfg will show the build configuration of an installed version of Apptainer, and lists the paths used by Apptainer. Use apptainer buildcfg to confirm paths are set correctly for your installation, and troubleshoot any ‘not-found’ errors at runtime.

$ apptainer buildcfg
PACKAGE_NAME=apptainer
PACKAGE_VERSION=1.1.3
BUILDDIR=/home/dtrudg/Sylabs/Git/apptainer/builddir
PREFIX=/usr/local
EXECPREFIX=/usr/local
BINDIR=/usr/local/bin
SBINDIR=/usr/local/sbin
LIBEXECDIR=/usr/local/libexec
DATAROOTDIR=/usr/local/share
DATADIR=/usr/local/share
SYSCONFDIR=/usr/local/etc
SHAREDSTATEDIR=/usr/local/com
LOCALSTATEDIR=/usr/local/var
RUNSTATEDIR=/usr/local/var/run
INCLUDEDIR=/usr/local/include
DOCDIR=/usr/local/share/doc/apptainer
INFODIR=/usr/local/share/info
LIBDIR=/usr/local/lib
LOCALEDIR=/usr/local/share/locale
MANDIR=/usr/local/share/man
APPTAINER_CONFDIR=/usr/local/etc/apptainer
SESSIONDIR=/usr/local/var/apptainer/mnt/session
PLUGIN_ROOTDIR=/usr/local/libexec/apptainer/plugin
APPTAINER_CONF_FILE=/usr/local/etc/apptainer/apptainer.conf
APPTAINER_SUID_INSTALL=0

Note that the LOCALSTATEDIR and SESSIONDIR should be on local, non-shared storage.

Test Suite

The Apptainer codebase includes a test suite that is run during development using CI services.

If you would like to run the test suite locally you can run the test targets from the builddir directory in the source tree:

  • make check runs source code linting and dependency checks

  • make unit-test runs basic unit tests

  • make integration-test runs integration tests

  • make e2e-test runs end-to-end tests, which exercise a large number of operations by calling the Apptainer CLI with different execution profiles.

Note

Running the full test suite requires a docker installation, and nc in order to test docker and instance/networking functionality.

Apptainer must be installed with suid in order to run the full test suite, as it must run the CLI with setuid privilege for the starter-suid binary.

Warning

sudo privilege is required to run the full tests, and you should not run the tests on a production system. We recommend running the tests in an isolated development or build environment.

Installation on Windows or Mac

Linux container runtimes like Apptainer cannot run natively on Windows or Mac because of basic incompatibilities with the host kernel. (Contrary to a popular misconception, MacOS does not run on a Linux kernel. It runs on a kernel called Darwin originally forked from BSD.)

In order to use Apptainer on these platforms, you can install Vagrant Boxes via Vagrant Cloud, one of Hashicorp’s open source tools, by following the instructions below. Then you can install Apptainer in the base VM of your choice by following the linux installation instructions above.

Windows

Install the following programs:

Mac

Apptainer is available via Vagrant (installable with Homebrew or manually)

To use Vagrant via Homebrew:

$ /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
$ brew install --cask virtualbox vagrant vagrant-manager