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Apptainer

Apptainer/Singularity is the most widely used container system for HPC. It is designed to execute applications at bare-metal performance while being secure, portable, and 100% reproducible. Apptainer is an open-source project with a friendly community of developers and users. The user base continues to expand, with Apptainer/Singularity now used across industry and academia in many areas of work.

Apptainer is a container platform. It allows you to create and run containers that package up pieces of software in a way that is portable and reproducible. You can build a container using Apptainer on your laptop, and then run it on many of the largest HPC clusters in the world, local university or company clusters, a single server, in the cloud, or on a workstation down the hall. Your container is a single file, and you don’t have to worry about how to install all the software you need on each different operating system.

Apptainer allows for more secure containers than docker without the need for root access.

Why use Apptainer?

From Why you should use Apptainer vs Docker | Medium.

Apptainer allows you to:

  1. Build on a personal computer with root or on a shared system with fakeroot.

  2. Move images between systems easily.

  3. Execute on a shared system without root.

Apptainer is designed for HPC:

  1. Defaults to running as the current user

  2. Defaults to mounting the home directory in /home/$USER

  3. Defaults to running as a program (not background process)

Apptainer also has great support with Docker images.

Systems with Apptainer installed

  • docker

  • thunderx

  • zenith

Other systems can have Apptainer installed by request.

Notes:

  • Apptainer mounts $HOME , /sys:/sys , /proc:/proc, /tmp:/tmp, /var/tmp:/var/tmp, /etc/resolv.conf:/etc/resolv.conf, /etc/passwd:/etc/passwd, and $PWD by default and run in ~ by default. This means you can change files in your home directory by running with Apptainer. This is different from Docker which creates a container (overlay in Apptainer) by default for the application to run in. See Bind Paths and Mounts.

  • To mount another location when running Apptainer, use the --bind option. For example to mount /noback use --bind /noback:/noback. See Bind Paths and Mounts.

  • Admins can specify default bind points in /etc/apptainer/apptainer.conf. See Apptainer Configuration Files

  • When creating a definition file, pay attention to the rules for each section. See Definition Files For example:

    • %setup is a scriplet which runs outside the container and can modify the host. Use ${APPTAINER_ROOTFS} to access the files in the Apptainer image.

    • Environment variables defined in %environment are available only after the build, so if you need access to them for the build, define them in the %post section.

  • To use --fakeroot you must first have fakeroot configured for that user. This can be done with the command sudo apptainer config fakeroot --add <user>. See User Namespaces & Fakeroot

  • To use X11 applications in Apptainer with over ThinLinc, you need to bind /var/opt/thinlinc with --bind /var/opt/thinlinc since that is where the user’s XAuthority file is stored.

  • sandbox image build mode along with fakeroot can help if one needs to apt-get install or yum install packages within a singularity / apptainer container and persist the mutable image out on disk: Build a Container — Apptainer User Guide main documentation.

NFS Limitations

From https://apptainer.org/docs/admin/main/installation.html#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.

Getting Started

System Admin Notes

  • It is helpful to add commonly needed bind paths to /etc/apptainer/apptainer.conf. I have added the following bind commands to Zenith:

bind path = /scratch
bind path = /etc/localtime
bind path = /etc/hosts
bind path = /noback
bind path = /var/opt/thinlinc
bind path = /auto

See also

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