9 ms·

Apptainer: Application Containers for Linux

123 points by cl3misch 1y ago

Simran-B 1y ago
Flatpak considers to move from OSTree to containers, citing the well-maintained tooling as a major plus point. How would that differ from Apptainers?
- Imustaskforhelp 1y ago
  Maybe the idea is that flatpak can have better sandbox control over applications running in flatpak using xdg-dbus ie. you can select the permissions that you want to give to a flatpak application and so sometimes it can act near native and not be completely isolated like containers. Also I am not sure if apptainers are completely isolated. Though I suppose through tools like https://containertoolbx.org/ https://containertoolbx.org/ such point also becomes moot & then I guess if they move to container, doesn't it sort of become like toolbx? To be honest, I think a lot of tools can have a huge overlap b/w them and I guess that's okay too
  - lotharcable 1y ago
    Containers in Linux are more a conceptual collection of different isolation techniques. Mostly just based on Linux namespaces. But things like cgroups, Linux capabilities, occasionally MAC (selinux, etc) and a few other items often get thrown in the mix. https://www.redhat.com/en/blog/7-linux-namespaces https://www.redhat.com/en/blog/7-linux-namespaces After a quick view of the apptainer documentation it looks like it minimally takes advantage of user and mount namespaces. So each apptainer gets its own idea of what the users/groups are and what the file system looks like. Flatpak is more about desktop application sandboxing. So while it does use user and mount namespaces like apptainer it takes advantage of more Linux features then that to help enhance the isolation. Which appears to be the opposite of the point of apptainer. Apptainer wants to use containers that integrate tightly with the rest of the system with very little isolation versus Flatpak wants to be maximally isolated with only the permissions necessary for the application. That isn't to say that apptainer can't use more Linux features to increase isolation. It supports the use of cgroups for resource quotas and can take advantage of different types of namespaces for network isolation among other things. Now as far as "OSTree vs containers" statement you are replying to... This is kinda misleading. OSTree is designed to manage binaries files in a way similar to git with text file. It isn't a type of container technology in itself. It just used for managing how objects on the file system are arranged and managed. It is used by some flatpak applications, but it is used for things besides flatpak. The 'containers' he mentioned is really a reference to OCI container image format. OCI container images is, again, a way to manage the file system contents typically used in containers. It isn't a container technology itself. It is like a tarball, but for file system images. OCI containers is a standardized version of Docker images. Due to the popularity and ubiquity of OCI image related tools and hosting software it makes sense for Flatpak to support it. OCI images, when combined with bootc, also can be used to deploy Linux container images to "bare hardware". Which is gaining popularity in helping to create and deploy "immutable" or "atomic" Linux distributions. Fedora Atomic-based OSes seem to be moving to use Bootc with OCI over pure OSTree approach... although they still use OSTree in some capacity. Incidentally Apptainer supports the use of OCI images (in addition to it's native SIF) as well as other commonly used container technologies like CNI. CNI is container network interface and is used with Kubernetes among other things.
    - Imustaskforhelp 1y ago
      Thanks a crazy lot for writing this as it actually made me genuinely understand the differences. And also, I must say that one of the most underrated parts which you told which I didn't knew about was that apptainer can be "unisolated?" ie. we don't have to do crazy shenanigans for it to access my files and it can just do it simply. Like someone else had mentioned https://nixery.dev/ https://nixery.dev/ and I wanted to see if I could use nix tools via docker and use them as if they were installed on my own system and apptainer really nailed it. I read that nixery.dev had to do some shenanigans to prevent the 150 layer or something but I suppose SIF doesn't have to deal with it so I am actually excited a little too haha. Thanks a lot!! Side Note: I think that there might be better ways to run nix apps like nix-appimage but I am just trying out things because why not. Its fun.
eisbaw 1y ago
Argh, yet another way to distribute userland images. AppImages does it right by including the run-time with the image itself - no prior installation needed. More nix less containers, btw. E.g. docker run -ti nixery.dev/shell/cowsay bash for on-the-fly containers based on Nix.
- _joel 1y ago
  fewer containers, surely :)
- Imustaskforhelp 1y ago
  Of course we ignore the taking shots at a project just for its existence thing aside I actually really like nixery.dev idea. Sounds kinda neat. If I am being really honest, there are a lot of ways to go around tbh, there are ways to run nix inside of docker and docker inside of nix too. There are ways to convert docker images into os too and there are tools like coreos. There is nix-shell and someone on hackernews told me about comma and I am still figuring out comma (haha! Thanks to them!) And if one just wants isolation, they can use bubblewrap or (pledge by jart) and I guess there is complete beauty and art in such container-esque space and I truly love this space a lot. I am actually wondering right now that using traefik (as load balancer) + nats (for a modular monolith) + podman/coreos + (cloudflare tunnels?) + any vps and you can use nix to build those containers too or you can go the other way around by having a nixos on vps with traefik + nats can be a really good alternative to kubernetes. I mean, There is docker swarm too if you don't want any of such complexity but people say that its less worked upon but still I guess there is a sort of fun in reinventing the wheel of kubernetes, but I guess I don't have tooo much problems with kubernetes I suppose because of the existence of helm charts (I haven't used kubernetes) but helm charts are written in go templates and I think they are a bit clunky but still I love golang and I feel like I would be okay with writing helm charts but I guess I am one of the people who just believes to scale horizontally first than vertically untill the economic scale gets broken and its more cheaper to use kubernetes / learn it than not.
- lotharcable 1y ago
  Appimage is terrible. It works by trying to make applications in appimages adhere to a lowest common denominator between Linux distros... which amounts to forcing application developers to develop for the oldest version of Linux appimage supports. Nix is a huge pain to deal with. Nix makes me think of the old Zawinski joke of: "Some people, when confronted with a problem, think 'I know, I'll use regular expressions.' Now they have two problems," Except there are less upsides for using Nix over something like OCI.
kinow 1y ago
Apptainer and singularity ce are quite common in HPC. While both implementations fork the old singularity project, they are not really identical. We use singularity in the HPCs (like Leonardo, LUMI, Fugaku, NeSI NZ, Levante) but some devs and researchers have apptainer installed locally. We found a timezone bug a few days ago in our Python code (matplotlib,xarray,etc.), but that didn't happen with apptainer. As the code bases are still a bit similar, I could confirm apptainer fixed it but singularity ce was still affected by the bug -- singularity replaces the UTC timezone file by the user's timezone, Helsinki EEST in our case in LUMI HPC. https://github.com/sylabs/singularity/issues/3686 https://github.com/sylabs/singularity/issues/3686
- markus92 1y ago
  Luckily they’re still compatible with each others containers. Can use Apptainer to build the container then run it on Singularity and vice-versa.
  - kinow 1y ago
    Yeah, we haven't found any issues so far besides this one with time zone. Other than that, we've been able to run the same containers with both.
- throw0101c 1y ago
  > Apptainer and singularity ce are quite common in HPC. While both implementations fork the old singularity project, they are not really identical. Apptainer is not a fork of the old Singularity project: Apptainer is the original project, but the community voted to change its name. It also came under the umbrella of the Linux Foundation: * https://apptainer.org/news/community-announcement-20211130/ https://apptainer.org/news/community-announcement-20211130/ Sylabs (where the original Singularity author first worked) was the one that forked off the original project.
  - kinow 1y ago
    Oh, that's correct. Thanks!
aa-jv 1y ago
Very interesting .. I was recently tasked with getting a bespoke AI/ML environment ready to ship/deploy to, what can only be considered, foreign environments .. and this has proven to be quite a hassle, because, of course: python. So I guess Apptainer is the solution to this use case - anyone had any experience with using it to bundle up an AI/ML application for redistribution? Thoughts/tips?
- SirHumphrey 1y ago
  I did start to use them for AI development on the HPC I have access to and it worked well (GPU pass-through basically automatically, the performace seemed basically the same) - but I mostly use them because I do not want to argue with administrators anymore that it's probably time they update Cuda 11.7 (as well as python 3.6) - the only version of Cuda currently installed on the cluster.
  - aa-jv 1y ago
    Ah, right. So, no matter what container comes along to solve this problem, there's still the BOFH factor to deal with .. Curious though, how are you doing this work without admin privs?
    - SirHumphrey 1y ago
      It's a bit annoying, but you can install conda without admin privileges and apptainer was installed for compliance with some EuroHPC project and luckily made accessible to all users. The container allows me to have an environment where I have "root" access and can install software. The most annoying thing is not the lack of privileges, but that the compute nodes do not have internet access (because "security") beside connecting to the headnode, so there is the whole song and dance of running the container (or installing conda packages) on the headnode so I can download everything I need, then saving the state and running them on the compute node.
      - aa-jv 1y ago
        Seems to me that you might benefit from containerizing your apptainer development environment. ;) /ducks
eraser215 1y ago
[flagged]
Havoc 1y ago
Wish these sort of projects would do a better job articulating what the value proposition is over leading existing ones. Like why should I put time into learning this instead of rootless podman? Aside from this secret management thing it sounds like same feature set
- v9v 1y ago
  You should put time into learning this if you are going to be running HPC jobs on clusters, because some HPC clusters support this for jobs and not much else.
  - tecleandor 1y ago
    So is this popular in science or data analysis / forecasting or something like that? I'm not familiar with it (I don't know if it changed names or just didn't notice)
    - misnome 1y ago
      Used to be called “Singularity”
    - v9v 1y ago
      I don't think people use it for reproducible environments on their own machines the same way Docker is sometimes used, I've mostly encountered it in academic compute clusters as a way to install the libraries/languages you're using onto the cluster in an easy to remove way. So it's popular in HPC clusters specifically and not really tied to a field of research beyond that.
    - elmolino89 1y ago
      Re science: yes and no. Meaning: the old way of compiling programs from sources on HPC systems while not dead is becoming rare. I can only speak about bioinformatics: the majority of programs one can get up and running in no time using either conda environments or apptainer containers. It may take few weeks for the brand new shiny version to get packaged by the maintainers, but this is seldom the problem. Even if you want to compile some program you will save yourself the time and frustration using either conda env or a container with a required toolchain/libraries. Even on a box with root access you need to avoid conflicting system wide installed library versions where program A requires lib version X and program B lib version Y.
IshKebab 1y ago
We tried to use this on our compute cluster for silicon design/verification. We gave up in the end and just went with the traditional TCL (now Lua) modules. The problems are: 1. You can't have apptainers that use each other. The most common case was things like Make, GCC, Git etc. If Make is in a different apptainer to GCC then it won't work because as soon as you go into Make then it can't see GCC any more. 2. It doesn't work if any of your output artefacts depend on things inside the container. For example you use your GCC apptainer to compile a program. It appears to work, but when you run it you find it actually linked to something in the apptainer that isn't visible any more. This is also a problem for C headers. 3. We had constant issues with PATH getting messed up so you can't see things outside the apptainer that should have been available. All in all it was a nice idea but ended up causing way more hassle than it was worth. It was much easier just to use an old OS (RHEL8) and get everything to work directly on that.
- mbreese 1y ago
  I think of using Apptainer/Singularity as more like Docker than anything else (without the full networking configs). These are all issues with traditional Docker containers as well, so I’m not sure how you were using the containers or what you were expecting. For my workflows on HPC, I use apptainers as basically drop-in replacements for Docker, and for that, they work quite well. These biggest benefit is that the containers are unprivileged. This means you can’t do a lot of things (in particular complex networking), but it also makes it much more secure for multi-tenant systems (like HPC). (I know Docker and Apptainer are slightly different beasts, but I’m speaking in broad strokes in a general sense without extra permissions).
  - d3Xt3r 1y ago
    You can also run Docker itself in rootless mode[1]. And if for some reason you don't want to run Docker, you can also use Podman or Incus instead, and they both support Docker images, as well as running unpriviliged. Finally, there's also Flox[2], which is a Nix-based application Sandbox, that I believe would align more towards your (and OP's) use case (unless you specifically require Docker image compatibility). So unfortunately your example doesn't illustrate why Apptainer is a better option. [1] https://docs.docker.com/engine/security/rootless/ https://docs.docker.com/engine/security/rootless/ [2] https://flox.dev/ https://flox.dev/
mrweasel 1y ago
To some extend I understand the problem that these solution are trying to address, I'm just not sure that simply stuff things into containers is really the right solution. Perhaps the problems need to be addressed on a more fundamental level.
- whatagreatboy 1y ago
  https://dl.acm.org/doi/10.1145/3126908.3126925 https://dl.acm.org/doi/10.1145/3126908.3126925 This paper might help
DrNosferatu 1y ago
It is very handy in SLURM clusters and servers where you have no sudo. Some attrition using it though: is there a good in-depth book about it?
- floro 1y ago
  I used it on a SLURM cluster before. The documentation is done well and should be a good introduction. The only issue I had was that the cluster didn't have fakeroot or sudo, so I had to build the apptainer locally and transfer it to the server.
  - DrNosferatu 1y ago
    Exactly: in most HPC clusters / servers one has no sudo.
cs_throwaway 1y ago
Funny this is here. Apptainer is Singularity, described here: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177459 https://journals.plos.org/plosone/article?id=10.1371/journal... If you ever use a shared cluster at a university or run by the government, Apptainer will be available, and Podman / Docker likely won't be. In these environments, it is best not to use containers at all, and instead get to know your sysadmin and understand how he expects the cluster to be used.
- shortrounddev2 1y ago
  Why are docker/podman less common? And why do you say it's better not to use containers? Performance?
  - kgxohxkhclhc 1y ago
    docker and podman expect to extract images to disk, then use fancy features like overlayfs, which doesn't work on network filesystems -- and in hpc, most filesystems users can write to persistently are network filesystems. apptainer images are straight filesystem images with no overlayfs or storage driver magic happening -- just a straight loop mount of a disk image. this means your container images can now live on your network filesystem.
    - 0xbadcafebee 1y ago
      Do the compute instances not have hard disks? Because it seems like whoever's running these systems doesn't understand Linux or containers all that well. If there's a hard disk on the compute nodes, then you just run the container from the remote image registry, and it downloads and extracts it temporarily to disk. No need for a network filesystem. If the containerized apps want to then work on common/shared files, they can still do that. You just mount the network filesystem on the host, then volume-mount that into the container's runtime. Now the containerized apps can access the network filesystem. This is standard practice in AWS ECS, where you can mount an EFS filesystem inside your running containers in ECS. (EFS is just NFS, and ECS is just a wrapper around Docker)
Tepix 1y ago
I agree with Havoc, the message is unclear: Is Apptainer a replacement for Flatpack on the desktop, or is it targeting the server?
- MillironX 1y ago
  Server - but this is kind of a wrong question. Apptainer is for running cli applications in immutable, rootless containers. The closest tool I can think of is Fedora Toolbx [1]. Apptainer is primarily used to distributing and reusing scientific computing tools b/c it doesn't allow root, doesn't allow for changes to the rootfs in each container, automatically mounts the working directory and works well with GPUs (that last point I can't personally attest to). [1]: https://docs.fedoraproject.org/en-US/fedora-silverblue/toolbox/ https://docs.fedoraproject.org/en-US/fedora-silverblue/toolb...
  - johnnyjeans 1y ago
    > Apptainer is for running cli applications in immutable, rootless containers. What's the appeal of using this over unshare + chroot to a mounted tarball with a tmpfs union mount where needed? Saner default configuration? Saner interface to cgroups?
    - lotharcable 1y ago
      Apptainer, like the vast majority of container solutions for Linux, take advantage of Linux namespaces. Which is a lot more robust and flexible then simple chroot. In Linux (docker, podman, lxc, apptainer, etc) containers are produced by combining underlying Linux features in different way. All of them use Linux namespaces. https://www.redhat.com/en/blog/7-linux-namespaces https://www.redhat.com/en/blog/7-linux-namespaces When using docker/podman/apptainer you can pick and choose when and how to use namespaces. Like I can use just use the 'mount' namespace to create a unique view of file systems, but not use the 'process', 'networking', and 'user' namespaces so that the container shares all of those things with the host OS. For example when using podman the default is to use the networking namespace so it gets its own IP address. When you are using rootless (unprivileged) mode it will use "usermode network" in the form of slirp4netns. This is good enough for most things, but it is limited and slow. Well I can turn that off. So that applications running in a podman container share the networking with the host OS. I do this for things like 'syncthing' so that the container version of that runs with the same performance as non-containered services without having to require special permissions for setting up rootful network (ie: macvlans or linux bridges with veth devices, etc) ) By default apptainer just uses mount and user namespaces. But it can take advantage of more Linux isolation features if you want it to. So the process ids, networking, and the rest of it is shared with the host OS. The mount namespace is like chroot on steroids. It is relatively trivial to break out of chroot jails. In fact it can happen accidentally. And it makes it easier to take adavantage of container image formats (like apptainer's SIF or more traditional OCI containers) This is Linux's approach as opposed to the BSD one of BSD Jails were the traditional limited Chroot feature was enhanced to make it robust.
exabrial 1y ago
Honestly switched to systemd isolation features (chroot, ro/rw mounts, etc) and never looked back.
- robertlagrant 1y ago
  How do you use them to give you portability and reproducibility of builds?
  - exabrial 1y ago
    use a proper build tool?
    - robertlagrant 1y ago
      Is...Docker one of those options?
      - exabrial 1y ago
        I mean when you download instagram does it require you to install an operating system?
amelius 1y ago
I have yet to see a container technology that doesn't break a myriad of things.
- Hilift 1y ago
  I thought the "hardened images" were a step in the right direction. It's a pain to have to deal with vulnerabilities on ephemeral short-lived containers/instances. Having something hyper up to date is welcome. https://www.docker.com/blog/introducing-docker-hardened-images/ https://www.docker.com/blog/introducing-docker-hardened-imag...
  - amelius 1y ago
    Could be, I have to see it before I believe it. This container tech is too fragile.
actinium226 1y ago
I tried looking into this, but I do development work on Mac, which is not supported, and so it became a non starter.
- thm 1y ago
  https://orbstack.dev https://orbstack.dev
- mbreese 1y ago
  See: https://apptainer.org/docs/admin/main/installation.html#mac https://apptainer.org/docs/admin/main/installation.html#mac Just like with Docker, it spins up a Linux VM that integrates with Apptainer. You can install/use it with Lima (much like Docker). You can also install it with `brew install lima` and then run `limactl start template://apptainer` to get a running Apptainer compatible VM running.
  - actinium226 1y ago
    Hm, not sure why I missed that, or maybe I didn't miss it and for some reason decided to just go with Docker. Either way thanks for pointing it out, I'll keep this in mind.
    - mbreese 1y ago
      It's not perfect... For example, I don't think there is an easy way to use Apptainer containers w/ VS Code. But it's there if you want to play with it. I was only partially aware of it as I tend to use Colima more than Lima, but have started to move towards Lima more in general. That said, I still stick to Docker-style containers personally as they are more widely supported (e.g. VS Code). However, I also work a lot in HPC, so migrating workflows cross-platform to Apptainer containers is a goal of mine.
harel 1y ago
Not a constructive comment, but I find the name "Apptainer" doesn't really work. Rolls funny on the tongue and feels just "wrong" to me.
evertheylen 1y ago
If any developers are looking to isolate different dev projects from each other using containers, I wrote a tool for it (using podman), maybe someone finds it useful or can thrash its security. Find the code on https://github.com/evertheylen/probox https://github.com/evertheylen/probox or read my blog post on https://evertheylen.eu/p/probox-intro/ https://evertheylen.eu/p/probox-intro/
- maweki 1y ago
  Why didn't toolbox fit your needs? I found toolbox to be a very reasonable way to install development dependencies on a per project basis while not managing multiple hidden filesystems.
  - evertheylen 1y ago
    toolbx is not actually intended to provide any security or isolation, see e.g. https://github.com/containers/toolbox/issues/183 https://github.com/containers/toolbox/issues/183
    - lotharcable 1y ago
      It would be more accurate to say that toolbx is based on Podman, but is intended to provide tight configuration with your user's outside environment. If you want to use toolbx for more isolation you'll have to end up turn off a bunch of features and configuring it in weird ways that ultimately defeats the purpose of having toolbx in the first place.... It is a lot easier to just to cut out the middle man and use podman directly.
      - evertheylen 1y ago
        Fully agree, that's why my python script is ultimately just a simple wrapper for podman but it makes my life a lot easier anyway.
mrbluecoat 1y ago
Great to see Apptainer getting some attention. It generally excels over other container options (like Docker and Podman) in these scenarios: - Need to run more than one activity in a single container (this is an anti-pattern in other container technologies) - HPC (and sometimes college) environments - Want single-file distribution model (although doesn't support deltas) - Cryptographically sign a SIF file without an external server - Robust GPU support
- actinium226 1y ago
  > Want single-file distribution model (although doesn't support deltas) You can achieve that with docker by `docker save image-name > image-name.tar.gz` and `docker load --input image-name.tar.gz`. It likewise doesn't support deltas but there was a link here on HN recently to something called "unregistry" which allows for doing "docker push" to deploy an image to a remote machine without a registry, and that thing does take deltas into account.
  - lotharcable 1y ago
    OCI image repositories are pretty ubiquitous nowadays and are trivial to setup. I am sure that a lot of people have them deployed and don't even realize it. If you are using Gitea, Gitlab, Github, or any of their major forks/variations of you probably already have a place to put your images. So I really don't know what the advantage of 'single file distribution model' is here. This is probably why people don't bother sharing tarballs of docker images with one another even though it is has been a option this entire time.
    - actinium226 1y ago
      If you're sharing with lots of people registries are great. If you're deploying to a server, I don't see a point in setting up a registry, regardless of how trivial it is. It seems even more trivial to just send the deployment package to the server.
      - 1y ago
0xbadcafebee 1y ago
Whoever made this is trying to sell something to people who don't know how containers work. The "encryptable" part is giving major snake oil vibes. Is there some clueless administrator somewhere demanding encryption, not really getting what it's for?
naikrovek 1y ago
Why doesn’t the OS simply provide this by default? I’ve never understood that. Process isolation should be the default. You should be able to opt out of certain parts of it as required by your application. This should not be something you add on top of the OS, nor should it be something that configures existing OS functionality for you. Isolation should be the default. Only MacOS does anything like this out of the box, that I’m aware of, and I’m not sure that it is granular enough for my liking as it is today. I often see apps asking for full disk access or local network access and deny them, because they don’t need those things, they maybe need a subset of it, but I can’t allow a subset of “full disk access” or “local network access” if the application is running as myself.
remram 1y ago
In my environment, the number one reason Apptainer is used has nothing to do with deployment, isolation, or software availability: it is to work around inode limits. On our HPC cluster, each user has a quota of inodes on the shared filesystem. This makes installing some software with lots of files problematic (like Anaconda). An Apptainer image is a single file on the filesystem though (basically squashfs) so you can have those with as many files as you want in each. Installing the same software normally is easy and works fine though, you just exchaust your quota.

123 points by cl3misch 1y ago

Flatpak considers to move from OSTree to containers, citing the well-maintained tooling as a major plus point. How would that differ from Apptainers?

Imustaskforhelp 1y ago
Maybe the idea is that flatpak can have better sandbox control over applications running in flatpak using xdg-dbus ie. you can select the permissions that you want to give to a flatpak application and so sometimes it can act near native and not be completely isolated like containers. Also I am not sure if apptainers are completely isolated. Though I suppose through tools like https://containertoolbx.org/ https://containertoolbx.org/ such point also becomes moot & then I guess if they move to container, doesn't it sort of become like toolbx? To be honest, I think a lot of tools can have a huge overlap b/w them and I guess that's okay too
- lotharcable 1y ago
  Containers in Linux are more a conceptual collection of different isolation techniques. Mostly just based on Linux namespaces. But things like cgroups, Linux capabilities, occasionally MAC (selinux, etc) and a few other items often get thrown in the mix. https://www.redhat.com/en/blog/7-linux-namespaces https://www.redhat.com/en/blog/7-linux-namespaces After a quick view of the apptainer documentation it looks like it minimally takes advantage of user and mount namespaces. So each apptainer gets its own idea of what the users/groups are and what the file system looks like. Flatpak is more about desktop application sandboxing. So while it does use user and mount namespaces like apptainer it takes advantage of more Linux features then that to help enhance the isolation. Which appears to be the opposite of the point of apptainer. Apptainer wants to use containers that integrate tightly with the rest of the system with very little isolation versus Flatpak wants to be maximally isolated with only the permissions necessary for the application. That isn't to say that apptainer can't use more Linux features to increase isolation. It supports the use of cgroups for resource quotas and can take advantage of different types of namespaces for network isolation among other things. Now as far as "OSTree vs containers" statement you are replying to... This is kinda misleading. OSTree is designed to manage binaries files in a way similar to git with text file. It isn't a type of container technology in itself. It just used for managing how objects on the file system are arranged and managed. It is used by some flatpak applications, but it is used for things besides flatpak. The 'containers' he mentioned is really a reference to OCI container image format. OCI container images is, again, a way to manage the file system contents typically used in containers. It isn't a container technology itself. It is like a tarball, but for file system images. OCI containers is a standardized version of Docker images. Due to the popularity and ubiquity of OCI image related tools and hosting software it makes sense for Flatpak to support it. OCI images, when combined with bootc, also can be used to deploy Linux container images to "bare hardware". Which is gaining popularity in helping to create and deploy "immutable" or "atomic" Linux distributions. Fedora Atomic-based OSes seem to be moving to use Bootc with OCI over pure OSTree approach... although they still use OSTree in some capacity. Incidentally Apptainer supports the use of OCI images (in addition to it's native SIF) as well as other commonly used container technologies like CNI. CNI is container network interface and is used with Kubernetes among other things.
  - Imustaskforhelp 1y ago
    Thanks a crazy lot for writing this as it actually made me genuinely understand the differences. And also, I must say that one of the most underrated parts which you told which I didn't knew about was that apptainer can be "unisolated?" ie. we don't have to do crazy shenanigans for it to access my files and it can just do it simply. Like someone else had mentioned https://nixery.dev/ https://nixery.dev/ and I wanted to see if I could use nix tools via docker and use them as if they were installed on my own system and apptainer really nailed it. I read that nixery.dev had to do some shenanigans to prevent the 150 layer or something but I suppose SIF doesn't have to deal with it so I am actually excited a little too haha. Thanks a lot!! Side Note: I think that there might be better ways to run nix apps like nix-appimage but I am just trying out things because why not. Its fun.

eisbaw 1y ago

Argh, yet another way to distribute userland images. AppImages does it right by including the run-time with the image itself - no prior installation needed. More nix less containers, btw. E.g. docker run -ti nixery.dev/shell/cowsay bash for on-the-fly containers based on Nix.

_joel 1y ago
fewer containers, surely :)
Imustaskforhelp 1y ago
Of course we ignore the taking shots at a project just for its existence thing aside I actually really like nixery.dev idea. Sounds kinda neat. If I am being really honest, there are a lot of ways to go around tbh, there are ways to run nix inside of docker and docker inside of nix too. There are ways to convert docker images into os too and there are tools like coreos. There is nix-shell and someone on hackernews told me about comma and I am still figuring out comma (haha! Thanks to them!) And if one just wants isolation, they can use bubblewrap or (pledge by jart) and I guess there is complete beauty and art in such container-esque space and I truly love this space a lot. I am actually wondering right now that using traefik (as load balancer) + nats (for a modular monolith) + podman/coreos + (cloudflare tunnels?) + any vps and you can use nix to build those containers too or you can go the other way around by having a nixos on vps with traefik + nats can be a really good alternative to kubernetes. I mean, There is docker swarm too if you don't want any of such complexity but people say that its less worked upon but still I guess there is a sort of fun in reinventing the wheel of kubernetes, but I guess I don't have tooo much problems with kubernetes I suppose because of the existence of helm charts (I haven't used kubernetes) but helm charts are written in go templates and I think they are a bit clunky but still I love golang and I feel like I would be okay with writing helm charts but I guess I am one of the people who just believes to scale horizontally first than vertically untill the economic scale gets broken and its more cheaper to use kubernetes / learn it than not.
lotharcable 1y ago
Appimage is terrible. It works by trying to make applications in appimages adhere to a lowest common denominator between Linux distros... which amounts to forcing application developers to develop for the oldest version of Linux appimage supports. Nix is a huge pain to deal with. Nix makes me think of the old Zawinski joke of: "Some people, when confronted with a problem, think 'I know, I'll use regular expressions.' Now they have two problems," Except there are less upsides for using Nix over something like OCI.

kinow 1y ago

Apptainer and singularity ce are quite common in HPC. While both implementations fork the old singularity project, they are not really identical. We use singularity in the HPCs (like Leonardo, LUMI, Fugaku, NeSI NZ, Levante) but some devs and researchers have apptainer installed locally. We found a timezone bug a few days ago in our Python code (matplotlib,xarray,etc.), but that didn't happen with apptainer. As the code bases are still a bit similar, I could confirm apptainer fixed it but singularity ce was still affected by the bug -- singularity replaces the UTC timezone file by the user's timezone, Helsinki EEST in our case in LUMI HPC. https://github.com/sylabs/singularity/issues/3686 https://github.com/sylabs/singularity/issues/3686

markus92 1y ago
Luckily they’re still compatible with each others containers. Can use Apptainer to build the container then run it on Singularity and vice-versa.
- kinow 1y ago
  Yeah, we haven't found any issues so far besides this one with time zone. Other than that, we've been able to run the same containers with both.
throw0101c 1y ago
> Apptainer and singularity ce are quite common in HPC. While both implementations fork the old singularity project, they are not really identical. Apptainer is not a fork of the old Singularity project: Apptainer is the original project, but the community voted to change its name. It also came under the umbrella of the Linux Foundation: * https://apptainer.org/news/community-announcement-20211130/ https://apptainer.org/news/community-announcement-20211130/ Sylabs (where the original Singularity author first worked) was the one that forked off the original project.
- kinow 1y ago
  Oh, that's correct. Thanks!

aa-jv 1y ago

Very interesting .. I was recently tasked with getting a bespoke AI/ML environment ready to ship/deploy to, what can only be considered, foreign environments .. and this has proven to be quite a hassle, because, of course: python. So I guess Apptainer is the solution to this use case - anyone had any experience with using it to bundle up an AI/ML application for redistribution? Thoughts/tips?

SirHumphrey 1y ago
I did start to use them for AI development on the HPC I have access to and it worked well (GPU pass-through basically automatically, the performace seemed basically the same) - but I mostly use them because I do not want to argue with administrators anymore that it's probably time they update Cuda 11.7 (as well as python 3.6) - the only version of Cuda currently installed on the cluster.
- aa-jv 1y ago
  Ah, right. So, no matter what container comes along to solve this problem, there's still the BOFH factor to deal with .. Curious though, how are you doing this work without admin privs?
  - SirHumphrey 1y ago
    It's a bit annoying, but you can install conda without admin privileges and apptainer was installed for compliance with some EuroHPC project and luckily made accessible to all users. The container allows me to have an environment where I have "root" access and can install software. The most annoying thing is not the lack of privileges, but that the compute nodes do not have internet access (because "security") beside connecting to the headnode, so there is the whole song and dance of running the container (or installing conda packages) on the headnode so I can download everything I need, then saving the state and running them on the compute node.
    - aa-jv 1y ago
      Seems to me that you might benefit from containerizing your apptainer development environment. ;) /ducks

eraser215 1y ago

[flagged]

Havoc 1y ago

Wish these sort of projects would do a better job articulating what the value proposition is over leading existing ones. Like why should I put time into learning this instead of rootless podman? Aside from this secret management thing it sounds like same feature set

v9v 1y ago
You should put time into learning this if you are going to be running HPC jobs on clusters, because some HPC clusters support this for jobs and not much else.
- tecleandor 1y ago
  So is this popular in science or data analysis / forecasting or something like that? I'm not familiar with it (I don't know if it changed names or just didn't notice)
  - misnome 1y ago
    Used to be called “Singularity”
  - v9v 1y ago
    I don't think people use it for reproducible environments on their own machines the same way Docker is sometimes used, I've mostly encountered it in academic compute clusters as a way to install the libraries/languages you're using onto the cluster in an easy to remove way. So it's popular in HPC clusters specifically and not really tied to a field of research beyond that.
  - elmolino89 1y ago
    Re science: yes and no. Meaning: the old way of compiling programs from sources on HPC systems while not dead is becoming rare. I can only speak about bioinformatics: the majority of programs one can get up and running in no time using either conda environments or apptainer containers. It may take few weeks for the brand new shiny version to get packaged by the maintainers, but this is seldom the problem. Even if you want to compile some program you will save yourself the time and frustration using either conda env or a container with a required toolchain/libraries. Even on a box with root access you need to avoid conflicting system wide installed library versions where program A requires lib version X and program B lib version Y.

IshKebab 1y ago

We tried to use this on our compute cluster for silicon design/verification. We gave up in the end and just went with the traditional TCL (now Lua) modules. The problems are: 1. You can't have apptainers that use each other. The most common case was things like Make, GCC, Git etc. If Make is in a different apptainer to GCC then it won't work because as soon as you go into Make then it can't see GCC any more. 2. It doesn't work if any of your output artefacts depend on things inside the container. For example you use your GCC apptainer to compile a program. It appears to work, but when you run it you find it actually linked to something in the apptainer that isn't visible any more. This is also a problem for C headers. 3. We had constant issues with PATH getting messed up so you can't see things outside the apptainer that should have been available. All in all it was a nice idea but ended up causing way more hassle than it was worth. It was much easier just to use an old OS (RHEL8) and get everything to work directly on that.

mbreese 1y ago
I think of using Apptainer/Singularity as more like Docker than anything else (without the full networking configs). These are all issues with traditional Docker containers as well, so I’m not sure how you were using the containers or what you were expecting. For my workflows on HPC, I use apptainers as basically drop-in replacements for Docker, and for that, they work quite well. These biggest benefit is that the containers are unprivileged. This means you can’t do a lot of things (in particular complex networking), but it also makes it much more secure for multi-tenant systems (like HPC). (I know Docker and Apptainer are slightly different beasts, but I’m speaking in broad strokes in a general sense without extra permissions).
- d3Xt3r 1y ago
  You can also run Docker itself in rootless mode[1]. And if for some reason you don't want to run Docker, you can also use Podman or Incus instead, and they both support Docker images, as well as running unpriviliged. Finally, there's also Flox[2], which is a Nix-based application Sandbox, that I believe would align more towards your (and OP's) use case (unless you specifically require Docker image compatibility). So unfortunately your example doesn't illustrate why Apptainer is a better option. [1] https://docs.docker.com/engine/security/rootless/ https://docs.docker.com/engine/security/rootless/ [2] https://flox.dev/ https://flox.dev/

mrweasel 1y ago

To some extend I understand the problem that these solution are trying to address, I'm just not sure that simply stuff things into containers is really the right solution. Perhaps the problems need to be addressed on a more fundamental level.

whatagreatboy 1y ago
https://dl.acm.org/doi/10.1145/3126908.3126925 https://dl.acm.org/doi/10.1145/3126908.3126925 This paper might help

DrNosferatu 1y ago

It is very handy in SLURM clusters and servers where you have no sudo. Some attrition using it though: is there a good in-depth book about it?

floro 1y ago
I used it on a SLURM cluster before. The documentation is done well and should be a good introduction. The only issue I had was that the cluster didn't have fakeroot or sudo, so I had to build the apptainer locally and transfer it to the server.
- DrNosferatu 1y ago
  Exactly: in most HPC clusters / servers one has no sudo.

cs_throwaway 1y ago

Funny this is here. Apptainer is Singularity, described here: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177459 https://journals.plos.org/plosone/article?id=10.1371/journal... If you ever use a shared cluster at a university or run by the government, Apptainer will be available, and Podman / Docker likely won't be. In these environments, it is best not to use containers at all, and instead get to know your sysadmin and understand how he expects the cluster to be used.

shortrounddev2 1y ago
Why are docker/podman less common? And why do you say it's better not to use containers? Performance?
- kgxohxkhclhc 1y ago
  docker and podman expect to extract images to disk, then use fancy features like overlayfs, which doesn't work on network filesystems -- and in hpc, most filesystems users can write to persistently are network filesystems. apptainer images are straight filesystem images with no overlayfs or storage driver magic happening -- just a straight loop mount of a disk image. this means your container images can now live on your network filesystem.
  - 0xbadcafebee 1y ago
    Do the compute instances not have hard disks? Because it seems like whoever's running these systems doesn't understand Linux or containers all that well. If there's a hard disk on the compute nodes, then you just run the container from the remote image registry, and it downloads and extracts it temporarily to disk. No need for a network filesystem. If the containerized apps want to then work on common/shared files, they can still do that. You just mount the network filesystem on the host, then volume-mount that into the container's runtime. Now the containerized apps can access the network filesystem. This is standard practice in AWS ECS, where you can mount an EFS filesystem inside your running containers in ECS. (EFS is just NFS, and ECS is just a wrapper around Docker)

Tepix 1y ago

I agree with Havoc, the message is unclear: Is Apptainer a replacement for Flatpack on the desktop, or is it targeting the server?

MillironX 1y ago
Server - but this is kind of a wrong question. Apptainer is for running cli applications in immutable, rootless containers. The closest tool I can think of is Fedora Toolbx [1]. Apptainer is primarily used to distributing and reusing scientific computing tools b/c it doesn't allow root, doesn't allow for changes to the rootfs in each container, automatically mounts the working directory and works well with GPUs (that last point I can't personally attest to). [1]: https://docs.fedoraproject.org/en-US/fedora-silverblue/toolbox/ https://docs.fedoraproject.org/en-US/fedora-silverblue/toolb...
- johnnyjeans 1y ago
  > Apptainer is for running cli applications in immutable, rootless containers. What's the appeal of using this over unshare + chroot to a mounted tarball with a tmpfs union mount where needed? Saner default configuration? Saner interface to cgroups?
  - lotharcable 1y ago
    Apptainer, like the vast majority of container solutions for Linux, take advantage of Linux namespaces. Which is a lot more robust and flexible then simple chroot. In Linux (docker, podman, lxc, apptainer, etc) containers are produced by combining underlying Linux features in different way. All of them use Linux namespaces. https://www.redhat.com/en/blog/7-linux-namespaces https://www.redhat.com/en/blog/7-linux-namespaces When using docker/podman/apptainer you can pick and choose when and how to use namespaces. Like I can use just use the 'mount' namespace to create a unique view of file systems, but not use the 'process', 'networking', and 'user' namespaces so that the container shares all of those things with the host OS. For example when using podman the default is to use the networking namespace so it gets its own IP address. When you are using rootless (unprivileged) mode it will use "usermode network" in the form of slirp4netns. This is good enough for most things, but it is limited and slow. Well I can turn that off. So that applications running in a podman container share the networking with the host OS. I do this for things like 'syncthing' so that the container version of that runs with the same performance as non-containered services without having to require special permissions for setting up rootful network (ie: macvlans or linux bridges with veth devices, etc) ) By default apptainer just uses mount and user namespaces. But it can take advantage of more Linux isolation features if you want it to. So the process ids, networking, and the rest of it is shared with the host OS. The mount namespace is like chroot on steroids. It is relatively trivial to break out of chroot jails. In fact it can happen accidentally. And it makes it easier to take adavantage of container image formats (like apptainer's SIF or more traditional OCI containers) This is Linux's approach as opposed to the BSD one of BSD Jails were the traditional limited Chroot feature was enhanced to make it robust.

exabrial 1y ago

Honestly switched to systemd isolation features (chroot, ro/rw mounts, etc) and never looked back.

robertlagrant 1y ago
How do you use them to give you portability and reproducibility of builds?
- exabrial 1y ago
  use a proper build tool?
  - robertlagrant 1y ago
    Is...Docker one of those options?
    - exabrial 1y ago
      I mean when you download instagram does it require you to install an operating system?

amelius 1y ago

I have yet to see a container technology that doesn't break a myriad of things.

Hilift 1y ago
I thought the "hardened images" were a step in the right direction. It's a pain to have to deal with vulnerabilities on ephemeral short-lived containers/instances. Having something hyper up to date is welcome. https://www.docker.com/blog/introducing-docker-hardened-images/ https://www.docker.com/blog/introducing-docker-hardened-imag...
- amelius 1y ago
  Could be, I have to see it before I believe it. This container tech is too fragile.

actinium226 1y ago

I tried looking into this, but I do development work on Mac, which is not supported, and so it became a non starter.

thm 1y ago
https://orbstack.dev https://orbstack.dev
mbreese 1y ago
See: https://apptainer.org/docs/admin/main/installation.html#mac https://apptainer.org/docs/admin/main/installation.html#mac Just like with Docker, it spins up a Linux VM that integrates with Apptainer. You can install/use it with Lima (much like Docker). You can also install it with `brew install lima` and then run `limactl start template://apptainer` to get a running Apptainer compatible VM running.
- actinium226 1y ago
  Hm, not sure why I missed that, or maybe I didn't miss it and for some reason decided to just go with Docker. Either way thanks for pointing it out, I'll keep this in mind.
  - mbreese 1y ago
    It's not perfect... For example, I don't think there is an easy way to use Apptainer containers w/ VS Code. But it's there if you want to play with it. I was only partially aware of it as I tend to use Colima more than Lima, but have started to move towards Lima more in general. That said, I still stick to Docker-style containers personally as they are more widely supported (e.g. VS Code). However, I also work a lot in HPC, so migrating workflows cross-platform to Apptainer containers is a goal of mine.

harel 1y ago

Not a constructive comment, but I find the name "Apptainer" doesn't really work. Rolls funny on the tongue and feels just "wrong" to me.

evertheylen 1y ago

If any developers are looking to isolate different dev projects from each other using containers, I wrote a tool for it (using podman), maybe someone finds it useful or can thrash its security. Find the code on https://github.com/evertheylen/probox https://github.com/evertheylen/probox or read my blog post on https://evertheylen.eu/p/probox-intro/ https://evertheylen.eu/p/probox-intro/

maweki 1y ago
Why didn't toolbox fit your needs? I found toolbox to be a very reasonable way to install development dependencies on a per project basis while not managing multiple hidden filesystems.
- evertheylen 1y ago
  toolbx is not actually intended to provide any security or isolation, see e.g. https://github.com/containers/toolbox/issues/183 https://github.com/containers/toolbox/issues/183
  - lotharcable 1y ago
    It would be more accurate to say that toolbx is based on Podman, but is intended to provide tight configuration with your user's outside environment. If you want to use toolbx for more isolation you'll have to end up turn off a bunch of features and configuring it in weird ways that ultimately defeats the purpose of having toolbx in the first place.... It is a lot easier to just to cut out the middle man and use podman directly.
    - evertheylen 1y ago
      Fully agree, that's why my python script is ultimately just a simple wrapper for podman but it makes my life a lot easier anyway.

mrbluecoat 1y ago

Great to see Apptainer getting some attention. It generally excels over other container options (like Docker and Podman) in these scenarios: - Need to run more than one activity in a single container (this is an anti-pattern in other container technologies) - HPC (and sometimes college) environments - Want single-file distribution model (although doesn't support deltas) - Cryptographically sign a SIF file without an external server - Robust GPU support

actinium226 1y ago
> Want single-file distribution model (although doesn't support deltas) You can achieve that with docker by `docker save image-name > image-name.tar.gz` and `docker load --input image-name.tar.gz`. It likewise doesn't support deltas but there was a link here on HN recently to something called "unregistry" which allows for doing "docker push" to deploy an image to a remote machine without a registry, and that thing does take deltas into account.
- lotharcable 1y ago
  OCI image repositories are pretty ubiquitous nowadays and are trivial to setup. I am sure that a lot of people have them deployed and don't even realize it. If you are using Gitea, Gitlab, Github, or any of their major forks/variations of you probably already have a place to put your images. So I really don't know what the advantage of 'single file distribution model' is here. This is probably why people don't bother sharing tarballs of docker images with one another even though it is has been a option this entire time.
  - actinium226 1y ago
    If you're sharing with lots of people registries are great. If you're deploying to a server, I don't see a point in setting up a registry, regardless of how trivial it is. It seems even more trivial to just send the deployment package to the server.
    - 1y ago

0xbadcafebee 1y ago

Whoever made this is trying to sell something to people who don't know how containers work. The "encryptable" part is giving major snake oil vibes. Is there some clueless administrator somewhere demanding encryption, not really getting what it's for?

naikrovek 1y ago

Why doesn’t the OS simply provide this by default? I’ve never understood that. Process isolation should be the default. You should be able to opt out of certain parts of it as required by your application. This should not be something you add on top of the OS, nor should it be something that configures existing OS functionality for you. Isolation should be the default. Only MacOS does anything like this out of the box, that I’m aware of, and I’m not sure that it is granular enough for my liking as it is today. I often see apps asking for full disk access or local network access and deny them, because they don’t need those things, they maybe need a subset of it, but I can’t allow a subset of “full disk access” or “local network access” if the application is running as myself.

remram 1y ago

In my environment, the number one reason Apptainer is used has nothing to do with deployment, isolation, or software availability: it is to work around inode limits. On our HPC cluster, each user has a quota of inodes on the shared filesystem. This makes installing some software with lots of files problematic (like Anaconda). An Apptainer image is a single file on the filesystem though (basically squashfs) so you can have those with as many files as you want in each. Installing the same software normally is easy and works fine though, you just exchaust your quota.