OCI Containers

This document shows how to build Fossil into OCI compatible containers and how to use those containers in interesting ways. We start off using the original and still most popular container development and runtime platform, Docker, but since you have more options than that, we will show some of these options later on.

1. Quick Start

Fossil ships a Dockerfile at the top of its source tree which you can build like so:

  $ docker build -t fossil .

If the image built successfully, you can create a container from it and test that it runs:

  $ docker run --name fossil -p 9999:8080/tcp fossil

This shows us remapping the internal TCP listening port as 9999 on the host. This feature of OCI runtimes means there’s little point to using the “fossil server --port” feature inside the container. We can let Fossil default to 8080 internally, then remap it to wherever we want it on the host instead.

Our stock Dockerfile configures Fossil with the default feature set, so you may wish to modify the Dockerfile to add configuration options, add APK packages to support those options, and so forth. It also strips out all but the default and darkmode skins to save executable space.

The Fossil Makefile provides two convenience targets, “make container-image” and “make container-run”. The first creates a versioned container image, and the second does that and then launches a fresh container based on that image. You can pass extra arguments to the first command via the Makefile’s DBFLAGS variable and to the second with the DRFLAGS variable. (DB is short for “docker build”, and DR is short for “docker run”.) To get the custom port setting as in second command above, say:

  $ make container-run DRFLAGS='-p 9999:8080/tcp'

Contrast the raw “docker” commands above, which create an unversioned image called fossil:latest and from that a container simply called fossil. The unversioned names are more convenient for interactive use, while the versioned ones are good for CI/CD type applications since they avoid a conflict with past versions; it lets you keep old containers around for quick roll-backs while replacing them with fresh ones.

2. Repository Storage Options

If you want the container to serve an existing repository, there are at least two right ways to do it.

The wrong way is to use the Dockerfile COPY command, because by baking the repo into the image at build time, it will become one of the image’s base layers. The end result is that each time you build a container from that image, the repo will be reset to its build-time state. Worse, restarting the container will do the same thing, since the base image layers are immutable in Docker. This is almost certainly not what you want.

The correct ways put the repo into the container created from the image, not in the image itself.

2.1 Storing the Repo Inside the Container

The simplest method is to stop the container if it was running, then say:

  $ docker cp /path/to/my-project.fossil fossil:/jail/museum/repo.fossil
  $ docker start fossil
  $ docker exec fossil chown -R 499 /jail/museum

That copies the local Fossil repo into the container where the server expects to find it, so that the “start” command causes it to serve from that copied-in file instead. Since it lives atop the immutable base layers, it persists as part of the container proper, surviving restarts.

Notice that the copy command changes the name of the repository database. The container configuration expects it to be called repo.fossil, which it almost certainly was not out on the host system. This is because there is only one repository inside this container, so we don’t have to name it after the project it contains, as is traditional. A generic name lets us hard-code the server start command.

If you skip the “chown” command above and put “http://localhost:9999/” into your browser, expecting to see the copied-in repo’s home page, you will get an opaque “Not Found” error. This is because the user and group ID of the file will be that of your local user on the container’s host machine, which is unlikely to map to anything in the container’s /etc/passwd and /etc/group files, effectively preventing the server from reading the copied-in repository file. 499 is the default “fossil” user ID inside the container, causing Fossil to run with that user’s privileges after it enters the chroot. (See below for how to change this default.) You don’t have to restart the server after fixing this with chmod: simply reload the browser, and Fossil will try again.

2.2 Storing the Repo Outside the Container

The simple storage method above has a problem: Docker containers are designed to be killed off at the slightest cause, rebuilt, and redeployed. If you do that with the repo inside the container, it gets destroyed, too. The solution is to replace the “run” command above with the following:

  $ docker run \
    --publish 9999:8080 \
    --name fossil-bind-mount \
    --volume ~/museum:/jail/museum \

Because this bind mount maps a host-side directory (~/museum) into the container, you don’t need to docker cp the repo into the container at all. It still expects to find the repository as repo.fossil under that directory, but now both the host and the container can see that repo DB.

Instead of a bind mount, you could instead set up a separate Docker volume, at which point you would need to docker cp the repo file into the container.

Either way, files in these mounted directories have a lifetime independent of the container(s) they’re mounted into. When you need to rebuild the container or its underlying image — such as to upgrade to a newer version of Fossil — the external directory remains behind and gets remapped into the new container when you recreate it with --volume/-v.

2.2.1 WAL Mode Interactions

You might be aware that OCI containers allow mapping a single file into the repository rather than a whole directory. Since Fossil repositories are specially-formatted SQLite databases, you might be wondering why we don’t say things like:

  --volume ~/museum/my-project.fossil:/jail/museum/repo.fossil

That lets us have a convenient file name for the project outside the container while letting the configuration inside the container refer to the generic “/museum/repo.fossil” name. Why should we have to name the repo generically on the outside merely to placate the container?

The reason is, you might be serving that repo with WAL mode enabled. If you map the repo DB alone into the container, the Fossil instance inside the container will write the -journal and -wal files alongside the mapped-in repository inside the container. That’s fine as far as it goes, but if you then try using the same repo DB from outside the container while there’s an active WAL, the Fossil instance outside won’t know about it. It will think it needs to write its own -journal and -wal files outside the container, creating a high risk of database corruption.

If we map a whole directory, both sides see the same set of WAL files, so there is at least a hope that WAL will work properly across that boundary. The success of the scheme depends on the mmap() and shared memory system calls being coordinated properly by the OS kernel the two worlds share.

There is a plan for proving to a reasonable level of confidence that using WAL across a container boundary is safe, but this effort is still in the early stages as of this writing.

Until that’s settled, my advice to those who want to use WAL mode on containerized servers is to map the whole directory as shown in these examples, but then isolate the two sides with a secondary clone. On the outside, you say something like this:

  $ fossil clone ~/museum/myproject.fossil

That lands you with two side-by-side clones of the repository on the server:

  ~/museum/myproject.fossil          ← local-use clone
  ~/museum/myproject/repo.fossil     ← served by container only

You open the secondary clone for local use, not the one being served by the container. When you commit, Fossil’s autosync feature pushes the change up through the HTTPS link to land safely inside the container.

3. Security

3.1 Why Chroot?

A potentially surprising feature of this container is that it runs Fossil as root. Since that causes the chroot jail feature to kick in, and a Docker container is a type of über-jail already, you may be wondering why we bother. Instead, why not either:

The reason is, although this container is quite stripped-down by today’s standards, it’s based on the surprisingly powerful Busybox project. (This author made a living for years in the early 1990s using Unix systems that were less powerful than this container.) If someone ever figured out how to make a Fossil binary execute arbitrary commands on the host or to open up a remote shell, the power available to them at that point would make it likely that they’d be able to island-hop from there into the rest of your network. That power is there for you as the system administrator alone, to let you inspect the container’s runtime behavior, change things on the fly, and so forth. Fossil proper doesn’t need that power; if we take it away via this cute double-jail dance, we keep any potential attacker from making use of it should they ever get in.

Having said this, know that we deem this risk low since a) it’s never happened, that we know of; and b) we haven’t enabled any of the risky features of Fossil such as TH1 docs. Nevertheless, we believe defense-in-depth strategies are wise.

If you say something like “docker exec fossil ps” while the system is idle, it’s likely to report a single fossil process running as root even though the chroot feature is documented as causing Fossil to drop its privileges in favor of the owner of the repository database or its containing folder. If the repo file is owned by the in-container user “fossil”, why is the server still running as root?

It’s because you’re seeing only the parent process, which assumes it’s running on bare metal or a VM and thus may need to do rootly things like listening on port 80 or 443 before forking off any children to handle HTTP hits. Fossil’s chroot feature only takes effect in these child processes. This is why you can fix broken permissions with chown after the container is already running, without restarting it: each hit reevaluates the repository file permissions when deciding what user to become when dropping root privileges.

3.2 Dropping Unnecessary Capabilities

The example commands above create the container with a default set of Linux kernel capabilities. Although Docker strips away almost all of the traditional root capabilities by default, and Fossil doesn’t need any of those it does take away, Docker does leave some enabled that Fossil doesn’t actually need. You can tighten the scope of capabilities by adding “--cap-drop” options to your container creation commands.


All together, we recommend adding the following options to your “docker run” commands, as well as to any “docker create” command that will be followed by “docker start”:

  --cap-drop AUDIT_WRITE \
  --cap-drop CHOWN \
  --cap-drop FSETID \
  --cap-drop KILL \
  --cap-drop MKNOD \
  --cap-drop NET_BIND_SERVICE \
  --cap-drop NET_RAW \
  --cap-drop SETFCAP \
  --cap-drop SETPCAP

In the next section, we’ll show a case where you create a container without ever running it, making these options pointless.

4. Extracting a Static Binary

Our 2-stage build process uses Alpine Linux only as a build host. Once we’ve got everything reduced to the two key static binaries — Fossil and BusyBox — we throw all the rest of it away.

A secondary benefit falls out of this process for free: it’s arguably the easiest way to build a purely static Fossil binary for Linux. Most modern Linux distros make this surprisingly difficult, but Alpine’s back-to-basics nature makes static builds work the way they used to, back in the day. If that’s all you’re after, you can do so as easily as this:

  $ docker build -t fossil .
  $ docker create --name fossil-static-tmp fossil
  $ docker cp fossil-static-tmp:/jail/bin/fossil .
  $ docker container rm fossil-static-tmp

The resulting binary is the single largest file inside that container, at about 4 MiB. (It’s built stripped and packed with UPX.)

5. Container Build Arguments

5.1 Package Versions

You can override the default versions of Fossil and BusyBox that get fetched in the build step. To get the latest-and-greatest of everything, you could say:

  $ docker build -t fossil \
    --build-arg FSLVER=trunk \
    --build-arg BBXVER=master .

(But don’t, for reasons we will get to.)

Because the BusyBox configuration file we ship was created with and tested against a specific stable release, that’s the version we pull by default. It does try to merge the defaults for any new configuration settings into the stock set, but since it’s possible this will fail, we don’t blindly update the BusyBox version merely because a new release came out. Someone needs to get around to vetting it against our stock configuration first.

As for Fossil, it defaults to fetching the same version as the checkout you’re running the build command from, based on checkin ID. The most common reason to override this is to get a release version:

  $ docker build -t fossil \
    --build-arg FSLVER=version-2.19 .

It’s best to use a specific version number rather than the generic “release” tag because Docker caches downloaded files and tries to reuse them across builds. If you ask for “release” before a new version is tagged and then immediately after, you might expect to get two different tarballs, but because the URL hasn’t changed, if you have an old release tarball in your Docker cache, you’ll get the old version even if you pass the “docker build --no-cache” option.

This is why we default to pulling the Fossil tarball by checkin ID rather than let it default to the generic “trunk” tag: so the URL will change each time you update your Fossil source tree, forcing Docker to pull a fresh tarball.

5.2 User & Group IDs

The “fossil” user and group IDs inside the container default to 499. Why? Regular user IDs start at 500 or 1000 on most Unix type systems, leaving those below it for system users like this Fossil daemon owner. Since it’s typical for these to start at 0 and go upward, we started at 500 and went down one instead to reduce the chance of a conflict to as close to zero as we can manage.

To change it to something else, say:

  $ docker build -t fossil --build-arg UID=501 .

This is particularly useful if you’re putting your repository on a Docker volume since the IDs “leak” out into the host environment via file permissions. You may therefore wish them to mean something on both sides of the container barrier rather than have “499” appear on the host in “ls -l” output.

6. Lightweight Alternatives to Docker

Those afflicted with sticker shock at seeing the size of a Docker Desktop installation — 1.65 GB here — might’ve immediately “noped” out of the whole concept of containers. The first thing to realize is that when it comes to actually serving simple containers like the ones shown above is that Docker Engine suffices, at about a quarter of the size.

Yet on a small server — say, a $4/month 10 GiB Digital Ocean droplet — that’s still a big chunk of your storage budget. It takes 100:1 overhead just to run a 4 MiB Fossil server container? Once again, I wouldn’t blame you if you noped right on out of here, but if you will be patient, you will find that there are ways to run Fossil inside a container even on entry-level cloud VPSes. These are well-suited to running Fossil; you don’t have to resort to raw Fossil service to succeed, leaving the benefits of containerization to those with bigger budgets.

For the sake of simple examples in this section, we’ll assume you’re integrating Fossil into a larger web site, such as with our Debian + nginx + TLS plan. This is why all of the examples below create the container with this option:


The assumption is that there’s a reverse proxy running somewhere that redirects public web hits to localhost port 9999, which in turn goes to port 8080 inside the container. This use of Docker/Podman port publishing effectively replaces the use of the “fossil server --localhost” option.

For the nginx case, you need to add --scgi to these commands, and you might also need to specify --baseurl.

Containers are a fine addition to such a scheme as they isolate the Fossil sections of the site from the rest of the back-end resources, thus greatly reducing the chance that they’ll ever be used to break into the host as a whole.

(If you wanted to be double-safe, you could put the web server into another container, restricting it to reading from the static web site directory and connecting across localhost to back-end dynamic content servers such as Fossil. That’s way outside the scope of this document, but you can find ready advice for that elsewhere. Seeing how we do this with Fossil should help you bridge the gap in extending this idea to the rest of your site.)

6.1 Stripping Docker Engine Down

The core of Docker Engine is its containerd daemon and the runc container runner. Add to this the out-of-core CLI program nerdctl and you have enough of the engine to run Fossil containers. The big things you’re missing are:

In exchange, you get a runtime that’s about half the size of Docker Engine. The commands are essentially the same as above, but you say “nerdctl” instead of “docker”. You might alias one to the other, because you’re still going to be using Docker to build and ship your container images.

6.2 Podman

A lighter-weight alternative to either of the prior options that doesn’t give up the image builder is Podman. Initially created by Red Hat and thus popular on that family of OSes, it will run on any flavor of Linux. It can even be made to run on macOS via Homebrew or on Windows via WSL2.

On Ubuntu 22.04, it’s about a quarter the size of Docker Engine, or half that of the “full” distribution of nerdctl and all its dependencies.

Although Podman bills itself as a drop-in replacement for the docker command and everything that sits behind it, some of the tool’s design decisions affect how our Fossil containers run, as compared to using Docker. The most important of these is that, by default, Podman wants to run your container “rootless,” meaning that it runs as a regular user. This is generally better for security, but we dealt with that risk differently above already. Since neither choice is unassailably correct in all conditions, we’ll document both options here.

6.2.1 Fossil in a Rootless Podman Container

If you build the stock Fossil container under podman, it will fail at two key steps:

  1. The mknod calls in the second stage, which create the /jail/dev nodes. For a rootless container, we want it to use the “real” /dev tree mounted into the container’s root filesystem instead.

  2. Anything that depends on the /jail directory and the fact that it becomes the file system’s root once the Fossil server is up and running.

The changes to fix this aren’t complicated. Simply apply that patch to our stock Dockerfile and rebuild:

  $ patch -p0 < containers/Dockerfile-nojail.patch
  $ docker build -t fossil:nojail .
  $ docker create \
    --name fossil-nojail \
    --publish \
    --volume ~/museum:/museum \

Do realize that by doing this, if an attacker ever managed to get shell access on your container, they’d have a BusyBox installation to play around in. That shouldn’t be enough to let them break out of the container entirely, but they’ll have powerful tools like wget, and they’ll be connected to the network the container runs on. Once the bad guy is inside the house, he doesn’t necessarily have to go after the residents directly to cause problems for them.

6.2.2 Fossil in a Rootful Podman Container

Simple Method

Fortunately, it’s easy enough to have it both ways. Simply run your podman commands as root:

  $ sudo podman build -t fossil --cap-add MKNOD .
  $ sudo podman create \
    --name fossil \
    --cap-drop CHOWN \
    --cap-drop FSETID \
    --cap-drop KILL \
    --cap-drop NET_BIND_SERVICE \
    --cap-drop SETFCAP \
    --cap-drop SETPCAP \
    --publish \
  $ sudo podman start fossil

It’s obvious why we have to start the container as root, but why create and build it as root, too? Isn’t that a regression from the modern practice of doing as much as possible with a normal user?

We have to do the build under sudo in part because we’re doing rootly things with the file system image layers we’re building up. Just because it’s done inside a container runtime’s build environment doesn’t mean we can get away without root privileges to do things like create the /jail/dev/null node.

The other reason we need “sudo podman build” is because it puts the result into root’s Podman image registry, where the next steps look for it.

That in turn explains why we need “sudo podman create:” because it’s creating a container based on an image that was created by root. If you ran that step without sudo, it wouldn’t be able to find the image.

If Docker is looking better and better to you as a result of all this, realize that it’s doing the same thing. It just hides it better by creating the docker group, so that when your user gets added to that group, you get silent root privilege escalation on your build machine. This is why Podman defaults to rootless containers. If you can get away with it, it’s a better way to work. We would not be recommending running podman under sudo if it didn’t buy us something we wanted badly.

Notice that we had to add the ability to run mknod(8) during the build. Podman sensibly denies this by default, which lets us leave off the corresponding --cap-drop option. Podman also denies CAP_NET_RAW and CAP_AUDIT_WRITE by default, which we don’t need, so we’ve simply removed them from the --cap-drop list relative to the commands for Docker above.

Building Under Docker, Running Under Podman

If you have a remote host where the Fossil instance needs to run, it’s possible to get around this need to build the image as root on the remote system. You still have to build as root on the local system, but as I said above, Docker already does this. What we’re doing is shifting the risk of running as root from the public host to the local one.

Once you have the image built on the local machine, create a “fossil” repository on your container repository of choice such as Docker Hub, then say:

  $ docker login
  $ docker tag fossil:latest mydockername/fossil:latest
  $ docker image push mydockername/fossil:latest

That will push the image up to your account, so that you can then switch to the remote machine and say:

  $ sudo podman create \
    --any-options-you-like \

This round-trip through the public image registry has another side benefit: your local system might be a lot faster than your remote one, as when the remote is a small VPS. Even with the overhead of schlepping container images across the Internet, it can be a net win in terms of build time.

6.3 Bare-Bones OCI Bundle Runners

If even the Podman stack is too big for you, you still have options for running containers that are considerably slimmer, at a high cost to administration complexity and loss of features.

Part of the OCI standard is the notion of a “bundle,” being a consistent way to present a pre-built and configured container to the runtime. Essentially, it consists of a directory containing a config.json file and a rootfs/ subdirectory containing the root filesystem image. Many tools can produce these for you. We’ll show only one method in the first section below, then reuse that in the following sections.

6.3.1 runc

We mentioned runc above, but it’s possible to use it standalone, without containerd or its CLI frontend nerdctl. You also lose the build engine, intelligent image layer sharing, image registry connections, and much more. The plus side is that runc alone is 18 MiB.

Using it without all the support tooling isn’t complicated, but it is cryptic enough to want a shell script. Let’s say we want to build on our big desktop machine but ship the resulting container to a small remote host. This should serve:

#!/bin/bash -ex
t=$(mktemp -d /tmp/$c-bundle.XXXXXX)

if [ -d "$t" ]
    docker container start  $c
    docker container export $c > $t/rootfs.tar
    id=$(docker inspect --format="{{.Id}}" $c)
    sudo cat $m/$id/config.json \
        | jq '.root.path = "'$b/rootfs'"'
        | jq '.linux.cgroupsPath = ""'
        | jq 'del(.linux.sysctl)'
        | jq 'del(.linux.namespaces[] | select(.type == "network"))'
        | jq 'del(.mounts[] | select(.destination == "/etc/hostname"))'
        | jq 'del(.mounts[] | select(.destination == "/etc/resolv.conf"))'
        | jq 'del(.mounts[] | select(.destination == "/etc/hosts"))'
        | jq 'del(.hooks)' > $t/config.json
    scp -r $t $h:tmp
    ssh -t $h "{
        mv ./$t/config.json $b &&
        sudo tar -C $b/rootfs -xf ./$t/rootfs.tar &&
        rm -r ./$t
    rm -r $t

The first several lines list configurables:

Why All That sudo Stuff?

This script uses sudo for two different purposes:

  1. To read the local config.json file out of the containerd managed directory, which is owned by root on Docker systems. Additionally, that input file is only available while the container is started, so we must ensure that before extracting it.

  2. To unpack the bundle onto the remote machine. If you try to get clever and unpack it locally, then rsync it to the remote host to avoid re-copying files that haven’t changed since the last update, you’ll find that it fails when it tries to copy device nodes, to create files owned only by the remote root user, and so forth. If the container bundle is small, it’s simpler to re-copy and unpack it fresh each time.

I point all this out because it might ask for your password twice: once for the local sudo command, and once for the remote.

Why All That jq Stuff?

We’re using jq for two separate purposes:

  1. To automatically transmogrify Docker’s container configuration so it will work with runc:

    • point it where we unpacked the container’s exported rootfs
    • accede to its wish to manage cgroups by itself
    • remove the sysctl calls that will break after…
    • …we remove the network namespace to allow Fossil’s TCP listening port to be available on the host; runc doesn’t offer the equivalent of docker create --publish, and we can’t be bothered to set up a manual mapping from the host port into the container
    • remove file bindings that point into the local runtime managed directories; one of the things we give up by using a bare container runner is automatic management of these files
    • remove the hooks for essentially the same reason
  2. To make the Docker-managed machine-readable config.json more human-readable, in case there are other things you want changed in this version of the container. Exposing the config.json file like this means you don’t have to rebuild the container merely to change a value like a mount point, the kernel capability set, and so forth.

Running the Bundle

With the container exported to a bundle like this, you can start it as:

  $ cd /path/to/bundle
  $ c=fossil-runc            ← …or anything else you prefer
  $ sudo runc create $c
  $ sudo runc start  $c
  $ sudo runc exec $c -t sh -l
  ~ $ ls museum
  ~ $ ps -eaf
      1 fossil    0:00 bin/fossil server --create …
  ~ $ exit
  $ sudo runc kill $c
  $ sudo runc delete $c

If you’re doing this on the export host, the first command is “cd $b” if we’re using the variables from the shell script above. Alternately, the runc subcommands that need to read the bundle files take a --bundle/-b flag to let you avoid switching directories.

The rest should be straightforward: create and start the container as root so the chroot(2) call inside the container will succeed, then get into it with a login shell and poke around to prove to ourselves that everything is working properly. It is. Yay!

The remaining commands show shutting the container down and destroying it, simply to show how these commands change relative to using the Docker Engine commands. It’s “kill,” not “stop,” and it’s “delete,” not “rm.”

Lack of Layer Sharing

The bundle export process collapses Docker’s union filesystem down to a single layer. Atop that, it makes all files mutable.

All of this is fine for tiny remote hosts with a single container, or at least one where none of the containers share base layers. Where it becomes a problem is when you have multiple Fossil containers on a single host, since they all derive from the same base image.

The full-featured container runtimes above will intelligently share these immutable base layers among the containers, storing only the differences in each individual container. More, when pulling images from a registry host, they’ll transfer only the layers you don’t have copies of locally, so you don’t have to burn bandwidth sending copies of Alpine and BusyBox each time, even though they’re unlikely to change from one build to the next.

6.3.2 crun

In the same way that Docker Engine is based on runc, Podman’s engine is based on crun, a lighter-weight alternative to runc. It’s only 1.4 MiB on the system I tested it on, yet it will run the same container bundles as in my runc examples above. We saved more than that by compressing the container’s Fossil executable with UPX, making the runtime virtually free in this case. The only question is whether you can put up with its limitations, which are the same as for runc.

6.3.3 systemd-nspawn

As of systemd version 242, its optional nspawn piece reportedly got the ability to run OCI bundles directly. You might have it installed already, but if not, it’s only about 2 MiB. It’s in the systemd-containers package as of Ubuntu 22.04 LTS:

  $ sudo apt install systemd-containers

It’s also in CentOS Stream 9, under the same name.

You create the bundles the same way as with the runc method above. The only thing that changes are the top-level management commands:

  $ sudo systemd-nspawn \
    --oci-bundle=/var/lib/machines/fossil \
    --machine=fossil \
    --network-veth \
  $ sudo machinectl list
  No machines.

This is why I wrote “reportedly” above: I couldn’t get it to work on two different Linux distributions, and I can’t see why. I’m leaving this here to give someone else a leg up, with the hope that they will work out what’s needed to get the container running and registered with machinectl.

As of this writing, the tool expects an OCI container version of “1.0.0”. I had to edit this at the top of my config.json file to get the first command to read the bundle. The fact that it errored out when I had “1.0.2-dev” in there proves it’s reading the file, but it doesn’t seem able to make sense of what it finds there, and it doesn’t give any diagnostics to say why.