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Thinking more about backups

2025-11-01T00:00:00Z

The Backblaze logo

Almost a year ago I wrote about how I do backups with Restic and Hetzner. That system has been ticking along well ever since, but recently I had some… thoughts. These backups are all well and good if I accidentally delete a file, or a database gets corrupted, or something, but there are two glaring issues:

Firstly, I’m backing up my Hetzner server to Hetzner cloud storage. If something happens to Hetzner — or my Hetzner account — then all my eggs go down with that basket. Obviously Hetzner are a big organisation and aren’t likely to just vanish overnight, but I’m less confident about my account. Could a false abuse report get it suspended? What if the UK passes even more dumb laws and Hetzner decide it’s easier just to not do business with people here? This is the same sort of concern I have about Google accounts: if you have half of your life in Google Drive and Google Mail, what happens if you comment on a YouTube video, get flagged by an AI moderation process, and your account gets suspended? It’s probably not very likely, but these are things my brain likes to dwell on.

Secondly, the credentials to access the backups sit on each machine that is backed up. If someone malicious gained access to the machine, they’d also have access to delete or tamper with all the backups. It feels a little silly that the same attack could take down both the originals and the backups. There’s no way to avoid that with Hetzner’s S3 implementation, as far as I can tell.

Exploring options

I toyed with the idea of making local copies of the backups, but the only way to avoid the same problems would be to keep them offline and do a manual copy every now and then. I didn’t really want to do that, and was concerned that if I did a monthly offline backup then I stood to lose up to a month of data in the worst case.

I then looked around at other S3 providers. Amazon’s glacier offering is tempting due to its very low storage costs, but you pay for that if you ever want to restore anything. There are also lots of weird pricing edge cases around moving data between storage classes, minimum file sizes, and so on. A much better option is Backblaze’s B2 product. Their pricing is much more straight-forward, and they have an interesting feature that’s particularly useful in this case: lifecycle rules. Coupled with the ability to create API keys that don’t have access to delete files (just “hide” them), this allows for what’s effectively an append-only store.

This works more-or-less out of the box with Restic. Joseph Price has a guide that goes into the setup in a bit more depth. Basically, whenever Restic would delete a file (e.g. during a “forget” or “prune” operation), it instead gets hidden and is only deleted when the B2 lifecycle rules decide it should be. I’ve kept the existing Hetzner S3 backups for now, and just added an extra step to the end of my script: a simple restic copy and a restic forget. B2 actually works out cheaper than the Hetzner storage, as they don’t bill you for a minimum of 1TB storage; my current usage is around $3/month. Not a bad price for some extra peace of mind!

Simple backups with Restic and Hetzner Cloud

2024-12-06T00:00:00Z

Restic’s mascot, who’s dual-wielding umbrellas to save you from a rainy day.

I have a confession: for the past few years I’ve not been backing up any of my computers. Everyone knows that you should do backups, but actually getting around to doing it is another story.

Don’t get me wrong: most of my important things are “backed up” by virtue of being committed to remote git repositories, or attached to e-mails, or re-obtainable from the original source, and so on. I don’t think any machine failing completely would be a disaster for me, but it would certainly be a pain.

This week I finally got around to doing something, and it ended up being a lot more straight forward than my previous forays into backup-land.

Restic

After soliciting a few opinions, the choice of backup software came down to either Borg or Restic. I’m pretty sure either would have done what I want, but I leaned towards Restic for a few reasons: it has a more informative website, it’s written in Go rather than Python¹, and Borg seems to be transitioning between major releases at the moment².

The way Restic works is pretty simple: you initialise a ‘repository’, and can then call restic backup /some/path and it’ll get backed up to the repository. Restic handles keeping different backups separate, and only sending data that’s changed, and deduplicating, and so on. You basically point it at a thing you don’t want to lose, and it sorts it out for you. Perfect.

There are equally straight-forward commands for removing old snapshots (restic forget) and verifying backups (restic check). One of the nice things about modern backup solutions is they support a whole range of backends. I was originally going to spin up a small VPS to host my backups, but noticed that Restic supported S3-compatible stores…

Hetzner Cloud Object Storage

I host my servers with Hetzner, and was going to use them to spin up a VPS as well. Despite the “Cloud” branding on a bunch of products, they offer reasonable prices and good service. A couple of months ago, they started offering S3-compatible object storage.

The pricing isn’t totally straight forward, but for continuous use the “free quota” amounts to 1TB of storage and 1TB of egress a month. Ingress is free, as is traffic within the eu-central region (where all my servers are). That quota is only awarded when you pay the “base price”, though, which is €4.99 a month. So basically it’s €5 a month for 1TB of storage and enough egress to fully restore every single byte. That’s better value than any VPS I can find, much cheaper than Amazon S3, and about the same as Backblaze B2.

Getting them to work together

Now you’d think making the tool that supports S3-compatible object storage work with your S3-compatible object storage would be easy, right? Well not quite. The library Restic uses to deal with S3 backends has some strange logic for figuring out the bucket name given a URL. It doesn’t quite seem to work right, though…

Hetzner buckets have URLs like s3://bucketname.hel1.your-objectstorage.com³, but just passing that to Restic gives an error that the bucket is not specified. The docs mention there’s an advanced option to make it use the virtual host for the bucket name: -o s3.bucket-lookup=dns. But that… also doesn’t work. What I ended up doing was specifying the URL as s3://hel1.your-objectstorage.com/bucketname, and also passing in the dns option. The library then seems to muddle its way back to a real, working URL. I’m not sure why it works like this: maybe it’s just a weird aspect of S3 that I’m oblivious to?

The next fun part is that you can configure Restic entirely by using environment variables, except for that -o s3.bucket-lookup=dns argument. That has to go on the command line. I ended up making a little wrapper script to invoke Restic correctly:

#!/bin/sh

# The password restic will use to encrypt your data. You should generate
# something nice and secure.
export RESTIC_PASSWORD=repo-password

# The path to the repository where restic will save the backup. In our case
# this takes the form `s3:<endpoint>/<bucket>`. Your endpoint might be different
# to mine depending on the region your bucket is in.
export RESTIC_REPOSITORY=s3:hel1.your-objectstorage.com/bucket-name

# The access and secret key generated in the 'S3 credentials' section of the
# Hetzner Cloud Console
export AWS_ACCESS_KEY_ID=hetzner-access-key-id
export AWS_SECRET_ACCESS_KEY=hetzner-access-key

# Pass any arguments on to the restic command, along with the magic
# `s3.bucket-lookup` option we need to resolve the S3 URL properly.
exec restic -o s3.bucket-lookup=dns "$@"

Then in the backup script I just alias restic to use the script:

#!/bin/bash

set -eu

# This means any time we use `restic` below, we'll actually execute our special
# script which supplies all the env vars and arguments needed to find the
# repository. Make sure the path matches where you saved the script!
alias restic='~/.bin/restic'

# Actually do the backup. Each directory in the list below will be backed up
# separately.
dirs=(
	"/some/path/to/backup/"
	"/some/other/path/"
)
for i in "${dirs[@]}" 
do
	echo $i
	(cd $i && restic --verbose backup .)
done

# Prune our snapshots. You can tweak the numbers here. Run with `--dry-run` to
# see what effect any changes would have before actually committing to them. 
restic forget --keep-daily 7 --keep-weekly 10 --keep-monthly 24 --keep-yearly 10

The only other notable thing here is that the script changes into the directory to be backed up. If you give Restic an absolute path, it will create a new snapshot if the metadata of any folder in the path changes, which is not what I want.

If it wasn’t for the S3 URL issues, the whole thing would’ve probably taken me about half an hour. That’s including setting up the object storage, installing Restic, and so on. It’s painfully easy. Why didn’t I do this three years ago?!

Addendum: a step-by-step guide

If you want to do this yourself, here’s a quick step-by-step guide:

Log in to the Hetzner Cloud Console, and create a project.
On the “Object Storage” tab, create a new bucket. Note the name and the endpoint.
On the “Security” tab, go to “S3 Credentials” and generate new credentials. Note down the access key and the secret key.
Copy the first shell script above, fill in the password (you can pick!), endpoint, bucket name, access key and secret key.
Run the script with the init argument (e.g. ~/.bin/restic init). This will create a new repository, and only needs to be done once even if you backup multiple machines.
Copy the second shell script above, making sure the restic alias points at the script you saved in step 4. Change the list of directories to whatever you want to backup.
Schedule the script to be run automatically, using crontab or systemd timers or however you prefer.

To check everything is working, you can use the snapshots subcommand to see a list of saved snapshots. You might also want to try to restore a snapshot using the restore subcommand.

I’m not trying to be a language snob, but given the choice between two otherwise equal projects one in Go and one in Python, I’ll take the Go one. I know I’m not going to have weird library issues down the line, and I’m much more comfortable rummaging around the source. ↩︎
With a “Don’t use this in production!” notice on the shiny new version. ↩︎
Aside: I really hate URLs like that. What is with the trend for completely generic domains divorced from the service they’re a part of? ↩︎

Reproducible Builds and Docker Images

2022-02-18T00:00:00Z

XKCD 2347: Dependency

Reproducible builds are builds which you are able to reproduce byte-for-byte, given the same source input. Your initial reaction to that statement might be “Aren’t nearly all builds ‘reproducible builds’, then? If I give my compiler a source file it will always give me the same binary, won’t it?” It sounds simple, like it’s something that should just be fundamentally true unless we go out of our way to break it, but in reality it’s actually quite a challenge. A group of Debian developers have been working on reproducible packages for the best part of a decade and while they’ve made fantastic progress, Debian still isn’t reproducible. Before we talk about why it’s a hard problem, let’s take a minute to ponder why it’s worth that much effort.

On supply chain attacks

Suppose you want to run some open-source software. One of the many benefits of open-source software is that anyone can look at the source and, in theory, spot bugs or malicious code. Some projects even have sponsored audits or penetration tests to affirm that the software is safe. But how do you actually deploy that software? You’re probably not building from source - more likely you’re using a package manager to install a pre-built version, or downloading a binary archive, or running a docker image. How do you know whoever prepared those binary artifacts did so from an un-doctored copy of the source? How do you know a middle-man hasn’t decided to add malware to the binaries to make money?

Even worse: if the software you’re trying to use includes any dependencies, you have the same issue of trust with them. Maybe your supplier isn’t compromising the software, but that doesn’t mean their supplier isn’t. The beauty-cum-horror of a supply chain attack is that it can target the weakest link anywhere along the supply chain. Even if there aren’t any binary files involved, dependencies can still be attacked: what if npmjs.com or proxy.golang.org or github.com return a different version of a dependency-of-a-dependency when the request comes from your IP address? It doesn’t even need to be a modified dependency, it could be a perfectly un-tampered, properly signed copy of the source, just from an older version with a known vulnerability.

Enter stage left: reproducible builds, here to save the day! If the build process is reproducible then you - or anyone else on the internet - can perform the same build on the same source and validate the output has the same checksum or hash. If Debian publish a binary package and an independent re-builder comes up with the exact same build artifact, there’s a reasonably good chance that the build is good. An attacker would have to compromise both the build machine and the re-build machine to do anything nefarious. The more re-builders there are, the less feasible a supply chain attack is.

So why isn’t software just reproducible?

Compilers

As a bit of an experiment, I asked some friends to run the following for me and report the answer:

echo -e "#include <stdio.h>\nint main() { printf(\"Hello\"); return 0; }" | \
  gcc -x c -o hello.out - && \
  sha256sum hello.out

This compiles a super-simple hello world program and then prints the SHA-256 hash of the resulting binary. Here are the results:

Hash	System	GCC
1f62feab5a06861dc575201d807781926d1ae49fb113da018fde8b670a1346f7	Arch	11.2.0
b8e6f2c7082be69f65ffa5e7a3d749eb47866a1b2e1ec19efb63cc59a8b160cd	Debian	8.3.0
cbad2e47a22c234b5e7fa55e029a8db4d64ac7a962e2176bd2e1373d78954088	Debian	8.3.0
e0f6bbc13b29fea8cfa2a975ba4661e781323298aec166c8311d342e6f93c4a6	Alpine	10.3.1
e379156895e06c7a0bf18ac4d648860edcb2655576b0ab9fab172bd6c8b92075	Debian	10.2.1
7ffdaee4eb64e016b89dc5e54d2c8eebab3cebafe2c7aa97de627b5972ecea46	Debian	11.2.0
8ae52cc166743b6ae1eb3e14179ef33de5061a04237f8f97088c896c41a2f698	Arch	11.1.0
8ae52cc166743b6ae1eb3e14179ef33de5061a04237f8f97088c896c41a2f698	Arch	11.1.0

As you can see, there are barely any duplicates. Even the same version of GCC on the same OS sometimes produces different results. And this is the most basic program I could write! Differences arise from the compiler version, the build flags, the libraries installed, and a whole host of other factors. If you compile a Go application instead of a C one, then by default the compiler will include debug information in the binary. This includes the full path to the source file on disk, so building a project in /home/chris/ will produce a different binary to building the same source in /tmp. Future versions of Go are also going to stamp in other meta-data such as VCS info, so building inside and outside a Git repository will produce different binaries.

Iteration order

So we’ve pinned our build environment, we’re manipulating timestamps when adding files to archives, now what? Imagine part of the build process involves looping through all the files in a directory and doing something. What order do these files get iterated in? Well, that very much depends on the filesystem and perhaps when the files themselves were created. To ensure this is reproducible we need to explicitly sort any such operation so that it’s always consistent. This iteration could be happening in a tool that’s called by another tool that’s called by a build script, so the fix isn’t necessarily straight-forward.

Side note: a bug war story

I’ve personally been victim to this kind of non-determinism. I was working on an Android app, and committed a new test that worked fine on my machine, and worked fine on the CI server. But it failed consistently for a colleague.

We both did fresh checkouts of the source, and ran the tests. Mine passed, his failed. He sent me an archive of his checkout in case there was something weird going on there, and the tests passed on my machine. We compared hashes of our checkouts, and they were the same. It was obviously environmental somehow, but everything else worked fine, and the build system went to great pains to ensure things were the same.

After a lot of debugging, I worked out that his test was running with a different version of a library to me, despite the libraries being defined in the build files and the build files being identical. After even more debugging it turned out there were two versions of the library on the classpath, and the ordering of them was different between my machine and his.

The actual issue turned out to be that the build tool generated the classpath by iterating over the library files, and that iteration was done in order of file creation time. The two libraries were added at different points in the project history, so the creation time in your local cache depended on which versions of the app you’d built in the past. With no cache everything worked as expected but there was a slim range of commits where only one library was in use, and if you had run the tests during that period your cache was effectively poisoned.

We fixed the issue by excluding the older version of the library (which was being pulled in as a transient dependency), and filed a bug against the build tool to make the classpath properly deterministic. I think that stands as the most difficult to diagnose bug I’ve ever dealt with.

Interestingly, if you iterate over a map in Go, the iteration is deliberately non-deterministic. That’s an attempt to defeat Hyrum’s Law and prevent developers from relying on whatever the current behaviour happens to be. This actually makes it easier to make things reproducible as the problem is loud and in-your-face, rather than subtle and hard to spot.

Other sources

There’s an awful lot of other places that non-determinism can come from. If the app pulls in dependencies, their versions have to be pinned, otherwise your build changes depending on the latest release of that dependency. If the build process pulls any information from a website, it’s liable to change. Hopefully the website is under your control so that you can version the resource and pin that version. Obviously, anything to do with dates or the current user will probably cause problems. Timezones and locales can cause subtle differences.

What about Docker?

Docker comes with some good and some bad points for reproducibility. The biggest advantage is that it inherently completely describes the build environment; it should work exactly the same from one system to another, even across different OS families. The biggest drawback is it sprays timestamps around like no-one’s business. Each layer in a container image is a .tar.gz file, meaning each file within it is timestamped as discussed above. Making an image involves a lot of copying of files around, so these timestamps invariably end up causing reproducibility issues.

Even worse than timestamps in the filesystem, the image format also contains some meta-data that includes the timestamp at which each layer was built. That means even if you go out of your way to set the timestamp of every single file in your image, the image itself will be different every time you rebuild it. There is no way to deal with this in Docker, which is a very sad state of affairs. Fortunately, Buildah provides a --timestamp flag for its build commands; this not only sets the layer timestamp but also the creation timestamp of any file within the layer.

The other major issue that affects Docker images is the pinning of packages pulled in by package managers. An awful lot of images are based on Alpine or Debian derivatives, and use apk or apt to install dependencies. These need to have a version specified as otherwise the package manager will just pull in the latest at the time of the build. But this isn’t quite enough: you also need to pin the version of any packages that they depend on, recursively. This means flattening the entire package hierarchy and installing all the packages explicitly and with pinned versions.

One more wrinkle in the package management space is that Alpine don’t keep old packages in their main repositories. If you have a Docker image with pinned alpine packages in, it will stop building if the package is updated. This isn’t necessarily fatal to making a reproducible build — as long as it’s reproducible for its useful lifetime, I don’t really see an issue.

Honestly, though, the biggest issue with making Docker images reproducible is getting people to care. Dockerfiles are a relatively new way of packaging software, and there’s no centralised organisation like you find with Linux distributions. There are enough challenges that most casual packagers aren’t going to bother, and no real incentive for them to. That won’t stop me trying, though!

Artisanal Docker images

2022-02-05T00:00:00Z

Artisanal containers…

I run a fair number of services as docker containers. Recently, I’ve been moving away from pre-built images pulled from Docker Hub in favour of those I’ve hand-crafted myself. If you’re thinking “that sounds like a lot of effort”, you’re right. It also comes with a number of advantages, though, and has been a fairly fun journey.

The problems with Docker Hub and its images

Rate limits

For the last few years, I’ve been getting increasingly unhappy with Docker Hub itself. Docker-the-technology is wonderful, but Docker-the-company has been making some rather large missteps. The biggest and most impactful of these has been introducing “pull rate” limits. At the time of writing, if you want to just pull a public image without logging in then you are limited to 100 pulls every 6 hours. If you log in then you’re limited to 200 pulls per 6 hours, but it’s account wide. This might seem like a big enough number, but I repeatedly hit it and there is no way to actually audit what is causing it. I have various containers that may all pull images at arbitrary times (e.g. continuous integration build agents), and the only information you get back from Docker Hub is the number of pulls remaining.

Obviously, I could start paying Docker Hub for a “Pro” plan. That gets you 5,000 pulls per day for $7/month. The downside is that every docker client would have to be authenticated, which presents a fair annoyance in terms of credential management. I also don’t really like how they positioned the service as a public utility with special treatment in the docker software, and then start tightening the ratchet to make money.

“Bad” images

I’m fairly opinionated about what a container image should look like: most importantly it should run just a single process, and only include the bare minimum dependencies required for that. Other people think differently, and it’s very hard to tell at a glance whether an image on Docker Hub contains just the application you want, or whether it also bundles MySQL, Redis, Elasticsearch, and a partridge in a pear tree. Some people want that kind of thing, but I really don’t. It’s also very hard to tell whether an image is officially endorsed by the upstream project, and where the source Dockerfile is. This used to be better because most projects used Docker Hub’s automatic builds, but they’re now a “pro” feature.

I quite often found that I’d be looking for an image for X, and there would be 5-10 images from different users. None of them looked official, some of them were out-of-date, some bundled the kitchen sink. Even when one looked good, it’s a bit of a gamble whether the author is going to keep it updated or not.

Doijanky

The rate limits and other problems were annoying, but they weren’t really annoying enough to force me to do anything about it. The straw that broke the camel’s back came later: I was looking at the official golang images, and noticed that all the tags were pushed by a random user account called “doijanky”:

An ‘official’ Docker Hub image pushed by user ‘doijanky’

I, perhaps naively, assumed that official images were built on Docker Hub’s own infrastructure. Why would all the Golang images be attributed to this user? Checking out their profile, they’re simply identified as a “Community User” like everyone else, with no repositories of their own. The only thing in the profile is their homepage, which is a link to a Jenkins dashboard: https://doi-janky.infosiftr.net/. It appears legitimate: “Infosiftr” are a container consultancy and the dashboard is linked to from the README in the official images git repository, but I find it baffling that they’re using third-party infrastructure and a normal user account (with a dubious name) to push these images. There doesn’t seem to be a good way to verify what you pull corresponds to the Dockerfile it came from; if infosiftr wanted to inject something into the build they could happily do so, and who knows how good their infosec posture is? If someone got access to the “doijanky” account, how long could they upload malicious images before someone noticed?

This little roller-coaster ride from “are all the official images compromised?!” to “oh, no, they’re not, it’s all just awful” finally convinced me to look at building my own images from scratch.

The implementation: templating with contempt

One of the big issues I needed to tackle was how to deal with updates. I didn’t want to have to go and edit a file every time some minor release was made of some software, or every time there was a security vulnerability in a common library. The official images use a shell-scripting based system to check for updates and generate Dockerfiles, I decided to do something similar but with Go templates. The result is a tool called contempt. It takes a template like:

FROM {{image "golang"}} AS build

ARG TAG="{{github_tag "example/project"}}"

RUN apk add --no-cache \
        {{range $key, $value := alpine_packages "git" -}}
        {{$key}}={{$value}}\
        {{end}}; \
# ...

Contempt has support for getting information from a variety of sources. In this case, it’s getting the latest digest of another Docker image, the latest tag from a Git repository, and the latest version of an alpine package and all its dependencies. The resulting Dockerfile looks something like this:

# Generated from https://github.com/csmith/dockerfiles/blob/master/miniflux/Dockerfile.gotpl
# BOM: {"apk:brotli-libs":"1.0.9-r5","apk:busybox":"1.34.1-r4", <snip> }

FROM reg.c5h.io/golang@sha256:ac8fa5f4078b0a697796b5d741... AS build

ARG TAG="2.0.35"

RUN apk add --no-cache \
        brotli-libs=1.0.9-r5\
        busybox=1.34.1-r4\
        # <snip>
        pcre2=10.39-r0\
        zlib=1.2.11-r3\
        ; \
# ...

I’ve cut out the longer parts for readability. You can see that it pins all versions of the alpine packages in use, as well as the base image. This ensures that if you build from the same Dockerfile at a later time it will build the same image (or will fail entirely, as Alpine doesn’t keep their old packages around indefinitely). It also produces a “bill of materials” as a really long JSON-encoded comment. If you let contempt commit the Dockerfile it uses the BOM to generate useful commit messages like: [project] apk:busybox: 1.34.1-r3->1.34.1-r4, so you can see exactly what changed.

Contempt also has support for building and pushing images whenever it changes the Dockerfile. I use it in a GitHub action that runs daily to check all my images are up-to-date and push those that aren’t. It understands the dependencies between images (by pre-analysing the templates) so it will always check and build base images before ones that require them. This means an update to, say, the “alpine” base image will cause anything that depends on it to get updated at the same time, ensuring security updates are rolled out promptly.

The result

You can see my collection of lovingly hand-crafted Dockerfiles in my dockerfiles repository.

There are a number of advantages to handwriting all the images I use. The obvious one is that they’re all built how I want: there are no extraneous dependencies, they’re all based on the same small set of base images (rather than pulling around 10 different versions of debian), nothing tries to also run a DBMS in its container, etc.

This level of customisation goes further, though. Because I’m packaging the software myself, I can tweak how it’s built to fit my needs. A couple of things I run need their own TLS certificates separate from my normal HTTPS setup, so I bake my certwrapper tool in to manage those; I can even set the build flags on certwrapper to only enable the particular DNS provider I personally need (thus avoiding dragging in clients for AWS, GCP, etc). Some software like Hashicorp Vault has an optional web interface that I don’t need, so I simply don’t enable it in the build. These changes save build time, reduce image sizes, in some cases improve runtime performance, and generally reduce the attack surface of what’s running in the container.

It’s also been a great way to learn more about how software is distributed. Writing a Dockerfile is not that distant from writing a PKGBUILD file for an Arch Linux package, or the equivalent for other distributions. In a couple of instances I’ve googled how to solve a particular issue, and found an Arch or Void linux maintainer asking the upstream project about the exact same issue.

Finally, all the images I build I push to my own registry so there are obviously no rate limiting issues. Standing up a service (assuming the Dockerfile has been written!) is amazingly quick because the base layers are all shared and cached, and the registry is a lot physically closer than Docker Hub. Bootstrapping this whole thing becomes an interesting problem because the image for the registry is stored on the registry, but I’ll leave that discussion for another post…

Debugging beyond the debugger

2019-05-08T00:00:00Z

Real-life debugging tools

Most programming — and sysadmin — problems can be debugged in a fairly straight forward manner using logs, print statements, educated guesses, or an actual debugger. Sometimes, though, the problem is more elusive. There’s a wider box of tricks that can be employed in these cases but I’ve not managed to find a nice overview of them, so here’s mine. I’m mainly focusing on Linux and similar systems, but there tend to be alternatives available for other Operating Systems or VMs if you seek them out.

Networking

tcpdump

tcpdump prints out descriptions of packets on a network interface. You can apply filters to limit which packets are displayed, chose to dump the entire content of the packet, and so forth.

Typical usage might look something like:

# tcpdump -nSi eth0 port 80
tcpdump: verbose output suppressed, use -v or -vv for full protocol decode
listening on eth0, link-type EN10MB (Ethernet), capture size 262144 bytes
16:03:35.577781 IP6 2001:db8::1.54742 > 2001:db8::2.80: Flags [S], seq 2815779044, win 64800, options [mss 1440,sackOK,TS val 2378811665 ecr 0,nop,wscale 7], length 0
16:03:35.586853 IP6 2001:db8::2.80 > 2001:db8::1.54742: Flags [S.], seq 1522609102, ack 2815779045, win 28560, options [mss 1440,sackOK,TS val 3063610173 ecr 2378811665,nop,wscale 7], length 0
16:03:35.586877 IP6 2001:db8::1.54742 > 2001:db8::2.80: Flags [.], ack 1522609103, win 507, options [nop,nop,TS val 2378811674 ecr 3063610173], length 0
16:03:35.620678 IP6 2001:db8::1.54742 > 2001:db8::2.80: Flags [P.], seq 2815779045:2815779399, ack 1522609103, win 507, options [nop,nop,TS val 2378811708 ecr 3063610173], length 354: HTTP: GET / HTTP/1.1

Here you can see the start of a plaintext HTTP request: the three-way handshake as the TCP connection is established followed by a GET request. Even if the data is encrypted as it will be in most cases, it’s often useful to see the “shape” of the transmissions: did the client start sending data when it connected, did the server ever respond, etc.

Daniel Miessler has a good tutorial on tcpdump if you’re not familiar with it and don’t want to jump straight into the man page.

… with Docker

Docker sets up separate network namespaces for each container. To see the traffic across the interfaces of a single container you can nsenter the container’s network namespace:

# nsenter -t $(docker inspect --format '{{.State.Pid}}' my_container) -n tcpdump -nS port 80

This retrieves the PID for the container, and tells nsenter to enter the network (-n) namespace from the given target (-t) PID, and then run the given command (in this case tcpdump ...).

openssl s_client / s_server

When a connection is using TLS it’s often useful to try connecting to the server and see what certificate it presents, algorithms it negotiates, and so forth. OpenSSL offers two useful subcommands which can help with this: s_client for connecting as a client, and s_server for listening to connections.

For example, using s_client to connect to google.com on the standard HTTPS port shows us details about the server cert and its verification status:

$ openssl s_client -connect google.com:443
CONNECTED(00000003)
depth=2 OU = GlobalSign Root CA - R2, O = GlobalSign, CN = GlobalSign
verify return:1
depth=1 C = US, O = Google Trust Services, CN = Google Internet Authority G3
verify return:1
depth=0 C = US, ST = California, L = Mountain View, O = Google LLC, CN = *.google.com
verify return:1
---
Certificate chain
 0 s:C = US, ST = California, L = Mountain View, O = Google LLC, CN = *.google.com
   i:C = US, O = Google Trust Services, CN = Google Internet Authority G3
 1 s:C = US, O = Google Trust Services, CN = Google Internet Authority G3
   i:OU = GlobalSign Root CA - R2, O = GlobalSign, CN = GlobalSign
---
# ...

Whereas connecting to my webserver and providing an unknown host in the SNI field results in an SSL alert 112 (“The server name sent was not recognized”) and no server certificate is sent:

$ openssl s_client -connect chameth.com:443 -servername example.com
CONNECTED(00000003)
140384831313024:error:14094458:SSL routines:ssl3_read_bytes:tlsv1 unrecognized name:../ssl/record/rec_layer_s3.c:1536:SSL alert number 112
---
no peer certificate available
---
# ...

Often if you hit this kind of alert in an application the exact error will be lost somewhere in the many layers between the SSL library and the logs, so being able to directly connect and test can help diagnose a lot of issues.

Once a connection is established you can read and write plain text and it will be encrypted and decrypted automatically.

Java apps

If a Java app is involved in the connection, you can enable a lot of built-in debugging with a simple JVM property: javax.net.debug. You can tweak what exactly gets logged, but the easiest thing to do is just set the property to all and you’ll see information about certificate chains, verification, and packet dumps:

$ java -Djavax.net.debug=all -jar ....
# ...
found key for : duke
chain [0] = [
[
  Version: V1
  Subject: CN=Duke, OU=Java Software, O="Sun Microsystems, Inc.",
  L=Cupertino, ST=CA, C=US
# ...

More information about Java’s debugging options is available on docs.oracle.com.

Thread and core dumps

Higher-level languages frequently provide an interactive way to dump the current execution state of all of their threads (a “thread dump”). This is useful to spot deadlocks, some types of race conditions, and as a quick and dirty method of investigating hangs or excessive CPU usage.

With both Java and Go applications you can send a QUIT signal to have a thread dump printed out; Go applications will quit after doing so, Java ones will carry on running. At most terminals you can hit Ctrl and \ to send a QUIT signal.

For Java you can also use the jstack tool from the JDK to dump threads by PID; this can be useful if the application is running in the background or has redirected sysout:

$ jstack 8321
Attaching to process ID 8321, please wait...
Debugger attached successfully.
Client compiler detected.

Thread t@5: (state = BLOCKED)
 - java.lang.Object.wait(long) @bci=-1107318896 (Interpreted frame)
 - java.lang.Object.wait(long) @bci=0 (Interpreted frame)
 - java.lang.ref.ReferenceQueue.remove(long) @bci=44, line=116 (Interpreted frame)
 - java.lang.ref.ReferenceQueue.remove() @bci=2, line=132 (Interpreted frame)
 - java.lang.ref.Finalizer$FinalizerThread.run() @bci=3, line=159 (Interpreted frame)

# ...

A core dump provides more complete information about the state of a process, but is often more complex to interpret. The gcore utility from GDB will create a core dump of a process with a given PID. You can then generally load the core file using your normal debugger, depending on the language in question.

System calls

strace is the swiss army knife for seeing what a process is doing. It details each system call made by a program (you can filter them down, of course). For example:

$ strace -e read curl https://google.com/
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0 \236\0\0\0\0\0\0"..., 832) = 832
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0P!\0\0\0\0\0\0"..., 832) = 832
read(3, "\177ELF\2\1\1\3\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\200l\2\0\0\0\0\0"..., 832) = 832
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\20Q\0\0\0\0\0\0"..., 832) = 832
# ...
read(3, "\0\0\0\0\0\0\0\4\25\345\366\302\273sE6\365wI\225\321|\3435Z\362\216\372\215\251aO"..., 253) = 253
<HTML><HEAD><meta http-equiv="content-type" content="text/html;charset=utf-8">
<TITLE>301 Moved</TITLE></HEAD><BODY>
<H1>301 Moved</H1>
The document has moved
<A HREF="https://www.google.com/">here</A>.
</BODY></HTML>
read(3, "\27\3\3\0!", 5)                = 5
# ...

Brendan Gregg has a nice guide on strace and alternatives.

… with docker

When the application is running in docker you can usually just strace it from the host with the correct PID (from e.g. docker inspect --format '{{.State.Pid}}' my_container). Sometimes you may need to trace the startup of an application though, which is a bit trickier. Instead you can run a new container using the same PID namespace as your target, and the permissions needed to strace:

$ docker run --rm -it --pid=container:my_container \
  --net=container:my_container \
  --cap-add sys_admin \
  --cap-add sys_ptrace \
  alpine

From within the new container you can install strace, and trace any running program within the target container using strace -p as normal. To start a new program you need access to the target container’s filesystem, which you can get to via /proc/1/root (PID 1 being the main process that docker started in the target container).

Files

Sometimes the problem might relate to file access. There are a couple of straight forward — but nonetheless useful — tools which might help here. inotifywait uses the Linux inotify subsystem to watch files or directories for operations. For example:

$ inotifywait -mr site/content
Setting up watches.  Beware: since -r was given, this may take a while!
Watches established.
site/content/post/ MODIFY 2019-05-08-debugging-beyond-the-debugger.md
site/content/post/ OPEN 2019-05-08-debugging-beyond-the-debugger.md
site/content/post/ MODIFY 2019-05-08-debugging-beyond-the-debugger.md
site/content/post/ MODIFY 2019-05-08-debugging-beyond-the-debugger.md
site/content/post/ CLOSE_WRITE,CLOSE 2019-05-08-debugging-beyond-the-debugger.md
# ...

Here the -m switch makes inotifywait monitor the files forever (instead of exiting on the first modification, which is the normal behaviour) and r makes it recurse into the directory and monitor each file and subdirectory in there.

If you want to see what processes currently have a file open, fuser is the go-to tool. For example:

$ fuser -v /
                     USER PID ACCESS COMMAND
/:                   root     kernel mount /
                     chris      2961 .rc.. systemd
                     chris      2986 .r... gdm-x-session
                     chris      2994 .r... dbus-daemon
                     chris      3001 .r... gnome-session-b
# ...

Honourable mentions

These aren’t really debugging tools, but I feel it’s worth mentioning as they often feature somewhere along the debugging-of-weird-problems journey.

I’ve seen some weird and wonderful problems happen because a disk is full, so a quick df early on in the debugging process never hurts. Some apps may hang, some may corrupt their config, some may fall over and die; sometimes the manner in which they fail doesn’t obviously point to a disk space issue.

Another issue that comes up now and then — especially inside VMs or other environment that don’t have a decent amount of “noise” happening — is entropy exhaustion. A quick look at /proc/sys/kernel/random/entropy_avail should be enough to confirm that everything is ticking along nicely. If it’s exceedingly low then you may find that anything involving random number generation stalls (TLS connections for example).