Chameth.com - posts like debugging-beyond-the-debugger, docker-automatic-nginx-proxy, thinking-more-about-backups but not intro-to-containers, why-you-should-be-using-https

An interesting Tailscale + Docker gotcha

2026-01-29T00:00:00Z

As I’ve written about before, I use Tailscale for a lot of things. I thought I had it set up in a reasonably secure manner, but I recently noticed a problem.

I use Tailscale’s ACLs to limit what each node can access, based on the tags I apply to it. So an app node can’t access anything via Tailscale, while an integration or server node can access things tagged with either app or integration. This is expressed pretty simply in the Tailscale ACL JSON:

{
	"tagOwners": {
		// Servers that can be SSH'd into
		"tag:server": [],
		// Applications that are exposed on tailscale but never connect out
		"tag:app": [],
		// Things which talk to other services over tailscale (connecting to apps etc)
		"tag:integration": [],
	},
	"grants": [
		{
			// Users can access everything
			"src": ["autogroup:member"],
			"dst": ["*"],
			"ip":  ["*"],
		},
		{
			// Servers and integrations can access integrations and apps
			"src": ["tag:server", "tag:integration"],
			"dst": ["tag:integration", "tag:app"],
			"ip":  ["*"],
		},
	],
}

Over the past week I’ve been setting up a private Forgejo instance behind Tailscale, complete with an actions runner that runs things using a docker-in-docker container. I didn’t want the runner knowing anything about Tailscale, so I had it configured to speak to Forgejo direct over HTTP (forgejo:3000) instead of using full Tailscale HTTPS URL that I use when accessing it (http://git.example-net.ts.net/)¹.

Everything was going fine, until I forgot to do that translation… and it worked. My Forgejo action runners could access anything on my tailnet. I run several things on Tailscale that just have authentication turned off, on the basis that only authorised devices can access them. Things like the admin interface for this website. I definitely didn’t intend for any workflow I run on my git server to have access to edit my website!

This wasn’t just limited to Forgejo, either. Any docker container I was running could access the tailnet. In hindsight it’s fairly obvious why: the host is running Tailscale, connected as a node tagged with my server tag. That creates a tailscale0 interface, and automagically sets up iptables rules to route Tailscale traffic over the interface. Docker also automagically sets up iptables rules to bridge traffic, and apparently these two sets of rules interact in such a way that traffic from Docker containers is allowed to route via the tailscale0 interface.

I say it’s fairly obvious in hindsight — there’s no reason why Docker would special case any particular host interface after all — but it still feels pretty surprising. Because both bits of software inject their own iptables rules, I never really had a good mental model for how they interact. The host Tailscale node was a completely separate building block to Docker. It would be a pain to use either of them if they didn’t do these rules, but it’s also one of the reasons I don’t really like “magical” things².

There are lots of ways to fix this, but none of them feel particularly great. You can configure both Tailscale and Docker to not automatically fiddle with iptables and handle the rules yourself, but I really hate dealing with iptables³. As a stopgap I did hold my nose and add some iptables rules to drop traffic to the tailscale0 interface if it originated from the IP ranges that Docker was configured to use:

iptables -I DOCKER-USER -s 192.168.0.0/16 -o tailscale0 -j DROP
iptables -I DOCKER-USER -s 172.17.0.0/12 -o tailscale0 -j DROP

The DOCKER-USER chain is a nice little escape hatch; it comes before the main auto-generated DOCKER chain, and Docker leaves the rules in it alone.

So I added these rules, and felt pretty good about myself, and then… everything started breaking in weird ways. After some debugging I realised the problem was DNS⁴. The server’s DNS resolver is 100.100.100.100, a special Tailscale address. This is so that it can resolve tailnet hostnames via MagicDNS (and so I don’t have to configure my custom DNS servers manually on each device; Tailscale does it for me). My new iptables rules inadvertently dropped all the DNS packets coming from docker containers. D’oh.

Obviously the solution here is to double down and add MORE iptables rules:

iptables -I DOCKER-USER -s 192.168.0.0/16 -d 100.100.100.100 -o tailscale0 -j ACCEPT
iptables -I DOCKER-USER -s 172.17.0.0/12 -d 100.100.100.100 -o tailscale0 -j ACCEPT

This got DNS working again, but it all feels a bit gross. Not least because to actually make these persist you need to use iptables-save, and then you also get all the rules that both Docker and Tailscale have inserted. I came across a script to filter out the Docker ones, but… yuck⁵.

I realised a cleaner idea might just be to lock down what server tagged nodes could access within Tailscale itself. That way I can avoid touching iptables at all. It’s handy to be able to curl services from the host when debugging, but it’s not really necessary. So I removed that access, and… stuff broke again. I’m using my Forgejo instance as a registry for some of the docker images I run, so the docker daemon needs to be able to reach it. I ended up making a new tag for infrastructure, which can be accessed from server devices. This does still allow all the docker containers to reach Forgejo, but I already have it set up with appropriate access controls and public/private repository splits. Forgejo is a service designed to run publicly, so this seems a reasonable trade-off for convenience. I used the tests feature of Tailscale’s ACL config to make sure I’d got the rules right:

{
	"tests": [
		{
			// Servers can only access infrastructure
			"src":   "tag:server",
			"proto": "tcp",
			"allow": [
				"tag:infrastructure:8080",
			],
			"deny": [
				"100.84.16.43:8080",
				"me@example.com:8080",
				"tag:server:8080",
				"tag:app:8080",
				"tag:integration:8080",
			],
		},
	],
}

The whole situation still feels a bit messy. If I ever get around to switching to nftables I might loop back and manually craft some rules for routing traffic, instead of leaving Tailscale and Docker to do their own thing.

I discovered later on that logging into the container registry at forgejo:3000 actually issued a redirect to https://git.example-net.ts.net/ so this was all basically for naught… ↩︎
I didn’t use Tailscale’s MagicDNS for a long time just because the word “magic” put me off. Only when I eventually got around to learning how it worked, and seeing that it wasn’t really that magical under the hood, did I change my mind. ↩︎
nftables seems far better in lots of ways, but I can’t really be bothered migrating. Maybe next time I reimage the server for whatever reason… ↩︎
It’s always DNS… ↩︎
Again, nftables would almost certainly help here. It actually has (gasp) configuration files. But again, I really didn’t want to spend the time migrating. ↩︎

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? ↩︎

Docker reverse proxying, redux

2022-12-06T00:00:00Z

Six years ago, I described my system for configuring a reverse proxy for docker containers. It involved six containers including a key-value store and a webserver. Nothing in that system has persisted to this day. Don’t get me wrong – it worked – but there were a lot of rough edges and areas for improvement.

Microservices and their limitations

My goal was to follow the UNIX philosophy of “do one thing and do it well”. Unfortunately, that doesn’t really work when applied to network services that have to interact with one and other. UNIX tools are built upon a common file system and simple data passed over STDIN. Microservices don’t have that shared foundation. You could make one: companies that use microservices in anger often have a team that deals with the “developer experience” of creating and using microservices. But as a solo developer that’s not something I wanted to spend my time doing.

This became very apparent when trying to debug issues. In the UNIX world, if your series of commands piped together does something strange you can simply echo the data at various stages. Not so much when that data is flying around on a network, going into and out of things like etcd. Trying to figure out why a certificate hadn’t been acquired was a case of searching through logs from four containers, none of which had particularly good logging. There are many ways to get insight into what’s happening with microservices but, again, that’s not something I wanted to do myself.

Over time, and with experience in other projects, I came to realise that microservices only really make sense if you’re unable to deploy a monolith. For tech companies this naturally happens when different teams contribute to the same service: splitting it out into smaller services that are wholly owned by individual teams makes sense. For solo developers, that never happens. You can still gain the other benefits of microservices – such as code separation and having clearly defined APIs – by sticking to certain coding standards.

Proxy inconveniences

As well as being unhappy with the microservice nature of the solution, I wasn’t pleased with nginx. If you requested an unknown domain, nginx would use the first server block in its config to serve a response, instead of sending an “unrecognised name” alert as I wanted. It was a minor issue, but it irked me.

So from nginx I switched to haproxy. It has a strict-sni option when configuring TLS connections which makes it behave properly. It also performs a lot better for this type of workload than nginx. All was well for a while, but then I started getting alerts that requests were occasionally failing. I couldn’t reproduce the issue, but my nightly jobs to build and push containers managed to hit it nearly every night, causing them to fail.

After some investigation, I found that the haproxy developers had refactored the header parsing code, and neglected to properly reset flags when multiple requests were sent over the same connection. There was a patch, but it wasn’t released. No problem, I thought, I’ll just cherry-pick it onto the last release… Except that haproxy use Git in the most convoluted manner I’ve ever seen – they have one repository per release. This makes it harder to patch, but it also made me question whether I trusted them to ship stable software: there were no tests for the header parsing code (which is both fundamental and finicky, the perfect target for tests), the source code management was weird, and they didn’t seem in any rush to patch this bug.

Not long after that issue, Greg managed to encounter another bug where haproxy returned a 500 error whenever the upstream server replied with a particular, perfectly valid, header. The die was cast – it was time to move to something else.

Not Invented Here syndrome

Looking for a new solution, there were many more options than back in 2016. I’m still convinced, however, that anything exposed to the Internet should not have access to run docker containers. It’s the modern equivalent of running a CGI script as root. That single requirement eliminates most off-the-shelf solutions. What do you do when nothing quite meets your specific requirements? You make something yourself! My new solution has two components: Dotege and Centauri.

Dotege is a replacement for the microservices that monitored containers and obtained certificates. It’s fundamentally a templating engine - whenever the containers change, it evaluates a template and saves the result to disk. The template has access to details about the containers, their labels, ports, and so on. Dotege can also obtain certificates from Let’s Encrypt, and raise a signal against another process whenever the template or certificates change. I used this to generate the configuration and certificates used by haproxy for a while, and more recently changed the template so that it works for Centauri.

Centauri is my own reverse proxy. It’s configured using a simple text file and can also obtain certificates from an ACME provider. It doesn’t serve static content, has no knowledge about docker, and avoids the other bells and whistles that adorn most reverse proxies. It also has good test coverage to ensure that I don’t, say, accidentally break header parsing.

As a software engineer I enjoy writing software, but I also enjoy running simple, easy to understand software. That’s what I’ve achieved here: it’s very easy to identify where the problem is if anything goes wrong, both are small Go programs rather than vast sprawling C monstrosities, and their interaction is primarily through a file written to disk that can be inspected or edited as needed.

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
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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).