Mehul Kar

02 May, 2017

How I Debugged The Last Thing


Early one morning, a few hours before my flight to RailsConf, a user emailed saying that downloads were erroring out on one of the services I maintain. I didn’t remember deploying anything that might have caused it, so I replied with the usual

Weird, I’ll look into it, can you file a bug report?

Side note: always file a bug report even if you’re reaching out personally. Bug reports are how maintainers track recurring issues, look up quick fixes, and update other users about the status of a thing. An email conversation doesn’t scale simply because it doesn’t have a URL. Side side note, aren’t URLs and linking such an amazing thing? For thousands of years we had books and we couldn’t hyperlink between them. Appreciate!

So downloads were breaking and I had a flight to catch. I drop everything and ssh into the server, because that’s the level of devops sophistication I have reached in my career. While I’m shush'ing, I remember that I’ve recently transferred all user uploaded artifacts to a 3rd party server, but I had continuing writing uploads to the VM for now, because I wasn’t 100% confident of the 3rd party server yet. “It’s been a while since I’ve started trusting the 3rd party”, I think to myself. “Did I remember to turn off writing files locally to my VM?” Even if I hadn’t, this is a pretty big VM, I shouldn’t run out of disk space from it.

I’m into the server now. I compulsively type ls into the terminal, because this is the first command I ever learned to type in a terminal and it will forever be the first command I always type into a terminal. All seems well. Then I type ls /s and the tab key and hit my first problem:

bash: cannot create temp file for here-document: No space left on device

Ok, well that’s a pretty strong clue. df -h comes next and it reveals that the disk is at 100% full. Oh geez. Flight leaves in 4 hours, which means I need to leave for the airport in 2 and I have not packed yet.

Ok, what’s taking up all this space? I look in my personal dotfiles for that one alias I have for the command that prints out the 10 largest directories in the current directory.

du -hsx * | sort -r | head -n 10

Ah, the log directory, of course. It’s the output from the 5 cache warmers that run every 5 minutes. Of course. The log file for each is a few gigs big. Gross, I should file another bug to enable log rotation for these at some point. I’ll file the bug later. rm *warmer.log.

Another df -h and we’re back at 70% disk space usage. Crisis averted.

I try out a couple downloads on the website and email the group and update the bug report that everything should be back to normal for now even though the underlying issue has not been resolved.

But something still seems off. Tab completion in bash still isn’t working and is throwing:

bash: cannot create temp file for here-document: No space left on device

A few minuter, the user responds to the ticket that downloads are still not working. I try again a few times and it looks like they’re failing every 2-3 times.

Clearly there is space left on the device now. I know it’s a good idea not to fill a disk over 50%, but at 70% it should be working fine and it should definitely have enough space to create a temp file for tab completion. What’s going on?

I remember that linux has a bunch of random caches that work pretty invisibly. For example, sudo permission is stored in a cache the first time you use it, so if you run three sudo commands in a row, you don’t have to type the sudo password three times. Another good example is that the path of executables (things found in locations in $PATH) are stored in a cache, so their location doesn’t have to be looked up every time they are executed. If the location of an executable changes, that cache needs to be refreshed.

So I wondered if the available space was also stored in a cache file somewhere. I exit and re-enter my ssh session. I wait a few minutes. No luck. I’m not even sure how to Google for this situation.

Then I remember something my old boss Andy said one time on the phone to someone else:

Yeah, the machine is out inodes. Can you add another disk?

Oh yes! inodes are a thing! I don’t really know what an inode is at this moment, but it has something to do with the number of files or the number of open files? I don’t really care right now. I need to finish diagnosing and hotfix this so I can get on my flight. I quickly Google how to investigate this. df -i. Viola! 100% usage. 5.2 million of them, all used up. Does that mean I have 5 million files on this machine? Is that normal? I have no idea. I don’t care.

Ok, so I need to delete some files. Where are all these files? A hunch says they’re in the tmp directory. Where else could there be a buildup of orphan files? This service has been running for more than a year without running out of inodes, so it must be tmp files.

ls /tmp

ls hangs forever. You won’t even let me look at what’s inside you? Smells like guilt. I’m panicking a little now, because I’m blind without ls. Combine that with having to type out every character instead of relying on tab completion, and I’m not feeling so great.

Ok, hail mary time: rm -rf /tmp/*. I should just be able to delete everything in here right? I know this is a bad idea because many services store essential pieces of information in tmp files for their runtime. And this is /tmp, so literally any system service could go down without its tmp files. But I’m willing to take that risk. System services should only store, well, temporary data in /tmp, so a restart or machine reboot should resolve any issues with that. Worst case scenario, spin up a new VM, provision it and deploy my app with a fresh database dump in ~1hr.

Luckily, rm hangs and eventually exits with a message “too many arguments”.

Oh ok, so at least that confirms there are a ton of files in /tmp. I also make a mental “cool!” note that rm -f /tmp/* looks like it’s expanding each file in /tmp and passing them as individual arguments to rm. Is that what the splat operator does? I know that it does something similar in Ruby.

Ok, so what now? I can’t delete files all together and I can’t see how many files are in there. But I really want to see what’s in /tmp before going any further. I remember that I have aliased ls to ls -al on this VM. I wonder if removing the arguments will help get some output. Google says I can run \ls to avoid the alias and run the program directly. /bin/ls would also do the same. Viola again! I have output, but it is taking a long time to print out. Hundreds of hundreds of lines of output. Filenames of garbled letters and numbers. This smells like Dir.mktmpdir. I know I’m doing this in app code somewhere. Looks like it isn’t getting cleaned up. It is probably part of the cache warming code.

I cancel out of the still-streaming output of ls. Clearly I need to run rm on each of these individually. What’s the fastest way for me to do this? I KNOW! I’ll send the output of ls to a file, open it in vim and substitute a rm -rf at the beginning of every line! Oh wait, I can’t create files on this machine. Ok, I’ll just remove a few files manually by copy pasting into the terminal, open up a few inodes and create a single file. But vim is so slow on this machine right now. I know! I’ll scp this file over to my local machine, add the rm -rf prefixes there and then paste the whole file back into my ssh session! Oh shit, the output of ls shows ~4.5 million files in /tmp. This could take a while.

I shut off all the other services on the VM and let 4.5 million lines of rm -rf run uninterrupted for the next 30 minutes. The nice thing is that each line runs individually, so all I have to do to stop deleting files is to close my Terminal tab.

To monitor my inode situation and feel cool at the same time, I ssh into the same machine and run

while true; do df -i; sleep 1; done

Surely enough, they’re going down! I feel happy.

When the inodes usage gets down to 70%, I turn off my rm -rf rager, turn off my cache warmers, and restart my web server. We’re back online and downloads should be stable.

I also mv /tmp /tmp-bak; sudo mkdir /tmp; sudo chmod 1777 /tmp to create an empty /tmp dir with the same octal mode for permissions. I’m not sure this is necessary, and it doesn’t help the disk space or inode situation, but I know I want /tmp to start from a blank slate. If I can’t reset /tmp entirely right now, I can at least swap it out for a new directory.

What a day.

In summary, the way to debug something when you’re all out of ideas is to remember what your boss said 2 years ago.

The lesson I learned was to avoid managing my own VMs and to hug a devops person today.

Want to talk about this blag? Email me or send me a toot @mehulkar!