AWS EC2 Disk Space Full

Mar 16, 2020

Estimated Reading Time: 8 minutes (1492 words)

Updates (4th June, 2020): Adding in another potential causes: logs

The company I am currently working for, uses AWS infrastructure extensively. For instance, we build our Elixir/Phoenix application release on a seperate EC2 instance.

Sometimes, if our engineers are unlucky, their build process will failed because of the lack of disk space in our build server.

Having to deal with this issue a couple of time have taught me a few things. Here, I am sharing the common approaches to clean up our EC2 disk space.

This post assume that you have run df -hT and have something as below:

Filesystem     Type      Size  Used Avail Use% Mounted on
udev           devtmpfs  2.0G     0  2.0G   0% /dev
tmpfs          tmpfs     396M   41M  355M  11% /run
/dev/xvda1     ext4      7.7G  7.7G   70M  59% /

Identifying the root cause

Before cleaning up our disk space, we need to know which directories are taking up most of the space.

To do this, you’ll probably need to have the sudo access. First, run the following command:

cd /
du -ah . | sort -rh | head -20

Let’s have a quick breakdown on what the commands above are doing:

After running this, you might see something like:

du: cannot read directory './proc/27089/task/27089/fd': Permission denied
du: cannot read directory './proc/27089/task/27089/fdinfo': Permission denied
du: cannot read directory './proc/27089/task/27089/ns': Permission denied
du: cannot read directory './proc/27089/fd': Permission denied

Don’t be afraid, nothing is breaking. By the end of the result, you will see something like this:

7.7G	.
3.7G	./usr
1.4G	./home/deploy
1.4G	./home
1.3G	./home/deploy/app/build
1.3G	./home/deploy/app
878M	./var
747M	./usr/lib
676M	./snap
530M	./var/lib
530M	./snap/core
355M	./usr/src
...

Now, we see that /usr are occupying a lot of the space. We can cd /usr and run du -ah . | sort -rh | head -20 again to see which directories in /usr take up the most spaces.

Based on my limited experience, the root cause could be one of the following:

Old Linux Header Files

If you happen to see /usr/src end up being the directory to occupy the most space, and ls /usr/src shows a lot of files in the form of linux-headers-* or linux-headers-*-generic, then you are facing the issue of linux header files occupying the space.

This is what happen to us during the first time.

Solution

After reading around Google Search results. I end up refering to this StackExchange ubuntu question to resolve the issue.

The author suggest running the following commds:

sudo apt-get update
sudo apt-get -f install
sudo apt-get autoremove

These commands will automatically remove older linux header files. You can refer to this StackExchange question regarding whether it’s safe to remove those files.

After runnning the above command, you’ll likely to see the following log (where I shamelessly copy from the StackExchange post mentioned above):

Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED:
  linux-aws-headers-4.4.0-1022 linux-aws-headers-4.4.0-1039 linux-aws-headers-4.4.0-1041 linux-aws-headers-4.4.0-1043
  linux-aws-headers-4.4.0-1044 linux-aws-headers-4.4.0-1048 linux-aws-headers-4.4.0-1049 linux-aws-headers-4.4.0-1052
  linux-aws-headers-4.4.0-1054 linux-aws-headers-4.4.0-1055 linux-aws-headers-4.4.0-1057 linux-aws-headers-4.4.0-1060
  linux-aws-headers-4.4.0-1061 linux-aws-headers-4.4.0-1062 linux-aws-headers-4.4.0-1065 linux-aws-headers-4.4.0-1066
  linux-aws-headers-4.4.0-1069 linux-aws-headers-4.4.0-1070 linux-aws-headers-4.4.0-1072 linux-aws-headers-4.4.0-1074
  linux-aws-headers-4.4.0-1075 linux-aws-headers-4.4.0-1077 linux-aws-headers-4.4.0-1079 linux-aws-headers-4.4.0-1083
  linux-headers-4.4.0-1022-aws linux-headers-4.4.0-1039-aws linux-headers-4.4.0-1041-aws linux-headers-4.4.0-1043-aws
  linux-headers-4.4.0-1044-aws linux-headers-4.4.0-1048-aws linux-headers-4.4.0-1049-aws linux-headers-4.4.0-1052-aws
  linux-headers-4.4.0-1054-aws linux-headers-4.4.0-1055-aws linux-headers-4.4.0-1057-aws linux-headers-4.4.0-1060-aws
  linux-headers-4.4.0-1061-aws linux-headers-4.4.0-1062-aws linux-headers-4.4.0-1065-aws linux-headers-4.4.0-1066-aws
  linux-headers-4.4.0-1069-aws linux-headers-4.4.0-1070-aws linux-headers-4.4.0-1072-aws linux-headers-4.4.0-1074-aws
  linux-headers-4.4.0-1075-aws linux-headers-4.4.0-1077-aws linux-headers-4.4.0-1079-aws linux-headers-4.4.0-1083-aws
  linux-image-4.4.0-1022-aws linux-image-4.4.0-1039-aws linux-image-4.4.0-1041-aws linux-image-4.4.0-1043-aws
  linux-image-4.4.0-1044-aws linux-image-4.4.0-1048-aws linux-image-4.4.0-1049-aws linux-image-4.4.0-1052-aws
  linux-image-4.4.0-1054-aws linux-image-4.4.0-1055-aws linux-image-4.4.0-1057-aws linux-image-4.4.0-1060-aws
  linux-image-4.4.0-1061-aws linux-image-4.4.0-1062-aws linux-image-4.4.0-1065-aws linux-image-4.4.0-1066-aws
  linux-image-4.4.0-1069-aws linux-image-4.4.0-1070-aws linux-image-4.4.0-1072-aws linux-image-4.4.0-1074-aws
  linux-image-4.4.0-1075-aws linux-image-4.4.0-1077-aws linux-image-4.4.0-1079-aws linux-image-4.4.0-1083-aws
  linux-modules-4.4.0-1077-aws linux-modules-4.4.0-1079-aws linux-modules-4.4.0-1083-aws
0 upgraded, 0 newly installed, 75 to remove and 205 not upgraded.
After this operation, 3214 MB disk space will be freed.

Try df -hT again and you should find your disk space get freed up.

Deleted, but opened files

If after running du, but the result doesn’t match up with df -hT, then it is possible that you have some files that is deleted but held open by some application or process.

The second time when our build server experiencing disk usage full issue, I tried removing linux header files as mentioend above, but it doesn’t free up much space.

It takes me a while to figure out what is happening. To summarize, I have learn that du and df sometimes give different disk usage because of these deleted but in use file, after searching about it and came across this StackExchange answer.

For instance, if your du returning something like this:

4.7G	.
1.7G	./usr
1.4G	./home/deploy
...

but your df -hT returning something like this:

Filesystem     Type      Size  Used Avail Use% Mounted on
udev           devtmpfs  2.0G     0  2.0G   0% /dev
tmpfs          tmpfs     396M   41M  355M  11% /run
/dev/xvda1     ext4      7.7G  7.7G   70M  59% /

where 4.7G is not equal to 7.7G. It’s very possible that you are facing the same issue.

Solution

The solution is found on this StackExchange answer. According to the author of the answer, we firstfind out what are the files that took up the spaces by running the following command:

sudo lsof | grep '(deleted)'

You might see something like this:

systemd-j   402                   root  txt       REG              202,1   326224       2308 /lib/systemd/systemd-journald (deleted)
dbus-daem  1032             messagebus  txt       REG              202,1   224208      24312 /usr/bin/dbus-daemon (deleted)
systemd-l  1054                   root  txt       REG              202,1   618520       2307 /lib/systemd/systemd-logind (deleted)
aws       19341                   root   1w       REG              202,1  1504932       3421 /var/log/awslogs.log.1 (deleted)

Then, look for the process that are not important or safe to kill and associated with large file.

For me, it’s aws logs file that is deleted but still help opened. It took up disk space of 1504932.

We can then proceed to kill the process to clear up the identified file by running the following:

# kill -9 <pid>
kill -9 19341

After that you can check your disk usage by using df -hT again and you should now have more free disk space. With this approach, we managed to free up 3.2G of disk space on our build server.

Huge undeleted log files

Recently, I have also came across another potential causes which is huge undeleted log files. It’s easy to locate the issues by simply running:

du -ah . | sort -rh | head -20

If your results is something like this, where /var/log come up as the top one, then it’s definitely due to logs.

7.6G	.
4.5G	./var
3.8G	./var/log
3.4G	./var/log/nginx
1.7G	./usr
1.6G	./var/log/nginx/access.log
882M	./var/log/nginx/error.log.1
696M	./snap
645M	./var/log/nginx/access.log.1
...
324M	./var/lib/snapd
276M	./usr/lib/x86_64-linux-gnu
275M	./snap/core/9066
275M	./snap/core/8935

As you can see from the results, in this case /var/log/nginx seems like the culprit. We can then change directory and ls -lah (-h to format the file size to human readable format), which result in:

total 3.4G
drwxr-xr-x  2 root   adm     4.0K May 31 06:25 .
drwxrwxr-x 11 root   syslog  4.0K Jun  1 01:30 ..
-rw-r-----  1 deploy adm     1.6G Jun  1 02:09 access.log
-rw-r-----  1 deploy adm     645M May 29 06:25 access.log.1
-rw-r-----  1 deploy adm      81K May 17 06:25 access.log.10.gz
-rw-r-----  1 deploy adm     268K May 16 06:25 access.log.11.gz
-rw-r-----  1 deploy adm    1019K May 15 06:25 access.log.12.gz
...
-rw-r-----  1 deploy adm     252M Jun  1 02:07 error.log
-rw-r-----  1 deploy adm     882M May 29 02:34 error.log.1
...

While it may seems like the straightforward solution is just rm access.log, but there are some caveat. Before deleting those logs directly, is good to google search around on how to do it properly, so this is what I found:

Browse those link if you want to learn more about it. But in my case, I am following the answer on the third link:

mv access.log access.log.old
# After this command, you should see a new empty access.log file created.
kill -USR1 `cat /var/run/nginx.pid`
rm access.log.old

If let’s say your largest log file is access.log.<number>, generally, it’s safe to delete it directly (you might need to double check on this, can’t manage to find a source to support my point and this time of writing).

At the end, here is the result when I run df -hT again:

Filesystem     Type      Size  Used Avail Use% Mounted on
udev           devtmpfs  2.0G     0  2.0G   0% /dev
tmpfs          tmpfs     396M   41M  355M  11% /run
/dev/xvda1     ext4      7.7G  4.3G  3.5G  56% /
...

All my space is back! And nginx is still working properly.

Conclusion

That’s all. These are the findings I discovered while attempting to solve disk space full issue in our EC2 instances. Hopefully it helps. All the information are actually available if we managed to search for the right term or key words.

Here are some other resources I refer to that are not mentioned in the article: