Docker container took too many storage of disk - docker

Question

I was use df -hl for check the status of my vps, but it is seem like,the Storage is took by docker mutil time(i only have 1 wordpress in this vps, there is no have other project)
today i recived a email from linode, they tell me my Storage is finished
Total: 25600 MB
Used: 25600 MB
i have a wordpress in this vps, which is builded by docker and wordpress
here is the code which from my vps
root#localhost:~# df -hl
Filesystem Size Used Avail Use% Mounted on
udev 463M 0 463M 0% /dev
tmpfs 99M 5.9M 93M 6% /run
/dev/sda 25G 5.0G 19G 22% /
tmpfs 493M 0 493M 0% /dev/shm
tmpfs 5.0M 0 5.0M 0% /run/lock
tmpfs 493M 0 493M 0% /sys/fs/cgroup
overlay 25G 5.0G 19G 22% /var/lib/docker/overlay2/2ebf8af06fccd1e3a455746e257c990e6d85f848832eaadd636f48d56e6fbefb/merged
overlay 25G 5.0G 19G 22% /var/lib/docker/overlay2/28044ad06cc4b50d58a331cd644a254c7c90480ad04c1686f2974503da1c98de/merged
shm 64M 0 64M 0% /var/lib/docker/containers/932928ba7b7ccbbb4dd9f05263fadda8c6764ec7185deefc37c0fc555a2c32d5/mounts/shm
shm 64M 0 64M 0% /var/lib/docker/containers/67d10956ef387af8327570b7013cc113114a48ccf3654f9ee01041e88e740192/mounts/shm
overlay 25G 5.0G 19G 22% /var/lib/docker/overlay2/b81fd707a47702b060b462fbb1424bf024c4e593071b0782f4c817ca46a188e2/merged
shm 64M 0 64M 0% /var/lib/docker/containers/ce2422fff8741ede110a730d1283e0f43792de05a14b2ae9bdb59874fefa5fc2/mounts/shm
tmpfs 99M 0 99M 0% /run/user/0
root#localhost:~# docker ps -a
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
932928ba7b7c wordpress:latest "docker-entrypoint.s…" 7 weeks ago Up 2 weeks 0.0.0.0:1994->80/tcp jujuzone_site
67d10956ef38 phpmyadmin/phpmyadmin "/run.sh supervisord…" 7 weeks ago Up 2 weeks 9000/tcp, 0.0.0.0:8081->80/tcp phpmyadmin
ce2422fff874 mysql:5.7 "docker-entrypoint.s…" 7 weeks ago Up 4 hours 3306/tcp, 33060/tcp db_jujuzone
root#localhost:~# docker system prune
WARNING! This will remove:
- all stopped containers
- all networks not used by at least one container
- all dangling images
- all dangling build cache
Are you sure you want to continue? [y/N] y
Total reclaimed space: 0B

Answer 1

It seems you've deleted some files that might still be in use by the system.
Keep in mind that in this case, the df command can show a different size from the du command.
You can check that with more precision using du -hc on the same directories and check if it's total differs from the df command.
You can also run lsof |grep '(deleted)' to verify which files were left open for the file descriptor.
In this case, you can kill this process and restart the responsible daemon.
After all, you must consider to run docker system prune with -a flag to also clear unused images and maybe reclaim a little bit more space.

Answer 2

I was experiencing this same issue recently on Ubuntu 20.04 with Docker v19.03.13. I searched through Docker docs and found that this maybe because of a new type of filesystem they introduced. You can read more about it from here. The way I fixed it was by editing (creating if not present already) the /etc/docker/daemon.json file and adding the following lines:
{
"storage-driver": "overlay"
}
Then restarting docker using the following command:
sudo systemctl restart docker
I have answered a similar question here.