Is it safe to clean docker/overlay2/

Question

I got some docker containers running on AWS EC2, the /var/lib/docker/overlay2 folder grows very fast in disk size.

I'm wondering if it is safe to delete its content? or if docker has some kind of command to free up some disk usage.

---

UPDATE:

I actually tried docker system prune -a already, which reclaimed 0Kb.

Also my /docker/overlay2 disk size is much larger than the output from docker system df

After reading docker documentation and BMitch's answer, I believe it is a stupid idea to touch this folder and I will try other ways to reclaim my disk space.

Answer 1

I found this worked best for me:

docker image prune --all

By default Docker will not remove named images, even if they are unused. This command will remove unused images.

Note each layer in an image is a folder inside the /usr/lib/docker/overlay2/ folder.

Answer 2

I used "docker system prune -a" it cleaned all files under volumes and overlay2

    [root@jasontest volumes]# docker system prune -a
    WARNING! This will remove:
            - all stopped containers
            - all networks not used by at least one container
            - all images without at least one container associated to them
            - all build cache
    Are you sure you want to continue? [y/N] y
    Deleted Images:
    untagged: ubuntu:12.04
    untagged: ubuntu@sha256:18305429afa14ea462f810146ba44d4363ae76e4c8dfc38288cf73aa07485005
    deleted: sha256:5b117edd0b767986092e9f721ba2364951b0a271f53f1f41aff9dd1861c2d4fe
    deleted: sha256:8c7f3d7534c80107e3a4155989c3be30b431624c61973d142822b12b0001ece8
    deleted: sha256:969d5a4e73ab4e4b89222136eeef2b09e711653b38266ef99d4e7a1f6ea984f4
    deleted: sha256:871522beabc173098da87018264cf3e63481628c5080bd728b90f268793d9840
    deleted: sha256:f13e8e542cae571644e2f4af25668fadfe094c0854176a725ebf4fdec7dae981
    deleted: sha256:58bcc73dcf4050a4955916a0dcb7e5f9c331bf547d31e22052f1b5fa16cf63f8
    untagged: osixia/openldap:1.2.1
    untagged: osixia/openldap@sha256:6ceb347feb37d421fcabd80f73e3dc6578022d59220cab717172ea69c38582ec
    deleted: sha256:a562f6fd60c7ef2adbea30d6271af8058c859804b2f36c270055344739c06d64
    deleted: sha256:90efa8a88d923fb1723bea8f1082d4741b588f7fbcf3359f38e8583efa53827d
    deleted: sha256:8d77930b93c88d2cdfdab0880f3f0b6b8be191c23b04c61fa1a6960cbeef3fe6
    deleted: sha256:dd9f76264bf3efd36f11c6231a0e1801c80d6b4ca698cd6fa2ff66dbd44c3683
    deleted: sha256:00efc4fb5e8a8e3ce0cb0047e4c697646c88b68388221a6bd7aa697529267554
    deleted: sha256:e64e6259fd63679a3b9ac25728f250c3afe49dbe457a1a80550b7f1ccf68458a
    deleted: sha256:da7d34d626d2758a01afe816a9434e85dffbafbd96eb04b62ec69029dae9665d
    deleted: sha256:b132dace06fa7e22346de5ca1ae0c2bf9acfb49fe9dbec4290a127b80380fe5a
    deleted: sha256:d626a8ad97a1f9c1f2c4db3814751ada64f60aed927764a3f994fcd88363b659
    untagged: centos:centos7
    untagged: centos@sha256:2671f7a3eea36ce43609e9fe7435ade83094291055f1c96d9d1d1d7c0b986a5d
    deleted: sha256:ff426288ea903fcf8d91aca97460c613348f7a27195606b45f19ae91776ca23d
    deleted: sha256:e15afa4858b655f8a5da4c4a41e05b908229f6fab8543434db79207478511ff7

    Total reclaimed space: 533.3MB
    [root@jasontest volumes]# ls -alth
    total 32K
    -rw-------  1 root root  32K May 23 21:14 metadata.db
    drwx------  2 root root 4.0K May 23 21:14 .
    drwx--x--x 14 root root 4.0K May 21 20:26 ..

Answer 3

also had problems with rapidly growing overlay2

/var/lib/docker/overlay2 - is a folder where docker store writable layers for your container. docker system prune -a - may work only if container is stopped and removed.

in my i was able to figure out what consumes space by going into overlay2 and investigating.

that folder contains other hash named folders. each of those has several folders including diff folder.

diff folder - contains actual difference written by a container with exact folder structure as your container (at least it was in my case - ubuntu 18...)

so i've used du -hsc /var/lib/docker/overlay2/LONGHASHHHHHHH/diff/tmp to figure out that /tmp inside of my container is the folder which gets polluted.

so as a workaround i've used -v /tmp/container-data/tmp:/tmp parameter for docker run command to map inner /tmp folder to host and setup a cron on host to cleanup that folder.

cron task was simple:

• sudo nano /etc/crontab
• */30 * * * * root rm -rf /tmp/container-data/tmp/*
• save and exit

NOTE: overlay2 is system docker folder, and they may change it structure anytime. Everything above is based on what i saw in there. Had to go in docker folder structure only because system was completely out of space and even wouldn't allow me to ssh into docker container.

Answer 4

WARNING: DO NOT USE IN A PRODUCTION SYSTEM

/# df
...
/dev/xvda1      51467016 39384516   9886300  80% /
...

Ok, let's first try system prune

#/ docker system prune --volumes
...
/# df
...
/dev/xvda1      51467016 38613596  10657220  79% /
...

Not so great, seems like it cleaned up a few megabytes. Let's go crazy now:

/# sudo su
/# service docker stop
/# cd /var/lib/docker
/var/lib/docker# rm -rf *
/# service docker start
/var/lib/docker# df
...
/dev/xvda1      51467016 8086924  41183892  17% /
...

Nice! Just remember that this is NOT recommended in anything but a throw-away server. At this point Docker's internal database won't be able to find any of these overlays and it may cause unintended consequences.

Answer 5

Docker uses /var/lib/docker to store your images, containers, and local named volumes. Deleting this can result in data loss and possibly stop the engine from running. The overlay2 subdirectory specifically contains the various filesystem layers for images and containers.

To cleanup unused containers and images, see docker system prune. There are also options to remove volumes and even tagged images, but they aren't enabled by default due to the possibility of data loss.

Answer 6

Backgroud

The blame for the issue can be split between our misconfiguration of container volumes, and a problem with docker leaking (failing to release) temporary data written to these volumes. We should be mapping (either to host folders or other persistent storage claims) all of out container's temporary / logs / scratch folders where our apps write frequently and/or heavily. Docker does not take responsibility for the cleanup of all automatically created so-called EmptyDirs located by default in /var/lib/docker/overlay2/*/diff/*. Contents of these "non-persistent" folders should be purged automatically by docker after container is stopped, but apparently are not (they may be even impossible to purge from the host side if the container is still running - and it can be running for months at a time).

Workaround

A workaround requires careful manual cleanup, and while already described elsewhere, you still may find some hints from my case study, which I tried to make as instructive and generalizable as possible.

So what happened is the culprit app (in my case clair-scanner) managed to write over a few months hundreds of gigs of data to the /diff/tmp subfolder of docker's overlay2

du -sch /var/lib/docker/overlay2/<long random folder name seen as bloated in df -h>/diff/tmp

271G total

So as all those subfolders in /diff/tmp were pretty self-explanatory (all were of the form clair-scanner-* and had obsolete creation dates), I stopped the associated container (docker stop clair) and carefully removed these obsolete subfolders from diff/tmp, starting prudently with a single (oldest) one, and testing the impact on docker engine (which did require restart [systemctl restart docker] to reclaim disk space):

rm -rf $(ls -at /var/lib/docker/overlay2/<long random folder name seen as bloated in df -h>/diff/tmp | grep clair-scanner | tail -1)

I reclaimed hundreds of gigs of disk space without the need to re-install docker or purge its entire folders. All running containers did have to be stopped at one point, because docker daemon restart was required to reclaim disk space, so make sure first your failover containers are running correctly on an/other node/s). I wish though that the docker prune command could cover the obsolete /diff/tmp (or even /diff/*) data as well (via yet another switch).

It's a 3-year-old issue now, you can read its rich and colorful history on Docker forums, where a variant aimed at application logs of the above solution was proposed in 2019 and seems to have worked in several setups: https://forums.docker.com/t/some-way-to-clean-up-identify-contents-of-var-lib-docker-overlay/30604