K
Q

Kubernetes node with high disk usage caused by docker overlay

6/22/2017

I am facing a problem with kubernetes nodes deployed on AWS. (Cluster with 3 nodes and 1 master running on m3.large instances with each about 25GB)

After (about 3 days) there is 0KB left on disk and the cluster get stuck.

All the storage (more or less) is used by /var/lib/docker/overlay/. Inside this folder are about 500 or more of those files:

drwx------ 3 root root 4096 Jun 20 15:33 ed4f90bd7a64806f9917e995a02974ac69883a06933033ffd5049dd31c13427a
drwx------ 3 root root 4096 Jun 20 15:28 ee9344fea422c38d71fdd2793ed517c5693b0c8a890964e6932befa1ebe5aa63
drwx------ 3 root root 4096 Jun 20 16:17 efed310a549243e730e9796e558b2ae282e07ea3ce0840a50c0917a435893d42
drwx------ 3 root root 4096 Jun 20 14:39 eff7f04f17c0f96cff496734fdc1903758af1dfdcd46011f6c3362c73c6086c2
drwx------ 3 root root 4096 Jun 20 15:29 f5bfb696f5a6cad888f7042d01bfe146c0621517c124d58d76e77683efa1034e
drwx------ 3 root root 4096 Jun 20 15:26 f5fa9d5d2066c7fc1c8f80970669634886dcaccc9e73ada33c7c250845d2fe8c
drwx------ 3 root root 4096 Jun 20 14:38 f8fd64fb1e0ab26708d5458dddd2d5a70018034237dfed3db48ada5666fcf77f
drwx------ 3 root root 4096 Jun 20 14:46 faa143ebd7a4079eaa45ddbf17dcfc9163e3035983f2e334e32a60e89452fa94
drwx------ 3 root root 4096 Jun 20 14:48 fb93c0c64e0d4935bf67fc8f70df2b8a4cffe59e294ee8a876dfdf6b57486da5
drwx------ 3 root root 4096 Jun 20 14:46 fd0a420d5655fb7d022c397effdb95968ff7e722c58fcc7915f97e8df47cd080

Cluster runs on Kubernetes 1.6.4 and Docker 1.12.6.

Seems to be a problem with the garbage collector of kubernetes. Running cAdvisor /validate gives me following message

 None of the devices support 'cfq' I/O scheduler. No disk stats can be reported.
     Disk "xvda" Scheduler type "none".

Running those statement journalctl -u kubelet | grep -i garbage gives also a error message: Jun 20 14:35:21 ip-172-21-4-239 kubelet[1551]: E0620 14:35:21.986898 1551 kubelet.go:1165] Image garbage collection failed: unable to find data for container /

Any ideas how to get the garbage collector working again?

-- nrhode
amazon-ec2
aws-ebs
cadvisor
docker
kubernetes

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1 Answer

5/21/2018

I was able to resolve a similar issue with recurring high IO on the nodes due to du -s /var/lib/docker/overlay/ by editing kops cluster.spec with kops edit cluster [cluster_name]. I added the following under specs:

docker:
    logDriver: json-file
    logLevel: warn
    storage: overlay2

It looks like by default kops configures docker to use overlay as default storage driver, while docker recommends using overlay2 as newer, more stable and faster.

-- Mark Hilton
Source: StackOverflow