Just recently I had the following issue while trying to stop my containers:
Error response from daemon: Cannot kill container: 9e81a44d4c79: Cannot kill container xxxx: unknown error after kill: runc did not terminate sucessfully: container_linux.go:392: signaling init process caused "permission denied"
The container was started regularly with docker-compose up, and after that, it wasn't reacting to:
docker-compose down
docker-compose stop xxx or docker container stop xxx
It turned out that AppArmor service was messing up with Docker. AppArmor (or "Application Armor") is a Linux kernel security module that allows the system administrator to restrict programs' capabilities with per-program profiles. For this problem with containers, it helped me to remove the unknown from AppArmor using the following command:
sudo aa-remove-unknown
After that, I was able to stop and kill my containers. To kill all running Docker containers, you can use the following command:
docker container kill $(docker ps -q)
If this didn't work for you, you can remove AppArmor, and then install it afterward if it's needed:
sudo apt-get purge --auto-remove apparmor`
`sudo service docker restart`
`docker system prune --all --volumes