docker mysql – Fatal error: Please read “Security” section of the manual to find out how to run mysqld as root!

Pulling the official MySQL image from the docker registry https://hub.docker.com/r/mysql/mysql-server to start a MySQL instance with your configuration file (and MySQL binary files). Adding the “–volume” option for the configuration directory (or file) and MySQL binary files and you stumble on the error:

2019-12-03 01:13:38 0 [Note] mysqld (mysqld 5.6.46-log) starting as process 67 ...
2019-12-03 01:13:38 67 [ERROR] Fatal error: Please read "Security" section of the manual to find out how to run mysqld as root!

2019-12-03 01:13:38 67 [ERROR] Aborting

2019-12-03 01:13:38 67 [Note] Binlog end
2019-12-03 01:13:38 67 [Note] mysqld: Shutdown complete

Apparently, the server option is not configured to run properly as a root user and you do not want to run it, but why it keeps insisting to run it as root?

Because of the entry point script will execute only “mysqld” as a command, which expects to have a “user” option in the “[mysqld]” section of your my.cnf configuration file!

Do not miss the user option in my.cnf! This is how the MySQL server will be using the “mysql” username not the root!

user=mysql

Typical error, because it is not so common to include the username in my.cnf configuration file of the mysqld process to run as. If you use the official docker MySQL image to create your configuration file you would not encounter the above error, but if you use an existing (probably old and from non virtualized environment) my.cnf make sure to include the username, which should be used to run the mysqld process as.

Here is our command to execute the container:

docker run --privileged -d -v /mnt/storage/docker/mysql-slave/files:/var/lib/mysql -v /mnt/storage/docker/mysql-slave/etc/my.cnf:/etc/my.cnf mysql/mysql-server:5.6

Build docker image with custom Dockerfile name – docker build requires exactly 1 argument

Docker uses the Dockerfile to build docker images, but what if you want to change the name and (or) the path of this file?
By default “docker build” command uses a file named Dockerfile on the same directory you execute the “docker build“. There is an option to change the path and name of this special file:

  -f, --file string             Name of the Dockerfile (Default is 'PATH/Dockerfile')

And the “-f” may include path and file name but it is mandatory to specify the path at the end “docker build” usually the current directory (context by the docker terminology) by adding “.” (the dot at the end of the command)

So if you want to build with a docker file mydockerfile in the current directory you must execute:

docker build -f mydockerfile .

If your file is in a sub-directory execute:

docker build -f subdirectory/mydockerfile .

The command will create a docker image in your local repository. Here is the output of the first command:

root@srv:~/docker# docker build -f mydockerfile .
Sending build context to Docker daemon  2.048kB
Step 1/3 : FROM ubuntu:bionic-20191029
bionic-20191029: Pulling from library/ubuntu
7ddbc47eeb70: Pull complete 
c1bbdc448b72: Pull complete 
8c3b70e39044: Pull complete 
45d437916d57: Pull complete 
Digest: sha256:6e9f67fa63b0323e9a1e587fd71c561ba48a034504fb804fd26fd8800039835d
Status: Downloaded newer image for ubuntu:bionic-20191029
 ---> 775349758637
Step 2/3 : MAINTAINER test@example.com
 ---> Running in 5fa42bca749c
Removing intermediate container 5fa42bca749c
 ---> 0a1ffa1728f4
Step 3/3 : RUN apt-get update && apt-get upgrade -y && apt-get install -y git wget
 ---> Running in 2e35040f247c
Get:1 http://security.ubuntu.com/ubuntu bionic-security InRelease [88.7 kB]
Get:2 http://archive.ubuntu.com/ubuntu bionic InRelease [242 kB]
Get:3 http://archive.ubuntu.com/ubuntu bionic-updates InRelease [88.7 kB]
Get:4 http://archive.ubuntu.com/ubuntu bionic-backports InRelease [74.6 kB]
.....
.....
Processing triggers for ca-certificates (20180409) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Removing intermediate container 2e35040f247c
 ---> 2382809739a4
Successfully built 2382809739a4

Here is the image:

REPOSITORY                            TAG                 IMAGE ID            CREATED              SIZE
root@srv:~# docker images
<none>                                <none>              2382809739a4        About a minute ago   186MB

Build command with custom name and registry URL and TAG

root@srv:~# docker build -t gitlab.ahelpme.com:4567/root/ubuntu-project/ubuntu18-manual-base:v0.1 -f mydockerfile .
Sending build context to Docker daemon  2.048kB
Step 1/3 : FROM ubuntu:bionic-20191029
 ---> 775349758637
Step 2/3 : MAINTAINER test@example.com
 ---> Using cache
 ---> 0a1ffa1728f4
Step 3/3 : RUN apt-get update && apt-get upgrade -y && apt-get install -y git wget
 ---> Using cache
 ---> 2382809739a4
Successfully built 2382809739a4
Successfully tagged gitlab.ahelpme.com:4567/root/ubuntu-project/ubuntu18-manual-base:v0.1
root@srv:~# docker push gitlab.ahelpme.com:4567/root/ubuntu-project/ubuntu18-manual-base:v0.1
The push refers to repository [gitlab.ahelpme.com:4567/root/ubuntu-project/ubuntu18-manual-base]
7cebba4bf6c3: Pushed 
e0b3afb09dc3: Pushed 
6c01b5a53aac: Pushed 
2c6ac8e5063e: Pushed 
cc967c529ced: Pushed 
v0.1: digest: sha256:acf42078bf46e320c402f09c6417a3dae8992ab4f4f685265486063daf30cb13 size: 1364

the registry URL is “gitlab.ahelpme.com:4567” and the project path is “/root/ubuntu-project/” and the name of the image is “ubuntu18-manual-base” with tag “v0.1“. The build command uses the cache from our first build example here (because the docker file is the same).

Typical errors with “-f”

Two errors you may encounter when trying the “-f” to change the name of the default Dockerfile name:

$ docker build -t gitlab.ahelpme.com:4567/root/ubuntu-project/ubuntu18-manual-base:v0.1 -f mydockerfile subdirectory/
unable to prepare context: unable to evaluate symlinks in Dockerfile path: lstat /builds/dev/docker-containers/mydockerfile: no such file or directory

$ docker build -t gitlab.ahelpme.com:4567/root/ubuntu-project/ubuntu18-manual-base:v0.1 -f subdirectory/mydockerfile
"docker build" requires exactly 1 argument.
See 'docker build --help'.

Usage:  docker build [OPTIONS] PATH | URL | -

First, you might think the -f would take the path and file name and this should be enough, but the errors above appears!

Our example Dockerfile

This is our simple example docker file:

FROM ubuntu:bionic-20191029
MAINTAINER test@example.com

RUN apt-get update && apt-get upgrade -y && apt-get install -y git wget

We are using the official docker image from Ubuntu. Always use official docker images!

Docker change the port mapping of an existing container

Unfortunately, it is not possible to change the port mapping (forwarded ports from the hosts to the container) of an existing RUNNING container!

Not only that, but you cannot change the mapped ports (forwarded ports) even when the container is stopped, so think twice when you run or start a container from the image you’ve chosen. Of course, you can always use docker’s commit command, which just creates a new image from you (running, in a sense of changes fro the original image) container and then you can run the new image with new mapped ports!

Still, there is a solution not involving the creation of new docker images and containers, but just to edit manually a configuration file while the Docker service is stopped.

So if you have several docker containers running you should stop all of them! When the Docker service stops, edit the “hostconfig.json” file! Here is the whole procedure:

  1. Stop the container.
  2. Stop the Docker container service.
  3. Edit the container’s file – hostconfig.json (usually in /var/lib/docker/containers/[ID]/hostconfig.json) and add or replace ports.
  4. Start the Docker container service.
  5. Start the docker container.

Real World Example

myuser@srv:~# sudo docker ps
CONTAINER ID        IMAGE                         COMMAND                  CREATED             STATUS                  PORTS                                                                                    NAMES
a9e21e92e2dd        gitlab/gitlab-runner:latest   "/usr/bin/dumb-init …"   2 days ago          Up 33 hours                                                                                                      gitlab-runner
5d025e7f93a4        gitlab/gitlab-ce:latest       "/assets/wrapper"        3 days ago          Up 34 hours (healthy)   0.0.0.0:80->80/tcp, 0.0.0.0:4567->4567/tcp, 0.0.0.0:1022->22/tcp   gitlab
myuser@srv:~# sudo docker ps
CONTAINER ID        IMAGE                         COMMAND                  CREATED             STATUS                  PORTS                                                                                    NAMES
a9e21e92e2dd        gitlab/gitlab-runner:latest   "/usr/bin/dumb-init …"   2 days ago          Up 33 hours                                                                                                      gitlab-runner
5d025e7f93a4        gitlab/gitlab-ce:latest       "/assets/wrapper"        3 days ago          Up 34 hours (healthy)   0.0.0.0:80->80/tcp, 0.0.0.0:4567->4567/tcp, 0.0.0.0:1022->22/tcp   gitlab
myuser@srv:~# sudo docker stop gitlab-runner
gitlab-runner
myuser@srv:~# sudo docker stop gitlab
gitlab
myuser@srv:~# sudo docker ps
CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES
myuser@srv:~# systemctl stop docker
myuser@srv:~# systemctl status docker
● docker.service - Docker Application Container Engine
   Loaded: loaded (/lib/systemd/system/docker.service; enabled; vendor preset: enabled)
   Active: inactive (dead) since Thu 2019-11-14 21:54:57 UTC; 5s ago
     Docs: https://docs.docker.com
  Process: 2340 ExecStart=/usr/bin/dockerd -H fd:// --containerd=/run/containerd/containerd.sock (code=exited, status=0/SUCCESS)
 Main PID: 2340 (code=exited, status=0/SUCCESS)

Nov 14 21:54:33 srv dockerd[2340]: time="2019-11-14T21:54:33.308531424Z" level=warning msg="a9e21e92e2dd297a68f68441353fc3bda39d0bb5564b60d402ae651fa80f5c72 cleanu
Nov 14 21:54:46 srv dockerd[2340]: time="2019-11-14T21:54:46.394643530Z" level=info msg="Container 5d025e7f93a45a50dbbaa87c55d7cdbbf6515bbe1d45ff599074f1cdcf320a0c
Nov 14 21:54:46 srv dockerd[2340]: time="2019-11-14T21:54:46.757171067Z" level=info msg="ignoring event" module=libcontainerd namespace=moby topic=/tasks/delete ty
Nov 14 21:54:47 srv dockerd[2340]: time="2019-11-14T21:54:47.031709355Z" level=warning msg="5d025e7f93a45a50dbbaa87c55d7cdbbf6515bbe1d45ff599074f1cdcf320a0c cleanu
Nov 14 21:54:57 srv systemd[1]: Stopping Docker Application Container Engine...
Nov 14 21:54:57 srv dockerd[2340]: time="2019-11-14T21:54:57.439296168Z" level=info msg="Processing signal 'terminated'"
Nov 14 21:54:57 srv dockerd[2340]: time="2019-11-14T21:54:57.447803201Z" level=info msg="Daemon shutdown complete"
Nov 14 21:54:57 srv dockerd[2340]: time="2019-11-14T21:54:57.449422219Z" level=info msg="stopping event stream following graceful shutdown" error="context canceled
Nov 14 21:54:57 srv dockerd[2340]: time="2019-11-14T21:54:57.449576789Z" level=info msg="stopping event stream following graceful shutdown" error="context canceled
Nov 14 21:54:57 srv systemd[1]: Stopped Docker Application Container Engine.
myuser@srv:~# cat /var/lib/docker/containers/5d025e7f93a45a50dbbaa87c55d7cdbbf6515bbe1d45ff599074f1cdcf320a0c/hostconfig.json 
{"Binds":["/srv/gitlab/config:/etc/gitlab","/srv/gitlab/logs:/var/log/gitlab","/srv/gitlab/data:/var/opt/gitlab"],"ContainerIDFile":"","LogConfig":{"Type":"json-file","Config":{}},"NetworkMode":"default","PortBindings":{"22/tcp":[{"HostIp":"","HostPort":"1022"}],"4567/tcp":[{"HostIp":"","HostPort":"4567"}],"80/tcp":[{"HostIp":"","HostPort":"80"}]},"RestartPolicy":{"Name":"always","MaximumRetryCount":0},"AutoRemove":false,"VolumeDriver":"","VolumesFrom":null,"CapAdd":null,"CapDrop":null,"Capabilities":null,"Dns":[],"DnsOptions":[],"DnsSearch":[],"ExtraHosts":null,"GroupAdd":null,"IpcMode":"private","Cgroup":"","Links":null,"OomScoreAdj":0,"PidMode":"","Privileged":false,"PublishAllPorts":false,"ReadonlyRootfs":false,"SecurityOpt":null,"UTSMode":"","UsernsMode":"","ShmSize":67108864,"Runtime":"runc","ConsoleSize":[0,0],"Isolation":"","CpuShares":0,"Memory":0,"NanoCpus":0,"CgroupParent":"","BlkioWeight":0,"BlkioWeightDevice":[],"BlkioDeviceReadBps":null,"BlkioDeviceWriteBps":null,"BlkioDeviceReadIOps":null,"BlkioDeviceWriteIOps":null,"CpuPeriod":0,"CpuQuota":0,"CpuRealtimePeriod":0,"CpuRealtimeRuntime":0,"CpusetCpus":"","CpusetMems":"","Devices":[],"DeviceCgroupRules":null,"DeviceRequests":null,"KernelMemory":0,"KernelMemoryTCP":0,"MemoryReservation":0,"MemorySwap":0,"MemorySwappiness":null,"OomKillDisable":false,"PidsLimit":null,"Ulimits":null,"CpuCount":0,"CpuPercent":0,"IOMaximumIOps":0,"IOMaximumBandwidth":0,"MaskedPaths":["/proc/asound","/proc/acpi","/proc/kcore","/proc/keys","/proc/latency_stats","/proc/timer_list","/proc/timer_stats","/proc/sched_debug","/proc/scsi","/sys/firmware"],"ReadonlyPaths":["/proc/bus","/proc/fs","/proc/irq","/proc/sys","/proc/sysrq-trigger"]
myuser@srv:~# nano /var/lib/docker/containers/5d025e7f93a45a50dbbaa87c55d7cdbbf6515bbe1d45ff599074f1cdcf320a0c/hostconfig.json 
myuser@srv:~# systemctl start docker
myuser@srv:~# systemctl status docker
● docker.service - Docker Application Container Engine
   Loaded: loaded (/lib/systemd/system/docker.service; enabled; vendor preset: enabled)
   Active: active (running) since Thu 2019-11-14 22:12:06 UTC; 2s ago
     Docs: https://docs.docker.com
 Main PID: 4693 (dockerd)
    Tasks: 54
   CGroup: /system.slice/docker.service
           ├─4693 /usr/bin/dockerd -H fd:// --containerd=/run/containerd/containerd.sock
           ├─4867 /usr/bin/docker-proxy -proto tcp -host-ip 0.0.0.0 -host-port 4567 -container-ip 172.17.0.3 -container-port 4567
           ├─4881 /usr/bin/docker-proxy -proto tcp -host-ip 0.0.0.0 -host-port 443 -container-ip 172.17.0.3 -container-port 443
           ├─4895 /usr/bin/docker-proxy -proto tcp -host-ip 0.0.0.0 -host-port 1022 -container-ip 172.17.0.3 -container-port 22
           └─4907 /usr/bin/docker-proxy -proto tcp -host-ip 0.0.0.0 -host-port 80 -container-ip 172.17.0.3 -container-port 80

Nov 14 22:12:04 srv dockerd[4693]: time="2019-11-14T22:12:04.034007956Z" level=warning msg="Your kernel does not support swap memory limit"
Nov 14 22:12:04 srv dockerd[4693]: time="2019-11-14T22:12:04.034062799Z" level=warning msg="Your kernel does not support cgroup rt period"
Nov 14 22:12:04 srv dockerd[4693]: time="2019-11-14T22:12:04.034074070Z" level=warning msg="Your kernel does not support cgroup rt runtime"
Nov 14 22:12:04 srv dockerd[4693]: time="2019-11-14T22:12:04.034361581Z" level=info msg="Loading containers: start."
Nov 14 22:12:04 srv dockerd[4693]: time="2019-11-14T22:12:04.344354207Z" level=info msg="Default bridge (docker0) is assigned with an IP address 172.17.0.0/16. Dae
Nov 14 22:12:05 srv dockerd[4693]: time="2019-11-14T22:12:05.916782317Z" level=info msg="Loading containers: done."
Nov 14 22:12:05 srv dockerd[4693]: time="2019-11-14T22:12:05.988204406Z" level=info msg="Docker daemon" commit=9013bf583a graphdriver(s)=overlay2 version=19.03.4
Nov 14 22:12:05 srv dockerd[4693]: time="2019-11-14T22:12:05.988317448Z" level=info msg="Daemon has completed initialization"
Nov 14 22:12:06 srv dockerd[4693]: time="2019-11-14T22:12:06.010801856Z" level=info msg="API listen on /var/run/docker.sock"
Nov 14 22:12:06 srv systemd[1]: Started Docker Application Container Engine.
myuser@srv:~# sudo docker start gitlab-runner
gitlab-runner
myuser@srv:~# sudo docker start gitlab
gitlab
myuser@srv:~# sudo docker ps
CONTAINER ID        IMAGE                         COMMAND                  CREATED             STATUS                             PORTS                                                                                    NAMES
a9e21e92e2dd        gitlab/gitlab-runner:latest   "/usr/bin/dumb-init …"   2 days ago          Up 19 seconds                                                                                                               gitlab-runner
5d025e7f93a4        gitlab/gitlab-ce:latest       "/assets/wrapper"        3 days ago          Up 19 seconds (health: starting)   0.0.0.0:80->80/tcp, 0.0.0.0:443->443/tcp, 0.0.0.0:4567->4567/tcp, 0.0.0.0:1022->22/tcp   gitlab
myuser@srv:~# wget --no-check-certificate https://192.168.0.238/
--2019-11-14 22:13:30--  https://192.168.0.238/
Connecting to 192.168.0.238:443... connected.
    WARNING: certificate common name ‘gitlab.ahelpme.com’ doesn't match requested host name ‘192.168.0.238’.
HTTP request sent, awaiting response... 302 Found
Location: https://192.168.0.238/users/sign_in [following]
--2019-11-14 22:13:30--  https://192.168.0.238/users/sign_in
Reusing existing connection to 192.168.0.238:443.
HTTP request sent, awaiting response... 200 OK
Length: unspecified 
Saving to: ‘index.html’

index.html                                     [ <=>                                                                                     ]  12.41K  --.-KB/s    in 0s      

2019-11-14 22:13:31 (134 MB/s) - ‘index.html’ saved [12708]


Change the ports or add more ports in “PortBindings”. The syntax is pretty straightforward just mind the comas, [] and {}.

"PortBindings":{"22/tcp":[{"HostIp":"","HostPort":"1022"}],"4567/tcp":[{"HostIp":"","HostPort":"4567"}],"80/tcp":[{"HostIp":"","HostPort":"80"}]}

Here we change the mapping from “host port 1022 to 22” to “host port 2222 to 22” just replacing the “1022” to “2222”:

"PortBindings":{"22/tcp":[{"HostIp":"","HostPort":"2222"}],"4567/tcp":[{"HostIp":"","HostPort":"4567"}],"80/tcp":[{"HostIp":"","HostPort":"80"}]}

And the second example is in addition to the 2222 change we want to add another mapping “host from 443 to 443” (open the HTTPS), just add new group with the above syntax:

"PortBindings":{"22/tcp":[{"HostIp":"","HostPort":"2222"}],"4567/tcp":[{"HostIp":"","HostPort":"4567"}],"80/tcp":[{"HostIp":"","HostPort":"80"}],"443/tcp":[{"HostIp":"","HostPort":"443"}]}

A note!

Probably there may be an idea not to be easy to add mapped ports when you think one of the main Docker goals is to isolate services per a Docker instance. It sounds strange to have a docker container for one service exporting a number of ports (or a single port) and later why you would need to expose another port? For another service in the same container, but you should use a separate container, not the same one!
But more and more Docker containers are used also to deliver a fine-tuned environment of a whole platform, which provides multiple services in a single docker container. Let’s take an example – GitLab, which offers installation in a Docker container hosting more than 10 services in a single container!