Permission Denied Errors on MySQL Files After Upgrading to New Docker Version

[alexandremsouza1]

Description

After upgrading to the latest Docker version, I encountered multiple permission-related errors when attempting to change ownership on MySQL files within the /var/lib/mysql directory. These errors prevent the application from accessing essential MySQL data and include the following messages:

2024-11-08 23:29:47 chown: changing ownership of '/var/lib/mysql/mysql.sock': Operation not permitted
2024-11-08 23:29:47 chown: cannot access '/var/lib/mysql/auto.cnf': Permission denied
2024-11-08 23:29:47 chown: cannot access '/var/lib/mysql/binlog.000004': Permission denied
2024-11-08 23:29:47 chown: cannot access '/var/lib/mysql/ib_buffer_pool': Permission denied
2024-11-08 23:29:47 chown: cannot access '/var/lib/mysql/binlog.000005': Permission denied
2024-11-08 23:29:47 chown: cannot access '/var/lib/mysql/binlog.000014': Permission denied

Reproduce

1. Update Docker to the latest version.
2. Use Docker Compose with version 4.34 to define a MySQL container. My docker-compose.yaml file is configured with MySQL and includes the following specifications: [ In Additional Info]
3. Run the MySQL container and attempt to set chown permissions on the /var/lib/mysql directory.
4. Observe permission errors on MySQL files as listed above.

Expected behavior

No response

docker version

Client: Docker Engine - Community
 Version:           27.3.1
 API version:       1.47
 Go version:        go1.22.7
 Git commit:        ce12230
 Built:             Fri Sep 20 11:40:59 2024
 OS/Arch:           linux/amd64
 Context:           desktop-linux

Server: Docker Desktop 4.35.1 (173168)
 Engine:
  Version:          27.3.1
  API version:      1.47 (minimum version 1.24)
  Go version:       go1.22.7
  Git commit:       41ca978
  Built:            Fri Sep 20 11:41:11 2024
  OS/Arch:          linux/amd64
  Experimental:     false
 containerd:
  Version:          1.7.21
  GitCommit:        472731909fa34bd7bc9c087e4c27943f9835f111
 runc:
  Version:          1.1.13
  GitCommit:        v1.1.13-0-g58aa920
 docker-init:
  Version:          0.19.0
  GitCommit:        de40ad0

docker info

Client: Docker Engine - Community
 Version:    27.3.1
 Context:    desktop-linux
 Debug Mode: false
 Plugins:
  buildx: Docker Buildx (Docker Inc.)
    Version:  v0.17.1-desktop.1
    Path:     /usr/lib/docker/cli-plugins/docker-buildx
  compose: Docker Compose (Docker Inc.)
    Version:  v2.29.7-desktop.1
    Path:     /usr/lib/docker/cli-plugins/docker-compose
  debug: Get a shell into any image or container (Docker Inc.)
    Version:  0.0.37
    Path:     /usr/lib/docker/cli-plugins/docker-debug
  desktop: Docker Desktop commands (Alpha) (Docker Inc.)
    Version:  v0.0.15
    Path:     /usr/lib/docker/cli-plugins/docker-desktop
  dev: Docker Dev Environments (Docker Inc.)
    Version:  v0.1.2
    Path:     /usr/lib/docker/cli-plugins/docker-dev
  extension: Manages Docker extensions (Docker Inc.)
    Version:  v0.2.27
    Path:     /usr/lib/docker/cli-plugins/docker-extension
  feedback: Provide feedback, right in your terminal! (Docker Inc.)
    Version:  v1.0.5
    Path:     /usr/lib/docker/cli-plugins/docker-feedback
  init: Creates Docker-related starter files for your project (Docker Inc.)
    Version:  v1.3.0
    Path:     /usr/lib/docker/cli-plugins/docker-init
  sbom: View the packaged-based Software Bill Of Materials (SBOM) for an image (Anchore Inc.)
    Version:  0.6.0
    Path:     /usr/lib/docker/cli-plugins/docker-sbom
  scout: Docker Scout (Docker Inc.)
    Version:  v1.14.0
    Path:     /usr/lib/docker/cli-plugins/docker-scout

Server:
 Containers: 7
  Running: 1
  Paused: 0
  Stopped: 6
 Images: 12
 Server Version: 27.3.1
 Storage Driver: overlay2
  Backing Filesystem: extfs
  Supports d_type: true
  Using metacopy: false
  Native Overlay Diff: true
  userxattr: false
 Logging Driver: json-file
 Cgroup Driver: cgroupfs
 Cgroup Version: 2
 Plugins:
  Volume: local
  Network: bridge host ipvlan macvlan null overlay
  Log: awslogs fluentd gcplogs gelf journald json-file local splunk syslog
 Swarm: inactive
 Runtimes: io.containerd.runc.v2 runc
 Default Runtime: runc
 Init Binary: docker-init
 containerd version: 472731909fa34bd7bc9c087e4c27943f9835f111
 runc version: v1.1.13-0-g58aa920
 init version: de40ad0
 Security Options:
  seccomp
   Profile: unconfined
  cgroupns
 Kernel Version: 6.10.11-linuxkit
 Operating System: Docker Desktop
 OSType: linux
 Architecture: x86_64
 CPUs: 8
 Total Memory: 3.714GiB
 Name: docker-desktop
 ID: d5dfc322-deca-4216-b4cb-a51c7db89840
 Docker Root Dir: /var/lib/docker
 Debug Mode: false
 HTTP Proxy: http.docker.internal:3128
 HTTPS Proxy: http.docker.internal:3128
 No Proxy: hubproxy.docker.internal
 Labels:
  com.docker.desktop.address=unix:///home/alexandre/.docker/desktop/docker-cli.sock
 Experimental: false
 Insecure Registries:
  hubproxy.docker.internal:5555
  127.0.0.0/8
 Live Restore Enabled: false

WARNING: daemon is not using the default seccomp profile

Diagnostics ID

6702D0A6-6A45-4CBD-9C89-5302B8B37473/20241109022826

Additional Info

version: "3.9" services: db: image: mysql:8.0.30 volumes:

• ./db_data:/var/lib/mysql restart: always environment: MYSQL_ROOT_PASSWORD: somewordpress MYSQL_DATABASE: wordpress MYSQL_USER: wordpress MYSQL_PASSWORD: wordpress wordpress: depends_on:
• db image: wordpress:latest volumes:
• ./wordpress:/var/www/html
• ./plugins:/var/www/html/wp-content/plugins ports:
• "8000:80" restart: always environment: WORDPRESS_DB_HOST: db:3306 WORDPRESS_DB_USER: wordpress WORDPRESS_DB_PASSWORD: wordpress WORDPRESS_DB_NAME: wordpress

[Nikhil-Gohil]

I am seeing similar permission issues after I updated from docker desktop 4.34.1 --> 4.35.1

All of my preexisting containers fail to spin up because inside the container, there are no permissions to write to the default "/config" folder that I have bind mount.

Docker compose has this setup for a container:

    volumes:
      - "~/config/sonarr:/config"
      - "/mnt/data:/data"

When I spin up the container, I see errors like:

2024-11-12 12:27:15 [v4.0.10.2624] NzbDrone.Common.Exceptions.SonarrStartupException: Sonarr failed to start: AppFolder /config is not writable

Inside the container:

/ # whoami
root

/ # ls -ld /config
drwxrwxr-x 8 root root 4096 Nov 11 12:03 /config

/ # touch  /config/write_test.txt
touch: cannot touch '/config/write_test.txt': Permission denied

From the host system:

UbuntuLTS-Server:~$ whoami
nikhil

UbuntuLTS-Server:~$ ls -ld ~/config/sonarr/
drwxrwxr-x 8 100999 100999 4096 Nov 11 12:03 /home/nikhil/config/sonarr/

UbuntuLTS-Server:~$ touch ~/config/sonarr/write_test.txt
touch: cannot touch '/home/nikhil/config/sonarr/write_test.txt': Permission denied

UbuntuLTS-Server:~$ sudo touch ~/config/sonarr/write_test.txt
UbuntuLTS-Server:~$ 

On the host system, the files show up as owned by uid 100999, and I can edit them after I become root. Inside the container, it shows the directory as owned by root, and even when I am the root user, I am unable to create/edit files in the directory.

I am unsure if this is a similar issue that you have flagged but thought I would post here first nonetheless. I attempted to --force-recreate, that did not help.

docker version
Client: Docker Engine - Community
 Version:           27.3.1
 API version:       1.47
 Go version:        go1.22.7
 Git commit:        ce12230
 Built:             Fri Sep 20 11:40:59 2024
 OS/Arch:           linux/amd64
 Context:           desktop-linux

Server: Docker Desktop 4.35.1 (173168)
 Engine:
  Version:          27.3.1
  API version:      1.47 (minimum version 1.24)
  Go version:       go1.22.7
  Git commit:       41ca978
  Built:            Fri Sep 20 11:41:11 2024
  OS/Arch:          linux/amd64
  Experimental:     false
 containerd:
  Version:          1.7.21
  GitCommit:        472731909fa34bd7bc9c087e4c27943f9835f111
 runc:
  Version:          1.1.13
  GitCommit:        v1.1.13-0-g58aa920
 docker-init:
  Version:          0.19.0
  GitCommit:        de40ad0

docker info
Client: Docker Engine - Community
 Version:    27.3.1
 Context:    desktop-linux
 Debug Mode: false
 Plugins:
  buildx: Docker Buildx (Docker Inc.)
    Version:  v0.17.1-desktop.1
    Path:     /usr/lib/docker/cli-plugins/docker-buildx
  compose: Docker Compose (Docker Inc.)
    Version:  v2.29.7-desktop.1
    Path:     /usr/lib/docker/cli-plugins/docker-compose
  debug: Get a shell into any image or container (Docker Inc.)
    Version:  0.0.37
    Path:     /usr/lib/docker/cli-plugins/docker-debug
  desktop: Docker Desktop commands (Alpha) (Docker Inc.)
    Version:  v0.0.15
    Path:     /usr/lib/docker/cli-plugins/docker-desktop
  dev: Docker Dev Environments (Docker Inc.)
    Version:  v0.1.2
    Path:     /usr/lib/docker/cli-plugins/docker-dev
  extension: Manages Docker extensions (Docker Inc.)
    Version:  v0.2.27
    Path:     /usr/lib/docker/cli-plugins/docker-extension
  feedback: Provide feedback, right in your terminal! (Docker Inc.)
    Version:  v1.0.5
    Path:     /usr/lib/docker/cli-plugins/docker-feedback
  init: Creates Docker-related starter files for your project (Docker Inc.)
    Version:  v1.3.0
    Path:     /usr/lib/docker/cli-plugins/docker-init
  sbom: View the packaged-based Software Bill Of Materials (SBOM) for an image (Anchore Inc.)
    Version:  0.6.0
    Path:     /usr/lib/docker/cli-plugins/docker-sbom
  scout: Docker Scout (Docker Inc.)
    Version:  v1.14.0
    Path:     /usr/lib/docker/cli-plugins/docker-scout

Server:
 Containers: 20
  Running: 18
  Paused: 0
  Stopped: 2
 Images: 65
 Server Version: 27.3.1
 Storage Driver: overlay2
  Backing Filesystem: extfs
  Supports d_type: true
  Using metacopy: false
  Native Overlay Diff: true
  userxattr: false
 Logging Driver: json-file
 Cgroup Driver: cgroupfs
 Cgroup Version: 2
 Plugins:
  Volume: local
  Network: bridge host ipvlan macvlan null overlay
  Log: awslogs fluentd gcplogs gelf journald json-file local splunk syslog
 Swarm: inactive
 Runtimes: io.containerd.runc.v2 runc
 Default Runtime: runc
 Init Binary: docker-init
 containerd version: 472731909fa34bd7bc9c087e4c27943f9835f111
 runc version: v1.1.13-0-g58aa920
 init version: de40ad0
 Security Options:
  seccomp
   Profile: unconfined
  cgroupns
 Kernel Version: 6.10.11-linuxkit
 Operating System: Docker Desktop
 OSType: linux
 Architecture: x86_64
 CPUs: 6
 Total Memory: 1.846GiB
 Name: docker-desktop
 ID: 1e6a09e0-54e0-459b-bf3b-85bf422b99a9
 Docker Root Dir: /var/lib/docker
 Debug Mode: false
 HTTP Proxy: http.docker.internal:3128
 HTTPS Proxy: http.docker.internal:3128
 No Proxy: hubproxy.docker.internal
 Labels:
  com.docker.desktop.address=unix:///home/nikhil/.docker/desktop/docker-cli.sock
 Experimental: false
 Insecure Registries:
  hubproxy.docker.internal:5555
  127.0.0.0/8
 Live Restore Enabled: false

WARNING: daemon is not using the default seccomp profile

version: "3.7"

services:
  sonarr:
    container_name: sonarr
    image: ghcr.io/hotio/sonarr:nightly
    ports:
      - "8989:8989"
    environment:
      - PUID=1000
      - PGID=1000
      - UMASK=002
      - TZ=America/Los_Angeles
    restart: unless-stopped
    volumes:
      - "~/config/sonarr:/config"
      - "/mnt/data:/data"