Containers stuck on "Fixing perms..."

[Jedediah04]

Support guidelines

• I've read the support guidelines

I've found a bug and checked that ...

• ... the documentation does not mention anything about my problem
• ... there are no open or closed issues that are related to my problem

Description

Hello
Trying to run the full stack (from this repo). Everything starts correctly, I see no error in containers logs, but most of them are stuck at the "Fixing perms..." step. Nothing happens after that and obviously, web ui's not working.

Expected behaviour

Containers should go trough the full setup and let me access web UI.

Actual behaviour

Web UI not accessible, db container see no connection from librenms and no "pure librenms" files are created in the directory (only folders).

Steps to reproduce

1. Setup the stack (copy pasting the compose file from the repo)
2. Ajusting env variables (PUID GUID set to a specific user thas have full access to the local files, but tried root also).
3. Start the stack
4. Wait for the containers to initialize
5. Nothing happens after "Fixing perms..."

Docker info

Client: Docker Engine - Community
 Version:    28.3.3
 Context:    default
 Debug Mode: false
 Plugins:
  buildx: Docker Buildx (Docker Inc.)
    Version:  v0.26.1
    Path:     /usr/libexec/docker/cli-plugins/docker-buildx
  compose: Docker Compose (Docker Inc.)
    Version:  v2.39.1
    Path:     /usr/libexec/docker/cli-plugins/docker-compose

Server:
 Containers: 8
  Running: 8
  Paused: 0
  Stopped: 0
 Images: 12
 Server Version: 28.3.3
 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: systemd
 Cgroup Version: 2
 Plugins:
  Volume: local
  Network: bridge host ipvlan macvlan null overlay
  Log: awslogs fluentd gcplogs gelf journald json-file local splunk syslog
 CDI spec directories:
  /etc/cdi
  /var/run/cdi
 Swarm: inactive
 Runtimes: runc io.containerd.runc.v2
 Default Runtime: runc
 Init Binary: docker-init
 containerd version: 05044ec0a9a75232cad458027ca83437aae3f4da
 runc version: v1.2.5-0-g59923ef
 init version: de40ad0
 Security Options:
  apparmor
  seccomp
   Profile: builtin
  cgroupns
 Kernel Version: 6.12.41+deb13-amd64
 Operating System: Debian GNU/Linux 13 (trixie)
 OSType: linux
 Architecture: x86_64
 CPUs: 2
 Total Memory: 3.826GiB
 Name: archium
 ID: bf0bca9c-3231-41d8-be34-6dc8a7f54b24
 Docker Root Dir: /var/lib/docker
 Debug Mode: false
 Experimental: false
 Insecure Registries:
  ::1/128
  127.0.0.0/8
 Live Restore Enabled: false

Docker Compose config

name: librenms

services:
  db:
    image: mariadb:10
    container_name: librenms_db
    command:
      - "mysqld"
      - "--innodb-file-per-table=1"
      - "--lower-case-table-names=0"
      - "--character-set-server=utf8mb4"
      - "--collation-server=utf8mb4_unicode_ci"
    volumes:
      - "/home/docker/librenms/db:/var/lib/mysql"
    environment:
      - "TZ=${TZ}"
      - "MARIADB_RANDOM_ROOT_PASSWORD=yes"
      - "MYSQL_DATABASE=${MYSQL_DATABASE}"
      - "MYSQL_USER=${MYSQL_USER}"
      - "MYSQL_PASSWORD=${MYSQL_PASSWORD}"
    restart: always

  redis:
    image: redis:7.2-alpine
    container_name: librenms_redis
    environment:
      - "TZ=${TZ}"
    restart: always

  msmtpd:
    image: crazymax/msmtpd:latest
    container_name: librenms_msmtpd
    env_file:
      - "stack.env"
    restart: always

  librenms:
    image: librenms/librenms:latest
    container_name: librenms
    hostname: librenms
    cap_add:
      - NET_ADMIN
      - NET_RAW
    ports:
      - target: 8000
        published: 8000
        protocol: tcp
    depends_on:
      - db
      - redis
      - msmtpd
    volumes:
      - "/home/docker/librenms/:/data"
    env_file:
      - "stack.env"
    environment:
      - "TZ=${TZ}"
      - "PUID=${PUID}"
      - "PGID=${PGID}"
      - "DB_HOST=db"
      - "DB_NAME=${MYSQL_DATABASE}"
      - "DB_USER=${MYSQL_USER}"
      - "DB_PASSWORD=${MYSQL_PASSWORD}"
      - "DB_TIMEOUT=60"
    restart: always

  dispatcher:
    image: librenms/librenms:latest
    container_name: librenms_dispatcher
    hostname: librenms-dispatcher
    cap_add:
      - NET_ADMIN
      - NET_RAW
    depends_on:
      - librenms
      - redis
    volumes:
      - "/home/docker/librenms/:/data"
    env_file:
      - "stack.env"
    environment:
      - "TZ=${TZ}"
      - "PUID=${PUID}"
      - "PGID=${PGID}"
      - "DB_HOST=db"
      - "DB_NAME=${MYSQL_DATABASE}"
      - "DB_USER=${MYSQL_USER}"
      - "DB_PASSWORD=${MYSQL_PASSWORD}"
      - "DB_TIMEOUT=60"
      - "DISPATCHER_NODE_ID=dispatcher1"
      - "SIDECAR_DISPATCHER=1"
    restart: always

  syslogng:
    image: librenms/librenms:latest
    container_name: librenms_syslogng
    hostname: librenms-syslogng
    cap_add:
      - NET_ADMIN
      - NET_RAW
    depends_on:
      - librenms
      - redis
    ports:
      - target: 514
        published: 514
        protocol: tcp
      - target: 514
        published: 514
        protocol: udp
    volumes:
      - "/home/docker/librenms/:/data"
    env_file:
      - "stack.env"
    environment:
      - "TZ=${TZ}"
      - "PUID=${PUID}"
      - "PGID=${PGID}"
      - "DB_HOST=db"
      - "DB_NAME=${MYSQL_DATABASE}"
      - "DB_USER=${MYSQL_USER}"
      - "DB_PASSWORD=${MYSQL_PASSWORD}"
      - "DB_TIMEOUT=60"
      - "SIDECAR_SYSLOGNG=1"
    restart: always

  snmptrapd:
    image: librenms/librenms:latest
    container_name: librenms_snmptrapd
    hostname: librenms-snmptrapd
    cap_add:
      - NET_ADMIN
      - NET_RAW
    depends_on:
      - librenms
      - redis
    ports:
      - target: 162
        published: 162
        protocol: tcp
      - target: 162
        published: 162
        protocol: udp
    volumes:
      - "/home/docker/librenms:/data"
    env_file:
      - "stack.env"
    environment:
      - "TZ=${TZ}"
      - "PUID=${PUID}"
      - "PGID=${PGID}"
      - "DB_HOST=db"
      - "DB_NAME=${MYSQL_DATABASE}"
      - "DB_USER=${MYSQL_USER}"
      - "DB_PASSWORD=${MYSQL_PASSWORD}"
      - "DB_TIMEOUT=60"
      - "SIDECAR_SNMPTRAPD=1"
    restart: always

Logs

Logs of "librenms" container
[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...
[fix-attrs.d] done.
[cont-init.d] executing container initialization scripts...
[cont-init.d] 00-fix-logs.sh: executing... 
[cont-init.d] 00-fix-logs.sh: exited 0.
[cont-init.d] 01-fix-uidgid.sh: executing... 
Switching to PGID 1001...
Switching to PUID 1001...
[cont-init.d] 01-fix-uidgid.sh: exited 0.
[cont-init.d] 02-fix-perms.sh: executing... 
Fixing perms...
[cont-init.d] 02-fix-perms.sh: exited 0.
[cont-init.d] 03-config.sh: executing... 
Setting timezone to Europe/Paris...
Setting PHP-FPM configuration...
Setting PHP INI configuration...
Setting OpCache configuration...
Setting Nginx configuration...
Updating SNMP community...
Initializing LibreNMS files / folders...
Setting LibreNMS configuration...
Checking LibreNMS plugins...
Fixing perms...

Logs of dispatcher container :
[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...
[fix-attrs.d] done.
[cont-init.d] executing container initialization scripts...
[cont-init.d] 00-fix-logs.sh: executing... 
[cont-init.d] 00-fix-logs.sh: exited 0.
[cont-init.d] 01-fix-uidgid.sh: executing... 
Switching to PGID 1001...
Switching to PUID 1001...
[cont-init.d] 01-fix-uidgid.sh: exited 0.
[cont-init.d] 02-fix-perms.sh: executing... 
Fixing perms...
[cont-init.d] 02-fix-perms.sh: exited 0.
[cont-init.d] 03-config.sh: executing... 
Setting timezone to Europe/Paris...
Setting PHP-FPM configuration...
Setting PHP INI configuration...
Setting OpCache configuration...
Setting Nginx configuration...
Updating SNMP community...
Initializing LibreNMS files / folders...
Setting LibreNMS configuration...
Checking LibreNMS plugins...
Fixing perms...

Additional info

All the librenms containers are stuck at this step.
db container seems to initialize correctly and is just waithing for librenms to connect.

Thanks :)

[Joren2087]

TLDR; Wait ~10-15min, it will continue.

I had the exact same issue. Latest build, fresh pull and all containers running the librenms/librenms image just get stuck on "Fixing perms".

I've managed to trace it back to this exact line that seem to just hangs indefinitely. By using Docker exec I traced down that the command chown -R librenms:librenms ${LIBRENMS_PATH}/vendor simply takes forever to run.

docker/rootfs/etc/cont-init.d/03-config.sh

Line 222 in 4959802

chown -R librenms:librenms /data/logs ${LIBRENMS_PATH}/composer* ${LIBRENMS_PATH}/config.d ${LIBRENMS_PATH}/bootstrap ${LIBRENMS_PATH}/logs ${LIBRENMS_PATH}/storage ${LIBRENMS_PATH}/vendor

According to find vendor/ -type f | wc -l there are over 10k files (recursively) in that directory, which is a lot, but not absurd.

To my own suprise, after waiting roughly 10-15 min, the script finally continued and librenms starts up as normal. It is possible it takes longer for you, but it seems like it is actually doing something.

Would still be preferred that someone looks into this issue. Having to wait 20 min on every recreate will get on a dev's nerves pretty fast.

Hope this helps!