Issue with netdata Docker agent. Failed to create SQLITE

RitZz · May 2, 2023, 5:39am

Heya, I am trying to add a netdata agent with docker. Here is my Docker compose

version: '3'
services:
  netdata:
    image: netdata/netdata:stable
    container_name: netdata
    ports:
      - 19999:19999
    restart: unless-stopped
    cap_add:
      - SYS_PTRACE
    security_opt:
      - apparmor:unconfined
    volumes:
      - /home/ritzz/server/netdata/etc:/etc/netdata
      - /home/ritzz/server/netdata/lib:/var/lib/netdata
      - /home/ritzz/server/netdata/cache:/var/cache/netdata
      - /home/ritzz/server/netdata/passwd:/host/etc/passwd
      - /home/ritzz/server/netdata/group:/host/etc/group
      - /home/ritzz/server/netdata/proc:/host/proc
      - /home/ritzz/server/netdata/sys:/host/sys
      - /home/ritzz/server/netdata/os-release:/host/etc/os-release
    environment:
      - NETDATA_CLAIM_TOKEN=EDrkQaLMgy1eCqBPGUNG1-hNDeNsQc2nm3ROZwnvAGuOpZb--lWTS7Jgc9IfV2UrltdM3_FRZbkAZF8CB92UIqkbAz72rRoeVCP1QGDu0qX1XOYuZ47FXHgmAwtL2YwsgGOMfYY
      - NETDATA_CLAIM_URL=https://app.netdata.cloud
      - NETDATA_CLAIM_ROOMS=
      - PUID=0
      - PGID=0
      - TZ=Asia/Calcutta

and here’s the log:

 # : Invalid argument
2023-05-02 05:30:47: netdata FATAL : netdata : Failed to initialize SQLite
2023-05-02 05:30:47: netdata INFO  : MAIN : /usr/libexec/netdata/plugins.d/anonymous-statistics.sh 'FATAL' 'netdata:netdata' '0942@database/r:rrd_init       /22'
2023-05-02 05:30:48: netdata ERROR : MAIN : Execution of anonymous statistics script returned http code 400.
2023-05-02 05:30:48: netdata INFO  : MAIN : NETDATA SHUTDOWN: initializing shutdown with code 1...
2023-05-02 05:30:48: netdata INFO  : MAIN : /usr/libexec/netdata/plugins.d/anonymous-statistics.sh 'EXIT' 'ERROR' '-'
2023-05-02 05:30:49: netdata ERROR : MAIN : Execution of anonymous statistics script returned http code 400.
2023-05-02 05:30:49: netdata INFO  : MAIN : NETDATA SHUTDOWN: next: create shutdown file
2023-05-02 05:30:49: netdata INFO  : MAIN : NETDATA SHUTDOWN: in       0 ms, create shutdown file - next: disable maintenance, new queries, new web requests, new streaming connections and aclk
2023-05-02 05:30:49: netdata INFO  : MAIN : NETDATA SHUTDOWN: in       0 ms, disable maintenance, new queries, new web requests, new streaming connections and aclk - next: stop replication, exporters, ML training, health and web servers threads
2023-05-02 05:30:49: netdata INFO  : MAIN : NETDATA SHUTDOWN: in       0 ms, stop replication, exporters, ML training, health and web servers threads - next: stop collectors and streaming threads
2023-05-02 05:30:49: netdata INFO  : MAIN : NETDATA SHUTDOWN: in       0 ms, stop collectors and streaming threads - next: stop ML prediction and context threads
2023-05-02 05:30:49: netdata INFO  : MAIN : NETDATA SHUTDOWN: in       0 ms, stop ML prediction and context threads - next: stop maintenance thread
2023-05-02 05:30:49: netdata INFO  : MAIN : NETDATA SHUTDOWN: in       0 ms, stop maintenance thread - next: clean rrdhost database
2023-05-02 05:30:49: netdata INFO  : MAIN : RRD: cleaning up database [0 hosts(s)]...
2023-05-02 05:30:49: netdata INFO  : MAIN : NETDATA SHUTDOWN: in       0 ms, clean rrdhost database - next: prepare metasync shutdown
2023-05-02 05:30:49: netdata INFO  : MAIN : METADATA: Sending a scan host command
Creating docker group 0
addgroup: gid '0' in use
Could not add group docker with ID 0, its already there probably
Assign netdata user to docker group 0
2023-05-02 05:30:55: netdata ERROR : MAIN : Ignoring host prefix '/host': path '/host/proc' is not a virtual file system (errno 22, Invalid argument)
2023-05-02 05:30:55: netdata INFO  : MAIN : TIMEZONE: using TZ variable 'Asia/Calcutta'
2023-05-02 05:30:55: netdata INFO  : MAIN : TIMEZONE: fixed as 'Asia/Calcutta'
2023-05-02 05:30:55: netdata INFO  : MAIN : NETDATA STARTUP: next: initialize ML
2023-05-02 05:30:55: netdata INFO  : MAIN : NETDATA STARTUP: in       0 ms, initialize ML - next: initialize signals
2023-05-02 05:30:55: netdata INFO  : MAIN : SIGNAL: Enabling reaper
2023-05-02 05:30:55: netdata INFO  : MAIN : process tracking enabled.
2023-05-02 05:30:55: netdata INFO  : MAIN : NETDATA STARTUP: in       0 ms, initialize signals - next: initialize static threads
2023-05-02 05:30:55: netdata INFO  : MAIN : NETDATA STARTUP: in       0 ms, initialize static threads - next: initialize web server
2023-05-02 05:30:55: netdata INFO  : MAIN : NETDATA STARTUP: in       0 ms, initialize web server - next: set resource limits
2023-05-02 05:30:55: netdata INFO  : MAIN : resources control: allowed file descriptors: soft = 1048576, max = 1048576
2023-05-02 05:30:55: netdata INFO  : MAIN : NETDATA STARTUP: in       0 ms, set resource limits - next: become daemon
2023-05-02 05:30:55: netdata INFO  : MAIN : Out-Of-Memory (OOM) score is already set to the wanted value 0
2023-05-02 05:30:55: netdata ERROR : MAIN : Cannot adjust netdata scheduling policy to batch (3), with priority 0. Falling back to nice. (errno 38, Function not implemented)
2023-05-02 05:30:55: netdata ERROR : MAIN : Cannot get my current process scheduling policy. (errno 38, Function not implemented)
2023-05-02 05:30:55: netdata INFO  : MAIN : netdata started on pid 1.
2023-05-02 05:30:55: netdata INFO  : MAIN : NETDATA STARTUP: in       0 ms, become daemon - next: initialize threads after fork
2023-05-02 05:30:55: netdata INFO  : MAIN : Set threads stack size to 131072 bytes
2023-05-02 05:30:55: netdata INFO  : MAIN : NETDATA STARTUP: in       0 ms, initialize threads after fork - next: initialize registry
2023-05-02 05:30:55: netdata INFO  : MAIN : NETDATA STARTUP: in       0 ms, initialize registry - next: fork the spawn server
2023-05-02 05:30:55: netdata INFO  : MAIN : Initializing spawn client.
2023-05-02 05:30:55: netdata INFO  : MAIN : NETDATA STARTUP: in       0 ms, fork the spawn server - next: collecting system info
2023-05-02 05:30:55: netdata INFO  : MAIN : Executing /usr/libexec/netdata/plugins.d/system-info.sh
Spawn server is up.
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_CONTAINER_OS_NAME=Alpine Linux
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_CONTAINER_OS_ID=alpine
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_CONTAINER_OS_ID_LIKE=unknown
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_CONTAINER_OS_VERSION=unknown
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_CONTAINER_OS_VERSION_ID=3.16.4
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_CONTAINER_OS_DETECTION=/etc/os-release
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_CONTAINER_IS_OFFICIAL_IMAGE=true
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_HOST_OS_NAME=unknown
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_HOST_OS_ID=unknown
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_HOST_OS_ID_LIKE=unknown
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_HOST_OS_VERSION=unknown
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_HOST_OS_VERSION_ID=unknown
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_HOST_OS_DETECTION=/host/etc/os-release
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_HOST_IS_K8S_NODE=false
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_KERNEL_NAME=Linux
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_KERNEL_VERSION=5.19.0-41-generic
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_ARCHITECTURE=x86_64
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_VIRTUALIZATION=none
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_VIRT_DETECTION=none
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_CONTAINER=docker
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_CONTAINER_DETECTION=dockerenv
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_CPU_LOGICAL_CPU_COUNT=4
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_CPU_VENDOR=GenuineIntel
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_CPU_MODEL=Intel(R) Core(TM) i3-4130 CPU @ 3.40GHz
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_CPU_FREQ=3400000000
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_CPU_DETECTION=lscpu
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_TOTAL_RAM=12432912384
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_RAM_DETECTION=procfs
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_TOTAL_DISK_SIZE=10120865472512
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_SYSTEM_DISK_DETECTION=sysfs
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_INSTANCE_CLOUD_TYPE=unknown
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_INSTANCE_CLOUD_INSTANCE_TYPE=unknown
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA_INSTANCE_CLOUD_INSTANCE_REGION=unknown
2023-05-02 05:30:56: netdata INFO  : MAIN : NETDATA STARTUP: in      56 ms, collecting system info - next: initialize RRD structures
2023-05-02 05:30:56: netdata ERROR : MAIN : Failed to initialize database at /var/cache/netdata/netdata-meta.db, due to "unable to open database file"

It fails to create an SQLite from what I see. How do I fix this?

Manolis_Vasilakis · May 2, 2023, 7:15am

Hi @RitZz . I’m not a docker expert, but likely this seems like a permissions problem. There is a similar issue here → [Bug]: Error trying to run in Docker for first time. · Issue #14215 · netdata/netdata · GitHub there might be some more info there.

RitZz · May 2, 2023, 7:28am

Tried that method already. I’ve tried running the container as root, gave proper chown and chgrp permission to the folders. But still facing the error

Manolis_Vasilakis · May 3, 2023, 9:00am

Ok, thanks. As a test, I did a similar setup, and chmod’ed the cache directory with 777 and that seemed to work. The user running netdata inside the container is 201.

But indeed even if I don’t chmod the e.g. lib directory to 777, netdata is still able to write into it. That needs some investigation, as to why just the sqlite db is having problems.

ilyam8 · May 3, 2023, 9:34am

@RitZz what are these directories?

      - /home/ritzz/server/netdata/passwd:/host/etc/passwd
      - /home/ritzz/server/netdata/group:/host/etc/group
      - /home/ritzz/server/netdata/proc:/host/proc
      - /home/ritzz/server/netdata/sys:/host/sys

Have you mounted the host syfs, procfs, etc to your home dir?

RitZz · May 3, 2023, 12:24pm

Yup, Works fine after chmod 777 but not sure why or how lib works.

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Issue with netdata Docker agent. Failed to create SQLITE

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