Docker - 如何将 /var/lib/mysql 挂载到 docker mysql 容器

Question

Is is possible to mount existing installed mysql /var/lib/mysql data to docker mysql container.

Because i dont want to migrate all my mysql and mongodb because i have 50+ Gb data and which is increasing daily.

I have set the volume to mount with the mysql data folder but unfortunately its not working for me.

I have tried but its not working am i missing something or doing something wrong?

version: "3"
services:
  app:
    build:
      context: ./app
      dockerfile: ./dockerfile      
    container_name: flaskPython
    links:
      - mysqldb
      - mongodb
    ports:
      - "5000:5000"
  myadmin:
        image: phpmyadmin/phpmyadmin
        container_name: phpmyadmin
        ports:
            - "8282:80"
        environment:
            - PMA_ARBITRARY=1
            - PMA_HOST=${MYSQL_HOST}
        restart: always
        depends_on:
            - mysqldb
            - mongodb  
  mysqldb:
        image: mysql:${MYSQL_VERSION}
        container_name: ${MYSQL_HOST}
        restart: 'always'
        expose:
            - '3306'
        env_file:
            - ".env"
        environment:
            - MYSQL_DATABASE=${MYSQL_DATABASE}
            - MYSQL_ROOT_PASSWORD=${MYSQL_ROOT_PASSWORD}
            - MYSQL_USER=${MYSQL_USER}
            - MYSQL_PASSWORD=${MYSQL_PASSWORD}
        ports:
            - "8989:3306"
        volumes:
            #- ./data/db/mysql:/var/lib/mysql
            - /var/lib/mysql:/var/lib/mysql
  mongodb:
        image: mongo
        container_name: mongodb
        restart: always
        environment:

          - MONGO_INITDB_ROOT_USERNAME=root
          - MONGO_INITDB_ROOT_PASSWORD=root
        # if you wish to setup additional user accounts specific per DB or with different roles you can use following entry point
        #no --auth is needed here as presence of username and password add this option automatically
        command: mongod
        ports:
            - "27017:27017"
        volumes:
          - ./mongo-entrypoint/:/docker-entrypoint-initdb.d/
          - ./data/db/mongo:/usr/data/db

Logs:

2019-02-01T16:08:20.100825Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2019-02-01T16:08:20.101919Z 0 [Note] mysqld (mysqld 5.7.22) starting as process 1 ...
2019-02-01T16:08:20.104031Z 0 [Note] InnoDB: PUNCH HOLE support available
2019-02-01T16:08:20.104043Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2019-02-01T16:08:20.104046Z 0 [Note] InnoDB: Uses event mutexes
2019-02-01T16:08:20.104048Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2019-02-01T16:08:20.104050Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2019-02-01T16:08:20.104052Z 0 [Note] InnoDB: Using Linux native AIO
2019-02-01T16:08:20.104214Z 0 [Note] InnoDB: Number of pools: 1
2019-02-01T16:08:20.104285Z 0 [Note] InnoDB: Using CPU crc32 instructions
2019-02-01T16:08:20.105476Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2019-02-01T16:08:20.110790Z 0 [Note] InnoDB: Completed initialization of buffer pool
2019-02-01T16:08:20.112288Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2019-02-01T16:08:20.123892Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2019-02-01T16:08:20.139921Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2019-02-01T16:08:20.139996Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2019-02-01T16:08:20.170786Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2019-02-01T16:08:20.173104Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2019-02-01T16:08:20.173143Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2019-02-01T16:08:20.174483Z 0 [Note] InnoDB: Waiting for purge to start
2019-02-01T16:08:20.224878Z 0 [Note] InnoDB: 5.7.22 started; log sequence number 1529088986
2019-02-01T16:08:20.225403Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
2019-02-01T16:08:20.225887Z 0 [Note] Plugin 'FEDERATED' is disabled.
2019-02-01T16:08:20.231185Z 0 [Note] InnoDB: Buffer pool(s) load completed at 190201 16:08:20
2019-02-01T16:08:20.233231Z 0 [Warning] Failed to set up SSL because of the following SSL library error: SSL context is not usable without certificate and private key
2019-02-01T16:08:20.233502Z 0 [Note] Server hostname (bind-address): '*'; port: 3306
2019-02-01T16:08:20.233535Z 0 [Note] IPv6 is available.
2019-02-01T16:08:20.233544Z 0 [Note]   - '::' resolves to '::';
2019-02-01T16:08:20.233556Z 0 [Note] Server socket created on IP: '::'.
2019-02-01T16:08:20.236451Z 0 [Warning] Insecure configuration for --pid-file: Location '/var/run/mysqld' in the path is accessible to all OS users. Consider choosing a different directory.
2019-02-01T16:08:20.248740Z 0 [Warning] 'user' entry 'root@localhost' ignored in --skip-name-resolve mode.
2019-02-01T16:08:20.248832Z 0 [Warning] 'user' entry 'mysql.session@localhost' ignored in --skip-name-resolve mode.
2019-02-01T16:08:20.248857Z 0 [Warning] 'user' entry 'mysql.sys@localhost' ignored in --skip-name-resolve mode.
2019-02-01T16:08:20.248875Z 0 [Warning] 'user' entry 'debian-sys-maint@localhost' ignored in --skip-name-resolve mode.
2019-02-01T16:08:20.248921Z 0 [Warning] 'db' entry 'performance_schema mysql.session@localhost' ignored in --skip-name-resolve mode.
2019-02-01T16:08:20.248935Z 0 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.
2019-02-01T16:08:20.249216Z 0 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.
2019-02-01T16:08:20.256300Z 0 [Warning] 'tables_priv' entry 'user mysql.session@localhost' ignored in --skip-name-resolve mode.
2019-02-01T16:08:20.256349Z 0 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.
2019-02-01T16:08:20.301149Z 0 [Note] Event Scheduler: Loaded 0 events
2019-02-01T16:08:20.301811Z 0 [Note] mysqld: ready for connections.
Version: '5.7.22'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  MySQL Community Server (GPL)

Getting different errors because i made some changes. sometime container crash, some time cant connect to mysql (111)

Answer 1

The problem

The problem may be the versions of Mysql and MongoDB and/or the user UID and GID for the /var/lib/mysql and /data/db/mongo .

Versions

First of all the Mysql versions and MongoDB versions running on the container need to be the same as the ones running on the host in order for you to be able to use the same folders used in the host.

Bear in mind that you cannot have the Mysql server and MongoDB server running at same time in the host and containers while sharing the same files.

By same files I mean /var/lib/mysql and /data/db/mongo on your host.

If you want to keep the servers running in localhost then you need to copy this folders elsewhere and have the same UID and GID for the user.

User UID and GID

The Mysql user and Mongo DB user inside the docker container and host must have same UID and GID.

Check them in both with:

$ sudo docker run --rm -it mysql bash
root@4c07b20e88c4:/# grep -irn mysql /etc/passwd
20:mysql:x:999:999::/home/mysql:
root@4c07b20e88c4:/# grep -irn mysql /etc/group
40:mysql:x:999:

or with:

root@4c07b20e88c4:/# id -u mysql
999
root@4c07b20e88c4:/# id -g mysql
999

As you can see UID is 999 and GID is also 999 for both user and group. Now just repeat the same in the host.

Possible Solution

Check the versions for Mysql and MongoDB in the host and in the container and if they mismatch, update the container to run the same versions of the host.

Also set the user of Mysql and MongoDB in the host to have the same UID and GID that is used inside the container or the other way around... choose the one that best suits your use case.

Changing UID and GID of a user

run in the shell:

root@4c07b20e88c4:/# usermod -u 800 mysql
root@4c07b20e88c4:/# id -u mysql
800
root@4c07b20e88c4:/# groupmod -g 800 mysql
root@4c07b20e88c4:/# id -g mysql
800

replace 800 with the id number you want and mysql with the user name you want to change the ids.

Next update the file permissions for that user:

find / -user <OLDUID> -exec chown -h <NEWUID> {} \;

and for the group:

find / -group <OLDGID> -exec chgrp -h <NEWGID> {} \;

More info here