MySQL container failing to run initialisation scripts in Docker Compose

Question

I am having issues getting my MySQL container to run some initialisation scripts (creating some databases) from Docker Compose. As per the documentation on Docker Hub, I mount the .sql files in /docker-entrypoint-initdb.d but to no avail.

My compose files is as follows:

version: '2'

services:
  database:
    image: mysql
    ports:
      - "3307:3306"
    environment:
      MYSQL_ROOT_PASSWORD: root
    volumes:
      - ./scripts/db:/docker-entrypoint-initdb.d

  myservice:
    image: company/myservice
    expose:
      - "10001"
    depends_on:
      - database
    links:
      - database
    environment:
      SERVICE_PORT: 10001
      DATABASE_URL: jdbc:mysql://database:3306/myservice?autoReconnect=true&useSSL=false&characterEncoding=UTF-8

And the contents of ./scripts/db is just 1 file init-databases.sql:

CREATE DATABASE myservice;

Once started up, MySQL is running, but the database is not created. The service container also successfully links to the MySQL container. Bashing into the MySQL container; the init scripts are successfully mounted in the correct location.

Can anyone see some obvious issues here?

LOGS FROM compose

database_1   | 2016-04-01T05:35:55.020279Z 0 [Note] mysqld (mysqld 5.7.11) starting as process 1 ...
database_1   | 2016-04-01T05:35:55.023277Z 0 [Note] InnoDB: PUNCH HOLE support available
database_1   | 2016-04-01T05:35:55.023305Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
database_1   | 2016-04-01T05:35:55.023316Z 0 [Note] InnoDB: Uses event mutexes
database_1   | 2016-04-01T05:35:55.023324Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
database_1   | 2016-04-01T05:35:55.023332Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.8
database_1   | 2016-04-01T05:35:55.023344Z 0 [Note] InnoDB: Using Linux native AIO
database_1   | 2016-04-01T05:35:55.023491Z 0 [Note] InnoDB: Number of pools: 1
database_1   | 2016-04-01T05:35:55.023566Z 0 [Note] InnoDB: Using CPU crc32 instructions
database_1   | 2016-04-01T05:35:55.028689Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
database_1   | 2016-04-01T05:35:55.041026Z 0 [Note] InnoDB: Completed initialization of buffer pool
database_1   | 2016-04-01T05:35:55.047324Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
database_1   | 2016-04-01T05:35:55.061537Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
database_1   | 2016-04-01T05:35:55.076895Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
database_1   | 2016-04-01T05:35:55.076987Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
database_1   | 2016-04-01T05:35:55.095683Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
database_1   | 2016-04-01T05:35:55.096484Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
database_1   | 2016-04-01T05:35:55.096540Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
database_1   | 2016-04-01T05:35:55.096931Z 0 [Note] InnoDB: Waiting for purge to start
database_1   | 2016-04-01T05:35:55.147986Z 0 [Note] InnoDB: 5.7.11 started; log sequence number 11992841
database_1   | 2016-04-01T05:35:55.148204Z 0 [Note] Plugin 'FEDERATED' is disabled.
database_1   | 2016-04-01T05:35:55.149262Z 0 [Note] Found ca.pem, server-cert.pem and server-key.pem in data directory. Trying to enable SSL support using them.
database_1   | 2016-04-01T05:35:55.149443Z 0 [Warning] CA certificate ca.pem is self signed.
database_1   | 2016-04-01T05:35:55.150272Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
database_1   | 2016-04-01T05:35:55.151068Z 0 [Note] InnoDB: Buffer pool(s) load completed at 160401  5:35:55
database_1   | 2016-04-01T05:35:55.152775Z 0 [Note] Server hostname (bind-address): '*'; port: 3306
database_1   | 2016-04-01T05:35:55.154441Z 0 [Note] IPv6 is available.
database_1   | 2016-04-01T05:35:55.154553Z 0 [Note]   - '::' resolves to '::';
database_1   | 2016-04-01T05:35:55.154571Z 0 [Note] Server socket created on IP: '::'.
database_1   | 2016-04-01T05:35:55.156680Z 0 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.
database_1   | 2016-04-01T05:35:55.156738Z 0 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.
database_1   | 2016-04-01T05:35:55.158280Z 0 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.
database_1   | 2016-04-01T05:35:55.165273Z 0 [Note] Event Scheduler: Loaded 0 events
database_1   | 2016-04-01T05:35:55.173462Z 0 [Note] mysqld: ready for connections.
database_1   | Version: '5.7.11'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  MySQL Community Server (GPL)

See if it is a permission issue. What is the owner id of the sql file on the container? — Xiongbing Jin
– Xiongbing Jin, Commented Apr 1, 2016 at 4:13
@warmoverflow - Doesn't seem like it, currently has permissions -rwxrwxrwx owned by staff. — Nico Huysamen
– Nico Huysamen, Commented Apr 1, 2016 at 4:25

VonC · Accepted Answer · 2016-04-01 06:38:48Z

2

Check if this is a docker-compose issue (like issue 115 which redirected to issue 2266)

I don't think the error is related to build, it's mostly likely volumes.
Compose preserves volumes so that you don't lose data (this will be better documented in the next release).

To remove those volumes run docker-compose rm -vf. The next time you docker-compose up it should start with fresh empty volumes.

According to hub.docker.com/mysql, check also if this is not a synchronization issue:

If there is no database initialized when the container starts, then a default database will be created. While this is the expected behavior, this means that it will not accept incoming connections until such initialization completes. This may cause issues when using automation tools, such as docker-compose, which start several containers simultaneously.

edited Apr 1, 2016 at 6:38

answered Apr 1, 2016 at 5:17

VonC

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8 Comments

Nico Huysamen Over a year ago

Not sure it's 1, the logs seem normal to me (added to question). I also don't think it's a sync issue, because of 3 reasons. 1, when I connect to the database after it starts accepting connections, the database is still not created. 2, when I add the MYSQL_DATABASE env variable, it still does not create the database. 3, when I add a echo.sh file in the same mount (which the image says it will run also), with a simple echo statement, it does not run.

VonC Over a year ago

@NicoHuysamen OK, I have added additional clues for you to consider.

Nico Huysamen Over a year ago

Yes, that solved the startup issue thanks! Now I'm sitting with the sync issue...

Nico Huysamen Over a year ago

Removing the volumes. Don't need to quote the password.

VonC Over a year ago

@NicoHuysamen Excellent! I have cleaned-up the answer accordingly.

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