Docker: Mysql crashes after few seconds when it has been started

Question

I am on Mac 10.11.3 (15D21)

About Docker I have:

$ docker version
Client:
 Version:      1.10.3
 API version:  1.22
 Go version:   go1.5.3
 Git commit:   20f81dd
 Built:        Thu Mar 10 21:49:11 2016
 OS/Arch:      darwin/amd64

Server:
 Version:      1.10.3
 API version:  1.22
 Go version:   go1.5.3
 Git commit:   20f81dd
 Built:        Thu Mar 10 21:49:11 2016
 OS/Arch:      linux/amd64

With the following Dockerfile (it to resolve Docker with mysql: The error means mysqld does not have the access rights to the directory):

FROM mysql:latest
RUN deluser mysql
RUN useradd mysql
RUN mkdir -p /Users/me/docker/mysql/data
RUN chmod -R 777 /Users/me/docker/mysql/data

I have created a new image docker build -t localmysql:latest . named localmysql

REPOSITORY                  TAG                 IMAGE ID            CREATED             SIZE
localmysql                  latest              ea0f7da32de8        15 hours ago        361.6 MB

I can create the manolitomysql new container from the localmysql new image (I am using multiple lines for better appreciation):

docker run -v /Users/me/docker/mysql/data:/var/lib/mysql 
--name manolitomysql 
-e MYSQL_DATABASE='mysqldb' -e MYSQL_USER='mysql' 
-e MYSQL_PASSWORD='mysql' -e MYSQL_ALLOW_EMPTY_PASSWORD='yes' 
-e MYSQL_ROOT_PASSWORD='' -d localmysql

The container runs:

CONTAINER ID        IMAGE               COMMAND                  CREATED             STATUS              PORTS               NAMES
06f15352aa7c        localmysql          "/entrypoint.sh mysql"   23 seconds ago      Up 22 seconds       3306/tcp            manolitomysql

Even I can enter to the console with docker exec -it manolitomysql /bin/bash

But after of more of 30 seconds the container crushes

#docker logs manolitomysql
Initializing database
2016-03-28T13:27:01.600230Z 0 [Warning] Setting lower_case_table_names=2 because file system for /var/lib/mysql/ is case insensitive
2016-03-28T13:27:03.355428Z 0 [Warning] InnoDB: New log files created, LSN=45790
2016-03-28T13:27:03.705206Z 0 [Warning] InnoDB: Creating foreign key constraint system tables.
2016-03-28T13:27:03.765510Z 0 [Warning] No existing UUID has been found, so we assume that this is the first time that this server has been started. Generating a new UUID: c2837bb5-f4e8-11e5-a856-0242ac110002.
2016-03-28T13:27:03.766641Z 0 [Warning] Gtid table is not ready to be used. Table 'mysql.gtid_executed' cannot be opened.
2016-03-28T13:27:03.767732Z 1 [Warning] root@localhost is created with an empty password ! Please consider switching off the --initialize-insecure option.
2016-03-28T13:27:04.960541Z 1 [Warning] 'user' entry 'root@localhost' ignored in --skip-name-resolve mode.
2016-03-28T13:27:04.960616Z 1 [Warning] 'user' entry 'mysql.sys@localhost' ignored in --skip-name-resolve mode.
2016-03-28T13:27:04.960716Z 1 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.
2016-03-28T13:27:04.960846Z 1 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.
2016-03-28T13:27:04.960962Z 1 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.
Database initialized
MySQL init process in progress...
2016-03-28T13:27:07.059842Z 0 [Note] mysqld (mysqld 5.7.11) starting as process 38 ...
2016-03-28T13:27:07.062158Z 0 [Warning] Setting lower_case_table_names=2 because file system for /var/lib/mysql/ is case insensitive
2016-03-28T13:27:07.063330Z 0 [ERROR] Plugin keyring_file reported: 'keyring_file initialization failure. Please check if the keyring_file_data points to readable keyring file or keyring file can be created in the specified location. The keyring_file will stay unusable until correct path to the keyring file gets provided'
2016-03-28T13:27:07.063747Z 0 [Note] InnoDB: PUNCH HOLE support available
2016-03-28T13:27:07.063766Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2016-03-28T13:27:07.063776Z 0 [Note] InnoDB: Uses event mutexes
2016-03-28T13:27:07.063785Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2016-03-28T13:27:07.063794Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.8
2016-03-28T13:27:07.063803Z 0 [Note] InnoDB: Using Linux native AIO
2016-03-28T13:27:07.063957Z 0 [Note] InnoDB: Number of pools: 1
2016-03-28T13:27:07.064037Z 0 [Note] InnoDB: Using CPU crc32 instructions
2016-03-28T13:27:07.069596Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2016-03-28T13:27:07.075441Z 0 [Note] InnoDB: Completed initialization of buffer pool
2016-03-28T13:27:07.076643Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2016-03-28T13:27:07.102198Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2016-03-28T13:27:07.133326Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2016-03-28T13:27:07.133809Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2016-03-28T13:27:07.185431Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2016-03-28T13:27:07.263862Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2016-03-28T13:27:07.263953Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2016-03-28T13:27:07.264530Z 0 [Note] InnoDB: Waiting for purge to start
2016-03-28T13:27:07.315152Z 0 [Note] InnoDB: 5.7.11 started; log sequence number 2492554
2016-03-28T13:27:07.315489Z 0 [Note] Plugin 'FEDERATED' is disabled.
2016-03-28T13:27:07.316620Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
2016-03-28T13:27:07.326420Z 0 [Warning] Failed to set up SSL because of the following SSL library error: SSL context is not usable without certificate and private key
2016-03-28T13:27:07.326507Z 0 [ERROR] Could not create unix socket lock file /var/run/mysqld/mysqld.sock.lock.
2016-03-28T13:27:07.326522Z 0 [ERROR] Unable to setup unix socket lock file.
2016-03-28T13:27:07.326531Z 0 [ERROR] Aborting

2016-03-28T13:27:07.326545Z 0 [Note] Binlog end
2016-03-28T13:27:07.326591Z 0 [Note] Shutting down plugin 'ngram'
2016-03-28T13:27:07.326605Z 0 [Note] Shutting down plugin 'BLACKHOLE'
2016-03-28T13:27:07.326614Z 0 [Note] Shutting down plugin 'partition'
2016-03-28T13:27:07.326623Z 0 [Note] Shutting down plugin 'ARCHIVE'
2016-03-28T13:27:07.326632Z 0 [Note] Shutting down plugin 'MEMORY'
2016-03-28T13:27:07.326641Z 0 [Note] Shutting down plugin 'INNODB_SYS_VIRTUAL'
2016-03-28T13:27:07.326650Z 0 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2016-03-28T13:27:07.326658Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2016-03-28T13:27:07.326673Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2016-03-28T13:27:07.326681Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2016-03-28T13:27:07.326690Z 0 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2016-03-28T13:27:07.326698Z 0 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2016-03-28T13:27:07.326706Z 0 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2016-03-28T13:27:07.326715Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2016-03-28T13:27:07.326723Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2016-03-28T13:27:07.326731Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2016-03-28T13:27:07.326740Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2016-03-28T13:27:07.326748Z 0 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2016-03-28T13:27:07.326757Z 0 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2016-03-28T13:27:07.326765Z 0 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2016-03-28T13:27:07.326773Z 0 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2016-03-28T13:27:07.326782Z 0 [Note] Shutting down plugin 'INNODB_METRICS'
2016-03-28T13:27:07.326790Z 0 [Note] Shutting down plugin 'INNODB_TEMP_TABLE_INFO'
2016-03-28T13:27:07.326798Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2016-03-28T13:27:07.326807Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2016-03-28T13:27:07.326816Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2016-03-28T13:27:07.326824Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2016-03-28T13:27:07.326832Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2016-03-28T13:27:07.326841Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2016-03-28T13:27:07.326850Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM'
2016-03-28T13:27:07.326858Z 0 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2016-03-28T13:27:07.326866Z 0 [Note] Shutting down plugin 'INNODB_CMP'
2016-03-28T13:27:07.326875Z 0 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2016-03-28T13:27:07.326883Z 0 [Note] Shutting down plugin 'INNODB_LOCKS'
2016-03-28T13:27:07.326894Z 0 [Note] Shutting down plugin 'INNODB_TRX'
2016-03-28T13:27:07.326903Z 0 [Note] Shutting down plugin 'InnoDB'
2016-03-28T13:27:07.326970Z 0 [Note] InnoDB: FTS optimize thread exiting.
2016-03-28T13:27:07.327081Z 0 [Note] InnoDB: Starting shutdown...
2016-03-28T13:27:07.327112Z 0 [Note] InnoDB: Buffer pool(s) load completed at 160328 13:27:07
2016-03-28T13:27:07.327946Z 0 [Note] InnoDB: Dumping buffer pool(s) to /var/lib/mysql/ib_buffer_pool
2016-03-28T13:27:07.328953Z 0 [Note] InnoDB: Buffer pool(s) dump completed at 160328 13:27:07
MySQL init process in progress...
MySQL init process in progress...
2016-03-28T13:27:08.954395Z 0 [Note] InnoDB: Shutdown completed; log sequence number 2492573
2016-03-28T13:27:08.956113Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2016-03-28T13:27:08.956170Z 0 [Note] Shutting down plugin 'MyISAM'
2016-03-28T13:27:08.956206Z 0 [Note] Shutting down plugin 'MRG_MYISAM'
2016-03-28T13:27:08.956221Z 0 [Note] Shutting down plugin 'CSV'
2016-03-28T13:27:08.956234Z 0 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2016-03-28T13:27:08.956293Z 0 [Note] Shutting down plugin 'sha256_password'
2016-03-28T13:27:08.956306Z 0 [Note] Shutting down plugin 'mysql_native_password'
2016-03-28T13:27:08.956317Z 0 [Note] Shutting down plugin 'keyring_file'
2016-03-28T13:27:08.956515Z 0 [Note] Shutting down plugin 'binlog'
2016-03-28T13:27:08.956853Z 0 [Note] mysqld: Shutdown complete

MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process in progress...
MySQL init process failed.
Manuels-MacBook-Pro:~ manueljordan$

Below the errors from above:

One

[ERROR] Plugin keyring_file reported: 'keyring_file initialization failure. Please check if the keyring_file_data points to readable keyring file or keyring file can be created in the specified location. The keyring_file will stay unusable until correct path to the keyring file gets provided'

Second

[ERROR] Could not create unix socket lock file /var/run/mysqld/mysqld.sock.lock.
[ERROR] Unable to setup unix socket lock file.
[ERROR] Aborting

What extra configuration is needed?

ThatsNinja · Accepted Answer

I'm guessing that you've got permissions issues, and that /var/run/mysqld is owned by the UID/GID of the mysql user created by the MySQL install process in the original Docker image. Try this in your Dockerfile:

FROM mysql:latest
RUN deluser mysql
RUN useradd mysql

RUN chown mysql:mysql /var/run/mysqld

RUN mkdir -p /Users/me/docker/mysql/data
RUN chmod -R 777 /Users/me/docker/mysql/data

Further guessing that the case is the same for the 'keyring_file', wherever that's located. Try running a docker run -it manolitomysql /bin/bash to get a shell prompt into your container, and see if you can draw a bead on it.

Docker: Mysql crashes after few seconds when it has been started

Answers (2)

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