Mysql root user is not initialized

[Kern046]

Hello there !

I am facing some kind of problem with the 5.7 image. The short description is that the container is set up properly, but it is impossible to connect with the root user. My suggestion is that the root password is not initialized properly.

I am using docker-toolbox with Windows (quite sad about it but due to VPN and company group strategies it is quite hard to setup a Unix environment here) and I think Windows permissions are the problem.

I copy here my files :

docker-compose.yml

mysql:
    container_name: my_mysql_container
    build: mysql
    environment:
        - MYSQL_DATABASES=my_database
        - MYSQL_ROOT_PASSWORD=root
        - MYSQL_HOST=127.0.0.1
        - MYSQL_PORT=33306
        - MYSQL_USER=helpless
        - MYSQL_PASSWORD=dev
        - MYSQL_LOYALTY_DATABASE=my_database
    ports:
        # MySQL
        - "33306:3306"
    volumes:
        # Mysql
        - "./volumes/mysql:/var/lib/mysql"

mysql/Dockerfile

FROM mysql:5.7
MAINTAINER Helpless Dev <helpless.dev@wonderful_company.com>

COPY conf.d/*.cnf /etc/mysql/conf.d/
COPY docker-entrypoint-initdb.d/databases.sh /docker-entrypoint-initdb.d/databases.sh
COPY docker-entrypoint-initdb.d/config.sh /docker-entrypoint-initdb.d/config.sh

RUN chmod a+x /docker-entrypoint-initdb.d/config.sh && chown root:root /docker-entrypoint-initdb.d/config.sh
RUN chmod a+x /docker-entrypoint-initdb.d/databases.sh && chown root:root /docker-entrypoint-initdb.d/databases.sh

mysql/conf.d/custom.cnf

[mysqld]
default-storage-engine=INNODB
init-connect='SET NAMES utf8'
character-set-server=utf8
collation-server=utf8_unicode_ci
bind-address        = 0.0.0.0
skip-external-locking
key_buffer      = 16M
max_allowed_packet  = 16M
thread_stack        = 192K
thread_cache_size       = 8
query_cache_limit   = 1M
query_cache_size        = 16M
expire_logs_days    = 10
max_binlog_size         = 100M

[mysqldump]
quick
quote-names
max_allowed_packet  = 16M

[isamchk]
key_buffer      = 16M

docker-entrypoint-initdb.d/config.sh

#!/bin/bash

chmod 644 /etc/mysql/conf.d/custom.cnf

echo "ok"

exec "$@"

docker-entrypoint-initdb.d/databases.sh

#!/bin/bash

mysql=( mysql --protocol=socket -uroot )

if [ ! -z "$MYSQL_ROOT_PASSWORD" ]; then
    mysql+=( -p"${MYSQL_ROOT_PASSWORD}" )
fi

IFS=',' read -a dbs <<< "$MYSQL_DATABASES"

if [ ${#dbs[@]} -gt 0 ];then
    for db in "${dbs[@]}"
    do
        if [ "$db" ]; then
            echo create database $db
            echo "CREATE DATABASE IF NOT EXISTS \`$db\` ;" | "${mysql[@]}"
        fi

    done

    if [ "${dbs[0]}" ]; then
        mysql+=( "${dbs[0]}" )
    fi
fi

if [ "$MYSQL_USER" -a "$MYSQL_PASSWORD" ]; then
    if [ ${#dbs[@]} -gt 0 ]; then
        for db in "${dbs[@]}"
        do
            if [ "$db" ]; then
                echo "GRANT ALL ON \`"$db"\`.* TO '"$MYSQL_USER"'@'%' ;" | "${mysql[@]}"
            fi
        done
    fi

    echo 'FLUSH PRIVILEGES ;' | "${mysql[@]}"
fi

I tried to change the permissions of custom.cnf because it is created in mode 666 and mysql ignores it with the message World writeable config file "custom.cnf" has been ignored. But my script is never executed, nor the databases.sh script which would fail anyway because the root user is not available.

I think the reason is that mysql cannot create the root user when failing at reading the config file, but when I removed the custom.cnf file, I had the following logs :

2016-09-26T11:40:30.936825Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2016-09-26T11:40:30.939713Z 0 [Note] mysqld (mysqld 5.7.15) starting as process 1 ...
2016-09-26T11:40:30.954868Z 0 [Warning] Setting lower_case_table_names=2 because file system for /var/lib/mysql/ is case insensitive
2016-09-26T11:40:30.956901Z 0 [Note] InnoDB: PUNCH HOLE support available
2016-09-26T11:40:30.959072Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2016-09-26T11:40:30.959141Z 0 [Note] InnoDB: Uses event mutexes
2016-09-26T11:40:30.959160Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2016-09-26T11:40:30.959348Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2016-09-26T11:40:30.959368Z 0 [Note] InnoDB: Using Linux native AIO
2016-09-26T11:40:30.959587Z 0 [Note] InnoDB: Number of pools: 1
2016-09-26T11:40:30.960271Z 0 [Note] InnoDB: Using CPU crc32 instructions
2016-09-26T11:40:30.966106Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2016-09-26T11:40:30.979996Z 0 [Note] InnoDB: Completed initialization of buffer pool
2016-09-26T11:40:30.981340Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2016-09-26T11:40:31.009740Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2016-09-26T11:40:31.081507Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2016-09-26T11:40:31.082573Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2016-09-26T11:40:31.188290Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2016-09-26T11:40:31.189949Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2016-09-26T11:40:31.190054Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2016-09-26T11:40:31.190480Z 0 [Note] InnoDB: Waiting for purge to start
2016-09-26T11:40:31.240774Z 0 [Note] InnoDB: 5.7.15 started; log sequence number 12135621
2016-09-26T11:40:31.241113Z 0 [Note] Plugin 'FEDERATED' is disabled.
2016-09-26T11:40:31.242288Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool



2016-09-26T11:40:31.248585Z 0 [Warning] World-writable config file './auto.cnf' is ignored.
2016-09-26T11:40:31.249364Z 0 [Warning] World-writable config file './auto.cnf' has been removed.





2016-09-26T11:40:31.249913Z 0 [Note] Salting uuid generator variables, current_pid: 1, server_start_time: 1474890030, bytes_sent: 0,
2016-09-26T11:40:31.250064Z 0 [Note] Generated uuid: '0775897e-83de-11e6-8440-0242ac110002', server_start_time: 281476451600687, bytes_sent: 68492832
2016-09-26T11:40:31.250115Z 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: 0775897e-83de-11e6-8440-0242ac110002.
2016-09-26T11:40:31.259733Z 0 [Warning] Failed to set up SSL because of the following SSL library error: SSL context is not usable without certificate and private key
2016-09-26T11:40:31.260256Z 0 [Note] Server hostname (bind-address): '*'; port: 3306
2016-09-26T11:40:31.260418Z 0 [Note] IPv6 is available.
2016-09-26T11:40:31.260458Z 0 [Note]   - '::' resolves to '::';
2016-09-26T11:40:31.260500Z 0 [Note] Server socket created on IP: '::'.
2016-09-26T11:40:31.274069Z 0 [Note] InnoDB: Buffer pool(s) load completed at 160926 11:40:31
2016-09-26T11:40:31.289454Z 0 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.
2016-09-26T11:40:31.289812Z 0 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.
2016-09-26T11:40:31.360977Z 0 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.
2016-09-26T11:40:31.487421Z 0 [Note] Event Scheduler: Loaded 0 events
2016-09-26T11:40:31.487685Z 0 [Note] mysqld: ready for connections.
Version: '5.7.15'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  MySQL Community Server (GPL)

I put in evidence the file permissions problems.

In the Dockerfile, I tried to run chmod 644, but after investigation, it is impossible with docker toolbox to modify the "o" permissions. I can do chmod u=rw,g=r but not u=rw,go=r or even a=r. I tried several combinations before concluding that it is impossible with docker toolbox on windows to change the "o" permissions during the building. I do not know if I have to do an issue in Docker Machine repository or Toolbox.

I would be glad if you can help me, that would avoid a Vagrant box on my Windows, which would be sad for me and my team :D !

Thanks a lot, and have a nice day !

[ltangvald]

Is there already a database (or any files or directories) in .volumes/mysql? If so, database init will be skipped, and that includes execution of the scripts in docker-entrypoint-initdb.d

Also, the scripts will be executed at the end of database init, so the script for fixing the permissions will be run after the first database startup, which might create an inconsistent setup for things like setting the default storage engine. A better solution might be to set the permission in Dockerfile.

[Kern046]

The problem is that the container exits with code 1 when I tried to change the permissions to 644 !

But I tried to build the container from scratch after removing the volumes/mysql folder, and I have new evidences of the problem :

Initializing database
mysqld: [Warning] World-writable config file '/etc/mysql/conf.d/custom.cnf' is ignored.
2016-09-26T13:18:03.829257Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2016-09-26T13:18:03.834098Z 0 [Warning] Setting lower_case_table_names=2 because file system for /var/lib/mysql/ is case insensitive
2016-09-26T13:18:04.328638Z 0 [Warning] InnoDB: New log files created, LSN=45790
2016-09-26T13:18:04.427158Z 0 [Warning] InnoDB: Creating foreign key constraint system tables.
2016-09-26T13:18:04.486357Z 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: a84283b1-83eb-11e6-81d6-0242ac110002.
2016-09-26T13:18:04.489057Z 0 [Warning] Gtid table is not ready to be used. Table 'mysql.gtid_executed' cannot be opened.
2016-09-26T13:18:04.490699Z 1 [Warning] root@localhost is created with an empty password ! Please consider switching off the --initialize-insecure option.
2016-09-26T13:18:05.518667Z 1 [Warning] 'user' entry 'root@localhost' ignored in --skip-name-resolve mode.
2016-09-26T13:18:05.518813Z 1 [Warning] 'user' entry 'mysql.sys@localhost' ignored in --skip-name-resolve mode.
2016-09-26T13:18:05.518934Z 1 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.
2016-09-26T13:18:05.519086Z 1 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.
2016-09-26T13:18:05.519221Z 1 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.
Database initialized
MySQL init process in progress...
mysqld: [Warning] World-writable config file '/etc/mysql/conf.d/custom.cnf' is ignored.
2016-09-26T13:18:08.561601Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2016-09-26T13:18:08.564188Z 0 [Note] mysqld (mysqld 5.7.15) starting as process 47 ...
2016-09-26T13:18:08.567039Z 0 [Warning] Setting lower_case_table_names=2 because file system for /var/lib/mysql/ is case insensitive
2016-09-26T13:18:08.568265Z 0 [Note] InnoDB: PUNCH HOLE support available
2016-09-26T13:18:08.568344Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2016-09-26T13:18:08.568377Z 0 [Note] InnoDB: Uses event mutexes
2016-09-26T13:18:08.568406Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2016-09-26T13:18:08.568492Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2016-09-26T13:18:08.568525Z 0 [Note] InnoDB: Using Linux native AIO
2016-09-26T13:18:08.568728Z 0 [Note] InnoDB: Number of pools: 1
2016-09-26T13:18:08.568831Z 0 [Note] InnoDB: Using CPU crc32 instructions
2016-09-26T13:18:08.569989Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2016-09-26T13:18:08.576881Z 0 [Note] InnoDB: Completed initialization of buffer pool
2016-09-26T13:18:08.578389Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2016-09-26T13:18:08.601909Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2016-09-26T13:18:08.636201Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2016-09-26T13:18:08.636991Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2016-09-26T13:18:08.686772Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2016-09-26T13:18:08.688076Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2016-09-26T13:18:08.688155Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2016-09-26T13:18:08.688563Z 0 [Note] InnoDB: Waiting for purge to start
2016-09-26T13:18:08.739186Z 0 [Note] InnoDB: 5.7.15 started; log sequence number 2528505
2016-09-26T13:18:08.739528Z 0 [Note] Plugin 'FEDERATED' is disabled.
2016-09-26T13:18:08.740724Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
2016-09-26T13:18:08.753770Z 0 [Warning] World-writable config file './auto.cnf' is ignored.
2016-09-26T13:18:08.755074Z 0 [Warning] World-writable config file './auto.cnf' has been removed.

2016-09-26T13:18:08.756082Z 0 [Note] Salting uuid generator variables, current_pid: 47, server_start_time: 1474895888, bytes_sent: 0,
2016-09-26T13:18:08.756541Z 0 [Note] Generated uuid: 'aace1830-83eb-11e6-84d6-0242ac110002', server_start_time: 13229325380296767, bytes_sent: 72023696
2016-09-26T13:18:08.756642Z 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: aace1830-83eb-11e6-84d6-0242ac110002.
2016-09-26T13:18:08.769161Z 0 [Warning] Failed to set up SSL because of the following SSL library error: SSL context is not usable without certificate and private key
2016-09-26T13:18:08.781724Z 0 [Note] InnoDB: Buffer pool(s) load completed at 160926 13:18:08
2016-09-26T13:18:09.267746Z 0 [Warning] 'user' entry 'root@localhost' ignored in --skip-name-resolve mode.
2016-09-26T13:18:09.267963Z 0 [Warning] 'user' entry 'mysql.sys@localhost' ignored in --skip-name-resolve mode.
2016-09-26T13:18:09.268322Z 0 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.
2016-09-26T13:18:09.268575Z 0 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.
2016-09-26T13:18:09.298055Z 0 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.
2016-09-26T13:18:09.400163Z 0 [Note] Event Scheduler: Loaded 0 events
2016-09-26T13:18:09.400387Z 0 [Note] mysqld: ready for connections.
Version: '5.7.15'  socket: '/var/run/mysqld/mysqld.sock'  port: 0  MySQL Community Server (GPL)
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 in progress...
MySQL init process in progress...
MySQL init process failed.

Ty for your quick answer :) !

[yosifkit]

@Kern046, it looks like you still need to add a chmod to the Dockerfile for your custom.cnf and do a docker build. Then you can get rid of docker-entrypoint-initdb.d/config.sh.

[Kern046]

@yosifkit, my problem actually was that I was unable to make the container run with a RUN chmod 644 /etc/mysql/conf.d/custom.cnf instruction in the Dockerfile. The container exited every time with 1 code without any log. That was the core of my problem and I think it is related to my Windows host, because running ``chmod u=rw,g=rworked fine but notchmod u=rw,go=r`.

My solution was to give up Docker Toolbox and Docker Machine and create a VM with Vagrant.

I do not have permissions problems anymore with Ubuntu Xenial (my VM OS), but the scripts in /docker-entrypoint-initdb.d are still not executed, root stills have empty password, and no host is able to connect except localhost (event 127.0.0.1 is forbidden)

[yosifkit]

If the container fails to start, then it is not a problem with the chown, but a problem with the config itself. The problem is that our entrypoint script does a mysqld --verbose --help to find out what the datadir is and if your config is improper, it will just fail at that point (we need to fix it to print the error rather than just dying; I'm going to look for a solution) (

mysql/5.7/docker-entrypoint.sh

Line 27 in de740a4

DATADIR="$(_datadir "$@")"

).

So to find the problem, I copied your cnf file and ran the following:

$ docker run -it --rm -v $PWD/my.cnf:/etc/mysql/conf.d/my.cnf --name mysql -e MYSQL_ROOT_PASSWORD=12345 mysql:5.7 bash
root@fd0ebe7e491c:/# mysqld --verbose --help > /dev/null
2016-09-30T18:06:45.828087Z 0 [ERROR] unknown variable 'key_buffer=16M'
2016-09-30T18:06:45.829979Z 0 [ERROR] Aborting

[yosifkit]

I made #218 to print the errors so that you don't get a stopped container with no output.

[ltangvald]

Ah right, I didn't spot that.
The key_buffer option has been deprecated for some time, and in 5.7 it was removed completely. It was simply renamed to key_buffer_size, so changing the name in the config should fix it.

[Kern046]

Hello there !

Thanks for the answers ! I updated the configuration file but it still does not work ! I tested also your useful command to detect any other error, but it does not produce any output !

I tried to just launch the mysqld command, which produces the following output :

2016-10-03T12:07:50.242779Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2016-10-03T12:07:50.243505Z 0 [Note] mysqld (mysqld 5.7.15) starting as process 16 ...
2016-10-03T12:07:50.245262Z 0 [ERROR] Fatal error: Please read "Security" section of the manual to find out how to run mysqld as root!

2016-10-03T12:07:50.247328Z 0 [ERROR] Aborting

2016-10-03T12:07:50.247882Z 0 [Note] Binlog end
2016-10-03T12:07:50.248365Z 0 [Note] mysqld: Shutdown complete

I've read the mentionned Security section and tried to launch mysqld --user=mysql. The following output was produced :

2016-10-03T12:14:31.822087Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2016-10-03T12:14:31.823143Z 0 [Note] mysqld (mysqld 5.7.15) starting as process 10 ...
2016-10-03T12:14:31.827072Z 0 [Note] InnoDB: PUNCH HOLE support available
2016-10-03T12:14:31.827108Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2016-10-03T12:14:31.827114Z 0 [Note] InnoDB: Uses event mutexes
2016-10-03T12:14:31.827117Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2016-10-03T12:14:31.827121Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2016-10-03T12:14:31.827125Z 0 [Note] InnoDB: Using Linux native AIO
2016-10-03T12:14:31.827344Z 0 [Note] InnoDB: Number of pools: 1
2016-10-03T12:14:31.827449Z 0 [Note] InnoDB: Using CPU crc32 instructions
2016-10-03T12:14:31.829139Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2016-10-03T12:14:31.835906Z 0 [Note] InnoDB: Completed initialization of buffer pool
2016-10-03T12:14:31.837815Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2016-10-03T12:14:31.848097Z 0 [Note] InnoDB: The first innodb_system data file 'ibdata1' did not exist. A new tablespace will be created!
2016-10-03T12:14:31.848374Z 0 [Note] InnoDB: Setting file './ibdata1' size to 12 MB. Physically writing the file full; Please wait ...
2016-10-03T12:14:32.335076Z 0 [Note] InnoDB: File './ibdata1' size is now 12 MB.
2016-10-03T12:14:32.335782Z 0 [Note] InnoDB: Setting log file ./ib_logfile101 size to 48 MB
2016-10-03T12:14:33.197097Z 0 [Note] InnoDB: Setting log file ./ib_logfile1 size to 48 MB
2016-10-03T12:14:34.177164Z 0 [Note] InnoDB: Renaming log file ./ib_logfile101 to ./ib_logfile0
2016-10-03T12:14:34.177351Z 0 [Warning] InnoDB: New log files created, LSN=45790
2016-10-03T12:14:34.177417Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2016-10-03T12:14:34.177483Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2016-10-03T12:14:34.486927Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2016-10-03T12:14:34.487217Z 0 [Note] InnoDB: Doublewrite buffer not found: creating new
2016-10-03T12:14:34.534460Z 0 [Note] InnoDB: Doublewrite buffer created
2016-10-03T12:14:34.539580Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2016-10-03T12:14:34.539628Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2016-10-03T12:14:34.539799Z 0 [Warning] InnoDB: Creating foreign key constraint system tables.
2016-10-03T12:14:34.542263Z 0 [Note] InnoDB: Foreign key constraint system tables created
2016-10-03T12:14:34.542343Z 0 [Note] InnoDB: Creating tablespace and datafile system tables.
2016-10-03T12:14:34.543018Z 0 [Note] InnoDB: Tablespace and datafile system tables created.
2016-10-03T12:14:34.543130Z 0 [Note] InnoDB: Creating sys_virtual system tables.
2016-10-03T12:14:34.543497Z 0 [Note] InnoDB: sys_virtual table created
2016-10-03T12:14:34.543984Z 0 [Note] InnoDB: Waiting for purge to start
2016-10-03T12:14:34.594451Z 0 [Note] InnoDB: 5.7.15 started; log sequence number 0
2016-10-03T12:14:34.594749Z 0 [Note] Plugin 'FEDERATED' is disabled.
mysqld: Table 'mysql.plugin' doesn't exist
2016-10-03T12:14:34.594973Z 0 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
2016-10-03T12:14:34.595625Z 0 [Note] Salting uuid generator variables, current_pid: 10, server_start_time: 1475496871, bytes_sent: 0,
2016-10-03T12:14:34.595844Z 0 [Note] Generated uuid: 'f2479c0c-8962-11e6-b935-0242ac110002', server_start_time: 2814751242603441, bytes_sent: 35373488
2016-10-03T12:14:34.595880Z 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: f2479c0c-8962-11e6-b935-0242ac110002.
2016-10-03T12:14:34.596584Z 0 [Warning] Gtid table is not ready to be used. Table 'mysql.gtid_executed' cannot be opened.
2016-10-03T12:14:34.596708Z 0 [Warning] Failed to set up SSL because of the following SSL library error: SSL context is not usable without certificate and private key
2016-10-03T12:14:34.597520Z 0 [Note] Server hostname (bind-address): '*'; port: 3306
2016-10-03T12:14:34.597564Z 0 [Note] IPv6 is available.
2016-10-03T12:14:34.597571Z 0 [Note]   - '::' resolves to '::';
2016-10-03T12:14:34.597661Z 0 [Note] Server socket created on IP: '::'.
2016-10-03T12:14:34.598733Z 0 [Warning] Failed to open optimizer cost constant tables

2016-10-03T12:14:34.599077Z 0 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.user' doesn't exist
2016-10-03T12:14:34.599480Z 0 [ERROR] Aborting

2016-10-03T12:14:34.599587Z 0 [Note] Binlog end
2016-10-03T12:14:34.599624Z 0 [Note] Shutting down plugin 'ngram'
2016-10-03T12:14:34.599700Z 0 [Note] Shutting down plugin 'BLACKHOLE'
2016-10-03T12:14:34.599708Z 0 [Note] Shutting down plugin 'partition'
2016-10-03T12:14:34.599710Z 0 [Note] Shutting down plugin 'ARCHIVE'
2016-10-03T12:14:34.599713Z 0 [Note] Shutting down plugin 'MEMORY'
2016-10-03T12:14:34.599716Z 0 [Note] Shutting down plugin 'INNODB_SYS_VIRTUAL'
2016-10-03T12:14:34.599719Z 0 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2016-10-03T12:14:34.599721Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2016-10-03T12:14:34.599724Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2016-10-03T12:14:34.599726Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2016-10-03T12:14:34.599729Z 0 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2016-10-03T12:14:34.599731Z 0 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2016-10-03T12:14:34.599733Z 0 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2016-10-03T12:14:34.599735Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2016-10-03T12:14:34.599840Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2016-10-03T12:14:34.599846Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2016-10-03T12:14:34.599848Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2016-10-03T12:14:34.599851Z 0 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2016-10-03T12:14:34.599865Z 0 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2016-10-03T12:14:34.599868Z 0 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2016-10-03T12:14:34.599870Z 0 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2016-10-03T12:14:34.599873Z 0 [Note] Shutting down plugin 'INNODB_METRICS'
2016-10-03T12:14:34.599875Z 0 [Note] Shutting down plugin 'INNODB_TEMP_TABLE_INFO'
2016-10-03T12:14:34.599889Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2016-10-03T12:14:34.599892Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2016-10-03T12:14:34.599895Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2016-10-03T12:14:34.599897Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2016-10-03T12:14:34.599948Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2016-10-03T12:14:34.599952Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2016-10-03T12:14:34.599955Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM'
2016-10-03T12:14:34.599957Z 0 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2016-10-03T12:14:34.599960Z 0 [Note] Shutting down plugin 'INNODB_CMP'
2016-10-03T12:14:34.599974Z 0 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2016-10-03T12:14:34.599977Z 0 [Note] Shutting down plugin 'INNODB_LOCKS'
2016-10-03T12:14:34.599979Z 0 [Note] Shutting down plugin 'INNODB_TRX'
2016-10-03T12:14:34.599982Z 0 [Note] Shutting down plugin 'InnoDB'
2016-10-03T12:14:34.600079Z 0 [Note] InnoDB: FTS optimize thread exiting.
2016-10-03T12:14:34.600288Z 0 [Note] InnoDB: Starting shutdown...
2016-10-03T12:14:34.701721Z 0 [Note] InnoDB: Dumping buffer pool(s) to /var/lib/mysql/ib_buffer_pool
2016-10-03T12:14:34.702082Z 0 [Note] InnoDB: Buffer pool(s) dump completed at 161003 12:14:34
2016-10-03T12:14:36.425461Z 0 [Note] InnoDB: Shutdown completed; log sequence number 1209961
2016-10-03T12:14:36.429470Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2016-10-03T12:14:36.429534Z 0 [Note] Shutting down plugin 'MyISAM'
2016-10-03T12:14:36.429632Z 0 [Note] Shutting down plugin 'MRG_MYISAM'
2016-10-03T12:14:36.429676Z 0 [Note] Shutting down plugin 'CSV'
2016-10-03T12:14:36.429685Z 0 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2016-10-03T12:14:36.429747Z 0 [Note] Shutting down plugin 'sha256_password'
2016-10-03T12:14:36.429822Z 0 [Note] Shutting down plugin 'mysql_native_password'
2016-10-03T12:14:36.430196Z 0 [Note] Shutting down plugin 'binlog'
2016-10-03T12:14:36.430937Z 0 [Note] mysqld: Shutdown complete

With docker-compose, my container stills start well, but without any password to my root user and without executing my scripts.

Thank you both for your answers :) !

[ltangvald]

I think you're missing the mysqld --initialize run that the container does when started with compose or default docker run command.
i.e. mysqld --initialize-insecure --user=mysql
(--initialize-insecure creates the root user with an empty password, while --intialize generates a random password for it)

[Kern046]

Indeed ! It starts fine.

I think I'm coming to get it. Reviewing the Dockerfile of the image, I notice the following piece of code :

for i in {30..0}; do
    if echo 'SELECT 1' | "${mysql[@]}" &> /dev/null; then
        break
    fi
    echo 'MySQL init process in progress...'
    sleep 1
done
if [ "$i" = 0 ]; then
    echo >&2 'MySQL init process failed.'
    exit 1
fi

This is exactly what is coming in my logs when I launch the container the first time after removing volumes/mysql :

Initializing database
2016-10-03T12:47:51.217644Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2016-10-03T12:47:51.604379Z 0 [Warning] InnoDB: New log files created, LSN=45790
2016-10-03T12:47:51.644572Z 0 [Warning] InnoDB: Creating foreign key constraint system tables.
2016-10-03T12:47:51.822911Z 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: 98b84632-8967-11e6-b063-0242ac110002.
2016-10-03T12:47:51.824140Z 0 [Warning] Gtid table is not ready to be used. Table 'mysql.gtid_executed' cannot be opened.
2016-10-03T12:47:51.824636Z 1 [Warning] root@localhost is created with an empty password ! Please consider switching off the --initialize-insecure option.
2016-10-03T12:47:52.702722Z 1 [Warning] 'user' entry 'root@localhost' ignored in --skip-name-resolve mode.
2016-10-03T12:47:52.702917Z 1 [Warning] 'user' entry 'mysql.sys@localhost' ignored in --skip-name-resolve mode.
2016-10-03T12:47:52.702972Z 1 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.
2016-10-03T12:47:52.703005Z 1 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.
2016-10-03T12:47:52.703129Z 1 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.
Database initialized
MySQL init process in progress...
2016-10-03T12:47:54.893601Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2016-10-03T12:47:54.905406Z 0 [Note] mysqld (mysqld 5.7.15) starting as process 49 ...
2016-10-03T12:47:54.909800Z 0 [Note] InnoDB: PUNCH HOLE support available
2016-10-03T12:47:54.915323Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2016-10-03T12:47:54.915331Z 0 [Note] InnoDB: Uses event mutexes
2016-10-03T12:47:54.915335Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2016-10-03T12:47:54.915338Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2016-10-03T12:47:54.915341Z 0 [Note] InnoDB: Using Linux native AIO
2016-10-03T12:47:54.915539Z 0 [Note] InnoDB: Number of pools: 1
2016-10-03T12:47:54.915617Z 0 [Note] InnoDB: Using CPU crc32 instructions
2016-10-03T12:47:54.922526Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2016-10-03T12:47:54.935973Z 0 [Note] InnoDB: Completed initialization of buffer pool
2016-10-03T12:47:54.942648Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2016-10-03T12:47:54.954253Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2016-10-03T12:47:54.966434Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2016-10-03T12:47:54.966490Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2016-10-03T12:47:55.062688Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2016-10-03T12:47:55.063293Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2016-10-03T12:47:55.063306Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2016-10-03T12:47:55.065968Z 0 [Note] InnoDB: Waiting for purge to start
2016-10-03T12:47:55.116747Z 0 [Note] InnoDB: 5.7.15 started; log sequence number 2528505
2016-10-03T12:47:55.121017Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
2016-10-03T12:47:55.121273Z 0 [Note] Plugin 'FEDERATED' is disabled.
2016-10-03T12:47:55.126550Z 0 [Note] InnoDB: Buffer pool(s) load completed at 161003 12:47:55
2016-10-03T12:47:55.133994Z 0 [Warning] Failed to set up SSL because of the following SSL library error: SSL context is not usable without certificate and private key
2016-10-03T12:47:55.146552Z 0 [Warning] 'user' entry 'root@localhost' ignored in --skip-name-resolve mode.
2016-10-03T12:47:55.146694Z 0 [Warning] 'user' entry 'mysql.sys@localhost' ignored in --skip-name-resolve mode.
2016-10-03T12:47:55.146765Z 0 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.
2016-10-03T12:47:55.146812Z 0 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.
2016-10-03T12:47:55.148147Z 0 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.
2016-10-03T12:47:55.163313Z 0 [Note] Event Scheduler: Loaded 0 events
2016-10-03T12:47:55.166612Z 0 [Note] mysqld: ready for connections.
Version: '5.7.15'  socket: '/var/run/mysqld/mysqld.sock'  port: 0  MySQL Community Server (GPL)
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 in progress...
MySQL init process in progress...
MySQL init process failed.

When I launched it the second time I haven't the initialization part and everything seemed to work, but the code modifying the root user is after the initialization code which failed. Everything is coming clear, unless the cause of the error :p !

We're getting close ! Thank for your patience !

EDIT : I don't know if I said it earlier, but the visible problem is that mysqld hasn't any binded port when initializing, maybe iet's a clue.

[RCooLeR]

Any success on this? How to resolve the issue?

[Kern046]

@RCooLeR None for the moment, I'd like to get some time to try to solve it myselfn I hope in the next few days. Did you experience the same issue ?

[RCooLeR]

Yes. I rebuild my docker with mysql/mysql-server but I think all thing is in timing... It just doesn't create/update users in time.

I have also noticed another issue with docker-compose

[Kern046]

In fact, I think the main clue is here :

Version: '5.7.15'  socket: '/var/run/mysqld/mysqld.sock'  port: 0  MySQL Community Server (GPL)

Why port 0 ? Why the port is not the configured one ? It seems quite logic that the check fails with this. The thing is that the second time that I launch the container, the port is set correctly, but due to the fact that there are files in the volumes/mysql folder, the initialization script is not triggered, and then the user scripts and database initialization are simply not executed.

If we succeed to fix the port 0 the first time after the container building, I think we would be done with that issue.