Error initialize specified but the data directory has files in it aborting

asked Jun 5, 2016 at 16:21

I faced the sample problem. i renamed the container directory from

/var/lib/mysql

to

/var/lib/minesql or some different name

. Now the container is started.

Previous Command:

docker container run --name=mysql -d -e MYSQL_ROOT_PASSWORD=abc1234 -e MYSQL_DATABASE=sample -e MYSQL_USER=ashik -e MYSQL_PASSWORD=abc123 -v mysql_volume:/var/lib/mysql mysql

Working Command:

docker container run --name=mysql -d -e MYSQL_ROOT_PASSWORD=abc1234 -e MYSQL_DATABASE=sample -e MYSQL_USER=ashik -e MYSQL_PASSWORD=abc123 -v mysql_volume:/var/lib/minesql mysql

answered May 24, 2019 at 12:37

Its usually means your data directory is not empty. If you remove or rename the data directory and the problem still exist, check your config file /etc/my.cnf and delete validate_password_policy variable in the initialize step. after starting the server you can set this variable to any things you want.

just remove /data directory. this is worked for me :

as simple like this :

image: mysql:5.7
volumes:
  - ./db:/var/lib/mysql

and make sure your «./db» directory is empty.

answered Feb 22, 2020 at 16:40

I had similar issue, but no mysql folder inside the /usr/local.

In my case mysql was located inside the /usr/local/var

so rm -rf /usr/local/var/mysql fixed the problem

answered May 24, 2021 at 12:41

answered Aug 16, 2021 at 14:09

Disable SElinux.

Setenforce 0

Also create log directory in /var/logs/ mysql folder
It have to mysql user owner

cd /var/log/
mkdir mysql
chown -R mysql:mysql mysql/

then change log direcotry in /etc/my.cnf

answered Mar 29, 2020 at 15:15

I have just installed MySQL 5.7 on a fresh CentOS 6.7(vm).

When I start the MySQL service with this command:

sudo service mysqld start

It doesn’t start and raise this error:

Initializing MySQL database: 2015-12-07T11:00:51.060114Z 0 [Warning]
TIMESTAMP with implicit DEFAULT value is deprecated. Please use
—explicit_defaults_for_timestamp server option (see documentation for more details). 2015-12-07T11:00:51.062305Z 0 [ERROR]
—initialize specified but the data directory has files in it.
Aborting. 2015-12-07T11:00:51.062347Z 0 [ERROR] Aborting [FAILED]

Do you know what is the problem?

I faced the same issue myself and I successfully resolved it.
What needs to be done is:
Open the my.conf file in vi editor and add a line under [mysqld]:

explicit_defaults_for_timestamp = 1

This will fix the first issue.
Now check the access rights of the location pointed by datadir field and make sure mysql can access it.
Worst case rename the location it points to. eg:

datadir=/var/lib/mysql1

Good luck.

answered Dec 23, 2016 at 12:40

You can follow the below steps

mysqld --initialize-insecure --user=username --datadir=datadir_path

you can also opt to --initialize-secure, but it would ask for root password as it was in previous versions with secure_installation.

Make sure the datadir is an empty created folder or else it will throw errors and then you can use following to start mysql:

./bin/mysqld_safe --defaults-file=path to cnf file

or

serivce mysqld start

Please check for error log file and share if you face any errors following above steps and do set root password once it is started.

I had a similar issue with Kubernetes and MySQL 5.7 as well.

Adding the suggestion from yosifki to my container’s definition got things working.

A new ext4 disk partition is not usually empty;
there is a lost+found directory, which mysql is known to choke on. You
could try adding —ignore-db-dir=lost+found to the CMD to know for
sure (from mysql docs)

Here’s an extract of my working YAML definition:

name: mysql-master
image: mysql:5.7
args:
  - "--ignore-db-dir=lost+found"

Here’s an example snippet in docker-compose to clarify:

version: '3'
services:
  mysql-master:
    image: mysql:5.7
    command: [--ignore-db-dir=lost+found]
    environment:
      - MYSQL_ROOT_PASSWORD=root

answered Feb 20, 2021 at 23:35