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I had a spring-boot project that used mysql docker-image so I didn't need to download the mysql benchwork. For other reasons I had to start over so I created a new project that uses the same mysql docker image I previously used. My docker-compose.yml mysql service looks like this

version: "3.7"

services:

  db:
    image: mysql:5.7
    command: --lower_case_table_names=1
    environment:
      MYSQL_ROOT_PASSWORD: root
      MYSQL_DATABASE: farming_db
      MYSQL_USER: root
      MYSQL_PASSWORD: root
    restart: always
    volumes:
      - "./database/farming_db/:/var/lib/mysql" #local
      - farming_db:/var/lib/mysql/data #docker
    ports:
      - "3306:3306"
    container_name: farming_mysql
    networks:
      - backend-network

When I run docker-compose up This is the error :

Attaching to farming_mysql, farming_server_springboot_1
farming_mysql | 2021-03-18 07:03:20+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.33-1debian10 started.
farming_mysql | 2021-03-18 07:03:20+00:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql'
farming_mysql | 2021-03-18 07:03:20+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.33-1debian10 started.
farming_mysql | 2021-03-18 07:03:21+00:00 [Note] [Entrypoint]: Initializing database files
farming_mysql | 2021-03-18T07:03:21.058436Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server opti
on (see documentation for more details).
farming_mysql | 2021-03-18T07:03:21.063630Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting.
farming_mysql | 2021-03-18T07:03:21.063710Z 0 [ERROR] Aborting
farming_mysql |
farming_mysql exited with code 1
springboot_1  |

I understood that my directory is not empty. I am trying to use "./database/farming_db/:/var/lib/mysql" and "farming_db:/var/lib/mysql/data" both as the volume directories. I think the problem is with the latter directory because the prior directory is empty. I'm having a problem deleting the contents in the latter directory because I don't know how to access it.

So this is what I've tried :

  1. I deleted all the containers and then deleted all the volumes.docker volume prune but didn't work.

  2. I searched that I could do rm -rf /usr/local/var/mysql but I don't know where I can execute this command since the container won't run properly at all.

  3. I deleted the mysql image and just ran docker-compose up again. This seems to pull a new mysql image from somewhere? but I still get the same error. I guess volume directory has nothing do with the docker image itself.

  4. I deleted the "- farming_db:/var/lib/mysql/data #docker" line from the docker-compose. But the same error is still occuring!

I'm using Windows10.

My question :

  1. How can I access the directory? I don't know where to use the rm -rf command.
  2. Why does this error still occur even when I erase "- farming_db:/var/lib/mysql/data #docker" from the docker-compose?
  3. And also could anyone explain what I am doing? I'm new to docker and I don't really understand these volume problems.
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  • In our case it didn't had anything to do with clearing the volumes. We just updated mysql in Dockerfile to 5.7.36 and everything worked as expected again. Commented Dec 23, 2021 at 14:35

8 Answers 8

Reset to default
24

Run docker system prune --volumes

This frees up the memory by removing all unused containers. Sometimes, the mentioned issue can occur due to memory limitations

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4

Generally I emptied the volume's data directory and just changed the versions of the MySQL. So in steps:

  1. empty volume directory content
  1. modify docker-compose.yml mysql version from 5.7 to 5.7.16
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2

This line indicate that mysql container is storing the data inside a directory database in the same directory than your docker-compose.yml:

    volumes:
      - "./database/farming_db/:/var/lib/mysql" #local

This kind of volume isn't managed by Docker, it's just a directory in your filesystem, this is why docker volume prune doesn't work. I know that, because it starts with a "path" relative or absolute.

The other volume, farming_db, are managed by Docker. I know that because it starts with a simple name. This kinds of volume are managed by Docker and are removed with prune.

So, answering:

  1. In the same directory than your docker-compose.yml you can remove that database folder.
  2. Because the first volume, the one with /var/lib/mysql still exists. MySQL keeps all files inside this directory and any other child directory are a database.
  3. You're just trying to put a container running and docker-compose hides a lot of details.
  4. This is just a detail, but MYSQL_USER should be different than root.

You can let Docker manage the entire volume, creating a single volume to hold all data, in this case I named it as mysql_data:

    volumes:
    - mysql_data:/var/lib/mysql

Or, you can explore a bit more the docker run equivalent command to get used with it:

docker run -d --name mysql \
-e MYSQL_ROOT_PASSWORD=root \
-e MYSQL_DATABASE=farming_db \
-e MYSQL_USER=myuser \
-e MYSQL_PASSWORD=mypass \
-v mysql_data:/var/lib/mysql \
-p 3306:3306 \
mysql:5.7
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1

I used docker-compose to run mysql image and encountered the error. I use the following configuration to set volume. - ./mysql/data:/var/lib/mysql/data

Then I changed it to the following and the error was solved. - ./mysql:/var/lib/mysql

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1

The error message is misleading: Problem resides in permission access by the process to read/write into it. If you create the mysql manually, the dir will be created with the appropriate rights and leave no issue.

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0

As vencedor's answer, it worked for me. If anyone need stay with mysql 5.7, you can add these lines to your db service in docker-compose.yml:

 - /etc/group:/etc/group:ro
 - /etc/passwd:/etc/passwd:ro
user: "1000:1000"
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0

If you are using Docker for Mac: Make sure there are no Volumes left that are not removed by docker volume prune.

Had a Volume from a failed docker-compose up attempt, which was not properly removed and it caused the error.

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0

Another cause for this problem (happened with me) it's a trivial thing, disk runs out of space. To fix the problem you have to delete the partially created volume/directory after freeing up some space.

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