Mysql not starting in a docker container on MacOS after docker update

Question

I just upgraded to Docker Desktop 2.4 on MacOS, from version 2.3. Suddenly none of my mysql containers will start. The logs show this as the reason:

Different lower_case_table_names settings for server ('2') and data dictionary ('0').
Data Dictionary initialization failed.
Aborting

The database files are mounted in a volume on my host machine, so that they persist between restarts.

I finally figured out why. Posting in order to answer.

Con

Answer 1

With the latest docker you can disable the gRPC Fuse for file sharing. (the gRPC Fuse setting is causing this problem, it's incompatible with the data dictionary of 0)

This fixes the problem... You can stop here if you're happy, but to use the new filesystem you can:

• Disable this checkbox
• Start the container
• Dump the database
• Enable this checkbox
• Make sure your data folder empty (so mysql creates a new data dictionary)
• Import the dumped database

UPDATE

Since version 2.5, the setting has been moved to the 'experimental features' page:

Idette

Doesn't work in my case :( Still can't persist the /var/lib/mysql/ as volume. As soon as I copy this folder from the container to my local project and restart the container (docker-compose up) mysql service fails to start – Tremolite

Worked for me too, thanks! My experience with docker so far has been quite mixed. – Salley

Or if your database is disposable/in a dev project, simply skip to step 5 and start over :-) – Churr

Thanks! Worked with Docker Desktop 2.5.0.1 on macOS 10.14.6 Mojave and mysql 8.0.13 – Bourgeon

Thanks for this you good human! This caught me off guard today at a very bad time, irritating stuff. Really appreciate this find it was beginning to manifest as a bad headache. – Eddaeddana

I can't see the gRPC option in Windows Docker Desktop 4.2.0. – Lifeblood

For some reason it is not getting unchecked when pressed save and restart button. Weird. macOS 12.5.1 and docker desktop 4.12.0 (85629) – Tune

Thanks! it solved my problem. you can find this option on Docker desktop 4.15 :: - Preferences -> General -> Choose file sharing implementation for your container. - you should choose osxfs( Legacy) – Corked

oh thanks...i was struggling for so long....it solved my exact probelm... – Mackenie

Answer 2

The lower_case_table_names setting tells mysql how to store and compare table names. If the file system the database is stored on is itself not case-sensitive, it will force you to use lower_case_table_names=2.

The MacOS filesystem is not case-sensitive. Up until Docker Desktop 2.4, the mysql container apparently didn't know that the underlying filesystem is not case-sensitive and set lower_case_table_names=0. However, since upgrading to Docker 2.4, Docker is apparently smarter about how it mounts volumes. So the container realizes its running on a case-insensitive filesystem and forces lower_case_table_names=2. The problem is that you cannot change the value of lower_case_table_names after initializing the database. And since the data dictionary was initialized with lower_case_table_names=0, it will fail to initialize with the server set to lower_case_table_names=2.

The only solution I've found is to:

1. Downgrade to Docker Desktop 2.3
2. Backup the entire database
3. Upgrade to Docker 2.4
4. Delete the volume storing the database.
5. Reinitialize the database.
6. Restore the database from backup.

UPDATE: See this answer below for a better solution. There is apparently no need to downgrade. You can instead disable "gRPC Fuse for filesharing", backup the database, re-enable gRPC fuse, delete your database data folder, and restore the database from backup.

Con

Thanks for you answer! Downgrade isn't required (See other post) – Idette

Answer 3

Another option is to create a case sensitive APFS volume using Disk Utility.

Unlike a partition, it is possible to share the free space, so you don't need to worry about reserving enough space to run your database.

Then create a symlink from your project to your case sensitive volume.

cd ~/my-project
ln -s /Volumes/MySQL/project-db mysql

Lavabo

This was an easy fix for MacOS thanks man. – Bartlett

Best, worked for MacOS. I had to delete and loss data in last iteration for similar issue. Thought it was due to mysql version change. But this time kept same version container but still it same issue. Not this method helped. Thanks – Tune

Answer 4

Docker removed this option on the recent updates , i manage to solve this issue on windows by doing this

Run a shell as administrator:

go to your local mounted mysql volume and run

fsutil file setCaseSensitiveInfo ./ enable 

credits to https://github.com/docker/for-win/issues/12384#issuecomment-972845031

Consciencestricken

Could you update your answer and include some details about what the command does, how it solves the problem? – Con

Answer 5

A small addition to Loic's H answer. Suppose your mapping is something like this:

docker run --name your_container_name ... -v //d/MySqlDockerData:/var/lib/mysql ...

if your try

fsutil file setCaseSensitiveInfo d:\MySqlDockerData

you will get an error "The directory is not empty"

To get around this follow these steps:

1. run docker container stop your_container_name
2. transfer the contents of the folder to the another place (clear the folder)
3. run again fsutil file setCaseSensitiveInfo d:\MySqlDockerData
4. transfer back saved data to the d:\MySqlDockerData
5. run docker container start your_container_name

voila

Wollastonite

The original question was related to macOS, but it looks like you're on Windows. Are you seeing this same issue on Windows as well? – Con

Cully, quite so and I reffered on the Loic H answer concerning Windows specifically – Wollastonite

I'm curious, do you know how you were able to get case-insensitive volume mounted on Windows in the first place (the thing that caused the problem)? – Con

As far as I know, prior to WSL2 it was common practice to map a Windows folder. Today it is recommended to use Linux folders for mapping to improve performance. But you can still map to a regular Windows folder, which has the attribute case-insensitive by default - the same problem as you perfectly described in your answer. – Wollastonite

Ah! I didn't realize Windows file systems were also case-insensitive. That's good to know. Thanks! – Con

Answer 6

As workaround on Windows OS I disabled WSL in Docker Desktop and it helped me

Update. After last Docker Desktop Updates I was forced to set Windows directory with DB data as case sensitive

Euplastic

This shouldn't be an issue in Windows since it uses a case-sensitive filesystem. I think you may be running into another problem. – Con

Can you confirm you're getting the same message in your logs (the message shown in the question)? – Con

Yes, first notice is Setting lower_case_table_names=2 because file system for /var/lib/mysql/ is case insensitive then InnoDB initialization has ended. Different lower_case_table_names settings for server ('2') and data dictionary ('0'). Data Dictionary initialization failed. – Euplastic

Do you have it mounted on a case-insensitive filesystem? – Con

I simply specified ./docker/dbdata:/var/lib/mysql in volumes in my docker-compose.yml, where docker/dbdata is my Windows directory (NTFS) – Euplastic

Answer 7

I just wanted to add this answer as I encountered the same issue in different context, and wanted to let everyone know how I solved it

The Problem:

So, I had a MySQL container running on my local machine, and it didn't have any persistent volume mounted. This basically means that if I killed the container, I would lose all the data. Since there was some useful data in the container, I didn't want that to happen.

Here's what I did:

I got into the container and copied the MySQL data directory to the host machine. Then, I killed the container and started a new one, mounting a volume with the copied directory on the host. To my surprise, I encountered the issue mentioned in the question as Windows and Linux systems have different case sensitivities for directories.

How did I solve it?

I created another directory, made it case-insensitive with the command

fsutil file setCaseSensitiveInfo ./ enable

and copied the content from the previously copied directory into it. After that, everything started working.

Bolan