Fix Docker OverlayFS Corruption on macOS

Fix Docker OverlayFS Corruption on macOS | Generated by AI

Home 2025.10

The error you’re seeing, driver "overlay2" failed to remove root filesystem: readdirnames /var/lib/docker/overlay2/.../merged: readdirent merged: bad message, indicates a deep corruption within Docker’s storage mechanism (OverlayFS) that is often caused by an interrupted operation or a host machine filesystem issue.

Since you’re on macOS (which runs Docker Desktop), the Docker daemon and its storage are managed inside a dedicated Linux Virtual Machine (VM). You don’t have direct access to /var/lib/docker/overlay2 like you would on native Linux, making the fix simpler and safer by focusing on the Docker Desktop app itself.

Here is the safest and most effective sequence of steps to resolve this on macOS:

1. Force-Stop and Force-Remove the Container

The container that failed is chat-mongodb (ID: ccd89a3f36a1528cb923c90de8755faeb36e229cab353c2285222948197b8d18). First, try a forced removal using its name or ID.

Stop the entire stack (to ensure no background process is holding a lock):
```
docker compose stop
```

Force-remove the specific container using the -f flag:

docker rm -f chat-mongodb
# OR using the ID:
# docker rm -f ccd89a3f36a1528cb923c90de8755faeb36e229cab353c2285222948197b8d18

Try running your original command again (docker compose down or equivalent). If the error persists, move to step 2.

2. Restart Docker Desktop

A simple restart often clears up transient lock issues or corrupted states within the internal VM.

Click the Docker Whale icon in your macOS menu bar.
Select Restart.

Option B: Using the Terminal

You can force quit and reopen the application:

killall Docker && open /Applications/Docker.app

After Docker restarts, wait about 30 seconds for it to fully start, then try running your original command again.

3. Clear Docker’s Cache and Unused Data (Prune)

If the restart fails, a powerful cleanup command can often resolve deeper corruption issues by removing unused or “dangling” components that might be related to the error.

WARNING: This command removes all stopped containers, unused networks, and dangling images. If you have containers you want to keep stopped (but not removed), back them up or skip this step.

Run the following command in your terminal:

docker system prune -a --volumes

-a (all) removes all unused images (not just dangling ones).
--volumes removes unused anonymous volumes (which might be the source of the overlay2 corruption).

You will be asked to confirm. Type y and press Enter. After the prune completes, try running your original command again.

4. Factory Reset Docker Desktop

This is the last resort as it will delete all your containers, images, and volumes (including any local data you have stored in non-mounted volumes). It forces a completely fresh start of the internal Docker VM.

Click the Docker Whale icon in your macOS menu bar.
Go to Settings (or Preferences) $\rightarrow$ Troubleshoot.
Click Reset to factory settings…

After the reset, Docker will restart with a clean slate, and you should be able to run your docker compose up command to rebuild your environment.

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