[Docker] "Operating system error number 28. Check that your OS and file system support files of this size" mysqlの容量エラーでコンテナが起動できない状態を解決する

環境
Docker for mac Version (2.0.0.0-mac78)
mac OS 10.13.13 (High Sierra)

mysqlのコンテナを起動しようとすると、以下のように容量が足りないとエラーがでる。

現象

Initializing database
2018-12-25T21:43:30.931202Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use for_timestamp server option (see documentation for more details).
2018-12-25T21:43:30.935205Z 0 [Warning] InnoDB: Using innodb_file_format is deprecated and the parameter may be removed in  http://dev.mysql.com/doc/refman/5.7/en/innodb-file-format.html
2018-12-25T21:43:30.961773Z 0 [Warning] InnoDB: Retry attempts for writing partial data failed.
2018-12-25T21:43:30.961810Z 0 [ERROR] InnoDB: Write to file ./ibdata1failed at offset 0, 1048576 bytes should have been  written. Operating system error number 28. Check that your OS and file system support files of this size. Check also that the a disk quota exceeded.
2018-12-25T21:43:30.961820Z 0 [ERROR] InnoDB: Error number 28 means 'No space left on device'
2018-12-25T21:43:30.961825Z 0 [ERROR] InnoDB: Could not set the file size of './ibdata1'. Probably out of disk space
2018-12-25T21:43:30.961828Z 0 [ERROR] InnoDB: InnoDB Database creation was aborted with error Generic error. You may need to ile before trying to start up again.
2018-12-25T21:43:31.565477Z 0 [ERROR] Plugin 'InnoDB' init function returned error.
2018-12-25T21:43:31.565514Z 0 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2018-12-25T21:43:31.565518Z 0 [ERROR] Failed to initialize builtin plugins.
2018-12-25T21:43:31.565520Z 0 [ERROR] Aborting

調査

対象のコンテナを起動して容量を確認すると
ルート以下が容量100%になっている

/# df -h
Filesystem      Size  Used Avail Use% Mounted on
overlay          59G   56G     0 100% /
tmpfs            64M     0   64M   0% /dev
tmpfs          1000M     0 1000M   0% /sys/fs/cgroup
osxfs           421G  333G   85G  80% /etc/mysql/conf.d
/dev/sda1        59G   56G     0 100% /etc/hosts
shm              64M     0   64M   0% /dev/shm
tmpfs          1000M     0 1000M   0% /proc/acpi
tmpfs          1000M     0 1000M   0% /sys/firmware

docker volumeコマンドでvolumeを確認すると、使っていなそうなvolumeがたくさんある

$ docker volume ls
local               0a147b310b327a732d452aba0da74e7fcb745641d53654cd6f6013efefba3f7e
local               0b86da4bcda4bbde206e02104a9449040cc3b9e22290a4583bda816910a23f50
local               0bd0f647f099ccde83a9ec7ac6fefe41d754cf28183cffeb66f01cc05dd32316
local               0e23c68d181912fc998c66e6f313de61ac97cf62fe5c0af99b5a9e8f5c2254f4
...

解決方法

不要なvolumeを消すコマンドを実行

docker volume prune

これで半分以上消えた。

この状態で、mysqlのコンテナを再起動すると、
正常に起動できるようになった。

参考：
https://www.pospome.work/entry/20160505/1462444972