【M1 Mac】lima + DockerでMySQLを起動する

2023-02-25

はじめに

limaを使って立ち上げたVMにdockerのmysqlを立ち上げようとした際に、以下のエラーでハマったので備忘録として残します。

• read-only file system
• permission denied
• exec format error
• [ERROR] [MY-010259] [Server] Another process with pid 63 is using unix socket file

環境

名前	バージョン
PC	MacBook Pro (13-inch, M1, 2020)
lima	0.14.2
Docker	20.10.12

結論

compose.yaml

services:
  db:
    image: mysql/mysql-server:latest
    user: mysql
    environment:
      MYSQL_ALLOW_EMPTY_PASSWORD: yes
    volumes:
      - db-data:/var/lib/mysql
    ports:
      - "3306:3306"

volumes:
  db-data:

limaのdocker exampleから大きく変更していません。
変更しているのは、mountsの部分です。

lima.yaml

lima.yaml

# Example to use Docker instead of containerd & nerdctl
# $ limactl start ./docker.yaml
# $ limactl shell docker docker run -it -v $HOME:$HOME --rm alpine

# To run `docker` on the host (assumes docker-cli is installed):
# $ export DOCKER_HOST=$(limactl list docker --format 'unix://{{.Dir}}/sock/docker.sock')
# $ docker ...

# This example requires Lima v0.8.0 or later
images:
# Try to use release-yyyyMMdd image if available. Note that release-yyyyMMdd will be removed after several months.
- location: "https://cloud-images.ubuntu.com/releases/22.04/release-20221201/ubuntu-22.04-server-cloudimg-amd64.img"
  arch: "x86_64"
  digest: "sha256:8a814737df484d9e2f4cb2c04c91629aea2fced6799fc36f77376f0da91dba65"
- location: "https://cloud-images.ubuntu.com/releases/22.04/release-20221201/ubuntu-22.04-server-cloudimg-arm64.img"
  arch: "aarch64"
  digest: "sha256:8a0477adcbdadefd58ae5c0625b53bbe618aedfe69983b824da8d02be0a8c961"
# Fallback to the latest release image.
# Hint: run `limactl prune` to invalidate the cache
- location: "https://cloud-images.ubuntu.com/releases/22.04/release/ubuntu-22.04-server-cloudimg-amd64.img"
  arch: "x86_64"
- location: "https://cloud-images.ubuntu.com/releases/22.04/release/ubuntu-22.04-server-cloudimg-arm64.img"
  arch: "aarch64"

# CPUs: if you see performance issues, try limiting cpus to 1.
# 🟢 Builtin default: 4
# cpus: null

# Memory size
# 🟢 Builtin default: "4GiB"
# memory: null

# Disk size
# 🟢 Builtin default: "100GiB"
# disk: null

mounts:
- # - location: "~"
- location: "~/Project"
  writable: true
- location: "/tmp/lima"
  writable: true
# containerd is managed by Docker, not by Lima, so the values are set to false here.
containerd:
  system: false
  user: false
provision:
- mode: system
  # This script defines the host.docker.internal hostname when hostResolver is disabled.
  # It is also needed for lima 0.8.2 and earlier, which does not support hostResolver.hosts.
  # Names defined in /etc/hosts inside the VM are not resolved inside containers when
  # using the hostResolver; use hostResolver.hosts instead (requires lima 0.8.3 or later).
  script: |
    #!/bin/sh
    sed -i 's/host.lima.internal.*/host.lima.internal host.docker.internal/' /etc/hosts
- mode: system
  script: |
    #!/bin/bash
    set -eux -o pipefail
    command -v docker >/dev/null 2>&1 && exit 0
    export DEBIAN_FRONTEND=noninteractive
    curl -fsSL https://get.docker.com | sh
    # NOTE: you may remove the lines below, if you prefer to use rootful docker, not rootless
    systemctl disable --now docker
    apt-get install -y uidmap dbus-user-session
- mode: user
  script: |
    #!/bin/bash
    set -eux -o pipefail
    systemctl --user start dbus
    dockerd-rootless-setuptool.sh install
    docker context use rootless
probes:
- script: |
    #!/bin/bash
    set -eux -o pipefail
    if ! timeout 30s bash -c "until command -v docker >/dev/null 2>&1; do sleep 3; done"; then
      echo >&2 "docker is not installed yet"
      exit 1
    fi
    if ! timeout 30s bash -c "until pgrep rootlesskit; do sleep 3; done"; then
      echo >&2 "rootlesskit (used by rootless docker) is not running"
      exit 1
    fi
  hint: See "/var/log/cloud-init-output.log". in the guest
hostResolver:
  # hostResolver.hosts requires lima 0.8.3 or later. Names defined here will also
  # resolve inside containers, and not just inside the VM itself.
  hosts:
    host.docker.internal: host.lima.internal
portForwards:
- guestSocket: "/run/user/{{.UID}}/docker.sock"
  hostSocket: "{{.Dir}}/sock/docker.sock"
message: |
  To run `docker` on the host (assumes docker-cli is installed), run the following commands:
  ------
  docker context create lima-{{.Name}} --docker "host=unix://{{.Dir}}/sock/docker.sock"
  docker context use lima-{{.Name}}
  docker run hello-world
  ------

調査

はじめにlimaのGitHubからテンプレートを取ってきます

$ curl -o lima.yaml https://raw.githubusercontent.com/lima-vm/lima/master/examples/docker.yaml

このときのファイルは以下の通りです

lima.yaml

# Example to use Docker instead of containerd & nerdctl
# $ limactl start ./docker.yaml
# $ limactl shell docker docker run -it -v $HOME:$HOME --rm alpine

# To run `docker` on the host (assumes docker-cli is installed):
# $ export DOCKER_HOST=$(limactl list docker --format 'unix://{{.Dir}}/sock/docker.sock')
# $ docker ...

# This example requires Lima v0.8.0 or later
images:
# Try to use release-yyyyMMdd image if available. Note that release-yyyyMMdd will be removed after several months.
- location: "https://cloud-images.ubuntu.com/releases/22.04/release-20221201/ubuntu-22.04-server-cloudimg-amd64.img"
  arch: "x86_64"
  digest: "sha256:8a814737df484d9e2f4cb2c04c91629aea2fced6799fc36f77376f0da91dba65"
- location: "https://cloud-images.ubuntu.com/releases/22.04/release-20221201/ubuntu-22.04-server-cloudimg-arm64.img"
  arch: "aarch64"
  digest: "sha256:8a0477adcbdadefd58ae5c0625b53bbe618aedfe69983b824da8d02be0a8c961"
# Fallback to the latest release image.
# Hint: run `limactl prune` to invalidate the cache
- location: "https://cloud-images.ubuntu.com/releases/22.04/release/ubuntu-22.04-server-cloudimg-amd64.img"
  arch: "x86_64"
- location: "https://cloud-images.ubuntu.com/releases/22.04/release/ubuntu-22.04-server-cloudimg-arm64.img"
  arch: "aarch64"

mounts:
- location: "~"
- location: "/tmp/lima"
  writable: true
# containerd is managed by Docker, not by Lima, so the values are set to false here.
containerd:
  system: false
  user: false
provision:
- mode: system
  # This script defines the host.docker.internal hostname when hostResolver is disabled.
  # It is also needed for lima 0.8.2 and earlier, which does not support hostResolver.hosts.
  # Names defined in /etc/hosts inside the VM are not resolved inside containers when
  # using the hostResolver; use hostResolver.hosts instead (requires lima 0.8.3 or later).
  script: |
    #!/bin/sh
    sed -i 's/host.lima.internal.*/host.lima.internal host.docker.internal/' /etc/hosts
- mode: system
  script: |
    #!/bin/bash
    set -eux -o pipefail
    command -v docker >/dev/null 2>&1 && exit 0
    export DEBIAN_FRONTEND=noninteractive
    curl -fsSL https://get.docker.com | sh
    # NOTE: you may remove the lines below, if you prefer to use rootful docker, not rootless
    systemctl disable --now docker
    apt-get install -y uidmap dbus-user-session
- mode: user
  script: |
    #!/bin/bash
    set -eux -o pipefail
    systemctl --user start dbus
    dockerd-rootless-setuptool.sh install
    docker context use rootless
probes:
- script: |
    #!/bin/bash
    set -eux -o pipefail
    if ! timeout 30s bash -c "until command -v docker >/dev/null 2>&1; do sleep 3; done"; then
      echo >&2 "docker is not installed yet"
      exit 1
    fi
    if ! timeout 30s bash -c "until pgrep rootlesskit; do sleep 3; done"; then
      echo >&2 "rootlesskit (used by rootless docker) is not running"
      exit 1
    fi
  hint: See "/var/log/cloud-init-output.log". in the guest
hostResolver:
  # hostResolver.hosts requires lima 0.8.3 or later. Names defined here will also
  # resolve inside containers, and not just inside the VM itself.
  hosts:
    host.docker.internal: host.lima.internal
portForwards:
- guestSocket: "/run/user/{{.UID}}/docker.sock"
  hostSocket: "{{.Dir}}/sock/docker.sock"
message: |
  To run `docker` on the host (assumes docker-cli is installed), run the following commands:
  ------
  docker context create lima-{{.Name}} --docker "host=unix://{{.Dir}}/sock/docker.sock"
  docker context use lima-{{.Name}}
  docker run hello-world
  ------

read-only file system

Linuxインスタンスを立ち上げます

$ limactl start --name docker --tty=false lima.yaml

出力結果

INFO[0000] Terminal is not available, proceeding without opening an editor
INFO[0000] Attempting to download the image from "https://cloud-images.ubuntu.com/releases/22.04/release-20221201/ubuntu-22.04-server-cloudimg-arm64.img"  digest="sha256:8a0477adcbdadefd58ae5c0625b53bbe618aedfe69983b824da8d02be0a8c961"
INFO[0000] Using cache "/Users/hoge/Library/Caches/lima/download/by-url-sha256/26ec58a84d273e5b19eebe2a555e5a63172532f1a7f8b0d6f0aaf5edc83ce1b3/data"
WARN[0001] [hostagent] Reducing the guest memory from 4GiB to 3GiB, to avoid host kernel panic on macOS <= 12.3 with QEMU >= 7.0; Please update macOS to 12.4 or later, or downgrade QEMU to 6.2; See https://github.com/lima-vm/lima/issues/795 for the further background.
INFO[0001] [hostagent] Starting QEMU (hint: to watch the boot progress, see "/Users/hoge/.lima/docker/serial.log")
INFO[0001] SSH Local Port: 58370
INFO[0001] [hostagent] Waiting for the essential requirement 1 of 5: "ssh"
cINFO[0022] [hostagent] The essential requirement 1 of 5 is satisfied
INFO[0022] [hostagent] Waiting for the essential requirement 2 of 5: "user session is ready for ssh"
INFO[0022] [hostagent] The essential requirement 2 of 5 is satisfied
INFO[0022] [hostagent] Waiting for the essential requirement 3 of 5: "sshfs binary to be installed"
INFO[0041] [hostagent] The essential requirement 3 of 5 is satisfied
INFO[0041] [hostagent] Waiting for the essential requirement 4 of 5: "/etc/fuse.conf (/etc/fuse3.conf) to contain \"user_allow_other\""
INFO[0045] [hostagent] The essential requirement 4 of 5 is satisfied
INFO[0045] [hostagent] Waiting for the essential requirement 5 of 5: "the guest agent to be running"
INFO[0045] [hostagent] The essential requirement 5 of 5 is satisfied
INFO[0045] [hostagent] Mounting "/Users/hoge" on "/Users/hoge"
INFO[0046] [hostagent] Mounting "/tmp/lima" on "/tmp/lima"
INFO[0046] [hostagent] Waiting for the optional requirement 1 of 1: "user probe 1/1"
INFO[0046] [hostagent] Forwarding "/run/user/501/docker.sock" (guest) to "/Users/hoge/.lima/docker/sock/docker.sock" (host)
INFO[0047] [hostagent] Forwarding "/run/lima-guestagent.sock" (guest) to "/Users/hoge/.lima/docker/ga.sock" (host)
INFO[0047] [hostagent] Not forwarding TCP 0.0.0.0:22
INFO[0047] [hostagent] Not forwarding TCP 127.0.0.53:53
INFO[0047] [hostagent] Not forwarding TCP [::]:22
INFO[0083] [hostagent] The optional requirement 1 of 1 is satisfied
INFO[0083] [hostagent] Waiting for the final requirement 1 of 1: "boot scripts must have finished"
INFO[0086] [hostagent] The final requirement 1 of 1 is satisfied
INFO[0086] READY. Run `limactl shell docker` to open the shell.
INFO[0086] Message from the instance "docker":
To run `docker` on the host (assumes docker-cli is installed), run the following commands:
------
docker context create lima-docker --docker "host=unix:///Users/hoge/.lima/docker/sock/docker.sock"
docker context use lima-docker
docker run hello-world
------

ちゃんと起動していますね。

$ limactl ls
NAME      STATUS     SSH                VMTYPE    ARCH       CPUS    MEMORY    DISK      DIR
docker    Running    127.0.0.1:58370    qemu      aarch64    4       4GiB      100GiB    ~/.lima/docker

完了したらdocker cliの向け先を先ほど作成したインスタンスに向けます

$ docker context create lima-docker --docker "host=unix:///Users/xxxxxx/.lima/docker/sock/docker.sock"
$ docker context use lima-docker

info: コンテキストやdocker cliの情報を表示できます

$ docker context ls
$ docker info

info: 環境変数DOCKER_HOSTを使うことで、docker contextを使うことなく、向け先を切り替えることもできます。
Docker デーモンソケットの保護

このときのcomposeファイルは以下の通りです。

compose.yaml

services:
  db:
    image: mysql:latest
    platform: linux/amd64
    environment:
      MYSQL_ALLOW_EMPTY_PASSWORD: yes
    volumes:
      - ./mysql/data:/var/lib/mysql
    ports:
      - "3306:3306"

docker compose upしてみると・・

$ docker compose up
[+] Running 12/12
 ⠿ db Pulled                                                                                                                     10.7s
   ⠿ b4ddc423e046 Pull complete                                                                                                   3.3s
   ⠿ b338d8e4ffd1 Pull complete                                                                                                   3.5s
   ⠿ b2b1b06949ab Pull complete                                                                                                   3.6s
   ⠿ daf393284da9 Pull complete                                                                                                   3.8s
   ⠿ 1cb8337ae65d Pull complete                                                                                                   3.8s
   ⠿ f6c2cc79221c Pull complete                                                                                                   3.9s
   ⠿ 4cec461351e0 Pull complete                                                                                                   5.2s
   ⠿ ab6bf0cba08e Pull complete                                                                                                   5.3s
   ⠿ 8df43cafbd11 Pull complete                                                                                                   7.4s
   ⠿ c6d0aac53df5 Pull complete                                                                                                   7.5s
   ⠿ b24148c7c251 Pull complete                                                                                                   7.5s
[+] Running 1/0
 ⠿ Container docker-lima-db-1  Created                                                                                            0.0s
Attaching to docker-lima-db-1
Error response from daemon: error while creating mount source path '/path/to/mysql/data': mkdir /path/to/mysql/data: read-only file system

mkdir /path/to/mysql/data: read-only file systemで拒否されました。

解決-1

- location: "~" は消して、特定のディレクトリのみwritable: trueにします。

mounts:
# - location: "~"
- location: "~/Project"
  writable: true
- location: "/tmp/lima"
  writable: true

Attempting to mount a writable directory under a read-only directory doesn’t work #873 - GitHub issues

補足

ホームディレクトリへの書き込み権限はdefaultでfalseなので、lima.yamlのmountsにwritable: trueを入れれば解消します。

mounts:
- location: "~"
  writable: true

Filesystem is not writable - GitHub lima README

しかし、公式ではtrueにすべきではないと書いているので、ホームディレクトリに対してwritableの設定するのは避けたほうが良いでしょう。

# CAUTION: `writable` SHOULD be false for the home directory.
# Setting `writable` to true is possible, but untested and dangerous.
# 🟢 Builtin default: false
writable: null

lima/examples/default.yaml

私のPCでは、ホームディレクトリ配下にProjectディレクトリを作成しているので、以下のように追記し、インスタンスを作り直しました。

mounts:
- location: "~"
- location: "~/Project"
  writable: true
- location: "/tmp/lima"
  writable: true

$ limactl stop docker
$ limactl delete docker

しかし、結局エラーは変わらず、read-only file systemでした。

limaのissueを探してみると、どうやらホームディレクトリはwritable:falseで、その配下のディレクトリをwritable:trueにするようなことはできないそうです。
Overlapping mounts don’t work correctly #302 - GitHub issues

permission denied

lima.yamlのmountsを修正してもう一度インスタンスを作成します。

$ limactl stop docker
$ limactl delete docker
$ limactl start --name docker --tty=false lima.yaml

compose.yamlはそのままです。

compose.yaml

services:
  db:
    image: mysql:latest
    platform: linux/amd64
    environment:
      MYSQL_ALLOW_EMPTY_PASSWORD: yes
    volumes:
      - ./mysql/data:/var/lib/mysql
    ports:
      - "3306:3306"

今度はpermission deniedで止まりました。

$ docker compose up
[+] Running 12/12
 ⠿ db Pulled                                                                                                                     10.8s
   ⠿ b4ddc423e046 Pull complete                                                                                                   3.3s
   ⠿ b338d8e4ffd1 Pull complete                                                                                                   3.6s
   ⠿ b2b1b06949ab Pull complete                                                                                                   3.6s
   ⠿ daf393284da9 Pull complete                                                                                                   3.8s
   ⠿ 1cb8337ae65d Pull complete                                                                                                   3.9s
   ⠿ f6c2cc79221c Pull complete                                                                                                   3.9s
   ⠿ 4cec461351e0 Pull complete                                                                                                   5.2s
   ⠿ ab6bf0cba08e Pull complete                                                                                                   5.3s
   ⠿ 8df43cafbd11 Pull complete                                                                                                   7.4s
   ⠿ c6d0aac53df5 Pull complete                                                                                                   7.4s
   ⠿ b24148c7c251 Pull complete                                                                                                   7.5s
[+] Running 2/1
 ⠿ Network docker-lima_default  Created                                                                                           0.0s
 ⠿ Container docker-lima-db-1   Created                                                                                           0.0s
Attaching to docker-lima-db-1
Error response from daemon: error while creating mount source path '/path/to/mysql/data': mkdir /path/to/Project: permission denied

解決-2

MySQLコンテナをlimaで起動するとPermission Deniedになる - Scrapboxの記事を参考にしました。

以下のようにuser: mysqlを入れます。

compose.yaml

services:
  db:
    image: mysql:latest
    platform: linux/amd64
    user: mysql
    environment:
      MYSQL_ALLOW_EMPTY_PASSWORD: yes
    volumes:
      - ./mysql/data:/var/lib/mysql
    ports:
      - "3306:3306"

exec format error

user:mysqlを入れて実行してみると、今度は、exec format errorが出ました。

$ docker compose up
[+] Running 1/0
 ⠿ Container docker-lima-db-1  Created                                                                                            0.0s
Attaching to docker-lima-db-1
docker-lima-db-1  | exec /usr/local/bin/docker-entrypoint.sh: exec format error
docker-lima-db-1 exited with code 1

解決-3

mysql/mysql-serverはarm64をサポートしているようなので、dockerイメージを代えます。

MySQL Server 8.0, the latest GA, for both x86 and AArch64(ARM64) architectures (tag: 8.0, latest) (mysql-server/8.0/Dockerfile)

mysql/mysql-server - DockerHub

compose.yaml

services:
  db:
    image: mysql/mysql-server:latest
    # platform: linux/amd64
    user: mysql
    environment:
      MYSQL_ALLOW_EMPTY_PASSWORD: yes
    volumes:
      - ./mysql/data:/var/lib/mysql
    ports:
      - "3306:3306"

[ERROR] [MY-010259] [Server] Another process with pid 63 is using unix socket file.

今度はunix socket fileでエラーが出ました。

$ docker compose up
[+] Running 1/1
 ⠿ Container docker-lima-db-1  Recreated                                                                                          0.4s
Attaching to docker-lima-db-1
docker-lima-db-1  | [Entrypoint] MySQL Docker Image 8.0.32-1.2.11-server
docker-lima-db-1  | [Entrypoint] Starting MySQL 8.0.32-1.2.11-server
docker-lima-db-1  | 2023-02-25T06:37:28.446867Z 0 [Warning] [MY-011068] [Server] The syntax '--skip-host-cache' is deprecated and will be removed in a future release. Please use SET GLOBAL host_cache_size=0 instead.
docker-lima-db-1  | 2023-02-25T06:37:28.446977Z 0 [Warning] [MY-010143] [Server] Ignoring user change to '27' because the user was set to 'mysql' earlier on the command line
docker-lima-db-1  | 2023-02-25T06:37:28.467339Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.32) starting as process 1
docker-lima-db-1  | 2023-02-25T06:37:28.492378Z 0 [Warning] [MY-010159] [Server] Setting lower_case_table_names=2 because file system for /var/lib/mysql/ is case insensitive
docker-lima-db-1  | 2023-02-25T06:37:28.732651Z 1 [System] [MY-013576] [InnoDB] InnoDB initialization has started.
docker-lima-db-1  | 2023-02-25T06:37:42.332168Z 1 [System] [MY-013577] [InnoDB] InnoDB initialization has ended.
docker-lima-db-1  | 2023-02-25T06:37:42.590346Z 0 [System] [MY-010229] [Server] Starting XA crash recovery...
docker-lima-db-1  | 2023-02-25T06:37:42.685470Z 0 [System] [MY-010232] [Server] XA crash recovery finished.
docker-lima-db-1  | 2023-02-25T06:37:42.736262Z 0 [Warning] [MY-010068] [Server] CA certificate ca.pem is self signed.
docker-lima-db-1  | 2023-02-25T06:37:42.736357Z 0 [System] [MY-013602] [Server] Channel mysql_main configured to support TLS. Encrypted connections are now supported for this channel.
docker-lima-db-1  | 2023-02-25T06:37:42.743300Z 0 [ERROR] [MY-010259] [Server] Another process with pid 63 is using unix socket file.
docker-lima-db-1  | 2023-02-25T06:37:42.743316Z 0 [ERROR] [MY-010268] [Server] Unable to setup unix socket lock file.
docker-lima-db-1  | 2023-02-25T06:37:42.743325Z 0 [ERROR] [MY-010119] [Server] Aborting
docker-lima-db-1  | 2023-02-25T06:37:44.374095Z 0 [System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.32)  MySQL Community Server - GPL.
docker-lima-db-1 exited with code 1

解決-4

[Error] [Server] Do you already have another mysqld server running on socket ? でMySQLがDockerで立ち上がらない現象 - Qiitaの記事を参考にしました！

名前付きボリュームをつけることで回避ができるそうです。

compose.yaml

services:
  db:
    image: mysql/mysql-server:latest
    # platform: linux/amd64
    user: mysql
    environment:
      MYSQL_ALLOW_EMPTY_PASSWORD: yes
    volumes:
      - db-data:/var/lib/mysql
    ports:
      - "3306:3306"

  volumes:
    db-data:

やってみましょう。

$ docker compose up

$ docker compose exec db mysql -uroot
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 16
Server version: 8.0.32 MySQL Community Server - GPL

Copyright (c) 2000, 2023, Oracle and/or its affiliates.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql>

無事mysqlに繋げることができました

Tags:

• MySQL
• lima
• docker compose
• Docker