Mysql: Shutdown after docker-compose up. [ERROR] InnoDB: Ignoring the redo log due to missing MLOG_CHECKPOINT between the checkpoint 2539618 and the end 2539872.

Created on 1 Sep 2017  路  7Comments  路  Source: docker-library/mysql

I am having a problem with the image when using it with docker-compose, something makes the container to shutdown after running docker-compose up.

Here is my docker-compose.yml file:

version: '2'
services:
  web:
    image: messenger
    ports:
     - "8000:8000"
    environment:
      MYSQL_USER: marwan
      MYSQL_PASSWORD: <pass>
      MYSQL_DATABASE: messenger
    depends_on:
      - mysql
      - elastic

  mysql:
    image: mysql
    environment:
      MYSQL_USER: marwan
      MYSQL_PASSWORD: <pass>
      MYSQL_DATABASE: messenger
      MYSQL_ROOT_PASSWORD: <pass>

  elastic:  
    image: docker.elastic.co/elasticsearch/elasticsearch:5.5.2
    ports:
      - 9200:9200

and here is the output:

Attaching to messenger_mysql_1, messenger_elastic_1, messenger_web_1
mysql_1    | 2017-09-01T10:01:43.480240Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
mysql_1    | 2017-09-01T10:01:43.481789Z 0 [Note] mysqld (mysqld 5.7.19) starting as process 1 ...
mysql_1    | 2017-09-01T10:01:43.485266Z 0 [Note] InnoDB: PUNCH HOLE support available
mysql_1    | 2017-09-01T10:01:43.485302Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
mysql_1    | 2017-09-01T10:01:43.485306Z 0 [Note] InnoDB: Uses event mutexes
mysql_1    | 2017-09-01T10:01:43.485310Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
mysql_1    | 2017-09-01T10:01:43.485314Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
mysql_1    | 2017-09-01T10:01:43.485321Z 0 [Note] InnoDB: Using Linux native AIO
mysql_1    | 2017-09-01T10:01:43.485652Z 0 [Note] InnoDB: Number of pools: 1
mysql_1    | 2017-09-01T10:01:43.485777Z 0 [Note] InnoDB: Using CPU crc32 instructions
mysql_1    | 2017-09-01T10:01:43.487402Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
mysql_1    | 2017-09-01T10:01:43.495110Z 0 [Note] InnoDB: Completed initialization of buffer pool
mysql_1    | 2017-09-01T10:01:43.497050Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
mysql_1    | 2017-09-01T10:01:43.509905Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
mysql_1    | 2017-09-01T10:01:43.510822Z 0 [Note] InnoDB: Log scan progressed past the checkpoint lsn 2539618
mysql_1    | 2017-09-01T10:01:43.510851Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 2539872
mysql_1    | 2017-09-01T10:01:43.510897Z 0 [ERROR] InnoDB: Ignoring the redo log due to missing MLOG_CHECKPOINT between the checkpoint 2539618 and the end 2539872.
mysql_1    | 2017-09-01T10:01:43.510934Z 0 [ERROR] InnoDB: Plugin initialization aborted with error Generic error
mysql_1    | 2017-09-01T10:01:44.111639Z 0 [ERROR] Plugin 'InnoDB' init function returned error.
mysql_1    | 2017-09-01T10:01:44.111678Z 0 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
mysql_1    | 2017-09-01T10:01:44.111690Z 0 [ERROR] Failed to initialize plugins.
mysql_1    | 2017-09-01T10:01:44.111695Z 0 [ERROR] Aborting
mysql_1    | 
mysql_1    | 2017-09-01T10:01:44.111711Z 0 [Note] Binlog end
mysql_1    | 2017-09-01T10:01:44.111801Z 0 [Note] Shutting down plugin 'CSV'
mysql_1    | 2017-09-01T10:01:44.112663Z 0 [Note] mysqld: Shutdown complete
mysql_1    | 
messenger_mysql_1 exited with code 1

What am I doing wrong?

picture marwan-nwh

Most helpful comment

I had this issue after a forced restart of the Docker daemon. What helped was connecting to the DB instance:

docker-compose run --rm db /bin/bash

Then deleting the following files:

rm -rf /var/lib/mysql/ib_logfile*

As far as I can tell, this did not cause any data loss, but be sure to have backups.

picture slhck on 13 Feb 2019
👍12

All 7 comments

Hi, I seem to have an identical error and it's got me stumped. Did you get yours fixed?

Attaching to website_db_1
db_1  | 2017-09-07T17:37:49.273674Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for mor
e details).
db_1  | 2017-09-07T17:37:49.279120Z 0 [Note] mysqld (mysqld 5.7.19) starting as process 1 ...
db_1  | 2017-09-07T17:37:49.289423Z 0 [Note] InnoDB: PUNCH HOLE support available
db_1  | 2017-09-07T17:37:49.289447Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
db_1  | 2017-09-07T17:37:49.289450Z 0 [Note] InnoDB: Uses event mutexes
db_1  | 2017-09-07T17:37:49.289453Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
db_1  | 2017-09-07T17:37:49.289455Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
db_1  | 2017-09-07T17:37:49.289463Z 0 [Note] InnoDB: Using Linux native AIO
db_1  | 2017-09-07T17:37:49.289743Z 0 [Note] InnoDB: Number of pools: 1
db_1  | 2017-09-07T17:37:49.289876Z 0 [Note] InnoDB: Using CPU crc32 instructions
db_1  | 2017-09-07T17:37:49.291077Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
db_1  | 2017-09-07T17:37:49.296618Z 0 [Note] InnoDB: Completed initialization of buffer pool
db_1  | 2017-09-07T17:37:49.297952Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
db_1  | 2017-09-07T17:37:49.326706Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
db_1  | 2017-09-07T17:37:49.329011Z 0 [Note] InnoDB: Log scan progressed past the checkpoint lsn 95265228
db_1  | 2017-09-07T17:37:49.329032Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 95267309
db_1  | 2017-09-07T17:37:49.329085Z 0 [ERROR] InnoDB: Ignoring the redo log due to missing MLOG_CHECKPOINT between the checkpoint 95265228 and the end 95267309.
db_1  | 2017-09-07T17:37:49.329097Z 0 [ERROR] InnoDB: Plugin initialization aborted with error Generic error
db_1  | 2017-09-07T17:37:49.930134Z 0 [ERROR] Plugin 'InnoDB' init function returned error.
db_1  | 2017-09-07T17:37:49.930205Z 0 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
db_1  | 2017-09-07T17:37:49.930217Z 0 [ERROR] Failed to initialize plugins.
db_1  | 2017-09-07T17:37:49.930223Z 0 [ERROR] Aborting
db_1  |
db_1  | 2017-09-07T17:37:49.930232Z 0 [Note] Binlog end
db_1  | 2017-09-07T17:37:49.930330Z 0 [Note] Shutting down plugin 'CSV'
db_1  | 2017-09-07T17:37:49.933545Z 0 [Note] mysqld: Shutdown complete
db_1  |
website_db_1 exited with code 1
ijmccallum picture ijmccallum on 7 Sep 2017

@ijmccallum It was two things:

  • Use the service name as your host
  • If you fail to connect, sleep for seconds then try to connect again, the database needs sometime to be ready for connections
marwan-nwh picture marwan-nwh on 7 Sep 2017

@ijmccallum This is my docker-compose.yml file:

version: '2'
services:
  web:
    build: .
    ports:
     - "8000:8000"
    environment:
      MYSQL_USER: marwan
      MYSQL_HOST: db
      MYSQL_PASSWORD: <password>
      MYSQL_DATABASE: messenger
    restart: always
    links:
      - db
      - elasticsearch

  db:
    image: mysql
    restart: always
    environment:
      MYSQL_USER: marwan
      MYSQL_PASSWORD: <password>
      MYSQL_DATABASE: messenger
      MYSQL_ROOT_PASSWORD: <password>

  elasticsearch:
    image: elasticsearch:5
    command: elasticsearch
    expose:
      - "9200"
      - "9300"
    volumes:
      - "/tmp/esdata:/usr/share/elasticsearch/data"

and this is the Go code where I connect to mysql:

func Init() {
    var err error
    dbj, err = jet.Open("mysql", fmt.Sprintf("%s:%s@tcp(%s:3306)/%s", os.Getenv("MYSQL_USER"), os.Getenv("MYSQL_PASSWORD"), os.Getenv("MYSQL_HOST"), os.Getenv("MYSQL_DATABASE")))
    if err != nil {
        fmt.Println(err)
        time.Sleep(5 * time.Second)
        Init()
        return
    }
    err = dbj.Ping()
    if err != nil {
        fmt.Println(err)
        time.Sleep(5 * time.Second)
        Init()
        return
    }
    println("Connected to MySql.")
}
marwan-nwh picture marwan-nwh on 8 Sep 2017

These sorts of questions/requests would be more appropriately posted to the Docker Community Forums, the Docker Community Slack, or Stack Overflow. :wink: Thanks!

tianon picture tianon on 4 Oct 2017

I had this issue after a forced restart of the Docker daemon. What helped was connecting to the DB instance:

docker-compose run --rm db /bin/bash

Then deleting the following files:

rm -rf /var/lib/mysql/ib_logfile*

As far as I can tell, this did not cause any data loss, but be sure to have backups.

slhck picture slhck on 13 Feb 2019
👍12

After a backup of my volumes i did what @slhck say and got my DB up with no data lose

barajas-victor picture barajas-victor on 26 Apr 2019

@slhck It causes data loss. Please make a backup before running those lines.

DarylAranha picture DarylAranha on 14 Jul 2020
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