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After trying to copy some columns of big tables (500k records) into another one, my MySQL dockers (5.7) images stoped. Trying to start it again I get the following error:

[ERROR] InnoDB: Trying to access page number 16384 in space 0, space name innodb_system, which is outside the tablespace bounds. Byte offset 0, len 16384, i/o type read. If you get t
    his error at mysqld startup, please check that your my.cnf matches the ibdata files that you have in the MySQL server.
[ERROR] InnoDB: Server exits.

It suggests checking my.cnf file. But I'm not sure what needs to be checked exactly. Can you help to start it again?

Here is the full log file

2020-07-05 21:11:06+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.30-1debian10 started.
2020-07-05 21:11:08+00:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql'
2020-07-05 21:11:08+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.30-1debian10 started.
2020-07-05T21:11:09.338116Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2020-07-05T21:11:09.347350Z 0 [Note] mysqld (mysqld 5.7.30) starting as process 1 ...
2020-07-05T21:11:09.367117Z 0 [Note] InnoDB: PUNCH HOLE support available
2020-07-05T21:11:09.367215Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2020-07-05T21:11:09.367229Z 0 [Note] InnoDB: Uses event mutexes
2020-07-05T21:11:09.367233Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2020-07-05T21:11:09.367237Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.11
2020-07-05T21:11:09.367240Z 0 [Note] InnoDB: Using Linux native AIO
2020-07-05T21:11:09.367540Z 0 [Note] InnoDB: Number of pools: 1
2020-07-05T21:11:09.367837Z 0 [Note] InnoDB: Using CPU crc32 instructions
2020-07-05T21:11:09.370078Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2020-07-05T21:11:09.383259Z 0 [Note] InnoDB: Completed initialization of buffer pool
2020-07-05T21:11:09.386104Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2020-07-05T21:11:09.436151Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2020-07-05T21:11:09.458334Z 0 [Note] InnoDB: Log scan progressed past the checkpoint lsn 7146120985
2020-07-05T21:11:09.537366Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 7151363584
2020-07-05T21:11:09.613422Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 7156606464
2020-07-05T21:11:09.678950Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 7161849344
2020-07-05T21:11:09.743568Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 7167092224
2020-07-05T21:11:09.814902Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 7172335104
2020-07-05T21:11:09.891447Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 7177577984
2020-07-05T21:11:09.961055Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 7182820864
2020-07-05T21:11:10.037062Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 7188063744
2020-07-05T21:11:10.115817Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 7193306624
2020-07-05T21:11:10.188869Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 7198549504
2020-07-05T21:11:10.258947Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 7203792384
2020-07-05T21:11:10.320226Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 7209035264
2020-07-05T21:11:10.394447Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 7214278144
2020-07-05T21:11:10.468725Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 7219521024
2020-07-05T21:11:10.501674Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 7221701778
2020-07-05T21:11:10.502002Z 0 [Note] InnoDB: Database was not shutdown normally!
2020-07-05T21:11:10.502062Z 0 [Note] InnoDB: Starting crash recovery.
2020-07-05T21:11:11.051988Z 0 [Note] InnoDB: 1 transaction(s) which must be rolled back or cleaned up in total 469959 row operations to undo
2020-07-05T21:11:11.052016Z 0 [Note] InnoDB: Trx id counter is 4498432
2020-07-05T21:11:11.052024Z 0 [Note] InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percent: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 6
    4 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
2020-07-05T21:11:12.544201Z 0 [Note] InnoDB: Apply batch completed
2020-07-05T21:11:13.012256Z 0 [Note] InnoDB: Starting in background the rollback of uncommitted transactions
2020-07-05T21:11:13.012289Z 0 [Note] InnoDB: Rolling back trx with id 4497948, 469959 rows to undo
    vajje2-mysql |
InnoDB: Progress in percents: 12020-07-05T21:11:13.013622Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2020-07-05T21:11:13.013643Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2020-07-05T21:11:13.018222Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2020-07-05T21:11:13.060735Z 0 [ERROR] InnoDB: Trying to access page number 16384 in space 0, space name innodb_system, which is outside the tablespace bounds. Byte offset 0, len 16384, i/o type read. If you get t
    his error at mysqld startup, please check that your my.cnf matches the ibdata files that you have in the MySQL server.
2020-07-05T21:11:13.060762Z 0 [ERROR] InnoDB: Server exits.

Trying to start MySQL using the native Windows version instead of Docker, I get a different error message

mysqld --console
2020-07-05T21:18:23.399589Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2020-07-05T21:18:23.399589Z 0 [Warning] 'NO_ZERO_DATE', 'NO_ZERO_IN_DATE' and 'ERROR_FOR_DIVISION_BY_ZERO' sql modes should be used with strict mode. They will be merged with strict mode in a future release.
2020-07-05T21:18:23.399589Z 0 [Warning] 'NO_AUTO_CREATE_USER' sql mode was not set.
2020-07-05T21:18:23.399589Z 0 [Warning] Insecure configuration for --secure-file-priv: Current value does not restrict location of generated files. Consider setting it to a valid, non-empty path.
2020-07-05T21:18:23.400089Z 0 [Note] mysqld (mysqld 5.7.12) starting as process 16596 ...
2020-07-05T21:18:23.406089Z 0 [Note] InnoDB: Mutexes and rw_locks use Windows interlocked functions
2020-07-05T21:18:23.406589Z 0 [Note] InnoDB: Uses event mutexes
2020-07-05T21:18:23.406589Z 0 [Note] InnoDB: _mm_lfence() and _mm_sfence() are used for memory barrier
2020-07-05T21:18:23.406589Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2020-07-05T21:18:23.407589Z 0 [Note] InnoDB: Number of pools: 1
2020-07-05T21:18:23.407589Z 0 [Note] InnoDB: Not using CPU crc32 instructions
2020-07-05T21:18:23.460113Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2020-07-05T21:18:23.466088Z 0 [Note] InnoDB: Completed initialization of buffer pool
2020-07-05T21:18:23.495090Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2020-07-05T21:18:23.498091Z 0 [Note] InnoDB: Log scan progressed past the checkpoint lsn 7146120985
2020-07-05T21:18:23.506129Z 0 [ERROR] InnoDB: ############### CORRUPT LOG RECORD FOUND ##################
2020-07-05T21:18:23.506625Z 0 [Note] InnoDB: Log record type 55, page 6632:0. Log parsing proceeded successfully up to 7147076749. Previous log record type 38, is multi 0 Recv offset 355267, prev 354841
2020-07-05T21:18:23.507094Z 0 [Note] InnoDB: Hex dump starting 100 bytes before and ending 100 bytes after the corrupted record:
 len 626; hex 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; asc         / ipairab            vre    rdn                       "                 "   -     I       }     F                 %M      U           }    D      -1:   J   T .   1   5   9   @   H    U  |        2  P _idfilewordmeaningmorphemepronunciation  '        $id 51d7caf6f7c2557465039093 f                                                j posmeaning  N             @ _iddesc  '        $id 50d2cf34f7c2553c16000008              )                                                                           "                      "7     ./mapper/word.ibd 7     ./mysql/innodb_table_stats.ibd 7     ./mysql/innodb_index_stats.ibd  8;
2020-07-05T21:18:23.589588Z 0 [Warning] InnoDB: The log file may have been corrupt and it is possible that the log scan did not proceed far enough in recovery! Please run CHECK TABLE on your InnoDB tables to check that they are ok! If mysqld crashes after this recovery; Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2020-07-05T21:18:23.590089Z 0 [ERROR] InnoDB: Ignoring the redo log due to missing MLOG_CHECKPOINT between the checkpoint 7146120985 and the end 7147103744.
2020-07-05T21:18:23.590089Z 0 [ERROR] InnoDB: Plugin initialization aborted with error Generic error
2020-07-05T21:18:23.791880Z 0 [ERROR] Plugin 'InnoDB' init function returned error.
2020-07-05T21:18:23.792342Z 0 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2020-07-05T21:18:23.792840Z 0 [ERROR] Failed to initialize plugins.
2020-07-05T21:18:23.792840Z 0 [ERROR] Aborting

2020-07-05T21:18:23.793339Z 0 [Note] Binlog end
2020-07-05T21:18:23.793339Z 0 [Note] Shutting down plugin 'CSV'
2020-07-05T21:18:23.794344Z 0 [Note] mysqld: Shutdown complete
2
  • First, your windows version is 5.7.12 while your docker image is 5.7.30. Update your Windows version if you want to use it on the same data. How did the original problem occur? Did you run out of space? Did the docker instance have a volume for its datadir? How where you doing the copies? Do not move/remove mysql files directly it will lead to this or more errors. Take a copy now so you have a preserved original. – danblack Jul 5 '20 at 23:33
  • Show us the command used to "copy some columns". – Rick James Aug 29 '20 at 23:59

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