Mysql 8.0.23 on CentOS 7.9 with WHM

I ended up with a corrupted InnoDB table. I gave up on a long query and killed it. Then the query was still blocking so I did a forceful server reboot. I know now that the query was still blocking because it was undoing the process. Killing it with a forceful server reboot corrupted my database. The rest is history.

So I've been trying to work through this process: https://dev.iserversupport.com/recover-crashed-innodb-tables-on-mysql-database-server/

But it seems MySQL doesn't want to recreate the ibdata1 file.


# For advice on how to change settings please see
# http://dev.mysql.com/doc/refman/8.0/en/server-configuration-defaults.html

[mysqld] disable-log-bin=1 default-authentication-plugin=mysql_native_password performance-schema=0
# Remove leading # and set to the amount of RAM for the most important data
# cache in MySQL. Start at 70% of total RAM for dedicated server, else 10%.
# innodb_buffer_pool_size = 128M
# Remove the leading "# " to disable binary logging
# Binary logging captures changes between backups and is enabled by
# default. It's default setting is log_bin=binlog
# disable_log_bin
# Remove leading # to set options mainly useful for reporting servers.
# The server defaults are faster for transactions and fast SELECTs.
# Adjust sizes as needed, experiment to find the optimal values.
# join_buffer_size = 128M
# sort_buffer_size = 2M
# read_rnd_buffer_size = 2M
# Remove leading # to revert to previous value for default_authentication_plugin,
# this will increase compatibility with older clients. For background, see:
# https://dev.mysql.com/doc/refman/8.0/en/server-system-variables.html#sysvar_default_authentication_plugin
# default-authentication-plugin=mysql_native_password

datadir=/var/lib/mysql socket=/var/lib/mysql/mysql.sock

log-error=/var/log/mysqld.log pid-file=/var/run/mysqld/mysqld.pid innodb_file_per_table=1

default-storage-engine=MyISAM interactive_timeout=300 key_cache_block_size=4096 max_heap_table_size=5G max_join_size=1000000000 max_allowed_packet=268435456 open_files_limit=40000 thread_cache_size=100 tmp_table_size=5G wait_timeout=7800 max_user_connections=500 myisam_recover_options=FORCE innodb_file_per_table=1 innodb_flush_log_at_trx_commit=0 innodb_purge_threads=1 innodb_thread_concurrency=8 pid-file=/var/lib/mysql/mysqld.pid

performance-schema=0 sql_mode='' interactive_timeout=30 wait_timeout=90

collation-server = utf8_unicode_ci character-set-server=utf8

key_buffer_size = 4G innodb_buffer_pool_size = 8G innodb_buffer_pool_chunk_size = 256M innodb_buffer_pool_instances = 8


And error log:

2021-01-19T18:18:18.543601Z 1 [ERROR] [MY-012592] [InnoDB] Operating system error number 2 in a file operation.
2021-01-19T18:18:18.543714Z 1 [ERROR] [MY-012593] [InnoDB] The error means the system cannot find the path specified.
2021-01-19T18:18:18.543792Z 1 [ERROR] [MY-012594] [InnoDB] If you are installing InnoDB, remember that you must create directories yourself, InnoDB does not create them.
2021-01-19T18:18:18.543895Z 1 [ERROR] [MY-012646] [InnoDB] File ./ibdata1: 'open' returned OS error 71. Cannot continue operation
2021-01-19T18:18:18.543986Z 1 [ERROR] [MY-012981] [InnoDB] Cannot continue operation.
2021-01-19T18:18:19.908326Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.23) starting as process 1777
2021-01-19T18:18:19.909547Z 0 [Warning] [MY-013242] [Server] --character-set-server: 'utf8' is currently an alias for the character set UTF8MB3, but will be an alias for UTF8MB4 in a future release. Please consider using UTF8MB4 in order to be unambiguous.
2021-01-19T18:18:19.909570Z 0 [Warning] [MY-013244] [Server] --collation-server: 'utf8_unicode_ci' is a collation of the deprecated character set UTF8MB3. Please consider using UTF8MB4 with an appropriate collation instead.
2021-01-19T18:18:19.959205Z 1 [System] [MY-013576] [InnoDB] InnoDB initialization has started.

This makes me think I have an ownership or read/write permissions error. But I checked the ownership on the /var/lib/mysql directory and it is mysql:mysql, permission is 751.

I was able to recover all of my data by forcing innodb_force_recovery = 3. But now that I've deleted those ibd files I can't get the server to start again either way. I did back them up, and I've tried copying them back but no dice.

I also attempted to re-install mysql via WHM. That failed.

Thank you Matt

  • mysql tries, but gets an error from the operating system, so it has no option than to stop. Did you check the harddrive for smart errors
    – nbk
    Jan 19, 2021 at 19:42
  • I deleted "ibdata1", "ib_logfile0", "ib_logfile1", "ib_buffer_pool", and "ibtmp1"
    – Matt
    Jan 20, 2021 at 19:37
  • Some questions after deleting /var/lib/mysql you lost all your databases? Do you have a backup? when ibdata1 is corrupted or deleted you cant start the server again(File ./ibdata1: 'open' returned OS error 71) and as a consequence of that you also cant to take a new dump. How do you synchronize the new ibdata1 with your old databases? Aug 4, 2021 at 2:40
  • @MatiasKloster, Before deleting /var/lib/mysql, you need to boot the database using --innodb-force-recovery=X. Then export your tables with mysqldump.
    – Matt
    Dec 29, 2021 at 6:28

1 Answer 1


I ended up resolving it by deleting the /var/lib/mysql directory and running

mysqld --initialize --datadir=/var/lib/mysql
  • Thank you, this is what I needed. I didn't want to recover tables or anything, I deleted the ib* files intentionally.
    – smido
    Sep 6, 2022 at 12:11

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