Error in MySQL upgrade from 5.6 to 5.7


Sep 6, 2017
United States
cPanel Access Level
Root Administrator
I tried to upgrade from mysql 5.6 to mysql 5.7 per a recommendation. It failed. When trying to start it, the error logs give me this:
2019-02-23T02:38:10.687444Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2019-02-23T02:38:10.687879Z 0 [Note] /usr/sbin/mysqld (mysqld 5.7.25) starting as process 9550 ...
2019-02-23T02:38:10.699726Z 0 [Warning] InnoDB: Using innodb_support_xa is deprecated and the parameter may be removed in future releases. Only innodb_support_xa=ON is allowed.
2019-02-23T02:38:10.699834Z 0 [Note] InnoDB: PUNCH HOLE support available
2019-02-23T02:38:10.699882Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2019-02-23T02:38:10.699894Z 0 [Note] InnoDB: Uses event mutexes
2019-02-23T02:38:10.699904Z 0 [Note] InnoDB: GCC builtin __sync_synchronize() is used for memory barrier
2019-02-23T02:38:10.699918Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.11
2019-02-23T02:38:10.699942Z 0 [Note] InnoDB: Using Linux native AIO
2019-02-23T02:38:10.700499Z 0 [Note] InnoDB: Number of pools: 1
2019-02-23T02:38:10.700793Z 0 [Note] InnoDB: Using CPU crc32 instructions
2019-02-23T02:38:10.704355Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2019-02-23T02:38:10.721659Z 0 [Note] InnoDB: Completed initialization of buffer pool
2019-02-23T02:38:10.727002Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2019-02-23T02:38:10.743571Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2019-02-23T02:38:10.743731Z 0 [ERROR] InnoDB: Operating system error number 40 in a file operation.
2019-02-23T02:38:10.743763Z 0 [ERROR] InnoDB: Error number 40 means 'Too many levels of symbolic links'
2019-02-23T02:38:10.743776Z 0 [Note] InnoDB: Some operating system error numbers are described at
2019-02-23T02:38:10.743794Z 0 [ERROR] InnoDB: File .//mysql.sock: 'stat' returned OS error 140.
2019-02-23T02:38:10.743821Z 0 [ERROR] InnoDB: os_file_readdir_next_file() returned -1 in directory ./, crash recovery may have failed for some .ibd files!
2019-02-23T02:38:10.743896Z 0 [ERROR] InnoDB: Plugin initialization aborted with error Generic error
2019-02-23T02:38:11.344488Z 0 [ERROR] Plugin 'InnoDB' init function returned error.
2019-02-23T02:38:11.344571Z 0 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2019-02-23T02:38:11.344600Z 0 [ERROR] Failed to initialize builtin plugins.
2019-02-23T02:38:11.344609Z 0 [ERROR] Aborting
2019-02-23T02:38:11.344624Z 0 [Note] Binlog end
2019-02-23T02:38:11.345357Z 0 [Note] /usr/sbin/mysqld: Shutdown complete
How do I fix this and restore the mysql service?
Last edited by a moderator:


Staff member
Apr 11, 2011
Hello @aries,

Can you share the contents of the /etc/my.cnf file on this system? EX:

cat /etc/my.cnf
Also, can you confirm if you've made any changes to the MySQL data directory storage location or storage type on this system? If you're unsure, please post the output from the following commands:

stat /var/lib/mysql
mount|grep mysql
Thank you.