MySQL Bugs: #90899: Failure to install MySQL 5.6.40 on Centos 7

Bug #90899	Failure to install MySQL 5.6.40 on Centos 7
Submitted:	16 May 2018 23:45	Modified:	17 May 2018 0:28
Reporter:	Ahmad Shamzuri	Email Updates:
Status:	Not a Bug	Impact on me:	None
Category:	MySQL Server: Installing	Severity:	S1 (Critical)
Version:	5.6.40	OS:	CentOS (7)
Assigned to:		CPU Architecture:	x86 (HPE)
Tags:	--initialize unknown option, mysql.plugin doesn't exist

Description:
I tried to install this version on my server but I got the issue below. I've tried both mysql-advanced-5.6.40-linux-glibc2.12-x86_64 and mysql-advanced-5.6.39-linux-glibc2.12-x86_64 installers. Both gave me the same errors after I run the command below.

[root@server1 mysql]# bin/mysqld --initialize --user=mysqladm --basedir=/home/mysqladm/software/mysql --datadir=/home/mysqladm/software/mysqldata/data
2018-05-16 17:15:52 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2018-05-16 17:15:52 0 [Note] --secure-file-priv is set to NULL. Operations related to importing and exporting data are disabled
2018-05-16 17:15:52 0 [Note] bin/mysqld (mysqld 5.6.39-enterprise-commercial-advanced) starting as process 17189 ...
2018-05-16 17:15:52 17189 [Note] Plugin 'FEDERATED' is disabled.
bin/mysqld: Table 'mysql.plugin' doesn't exist
2018-05-16 17:15:52 17189 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
2018-05-16 17:15:52 17189 [Note] InnoDB: Using atomics to ref count buffer pool pages
2018-05-16 17:15:52 17189 [Note] InnoDB: The InnoDB memory heap is disabled
2018-05-16 17:15:52 17189 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2018-05-16 17:15:52 17189 [Note] InnoDB: Memory barrier is not used
2018-05-16 17:15:52 17189 [Note] InnoDB: Compressed tables use zlib 1.2.3
2018-05-16 17:15:52 17189 [Note] InnoDB: Using Linux native AIO
2018-05-16 17:15:52 17189 [Note] InnoDB: Using CPU crc32 instructions
2018-05-16 17:15:52 17189 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2018-05-16 17:15:52 17189 [Note] InnoDB: Completed initialization of buffer pool
2018-05-16 17:15:52 17189 [Note] InnoDB: The first specified data file ./ibdata1 did not exist: a new database to be created!
2018-05-16 17:15:52 17189 [Note] InnoDB: Setting file ./ibdata1 size to 12 MB
2018-05-16 17:15:52 17189 [Note] InnoDB: Database physically writes the file full: wait...
2018-05-16 17:15:52 17189 [Note] InnoDB: Setting log file ./ib_logfile101 size to 48 MB
2018-05-16 17:15:52 17189 [Note] InnoDB: Setting log file ./ib_logfile1 size to 48 MB
2018-05-16 17:15:52 17189 [Note] InnoDB: Renaming log file ./ib_logfile101 to ./ib_logfile0
2018-05-16 17:15:52 17189 [Warning] InnoDB: New log files created, LSN=45781
2018-05-16 17:15:52 17189 [Note] InnoDB: Doublewrite buffer not found: creating new
2018-05-16 17:15:52 17189 [Note] InnoDB: Doublewrite buffer created
2018-05-16 17:15:52 17189 [Note] InnoDB: 128 rollback segment(s) are active.
2018-05-16 17:15:52 17189 [Warning] InnoDB: Creating foreign key constraint system tables.
2018-05-16 17:15:52 17189 [Note] InnoDB: Foreign key constraint system tables created
2018-05-16 17:15:52 17189 [Note] InnoDB: Creating tablespace and datafile system tables.
2018-05-16 17:15:52 17189 [Note] InnoDB: Tablespace and datafile system tables created.
2018-05-16 17:15:52 17189 [Note] InnoDB: Waiting for purge to start
2018-05-16 17:15:52 17189 [Note] InnoDB: 5.6.39 started; log sequence number 0
2018-05-16 17:15:52 17189 [ERROR] bin/mysqld: unknown option '--initialize'
2018-05-16 17:15:52 17189 [ERROR] Aborting

2018-05-16 17:15:52 17189 [Note] Binlog end
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'partition'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_METRICS'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_CMPMEM'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_CMP'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_LOCKS'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'INNODB_TRX'
2018-05-16 17:15:52 17189 [Note] Shutting down plugin 'InnoDB'
2018-05-16 17:15:52 17189 [Note] InnoDB: FTS optimize thread exiting.
2018-05-16 17:15:52 17189 [Note] InnoDB: Starting shutdown...
2018-05-16 17:15:54 17189 [Note] InnoDB: Shutdown completed; log sequence number 1600607
2018-05-16 17:15:54 17189 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2018-05-16 17:15:54 17189 [Note] Shutting down plugin 'BLACKHOLE'
2018-05-16 17:15:54 17189 [Note] Shutting down plugin 'ARCHIVE'
2018-05-16 17:15:54 17189 [Note] Shutting down plugin 'MEMORY'
2018-05-16 17:15:54 17189 [Note] Shutting down plugin 'MRG_MYISAM'
2018-05-16 17:15:54 17189 [Note] Shutting down plugin 'MyISAM'
2018-05-16 17:15:54 17189 [Note] Shutting down plugin 'CSV'
2018-05-16 17:15:54 17189 [Note] Shutting down plugin 'sha256_password'
2018-05-16 17:15:54 17189 [Note] Shutting down plugin 'mysql_old_password'
2018-05-16 17:15:54 17189 [Note] Shutting down plugin 'mysql_native_password'
2018-05-16 17:15:54 17189 [Note] Shutting down plugin 'binlog'
2018-05-16 17:15:54 17189 [Note] bin/mysqld: Shutdown complete

How to repeat:
I've deleted the database in datadir directories and re-run the same commands above. It still gave me the same error. There's no MySQL files/folders in /var/log or /var/lib. There's even no my.cnf in the /etc folder

Suggested fix:
Please help to find one

We're sorry, but the bug system is not the appropriate forum for asking help on using MySQL products. Your problem is not the result of a bug.

Support on using our products is available both free in our forums at http://forums.mysql.com/ and for a reasonable fee direct from our skilled support engineers at http://www.mysql.com/support/

Thank you for your interest in MySQL.

bin/mysqld --initialize --user=mysqladm 'that's for server 5.7 and 8.0'
Please read the manual about mysql_install_db