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What version are you running? 5.6 doc gives the details: innodb_flush_log_at_trx_commit can be set (1) on the commandline, (2) in my.cnf, or (3) via SET GLOBAL. sql_safe_updates can only be set via SET SESSION or SET GLOBAL. Note that SET GLOBAL does not impact anyone currently connected (including yourself). It will effect anyone connecting later, but ...


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That is not how you start mysql from the command line. When you type mysql in the command line it will launch the mysql-client not the mysql-server, which looks for the user/password options to be provided as arguments, if they aren't provided it will expect them to be specified in ~/.my.cnf or /etc/mysql/my.cnf. If it still can't find the details there ...



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