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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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