Set these as follows in my.cnf (takes effect after mysqld is restarted):
[mysqld]
interactive_timeout=180
wait_timeout=180
If you do not want to restart mysql, then run these two commands:
SET GLOBAL interactive_timeout = 180;
SET GLOBAL wait_timeout = 180;
This will not close the connections already open. This will cause new connections to close in 180 seconds.
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