From: Kamalakar Reddy Y
Date: September 10 2012 10:28am
Subject: Help with mysql connect_timeout
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But connect-timeout has nothing to do with termination of query. It is no.
of secs that mysqld server waits for a connect packet before responding
with Bad handshake, default value is 10 seconds.

Probably you should adjust net_read /write_ timeout.

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