We're using Nginx + PHP in fastcgi mode, and using PHP-FPM as cgi process manager. In our scripts we use PDO to connect MySQL and definitely NOT in persistent mode.
But recently we found we still got too many connections in MySQL, any suggestions (or any possible reasons)?
Take a look at mysql's threads (show processlist). Is it possible that you just have a bunch of idle connections because your scripts aren't closing their connections?
what do you means by 'connections'? do you mean the connections value in SHOW STATUS? I think this should be normally high..
could you provide the report generated from this script: http://hackmysql.com/mysqlreport
It gives a nice view about the database.