Ubuntu – the difference between apt-get update and upgrade

You should be just fine extending wait_timeout

Notice the maximum value for wait_timeout for MySQL 5.0, 5.1, 5.5, 5.6

• Linux : 31536000 seconds (365 days, one year)
• Windows : 2147483 seconds (2^31 milliseconds, 24 days 20 hours 31 min 23 seconds)

These maximums would not exist of mysqld could not handle them.

Connection pooling only saves on overhead in terms the alternative: destroying and reallocating memory for new DB Connections. This could cause the OS on the DB Server to engage in a lot more swapping to juggle memory.

I wrote about this over a year ago : How costly is opening and closing of a DB connection?

Lowering the wait_timeout could definitely throw Apache into confusion because there and PHP and Apache objects for DB Connections still instantiated while the DB Connection decides to terminate early and without warning. In that event, you may have to scan your netstat for any TIME_WAIT on connections over port 3306 or whatever port MySQL is using.

• May 20, 2011 : Why is MySQL caching data on our dynamic PHP site?
• Aug 17, 2011 : Too Many Connections
• Oct 26, 2011 : What could be causing strange query timeouts between PHP and MySQL?
• Feb 27, 2012 : MySQL connection count much larger than query count

If such exist and impedes Apache from opening a new connection, you would have to kill the TIME_WAITs yourself. See my Feb 01, 2012 ServerFault post MySQL lowering wait_timeout value to lower number of open connections on how to do so.

In your configuration you got max-connecions = 500 this means you acutally have 500 connections available to your server, and mysql adds an extraslot for and adminuser who's able to access over a terminal.

So you actually should always be able to connect to your Database even when all connections are used up.

Try to evaluate who/what is using up your administration connection, and get rid of it. Reasons i encountered are poorly written cronjobs which connect via shellscript to your DB (for example a self written backupscript) this takes a long time to run and locks you out of your Database.

Also check your open files limit on your OS in most distribution these values need to be raised when you have some heavy traffic on your server.