Try running and analysing a tcpdump on the mysql port. Wireshark could provide some answers, or you may even get a visual clue just running tcpdump in a terminal.
What happens if you run the db locally?
On Thu, 2012-01-05 at 10:19 -0700, John Pagakis wrote:
Posted by toolsmythe on January 4, 2012 at 8:18pm
I'm dealing with an odd performance issue on a production Drupal 7.7 site.
I have a machine that is configured thus:
4gig Quad proc 900GB disk
OS: Debian 6
For apache we are using version ii apache2 2.2.16-6+squeeze1 Apache HTTP Server metapackage ii apache2-mpm-prefork 2.2.16-6+squeeze1 Apache HTTP Server - traditional non-threaded model
For PHP we are running version ii php5 5.3.3-7+squeeze3 server-side, HTML-embedded scripting language (metapackage) ii libapache2-mod-php5 5.3.3-7+squeeze3 server-side, HTML-embedded scripting language (Apache 2 module)
ii mysql-client-5.1 5.1.49-3 MySQL database client binaries
Database is on a seperate server.
The Problem We are getting a pretty consistant 5+ second delay before any page on the site renders. It renders quickly once it starts to render, but there is a delay of 5 or more seconds before that happens.