Troubleshooting / Identifying Slow Queries

[Tama]

Hi there

I run a MySQL/PHP website (using the PHPNuke platform) and have been running into performance issues after a recent upgrade (of software and server.)

My Sun Cobalt RAQ runs slow when I get more than around 50 users. I've been checking the SQL processes and it seems that sometimes some of them are hanging. I haven't been able to work out which queries are messing up. I'm using phpMyAdmin to administer/ monitor the database.

The SQL server has been averaging 13.21 queries a second since started (10 days ago.)

To troubleshoot this I have a number of questions:

1. Is it possible to log the commands/ time the commands took to process on a SQL database?
2. Is it possible to log the commands/ time the commands took to process via PHP?
3. Is there any variable that would drop "stalled" processes quickly?
4. Is there any other variables I should be checking that could cause this?
5. Is there any server setting that would make a difference?

Thank you in advance
Tama

P.S. My website is

http://www.vorb.org.nz

- page generation is displayed at the bottom of the page.