MySQL tuning procedures, steps and tips

You need to provide a lot more information:

1) How much RAM is available on the box? Is Tomcat the only thing running?
2) Is this a 32bit or 64bit VM?
3) How many CPU's/cores are on this box?
4) What major version of the jdk are you running? 1.4, 5, or 6?

The answers to those questions will allow you to set boundaries for the heap.

Once you get past that, questions about the application may need to be answered - how many objects are long-lived (ie cache), and how many are short lived (less than 5 seconds before they go out of scope).

These questions will tell us what % of the heap can be used for Eden, and what percent needs to be used for the old generation.

Update

Well, if your Tomcat is long-running, then adding the '-server' flag would likely be beneficial. Given your constraints, unless you know your apps inside and out, it's probably best to leave it up to ergonomics to determine the best ratios and collector. Java tuning is much more an art than it is a science. Start here: http://java.sun.com/javase/technologies/hotspot/gc/gc_tuning_6.html, then look for tools like GCHisto, and VisualGC to help you visualize what's going on inside the VM.

Here are a few of the things I've run into with MySQL optimization:

If you see that your database server (the MySQL processes in particular) are using the majority of the CPU time, it probably means that you are either missing indexes or you need to optimize queries.

Turn on the slow query logging and pursue those slow queries to find out how they can be optimized. Use "explain" with the slow queries to find out why they are slow. The MySQL documentation has several sections about how to interpret these results.

Use memcached to cache the result of any queries you can for as long as you can. This is extremely fast, and able to cache many things that the internal MySQL query caching cannot, but can only be used in cases where you know the data can be cached long-term or you manually expire the cache.

Set up "munin" on the database system to begin collecting information about the system utilization and database query load.

Make sure your system has enough RAM that you aren't swapping, and hopefully also enough that you do few if any disc reads (use vmstat or munin to monitor this). Meaning that the data is served out of MySQL or disc buffer caches.

Sean