It is often necessary to divide many real-world applications into multiple distinct phases.  As a result, the search for performance problems can often be constrained to a particular phase of an application's execution.  One of the most effective ways to narrow focus onto a specific region is to use the Scenario API on Code Gallery in conjunction with the Concurrency Visualizer to isolate areas of interest.  The Architect on our team, Hazim Shafi, has written a blog entry which describes this process and gives examples of using the Scenario API along with the Concurrency Visualizer to solve such problems.  I highly encourage you to check out his entry and then try it for yourself!

James Rapp - Parallel Computing Platform