Profiling code running in the context of an application server requires configuration of that server in addition to configuring settings for PurifyPlus. These various configurations are described in detail on the IBM web site.
The developerWorks section on the IBM web site has several articles about this topic. Go to: http://www.ibm.com/developerworks/rational and search for "Testing J2EE applications with Rational PurifyPlus" to find one document. For others broaden the search to "J2EE Purify".
The PurifyPlus support site at: http://www.ibm.com/software/awdtools/purifyplus/support also contains up to date Technotes that offer explanations dealing with this topic. You can search them for more related information.
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