OK, I haven't removed the @Target annotation yet, cos thats a lot of work... but I created a standard hibernate session within the EJB, so know I run the same query via the app server managed EntityManager and via a hibernate session created from a standalone hiberbate.cfg.xml....
EntityManager query time = 26.6 seconds
Hibernate session query time = 12.3 seconds
So, they are both slower than the same code run in JSE, and the EntityManager is still considerably slower than a standard hibernate session.
Still more investigation needed
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