Have you considered breaking up your EJB into two EJBs joined via a JMS queue?  
Basically have the first EJB generate the messages for the web service, and as 
it generates say 100 web service requests, it tosses those requests onto a 
queue instead of making those requests itself.  Then have another EJB (MDB) 
consuming off of that queue and this EJB can have its own custom timeout based 
on when it should timeout on 100 web service requests.

This lets your first EJB reduce its work load to beat the timeout, and then the 
other EJB that is doing the web service requests will have its own timeout.  
Not only that, but since there is the second EJB doing the web requests, you 
can allow it do run those in parallel and get all your work done much faster 
and have it broken up with reasonable transaction timeouts.


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