I don't know if it is related to your problem but I have a memory problem 
with transactions too.

I have a program that reads some web pages, perform some analysis on them 
and then save results in a local H2 database.

Every 50 or 100 pages, the program would flush the session and commit the 
transaction and yet, after reading 1500 pages or so (depending on the 
average size of the saved data), I would get an out of memory error in 
java.  To solve my problem I actually had to close the session every 50 
pages and create a new one and a new transaction.

Not very efficient, but I didn't care much about efficiency in a program 
meant to run for a few hours once a month or so. 

I still don't understand why my memory usage was blowing up though. 

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