I'm using Berkeley DB Java Edition(6.3.8), but I'm not sure if the database is supposed to be accessed by one JVM instance. Can two JVM instance access it simultaneously(assume one instance do put and get, and the other do get only)?
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No, BDB-JE is an embeddable database, it runs within the JVM running your application and it can be accessed only by this JVM.
See http://www.oracle.com/technetwork/database/berkeleydb/overview/index-093405.html