On startup GemFire tries to find an existing JTA TransactionManager by doing a JNDI lookup. If no JTATransactionManager is found, we try to bind our own JTATransactionManager. According to your log, this step is failing. I could not get to the javadocs of Atomikos, do you know under what name their TransactionManager binds to JNDI? Also, is their TransactionManager an implementation of javax.transaction.TransactionManager?
Can you run with finer logs and post them?