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Agents take longer to run with transaction logging after upgrade to Domino 6.51

I'm using Domino 6.51 and selected nightly agents run out of time when transaction logging is enabled. These agents ran perfectly fine on Domino 5.08 with transaction logging enabled. What is classified as a transaction? And why on 5.08 did the agents complete within 90 minutes but now run out of time after 6 hours?

How has transaction logging changed in Domino 6? The agents also crash the server if run during the day when transaction logging is enabled. Any advice on this matter is greatly appreciated.
I can't specifically say what would cause this from the information you provided. My guess is that your agent is somehow locking the database and coming in conflict with Logasio (translogger). Transactional logging was changed in D6, but for the better. Rather than locking the entire database, it only locks the elements that are to be hardened. It also has an improved flushing algorithm for less frequent tie-ups of system resources. I would suggest turning on agent manager debugging and sending all agent activity to that output file. From there, your developers or Lotus Support should be able to pinpoint the issue.

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