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I have a large database with a file stream located on a different disk the server that hosts this database has a large number of another none related databases but the specifications of this server are great, my database throws a timeout exception for some queries from time to time,

every time I rebuild and reorganize the indexes the queries back to work normally, I have created a maintenance plan that do Rebuild, Reorganize and update statistics every 3 hours to avoid such issues, the fill factor for the indexes is 90%,

What are the reasons for this? and how I can avoid this issue without the maintenance plan as it adds an extra overhead on the CPU and the RAM.

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You have a performance issue at your hands. Investigate it appropriately, using a performance investigation methodology like Waits and Queues. USE is also a great performance troubleshooting framework.

Stop doing random changes in hope something improves. Measure, identify, then act appropriately. Establish baselines. Read the entire Monitor and Tune for Performance chapter on MSDN.

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