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Our production MySql database lives on single data partition. There really isn't anything else on that partition other than the databases. Is it safe to run a windows defrag on that partition? Will MySql lock tables, could it slow down query times? We have Server 2008 and MySql 5.1.

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Yes, it is safe to run a Windows defrag on the partition. To reduce performance impact, you might consider a third-party defragger (e.g. PerfectDisk www.raxco.com), which will have minimal performance overhead. This tool can also prevent most fragmentation and reduce the rate of fragmentation, further reducing the issues you are experiencnig.

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