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Here is the case

A week ago SuperMicro Server started beeping due to one HDD failure which is part of Raid, This server has Physical Raid Controller .. Now i replaced the faulty HDD with New HDD and now new HDD is blinking with both Blue LED and Red LED and server is still beeping

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    It would be good if you post exact HW controller and server model. Did you try to enter HW (I assume its some sort of LSI MegaRaid?) controller menu and check there status of array? When did you replace this disk? It may also beep because RAID has not yet rebuild and there is danger of data loss. – adoado0 Feb 9 '17 at 9:18
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Normally you need to add the new disk as a spare disk to the existing array in the CLI oder GUI tool of the RAID controller or via BIOS. Just plugging a new disk does not tell anything to the controller, your intention might be to do some new raid array with it, so it will not automatically take this disk for rebuild.

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