TLER is the biggest difference.. I have a pair of these in raid 1
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Hard drives typically perform error recovery on their own, pausing for extended periods of time to save data that might otherwise be lost. That works well enough for drives acting independently, but it can be problematic when multiple drives are bound together in a RAID array. RAID controllers prefer to handle error recovery on their own, so they don't want to waste too much time waiting around for a single drive's heroic attempt at solo error recovery.
If a drive pauses for too long trying to recover from an error, it may be tagged as a failed disk and dropped from the array, even if its attempt at error recovery is ultimately successful. To prevent this premature array ejection, TLER limits the amount of time that a drive will pause to recover an error before it resumes normal operation. If the error isn't quickly recovered by the drive, the RAID controller will sort it out. However, if the drive isn't connected to a RAID controller that supports error recovery, data could become corrupted or lost. That's why Western Digital doesn't recommend TLER-equipped drives for non-RAID applications.
Since it's designed for multi-drive RAID environments, the RE2 naturally supports TLER. Drives even ship with it enabled, although Western Digital says the feature can be disabled by end users. Users can avoid TLER completely with the Caviar SE16, which doesn't support the feature.
In addition to its lack of TLER, the SE16 also misses out on the RE2's support for Rotary Acceleration Feed Forward (RAFF), which detects rotational vibration and adjusts the drive head accordingly. RAFF isn't particularly necessary for single-drive systems, but it's considerably more useful in RAID environments where multiple drives are tightly packed together.
Cramming multi-drive RAID arrays into rackmount server chassis generally puts drives into an environment with higher temperatures and vibration levels than the average desktop PC. That doesn't bode well for a drive's longevity, but Western Digital is confident enough in the RE2's robustness to give it a mean time between failure (MTBF) rating of 1.2 million hours. Unfortunately, Western Digital won't disclose the MTBF of the SE16, saying only that it's in line with other desktop drives. Desktop drives typically have a 1-million-hour MTBF.
Given its longer MTBF rating, it's only fitting that the RE2 is covered by a longer warranty than the SE16. The RE2 is covered for five years. The SE16 gets one year of coverage when sold in a retail kit or three years when sold as a bare drive. Five-year warranties are commonplace for enterprise hard drives, and so are three-year warranties for desktop drives. However, it's a little odd to see the SE16's warranty coverage drop to a single year when the drive is sold as a retail kit. Perhaps Western Digital is banking on retail customers not being savvy enough to compare hard drive warranties in the aisles of Best Buy. Enthusiasts should know better, and since we tend to buy bare drives rather than retail kits, we shouldn't end up with the short end of the stick.