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These two options seem confusing. For example: according to the man page -B 254 "does not permit spin-down". However, testing with -B 254 -S 1 the drive does spin down after 5 seconds.

-B Query/set Advanced Power Management feature, if the drive supports it. A low value means aggressive power management and a high value means better performance. Possible settings range from values 1 through 127 (which permit spin-down), and values 128 through 254 (which do not permit spin-down). The highest degree of power management is attained with a setting of 1, and the highest I/O performance with a setting of 254. A value of 255 tells hdparm to disable Advanced Power Management altogether on the drive (not all drives support disabling it, but most do).

-S Put the drive into idle (low-power) mode, and also set the standby (spindown) timeout for the drive. This timeout value is used by the drive to determine how long to wait (with no disk activity) before turning off the spindle motor to save power. Under such circumstances, the drive may take as long as 30 seconds to respond to a subsequent disk access, though most drives are much quicker. The encoding of the timeout value is somewhat peculiar. A value of zero means "timeouts are disabled": the device will not automatically enter standby mode. Values from 1 to 240 specify multiples of 5 seconds, yielding timeouts from 5 seconds to 20 minutes. Values from 241 to 251 specify from 1 to 11 units of 30 minutes, yielding timeouts from 30 minutes to 5.5 hours. A value of 252 signifies a timeout of 21 minutes. A value of 253 sets a vendor-defined timeout period between 8 and 12 hours, and the value 254 is reserved. 255 is interpreted as 21 minutes plus 15 seconds. Note that some older drives may have very different interpretations of these values.

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I think the -B switch affects the drive's internal, automatic energy saving features, so it stops the drive spinning itself down, but it doesn't stop the OS spinning it down upon request. – Jamie Kitson Sep 10 '13 at 19:05
I try -B127 -S240 on my notebook sata disk. But it makes Load_Cycle_Count increase too fast about 4/minute. – waterloo2005 Dec 15 '13 at 3:36

According to the ATA Spec, they don't affect each other at all:

Advanced Power Management is independent of the Standby timer setting. If both Advanced Power Management and the Standby timer are set, the device will go to the Standby state when the timer times out or the device’s Advanced Power Management algorithm indicates that the Standby state should be entered.

So you can use -B 254 to not let the Advanced Power Management part of the drive spin it down, but still use -S 1 to have the Standby timer spin it down after 5 seconds.

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