This article wants to shed some light on how hdparm in connection with advanced power management works and how some default values might keep the disk from spinning down. You might go to the following articles, if you want to know how to configure your system to permanently set a disk to spin-down after a given idle time or how to distinctively identify the hard disk you want to configure and why this is an important issue.
1. Check the status of your hard disks
Open up a terminal and copy/paste the following command to get the status off all hard disk connected to your computer:
sudo hdparm -B /dev/sd? (strange but yes: it's really a question mark for a wild card)
2. Understanding the values
Studying the man hdparm a bit, you'll get the first clue why some disks aren't spinning down by just applying the spin down time with hdparm -S:
"Possible settings range from values 1 through 127 (which permit spin-down), and values 128 through 254 (which do not permit spin-down).[...]A value of 255 tells hdparm to disable Advanced Power Management altogether on the drive (not all drives support disabling it, but most do)."
The output resulting from the command above most possibly show you, that your disks are set to APM_level=254. With the information from the manual this tells you, that it somehow is still configured to use Advanced Power Management features, but won't spin down. If you own a "green drive" that comes with built-in power saving features, you might also see "APM_level=not supported" here. In that case you can't set the APM_level manually, but you can still change the spin-down time by using e.g. "sudo hdparm -S180 /dev/sda" to spin down sda after 15 minutes.
Important note: With many systems there is a bug (or bad documented problem) right now, resulting in your hard drive spinning down every minute or so when using hdparm -B127, no matter which hdparm -S you used. If you experience this, set your drive to hdparm -B255 and define a spin-down time. As strange as it sounds, the spin-down times will then work also the documentation tells you, that 255 disables advanced power management.
3. Change settings temporarily and try spinning down the hard disk in question
If the hard disk causing you trouble is /dev/sda right now first copy/paste the following command:
sudo hdparm -B127 /dev/sda
in connection with the issue mentioned above it might be even better to check whether it works with
sudo hdparm -B255 /dev/sda
The flag -B127, in theory, should set the hard drive to a level that allows the most performance while still allowing it to spin down. As mentioned this might not work, giving you the only work around of setting it to 255
To check whether it really will spin down now, you can use the following command to instantly make it spin down:
sudo hdparm -y /dev/sda
You should hear it spin down now, what is unfortunately the best way to check it. You can use sudo hdparm -C /dev/sd? to check the status, but nevertheless "standby" tell you it spun down, it might not really have done so. If -B255 works and the hard drive spins down, you should use it instead of -B127