I've got a lvm volume, which is composed of two hard drives enclosed in external enclosure connected through usb.

As it's external and not used too much, I like to spin it down if it is not used.

I'm using Linux Mint 18.3

Disk utility (gnome-disk-utility) doesn't support disk power management on disks containing lvm volumes.

I can do it with command

hdparm -y /dev/sde /dev/sdf

I can check beforehand if there is any process accessing mounted volume through

fuser -m /dev/lvm/volume

Is it safe to run hdparm command on lvm volume in such a situation?

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Yes; all the command does is ask the drive to spin down. As soon as it is accessed again, it will automatically spin up again.

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