Comment by tlikonen

Usually in Linux the system is installed on an encrypted filesystem (cryptsetup, LUKS). Only kernel and so called initrd image (early boot stuff) is outside the encryption. The disk is opened at very early stage in boot when just about the kernel is loaded. Thus, the encryption is open whenever the operating system is running. Everything is of course still transparently encrypted on disk but the "lock" is open. One must shut down the computer to close the filesystem's encryption.