I'm on Ubuntu 16.06 LTS server and I've encrypted my home with ecryptfs following this procedure. So far so good.
What I like with ecryptfs is that it's possible to remotely reboot the machine and files are unencrypted on user login (not possible with Cryptsetup/LUKS and whole disk encryption).
Nevertheless, is it possible to have the user's home directory not being re-encrypted when he logs out? So that you just can't read things if the machine is stolen but it's possible to have cron tasks read and write from user's home.