I had the same issue, too... Lots of messages saying "Timed out stoppping ...". The system never rebooted.
Here is what fixed the problem for me: Firstly, I activated systemd's debug shell using 'systemctl enable debug-shell.service'. Then I initiated a reboot and when the problem occured, I switched to debug shell (alt+F9 [/F10 ?] ). Using 'systemctl list-jobs', I figured out what jobs were running while the system hung. One of the jobs was an "unattended-upgrdes" job. This job held one ore more files on my root filesystem open. When I killed that process, the system finished its shutdown and rebooted. After having removed the package by 'apt-get --purge remove unattended-upgrades' the problem didn't arise again. I am using cron-apt on my servers - therefore I do not necessarily need unattended-upgrades. Hopefully this helps as workaround and to find the real cause of the problem. ** Attachment added: "Screenshots debug shell and shutdown messages" https://bugs.launchpad.net/ubuntu/+source/systemd/+bug/1554795/+attachment/4861267/+files/no-reboot-with-unattended-upgrades.png -- You received this bug notification because you are a member of Ubuntu Touch seeded packages, which is subscribed to initramfs-tools in Ubuntu. https://bugs.launchpad.net/bugs/1554795 Title: timeout on restart or shutdown with LUKS root Status in initramfs-tools package in Ubuntu: Confirmed Status in systemd package in Ubuntu: Confirmed Bug description: Using the server install ISO, it's possible to specify root on LUKS and variations thereof - for instance, root on LUKS on MD-RAID, root on LVM on LUKS on MD-RAID, and so forth. The installer does the right thing and initramfs-tools does everything necessary to support booting this sort of thing. However, systemd gives a 90-second timeout on restart or shutdown, presumably because it cannot dispose of the things beneath root. It's wholly unclear to me where the 90-second timeout is specified, should I wish to shorten it to reboot without the futile delay, but more to the point, there seems to be infrastructure for handling this kind of situation that doesn't exist in Ubuntu at present. I was pointed at this: https://www.freedesktop.org/wiki/Software/systemd/InitrdInterface/ However, Ubuntu seems not to have anything in its initramfs-tools to facilitate "shutdown-initrd" functionality. I haven't tested this, but I suspect this problem will exist for folks running root on MD-RAID without the LUKS as well. Either way, a relatively common vanilla install will force 90-second timeouts on users, which is unfortunate. ProblemType: Bug DistroRelease: Ubuntu 16.04 Package: systemd 229-2ubuntu1 [modified: usr/share/dbus-1/system-services/org.freedesktop.systemd1.service] ProcVersionSignature: Ubuntu 4.4.0-11.26-generic 4.4.4 Uname: Linux 4.4.0-11-generic x86_64 NonfreeKernelModules: zfs zunicode zcommon znvpair zavl nvidia_uvm nvidia_modeset nvidia ApportVersion: 2.20-0ubuntu3 Architecture: amd64 Date: Tue Mar 8 18:06:45 2016 InstallationDate: Installed on 2016-02-24 (13 days ago) InstallationMedia: Ubuntu-Server 16.04 LTS "Xenial Xerus" - Alpha amd64 (20160219) Lsusb: Bus 002 Device 002: ID 1058:0820 Western Digital Technologies, Inc. My Passport Ultra (WDBMWV, WDBZFP) Bus 002 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub Bus 001 Device 003: ID 046d:c408 Logitech, Inc. Marble Mouse (4-button) Bus 001 Device 002: ID 046d:c318 Logitech, Inc. Illuminated Keyboard Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub MachineType: Gigabyte Technology Co., Ltd. To be filled by O.E.M. ProcEnviron: TERM=xterm-color PATH=(custom, no user) XDG_RUNTIME_DIR=<set> LANG=en_US.UTF-8 SHELL=/bin/bash ProcKernelCmdLine: BOOT_IMAGE=/vmlinuz-4.4.0-11-generic.efi.signed root=/dev/mapper/hostname-root ro net.ifnames=0 biosdevname=0 SourcePackage: systemd SystemdDelta: [EXTENDED] /lib/systemd/system/systemd-timesyncd.service → /lib/systemd/system/systemd-timesyncd.service.d/disable-with-time-daemon.conf [EXTENDED] /lib/systemd/system/rc-local.service → /lib/systemd/system/rc-local.service.d/debian.conf 2 overridden configuration files found. UpgradeStatus: No upgrade log present (probably fresh install) dmi.bios.date: 12/04/2015 dmi.bios.vendor: American Megatrends Inc. dmi.bios.version: F1 dmi.board.asset.tag: To be filled by O.E.M. dmi.board.name: X150M-PRO ECC-CF dmi.board.vendor: Gigabyte Technology Co., Ltd. dmi.board.version: x.x dmi.chassis.asset.tag: To Be Filled By O.E.M. dmi.chassis.type: 3 dmi.chassis.vendor: To Be Filled By O.E.M. dmi.chassis.version: To Be Filled By O.E.M. dmi.modalias: dmi:bvnAmericanMegatrendsInc.:bvrF1:bd12/04/2015:svnGigabyteTechnologyCo.,Ltd.:pnTobefilledbyO.E.M.:pvrTobefilledbyO.E.M.:rvnGigabyteTechnologyCo.,Ltd.:rnX150M-PROECC-CF:rvrx.x:cvnToBeFilledByO.E.M.:ct3:cvrToBeFilledByO.E.M.: dmi.product.name: To be filled by O.E.M. dmi.product.version: To be filled by O.E.M. dmi.sys.vendor: Gigabyte Technology Co., Ltd. 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