This issue still exists on 
Laptop: Macbook Pro 11,1 (2014 13" model)
Ubuntu: Yakkety (16.10)
Kernel: Linux version 4.8.0-41-generic (buildd@lgw01-18)

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https://bugs.launchpad.net/bugs/1413440

Title:
  USB stops working after a while (xhci_hcd 0000:00:14.0: Timeout while
  waiting for setup device command)

Status in System76:
  Triaged
Status in linux package in Ubuntu:
  Triaged

Bug description:
  On my laptop the kernel will sometimes drop the USB hub. After this,
  the laptop doesn't recognise any device plugged in to the USB ports -
  plugging and unplugging any device I've tried into any of the USB
  ports produces no response, not even dmesg entries.

  Strangely this also applies to bluetooth - it no longer works once USB
  has dropped (possibly the module is hung of the bus internally).

  Once this has happened only a reboot fixes it; I've not managed to
  find any combination of module unload/reload or suspend cycles to
  reinitialise things correctly.

  Relevant snippet of dmesg:
  [48830.625057] xhci_hcd 0000:00:14.0: Timeout while waiting for setup device 
command
  [48838.079718] xhci_hcd 0000:00:14.0: Stopped the command ring failed, maybe 
the host is dead
  [48838.079742] xhci_hcd 0000:00:14.0: Abort command ring failed
  [48838.079746] xhci_hcd 0000:00:14.0: HC died; cleaning up
  [48838.079770] xhci_hcd 0000:00:14.0: Timeout while waiting for setup device 
command
  [48838.079806] sched: RT throttling activated
  [48838.079981] usb 1-1: USB disconnect, device number 16
  [48838.079985] usb 1-1.2: USB disconnect, device number 18
  [48838.079987] usb 1-1.2.3: USB disconnect, device number 19
  [48838.080285] usb 1-1.2.4: USB disconnect, device number 20
  [48838.111892] usb 1-1.4: USB disconnect, device number 17
  [48838.191292] usb 1-4: USB disconnect, device number 6
  [48838.267550] usb 1-10: USB disconnect, device number 8
  [48838.282968] usb 2-1: device not accepting address 8, error -62
  [48838.282983] usb 2-1: USB disconnect, device number 8
  [48838.282986] usb 2-1.2: USB disconnect, device number 9

  ProblemType: Bug
  DistroRelease: Ubuntu 15.04
  Package: linux-image-3.18.0-9-generic 3.18.0-9.10
  ProcVersionSignature: Ubuntu 3.18.0-9.10-generic 3.18.2
  Uname: Linux 3.18.0-9-generic x86_64
  ApportVersion: 2.15.1-0ubuntu2
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC1:  chris      4255 F.... pulseaudio
   /dev/snd/controlC0:  chris      4255 F.... pulseaudio
  CRDA:
   country AU: DFS-UNSET
        (2402 - 2482 @ 40), (N/A, 20), (N/A)
        (5170 - 5250 @ 40), (3, 23), (N/A)
        (5250 - 5330 @ 40), (3, 23), (0 ms), DFS
        (5735 - 5835 @ 40), (3, 30), (N/A)
  CurrentDesktop: Unity
  Date: Thu Jan 22 12:59:27 2015
  InstallationDate: Installed on 2013-08-06 (533 days ago)
  InstallationMedia: Ubuntu 13.04 "Raring Ringtail" - Release amd64 (20130424)
  MachineType: System76, Inc. Galago UltraPro
  ProcFB: 0 inteldrmfb
  ProcKernelCmdLine: BOOT_IMAGE=/vmlinuz-3.18.0-9-generic.efi.signed 
root=UUID=92c2fa03-f29c-4bcc-87ab-f0fe28c134f2 ro quiet splash vt.handoff=7 
init=/lib/systemd/systemd break=mount
  RelatedPackageVersions:
   linux-restricted-modules-3.18.0-9-generic N/A
   linux-backports-modules-3.18.0-9-generic  N/A
   linux-firmware                            1.141
  RfKill:
   1: phy0: Wireless LAN
        Soft blocked: no
        Hard blocked: no
  SourcePackage: linux
  UpgradeStatus: Upgraded to vivid on 2013-08-06 (533 days ago)
  dmi.bios.date: 07/09/2013
  dmi.bios.vendor: American Megatrends Inc.
  dmi.bios.version: 4.6.5
  dmi.board.asset.tag: Tag 12345
  dmi.board.name: Galago UltraPro
  dmi.board.vendor: System76, Inc.
  dmi.board.version: galu1
  dmi.chassis.asset.tag: No Asset Tag
  dmi.chassis.type: 9
  dmi.chassis.vendor: System76, Inc,
  dmi.chassis.version: galu1
  dmi.modalias: 
dmi:bvnAmericanMegatrendsInc.:bvr4.6.5:bd07/09/2013:svnSystem76,Inc.:pnGalagoUltraPro:pvrgalu1:rvnSystem76,Inc.:rnGalagoUltraPro:rvrgalu1:cvnSystem76,Inc,:ct9:cvrgalu1:
  dmi.product.name: Galago UltraPro
  dmi.product.version: galu1
  dmi.sys.vendor: System76, Inc.

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