Hi, the BIOS is expected to configure the PCI bridges leading to the TBT
controller but it does not seem to do that:

[    3.725792] pci 0000:06:00.0: bridge configuration invalid ([bus 00-00]), 
reconfiguring
[    3.725799] pci 0000:06:01.0: bridge configuration invalid ([bus 00-00]), 
reconfiguring
[    3.725807] pci 0000:06:02.0: bridge configuration invalid ([bus 00-00]), 
reconfiguring
[    3.725814] pci 0000:06:04.0: bridge configuration invalid ([bus 00-00]), 
reconfiguring

to me this looks like a BIOS issue.

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https://bugs.launchpad.net/bugs/1696325

Title:
  USB, display and ethernet ports in HP Thunderbolt dock don't work

Status in linux package in Ubuntu:
  Confirmed

Bug description:
  I have laptop HP ZBook G3 Studio with Thunderbolt dock P5Q58AA.
  Installed OS is Ubuntu 16.04.2 LTS

  When I connect dock into laptop only power works and laptop can be
  shutdown by pressing power button in dock. USB ports, display ports,
  ethernet port and audio plug are not working.

  
  $ lsb_release -rd
  Description:  Ubuntu 16.04.2 LTS
  Release:      16.04

  $ apt-cache policy linux-image-generic-hwe-16.04
  linux-image-generic-hwe-16.04:
    Installed: 4.8.0.54.25
    Candidate: 4.8.0.54.25
    Version table:
   *** 4.8.0.54.25 500
          500 http://fi.archive.ubuntu.com/ubuntu xenial-updates/main amd64 
Packages
          500 http://security.ubuntu.com/ubuntu xenial-security/main amd64 
Packages
          100 /var/lib/dpkg/status
  --- 
  ApportVersion: 2.20.1-0ubuntu2.6
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC1:  markus     3304 F.... pulseaudio
   /dev/snd/controlC0:  markus     3304 F.... pulseaudio
  CurrentDesktop: Unity
  DistroRelease: Ubuntu 16.04
  EcryptfsInUse: Yes
  InstallationDate: Installed on 2017-04-07 (61 days ago)
  InstallationMedia: Ubuntu 16.04.2 LTS "Xenial Xerus" - Release amd64 
(20170215.2)
  Lsusb:
   Bus 002 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
   Bus 001 Device 003: ID 045e:00cb Microsoft Corp. Basic Optical Mouse v2.0
   Bus 001 Device 002: ID 045e:07f8 Microsoft Corp. Wired Keyboard 600 (model 
1576)
   Bus 001 Device 004: ID 8087:0a2b Intel Corp. 
   Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
  MachineType: HP HP ZBook Studio G3
  NonfreeKernelModules: nvidia_uvm nvidia_drm nvidia_modeset nvidia
  Package: linux (not installed)
  ProcFB: 0 EFI VGA
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.8.0-54-generic.efi.signed 
root=UUID=2b78b572-05a1-4c01-b97d-9c1fea406faf ro quiet splash nomodeset 
pnpacpi=off vt.handoff=7
  ProcVersionSignature: Ubuntu 4.8.0-54.57~16.04.1-generic 4.8.17
  RelatedPackageVersions:
   linux-restricted-modules-4.8.0-54-generic N/A
   linux-backports-modules-4.8.0-54-generic  N/A
   linux-firmware                            1.157.10
  Tags:  xenial
  Uname: Linux 4.8.0-54-generic x86_64
  UpgradeStatus: No upgrade log present (probably fresh install)
  UserGroups: adm cdrom dip docker lpadmin plugdev sambashare sudo
  _MarkForUpload: True
  dmi.bios.date: 11/02/2016
  dmi.bios.vendor: HP
  dmi.bios.version: N82 Ver. 01.15
  dmi.board.name: 80D4
  dmi.board.vendor: HP
  dmi.board.version: KBC Version 11.67
  dmi.chassis.type: 10
  dmi.chassis.vendor: HP
  dmi.modalias: 
dmi:bvnHP:bvrN82Ver.01.15:bd11/02/2016:svnHP:pnHPZBookStudioG3:pvr:rvnHP:rn80D4:rvrKBCVersion11.67:cvnHP:ct10:cvr:
  dmi.product.name: HP ZBook Studio G3
  dmi.sys.vendor: HP

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