I'm running ubuntu 18.04 and have the same problems with USB 3.0.
The ONLY way to get it to work at all ever is to turn iommu off in the bios
and use iommu=soft as kernel parameter (as is described as the "solution"
on many forums) AND I need to have certain device plugged into USB and/or
something else magical that I didn't pin point.

Anyway, once USB 3 works, it keeps working until I turn off a device
(Valve Index headset), or rather when I quit steam, I get the following
dmesg:

[ 7211.963003] xhci_hcd 0000:04:00.0: xHCI host not responding to stop endpoint 
command.
[ 7211.963019] xhci_hcd 0000:04:00.0: xHCI host controller not responding, 
assume dead
[ 7211.963037] xhci_hcd 0000:04:00.0: HC died; cleaning up
[ 7211.963053] usb 10-1: USB disconnect, device number 9
[ 7211.963222] usb 11-2: USB disconnect, device number 7
[ 7212.211386] usb 10-2: USB disconnect, device number 10
[ 7212.211390] usb 10-2.3: USB disconnect, device number 11
[ 7212.211392] usb 10-2.3.1: USB disconnect, device number 12
[ 7212.212041] usb 10-2.3.2: USB disconnect, device number 14
[ 7212.212529] usb 10-2.3.3: USB disconnect, device number 15
[ 7212.213010] usb 10-2.3.5: USB disconnect, device number 13

which were the connected USB 3 devices.

After that those USB plugs are dead. I have no figured out how
or even if it is possible to revive them without a reboot.

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You received this bug notification because you are a member of Kernel
Packages, which is subscribed to linux in Ubuntu.
https://bugs.launchpad.net/bugs/1313279

Title:
  xHCI host not responding to stop endpoint command

Status in Linux:
  Unknown
Status in linux package in Ubuntu:
  Confirmed

Bug description:
  Description:  Ubuntu 14.04 LTS
  Release:      14.04
  Hardware: Intel NUC D34010WYK (Core i3 4010U)
  Memory: 4 gigabytes
  USD device: PCTV 292e DVB-T tuner

  I have 2 PCTV 292e DVB-T tuners connected to the system. When I start
  to use either of the tuner, the xHCI host crashes. Since I'm booting
  from an USB disk. If I only connect 1 of the tuners, the system works
  ok. It does not matter which one of the tuners I connect.

  [   68.990396] xhci_hcd 0000:00:14.0: xHCI host not responding to stop 
endpoint command.
  [   68.990402] xhci_hcd 0000:00:14.0: Assuming host is dying, halting host.

  Sometimes this also leads to this:

  [  638.183002] IP: [<ffffffff815325dd>] usb_enable_link_state+0x2d/0x2f0
  [  638.183057] PGD 0 
  [  638.183077] Oops: 0000 [#1] SMP 

  I can also observe the same fault with OpenELEC Linux distribution
  that runs kernel 3.14 when I run the system from an internal SATA SSD
  drive (not from an external USB disk).

  lsusb -v: http://paste.ubuntu.com/7343384/
  dmesg: http://sprunge.us/HMXH
  dmesg (crash type 2): http://sprunge.us/PSiX

  ProblemType: Bug
  DistroRelease: Ubuntu 14.04
  Package: lubuntu-desktop 0.55
  ProcVersionSignature: Ubuntu 3.13.0-24.46-generic 3.13.9
  Uname: Linux 3.13.0-24-generic x86_64
  ApportVersion: 2.14.1-0ubuntu3
  Architecture: amd64
  Date: Sun Apr 27 11:12:22 2014
  InstallationDate: Installed on 2014-04-07 (19 days ago)
  InstallationMedia: Lubuntu 13.10 "Saucy Salamander" - Release amd64 
(20131016.1)
  SourcePackage: lubuntu-meta
  UpgradeStatus: Upgraded to trusty on 2014-04-26 (0 days ago)

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