Debugging USB 3.0 Speeds

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I've added a USB 3.0 card that should support super speed to a server I have, but it's not working at super-speed speeds for the external hard drives I connect, and a having a hard time diagnosing why (hardware issue/quirk? driver issue?)

Before installing the card, xhci wasn't ever used, now it is, so that makes it clear that it is a usb 3.0 card. It's a 4 port card, but what's weird is that the card seems to expose 2 USB hubs with 4 ports.

i.e.

[    2.086988] xhci_hcd 0000:07:00.0: xHCI Host Controller
[ 2.086996] xhci_hcd 0000:07:00.0: new USB bus registered, assigned bus number 2 [ 2.092364] xhci_hcd 0000:07:00.0: hcc params 0x014051cf hci version 0x100 quirks 0x00000010 [ 2.092561] usb usb2: New USB device found, idVendor=1d6b, idProduct=0002 [ 2.092563] usb usb2: New USB device strings: Mfr=3, Product=2, SerialNumber=1
[    2.092564] usb usb2: Product: xHCI Host Controller
[    2.092565] usb usb2: Manufacturer: Linux 4.9.0-3-amd64 xhci-hcd
[    2.092566] usb usb2: SerialNumber: 0000:07:00.0
[    2.092741] hub 2-0:1.0: USB hub found
[    2.092749] hub 2-0:1.0: 4 ports detected

quickly followed by

[    2.092881] xhci_hcd 0000:07:00.0: xHCI Host Controller
[ 2.092884] xhci_hcd 0000:07:00.0: new USB bus registered, assigned bus number 3 [ 2.095951] usb usb3: We don't know the algorithms for LPM for this host, disabling LPM. [ 2.095965] usb usb3: New USB device found, idVendor=1d6b, idProduct=0003 [ 2.095966] usb usb3: New USB device strings: Mfr=3, Product=2, SerialNumber=1
[    2.095967] usb usb3: Product: xHCI Host Controller
[    2.095968] usb usb3: Manufacturer: Linux 4.9.0-3-amd64 xhci-hcd
[    2.095969] usb usb3: SerialNumber: 0000:07:00.0
[    2.096100] hub 3-0:1.0: USB hub found
[    2.096116] hub 3-0:1.0: 4 ports detected

lsusb -t shows the hubs and the problem

/:  Bus 03.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/4p, 5000M
/:  Bus 02.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/4p, 480M
    |__ Port 3: Dev 5, If 0, Class=Mass Storage, Driver=uas, 480M
    |__ Port 4: Dev 6, If 0, Class=Hub, Driver=hub/3p, 480M
        |__ Port 1: Dev 11, If 0, Class=Mass Storage, Driver=uas, 480M

the hard drives I plug in are connecting to the 480Mbps "hub", not the 5000Mbps hub.

and this is clear from the kernel logs when connecting the external hard drive

[538663.101097] usb 2-4: new high-speed USB device number 6 using xhci_hcd
[538663.246919] usb 2-4: New USB device found, idVendor=0bc2, idProduct=ab44 [538663.246922] usb 2-4: New USB device strings: Mfr=1, Product=2, SerialNumber=3
[538663.246923] usb 2-4: Product: Backup+ Hub
[538663.246924] usb 2-4: Manufacturer: Seagate
[538663.248429] hub 2-4:1.0: USB hub found
[538663.248973] hub 2-4:1.0: 3 ports detected
[538664.169034] usb 2-4.1: new high-speed USB device number 11 using xhci_hcd [538664.319996] usb 2-4.1: New USB device found, idVendor=0bc2, idProduct=ab38 [538664.319999] usb 2-4.1: New USB device strings: Mfr=2, Product=3, SerialNumber=1
[538664.320000] usb 2-4.1: Product: Backup+ Hub BK
[538664.320001] usb 2-4.1: Manufacturer: Seagate

I have tested these drives in other computers (windows) and they seemed to work at super-speed speeds, plan is to try a different usb 3.0 card as well in this machine which I also know worked in windows at super-speed speeds, but trying to understand f there are other ways to debug it.

i.e. even lsusb -v shows that these devices should be capable of super-speed speeds

  SuperSpeed USB Device Capability:
    bLength                10
    bDescriptorType        16
    bDevCapabilityType      3
    bmAttributes         0x00
    wSpeedsSupported   0x000e
      Device can operate at Full Speed (12Mbps)
      Device can operate at High Speed (480Mbps)
      Device can operate at SuperSpeed (5Gbps)

For reference, this is the stock Debian 4.9 kernel in Debian stretch

Linux spotter 4.9.0-3-amd64 #1 SMP Debian 4.9.30-2+deb9u3 (2017-08-06) x86_64 GNU/Linux

any help in understanding what's going on would be appreciated.
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