I recently purchased a PCI Express x1 USB 3.0 controller card (containing the NEC USB 3.0 controller) with the intent of using a USB 3.0 external hard drive with my Linux box. I installed the card in an empty PCIe slot on my motherboard, connected the card to a power cable, strung a USB 3.0 cable between one of the new ports and my external HDD, and connected the HDD to a wall socket for power. Booting the system, the drive works 100% as intended, with the one exception of throughput: rather than using SuperSpeed 4.8 Gbps connectivity, it seems to be falling back to High Speed 480 Mbps USB 2.0-style throughput. Disk Utility shows it as a 480 Mbps device, and running a couple Disk Utility and dd benchmarks confirms that the drive fails to exceed ~40 MB/s (the approximate limit of USB 2.0), despite it being an SSD capable of far more than that.

When I connect my USB 3.0 HDD, dmesg shows this:

[ 3923.280018] usb 3-2: new high speed USB device using ehci_hcd and address 6

where I would expect to find this:

[ 3923.280018] usb 3-2: new SuperSpeed USB device using xhci_hcd and address 6

My system was running on kernel 2.6.35-25-generic at the time. Then, I stumbled upon this forum thread by an individual who found that a bug, which was present in kernels prior to 2.6.37-rc5, could be the culprit for this type of problem. Consequently, I installed the 2.6.37-generic mainline Ubuntu kernel to determine if the problem would go away. It didn't, so I tried 2.6.38-rc3-generic, and even the 2.6.38 nightly from 2010.02.01, to no avail.

In short, I'm trying to determine why, with USB 3.0 support in the kernel, my USB 3.0 drive fails to run at full SuperSpeed throughput.

See the comments under this question for additional details.

Output that might be relevant to the problem (when booting from 2.6.38-rc3):

Relevant lines from dmesg:

[   19.589491] xhci_hcd 0000:03:00.0: PCI INT A -> GSI 17 (level, low) -> IRQ 17
[   19.589512] xhci_hcd 0000:03:00.0: setting latency timer to 64
[   19.589516] xhci_hcd 0000:03:00.0: xHCI Host Controller
[   19.589623] xhci_hcd 0000:03:00.0: new USB bus registered, assigned bus number 12
[   19.650492] xhci_hcd 0000:03:00.0: irq 17, io mem 0xf8100000
[   19.650556] xhci_hcd 0000:03:00.0: irq 47 for MSI/MSI-X
[   19.650560] xhci_hcd 0000:03:00.0: irq 48 for MSI/MSI-X
[   19.650563] xhci_hcd 0000:03:00.0: irq 49 for MSI/MSI-X
[   19.653946] xHCI xhci_add_endpoint called for root hub
[   19.653948] xHCI xhci_check_bandwidth called for root hub

Relevant section of sudo lspci -v:

03:00.0 USB Controller: NEC Corporation uPD720200 USB 3.0 Host Controller (rev 03) (prog-if 30)
    Flags: bus master, fast devsel, latency 0, IRQ 17
    Memory at f8100000 (64-bit, non-prefetchable) [size=8K]
    Capabilities: [50] Power Management version 3
    Capabilities: [70] MSI: Enable- Count=1/8 Maskable- 64bit+
    Capabilities: [90] MSI-X: Enable+ Count=8 Masked-
    Capabilities: [a0] Express Endpoint, MSI 00
    Capabilities: [100] Advanced Error Reporting
    Capabilities: [140] Device Serial Number ff-ff-ff-ff-ff-ff-ff-ff
    Capabilities: [150] #18
    Kernel driver in use: xhci_hcd
    Kernel modules: xhci-hcd

Relevant section of sudo lsusb -v:

Bus 012 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
Device Descriptor:
  bLength                18
  bDescriptorType         1
  bcdUSB               3.00
  bDeviceClass            9 Hub
  bDeviceSubClass         0 Unused
  bDeviceProtocol         3 
  bMaxPacketSize0         9
  idVendor           0x1d6b Linux Foundation
  idProduct          0x0003 3.0 root hub
  bcdDevice            2.06
  iManufacturer           3 Linux 2.6.38-020638rc3-generic xhci_hcd
  iProduct                2 xHCI Host Controller
  iSerial                 1 0000:03:00.0
  bNumConfigurations      1
  Configuration Descriptor:
    bLength                 9
    bDescriptorType         2
    wTotalLength           25
    bNumInterfaces          1
    bConfigurationValue     1
    iConfiguration          0 
    bmAttributes         0xe0
      Self Powered
      Remote Wakeup
    MaxPower                0mA
    Interface Descriptor:
      bLength                 9
      bDescriptorType         4
      bInterfaceNumber        0
      bAlternateSetting       0
      bNumEndpoints           1
      bInterfaceClass         9 Hub
      bInterfaceSubClass      0 Unused
      bInterfaceProtocol      0 Full speed (or root) hub
      iInterface              0 
      Endpoint Descriptor:
        bLength                 7
        bDescriptorType         5
        bEndpointAddress     0x81  EP 1 IN
        bmAttributes            3
          Transfer Type            Interrupt
          Synch Type               None
          Usage Type               Data
        wMaxPacketSize     0x0004  1x 4 bytes
        bInterval              12
Hub Descriptor:
  bLength               9
  bDescriptorType      41
  nNbrPorts             4
  wHubCharacteristic 0x0009
    Per-port power switching
    Per-port overcurrent protection
    TT think time 8 FS bits
  bPwrOn2PwrGood       10 * 2 milli seconds
  bHubContrCurrent      0 milli Ampere
  DeviceRemovable    0x00
  PortPwrCtrlMask    0xff
 Hub Port Status:
   Port 1: 0000.0100 power
   Port 2: 0000.0100 power
   Port 3: 0000.0100 power
   Port 4: 0000.0100 power
Device Status:     0x0003
  Self Powered
  Remote Wakeup Enabled

Full, non-verbose lsusb:

Bus 012 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
Bus 011 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 010 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 009 Device 003: ID 04d9:0702 Holtek Semiconductor, Inc. 
Bus 009 Device 002: ID 046d:c068 Logitech, Inc. G500 Laser Mouse
Bus 009 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 008 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 007 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 006 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 005 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 004 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 003 Device 006: ID 174c:5106 ASMedia Technology Inc. 
Bus 003 Device 004: ID 0bda:0151 Realtek Semiconductor Corp. Mass Storage Device (Multicard Reader)
Bus 003 Device 002: ID 058f:6366 Alcor Micro Corp. Multi Flash Reader
Bus 003 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 002 Device 006: ID 1687:0163 Kingmax Digital Inc. 
Bus 002 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 001 Device 002: ID 046d:081b Logitech, Inc. 
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub

Full output:

• full dmesg
• full lspci
• full lsusb