3

9/22/2022 Edit: We got another couple systems for a client with the same issue, and adding the following to /etc/default/grub has resolved it.

"pci=nommconf"

Per the title, I am having issues that are currently limited to only Ubuntu (is not happening with Fedora or Arch/Manjaro).

  • 1 of the 3 M.2 SSDs stops being detected.
  • 7 of 13 USB ports drop power/connectivity while loading OS (2 type-a and 1 type-c on the front panel as well as 2 type-c and 4 type-a on the rear do not work).

The system is as follows:

AMD Threadripper Pro 3975WX
Asus WRX80E Sage Wifi
32GB ECC/Registered x4
WD Black SN850 2TB x3
Nvidia RTX 3090 (EVGA FTW3 Ultra)
1000W PSU (EVGA G6)

Output of 'lspci -k' from liveiso

00:00.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Root Complex
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse Root Complex
00:00.2 IOMMU: Advanced Micro Devices, Inc. [AMD] Starship/Matisse IOMMU
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse IOMMU
00:01.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
00:02.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
    DeviceName:  Onboard IGD
00:03.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
00:04.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
00:05.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
00:07.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
00:07.1 PCI bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Internal PCIe GPP Bridge 0 to bus[E:B]
    Kernel driver in use: pcieport
00:08.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
00:08.1 PCI bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Internal PCIe GPP Bridge 0 to bus[E:B]
    Kernel driver in use: pcieport
00:14.0 SMBus: Advanced Micro Devices, Inc. [AMD] FCH SMBus Controller (rev 61)
    Subsystem: ASUSTeK Computer Inc. FCH SMBus Controller
    Kernel driver in use: piix4_smbus
    Kernel modules: i2c_piix4, sp5100_tco
00:14.3 ISA bridge: Advanced Micro Devices, Inc. [AMD] FCH LPC Bridge (rev 51)
    Subsystem: ASUSTeK Computer Inc. FCH LPC Bridge
00:18.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship Device 24; Function 0
00:18.1 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship Device 24; Function 1
00:18.2 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship Device 24; Function 2
00:18.3 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship Device 24; Function 3
    Kernel driver in use: k10temp
    Kernel modules: k10temp
00:18.4 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship Device 24; Function 4
00:18.5 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship Device 24; Function 5
00:18.6 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship Device 24; Function 6
00:18.7 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship Device 24; Function 7
01:00.0 Non-Essential Instrumentation [1300]: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Function
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse PCIe Dummy Function
02:00.0 Non-Essential Instrumentation [1300]: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Reserved SPP
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse Reserved SPP
02:00.3 USB controller: Advanced Micro Devices, Inc. [AMD] Starship USB 3.0 Host Controller
    Subsystem: ASUSTeK Computer Inc. Starship USB 3.0 Host Controller
    Kernel driver in use: xhci_hcd
    Kernel modules: xhci_pci
20:00.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Root Complex
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse Root Complex
20:00.2 IOMMU: Advanced Micro Devices, Inc. [AMD] Starship/Matisse IOMMU
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse IOMMU
20:01.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
20:01.1 PCI bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse GPP Bridge
    Kernel driver in use: pcieport
20:01.2 PCI bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse GPP Bridge
    Kernel driver in use: pcieport
20:01.3 PCI bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse GPP Bridge
    Kernel driver in use: pcieport
20:02.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
20:03.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
20:04.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
20:05.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
20:07.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
20:07.1 PCI bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Internal PCIe GPP Bridge 0 to bus[E:B]
    Kernel driver in use: pcieport
20:08.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
20:08.1 PCI bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Internal PCIe GPP Bridge 0 to bus[E:B]
    Kernel driver in use: pcieport
21:00.0 PCI bridge: Advanced Micro Devices, Inc. [AMD] Matisse Switch Upstream
    Kernel driver in use: pcieport
22:00.0 PCI bridge: Advanced Micro Devices, Inc. [AMD] Matisse PCIe GPP Bridge
    Kernel driver in use: pcieport
22:01.0 PCI bridge: Advanced Micro Devices, Inc. [AMD] Matisse PCIe GPP Bridge
    Kernel driver in use: pcieport
22:02.0 PCI bridge: Advanced Micro Devices, Inc. [AMD] Matisse PCIe GPP Bridge
    Kernel driver in use: pcieport
22:03.0 PCI bridge: Advanced Micro Devices, Inc. [AMD] Matisse PCIe GPP Bridge
    Kernel driver in use: pcieport
22:04.0 PCI bridge: Advanced Micro Devices, Inc. [AMD] Matisse PCIe GPP Bridge
    Kernel driver in use: pcieport
22:05.0 PCI bridge: Advanced Micro Devices, Inc. [AMD] Matisse PCIe GPP Bridge
    Kernel driver in use: pcieport
22:06.0 PCI bridge: Advanced Micro Devices, Inc. [AMD] Matisse PCIe GPP Bridge
    Kernel driver in use: pcieport
22:08.0 PCI bridge: Advanced Micro Devices, Inc. [AMD] Matisse PCIe GPP Bridge
    Kernel driver in use: pcieport
23:00.0 Non-Volatile memory controller: Sandisk Corp WD PC SN810 / Black SN850 NVMe SSD (rev 01)
    Subsystem: Sandisk Corp WD Black SN850
    Kernel modules: nvme
24:00.0 USB controller: ASMedia Technology Inc. ASM3242 USB 3.2 Host Controller
    Subsystem: ASUSTeK Computer Inc. ASM3242 USB 3.2 Host Controller
    Kernel modules: xhci_pci
25:00.0 Ethernet controller: Intel Corporation Ethernet Controller 10G X550T (rev 01)
    Subsystem: ASUSTeK Computer Inc. Ethernet Controller 10G X550T
    Kernel driver in use: ixgbe
    Kernel modules: ixgbe
25:00.1 Ethernet controller: Intel Corporation Ethernet Controller 10G X550T (rev 01)
    Subsystem: ASUSTeK Computer Inc. Ethernet Controller 10G X550T
    Kernel driver in use: ixgbe
    Kernel modules: ixgbe
26:00.0 Network controller: Intel Corporation Wi-Fi 6 AX200 (rev 1a)
    Subsystem: Intel Corporation Wi-Fi 6 AX200NGW
    Kernel modules: iwlwifi
27:00.0 SATA controller: ASMedia Technology Inc. ASM1062 Serial ATA Controller (rev 02)
    Subsystem: ASUSTeK Computer Inc. ASM1062 Serial ATA Controller
    Kernel modules: ahci
28:00.0 SATA controller: ASMedia Technology Inc. ASM1062 Serial ATA Controller (rev 02)
    Subsystem: ASUSTeK Computer Inc. ASM1062 Serial ATA Controller
    Kernel modules: ahci
29:00.0 PCI bridge: ASPEED Technology, Inc. AST1150 PCI-to-PCI Bridge (rev 04)
2a:00.0 VGA compatible controller: ASPEED Technology, Inc. ASPEED Graphics Family (rev 41)
    Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family
    Kernel modules: ast
2b:00.0 Non-Essential Instrumentation [1300]: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Reserved SPP
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse Reserved SPP
2b:00.1 USB controller: Advanced Micro Devices, Inc. [AMD] Matisse USB 3.0 Host Controller
    Subsystem: ASUSTeK Computer Inc. Matisse USB 3.0 Host Controller
    Kernel modules: xhci_pci
2b:00.3 USB controller: Advanced Micro Devices, Inc. [AMD] Matisse USB 3.0 Host Controller
    Subsystem: Advanced Micro Devices, Inc. [AMD] Matisse USB 3.0 Host Controller
    Kernel modules: xhci_pci
2c:00.0 Non-Volatile memory controller: Sandisk Corp WD PC SN810 / Black SN850 NVMe SSD (rev 01)
    Subsystem: Sandisk Corp WD Black SN850
    Kernel driver in use: nvme
    Kernel modules: nvme
2d:00.0 Non-Volatile memory controller: Sandisk Corp WD PC SN810 / Black SN850 NVMe SSD (rev 01)
    Subsystem: Sandisk Corp WD Black SN850
    Kernel driver in use: nvme
    Kernel modules: nvme
2e:00.0 Non-Essential Instrumentation [1300]: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Function
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse PCIe Dummy Function
2f:00.0 Non-Essential Instrumentation [1300]: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Reserved SPP
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse Reserved SPP
2f:00.1 Encryption controller: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Cryptographic Coprocessor PSPCPP
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse Cryptographic Coprocessor PSPCPP
    Kernel driver in use: ccp
    Kernel modules: ccp
2f:00.3 USB controller: Advanced Micro Devices, Inc. [AMD] Starship USB 3.0 Host Controller
    Subsystem: ASUSTeK Computer Inc. Starship USB 3.0 Host Controller
    Kernel driver in use: xhci_hcd
    Kernel modules: xhci_pci
2f:00.4 Audio device: Advanced Micro Devices, Inc. [AMD] Starship/Matisse HD Audio Controller
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse HD Audio Controller
    Kernel modules: snd_hda_intel
40:00.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Root Complex
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse Root Complex
40:00.2 IOMMU: Advanced Micro Devices, Inc. [AMD] Starship/Matisse IOMMU
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse IOMMU
40:01.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
40:01.1 PCI bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse GPP Bridge
    Kernel driver in use: pcieport
40:02.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
40:03.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
40:04.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
40:05.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
40:07.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
40:07.1 PCI bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Internal PCIe GPP Bridge 0 to bus[E:B]
    Kernel driver in use: pcieport
40:08.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
40:08.1 PCI bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Internal PCIe GPP Bridge 0 to bus[E:B]
    Kernel driver in use: pcieport
41:00.0 VGA compatible controller: NVIDIA Corporation GA102 [GeForce RTX 3090] (rev a1)
    Subsystem: eVga.com. Corp. GA102 [GeForce RTX 3090]
    Kernel driver in use: nouveau
    Kernel modules: nvidiafb, nouveau
41:00.1 Audio device: NVIDIA Corporation GA102 High Definition Audio Controller (rev a1)
    Subsystem: eVga.com. Corp. GA102 High Definition Audio Controller
    Kernel driver in use: snd_hda_intel
    Kernel modules: snd_hda_intel
42:00.0 Non-Essential Instrumentation [1300]: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Function
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse PCIe Dummy Function
43:00.0 Non-Essential Instrumentation [1300]: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Reserved SPP
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse Reserved SPP
60:00.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Root Complex
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse Root Complex
60:00.2 IOMMU: Advanced Micro Devices, Inc. [AMD] Starship/Matisse IOMMU
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse IOMMU
60:01.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
60:02.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
60:03.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
60:04.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
60:05.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
60:07.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
60:07.1 PCI bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Internal PCIe GPP Bridge 0 to bus[E:B]
    Kernel driver in use: pcieport
60:08.0 Host bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Host Bridge
60:08.1 PCI bridge: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Internal PCIe GPP Bridge 0 to bus[E:B]
    Kernel driver in use: pcieport
61:00.0 Non-Essential Instrumentation [1300]: Advanced Micro Devices, Inc. [AMD] Starship/Matisse PCIe Dummy Function
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse PCIe Dummy Function
62:00.0 Non-Essential Instrumentation [1300]: Advanced Micro Devices, Inc. [AMD] Starship/Matisse Reserved SPP
    Subsystem: ASUSTeK Computer Inc. Starship/Matisse Reserved SPP

1
  • 2
    Please don't put "Solved" in the question title and the solution inside the question. This is a question answer site. You are most welcome to answer your own question. You should accept the correct answer by clicking on the gray check ✔️ and turn it green ✅. This will mark the question as solved and help others.
    – user68186
    Oct 25, 2022 at 0:17

3 Answers 3

4

TLDR: Flip the physical VGA switch to Off to completely disable the onboard VGA.

I know this is marked as solved, but I wanted to chime in with another potential solution.

I was having the same issue, certain USB ports not working, WiFi & Bluetooth not working, etc. Went down the rabbit hole of BIOS settings and ended up here. pci=nommconf did solve the issue, but it was really bothering me and I knew there was something weird going on with the PCIe bus that was causing the issue in the first place - so I started disabling as much as I could.

Turns out, it was a super simple solution - just took forever to figure out. Flip the physical VGA switch to off. That solved all the issues I was having and I no longer need the kernel flags in GRUB. USB Ports, Wifi & Bluetooth are all working with no more dmesg errors.

When I first built my machine, I used the onboard VGA adapter to connect to a monitor in order to install Ubuntu. Once I got Ubuntu installed, I installed my GPU, and I changed the BIOS setting BootBoot ConfigurationPrimary Display from Onboard VGA Header to Discrete graphics card. Turns out, this does not actually disable the onboard VGA header - so I’m assuming it was causing issues for other PCIe devices. In order to completely disable the onboard VGA, you need to flip the physical switch to off. If you have a discrete GPU, you shouldn’t need the motherboard’s VGA anyway.

The switch is located in the bottom right portion of the motherboard right above the VGA header.

VGA Switch Location

Hope this helps.

2
  • This indeed worked perfectly!
    – rept
    Dec 28, 2022 at 9:57
  • This just plagued me too. Any idea why this interfered with USBs?
    – Josh.F
    Mar 11, 2023 at 0:10
1

I'm just re-posting the OP's solution as an answer (with more detailed explanation), given that this actually solved my issue after many hours of research and desperation.

When booting from USB and arriving to the menu to select "Try or Install Ubuntu", press e to edit the GRUB settings. Then, add pci=nommconf and press Ctrl+X or F10 to save and boot.

0

I confirm, turning off VGA header on motherboard works!! My very painful story:

Home server spec:

  • ASUS Pro WS WRX80E-SAGE SE WIFI II
  • 5975wx
  • 256gb ram
  • 4x Seagate Exos 20tb (in zpool1)

I had 2 weeks of insane issues with sata ports and my HDDs. My zpool was falling apart every 2hrs or so with read and/or write errors and dmesg had cryptic messages all over the place. What i've done (and nothing helped):

  • bios updates
  • bcm firmware update
  • HDDs firmware updates
  • Reseated CPU couple of times, making sure I follow the instructuons
  • Bought external hdd box (qnap TR-004), in attempt to separate hdd problem from possible issues with cpu/motherboard/etc.

But the issue persisted even with external enclosure! Reading dmesg log closer i've noticed that my xHCI host controller was dying.

[Sun Apr 16 03:45:15 2023] xhci_hcd 0000:2b:00.1: AMD-Vi: Event logged [IO_PAGE_FAULT domain=0x002b address=0xfffffff00000 flags=0x0000]
... <skipped> ...
[Sun Apr 16 03:45:15 2023] xhci_hcd 0000:2b:00.1: AMD-Vi: Event logged [IO_PAGE_FAULT domain=0x002b address=0xfffffff03f80 flags=0x0000]
[Sun Apr 16 03:45:51 2023] xhci_hcd 0000:2b:00.1: xHCI host not responding to stop endpoint command
[Sun Apr 16 03:45:51 2023] xhci_hcd 0000:2b:00.1: xHCI host controller not responding, assume dead
[Sun Apr 16 03:45:51 2023] xhci_hcd 0000:2b:00.1: HC died; cleaning up
[Sun Apr 16 03:45:51 2023] usb 3-5: USB disconnect, device number 2

After two hours of googling I finally found this post and can't thank enough everyone in this thread, especially @SteveMG9! Whew, I was ready to RMA the motherboard and disks...

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