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Explanation

I just built a new computer. Here are the specs:

Motherboard: Gigabyte 990FXA-UD3

CPU: AMD FX 8350

SSD: SAMSUNG 840 Pro Series MZ-7PD256BW

RAM: G.SKILL F3-1600C9Q-32GXM

Initially I tried to install Linux Mint 15 with XFCE from a Live DVD. The live DVD loaded, but my keyboard and mouse where not detected or mounted, so I couldn't install it. After some googling I discovered that some of my BIOS settings were probably causing the problem. I enabled the network stack and the IOMMU controller (described here and here) and then usb devices started to work and I was able to install Ubuntu 12.04.3 LTS. But I really wanted Mint 15 with XFCE, so I installed that again and it worked this time! But then I noticed that I "couldn't" get a network connection. So then I reinstalled Ubuntu again. After installing Ubuntu, I realized that for some reason or another the Automatic DHCP wasn't working. I switched it to a manual configuration, and after rebooting the computer (not sure why I had to reboot to get the config to work) I had network connectivity. Well geez, I still wanted Mint, so I reinstalled yet again!

Long story short - I now have Mint 15 with XFCE up and running. But its still not perfect. The boot time takes forever and there is no indication that the computer is booting other than the color of the LED on my monitor. The screen is black, no graphical information whatsoever indicating the OS is loading. After waiting a few minutes (I haven't timed it but I think its about 4 or 5 minutes) I finally get the login screen. But when I try to use the USB keyboard or mouse, they still don't work. I know this sounds confusing because I said everything is up and running. Well, the problem is that I have to wait somewhere between 1 to 2 minutes before the keyboard and mouse are functional. I can live with this, but it feels like something still isn't working right.

I get the same results with Mint 15 and Ubuntu 12.04.3 LTS.

I made sure the motherboard has the latest BIOS installed. I tried to update the drivers for the LAN, Realtek 8111E (the website says "LINUX driver for kernel 3.x and 2.6.x and 2.4.x") but when I untar r8168-8.037.00.tar.bz2 the README file states "Kernel source tree (supported Linux kernel 2.6.x and 2.4.x)" so I didn't install it because I'm running:

$ uname -a
Linux bugger 3.8.0-25-generic #37-Ubuntu SMP Thu Jun 6 20:47:07 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

Here are snipets from /var/log/syslog. I just included the parts pertinent to the warnings or errors that are reported:

...
Oct 27 19:34:07 bugger kernel: [    1.531599] AMD-Vi: Event logged [IO_PAGE_FAULT device=01:00.0 domain=0x0014 address=0x00000000be9f9880 flags=0x0010]
Oct 27 19:34:07 bugger kernel: [    1.850302] usb 3-2: new high-speed USB device number 2 using ehci-pci
Oct 27 19:34:07 bugger kernel: [   16.912757] usb 3-2: device descriptor read/64, error -110
Oct 27 19:34:07 bugger kernel: [   18.217346] xhci_hcd 0000:01:00.0: can't setup
Oct 27 19:34:07 bugger kernel: [   18.217348] xhci_hcd 0000:01:00.0: USB bus 8 deregistered
Oct 27 19:34:07 bugger kernel: [   18.217375] Switching to clocksource tsc
Oct 27 19:34:07 bugger kernel: [   18.217377] xhci_hcd 0000:01:00.0: init 0000:01:00.0 fail, -110
Oct 27 19:34:07 bugger kernel: [   18.217379] xhci_hcd: probe of 0000:01:00.0 failed with error -110
...
Oct 27 19:34:07 bugger kernel: [   19.795759] [drm] Initialized nouveau 1.1.0 20120801 for 0000:03:00.0 on minor 0
Oct 27 19:34:07 bugger kernel: [   32.079049] usb 3-2: device descriptor read/64, error -110
Oct 27 19:34:07 bugger kernel: [   32.294288] usb 3-2: new high-speed USB device number 3 using ehci-pci
Oct 27 19:34:07 bugger kernel: [   47.356778] usb 3-2: device descriptor read/64, error -110
Oct 27 19:34:07 bugger kernel: [   62.522954] usb 3-2: device descriptor read/64, error -110
Oct 27 19:34:07 bugger kernel: [   62.738247] usb 3-2: new high-speed USB device number 4 using ehci-pci
Oct 27 19:34:07 bugger kernel: [   73.112154] usb 3-2: device not accepting address 4, error -110
Oct 27 19:34:07 bugger kernel: [   73.223791] usb 3-2: new high-speed USB device number 5 using ehci-pci
Oct 27 19:34:07 bugger kernel: [   83.597693] usb 3-2: device not accepting address 5, error -110
Oct 27 19:34:07 bugger kernel: [   83.597715] hub 3-0:1.0: unable to enumerate USB device on port 2
Oct 27 19:34:07 bugger kernel: [   83.733056] xor: automatically using best checksumming function:
Oct 27 19:34:07 bugger kernel: [   83.769049]    avx       :  5053.000 MB/sec
Oct 27 19:34:07 bugger kernel: [   83.770733] device-mapper: dm-raid45: initialized v0.2594b
Oct 27 19:34:07 bugger kernel: [   83.792131] Btrfs loaded
Oct 27 19:34:07 bugger kernel: [   83.813183] EXT4-fs (sda1): mounted filesystem with ordered data mode. Opts: (null)
Oct 27 19:34:07 bugger kernel: [   83.872709] usb 5-3: new full-speed USB device number 2 using ohci_hcd
Oct 27 19:34:07 bugger kernel: [   83.938145] Adding 33516540k swap on /dev/sda5.  Priority:-1 extents:1 across:33516540k SS
Oct 27 19:34:07 bugger kernel: [   83.958737] EXT4-fs (sda1): re-mounted. Opts: errors=remount-ro
Oct 27 19:34:07 bugger kernel: [   83.983172] IPv6: ADDRCONF(NETDEV_UP): eth0: link is not ready
Oct 27 19:34:07 bugger kernel: [   84.009284] lp: driver loaded but no devices found
Oct 27 19:34:07 bugger kernel: [   84.033058] usb 5-3: New USB device found, idVendor=0557, idProduct=7000
Oct 27 19:34:07 bugger kernel: [   84.033064] usb 5-3: New USB device strings: Mfr=0, Product=0, SerialNumber=0
Oct 27 19:34:07 bugger kernel: [   84.035104] hub 5-3:1.0: USB hub found
Oct 27 19:34:07 bugger kernel: [   84.037248] hub 5-3:1.0: 4 ports detected
Oct 27 19:34:07 bugger bluetoothd[626]: Bluetooth daemon 4.101
Oct 27 19:34:07 bugger bluetoothd[626]: Starting SDP server
Oct 27 19:34:07 bugger bluetoothd[626]: DIS cannot start: GATT is disabled
Oct 27 19:34:07 bugger bluetoothd[626]: Failed to init deviceinfo plugin
Oct 27 19:34:07 bugger bluetoothd[626]: Failed to init proximity plugin
Oct 27 19:34:07 bugger bluetoothd[626]: Failed to init time plugin
Oct 27 19:34:07 bugger bluetoothd[626]: Failed to init alert plugin
Oct 27 19:34:07 bugger bluetoothd[626]: Failed to init thermometer plugin
Oct 27 19:34:07 bugger kernel: [   84.064980] Bluetooth: Core ver 2.16
Oct 27 19:34:07 bugger kernel: [   84.064995] NET: Registered protocol family 31
Oct 27 19:34:07 bugger kernel: [   84.064996] Bluetooth: HCI device and connection manager initialized
Oct 27 19:34:07 bugger kernel: [   84.065002] Bluetooth: HCI socket layer initialized
Oct 27 19:34:07 bugger kernel: [   84.065005] Bluetooth: L2CAP socket layer initialized
Oct 27 19:34:07 bugger kernel: [   84.065009] Bluetooth: SCO socket layer initialized
Oct 27 19:34:07 bugger bluetoothd[626]: Failed to init gatt_example plugin
...
Oct 27 19:34:07 bugger NetworkManager[979]: <info> monitoring kernel firmware directory '/lib/firmware'.
Oct 27 19:34:07 bugger NetworkManager[979]: <info> WiFi hardware radio set enabled
Oct 27 19:34:07 bugger NetworkManager[979]: <info> WiFi enabled by radio killswitch; enabled by state file
Oct 27 19:34:07 bugger NetworkManager[979]: <info> WWAN enabled by radio killswitch; enabled by state file
Oct 27 19:34:07 bugger NetworkManager[979]: <info> WiMAX enabled by radio killswitch; enabled by state file
Oct 27 19:34:07 bugger NetworkManager[979]: <info> Networking is enabled by state file
Oct 27 19:34:07 bugger NetworkManager[979]: <warn> failed to allocate link cache: (-10) Operation not supported
Oct 27 19:34:07 bugger NetworkManager[979]: <info> (eth0): carrier is OFF
Oct 27 19:34:07 bugger NetworkManager[979]: <info> (eth0): new Ethernet device (driver: 'r8169' ifindex: 2)
Oct 27 19:34:07 bugger NetworkManager[979]: <info> (eth0): exported as /org/freedesktop/NetworkManager/Devices/0
Oct 27 19:34:07 bugger NetworkManager[979]: <info> (eth0): device state change: unmanaged -> unavailable (reason 'managed') [10 20 2]
Oct 27 19:34:07 bugger NetworkManager[979]: <info> (eth0): bringing up device.
Oct 27 19:34:07 bugger NetworkManager[979]: <info> monitoring kernel firmware directory '/lib/firmware'.
Oct 27 19:34:07 bugger NetworkManager[979]: <info> WiFi hardware radio set enabled
Oct 27 19:34:07 bugger NetworkManager[979]: <info> WiFi enabled by radio killswitch; enabled by state file
Oct 27 19:34:07 bugger NetworkManager[979]: <info> WWAN enabled by radio killswitch; enabled by state file
Oct 27 19:34:07 bugger NetworkManager[979]: <info> WiMAX enabled by radio killswitch; enabled by state file
Oct 27 19:34:07 bugger NetworkManager[979]: <info> Networking is enabled by state file
Oct 27 19:34:07 bugger NetworkManager[979]: <warn> failed to allocate link cache: (-10) Operation not supported
Oct 27 19:34:07 bugger NetworkManager[979]: <info> (eth0): carrier is OFF
Oct 27 19:34:07 bugger NetworkManager[979]: <info> (eth0): new Ethernet device (driver: 'r8169' ifindex: 2)
Oct 27 19:34:07 bugger NetworkManager[979]: <info> (eth0): exported as /org/freedesktop/NetworkManager/Devices/0
Oct 27 19:34:07 bugger NetworkManager[979]: <info> (eth0): device state change: unmanaged -> unavailable (reason 'managed') [10 20 2]
Oct 27 19:34:07 bugger NetworkManager[979]: <info> (eth0): bringing up device.
...
Oct 27 19:34:08 bugger ntpdate[1265]: Can't find host ntp.ubuntu.com: System error (-11)
Oct 27 19:34:08 bugger ntpdate[1265]: no servers can be used, exiting
Oct 27 19:34:08 bugger mdm[1277]: WARNING: Plymouth is running, asking it to stop...
Oct 27 19:34:08 bugger mdm[1277]: WARNING: Plymouth stopped
Oct 27 19:34:08 bugger acpid: client connected from 1335[0:0]
Oct 27 19:34:08 bugger acpid: 1 client rule loaded
Oct 27 19:34:08 bugger kernel: [   84.925348] input: HDA NVidia HDMI/DP,pcm=9 as /devices/pci0000:00/0000:00:0b.0/0000:03:00.1/sound/card1/input10
Oct 27 19:34:08 bugger kernel: [   84.925422] input: HDA NVidia HDMI/DP,pcm=8 as /devices/pci0000:00/0000:00:0b.0/0000:03:00.1/sound/card1/input11
Oct 27 19:34:08 bugger kernel: [   84.925480] input: HDA NVidia HDMI/DP,pcm=7 as /devices/pci0000:00/0000:00:0b.0/0000:03:00.1/sound/card1/input12
Oct 27 19:34:08 bugger kernel: [   84.925540] input: HDA NVidia HDMI/DP,pcm=3 as /devices/pci0000:00/0000:00:0b.0/0000:03:00.1/sound/card1/input13
Oct 27 19:34:08 bugger mdm[1277]: WARNING: failed to get file info for accountService pic file: Error when getting information for file '/var/lib/AccountsService/icons/axiopisty': No such file or directory
Oct 27 19:34:08 bugger mdm[1277]: WARNING: failed to get file info for accountService pic file: Error when getting information for file '/home/axiopisty/.face': No such file or directory
Oct 27 19:34:08 bugger mdm[1277]: GLib-GIO-CRITICAL: g_file_info_get_attribute_uint64: assertion `G_IS_FILE_INFO (info)' failed
Oct 27 19:34:08 bugger mdm[1277]: GLib-GIO-CRITICAL: g_file_info_get_attribute_uint64: assertion `G_IS_FILE_INFO (info)' failed
...
Oct 27 19:34:10 bugger NetworkManager[979]: <warn> dnsmasq not available on the bus, can't update servers.
Oct 27 19:34:10 bugger NetworkManager[979]: <error> [1382924050.590066] [nm-dns-dnsmasq.c:402] update(): dnsmasq owner not found on bus: Could not get owner of name 'org.freedesktop.NetworkManager.dnsmasq': no such name
Oct 27 19:34:10 bugger NetworkManager[979]: <warn> DNS: plugin dnsmasq update failed
Oct 27 19:34:10 bugger NetworkManager[979]: <info> Writing DNS information to /sbin/resolvconf
...
Oct 27 19:34:19 bugger kernel: [   99.525358] usb 7-2: device descriptor read/64, error -110
Oct 27 19:34:26 bugger NetworkManager[979]: <info> (eth0): IP6 addrconf timed out or failed.
Oct 27 19:34:26 bugger NetworkManager[979]: <info> Activation (eth0) Stage 4 of 5 (IPv6 Configure Timeout) scheduled...
Oct 27 19:34:26 bugger NetworkManager[979]: <info> Activation (eth0) Stage 4 of 5 (IPv6 Configure Timeout) started...
Oct 27 19:34:26 bugger NetworkManager[979]: <info> Activation (eth0) Stage 4 of 5 (IPv6 Configure Timeout) complete.
Oct 27 19:34:35 bugger kernel: [  114.715442] usb 7-2: device descriptor read/64, error -110
Oct 27 19:34:35 bugger kernel: [  114.954663] usb 7-2: new full-speed USB device number 3 using ohci_hcd
Oct 27 19:34:50 bugger kernel: [  130.041088] usb 7-2: device descriptor read/64, error -110
Oct 27 19:35:05 bugger kernel: [  145.231222] usb 7-2: device descriptor read/64, error -110
Oct 27 19:35:06 bugger kernel: [  145.470436] usb 7-2: new full-speed USB device number 4 using ohci_hcd
Oct 27 19:35:16 bugger kernel: [  155.844341] usb 7-2: device not accepting address 4, error -110
Oct 27 19:35:16 bugger kernel: [  155.979888] usb 7-2: new full-speed USB device number 5 using ohci_hcd
Oct 27 19:35:27 bugger kernel: [  166.353805] usb 7-2: device not accepting address 5, error -110
Oct 27 19:35:27 bugger kernel: [  166.353824] hub 7-0:1.0: unable to enumerate USB device on port 2
Oct 27 19:35:27 bugger kernel: [  166.553694] usb 5-3.1: new low-speed USB device number 3 using ohci_hcd
Oct 27 19:35:27 bugger kernel: [  166.728143] usb 5-3.1: New USB device found, idVendor=045e, idProduct=00db
Oct 27 19:35:27 bugger kernel: [  166.728150] usb 5-3.1: New USB device strings: Mfr=1, Product=2, SerialNumber=0
Oct 27 19:35:27 bugger kernel: [  166.728156] usb 5-3.1: Product: Natural® Ergonomic Key
Oct 27 19:35:27 bugger kernel: [  166.728160] usb 5-3.1: Manufacturer: Microsoft
Oct 27 19:35:27 bugger mtp-probe: checking bus 5, device 3: "/sys/devices/pci0000:00/0000:00:13.0/usb5/5-3/5-3.1"
Oct 27 19:35:27 bugger mtp-probe: bus: 5, device: 3 was not an MTP device
Oct 27 19:35:27 bugger kernel: [  166.824938] usbcore: registered new interface driver usbhid
Oct 27 19:35:27 bugger kernel: [  166.824943] usbhid: USB HID core driver
...
Oct 27 21:19:55 bugger xscreensaver: pam_ecryptfs: seteuid error
...
Oct 28 08:44:31 bugger xscreensaver: pam_ecryptfs: seteuid error
...
Oct 28 15:47:38 bugger kernel: [72659.857778] nspluginwrapper[15024]: segfault at 7f856cdf91aa ip 00007f85730d97d6 sp 00007fff8719d3c8 error 4 in libc-2.17.so[7f8572fa0000+1bf000]
...
Oct 28 16:10:05 bugger NetworkManager[979]: <error> [1382998205.711047] [nm-system.c:145] nm_system_device_set_ip4_route(): (tun0): failed to set IPv4 route: Object exists
Oct 28 16:10:05 bugger NetworkManager[979]: <error> [1382998205.711229] [nm-system.c:145] nm_system_device_set_ip4_route(): (tun0): failed to set IPv4 route: Object exists
Oct 28 16:10:05 bugger NetworkManager[979]: <error> [1382998205.711388] [nm-system.c:145] nm_system_device_set_ip4_route(): (tun0): failed to set IPv4 route: Object exists
...
Oct 28 18:32:30 bugger NetworkManager[979]: <warn> DNS: plugin dnsmasq update failed
...
Oct 28 18:32:50 bugger NetworkManager[979]: <info> (eth0): IP6 addrconf timed out or failed.

To be clear, the LAN is hit and miss. Sometimes it works (with manual configuration, not with auto DHCP) after starting the computer, and sometimes it does not. The USB devices will work, after waiting about 2 minutes after the login screen apears. But if both the USB devices and the LAN are working after a system boot, then they seem to work fine... until the next time the system boots up again. Its just hit and miss.

Question

As can be seen from the log file, I'm still having problems with the USB and LAN devices. How can I fix these problems? Maybe some other BIOS settings, other drivers, or maybe submit a bug somewhere?

Thanks.

EDIT

I used a stopwatch to know the boot/mouse ready times.

Boot  time: 1:53.50
Mouse time: 1:22.16
Total time: 3:15.66

This means from the time I pressed the power on button to the time I got a login screen it took 1:53. Then it took an additional 1:22 before the mouse and keyboard were operational (with "ohci_hcd" usb 1.0 support rather that "ehci-pci" usb 2.0 support). The total time before I could log into the machine was 3:15.

Is 1:53 a normal amount of time for the OS to boot given the specified hardware?

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1 Answer 1

Try turning off IOMMU support in the BIOS. I have the same system and I'm just starting to set it up. With IOMMU enabled, I see the same IO_PAGE_FAULT device:01:00.0 errors; with it disabled, those errors went away, as did related errors from xhci_hcd (USB 3.0).

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