7i77 problem

Debug file information:
Can not find -sec MOT -var MOT -num 1
Can not find -sec IO -var IO -num 1
Can not find -sec LINUXCNC -var NML_FILE -num 1
Can not find -sec EMC -var NML_FILE -num 1
insmod: error inserting '/usr/realtime-2.6.32-122-rtai/modules/linuxcnc/hm2_pci.ko': -1 No such device
test.hal:9: exit value: 1
test.hal:9: insmod failed, returned -1
See the output of 'dmesg' for more information.
2080
PID TTY STAT TIME COMMAND
Stopping realtime threads
Unloading hal components



but I looked at this directory, hm2_pci.ko is there? any advice here please?

this same configuration works perfectly on another machine with the same motherboard etc

[ 0.000337] Initializing cgroup subsys freezer
[ 0.000341] Initializing cgroup subsys net_cls
[ 0.000372] CPU: L1 I cache: 32K, L1 D cache: 24K
[ 0.000377] CPU: L2 cache: 512K
[ 0.000382] CPU: Physical Processor ID: 0
[ 0.000385] CPU: Processor Core ID: 0
[ 0.000391] mce: CPU supports 5 MCE banks
[ 0.000403] CPU0: Thermal monitoring enabled (TM1)
[ 0.000415] Performance Events: Nehalem/Corei7 events, Intel PMU driver.
[ 0.000431] ... version: 3
[ 0.000435] ... bit width: 40
[ 0.000439] ... generic registers: 2
[ 0.000443] ... value mask: 000000ffffffffff
[ 0.000447] ... max period: 000000007fffffff
[ 0.000451] ... fixed-purpose events: 3
[ 0.000455] ... event mask: 0000000700000003
[ 0.000463] Checking 'hlt' instruction... OK.
[ 0.014864] ACPI: Core revision 20090903
[ 0.027591] ftrace: converting mcount calls to 0f 1f 44 00 00
[ 0.027601] ftrace: allocating 21003 entries in 42 pages
[ 0.034983] Enabling APIC mode: Flat. Using 1 I/O APICs
[ 0.035389] ..TIMER: vector=0x30 apic1=0 pin1=2 apic2=-1 pin2=-1
[ 0.075039] ..MP-BIOS bug: 8254 timer not connected to IO-APIC
[ 0.075044] ...trying to set up timer (IRQ0) through the 8259A ...
[ 0.075048] ..... (found apic 0 pin 2) ...
[ 0.114713] ....... works.
[ 0.114718] CPU0: Intel(R) Atom(TM) CPU D2500 @ 1.86GHz stepping 01
[ 0.222115] Booting processor 1 APIC 0x1 ip 0x6000
[ 0.232060] Initializing CPU#1
[ 0.309718] CPU: L1 I cache: 32K, L1 D cache: 24K
[ 0.309723] CPU: L2 cache: 512K
[ 0.309727] CPU: Physical Processor ID: 0
[ 0.309730] CPU: Processor Core ID: 1
[ 0.309746] CPU1: Thermal monitoring enabled (TM1)
[ 0.309795] CPU1: Intel(R) Atom(TM) CPU D2500 @ 1.86GHz stepping 01
[ 0.309814] checking TSC synchronization [CPU#0 -> CPU#1]: passed.
[ 0.329822] Brought up 2 CPUs
[ 0.329828] Total of 2 processors activated (7467.12 BogoMIPS).
[ 0.329964] CPU0 attaching sched-domain:
[ 0.329969] domain 0: span 0-1 level CPU
[ 0.329974] groups: 0 1
[ 0.329984] CPU1 attaching sched-domain:
[ 0.329988] domain 0: span 0-1 level CPU
[ 0.329993] groups: 1 0
[ 0.330330] devtmpfs: initialized
[ 0.330989] regulator: core version 0.5
[ 0.331086] NET: Registered protocol family 16
[ 0.331311] Trying to unpack rootfs image as initramfs...
[ 0.331371] EISA bus registered
[ 0.331386] ACPI FADT declares the system doesn't support PCIe ASPM, so disable it
[ 0.331391] ACPI: bus type pci registered
[ 0.331508] PCI: MCFG configuration 0: base e0000000 segment 0 buses 0 - 63
[ 0.331515] PCI: MCFG area at e0000000 reserved in E820
[ 0.331518] PCI: Using MMCONFIG for extended config space
[ 0.331523] PCI: Using configuration type 1 for base access
[ 0.333154] bio: create slab <bio-0> at 0
[ 0.334748] ACPI: EC: Look up EC in DSDT
[ 0.338157] ACPI: Executed 1 blocks of module-level executable AML code
[ 0.342316] ACPI: BIOS _OSI(Linux) query ignored
[ 0.345592] ACPI: Interpreter enabled
[ 0.345597] ACPI: (supports S0 S5)
[ 0.345620] ACPI: Using IOAPIC for interrupt routing
[ 0.359347] ACPI: No dock devices found.
[ 0.360137] _OSC invalid UUID
[ 0.360144] ACPI: PCI Root Bridge [PCI0] (0000:00)
[ 0.360278] pci 0000:00:02.0: reg 10 32bit mmio: [0x80100000-0x801fffff]
[ 0.360287] pci 0000:00:02.0: reg 14 io port: [0x20d0-0x20d7]
[ 0.360416] pci 0000:00:1b.0: reg 10 64bit mmio: [0x80300000-0x80303fff]
[ 0.360491] pci 0000:00:1b.0: PME# supported from D0 D3hot D3cold
[ 0.360499] pci 0000:00:1b.0: PME# disabled
[ 0.360611] pci 0000:00:1c.0: PME# supported from D0 D3hot D3cold
[ 0.360619] pci 0000:00:1c.0: PME# disabled
[ 0.360699] pci 0000:00:1d.0: reg 20 io port: [0x20a0-0x20bf]
[ 0.360780] pci 0000:00:1d.1: reg 20 io port: [0x2080-0x209f]
[ 0.360870] pci 0000:00:1d.2: reg 20 io port: [0x2060-0x207f]
[ 0.360960] pci 0000:00:1d.3: reg 20 io port: [0x2040-0x205f]
[ 0.361047] pci 0000:00:1d.7: reg 10 32bit mmio: [0x80204400-0x802047ff]
[ 0.361127] pci 0000:00:1d.7: PME# supported from D0 D3hot D3cold
[ 0.361135] pci 0000:00:1d.7: PME# disabled
[ 0.361410] pci 0000:00:1f.2: reg 10 io port: [0x20c8-0x20cf]
[ 0.361421] pci 0000:00:1f.2: reg 14 io port: [0x20dc-0x20df]
[ 0.361434] pci 0000:00:1f.2: reg 18 io port: [0x20c0-0x20c7]
[ 0.361446] pci 0000:00:1f.2: reg 1c io port: [0x20d8-0x20db]
[ 0.361457] pci 0000:00:1f.2: reg 20 io port: [0x2020-0x202f]
[ 0.361469] pci 0000:00:1f.2: reg 24 32bit mmio: [0x80204000-0x802043ff]
[ 0.361511] pci 0000:00:1f.2: PME# supported from D3hot
[ 0.361518] pci 0000:00:1f.2: PME# disabled
[ 0.361597] pci 0000:00:1f.3: reg 20 io port: [0x2000-0x201f]
[ 0.361737] pci 0000:01:00.0: reg 10 32bit mmio: [0x80020000-0x8003ffff]
[ 0.361754] pci 0000:01:00.0: reg 14 32bit mmio: [0x80000000-0x8001ffff]
[ 0.361771] pci 0000:01:00.0: reg 18 io port: [0x1000-0x101f]
[ 0.361789] pci 0000:01:00.0: reg 1c 32bit mmio: [0x80040000-0x80043fff]
[ 0.361901] pci 0000:01:00.0: PME# supported from D0 D3hot D3cold
[ 0.361912] pci 0000:01:00.0: PME# disabled
[ 0.362008] pci 0000:00:1c.0: bridge io port: [0x1000-0x1fff]
[ 0.362016] pci 0000:00:1c.0: bridge 32bit mmio: [0x80000000-0x800fffff]
[ 0.362097] pci 0000:00:1e.0: transparent bridge
[ 0.362131] pci_bus 0000:00: on NUMA node 0
[ 0.362142] ACPI: PCI Interrupt Routing Table [\_SB_.PCI0._PRT]
[ 0.362339] ACPI: PCI Interrupt Routing Table [\_SB_.PCI0.P0P1._PRT]
[ 0.362682] ACPI: PCI Interrupt Routing Table [\_SB_.PCI0.RP01._PRT]
[ 0.362988] _OSC invalid UUID
[ 0.373756] ACPI: PCI Interrupt Link [LNKA] (IRQs 1 3 4 5 6 7 10 12 14 15) *11
[ 0.373962] ACPI: PCI Interrupt Link [LNKB] (IRQs 1 3 4 5 6 7 11 12 14 15) *0, disabled.
[ 0.374166] ACPI: PCI Interrupt Link [LNKC] (IRQs 1 3 4 5 6 7 10 12 14 15) *9
[ 0.374368] ACPI: PCI Interrupt Link [LNKD] (IRQs 1 3 4 5 6 7 *11 12 14 15)
[ 0.374563] ACPI: PCI Interrupt Link [LNKE] (IRQs 1 3 4 5 6 7 10 12 14 15) *0, disabled.
[ 0.374762] ACPI: PCI Interrupt Link [LNKF] (IRQs 1 3 4 5 6 7 11 12 14 15) *0, disabled.
[ 0.374964] ACPI: PCI Interrupt Link [LNKG] (IRQs 1 3 4 5 6 7 10 12 14 15) *9
[ 0.375163] ACPI: PCI Interrupt Link [LNKH] (IRQs 1 3 4 5 6 7 11 12 14 15) *10
[ 0.375386] vgaarb: device added: PCI:0000:00:02.0,decodes=io+mem,owns=io+mem,locks=none
[ 0.375402] vgaarb: loaded
[ 0.375645] SCSI subsystem initialized
[ 0.375827] libata version 3.00 loaded.
[ 0.376009] usbcore: registered new interface driver usbfs
[ 0.376035] usbcore: registered new interface driver hub
[ 0.376101] usbcore: registered new device driver usb
[ 0.376388] ACPI: WMI: Mapper loaded
[ 0.376393] PCI: Using ACPI for IRQ routing
[ 0.376659] NetLabel: Initializing
[ 0.376664] NetLabel: domain hash size = 128
[ 0.376667] NetLabel: protocols = UNLABELED CIPSOv4
[ 0.376690] NetLabel: unlabeled traffic allowed by default
[ 0.376761] Switching to clocksource tsc
[ 0.380177] AppArmor: AppArmor Filesystem Enabled
[ 0.380201] pnp: PnP ACPI init
[ 0.380230] ACPI: bus type pnp registered
[ 0.382937] pnp 00:09: IRQ 4 override to edge, high
[ 0.383507] pnp 00:0a: IRQ 3 override to edge, high
[ 0.384701] pnp: PnP ACPI: found 12 devices
[ 0.384706] ACPI: ACPI bus type pnp unregistered
[ 0.384713] PnPBIOS: Disabled by ACPI PNP
[ 0.384736] system 00:03: iomem range 0xfed00000-0xfed003ff has been reserved
[ 0.384750] system 00:05: ioport range 0x680-0x69f has been reserved
[ 0.384757] system 00:05: ioport range 0xffff-0xffff has been reserved
[ 0.384763] system 00:05: ioport range 0xffff-0xffff has been reserved
[ 0.384769] system 00:05: ioport range 0xffff-0xffff has been reserved
[ 0.384776] system 00:05: ioport range 0x400-0x47f has been reserved
[ 0.384782] system 00:05: ioport range 0x500-0x57f has been reserved
[ 0.384788] system 00:05: ioport range 0x600-0x61f has been reserved
[ 0.384799] system 00:06: ioport range 0x6a0-0x6af has been reserved
[ 0.384805] system 00:06: ioport range 0x6b0-0x6ff has been reserved
[ 0.384818] system 00:0b: iomem range 0xfed1c000-0xfed1ffff has been reserved
[ 0.384825] system 00:0b: iomem range 0x0-0x3fff could not be reserved
[ 0.384831] system 00:0b: iomem range 0x0-0xfff could not be reserved
[ 0.384838] system 00:0b: iomem range 0x0-0xfff could not be reserved
[ 0.384844] system 00:0b: iomem range 0xfed45000-0xfed8ffff has been reserved
[ 0.421056] pci 0000:00:1c.0: PCI bridge, secondary bus 0000:01
[ 0.421064] pci 0000:00:1c.0: IO window: 0x1000-0x1fff
[ 0.421074] pci 0000:00:1c.0: MEM window: 0x80000000-0x800fffff
[ 0.421084] pci 0000:00:1c.0: PREFETCH window: 0x00000080400000-0x000000805fffff
[ 0.421096] pci 0000:00:1e.0: PCI bridge, secondary bus 0000:02
[ 0.421100] pci 0000:00:1e.0: IO window: disabled
[ 0.421108] pci 0000:00:1e.0: MEM window: disabled
[ 0.421116] pci 0000:00:1e.0: PREFETCH window: disabled
[ 0.421141] alloc irq_desc for 16 on node -1
[ 0.421147] alloc kstat_irqs on node -1
[ 0.421158] pci 0000:00:1c.0: PCI INT A -> GSI 16 (level, low) -> IRQ 16
[ 0.421168] pci 0000:00:1c.0: setting latency timer to 64
[ 0.421183] pci 0000:00:1e.0: setting latency timer to 64
[ 0.421192] pci_bus 0000:00: resource 0 io: [0x00-0xffff]
[ 0.421197] pci_bus 0000:00: resource 1 mem: [0x000000-0xffffffff]
[ 0.421203] pci_bus 0000:01: resource 0 io: [0x1000-0x1fff]
[ 0.421208] pci_bus 0000:01: resource 1 mem: [0x80000000-0x800fffff]
[ 0.421214] pci_bus 0000:01: resource 2 pref mem [0x80400000-0x805fffff]
[ 0.421220] pci_bus 0000:02: resource 3 io: [0x00-0xffff]
[ 0.421225] pci_bus 0000:02: resource 4 mem: [0x000000-0xffffffff]
[ 0.421291] NET: Registered protocol family 2
[ 0.421470] IP route cache hash table entries: 32768 (order: 5, 131072 bytes)
[ 0.422054] TCP established hash table entries: 131072 (order: 8, 1048576 bytes)
[ 0.422918] TCP bind hash table entries: 65536 (order: 7, 524288 bytes)
[ 0.423329] TCP: Hash tables configured (established 131072 bind 65536)
[ 0.423336] TCP reno registered
[ 0.423530] NET: Registered protocol family 1
[ 0.423572] pci 0000:00:02.0: Boot video device
[ 0.438057] Scanning for low memory corruption every 60 seconds
[ 0.438239] audit: initializing netlink socket (disabled)
[ 0.438261] type=2000 audit(1367583721.284:1): initialized
[ 0.450938] highmem bounce pool size: 64 pages
[ 0.450949] HugeTLB registered 4 MB page size, pre-allocated 0 pages
[ 0.454011] VFS: Disk quotas dquot_6.5.2
[ 0.454130] Dquot-cache hash table entries: 1024 (order 0, 4096 bytes)
[ 0.455331] fuse init (API version 7.13)
[ 0.455506] msgmni has been set to 1680
[ 0.455942] alg: No test for stdrng (krng)
[ 0.456066] Block layer SCSI generic (bsg) driver version 0.4 loaded (major 253)
[ 0.456073] io scheduler noop registered
[ 0.456077] io scheduler anticipatory registered
[ 0.456081] io scheduler deadline registered
[ 0.456171] io scheduler cfq registered (default)
[ 0.456391] alloc irq_desc for 24 on node -1
[ 0.456396] alloc kstat_irqs on node -1
[ 0.456415] pcieport 0000:00:1c.0: irq 24 for MSI/MSI-X
[ 0.456429] pcieport 0000:00:1c.0: setting latency timer to 64
[ 0.456590] pci_hotplug: PCI Hot Plug PCI Core version: 0.5
[ 0.456795] _OSC invalid UUID
[ 0.457004] _OSC invalid UUID
[ 0.457040] pciehp: PCI Express Hot Plug Controller Driver version: 0.4
[ 0.457207] input: Power Button as /devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0C:00/input/input0
[ 0.457221] ACPI: Power Button [PWRB]
[ 0.457308] input: Sleep Button as /devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0E:00/input/input1
[ 0.457315] ACPI: Sleep Button [SLPB]
[ 0.457401] input: Power Button as /devices/LNXSYSTM:00/LNXPWRBN:00/input/input2
[ 0.457407] ACPI: Power Button [PWRF]
[ 0.460520] hpet_acpi_add: no address or irqs in _CRS
[ 0.460629] Serial: 8250/16550 driver, 4 ports, IRQ sharing enabled
[ 0.460773] serial8250: ttyS0 at I/O 0x3f8 (irq = 4) is a 16550A
[ 0.460931] serial8250: ttyS1 at I/O 0x2f8 (irq = 3) is a 16550A
[ 0.461446] 00:09: ttyS0 at I/O 0x3f8 (irq = 4) is a 16550A
[ 0.461691] 00:0a: ttyS1 at I/O 0x2f8 (irq = 3) is a 16550A
[ 0.463751] brd: module loaded
[ 0.464734] loop: module loaded
[ 0.464914] input: Macintosh mouse button emulation as /devices/virtual/input/input3
[ 0.465813] Fixed MDIO Bus: probed
[ 0.465884] PPP generic driver version 2.4.2
[ 0.465959] tun: Universal TUN/TAP device driver, 1.6
[ 0.465963] tun: (C) 1999-2004 Max Krasnyansky <This email address is being protected from spambots. You need JavaScript enabled to view it.>
[ 0.466075] isapnp: Scanning for PnP cards...
[ 0.466134] ehci_hcd: USB 2.0 'Enhanced' Host Controller (EHCI) Driver
[ 0.466179] alloc irq_desc for 23 on node -1
[ 0.466184] alloc kstat_irqs on node -1
[ 0.466196] ehci_hcd 0000:00:1d.7: PCI INT A -> GSI 23 (level, low) -> IRQ 23
[ 0.466223] ehci_hcd 0000:00:1d.7: setting latency timer to 64
[ 0.466230] ehci_hcd 0000:00:1d.7: EHCI Host Controller
[ 0.466300] ehci_hcd 0000:00:1d.7: new USB bus registered, assigned bus number 1
[ 0.466336] ehci_hcd 0000:00:1d.7: using broken periodic workaround
[ 0.466353] ehci_hcd 0000:00:1d.7: debug port 1
[ 0.470251] ehci_hcd 0000:00:1d.7: cache line size of 32 is not supported
[ 0.470279] ehci_hcd 0000:00:1d.7: irq 23, io mem 0x80204400
[ 0.517682] ehci_hcd 0000:00:1d.7: USB 2.0 started, EHCI 1.00
[ 0.517875] usb usb1: configuration #1 chosen from 1 choice
[ 0.517931] hub 1-0:1.0: USB hub found
[ 0.517947] hub 1-0:1.0: 8 ports detected
[ 0.518068] ohci_hcd: USB 1.1 'Open' Host Controller (OHCI) Driver
[ 0.518096] uhci_hcd: USB Universal Host Controller Interface driver
[ 0.518149] uhci_hcd 0000:00:1d.0: PCI INT A -> GSI 23 (level, low) -> IRQ 23
[ 0.518161] uhci_hcd 0000:00:1d.0: setting latency timer to 64
[ 0.518168] uhci_hcd 0000:00:1d.0: UHCI Host Controller
[ 0.518237] uhci_hcd 0000:00:1d.0: new USB bus registered, assigned bus number 2
[ 0.518276] uhci_hcd 0000:00:1d.0: irq 23, io base 0x000020a0
[ 0.518455] usb usb2: configuration #1 chosen from 1 choice
[ 0.518509] hub 2-0:1.0: USB hub found
[ 0.518522] hub 2-0:1.0: 2 ports detected
[ 0.518605] alloc irq_desc for 19 on node -1
[ 0.518610] alloc kstat_irqs on node -1
[ 0.518620] uhci_hcd 0000:00:1d.1: PCI INT B -> GSI 19 (level, low) -> IRQ 19
[ 0.518632] uhci_hcd 0000:00:1d.1: setting latency timer to 64
[ 0.518639] uhci_hcd 0000:00:1d.1: UHCI Host Controller
[ 0.518716] uhci_hcd 0000:00:1d.1: new USB bus registered, assigned bus number 3
[ 0.518766] uhci_hcd 0000:00:1d.1: irq 19, io base 0x00002080
[ 0.518946] usb usb3: configuration #1 chosen from 1 choice
[ 0.519000] hub 3-0:1.0: USB hub found
[ 0.519015] hub 3-0:1.0: 2 ports detected
[ 0.519099] alloc irq_desc for 18 on node -1
[ 0.519104] alloc kstat_irqs on node -1
[ 0.519113] uhci_hcd 0000:00:1d.2: PCI INT C -> GSI 18 (level, low) -> IRQ 18
[ 0.519123] uhci_hcd 0000:00:1d.2: setting latency timer to 64
[ 0.519129] uhci_hcd 0000:00:1d.2: UHCI Host Controller
[ 0.519195] uhci_hcd 0000:00:1d.2: new USB bus registered, assigned bus number 4
[ 0.519240] uhci_hcd 0000:00:1d.2: irq 18, io base 0x00002060
[ 0.519423] usb usb4: configuration #1 chosen from 1 choice
[ 0.519476] hub 4-0:1.0: USB hub found
[ 0.519491] hub 4-0:1.0: 2 ports detected
[ 0.519576] uhci_hcd 0000:00:1d.3: PCI INT D -> GSI 16 (level, low) -> IRQ 16
[ 0.519587] uhci_hcd 0000:00:1d.3: setting latency timer to 64
[ 0.519593] uhci_hcd 0000:00:1d.3: UHCI Host Controller
[ 0.519661] uhci_hcd 0000:00:1d.3: new USB bus registered, assigned bus number 5
[ 0.519709] uhci_hcd 0000:00:1d.3: irq 16, io base 0x00002040
[ 0.519890] usb usb5: configuration #1 chosen from 1 choice
[ 0.519943] hub 5-0:1.0: USB hub found
[ 0.519957] hub 5-0:1.0: 2 ports detected
[ 0.520134] PNP: No PS/2 controller found. Probing ports directly.
[ 0.521998] serio: i8042 KBD port at 0x60,0x64 irq 1
[ 0.522015] serio: i8042 AUX port at 0x60,0x64 irq 12
[ 0.522269] mice: PS/2 mouse device common for all mice
[ 0.522529] rtc_cmos 00:07: RTC can wake from S4
[ 0.522601] rtc_cmos 00:07: rtc core: registered rtc_cmos as rtc0
[ 0.522640] rtc0: alarms up to one month, y3k, 242 bytes nvram
[ 0.522856] device-mapper: uevent: version 1.0.3
[ 0.523070] device-mapper: ioctl: 4.15.0-ioctl (2009-04-01) initialised: This email address is being protected from spambots. You need JavaScript enabled to view it.
[ 0.523212] device-mapper: multipath: version 1.1.0 loaded
[ 0.523218] device-mapper: multipath round-robin: version 1.0.0 loaded
[ 0.523456] EISA: Probing bus 0 at eisa.0
[ 0.523466] Cannot allocate resource for EISA slot 1
[ 0.523471] Cannot allocate resource for EISA slot 2
[ 0.523501] EISA: Detected 0 cards.
[ 0.523506] cpuidle: using governor ladder
[ 0.523512] cpuidle: using governor menu
[ 0.524322] TCP cubic registered
[ 0.524642] NET: Registered protocol family 10
[ 0.525447] lo: Disabled Privacy Extensions
[ 0.526046] NET: Registered protocol family 17
[ 0.526102] Using IPI No-Shortcut mode
[ 0.526292] registered taskstats version 1
[ 0.526746] rtc_cmos 00:07: setting system clock to 2013-05-03 12:22:02 UTC (1367583722)
[ 0.526752] BIOS EDD facility v0.16 2004-Jun-25, 0 devices found
[ 0.526756] EDD information not available.
[ 0.831803] isapnp: No Plug & Play device found
[ 0.852208] Freeing initrd memory: 12833k freed
[ 0.862675] Freeing unused kernel memory: 620k freed
[ 0.863105] Write protecting the kernel text: 4540k
[ 0.863152] Write protecting the kernel read-only data: 1668k
[ 0.899583] udev: starting version 151
[ 1.044711] vga16fb: initializing
[ 1.044720] vga16fb: mapped to 0xc00a0000
[ 1.044821] fb0: VGA16 VGA frame buffer device
[ 1.066653] ahci 0000:00:1f.2: version 3.0
[ 1.066685] ahci 0000:00:1f.2: PCI INT B -> GSI 19 (level, low) -> IRQ 19
[ 1.066759] alloc irq_desc for 25 on node -1
[ 1.066765] alloc kstat_irqs on node -1
[ 1.066784] ahci 0000:00:1f.2: irq 25 for MSI/MSI-X
[ 1.066849] ahci: SSS flag set, parallel bus scan disabled
[ 1.066899] ahci 0000:00:1f.2: AHCI 0001.0100 32 slots 4 ports 3 Gbps 0x3 impl SATA mode
[ 1.066907] ahci 0000:00:1f.2: flags: 64bit ncq stag pm led clo pio slum part
[ 1.066915] ahci 0000:00:1f.2: setting latency timer to 64
[ 1.081081] usb 4-2: new low speed USB device using uhci_hcd and address 2
[ 1.090747] e1000e: Intel(R) PRO/1000 Network Driver - 1.0.2-k2
[ 1.090755] e1000e: Copyright (c) 1999-2008 Intel Corporation.
[ 1.090847] e1000e 0000:01:00.0: PCI INT A -> GSI 16 (level, low) -> IRQ 16
[ 1.090894] e1000e 0000:01:00.0: setting latency timer to 64
[ 1.091147] alloc irq_desc for 26 on node -1
[ 1.091152] alloc kstat_irqs on node -1
[ 1.091163] e1000e 0000:01:00.0: irq 26 for MSI/MSI-X
[ 1.091167] alloc irq_desc for 27 on node -1
[ 1.091171] alloc kstat_irqs on node -1
[ 1.091178] e1000e 0000:01:00.0: irq 27 for MSI/MSI-X
[ 1.091182] alloc irq_desc for 28 on node -1
[ 1.091186] alloc kstat_irqs on node -1
[ 1.091192] e1000e 0000:01:00.0: irq 28 for MSI/MSI-X
[ 1.095567] scsi0 : ahci
[ 1.110878] scsi1 : ahci
[ 1.129321] scsi2 : ahci
[ 1.141057] scsi3 : ahci
[ 1.141208] ata1: SATA max UDMA/133 abar m1024@0x80204000 port 0x80204100 irq 25
[ 1.141215] ata2: SATA max UDMA/133 abar m1024@0x80204000 port 0x80204180 irq 25
[ 1.141220] ata3: DUMMY
[ 1.141224] ata4: DUMMY
[ 1.207247] 0000:01:00.0: eth0: (PCI Express:2.5GB/s:Width x1) 00:22:4d:a0:6d:7c
[ 1.207254] 0000:01:00.0: eth0: Intel(R) PRO/1000 Network Connection
[ 1.207272] 0000:01:00.0: eth0: MAC: 3, PHY: 8, PBA No: ffffff-0ff
[ 1.259728] usb 4-2: configuration #1 chosen from 1 choice
[ 1.295932] usbcore: registered new interface driver hiddev
[ 1.309962] input: CHESEN PS2 to USB Converter as /devices/pci0000:00/0000:00:1d.2/usb4/4-2/4-2:1.0/input/input4
[ 1.310141] generic-usb 0003:0A81:0205.0001: input,hidraw0: USB HID v1.10 Keyboard [CHESEN PS2 to USB Converter] on usb-0000:00:1d.2-2/input0
[ 1.338062] input: CHESEN PS2 to USB Converter as /devices/pci0000:00/0000:00:1d.2/usb4/4-2/4-2:1.1/input/input5
[ 1.338274] generic-usb 0003:0A81:0205.0002: input,hidraw1: USB HID v1.10 Mouse [CHESEN PS2 to USB Converter] on usb-0000:00:1d.2-2/input1
[ 1.338318] usbcore: registered new interface driver usbhid
[ 1.338324] usbhid: v2.6:USB HID core driver
[ 1.463894] ata1: SATA link up 3.0 Gbps (SStatus 123 SControl 300)
[ 1.464150] ata1.00: ATA-8: InnoLite II 2.5 SATA SSD, 120319, max UDMA/133
[ 1.464157] ata1.00: 62533296 sectors, multi 16: LBA48 NCQ (depth 31/32), AA
[ 1.464525] ata1.00: configured for UDMA/133
[ 1.480057] scsi 0:0:0:0: Direct-Access ATA InnoLite II 2.5 1203 PQ: 0 ANSI: 5
[ 1.480360] sd 0:0:0:0: Attached scsi generic sg0 type 0
[ 1.480647] sd 0:0:0:0: [sda] 62533296 512-byte logical blocks: (32.0 GB/29.8 GiB)
[ 1.480769] sd 0:0:0:0: [sda] Write Protect is off
[ 1.480776] sd 0:0:0:0: [sda] Mode Sense: 00 3a 00 00
[ 1.480838] sd 0:0:0:0: [sda] Write cache: enabled, read cache: enabled, doesn't support DPO or FUA
[ 1.481176] sda: sda1 sda2 < sda5 >
[ 1.482373] sd 0:0:0:0: [sda] Attached SCSI disk
[ 1.799539] ata2: SATA link down (SStatus 0 SControl 300)
[ 1.917023] Console: switching to colour frame buffer device 80x30
[ 2.314719] xor: automatically using best checksumming function: pIII_sse
[ 2.330953] pIII_sse : 5751.000 MB/sec
[ 2.330959] xor: using function: pIII_sse (5751.000 MB/sec)
[ 2.336931] device-mapper: dm-raid45: initialized v0.2594b
[ 2.393476] EXT4-fs (sda1): mounted filesystem with ordered data mode
[ 2.911847] Adding 1332216k swap on /dev/sda5. Priority:-1 extents:1 across:1332216k SS
[ 2.932059] udev: starting version 151
[ 3.344991] lp: driver loaded but no devices found
[ 3.479953] parport_pc 00:08: reported by Plug and Play ACPI
[ 3.480033] parport0: PC-style at 0x378, irq 7 [PCSPP,TRISTATE]
[ 3.529416] ppdev: user-space parallel port driver
[ 3.577990] lp0: using parport0 (interrupt-driven).
[ 3.715727] type=1505 audit(1367583725.690:2): operation="profile_load" pid=623 name="/sbin/dhclient3"
[ 3.716223] type=1505 audit(1367583725.690:3): operation="profile_load" pid=623 name="/usr/lib/NetworkManager/nm-dhcp-client.action"
[ 3.716441] type=1505 audit(1367583725.690:4): operation="profile_replace" pid=638 name="/sbin/dhclient3"
[ 3.716516] type=1505 audit(1367583725.690:5): operation="profile_load" pid=623 name="/usr/lib/connman/scripts/dhclient-script"
[ 3.716987] type=1505 audit(1367583725.690:6): operation="profile_replace" pid=638 name="/usr/lib/NetworkManager/nm-dhcp-client.action"
[ 3.717296] type=1505 audit(1367583725.690:7): operation="profile_replace" pid=638 name="/usr/lib/connman/scripts/dhclient-script"
[ 3.814786] alloc irq_desc for 22 on node -1
[ 3.814792] alloc kstat_irqs on node -1
[ 3.814805] HDA Intel 0000:00:1b.0: PCI INT A -> GSI 22 (level, low) -> IRQ 22
[ 3.814871] HDA Intel 0000:00:1b.0: setting latency timer to 64
[ 3.928030] hda_codec: ALC662 rev1: BIOS auto-probing.
[ 3.930040] input: HDA Digital PCBeep as /devices/pci0000:00/0000:00:1b.0/input/input6
[ 4.077802] type=1505 audit(1367583726.054:8): operation="profile_replace" pid=770 name="/sbin/dhclient3"
[ 4.078316] type=1505 audit(1367583726.054:9): operation="profile_replace" pid=770 name="/usr/lib/NetworkManager/nm-dhcp-client.action"
[ 4.078637] type=1505 audit(1367583726.054:10): operation="profile_replace" pid=770 name="/usr/lib/connman/scripts/dhclient-script"
[ 4.084975] ADDRCONF(NETDEV_UP): eth0: link is not ready
[ 4.621666] CPU0 attaching NULL sched-domain.
[ 4.621678] CPU1 attaching NULL sched-domain.
[ 4.652619] CPU0 attaching sched-domain:
[ 4.652625] domain 0: span 0-1 level CPU
[ 4.652631] groups: 0 1
[ 4.652641] CPU1 attaching sched-domain:
[ 4.652645] domain 0: span 0-1 level CPU
[ 4.652650] groups: 1 0
[ 7.156405] CPU0 attaching NULL sched-domain.
[ 7.156416] CPU1 attaching NULL sched-domain.
[ 7.174521] CPU0 attaching sched-domain:
[ 7.174530] domain 0: span 0-1 level CPU
[ 7.174536] groups: 0 1
[ 7.174547] CPU1 attaching sched-domain:
[ 7.174551] domain 0: span 0-1 level CPU
[ 7.174556] groups: 1 0
[ 14.548135] I-pipe: Domain RTAI registered.
[ 14.548149] RTAI[hal]: <3.8.1> mounted over IPIPE-NOTHREADS 2.6-03.
[ 14.548154] RTAI[hal]: compiled with gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5) .
[ 14.548218] RTAI[hal]: mounted (IPIPE-NOTHREADS, IMMEDIATE (INTERNAL IRQs DISPATCHED), ISOL_CPUS_MASK: 0).
[ 14.548223] PIPELINE layers:
[ 14.548228] f8331e20 9ac15d93 RTAI 200
[ 14.548233] c085cb20 0 Linux 100
[ 14.592292] RTAI[malloc]: global heap size = 2097152 bytes, <BSD>.
[ 14.598597] RTAI[sched]: IMMEDIATE, MP, USER/KERNEL SPACE: <with RTAI OWN KTASKs>, kstacks pool size = 524288 bytes.
[ 14.598609] RTAI[sched]: hard timer type/freq = APIC/8333598(Hz); default timing: periodic; linear timed lists.
[ 14.598617] RTAI[sched]: Linux timer freq = 250 (Hz), TimeBase freq = 1866666000 hz.
[ 14.598622] RTAI[sched]: timer setup = 999 ns, resched latency = 2944 ns.
[ 14.598776] RTAI[usi]: enabled.
[ 14.685118] RTAI[math]: loaded.
[ 14.813507] hm2: loading Mesa HostMot2 driver version 0.15
[ 14.819086] hm2_pci: loading Mesa AnyIO HostMot2 driver version 0.7
[ 15.382687] hm2: unloading
[ 15.447739] RTAI[math]: unloaded.
[ 15.499874] SCHED releases registered named ALIEN RTGLBH
[ 15.529580] RTAI[malloc]: unloaded.
[ 15.629107] RTAI[sched]: unloaded (forced hard/soft/hard transitions: traps 0, syscalls 0).
[ 15.633526] I-pipe: Domain RTAI unregistered.
[ 15.633628] RTAI[hal]: unmounted.
[ 459.926153] I-pipe: Domain RTAI registered.
[ 459.926166] RTAI[hal]: <3.8.1> mounted over IPIPE-NOTHREADS 2.6-03.
[ 459.926171] RTAI[hal]: compiled with gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5) .
[ 459.926266] RTAI[hal]: mounted (IPIPE-NOTHREADS, IMMEDIATE (INTERNAL IRQs DISPATCHED), ISOL_CPUS_MASK: 0).
[ 459.926271] PIPELINE layers:
[ 459.926277] f8331e20 9ac15d93 RTAI 200
[ 459.926282] c085cb20 0 Linux 100
[ 459.967936] RTAI[malloc]: global heap size = 2097152 bytes, <BSD>.
[ 459.968792] RTAI[sched]: IMMEDIATE, MP, USER/KERNEL SPACE: <with RTAI OWN KTASKs>, kstacks pool size = 524288 bytes.
[ 459.968804] RTAI[sched]: hard timer type/freq = APIC/8333598(Hz); default timing: periodic; linear timed lists.
[ 459.968811] RTAI[sched]: Linux timer freq = 250 (Hz), TimeBase freq = 1866666000 hz.
[ 459.968817] RTAI[sched]: timer setup = 999 ns, resched latency = 2944 ns.
[ 459.968932] RTAI[usi]: enabled.
[ 460.052469] RTAI[math]: loaded.
[ 460.173791] hm2: loading Mesa HostMot2 driver version 0.15
[ 460.178777] hm2_pci: loading Mesa AnyIO HostMot2 driver version 0.7
[ 460.703887] hm2: unloading
[ 460.768266] RTAI[math]: unloaded.
[ 460.803039] SCHED releases registered named ALIEN RTGLBH
[ 460.833165] RTAI[malloc]: unloaded.
[ 460.932677] RTAI[sched]: unloaded (forced hard/soft/hard transitions: traps 0, syscalls 0).
[ 460.936568] I-pipe: Domain RTAI unregistered.
[ 460.936648] RTAI[hal]: unmounted.

You might also run
sudo dmesg -c
before you start. This will clear the kernel log.
The only interesting parts are what are added to the log
by Andys command sequence.

Thank you for the help,

I later discovered that the pci riser card that i was using, was the actual problem.