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["Christopher M. Penalver" <christopher.m.penalver@xxxxxxxxx>]

MvW, thank you for your comment. So your hardware and problem may be tracked, could you please file a new report with Ubuntu by executing the following in a terminal while booted into a Ubuntu repository kernel (not a mainline one) via:
ubuntu-bug linux

For more on this, please read the official Ubuntu documentation:
Ubuntu Bug Control and Ubuntu Bug Squad: https://wiki.ubuntu.com/Bugs/BestPractices#X.2BAC8-Reporting.Focus_on_One_Issue
Ubuntu Kernel Team: https://wiki.ubuntu.com/KernelTeam/KernelTeamBugPolicies#Filing_Kernel_Bug_reports
Ubuntu Community: https://help.ubuntu.com/community/ReportingBugs#Bug_reporting_etiquette

When opening up the new report, please feel free to subscribe me to it.

Thank you for your understanding.

Helpful bug reporting tips:
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https://bugs.launchpad.net/bugs/1089768

Title:
  Marvell Sata controller and AMD-Vi problems

Status in “linux” package in Ubuntu:
  Expired

Bug description:
  This bug is to confirm that the Marvell 88SE9128 chipset bug presents
  under AMD's IOMMU implementation as well as Intel's VT-D. I've tested
  this with a Syba SD-PEX40035 and a Highpoint Rocket 620 (both use the
  same Marvell chipset) PCIe card, under both the stock Quantal kernel
  and the 3.7.0rc8 kernel from the mainline kernel PPA. It sounds like
  the preferred solution is PCI quirk, and some of the infrastructure is
  in place, but it hasn't been implemented yet. Symptoms consist of a
  much longer boot process, and failure to identify any devices attached
  to the Marvell controllers.

  WORKAROUND: Works fine as long as I disable the IOMMU in the BIOS.

  My system consists of an AMD A10-5800K in a Gigabyte GA-F2A85X-D3H
  motherboard, 5x Seagate 1.5 TB drives in software Raid5, 4x Seagate 3
  TB drives in a native ZFS raidz (not yet used), a Sata BD-ROM, and a
  500 GB sata drive (not yet used).

  https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1005226
  http://lists.linuxfoundation.org/pipermail/iommu/2012-September/004551.html
  https://bugzilla.kernel.org/show_bug.cgi?id=42679
  https://bugzilla.redhat.com/show_bug.cgi?id=757166

  pci 02:00.1 is the IDE endpoint, but there are no PATA devices in the
  system, which matches the behavior of the other chips (emitting DMA
  operations from the wrong PCI endpoint, which the IOMMU rejects.)

  ##########################################################
  02:00.1 IDE interface: Marvell Technology Group Ltd. 88SE9128 IDE Controller (rev 11) (prog-if 8f [Master SecP SecO PriP PriO])
          Subsystem: Marvell Technology Group Ltd. 88SE9128 IDE Controller
          Flags: bus master, fast devsel, latency 0, IRQ 18
          I/O ports at d040 [size=8]
          I/O ports at d030 [size=4]
          I/O ports at d020 [size=8]
          I/O ports at d010 [size=4]
          I/O ports at d000 [size=16]
          Memory at fea20000 (32-bit, non-prefetchable) [size=16]
          Expansion ROM at fea00000 [disabled] [size=64K]
          Capabilities: [40] Power Management version 3
          Capabilities: [50] MSI: Enable- Count=1/1 Maskable- 64bit-
          Capabilities: [70] Express Legacy Endpoint, MSI 00
          Capabilities: [100] Advanced Error Reporting
          Kernel driver in use: pata_marvell
          Kernel modules: pata_marvell

  ##########################################################
  [    1.225703] AMD-Vi: Event logged [IO_PAGE_FAULT device=02:00.1 domain=0x001d address=0x00000000001003c0 flags=0x0000]
  <snip>
  [    6.207818] ata16.00: qc timeout (cmd 0xa1)
  [    6.215674] ata9.00: qc timeout (cmd 0xa1)
  [    6.215681] ata9.00: failed to IDENTIFY (I/O error, err_mask=0x4)
  [    6.223640] ata24.00: qc timeout (cmd 0xa1)
  [    6.231606] ata17.00: qc timeout (cmd 0xec)
  [    6.231627] ata24.00: failed to IDENTIFY (I/O error, err_mask=0x4)
  [    6.239574] ata17.00: failed to IDENTIFY (I/O error, err_mask=0x4)
  [    6.343207] ata18.00: qc timeout (cmd 0xec)
  [    6.351204] ata18.00: failed to IDENTIFY (I/O error, err_mask=0x4)
  [    6.534578] ata9: SATA link up 1.5 Gbps (SStatus 113 SControl 300)
  [    6.558489] ata24: SATA link up 1.5 Gbps (SStatus 113 SControl 300)
  [    6.709935] ata16.00: failed to IDENTIFY (I/O error, err_mask=0x4)
  [    7.531002] ata16: SATA link up 1.5 Gbps (SStatus 113 SControl 300)
  [   11.588451] ata17: link is slow to respond, please be patient (ready=0)
  [   11.700054] ata18: link is slow to respond, please be patient (ready=0)
  [   16.219859] ata17: COMRESET failed (errno=-16)
  [   16.331454] ata18: COMRESET failed (errno=-16)
  [   16.498853] ata9.00: qc timeout (cmd 0xa1)
  [   16.498865] ata9.00: failed to IDENTIFY (I/O error, err_mask=0x4)
  [   16.498870] ata9: limiting SATA link speed to 1.5 Gbps
  [   16.522792] ata24.00: qc timeout (cmd 0xa1)
  [   16.522804] ata24.00: failed to IDENTIFY (I/O error, err_mask=0x4)
  [   16.522807] ata24: limiting SATA link speed to 1.5 Gbps
  [   16.817725] ata9: SATA link up 1.5 Gbps (SStatus 113 SControl 310)
  [   16.849613] ata24: SATA link up 1.5 Gbps (SStatus 113 SControl 310)
  [   17.495260] ata16.00: qc timeout (cmd 0xa1)
  [   17.997499] ata16.00: failed to IDENTIFY (I/O error, err_mask=0x4)
  [   17.997504] ata16: limiting SATA link speed to 1.5 Gbps
  [   18.818556] ata16: SATA link up 1.5 Gbps (SStatus 113 SControl 310)
  [   21.568700] ata17: link is slow to respond, please be patient (ready=0)
  [   21.680300] ata18: link is slow to respond, please be patient (ready=0)
  [   26.200104] ata17: COMRESET failed (errno=-16)
  [   26.311693] ata18: COMRESET failed (errno=-16)
  [   31.548931] ata17: link is slow to respond, please be patient (ready=0)
  [   31.660534] ata18: link is slow to respond, please be patient (ready=0)
  [   46.710611] ata9.00: qc timeout (cmd 0xa1)
  [   46.710618] ata9.00: failed to IDENTIFY (I/O error, err_mask=0x4)
  [   46.742498] ata24.00: qc timeout (cmd 0xa1)
  [   46.750464] ata24.00: failed to IDENTIFY (I/O error, err_mask=0x4)
  [   47.029478] ata9: SATA link up 1.5 Gbps (SStatus 113 SControl 310)
  [   47.077301] ata24: SATA link up 1.5 Gbps (SStatus 113 SControl 310)
  [   48.711438] ata16.00: qc timeout (cmd 0xa1)
  [   49.213639] ata16.00: failed to IDENTIFY (I/O error, err_mask=0x4)
  [   50.034704] ata16: SATA link up 1.5 Gbps (SStatus 113 SControl 310)
  [   61.122962] ata17: COMRESET failed (errno=-16)
  [   61.122971] ata17: limiting SATA link speed to 1.5 Gbps
  [   61.234560] ata18: COMRESET failed (errno=-16)
  [   61.234569] ata18: limiting SATA link speed to 3.0 Gbps
  [   66.137000] ata17: COMRESET failed (errno=-16)
  [   66.137009] ata17: reset failed, giving up
  [   66.248595] ata18: COMRESET failed (errno=-16)
  [   66.248603] ata18: reset failed, giving up
  <snip>

  -R C
  --- 
  ApportVersion: 2.6.1-0ubuntu6
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC1:  zarquon    9636 F.... xfce4-volumed
                        zarquon    9639 F.... pulseaudio
   /dev/snd/controlC0:  zarquon    9636 F.... xfce4-volumed
                        zarquon    9639 F.... pulseaudio
  CRDA: Error: command ['iw', 'reg', 'get'] failed with exit code 1: nl80211 not found.
  DistroRelease: Ubuntu 12.10
  IwConfig:
   ctn0      no wireless extensions.
   
   eth0      no wireless extensions.
   
   lo        no wireless extensions.
  MachineType: Gigabyte Technology Co., Ltd. To be filled by O.E.M.
  MarkForUpload: True
  NonfreeKernelModules: fglrx zfs zcommon zavl znvpair zunicode
  Package: linux (not installed)
  ProcFB:
   
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.5.0-17-generic root=UUID=fa2f74cd-e56f-435d-93a2-6dfc3685d3de ro crashkernel=384M-2G:64M,2G-:128M quiet splash vt.handoff=7
  ProcVersionSignature: Ubuntu 3.5.0-17.28-generic 3.5.5
  RelatedPackageVersions:
   linux-restricted-modules-3.5.0-17-generic N/A
   linux-backports-modules-3.5.0-17-generic  N/A
   linux-firmware                            1.95
  RfKill:
   
  Tags:  quantal
  Uname: Linux 3.5.0-17-generic x86_64
  UpgradeStatus: Upgraded to quantal on 2012-10-23 (51 days ago)
  UserGroups: adm admin audio cdrom dialout disk lpadmin mythtv plugdev sambashare video
  WpaSupplicantLog:
   
  dmi.bios.date: 10/09/2012
  dmi.bios.vendor: American Megatrends Inc.
  dmi.bios.version: F1
  dmi.board.asset.tag: To be filled by O.E.M.
  dmi.board.name: F2A85X-D3H
  dmi.board.vendor: Gigabyte Technology Co., Ltd.
  dmi.board.version: x.x
  dmi.chassis.asset.tag: To Be Filled By O.E.M.
  dmi.chassis.type: 3
  dmi.chassis.vendor: Gigabyte Technology Co., Ltd.
  dmi.chassis.version: To Be Filled By O.E.M.
  dmi.modalias: dmi:bvnAmericanMegatrendsInc.:bvrF1:bd10/09/2012:svnGigabyteTechnologyCo.,Ltd.:pnTobefilledbyO.E.M.:pvrTobefilledbyO.E.M.:rvnGigabyteTechnologyCo.,Ltd.:rnF2A85X-D3H:rvrx.x:cvnGigabyteTechnologyCo.,Ltd.:ct3:cvrToBeFilledByO.E.M.:
  dmi.product.name: To be filled by O.E.M.
  dmi.product.version: To be filled by O.E.M.
  dmi.sys.vendor: Gigabyte Technology Co., Ltd.

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