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

Daniel, it will help immensely if you filed a new report with the Ubuntu repository kernel (not mainline/upstream) via a terminal:
ubuntu-bug linux

Please feel free to subscribe me to it.

For more on why this is helpful, please see
https://wiki.ubuntu.com/ReportingBugs.

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https://bugs.launchpad.net/bugs/1582858

Title:
  kernel 4.4.0-22-generic in 16.04 sees no disks on HP Proliant DL165 G7
  if IOMMU is enabled

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  On a HP Proliant DL165 G7 I upgraded from 14.04.3 LTS to 16.04 LTS (I
  know, not supported).

  After reboot, the new kernel was loaded by GRUB, but failed to find
  the disks installed in the system (setup working for almost 2 years,
  standard HP setup with the SATA controller in AHCI mode and AHCI
  enabled during BIOS). It then dropped to a shell in initramfs, after
  hundreds (thousands?) of identical errors:

  [...] AMD-Vi: Event Logged [IO_PAGE_FAULT] device=xxx adress=yyy
  flags=0x...

  and the final error messages:

  ata3: softreset failed (1st FIS failed)
  ata4: softreset failed (1st FIS failed)
  ata3: limiting SATA link speed to 1.5 Gbps
  ata3: softreset failed (1st FIS failed)
  ata4: limiting SATA link speed to 1.5 Gbps
  ata4: softreset failed (1st FIS failed)
  ata3: reset failed, giving up
  ata4: reset failed, giving up

  The system disks are on ata1 and ata2, though.

  
  I tried booting the system from different other 16.04 boot media (ubuntu-16.04-server-amd64.iso, ubuntu-16.04-desktop-amd64.iso) into a rescue system. I also got the 
  [...] AMD-Vi: Event Logged ... messages. When the rescue shell was running, the system disks were also not detected, the installer I started as an experiment only offered the (USB disk) boot medium itself as installation target. The desktop installer and kernel then crashed with error messages about squashfs (sorry, didn't record those).

  Without any change, the same system boots without issues from a 14.04
  boot image, all disks present. Also, the 16.04 system boots fine if
  the old 3.13.0-86 kernel is selected in the GRUB menu.

  After some fiddling around, I turned off the IOMMU in the server's
  BIOS (under PCiExpress) - and all went back to normal, without any
  change on the installed system. Kernel 4.4.0-22-generic now boots just
  fine from the LVM-Root.

  So this is WORKSFORME now, but maybe somebody should look into it. I do believe that Proliants are quite common out there. If needed, I'll provide more info if possible - but currently I wouldn't know what.
  --- 
  AlsaDevices:
   total 0
   crw-rw---- 1 root audio 116,  1 May 17 18:50 seq
   crw-rw---- 1 root audio 116, 33 May 17 18:50 timer
  AplayDevices: Error: [Errno 2] No such file or directory
  ApportVersion: 2.20.1-0ubuntu2
  Architecture: amd64
  ArecordDevices: Error: [Errno 2] No such file or directory
  AudioDevicesInUse: Error: command ['fuser', '-v', '/dev/snd/seq', '/dev/snd/timer'] failed with exit code 1:
  DistroRelease: Ubuntu 16.04
  HibernationDevice: RESUME=UUID=d46c7c15-9d36-4d87-930d-e43d447e8855
  InstallationDate: Installed on 2012-12-22 (1244 days ago)
  InstallationMedia: Ubuntu-Server 12.10 "Quantal Quetzal" - Release amd64 (20121017.2)
  IwConfig: Error: [Errno 2] No such file or directory
  MachineType: HP ProLiant DL165 G7
  Package: linux (not installed)
  PciMultimedia:
   
  ProcEnviron:
   LANGUAGE=en_US:en
   TERM=xterm
   PATH=(custom, no user)
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  ProcFB: 0 VESA VGA
  ProcKernelCmdLine: BOOT_IMAGE=/vmlinuz-4.4.0-22-generic root=/dev/mapper/vg0-root ro net.ifnames=0 rootfstype=ext4
  ProcVersionSignature: Ubuntu 4.4.0-22.40-generic 4.4.8
  RelatedPackageVersions:
   linux-restricted-modules-4.4.0-22-generic N/A
   linux-backports-modules-4.4.0-22-generic  N/A
   linux-firmware                            1.157
  RfKill: Error: [Errno 2] No such file or directory
  Tags:  xenial
  Uname: Linux 4.4.0-22-generic x86_64
  UpgradeStatus: Upgraded to xenial on 2014-05-25 (725 days ago)
  UserGroups:
   
  _MarkForUpload: True
  dmi.bios.date: 07/27/2012
  dmi.bios.vendor: HP
  dmi.bios.version: O37
  dmi.chassis.type: 23
  dmi.chassis.vendor: HP
  dmi.modalias: dmi:bvnHP:bvrO37:bd07/27/2012:svnHP:pnProLiantDL165G7:pvr:cvnHP:ct23:cvr:
  dmi.product.name: ProLiant DL165 G7
  dmi.sys.vendor: HP

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