This affects me and all other linux users with a mac pro (2006).   It
might affect other mac pro machines.  The output from the front jack is
line level, so needs to be put through and amplifier in order to boost
the signal.  You might be able to use the alsa-tools 'route' plugin to
re-route the outputs.  I haven't had time to investigate this personally
yet.

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https://bugs.launchpad.net/bugs/1175638

Title:
  extremely low volume macpro

Status in “alsa-driver” package in Ubuntu:
  Confirmed

Bug description:
  The volume is extremely low, at first I thought it wasn't working.  If
  I turn it up to 150% I can hear it but its grainy/crackly.  When I
  dual boot into OSX it's fine.

  ProblemType: Bug
  DistroRelease: Ubuntu 13.04
  Package: alsa-base 1.0.25+dfsg-0ubuntu4
  ProcVersionSignature: Ubuntu 3.8.0-19.29-generic 3.8.8
  Uname: Linux 3.8.0-19-generic x86_64
  NonfreeKernelModules: nvidia wl
  ApportVersion: 2.9.2-0ubuntu8
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC0:  amir       2378 F.... pulseaudio
   /dev/snd/pcmC0D0p:   amir       2378 F...m pulseaudio
   /dev/snd/pcmC0D1c:   amir       2378 F...m pulseaudio
  Date: Thu May  2 10:56:33 2013
  InstallationDate: Installed on 2013-04-29 (2 days ago)
  InstallationMedia: Ubuntu 13.04 "Raring Ringtail" - Release amd64+mac 
(20130424)
  MarkForUpload: True
  PackageArchitecture: all
  ProcEnviron:
   TERM=xterm
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  SourcePackage: alsa-driver
  Symptom: audio
  Symptom_Card: Built-in Audio - HDA Intel
  Symptom_Jack: Green Headphone Out, Front
  Symptom_Type: Volume slider, or mixer problems
  Title: [MacPro1,1, Realtek ALC889A, Green Headphone Out, Front] volume slider 
problem
  UpgradeStatus: No upgrade log present (probably fresh install)
  dmi.bios.date: 07/02/07
  dmi.bios.vendor: Apple Computer, Inc.
  dmi.bios.version: MP11.88Z.005C.B08.0707021221
  dmi.board.asset.tag: Base Board Asset Tag#
  dmi.board.name: Mac-F4208DC8
  dmi.board.vendor: Apple Computer, Inc.
  dmi.board.version: PVT
  dmi.chassis.asset.tag: Asset Tag#
  dmi.chassis.type: 2
  dmi.chassis.vendor: Apple Computer, Inc.
  dmi.chassis.version: Mac-F4208DC8
  dmi.modalias: 
dmi:bvnAppleComputer,Inc.:bvrMP11.88Z.005C.B08.0707021221:bd07/02/07:svnAppleComputer,Inc.:pnMacPro1,1:pvr1.0:rvnAppleComputer,Inc.:rnMac-F4208DC8:rvrPVT:cvnAppleComputer,Inc.:ct2:cvrMac-F4208DC8:
  dmi.product.name: MacPro1,1
  dmi.product.version: 1.0
  dmi.sys.vendor: Apple Computer, Inc.

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