Tuhu, if you type the following three commands into a terminal window
what is printed after each command?

sudo stop network-manager
initctl status modemmanager
ps p $(pgrep modem-manager) 2>/dev/null

The third command should print something only if modem-manager is still
running. It shouldn't be, but your /DEBUG file showed that it was and
that's part of the problem.  You'll want to restart network-manager by
typing:

sudo start network-manager

What network devices are active on your computer whenever the problem
occurs?  Any mobile broadband devices at all?  Have you looked at the
log file /var/log/upstart/modemmanager.log to see if there are any error
messages or warnings there?

Bug #974187 reports modem-manager taking a very long time to shut
down. That bug is unresolved and due to expire soon due to lack of
activity.  You might want to subscribe to that bug and add a "me too".

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Packages, which is subscribed to network-manager in Ubuntu.
https://bugs.launchpad.net/bugs/963106

Title:
  NetworkManager causes orphaned inodes

Status in “network-manager” package in Ubuntu:
  Fix Released
Status in “network-manager” source package in Precise:
  Fix Released

Bug description:
  [Impact]
  On shutdown, dhclient isn't getting reaped by NetworkManager, despite being 
kept running through sendsigs so as not to disrupt remote filesystems (and 
their unmounting at shutdown). dhclient may be keeping open files for its lease 
files, which causes issues when unmounting /var/lib, which contains those lease 
files.

  [Development Fix]
  Remove support for connection assumption, which is meant to bring 
NetworkManager up to speed with connections that may have already be up during 
a restart of the daemon. Since we don't actually restart the daemon 
automatically (and instead suggest a restart of the system after upgrade) and 
the advantage is minimal compared to the impact on users of this interacting 
with the shutdown sequence, patch connection assumption out of the NM code and 
just always take down dhclient when NM stops.

  [Stable Fix]
  See above "Development fix".

  [Test Case]
  1) Shut down coputer.
  2) In the shutdown process, perhaps as a post-stop script in 
/etc/init/network-manager, track down open files for the dhclient pid (which 
should be available from /run/sendsigs.omit.d/network-manager.dhclient{6,}.pid)

  [Regression Potential]
  Minimal, only affects bringing NetworkManager up on a restart of the daemon 
(sudo restart network-manager or /etc/init.d/network-manager restart), which 
improves on the speed of this operation and avoid resetting the connection if 
it's already up.

  ---------

  During system shutdown, NetworkManager neither kills dhclient nor does
  it remove the dhclient pid file from the directory
  /var/run/sendsigs.omit.d.  As a result, dhclient continues to hold the
  pid file open for write and when /etc/init.d/umountroot tries to
  remount the root filesystem read-only, the remount fails.  The
  message:

  mount: / is busy

  is seen in the console, and the filesystem must be recovered at boot
  time:

  [    8.946427] EXT4-fs (sda1): INFO: recovery required on readonly filesystem
  [    8.947057] EXT4-fs (sda1): write access will be enabled during recovery
  [   11.234075] EXT4-fs (sda1): recovery complete

  If shared libraries used by dhclient are updated before the reboot,
  orphaned inodes associated with the .so files are created.  For
  example, doing "sudo apt-get install --reinstall libc6" and then
  rebooting leads to:

  [    8.356521] EXT4-fs (sda1): INFO: recovery required on readonly filesystem
  [    8.356521] EXT4-fs (sda1): write access will be enabled during recovery
  [    8.716544] EXT4-fs (sda1): orphan cleanup on readonly fs
  [    8.716544] EXT4-fs (sda1): ext4_orphan_cleanup: deleting unreferenced 
inode 313749
  [    8.724544] EXT4-fs (sda1): ext4_orphan_cleanup: deleting unreferenced 
inode 313733
  [    8.724544] EXT4-fs (sda1): ext4_orphan_cleanup: deleting unreferenced 
inode 313725
  [    8.724544] EXT4-fs (sda1): 3 orphan inodes deleted
  [    8.728544] EXT4-fs (sda1): recovery complete

  This is network-manager 0.9.3.995+git201203152001.04b2a74-0ubuntu1
  running under 12.04.   I don't believe any actual data loss will occur
  as a result of this bug, but it's likely to produce much user anxiety.
  Also see Bug 952315, which misidentifies the cause of the problems as
  upstart.

  ProblemType: Bug
  DistroRelease: Ubuntu 12.04
  Package: network-manager 0.9.3.995+git201203152001.04b2a74-0ubuntu1
  ProcVersionSignature: Ubuntu 3.2.0-20.32-generic 3.2.12
  Uname: Linux 3.2.0-20-generic i686
  ApportVersion: 1.95-0ubuntu1
  Architecture: i386
  CRDA: Error: command ['iw', 'reg', 'get'] failed with exit code 1: nl80211 
not found.
  Date: Fri Mar 23 07:42:20 2012
  InstallationMedia: Ubuntu 11.10 "Oneiric Ocelot" - Release i386 (20111011)
  IwConfig:
   lo        no wireless extensions.

   eth0      no wireless extensions.
  NetworkManager.state:
   [main]
   NetworkingEnabled=true
   WirelessEnabled=true
   WWANEnabled=true
   WimaxEnabled=true
  ProcEnviron:
   TERM=xterm
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  RfKill:

  SourcePackage: network-manager
  UpgradeStatus: Upgraded to precise on 2012-03-02 (20 days ago)

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