Just to make it clear: I formatted and did a fresh install of Kubuntu
14.04. The problem has been solved.

Probably it was due to some configuration problems.

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https://bugs.launchpad.net/bugs/1305237

Title:
  100% I/O usage due to jbd2

Status in “linux” package in Ubuntu:
  Triaged

Bug description:
  
  I have 14.04 Beta 2 64-bit and Intel i7 Processor with 2.2Ghz clock, 4 GB RAM 
and 500 GB Harddrive.

  After using Ubuntu for some time, everything goes so slow and I cannot
  even move my USB mouse cursor, but only touchpad. Not possible to open
  even a terminal window.

  Here is the iotop output:

  http://pastebin.ubuntu.com/7227394/

  Also the cpu usage is around 3% only by chromium.

  I unmounted all ntfs disks (I even don't have sda8), but the problem is the 
same.
  --- 
  ApportVersion: 2.13.3-0ubuntu1
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC0:  volkan     4336 F.... pulseaudio
                        volkan     5310 F.... pulseaudio
  CurrentDesktop: KDE
  DistroRelease: Ubuntu 14.04
  InstallationDate: Installed on 2013-04-16 (357 days ago)
  InstallationMedia: Kubuntu 12.10 "Quantal Quetzal" - Release amd64 
(20121017.1)
  MachineType: SAMSUNG ELECTRONICS CO., LTD. 300V3A/300V4A/300V5A/200A4B/200A5B
  Package: linux 3.11.0.18.19 [origin: unknown]
  PackageArchitecture: amd64
  ProcFB: 0 inteldrmfb
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.13.0-20-generic 
root=UUID=69512adb-ab15-463f-85d4-29a19b1e8668 ro quiet splash vt.handoff=7
  ProcVersionSignature: Ubuntu 3.13.0-20.42-generic 3.13.7
  RelatedPackageVersions:
   linux-restricted-modules-3.13.0-20-generic N/A
   linux-backports-modules-3.13.0-20-generic  N/A
   linux-firmware                             1.126
  StagingDrivers: zram
  Tags: trusty third-party-packages staging
  Uname: Linux 3.13.0-20-generic x86_64
  UnreportableReason: Bu resmi bir Ubuntu paketi değil. Lütfen herhangi bir 
üçüncü parti paketini kaldırıp tekrar deneyin.
  UpgradeStatus: Upgraded to trusty on 2014-03-10 (30 days ago)
  UserGroups: adm audio cdrom debian-tor dip libvirtd lpadmin netdev plugdev 
sambashare sudo www-data
  _MarkForUpload: True
  dmi.bios.date: 11/02/2012
  dmi.bios.vendor: Phoenix Technologies Ltd.
  dmi.bios.version: 10FI
  dmi.board.asset.tag: Base Board Asset Tag
  dmi.board.name: 300V3A/300V4A/300V5A/200A4B/200A5B
  dmi.board.vendor: SAMSUNG ELECTRONICS CO., LTD.
  dmi.board.version: FAB1
  dmi.chassis.asset.tag: Asset Tag
  dmi.chassis.type: 9
  dmi.chassis.vendor: SAMSUNG ELECTRONICS CO., LTD.
  dmi.chassis.version: 0.1
  dmi.modalias: 
dmi:bvnPhoenixTechnologiesLtd.:bvr10FI:bd11/02/2012:svnSAMSUNGELECTRONICSCO.,LTD.:pn300V3A/300V4A/300V5A/200A4B/200A5B:pvr0.1:rvnSAMSUNGELECTRONICSCO.,LTD.:rn300V3A/300V4A/300V5A/200A4B/200A5B:rvrFAB1:cvnSAMSUNGELECTRONICSCO.,LTD.:ct9:cvr0.1:
  dmi.product.name: 300V3A/300V4A/300V5A/200A4B/200A5B
  dmi.product.version: 0.1
  dmi.sys.vendor: SAMSUNG ELECTRONICS CO., LTD.

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