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I have been running 12.04 on my Fujitsu Siemens Lifebook E751 for almost a year without any problems, and then several days ago I noticed a very high CPU IOwait that makes the system poorly responsive (it freezes for fractions of a second, but this happens very often making the computer very unpleasant to use). I tried to debug and iotop identifies jbd2 (Journaling block device) as the process responsible. This process is only called while I do regular activities and not when the computer is idle. It did not seem that the problem is that it is called too often, but that when it is called, it takes too much time to do its job. So I have tried to check my disk and was unpleasantly surprised by its extremely slow performance parameters.

sudo hdparm -tT /dev/sdb6

/dev/sdb6:
  Timing cached reads:     2 MB in  2.43 seconds = 842.41 kB/sec
  Timing buffered disk reads:  22 MB in  3.01 seconds =   7.30 MB/sec

I did a fresh install of 13.04 (I had all my data backed up so it was not so radical) and that did not fix anything. I also checked the disk performance while booted from USB and the disk performance is the same (the system booted from USB is very responsive so I assume that this cannot be cpu or memory problem). Could this be fixed (is this a software or a hardware failure)?

Thank you for your advices.

Filip

PS: Here is some more data that might be useful.

sync ; time sh -c "dd if=/dev/zero of=testfile bs=100k count=1k  && sync" ; rm testfile 
1024+0 records in
1024+0 records out
104857600 bytes (105 MB) copied, 0,0837853 s, 1,3 GB/s

real    0m1.250s
user    0m0.000s
sys     0m0.100s


sudo hdparm /dev/sdb6

/dev/sdb6:
multcount     = 16 (on)
IO_support    =  1 (32-bit)
readonly      =  0 (off)
readahead     = 256 (on)
geometry      = 60801/255/63, sectors = 731281408, start = 198688768

sudo hdparm -i /dev/sdb6

/dev/sdb6:

Model=TOSHIBA MK5061GSYN, FwRev=MH000K, SerialNo=629GF6JIS
Config={ Fixed }
RawCHS=16383/16/63, TrkSize=0, SectSize=0, ECCbytes=0
BuffType=unknown, BuffSize=16384kB, MaxMultSect=16, MultSect=16
CurCHS=65535/1/63, CurSects=4128705, LBA=yes, LBAsects=976773168
IORDY=on/off, tPIO={min:120,w/IORDY:120}, tDMA={min:120,rec:120}
PIO modes:  pio0 pio1 pio2 pio3 pio4 
DMA modes:  sdma0 sdma1 sdma2 mdma0 mdma1 mdma2 
UDMA modes: udma0 udma1 udma2 udma3 udma4 *udma5 
AdvancedPM=yes: unknown setting WriteCache=enabled
Drive conforms to: Unspecified:  ATA/ATAPI-3,4,5,6,7

* signifies the current active mode

sudo smartctl -a /dev/sdb6
smartctl 5.43 2012-06-30 r3573 [x86_64-linux-3.8.0-23-generic] (local build)
Copyright (C) 2002-12 by Bruce Allen, http://smartmontools.sourceforge.net

=== START OF INFORMATION SECTION ===
Model Family:     Toshiba 2.5" HDD MK..61GSYN
Device Model:     TOSHIBA MK5061GSYN
Serial Number:    629GF6JIS
LU WWN Device Id: 5 000039 416f03c89
Firmware Version: MH000K
User Capacity:    500,107,862,016 bytes [500 GB]
Sector Size:      512 bytes logical/physical
Device is:        In smartctl database [for details use: -P show]
ATA Version is:   8
ATA Standard is:  Exact ATA specification draft version not indicated
Local Time is:    Fri Jul  5 22:01:13 2013 CEST
SMART support is: Available - device has SMART capability.
SMART support is: Enabled

=== START OF READ SMART DATA SECTION ===
SMART overall-health self-assessment test result: PASSED

General SMART Values:
Offline data collection status:  (0x00) Offline data collection activity
                was never started.
                Auto Offline Data Collection: Disabled.
Self-test execution status:      (  25) The self-test routine was aborted by
                the host.
Total time to complete Offline data collection:         (  120) seconds.
Offline data collection 
capabilities:   (0x5b) SMART execute Offline immediate.
                Auto Offline data collection on/off support.
                Suspend Offline collection upon new
                command.
                Offline surface scan supported.
                Self-test supported.
                No Conveyance Self-test supported.
                Selective Self-test supported.
SMART capabilities:            (0x0003) Saves SMART data before entering
                power-saving mode.
                Supports SMART auto save timer.
Error logging capability:        (0x01) Error logging supported.
                General Purpose Logging supported.
Short self-test routine 
recommended polling time:    (   2) minutes.
Extended self-test routine
recommended polling time:    ( 126) minutes.
SCT capabilities:          (0x003d) SCT Status supported.
                SCT Error Recovery Control supported.
                SCT Feature Control supported.
                SCT Data Table supported.

SMART Attributes Data Structure revision number: 16
Vendor Specific SMART Attributes with Thresholds:
ID# ATTRIBUTE_NAME          FLAG     VALUE WORST THRESH TYPE      UPDATED WHEN_FAILED RAW_VALUE
1 Raw_Read_Error_Rate     0x000b   100   100   050    Pre-fail  Always       -       0
2 Throughput_Performance  0x0005   100   100   050    Pre-fail  Offline      -       0
3 Spin_Up_Time            0x0027   100   100   001    Pre-fail  Always       -       2356
4 Start_Stop_Count        0x0032   100   100   000    Old_age   Always       -       1413
5 Reallocated_Sector_Ct   0x0033   100   100   050    Pre-fail  Always       -       0
7 Seek_Error_Rate         0x000b   100   100   050    Pre-fail  Always       -       0
8 Seek_Time_Performance   0x0005   100   100   050    Pre-fail  Offline      -       0
9 Power_On_Hours          0x0032   093   093   000    Old_age   Always       -       3160
10 Spin_Retry_Count        0x0033   128   100   030    Pre-fail  Always       -       0
12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       1149
191 G-Sense_Error_Rate      0x0032   100   100   000    Old_age   Always       -       26
192 Power-Off_Retract_Count 0x0032   100   100   000    Old_age   Always       -       7
193 Load_Cycle_Count        0x0032   098   098   000    Old_age   Always       -       22993
194 Temperature_Celsius     0x0022   100   100   000    Old_age   Always       -       59 (Min/Max 18/61)
196 Reallocated_Event_Count 0x0032   100   100   000    Old_age   Always       -       0
197 Current_Pending_Sector  0x0032   100   100   000    Old_age   Always       -       0
198 Offline_Uncorrectable   0x0030   100   100   000    Old_age   Offline      -       0
199 UDMA_CRC_Error_Count    0x0032   200   200   000    Old_age   Always       -       0
220 Disk_Shift              0x0002   100   100   000    Old_age   Always       -       8364
222 Loaded_Hours            0x0032   094   094   000    Old_age   Always       -       2550
223 Load_Retry_Count        0x0032   100   100   000    Old_age   Always       -       0
224 Load_Friction           0x0022   100   100   000    Old_age   Always       -       0
226 Load-in_Time            0x0026   100   100   000    Old_age   Always       -       266
240 Head_Flying_Hours       0x0001   100   100   001    Pre-fail  Offline      -       0

SMART Error Log Version: 1
ATA Error Count: 1
CR = Command Register [HEX]
FR = Features Register [HEX]
SC = Sector Count Register [HEX]
SN = Sector Number Register [HEX]
CL = Cylinder Low Register [HEX]
CH = Cylinder High Register [HEX]
DH = Device/Head Register [HEX]
DC = Device Command Register [HEX]
ER = Error register [HEX]
ST = Status register [HEX]
Powered_Up_Time is measured from power on, and printed as
DDd+hh:mm:SS.sss where DD=days, hh=hours, mm=minutes, SS=sec, and sss=millisec. It "wraps" after 49.710 days.

Error 1 occurred at disk power-on lifetime: 310 hours (12 days + 22 hours)
When the command that caused the error occurred, the device was active or idle.

  After command completion occurred, registers were:
  ER ST SC SN CL CH DH
  -- -- -- -- -- -- --
  84 41 30 ff ff 25 65  Error: ICRC, ABRT at LBA = 0x0525ffff = 86376447

  Commands leading to the command that caused the error were:
  CR FR SC SN CL CH DH DC   Powered_Up_Time  Command/Feature_Name
  -- -- -- -- -- -- -- --  ----------------  --------------------
  61 00 40 00 01 26 40 00      05:26:41.826  WRITE FPDMA QUEUED
  61 00 38 00 00 26 40 00      05:26:41.826  WRITE FPDMA QUEUED
  61 00 30 00 ff 25 40 00      05:26:41.826  WRITE FPDMA QUEUED
  61 00 28 00 fe 25 40 00      05:26:41.826  WRITE FPDMA QUEUED
  61 00 20 00 fd 25 40 00      05:26:41.823  WRITE FPDMA QUEUED

 SMART Self-test log structure revision number 1
 Num  Test_Description    Status                  Remaining  LifeTime(hours) LBA_of_first_error
 # 1  Extended offline    Aborted by host               90%      3155         -
 # 2  Short offline       Completed without error       00%      3155         -

SMART Selective self-test log data structure revision number 1
SPAN  MIN_LBA  MAX_LBA  CURRENT_TEST_STATUS
   1        0        0  Not_testing
   2        0        0  Not_testing
   3        0        0  Not_testing
   4        0        0  Not_testing
   5        0        0  Not_testing
 Selective self-test flags (0x0):
 After scanning selected spans, do NOT read-scan remainder of disk.
 If Selective self-test is pending on power-up, resume after 0 minute delay.
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1 Answer 1

This could be caused by the fact that your harddisk has some bad blocks. I would recommend you to boot from the USB stick again and run the following command from a terminal:

sudo fsck -c /dev/sdb6

This will add those bad blocks to the bad block list, meaning that they should not be used any more.

Another option is to run gparted and trigger a check of your disk there.

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