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Re: excessive CPU usage



On 09/21/2014 11:54 AM, Gary Roach wrote:
Hi all

For the last few months I have been plagued by very slow response from my system. As an example, it takes 2 1/2 minutes to drag and drop 80 files from my email inbox to the trash bin in icedove. It has taken as high as 5 minutes for iceweasel to load. This problem is not just these packages but also applies to all of the rest of my programs.

I am using Debian Wheezy with a i5750 4 core processor on a fast Intel board. I run a kde desktop. All the software is up to date.

I have checked all of the log files and can't find any anomalies. Rebooting doesn't help.

Using the KDE System Monitor (ksysguard) I have noticed that at least one of the processors goes to 100% and stays there for long periods even though there is no noticeable activity in the process tables. The only other thing I have noticed (the printing just hung up while I am writing this) is that the hard drive indicator comes on and stays on during the processor activity. I ran some checks on the hard drive but found no indication of any hard drive problems.

Has anyone else had a similar problem or have any idea what is going on.

Thanks in advance

Gary R.


After several days of investigation, I am still not sure what is causing the problem. I have noted the following:

The journaling program jbd2/sda1-8 is taking up most of the I/O time. I do have noatime set in fstab.

Having two identical machines is very helpful. My wifes system is fast and never bogs down. Mine is a real dog at this time. I ran iotop on both systems. In my wifes kjournal will pop to the top of the list for a very short period when loading a new application. Otherwise iotop is quiet. On mine kjournal doesn't show at all but jbd2/sda1-8 shows up all of the time. There is constant activity on my system even when nothing is happening.

Below is the output from gsmartcontrol. Note that vendor specific attributes 197 and 198 raw values are 757 and 232 respectively and are highlighted in pink on the gsmartcontrol program. My wifes computer's raw values are included in the last column of the smart attributes table for comparison. Also note that there were no errors reported for my wifes  system. Do I need to replace the drive or is this fixable. Is this even the root cause of my problems. I'm not too sharp on reading this data an will appreciate comments from a more knowledgeable person.




smartctl 5.41 2011-06-09 r3365 [x86_64-linux-3.2.0-4-amd64] (local build)
Copyright (C) 2002-11 by Bruce Allen, http://smartmontools.sourceforge.net

=== START OF INFORMATION SECTION ===
Model Family:     Western Digital Caviar Green
Device Model:     WDC WD5000AADS-00M2B0
Serial Number:    WD-WCAV59765616
LU WWN Device Id: 5 0014ee 25992fc38
Firmware Version: 01.00A01
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:    Sun Sep 28 18:12:56 2014 PDT
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:  (0x84)    Offline data collection activity
                    was suspended by an interrupting command from host.
                    Auto Offline Data Collection: Enabled.
Self-test execution status:      ( 121)    The previous self-test completed having
                    the read element of the test failed.
Total time to complete Offline
data collection:         ( 9960) seconds.
Offline data collection
capabilities:              (0x7b) SMART execute Offline immediate.
                    Auto Offline data collection on/off support.
                    Suspend Offline collection upon new
                    command.
                    Offline surface scan supported.
                    Self-test supported.
                    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:      ( 118) minutes.
Conveyance self-test routine
recommended polling time:      (   5) minutes.
SCT capabilities:            (0x3037)    SCT Status 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 (Wife Raw)
  1 Raw_Read_Error_Rate     0x002f    200      200        051     Pre-fail      Always               -                  84123                0
  3 Spin_Up_Time                  0x0027   114      108        021     Pre-fail      Always               -                    7283            3575
  4 Start_Stop_Count            0x0032   100      100        000     Old_age    Always               -                      269                64
  5 Reallocated_Sector_Ct     0x0033    200      200       140     Pre-fail      Always               -                          0                  0
  7 Seek_Error_Rate              0x002e   200      200        000     Old_age    Always               -                          0                  0
  9 Power_On_Hours            0x0032    051      051       000     Old_age    Always                -                  35966          31847
 10 Spin_Retry_Count           0x0032   100      100        000     Old_age    Always                -                         0                  0
 11 Calibration_Retry_Count 0x0032   100       100       000     Old_age    Always                -                          0                 0
 12 Power_Cycle_Count        0x0032   100       100       000     Old_age    Always                -                     267                62
192 Power-Off_Retract_Count 0x0032 200       200       000     Old_age   Always                -                     214                48
193 Load_Cycle_Count         0x0032    001       001      000     Old_age    Always                -             4000934      2618304
194 Temperature_Celsius      0x0022   110       106       000     Old_age    Always                -                      37                33
196 Reallocated_Event_Count 0x0032  200      200       000     Old_age    Always                -                        0                  0
197 Current_Pending_Sector  0x0032  191      187       000     Old_age    Always                -                    757                  0
198 Offline_Uncorrectable     0x0030   198      189       000     Old_age    Offline                 -                    232                  0

199 UDMA_CRC_Error_Count 0x0032   200     200       000     Old_age    Always                -                        0                  0
200 Multi_Zone_Error_Rate    0x0008   197     193       000     Old_age    Offline                 -                    723                  0

SMART Error Log Version: 1
ATA Error Count: 54177 (device log contains only the most recent five errors)
    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 54177 occurred at disk power-on lifetime: 35960 hours (1498 days + 8 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
  -- -- -- -- -- -- --
  40 51 00 34 54 50 e0  Error: UNC at LBA = 0x00505434 = 5264436

  Commands leading to the command that caused the error were:
  CR FR SC SN CL CH DH DC   Powered_Up_Time  Command/Feature_Name
  -- -- -- -- -- -- -- --  ----------------  --------------------
  c8 00 00 20 54 50 e0 08  27d+02:56:44.789  READ DMA
  ec 00 00 00 00 00 a0 08  27d+02:56:44.781  IDENTIFY DEVICE
  ef 03 46 00 00 00 a0 08  27d+02:56:44.781  SET FEATURES [Set transfer mode]

Error 54176 occurred at disk power-on lifetime: 35960 hours (1498 days + 8 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
  -- -- -- -- -- -- --
  40 51 00 34 54 50 e0  Error: UNC at LBA = 0x00505434 = 5264436

  Commands leading to the command that caused the error were:
  CR FR SC SN CL CH DH DC   Powered_Up_Time  Command/Feature_Name
  -- -- -- -- -- -- -- --  ----------------  --------------------
  c8 00 00 20 54 50 e0 08  27d+02:56:41.592  READ DMA
  ec 00 00 00 00 00 a0 08  27d+02:56:41.584  IDENTIFY DEVICE
  ef 03 46 00 00 00 a0 08  27d+02:56:41.584  SET FEATURES [Set transfer mode]

Error 54175 occurred at disk power-on lifetime: 35960 hours (1498 days + 8 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
  -- -- -- -- -- -- --
  40 51 00 34 54 50 e0  Error: UNC at LBA = 0x00505434 = 5264436

  Commands leading to the command that caused the error were:
  CR FR SC SN CL CH DH DC   Powered_Up_Time  Command/Feature_Name
  -- -- -- -- -- -- -- --  ----------------  --------------------
  c8 00 00 20 54 50 e0 08  27d+02:56:38.459  READ DMA
  ec 00 00 00 00 00 a0 08  27d+02:56:38.451  IDENTIFY DEVICE
  ef 03 46 00 00 00 a0 08  27d+02:56:38.451  SET FEATURES [Set transfer mode]

Error 54174 occurred at disk power-on lifetime: 35960 hours (1498 days + 8 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
  -- -- -- -- -- -- --
  40 51 00 34 54 50 e0  Error: UNC at LBA = 0x00505434 = 5264436

  Commands leading to the command that caused the error were:
  CR FR SC SN CL CH DH DC   Powered_Up_Time  Command/Feature_Name
  -- -- -- -- -- -- -- --  ----------------  --------------------
  c8 00 00 20 54 50 e0 08  27d+02:56:35.518  READ DMA
  ec 00 00 00 00 00 a0 08  27d+02:56:35.510  IDENTIFY DEVICE
  ef 03 46 00 00 00 a0 08  27d+02:56:35.510  SET FEATURES [Set transfer mode]

Error 54173 occurred at disk power-on lifetime: 35960 hours (1498 days + 8 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
  -- -- -- -- -- -- --
  40 51 00 34 54 50 e0  Error: UNC at LBA = 0x00505434 = 5264436

  Commands leading to the command that caused the error were:
  CR FR SC SN CL CH DH DC   Powered_Up_Time  Command/Feature_Name
  -- -- -- -- -- -- -- --  ----------------  --------------------
  c8 00 00 20 54 50 e0 08  27d+02:56:32.353  READ DMA
  c8 00 88 68 57 50 e0 08  27d+02:56:32.338  READ DMA
  c8 00 20 00 54 50 e0 08  27d+02:56:31.798  READ DMA

SMART Self-test log structure revision number 1
Num  Test_Description    Status                  Remaining  LifeTime(hours)  LBA_of_first_error
# 1  Extended offline    Completed: read failure       90%     35888         307316
# 2  Short offline       Completed: read failure       90%     35887         330254
# 3  Extended offline    Completed: read failure       90%     35887         410646

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.

Thanks for you help

Gary R.

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