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I'm having high IOWait and and generally slow disk speed.(on 7200 RPM TOSHIBA MK5061GSYN Hard Drive) My disk usage is %100 on Windows 8 too, so I don't think this is Linux related. I know I have 182 bad blocks but all of them are reallocated so I don't think they will cause any problem. "sudo hdparm -tT /dev/sda"

/dev/sda:
 Timing cached reads:     2 MB in  2.87 seconds = 713.09 kB/sec
 Timing buffered disk reads: 198 MB in  3.02 seconds =  65.67 MB/sec

My external 160 GB 5400 RPM SAMSUNG HM161HI drive "sudo hdparm -tT /dev/sdb"

/dev/sdb:
 Timing cached reads:   14614 MB in  1.99 seconds = 7330.51 MB/sec
 Timing buffered disk reads:  94 MB in  3.03 seconds =  31.06 MB/sec

S.M.A.R.T. status:

smartctl 6.2 2013-07-26 r3841 [x86_64-linux-3.13.0-32-generic] (local build)
Copyright (C) 2002-13, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Model Family:     Toshiba 2.5" HDD MK..61GSY[N]
Device Model:     TOSHIBA MK5061GSYN
Serial Number:    82NRT1ZLT
LU WWN Device Id: 5 000039 431d06641
Firmware Version: MH000C
User Capacity:    500.107.862.016 bytes [500 GB]
Sector Size:      512 bytes logical/physical
Rotation Rate:    7200 rpm
Device is:        In smartctl database [for details use: -P show]
ATA Version is:   ATA8-ACS (minor revision not indicated)
SATA Version is:  SATA 2.6, 3.0 Gb/s (current: 3.0 Gb/s)
Local Time is:    Fri Oct 31 21:45:02 2014 EET
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:  (0x05) Offline data collection activity
                    was aborted by an interrupting command from host.
                    Auto Offline Data Collection: Disabled.
Self-test execution status:      (   0) The previous self-test routine completed
                    without error or no self-test has ever 
                    been run.
Total time to complete Offline 
data collection:        (  120) seconds.
Offline data collection
capabilities:            (0x51) SMART execute Offline immediate.
                    No Auto Offline data collection support.
                    Suspend Offline collection upon new
                    command.
                    No 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:    ( 113) minutes.
SCT capabilities:          (0x003f) 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     0x002f   100   100   050    Pre-fail  Always       -       0
  2 Throughput_Performance  0x0027   100   100   050    Pre-fail  Always       -       0
  3 Spin_Up_Time            0x0023   100   100   002    Pre-fail  Always       -       2280
  4 Start_Stop_Count        0x0032   100   100   000    Old_age   Always       -       1060
  5 Reallocated_Sector_Ct   0x0033   092   092   010    Pre-fail  Always       -       182
  7 Seek_Error_Rate         0x002f   100   100   050    Pre-fail  Always       -       0
  8 Seek_Time_Performance   0x0025   100   100   050    Pre-fail  Offline      -       0
  9 Power_On_Hours          0x0032   100   100   000    Old_age   Always       -       357
 10 Spin_Retry_Count        0x0033   121   100   030    Pre-fail  Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       396
183 Runtime_Bad_Block       0x0032   100   100   001    Old_age   Always       -       0
184 End-to-End_Error        0x0033   100   100   097    Pre-fail  Always       -       0
185 Unknown_Attribute       0x0032   100   100   001    Old_age   Always       -       65535
187 Reported_Uncorrect      0x0032   100   100   000    Old_age   Always       -       0
188 Command_Timeout         0x0032   100   097   000    Old_age   Always       -       11
189 High_Fly_Writes         0x003a   100   100   001    Old_age   Always       -       0
190 Airflow_Temperature_Cel 0x0022   055   048   040    Old_age   Always       -       45 (Min/Max 29/45)
191 G-Sense_Error_Rate      0x0032   100   100   000    Old_age   Always       -       1
192 Power-Off_Retract_Count 0x0022   100   100   000    Old_age   Always       -       983055
193 Load_Cycle_Count        0x0032   100   100   000    Old_age   Always       -       7139
196 Reallocated_Event_Count 0x0032   100   100   000    Old_age   Always       -       16
197 Current_Pending_Sector  0x0032   100   100   000    Old_age   Always       -       0
199 UDMA_CRC_Error_Count    0x0032   200   253   000    Old_age   Always       -       0

SMART Error Log Version: 1
No Errors Logged

SMART Self-test log structure revision number 1
Num  Test_Description    Status                  Remaining  LifeTime(hours)  LBA_of_first_error
# 1  Short offline       Completed without error       00%       357         -
# 2  Short offline       Aborted by host               60%       350         -
# 3  Short offline       Completed without error       00%       292         -
# 4  Short offline       Completed without error       00%       290         -
# 5  Short offline       Aborted by host               10%       289         -
# 6  Short offline       Aborted by host               10%       288         -
# 7  Short offline       Completed without error       00%       195         -
# 8  Short offline       Completed without error       00%       143         -
# 9  Short offline       Completed without error       00%       142         -
#10  Short offline       Completed without error       00%         3         -

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.

System Information:

System:    Host: ege-LIFEBOOK-AH532-G21 Kernel: 3.13.0-32-generic x86_64 (64 bit) Desktop: Gnome Distro: Ubuntu 14.04 trusty
Machine:   System: FUJITSU (portable) product: LIFEBOOK AH532/G21
           Mobo: FUJITSU model: FJNBB2B Bios: FUJITSU // Phoenix version: Version 2.09 date: 02/20/2013
CPU:       Dual core Intel Core i5-3210M CPU (-HT-MCP-) cache: 3072 KB flags: (lm nx sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx) 
           Clock Speeds: 1: 1200.00 MHz 2: 1200.00 MHz 3: 2400.00 MHz 4: 1200.00 MHz
Graphics:  Card-1: Intel 3rd Gen Core processor Graphics Controller 
           Card-2: NVIDIA GF108M [GeForce GT 620M] 
           X.Org: 1.15.1 drivers: intel (unloaded: fbdev,vesa) FAILED: nouveau Resolution: [email protected] 
           GLX Renderer: Mesa DRI Intel Ivybridge Mobile GLX Version: 3.0 Mesa 10.1.3
Audio:     Card: Intel 7 Series/C210 Series Family High Definition Audio Controller driver: snd_hda_intel 
           Sound: Advanced Linux Sound Architecture ver: k3.13.0-32-generic
Network:   Card-1: Intel Centrino Wireless-N 2230 driver: iwlwifi 
           IF: wlan0 state: up mac: 84:a6:c8:1a:1e:4a
           Card-2: Realtek RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller driver: r8169 
           IF: eth0 state: down mac: 2c:d4:44:91:7c:60
Drives:    HDD Total Size: 664.2GB (11.9% used) 1: id: /dev/sda model: TOSHIBA_MK5061GS size: 500.1GB 
           2: USB id: /dev/sdc model: USB_Flash_Disk size: 4.0GB 3: USB id: /dev/sdb model: HM161HI size: 160.0GB 
Partition: ID: / size: 147G used: 4.2G (3%) fs: ext4 ID: swap-1 size: 4.10GB used: 0.00GB (0%) fs: swap 
RAID:      No RAID devices detected - /proc/mdstat and md_mod kernel raid module present
Sensors:   System Temperatures: cpu: 57.0C mobo: N/A 
           Fan Speeds (in rpm): cpu: N/A 
Info:      Processes: 211 Uptime: 25 min Memory: 876.4/3811.2MB Client: Shell (bash) inxi: 1.9.17 

EDIT: I issued "hdparm -tT /dev/sda" on live USB and speed seems to be fine:

/dev/sda:
 Timing cached reads:   15282 MB in  1.99 seconds = 7667.29 MB/sec
 Timing buffered disk reads: 288 MB in  3.01 seconds =  95.63 MB/sec

What can cause this problem on the installed system?

EDIT 2: My HDD died yesterday. My computer does not even recognize it anymore. I will replace it soon.

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  • I am sorry you where having issues and your drive failed. A few bad sectors are not a problem but it's better to replace it as it's better for your data. So to avoid this in the future just replace the drive when it detects some bad sectors. It's physical damage so one bad sector can be very quickly turn into 200 bad sectors and so on.
    – Jon
    Oct 18, 2021 at 13:31

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