Slow hard drive?

Question

Some time ago I noticed, that my desktop has become slower, than usual. It looks like a source of troubles is the hard drive (there is no such issue with Live USB) - but I don't understand the reason for this. There is an info from smartctl - can anybody explain, what may be wrong?

smartctl --all /dev/sda

smartctl 6.1 2013-03-16 r3800 [x86_64-linux-3.8.2] (local build)
Copyright (C) 2002-13, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Model Family:     Western Digital Scorpio Blue Serial ATA (AF)
Device Model:     WDC WD5000BPVT-00HXZT3
Serial Number:    WD-WXF1E62KSHM2
LU WWN Device Id: 5 0014ee 658207174
Firmware Version: 01.01A01
User Capacity:    500 107 862 016 bytes [500 GB]
Sector Sizes:     512 bytes logical, 4096 bytes physical
Rotation Rate:    5400 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
Local Time is:    Sun May  4 23:07:15 2014 NOVT
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:      (   0) The previous self-test routine completed
                    without error or no self-test has ever 
                    been run.
Total time to complete Offline 
data collection:        (12060) 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:    ( 120) minutes.
Conveyance self-test routine
recommended polling time:    (   5) minutes.
SCT capabilities:          (0x7035) 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
  1 Raw_Read_Error_Rate     0x002f   200   200   051    Pre-fail  Always       -       8
  3 Spin_Up_Time            0x0027   178   177   021    Pre-fail  Always       -       2083
  4 Start_Stop_Count        0x0032   100   100   000    Old_age   Always       -       966
  5 Reallocated_Sector_Ct   0x0033   200   200   140    Pre-fail  Always       -       0
  7 Seek_Error_Rate         0x002e   200   200   000    Old_age   Always       -       0
  9 Power_On_Hours          0x0032   095   095   000    Old_age   Always       -       3887
 10 Spin_Retry_Count        0x0032   100   100   000    Old_age   Always       -       0
 11 Calibration_Retry_Count 0x0032   100   100   000    Old_age   Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       966
192 Power-Off_Retract_Count 0x0032   200   200   000    Old_age   Always       -       48
193 Load_Cycle_Count        0x0032   185   185   000    Old_age   Always       -       46771
194 Temperature_Celsius     0x0022   103   100   000    Old_age   Always       -       44
196 Reallocated_Event_Count 0x0032   200   200   000    Old_age   Always       -       0
197 Current_Pending_Sector  0x0032   200   200   000    Old_age   Always       -       0
198 Offline_Uncorrectable   0x0030   100   253   000    Old_age   Offline      -       0
199 UDMA_CRC_Error_Count    0x0032   200   200   000    Old_age   Always       -       0
200 Multi_Zone_Error_Rate   0x0008   100   253   000    Old_age   Offline      -       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%      3884         -
# 2  Short offline       Completed without error       00%      2834         -

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.

Answer 1

If the HDD is having to re-read either a bad block or bad sector, which is beginning to fail, it will try to re-read a given section several times until it's able to do so. This behavior will manifest as the HDD "slowing down" but it's the act of having to read a given area from the disk a multitude of times that you're experiencing.

Typically when this occurs I'll run the HDD through either HDAT2 or SpinRite to determine if there are any bad blocks on the disk and instruct either of these two tools to attempt to repair and/or recover the data from defective blocks.

This is only a short-term fix; typically if it continues to happen then it's oftentimes a symptom of a larger problem looming that the HDD is going to fail in the not-too-distant future. If this is the case then I would begin planning on getting a replacement and migrating the data from the problem drive before it actually fails.