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I am running ubuntu 12.04(32 bit). Suddenly after a reboot my laptop did not detect HDD. After couple of restart it failed to detect HDD. Then i change sata mode to IDE from AHCI in BIOS. Then it detect HDD again. And now HDD performance is very slow. I run a short test in disk utility. It shows no error or warning.

hdparm -i /dev/sda

 Model=TOSHIBA MK3259GSXP, FwRev=GN003J, SerialNo=61OJC86CT
 Config={ Fixed }
 RawCHS=16383/16/63, TrkSize=0, SectSize=0, ECCbytes=0
 BuffType=unknown, BuffSize=8192kB, MaxMultSect=16, MultSect=16
 CurCHS=16383/16/63, CurSects=16514064, LBA=yes, LBAsects=625142448
 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

hdparm -tT /dev/sda

/dev/sda:
 Timing cached reads:     2 MB in  2.70 seconds = 759.55 kB/sec
 Timing buffered disk reads: 172 MB in  3.02 seconds =  56.99 MB/sec

These are the result of hdparm command. Does it normal? please help.

Specification:

Laptop: Acer Aspire 4250
HDD: 320
RAM: 2GB
Processor: dual core (1.6GHZ)

EDITED

I found something. After some ideal time SDA link goes down (speed 700 kb/sec). It's back after a minitue (speed in MB/sec). Kernel Log:

1.194927] ahci 0000:00:11.0: version 3.0
Jul 14 01:07:32 ubuntu kernel: [    1.195121] ahci 0000:00:11.0: AHCI 0001.0200 32 slots 4 ports 6 Gbps 0xf impl SATA mode
Jul 14 01:07:32 ubuntu kernel: [    1.196190] scsi0 : ahci
Jul 14 01:07:32 ubuntu kernel: [    1.196326] scsi1 : ahci
Jul 14 01:07:32 ubuntu kernel: [    1.196417] scsi2 : ahci
Jul 14 01:07:32 ubuntu kernel: [    1.196508] scsi3 : ahci
Jul 14 01:07:32 ubuntu kernel: [    1.196951] ata1: SATA max UDMA/133 abar m1024@0x9034b000 port 0x9034b100 irq 19
Jul 14 01:07:32 ubuntu kernel: [    1.196957] ata2: SATA max UDMA/133 abar m1024@0x9034b000 port 0x9034b180 irq 19
Jul 14 01:07:32 ubuntu kernel: [    1.196961] ata3: SATA max UDMA/133 abar m1024@0x9034b000 port 0x9034b200 irq 19
Jul 14 01:07:32 ubuntu kernel: [    1.196965] ata4: SATA max UDMA/133 abar m1024@0x9034b000 port 0x9034b280 irq 19
#Jul 14 01:07:32 ubuntu kernel: [    1.528890] ata4: SATA link down (SStatus 0 SControl 300)
#Jul 14 01:07:32 ubuntu kernel: [    1.528970] ata3: SATA link down (SStatus 0 SControl 300)
#Jul 14 01:07:32 ubuntu kernel: [    1.701010] ata2: SATA link up 1.5 Gbps (SStatus 113 SControl 300)
Jul 14 01:07:32 ubuntu kernel: [    2.172883] Switching to clocksource tsc
Jul 14 01:07:32 ubuntu kernel: [    3.380557] ata1: SATA link up 3.0 Gbps (SStatus 123 SControl 300)
Jul 14 01:07:32 ubuntu kernel: [    3.424635] ata1.00: ATA-8: TOSHIBA MK3259GSXP, GN003J, max UDMA/100
Jul 14 01:07:32 ubuntu kernel: [    3.424644] ata1.00: 625142448 sectors, multi 16: LBA48 NCQ (depth 31/32), AA
Jul 14 01:07:32 ubuntu kernel: [    3.425731] ata1.00: configured for UDMA/100
Jul 14 01:07:32 ubuntu kernel: [    3.426226] scsi 0:0:0:0: Direct-Access     ATA      TOSHIBA MK3259GS GN00 PQ: 0 ANSI: 5
Jul 14 01:07:32 ubuntu kernel: [    3.426483] sd 0:0:0:0: [sda] 625142448 512-byte logical blocks: (320 GB/298 GiB)
Jul 14 01:07:32 ubuntu kernel: [    3.426488] sd 0:0:0:0: [sda] 4096-byte physical blocks
Jul 14 01:07:32 ubuntu kernel: [    3.426550] sd 0:0:0:0: Attached scsi generic sg0 type 0
Jul 14 01:07:32 ubuntu kernel: [    3.426568] sd 0:0:0:0: [sda] Write Protect is off
Jul 14 01:07:32 ubuntu kernel: [    3.426574] sd 0:0:0:0: [sda] Mode Sense: 00 3a 00 00
Jul 14 01:07:32 ubuntu kernel: [    3.426608] sd 0:0:0:0: [sda] Write cache: enabled, read cache: enabled, doesn't support DPO or FUA
Jul 14 01:07:32 ubuntu kernel: [    3.537077]  sda: sda1 sda2 sda3 sda4 < sda5 sda6 sda7 >
Jul 14 01:07:32 ubuntu kernel: [    3.538831] sd 0:0:0:0: [sda] Attached SCSI disk
Jul 14 01:07:32 ubuntu kernel: [    3.540782] scsi 1:0:0:0: CD-ROM            MATSHITA DVD-RAM UJ8B0AW  1.00 PQ: 0 ANSI: 5
Jul 14 01:07:32 ubuntu kernel: [    3.542788] sr0: scsi3-mmc drive: 24x/24x writer dvd-ram cd/rw xa/form2 cdda tray
Jul 14 01:07:32 ubuntu kernel: [    3.542796] cdrom: Uniform CD-ROM driver Revision: 3.20
Jul 14 01:07:32 ubuntu kernel: [    3.543116] sr 1:0:0:0: Attached scsi CD-ROM sr0
Jul 14 01:07:32 ubuntu kernel: [    3.543254] sr 1:0:0:0: Attached scsi generic sg1 type 5
Jul 14 01:07:32 ubuntu kernel: [    3.543485] Freeing unused kernel memory: 748k freed 

I am having exactly the same problem, https://answers.launchpad.net/ubuntu/+source/linux/+question/166624

ADDED INFO

smartctl 5.43 2012-06-05 r3561 [i686-linux-3.5.0-3-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..59GSXP (Adv. Format)
Device Model:     TOSHIBA MK3259GSXP
Serial Number:    61OJC86CT
LU WWN Device Id: 5 000039 353c09e33
Firmware Version: GN003J
User Capacity:    320,072,933,376 bytes [320 GB]
Sector Sizes:     512 bytes logical, 4096 bytes 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 Jul 15 00:36:16 2012 BDT
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:        (  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:    ( 103) 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       -       1206
  4 Start_Stop_Count        0x0032   100   100   000    Old_age   Always       -       5171
  5 Reallocated_Sector_Ct   0x0033   100   100   050    Pre-fail  Always       -       736
  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   096   096   000    Old_age   Always       -       1726
 10 Spin_Retry_Count        0x0033   202   100   030    Pre-fail  Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       1208
191 G-Sense_Error_Rate      0x0032   100   100   000    Old_age   Always       -       15
192 Power-Off_Retract_Count 0x0032   100   100   000    Old_age   Always       -       89
193 Load_Cycle_Count        0x0032   098   098   000    Old_age   Always       -       24439
194 Temperature_Celsius     0x0022   100   100   000    Old_age   Always       -       42 (Min/Max 18/48)
196 Reallocated_Event_Count 0x0032   100   100   000    Old_age   Always       -       14
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       -       49
222 Loaded_Hours            0x0032   097   097   000    Old_age   Always       -       1362
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       -       297
240 Head_Flying_Hours       0x0001   100   100   001    Pre-fail  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%      1726         -
# 2  Short offline       Aborted by host               60%      1726         -
# 3  Short offline       Completed without error       00%      1714         -
# 4  Short offline       Completed without error       00%      1707         -

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.

enter image description here

New

I have found another issue. The result of #hdparm -tT /dev/sda is different in installed system and liveCD

LIVECD:

Timing cached reads:     2630 MB in  3.00 seconds = 878.32 MB/sec
Timing buffered disk reads: 218 MB in  3.00 seconds =  72.62 MB/sec

Installed system

 Timing cached reads:     2 MB in  3.37 seconds = 607.20 kB/sec
 Timing buffered disk reads: 218 MB in  3.00 seconds =  72.62 MB/sec
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Can you search for relevant errors in dmesg output? –  int_ua Jul 14 '12 at 6:12
    
there are no error in dmesg and log. I have checked both. –  shantanu Jul 14 '12 at 8:25
    
Can you check the SMART status of your hard drive , by referring this. Or simply launching the DISKS from application and through option select view SMART data. And post so. –  tijybba Jul 14 '12 at 18:02
    
@tijybba i have added the info –  shantanu Jul 14 '12 at 18:41
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3 Answers

up vote 2 down vote accepted

Thanks for posting the Output,

The above results suggest that they have already crossed their Threshold values, it would be wise to take backup , and Replace it if is under Warranty period. Further pressing to get the desired performance may damage it.

Reallocated Sectors Count showing 736 , While primarily used as a metric of the life expectancy of the drive, this number also affects performance. As the count of reallocated sectors increases, the read/write speed tends to become worse because the drive head is forced to seek to the reserved area whenever a remap is accessed.

Spin Retry Count showing 202 It is the count of retry of spin start attempts. This attribute stores a total count of the spin start attempts to reach the fully operational speed (under the condition that the first attempt was unsuccessful). An increase of this attribute value is a sign of problems in the hard disk mechanical subsystem.

For further reading refer here and S.M.A.R.T. wiki

P.S: A low health value alone does not neccessary mean that the hard disk will surely die in the near future (to verify this, a complete (hardware) examination is required), but there is a real chance for failure.

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I consider any drive showing a non-zero value for Reallocated Sector Count or Reallocation Event Count to be a candidate for warranty replacement. Combined with the inability to detect the drive in SATA mode, I think you have a bad drive. If it is still under warranty, have the drive replaced.

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Replace the drive. Any drive that has bad sectors is doomed to fail some day.

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1  
You may want to expand on this, at least slightly. Every drive has some bad sectors. –  Eliah Kagan Jul 20 '12 at 8:23
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