Questions[smart](ubuntu)

My laptop SSD is acting up and the number of errors soared since the last time I posted.

Is this drive dead / dying?
It's on now and I'm writing this on it - I have all my data backed up and all, but I am still unsure if it's usable or not?

Contacting the manufacturer didn't help much: they asked me to install Windows and run the disk check utility from there or connect it as an external drive to a Windows host and test it there.
I did both and no errors were encountered.

I also checked it with the utility they provide (see screenshot below). I then used the image I made with clonezilla to return to Ubuntu, and I found that the SATA PHY error count is nearing 300 errors!

I've also checked the connectors, but since the SSD is in a laptop I cannot change the cable (easily).

These are the test results generated by the manufacturer's utility

And the smartctl output on Ubuntu, later:

smartctl 6.5 2016-05-07 r4318 [x86_64-linux-4.14.0-041400-generic] (local build)
Copyright (C) 2002-16, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Device Model:     SPCC Solid State Disk
Serial Number:    XXXXXXXXXX
Firmware Version: S9FM02.8
User Capacity:    120,034,123,776 bytes [120 GB]
Sector Size:      512 bytes logical/physical
Rotation Rate:    Solid State Device
Form Factor:      2.5 inches
Device is:        Not in smartctl database [for details use: -P showall]
ATA Version is:   ACS-3 (minor revision not indicated)
SATA Version is:  SATA 3.1, 6.0 Gb/s (current: 3.0 Gb/s)
Local Time is:    Sun Feb 18 02:22:56 2018 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:  (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:        (   30) 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:    (   1) minutes.
Extended self-test routine
recommended polling time:    (   2) minutes.
Conveyance self-test routine
recommended polling time:    (   2) minutes.

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     0x000a   100   100   000    Old_age   Always       -       0
  9 Power_On_Hours          0x0012   100   100   000    Old_age   Always       -       6352
 12 Power_Cycle_Count       0x0012   100   100   000    Old_age   Always       -       2717
168 Unknown_Attribute       0x0012   100   100   000    Old_age   Always       -       0
170 Unknown_Attribute       0x0013   100   100   010    Pre-fail  Always       -       25
173 Unknown_Attribute       0x0000   100   100   000    Old_age   Offline      -       105447539
192 Power-Off_Retract_Count 0x0012   100   100   000    Old_age   Always       -       77
194 Temperature_Celsius     0x0023   070   070   000    Pre-fail  Always       -       30
196 Reallocated_Event_Count 0x0000   100   100   000    Old_age   Offline      -       0
218 Unknown_Attribute       0x0000   100   100   000    Old_age   Offline      -       15431
241 Total_LBAs_Written      0x0012   100   100   000    Old_age   Always       -       6281157

SMART Error Log Version: 1
ATA Error Count: 298 (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 298 occurred at disk power-on lifetime: 0 hours (0 days + 0 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 51 01 01 00 00 00

  Commands leading to the command that caused the error were:
  CR FR SC SN CL CH DH DC   Powered_Up_Time  Command/Feature_Name
  -- -- -- -- -- -- -- --  ----------------  --------------------
  ff d5 01 01 00 00 00 ff      00:11:08.077  [VENDOR SPECIFIC]
  ca 00 80 b0 8f 12 e1 00      00:11:08.076  WRITE DMA
  ca 00 80 30 8f 12 e1 00      00:11:08.076  WRITE DMA
  ca 00 80 b0 8e 12 e1 00      00:11:08.075  WRITE DMA
  ca 00 80 30 8e 12 e1 00      00:11:08.074  WRITE DMA

Error 297 occurred at disk power-on lifetime: 0 hours (0 days + 0 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 51 01 01 00 00 00

  Commands leading to the command that caused the error were:
  CR FR SC SN CL CH DH DC   Powered_Up_Time  Command/Feature_Name
  -- -- -- -- -- -- -- --  ----------------  --------------------
  ff d5 01 01 00 00 00 ff      00:11:08.039  [VENDOR SPECIFIC]
  ca 00 80 b0 7c 12 e1 00      00:11:08.038  WRITE DMA
  ca 00 80 30 7c 12 e1 00      00:11:08.038  WRITE DMA
  ca 00 80 b0 7b 12 e1 00      00:11:08.037  WRITE DMA
  ca 00 80 30 7b 12 e1 00      00:11:08.037  WRITE DMA

Error 296 occurred at disk power-on lifetime: 0 hours (0 days + 0 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 51 01 01 00 00 00

  Commands leading to the command that caused the error were:
  CR FR SC SN CL CH DH DC   Powered_Up_Time  Command/Feature_Name
  -- -- -- -- -- -- -- --  ----------------  --------------------
  ff d5 01 01 00 00 00 ff      00:11:07.974  [VENDOR SPECIFIC]
  ca 00 80 b0 48 12 e1 00      00:11:07.973  WRITE DMA
  ca 00 80 30 48 12 e1 00      00:11:07.972  WRITE DMA
  ca 00 80 b0 47 12 e1 00      00:11:07.972  WRITE DMA
  ca 00 80 30 47 12 e1 00      00:11:07.972  WRITE DMA

Error 295 occurred at disk power-on lifetime: 0 hours (0 days + 0 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 51 01 01 00 00 00

  Commands leading to the command that caused the error were:
  CR FR SC SN CL CH DH DC   Powered_Up_Time  Command/Feature_Name
  -- -- -- -- -- -- -- --  ----------------  --------------------
  ff d5 01 01 00 00 00 ff      00:11:07.927  [VENDOR SPECIFIC]
  ca 00 80 b0 2a 12 e1 00      00:11:07.926  WRITE DMA
  ca 00 80 30 2a 12 e1 00      00:11:07.925  WRITE DMA
  ca 00 80 b0 29 12 e1 00      00:11:07.925  WRITE DMA
  ca 00 80 30 29 12 e1 00      00:11:07.924  WRITE DMA

Error 294 occurred at disk power-on lifetime: 0 hours (0 days + 0 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 51 01 01 00 00 00

  Commands leading to the command that caused the error were:
  CR FR SC SN CL CH DH DC   Powered_Up_Time  Command/Feature_Name
  -- -- -- -- -- -- -- --  ----------------  --------------------
  ff d5 01 01 00 00 00 ff      00:11:07.899  [VENDOR SPECIFIC]
  ca 00 80 b0 22 12 e1 00      00:11:07.898  WRITE DMA
  ca 00 80 30 22 12 e1 00      00:11:07.897  WRITE DMA
  ca 00 80 b0 21 12 e1 00      00:11:07.897  WRITE DMA
  ca 00 80 30 21 12 e1 00      00:11:07.896  WRITE DMA

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%      6288         -
# 2  Conveyance offline  Completed without error       00%      6285         -
# 3  Short offline       Completed without error       00%      6285         -
# 4  Extended offline    Completed without error       00%      6283         -
# 5  Extended offline    Completed without error       00%      6283         -
# 6  Short offline       Completed without error       00%      6283         -
# 7  Extended offline    Completed without error       00%      6262         -
# 8  Conveyance offline  Completed without error       00%      6262         -
# 9  Conveyance offline  Completed without error       00%      6262         -
#10  Extended offline    Completed without error       00%      6262         -
#11  Short offline       Completed without error       00%      6262         -
#12  Conveyance offline  Completed without error       00%      6211         -
#13  Extended offline    Completed without error       00%      6211         -
#14  Short offline       Completed without error       00%      6211         -
#15  Short offline       Completed without error       00%      6075         -
#16  Conveyance offline  Completed without error       00%      5564         -
#17  Extended offline    Completed without error       00%      5564         -
#18  Short offline       Completed without error       00%      5564         -
#19  Conveyance offline  Completed without error       00%      5319         -
#20  Short offline       Completed without error       00%      5319         -
#21  Conveyance offline  Completed without error       00%      4403         -

SMART Selective self-test log data structure revision number 0
Note: revision number not 1 implies that no selective self-test has ever been run
 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.

I have a year-old drive that's giving me trouble. Copying data to it fails after about 8-10GB of transfers. It spontaneously changes to 'read only'. It's properly formatted ext4, I'm the owner. Searching online, it looks like this is a symptom of a failing drive.

How do I confirm this, since the SMART tests indicate otherwise?

I did the obvious like check the Disk Utility, and ran the extended SMART test. All results from Disk Utility come back perfect. Read error rate and reallocated sectors are showing zero.

I'm guessing this disk is bad and SMART isn't detecting it, though I don't understand why. I'd like to confirm what the problem is.

I'm having no problems with the other disks in the machine.

fstab:

proc /proc proc nodev,noexec,nosuid 0 0 UUID=62e11126-3f06-43f0-bd5a-29b411bb8160 / ext4
errors=remount-ro 0 1
UUID=5e2d6348-be6e-4d5d-8f7f-1a5c1cab7db2 /home ext4
defaults 0 2 UUID=97e594a3-c783-4c73-97c0-682afcdc88b6 none swap sw 0 0
/dev/disk/by-label/Media /media/Media ntfs-3g defaults,user,locale=en_GB.utf8 0 0

Output of dmesg | less: (There are hundreds more 'Buffer I/O error' lines above)

[22734.511487] Buffer I/O error on device sda1, logical block 302203
[22734.511489] Buffer I/O error on device sda1, logical block 302204
[22734.511490] Buffer I/O error on device sda1, logical block 302205
[22734.511492] Buffer I/O error on device sda1, logical block 302206
[22734.511494] Buffer I/O error on device sda1, logical block 302207
[22734.511496] EXT4-fs warning (device sda1): ext4_end_bio:251: I/O error writing to inode 9437465 (offset 4194304 size 524288 starting block 302215)
[22734.511500] ata1: EH complete
[22734.511616] EXT4-fs error (device sda1): ext4_journal_start_sb:327: Detected aborted journal
[22734.511619] EXT4-fs (sda1): Remounting filesystem read-only
[22734.519343] EXT4-fs error (device sda1) in ext4_da_writepages:2298: IO failure
[22734.538566] EXT4-fs (sda1): ext4_da_writepages: jbd2_start: 601 pages, ino 9437474; err -30
[22734.560225] ata1.00: exception Emask 0x10 SAct 0x1 SErr 0x400100 action 0x6 frozen
[22734.560253] ata1.00: irq_stat 0x08000000, interface fatal error
[22734.560256] ata1: SError: { UnrecovData Handshk }
[22734.560258] ata1.00: failed command: WRITE FPDMA QUEUED
[22734.560262] ata1.00: cmd 61/00:00:3f:68:25/04:00:00:00:00/40 tag 0 ncq 524288 out
[22734.560263]          res 40/00:04:3f:68:25/00:00:00:00:00/40 Emask 0x10 (ATA bus error)
[22734.560264] ata1.00: status: { DRDY }
[22734.560268] ata1: hard resetting link
[22735.047845] ata1: SATA link up 1.5 Gbps (SStatus 113 SControl 310)
[22735.052069] ata1.00: configured for UDMA/33
[22735.067810] ata1: EH complete
[22735.136249] ata1.00: exception Emask 0x10 SAct 0x3f SErr 0x400100 action 0x6 frozen  

fsck result:

tom@1204-Desktop:~$ sudo fsck /dev/sda1
[sudo] password for tom: 
fsck from util-linux 2.20.1
e2fsck 1.42 (29-Nov-2011)
New_Volume: recovering journal
New_Volume contains a file system with errors, check forced.
Pass 1: Checking inodes, blocks, and sizes
Pass 2: Checking directory structure
Pass 3: Checking directory connectivity
Pass 4: Checking reference counts
Pass 5: Checking group summary information
Free blocks count wrong (236669077, counted=236701938).
Fix<y>? yes

Free inodes count wrong (61048336, counted=61048349).
Fix<y>? yes

Last but not least is the read/write screengrab, this is new. It used to stay pretty consistent over the duration of the test.

EDIT- When I powered on this morning the drive had changed from /dev/sda to /dev/sdc, strange. I'm certain that hasn't happened before and I'm certain it was /dev/sda. I swapped SATA cables with a known good one and saw that same failure at about 10GB transfers. I didn't change SATA ports yet, I'll try that next. (Edit #2, it was the SATA port, changing it fixed the problem. Flagging this as too localized.)

Output of sudo smartctl -a /dev/sda

=== START OF INFORMATION SECTION === Model Family:     Western Digital Caviar Black Device Model:     WDC WD1002FAEX-00Y9A0 Serial Number:    WD-WCAW30776630 LU WWN Device Id: 5 0014ee 25acf2868 Firmware Version:
05.01D05 User Capacity:    1,000,204,886,016 bytes [1.00 TB] 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 May 25 07:16:18 2012 BST 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:  (0x82)   Offline data collection activity
                    was completed without error.
                    Auto Offline Data Collection: Enabled. 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:      (16500) 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:    ( 170) minutes. Conveyance self-test routine recommended polling time:      (   5) minutes. SCT capabilities:
           (0x3035) 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  
-       0   3 Spin_Up_Time            0x0027   176   173   021    Pre-fail  Always       -       4183   4 Start_Stop_Count        0x0032 100   100   000    Old_age   Always       -       774   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   093   093   000    Old_age   Always       -       5518  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       -       772 192 Power-Off_Retract_Count 0x0032   200   200   000    Old_age   Always  
-       39 193 Load_Cycle_Count        0x0032   200   200   000    Old_age   Always       -       736 194 Temperature_Celsius     0x0022  118   111   000    Old_age   Always       -       29 196 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   200   200   000    Old_age   Offline      -       0 199 UDMA_CRC_Error_Count    0x0032   200   200   000    Old_age   Always  
-       0 200 Multi_Zone_Error_Rate   0x0008   200   200   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  Extended offline    Completed without error       00%      5514         -

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.

I'm getting these errors ramdomly, and I don't know if its normal or not.

[39441.061856] ata3.00: failed to read SCR 1 (Emask=0x40)
[39441.061866] ata3.01: failed to read SCR 1 (Emask=0x40)
[39441.061892] ata3.15: exception Emask 0x10 SAct 0x0 SErr 0x280100 action 0x6 frozen
[39441.061897] ata3.15: irq_stat 0x08000000, interface fatal error
[39441.061904] ata3.15: SError: { UnrecovData 10B8B BadCRC }
[39441.061910] ata3.00: exception Emask 0x100 SAct 0x0 SErr 0x0 action 0x6 frozen
[39441.061917] ata3.01: exception Emask 0x100 SAct 0xe SErr 0x0 action 0x6 frozen
[39441.061923] ata3.01: failed command: READ FPDMA QUEUED
[39441.061933] ata3.01: cmd 60/a8:08:b0:48:62/00:00:00:00:00/40 tag 1 ncq 86016 in
[39441.061940] ata3.01: status: { DRDY }
[39441.061944] ata3.01: failed command: READ FPDMA QUEUED
[39441.061953] ata3.01: cmd 60/a8:10:b0:49:62/00:00:00:00:00/40 tag 2 ncq 86016 in
[39441.061959] ata3.01: status: { DRDY }
[39441.061963] ata3.01: failed command: READ FPDMA QUEUED
[39441.061972] ata3.01: cmd 60/58:18:58:4a:62/00:00:00:00:00/40 tag 3 ncq 45056 in
[39441.061978] ata3.01: status: { DRDY }
[39441.061987] ata3.15: hard resetting link
[39441.608302] ata3.15: SATA link up 3.0 Gbps (SStatus 123 SControl 300)
[39441.609090] ata3.00: hard resetting link
[39441.929246] ata3.00: SATA link up 3.0 Gbps (SStatus 123 SControl 320)
[39441.929333] ata3.01: hard resetting link
[39442.249184] ata3.01: SATA link up 3.0 Gbps (SStatus 123 SControl 320)
[39442.263242] ata3.00: configured for UDMA/133
[39442.277570] ata3.01: configured for UDMA/133
[39442.277725] ata3: EH complete

I'm also pasting smartctl -a for sda, sdb and sdc.

Thanks in advance for your help.

Whenever I start my computer Ubuntu pops up the following error:

A hard disk may be failing
one or more hard disk report health problems

A friend of mine ran some test and it was found that my hard disk has 74 bad sectors.

Is this merely a software issue that will be solved after a complete format of my hard disk, or is it a hardware issue and I will have to replace my hard disk?

Awaiting your responses.

Thanks,
Sneha Kamath.

My system has started behaving strangely, intermittently locking up. I see messages like the following in syslog:

Nov 18 22:22:00 claypool kernel: [ 3428.078156] ata3.00: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x0
Nov 18 22:22:00 claypool kernel: [ 3428.078163] ata3.00: irq_stat 0x40000000
Nov 18 22:22:00 claypool kernel: [ 3428.078167] sr 2:0:0:0: CDB: Test Unit Ready: 00 00 00 00 00 00
Nov 18 22:22:00 claypool kernel: [ 3428.078182] ata3.00: cmd a0/00:00:00:00:00/00:00:00:00:00/a0 tag 0
Nov 18 22:22:00 claypool kernel: [ 3428.078184]          res 50/00:03:00:00:00/00:00:00:00:00/a0 Emask 0x1 (device error)
Nov 18 22:22:00 claypool kernel: [ 3428.078188] ata3.00: status: { DRDY }
Nov 18 22:22:00 claypool kernel: [ 3428.080887] ata3.00: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x0
Nov 18 22:22:00 claypool kernel: [ 3428.080890] ata3.00: irq_stat 0x40000000
Nov 18 22:22:00 claypool kernel: [ 3428.080893] sr 2:0:0:0: CDB: Test Unit Ready: 00 00 00 00 00 00
Nov 18 22:22:00 claypool kernel: [ 3428.080905] ata3.00: cmd a0/00:00:00:00:00/00:00:00:00:00/a0 tag 0
Nov 18 22:22:00 claypool kernel: [ 3428.080906]          res 50/00:03:00:00:00/00:00:00:00:00/a0 Emask 0x1 (device error)
Nov 18 22:22:00 claypool kernel: [ 3428.080910] ata3.00: status: { DRDY }

And then this:

Nov 18 23:13:56 claypool kernel: [ 6544.000798] ata1.00: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x6 frozen
Nov 18 23:13:56 claypool kernel: [ 6544.000804] ata1.00: failed command: FLUSH CACHE EXT
Nov 18 23:13:56 claypool kernel: [ 6544.000814] ata1.00: cmd ea/00:00:00:00:00/00:00:00:00:00/a0 tag 0
Nov 18 23:13:56 claypool kernel: [ 6544.000815]          res 40/00:00:00:4f:c2/00:00:00:00:00/40 Emask 0x4 (timeout)
Nov 18 23:13:56 claypool kernel: [ 6544.000819] ata1.00: status: { DRDY }
Nov 18 23:13:56 claypool kernel: [ 6544.000825] ata1: hard resetting link
Nov 18 23:14:01 claypool kernel: [ 6549.360324] ata1: link is slow to respond, please be patient (ready=0)
Nov 18 23:14:06 claypool kernel: [ 6554.008091] ata1: COMRESET failed (errno=-16)
Nov 18 23:14:06 claypool kernel: [ 6554.008103] ata1: hard resetting link
Nov 18 23:14:11 claypool kernel: [ 6559.372246] ata1: link is slow to respond, please be patient (ready=0)
Nov 18 23:14:16 claypool kernel: [ 6564.020228] ata1: COMRESET failed (errno=-16)
Nov 18 23:14:16 claypool kernel: [ 6564.020235] ata1: hard resetting link
Nov 18 23:14:21 claypool kernel: [ 6569.380109] ata1: link is slow to respond, please be patient (ready=0)
Nov 18 23:14:31 claypool kernel: [ 6579.460243] ata1: SATA link up 3.0 Gbps (SStatus 123 SControl 300)
Nov 18 23:14:31 claypool kernel: [ 6579.486595] ata1.00: configured for UDMA/133
Nov 18 23:14:31 claypool kernel: [ 6579.486601] ata1.00: retrying FLUSH 0xea Emask 0x4
Nov 18 23:14:31 claypool kernel: [ 6579.486939] ata1.00: device reported invalid CHS sector 0
Nov 18 23:14:31 claypool kernel: [ 6579.486952] ata1: EH complete
Nov 18 23:17:01 claypool CRON[3910]: (root) CMD (   cd / && run-parts --report /etc/cron.hourly)
Nov 18 23:17:01 claypool CRON[3908]: (CRON) error (grandchild #3910 failed with exit status 1)
Nov 18 23:17:01 claypool postfix/sendmail[3925]: fatal: open /etc/postfix/main.cf: No such file or directory
Nov 18 23:17:01 claypool CRON[3908]: (root) MAIL (mailed 1 byte of output; but got status 0x004b, #012)
Nov 18 23:39:01 claypool CRON[4200]: (root) CMD (  [ -x /usr/lib/php5/maxlifetime ] && [ -d /var/lib/php5 ] && find /var/lib/php5/ -type f -cmin +$(/usr/lib/php5/maxlifetime) -print0 | xargs -n 200 -r -0 rm)

There are no messages marked after 23:39. When I next tried to use the machine, it would not return from the screensaver (blank screen), nor switch to another terminal, and I had to hard reboot it.

[UPDATE] The output of smartctl is here. I had trouble getting this, because / is being mounted read-only (?!), which prevents most applications from running.

Also, it may not be related, but I have the following worrying messages in dmesg:

[   10.084596] k8temp 0000:00:18.3: Temperature readouts might be wrong - check erratum #141
[   10.098477] i2c i2c-0: nForce2 SMBus adapter at 0x600
[   10.098483] ACPI: resource nForce2_smbus [io  0x0700-0x073f] conflicts with ACPI region SM00 [??? 0x00000700-0x0000073f flags 0x30]
[   10.098486] ACPI: This conflict may cause random problems and system instability
[   10.098487] ACPI: If an ACPI driver is available for this device, you should use it instead of the native driver
[   10.098509] i2c i2c-1: nForce2 SMBus adapter at 0x700
[   10.112570] Linux agpgart interface v0.103
[   10.155329] atk: Resources not safely usable due to acpi_enforce_resources kernel parameter
[   10.161506] it87: Found IT8712F chip at 0x290, revision 8
[   10.161517] it87: VID is disabled (pins used for GPIO)
[   10.161527] it87: in3 is VCC (+5V)
[   10.161528] it87: in7 is VCCH (+5V Stand-By)
[   10.161560] ACPI: resource it87 [io  0x0295-0x0296] conflicts with ACPI region ECRE [??? 0x00000290-0x000002af flags 0x45]
[   10.161562] ACPI: This conflict may cause random problems and system instability
[   10.161564] ACPI: If an ACPI driver is available for this device, you should use it instead of the native driver

[UPDATE 2] I swapped in a new SATA cable, per Phil's suggestion. The current output of smartctl is here, if it helps.

[UPDATE 3] I don't think the cable fixed it. The system hasn't locked up yet, but my media player crashed a few minutes ago and I have the following in the syslog:

Nov 20 16:07:17 claypool kernel: [ 2294.400033] ata1: link is slow to respond, please be patient (ready=0)
Nov 20 16:07:47 claypool kernel: [ 2324.084581] ata1: COMRESET failed (errno=-16)
Nov 20 16:07:47 claypool kernel: [ 2324.084588] ata1: limiting SATA link speed to 1.5 Gbps
Nov 20 16:07:47 claypool kernel: [ 2324.084592] ata1: hard resetting link

I get the following response from smartctl:

$ sudo smartctl -a /dev/sda
[sudo] password for chris: 
sudo: Can't open /var/lib/sudo/chris/0: Read-only file system
smartctl 5.40 2010-03-16 r3077 [i686-pc-linux-gnu] (local build)
Copyright (C) 2002-10 by Bruce Allen, http://smartmontools.sourceforge.net

Device: /0:0:0:0  Version: 
scsiModePageOffset: response length too short, resp_len=47 offset=50 bd_len=46
>> Terminate command early due to bad response to IEC mode page
A mandatory SMART command failed: exiting. To continue, add one or more '-T permissive' options.