[SOLVED] EXT3 Aborting Journal / Kernel Soft Lockup Help

pawprint_net · 02-02-2011, 10:55 AM

I have a system running CentOS 5.5 (194.32 Kernel) that has been working fine for about 8 months. I found it stuck one morning dumping a Soft Lockup Kernel message every 10 seconds and have been trying to find out what is going on - here is what I've done and found.

System is a Core i3 with 4Gb DDR3 ram and 2 1.5Tb SATA drives - everything is less then 1 year old with not too much load (this is a backup system for my server - a twin and the other works fine)
Intel Mobo: DM55HC

Rebooting the system (after doing a fsck on the drives with lots of errors) it runs for about 20 hours or so and then drops back into this problem.

Prior to going into the soft lockup it reports that the Journal has aborted on one drive or the other and drops into a Read Only FS.

There is nothing in the logs apart from the aborting journal message and the soft-lockup)

Tried fsck with badblocks check on the 2 mountpoints for both drives (dunno how to check the swap partition) - nothing I could see there.
I have tried memtest for about 36hours. No errors
I ran smartctl long tests on both drives. No Errors

I'm beginning to think it's the SATA controller on the motherboard but I have no idea how to test this.

I'd appreciate any thoughts of what I can do next.

business_kid · 02-02-2011, 01:02 PM

It's the backup; can it come offline? What's the output of smartctl?
BTW have you tried remounting ext2?

pawprint_net · 02-02-2011, 02:57 PM

Yes, in fact, it's offline now - I have tried rebooting and remounting and running at different run levels several times - When I switched to "init 1" and unmounted everything it seemed to sit there without incident for 24h - which would make me think it's not a CPU thing but as soon as the drives come into play it seems to be just a matter of time before it fails.

Ambient, motherboard, and CPU temps are all < 30C so I don't think it's overheating either.

The output from smartctl was basically that the test had completed and there were no errors detected - that's all it said.

I can run a specific smartctl report if that would help just let me know.

business_kid · 02-03-2011, 02:41 AM

Ok, basics all good.
Next I would look into the specific error. Exactly what has gone wrong when a kernel goes into soft lockup? I've never seen that. Check the kernel bugzilla.
Can you make the journal external? e.g. the journal for drive a on drive b, & vice versa? tune2fs -J I think.
You might end up emailing support - in the drive manufacturer, chipset or CentOS.
I would also change what you can painlessly change for the sake of changing it, so you can eliminate it from suspicion.

pawprint_net · 02-03-2011, 03:02 PM

After asking around a lot I may have a solution - someone suggested turning off acpi in the kernel they though it might be an IRQ conflict and I had seen some messages about a certain IRQ getting disabled upon boot. I have tried this and I'm waiting to see what the system does in 24-36 hours.

I'll post a followup in either case.

unSpawn · 02-03-2011, 04:30 PM

Quote:

Originally Posted by pawprint_net

I'll post a followup in either case.

When you do please consider posting exact HW specs and error messages. YMMV but it just may help.

pawprint_net · 02-07-2011, 09:31 PM

More info...

Tried the IRQ and Kernel options to no avail... Since then I have also tried the following:

Installing a new Centos5.5 on a different HD (same make/model) and let the system run for 3 days - no problems at all with this.

Tried booting again from the old HD and got the same problems after various lengths of time.

I have just found something new though - after the system crashes and I get into the repair filesystem prompt and start running fsck I can do this over and over and every single time I run it I always get errors being fixed - I have run repeated SMART tests and badblocks tests all showing that everything is fine - but every time I run fsck it finds and corrects errors. This makes no sense to me. Any ideas?

Detailed Hardware description:

Intel DH55HC Motherboard
Core i3 530 @ 2.93GHz
4Gb OCZ DDR3 - 1333 Ram
1Tb ST31000528AS Segate HD (boot Drive)
1.5Tb WDC WD15EARS-00Z5B1 WD HD (data Drive)

I will try to get exact error messages but it's hard because the system keeps failing.

business_kid · 02-08-2011, 02:24 AM

Quote:

Originally Posted by pawprint_net

I have just found something new though - after the system crashes and I get into the repair filesystem prompt and start running fsck I can do this over and over and every single time I run it I always get errors being fixed - I have run repeated SMART tests and badblocks tests all showing that everything is fine - but every time I run fsck it finds and corrects errors. This makes no sense to me. Any ideas?

Yeah, classic symptoms of the disk falling apart. try du -sh /lost+found. If it's going up, your disk is gone.

unSpawn · 02-08-2011, 03:27 AM

Quote:

Originally Posted by pawprint_net

1Tb ST31000528AS Segate HD (boot Drive)
1.5Tb WDC WD15EARS-00Z5B1 WD HD (data Drive)

Looking on the 'net for nfo you'll find more than a few hints at ST31000528AS 1TB disks to have firmware problems and even a hint of one company saying there's a higher than average return rate for these disks. The amount of problems with WD15EARS-00Z5B1 1.5TB disks by comparison seem lower but it's not like Caviar Green EADS/EARS-type drives are without problems...

Quote:

Originally Posted by business_kid

try du -sh /lost+found. If it's going up, your disk is gone.

I'd mark looking at /lost+found as "circumstantial evidence" because it only gets filled if fsck detects VFS-level problems, actually can correct things and manages to save files there. I mean there may be types of problems where saving may not be possible or not relevant, right?

Quote:

Originally Posted by pawprint_net

I have run repeated SMART tests and badblocks tests all showing that everything is fine

There's a rather large difference between just running 'smartd' and running (scheduled?) long self tests. Besides saying "everything is fine" doesn't mean a thing to me, I'd rather see 'smartctl -Ha /dev/devicename'-style output. I agree problems you reported should only lead to you backing up valuable data as soon as possible and replacing the failing disk(s).

pawprint_net · 02-08-2011, 06:43 AM

I have been running long self tests in smartctl I finally managed to capture some results.

I'd love to replace the drive - but to do that I must get segate's seatools to give me a code so I can get an RMA or somehow convince them it IS the drive failing - unfortunately when I use their seatools bootable ISO the thing crashes (which seems to be a common problem) and so looking for an alternative the SMART output below really isn't helping my case (the results here look just fine to me no?).

du -sh /lost+found gives 172K but doesn't seem to be increasing.

Code:

smartctl version 5.38 [x86_64-redhat-linux-gnu] Copyright (C) 2002-8 Bruce Allen
Home page is http://smartmontools.sourceforge.net/

=== START OF INFORMATION SECTION ===
Device Model:     ST31000528AS
Serial Number:    9VP78WVQ
Firmware Version: CC38
User Capacity:    1,000,204,886,016 bytes
Device is:        Not in smartctl database [for details use: -P showall]
ATA Version is:   8
ATA Standard is:  ATA-8-ACS revision 4
Local Time is:    Tue Feb  8 04:35:48 2011 PST
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:                 ( 600) 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:        ( 179) minutes.
Conveyance self-test routine
recommended polling time:        (   2) minutes.
SCT capabilities:              (0x103f) SCT Status supported.
                                        SCT Feature Control supported.
                                        SCT Data Table supported.

SMART Attributes Data Structure revision number: 10
Vendor Specific SMART Attributes with Thresholds:
ID# ATTRIBUTE_NAME          FLAG     VALUE WORST THRESH TYPE      UPDATED  WHEN_FAILED RAW_VALUE
  1 Raw_Read_Error_Rate     0x000f   116   099   006    Pre-fail  Always       -       109041358
  3 Spin_Up_Time            0x0003   095   095   000    Pre-fail  Always       -       0
  4 Start_Stop_Count        0x0032   100   100   020    Old_age   Always       -       56
  5 Reallocated_Sector_Ct   0x0033   100   100   036    Pre-fail  Always       -       0
  7 Seek_Error_Rate         0x000f   075   060   030    Pre-fail  Always       -       37883900
  9 Power_On_Hours          0x0032   096   096   000    Old_age   Always       -       3818
 10 Spin_Retry_Count        0x0013   100   100   097    Pre-fail  Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   020    Old_age   Always       -       28
183 Unknown_Attribute       0x0032   100   100   000    Old_age   Always       -       0
184 Unknown_Attribute       0x0032   100   100   099    Old_age   Always       -       0
187 Reported_Uncorrect      0x0032   100   100   000    Old_age   Always       -       0
188 Unknown_Attribute       0x0032   099   098   000    Old_age   Always       -       34
189 High_Fly_Writes         0x003a   100   100   000    Old_age   Always       -       0
190 Airflow_Temperature_Cel 0x0022   081   050   045    Old_age   Always       -       19 (Lifetime Min/Max 18/19)
194 Temperature_Celsius     0x0022   019   050   000    Old_age   Always       -       19 (0 13 0 0)
195 Hardware_ECC_Recovered  0x001a   037   023   000    Old_age   Always       -       109041358
197 Current_Pending_Sector  0x0012   100   100   000    Old_age   Always       -       0
198 Offline_Uncorrectable   0x0010   100   100   000    Old_age   Offline      -       0
199 UDMA_CRC_Error_Count    0x003e   200   200   000    Old_age   Always       -       0
240 Head_Flying_Hours       0x0000   100   253   000    Old_age   Offline      -       89661737275179
241 Unknown_Attribute       0x0000   100   253   000    Old_age   Offline      -       2679377008
242 Unknown_Attribute       0x0000   100   253   000    Old_age   Offline      -       1829373452

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%      3817         -
# 2  Extended offline    Completed without error       00%      3745         -

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.

and the other drive...

Code:

smartctl version 5.38 [x86_64-redhat-linux-gnu] Copyright (C) 2002-8 Bruce Allen
Home page is http://smartmontools.sourceforge.net/

=== START OF INFORMATION SECTION ===
Device Model:     WDC WD15EARS-00Z5B1
Serial Number:    WD-WCAVU0461015
Firmware Version: 80.00A80
User Capacity:    1,500,301,910,016 bytes
Device is:        Not in smartctl database [for details use: -P showall]
ATA Version is:   8
ATA Standard is:  Exact ATA specification draft version not indicated
Local Time is:    Tue Feb  8 04:40:58 2011 PST
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:                 (34200) 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:        ( 255) minutes.
Conveyance self-test routine
recommended polling time:        (   5) minutes.
SCT capabilities:              (0x3031) 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   181   180   021    Pre-fail  Always       -       5950
  4 Start_Stop_Count        0x0032   100   100   000    Old_age   Always       -       27
  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       -       3749
 10 Spin_Retry_Count        0x0032   100   253   000    Old_age   Always       -       0
 11 Calibration_Retry_Count 0x0032   100   253   000    Old_age   Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       25
192 Power-Off_Retract_Count 0x0032   200   200   000    Old_age   Always       -       17
193 Load_Cycle_Count        0x0032   198   198   000    Old_age   Always       -       8923
194 Temperature_Celsius     0x0022   127   098   000    Old_age   Always       -       23
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%      3699         -
# 2  Extended offline    Completed without error       00%      3693         -

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.

pawprint_net · 02-08-2011, 08:04 AM

Update: Just found a firmware update for the ST31000528AS - I have applied it and am running another smartctl -t long

Strange because if you search for the update on the segate site using the drive serial you don't find it - but doing a search on google you do - else I would have found this ages ago.

... again I'll post an update when I have one.

pawprint_net · 02-08-2011, 08:36 AM

now the other drive goes into error mode again - this is from the WD - seems highly unlikely to me that 2 drives from 2 different manufacturers would fail at exactly the same time both showing no SMART errors nor badblocks errors. This must be the Mobo or the OS no?

Code:

Feb  8 06:03:00 backup kernel: EXT3-fs error (device sdb2): ext3_lookup: unlinked inode 281804899 in dir #298582113
Feb  8 06:03:00 backup kernel: Aborting journal on device sdb2.
Feb  8 06:03:00 backup kernel: EXT3-fs error (device sdb2): ext3_lookup: unlinked inode 281804901 in dir #298582113
Feb  8 06:03:00 backup kernel: ext3_abort called.
Feb  8 06:03:00 backup kernel: EXT3-fs error (device sdb2): ext3_journal_start_sb: Detected aborted journal
Feb  8 06:03:00 backup kernel: Remounting filesystem read-only
Feb  8 06:03:05 backup kernel: EXT3-fs error (device sdb2): ext3_lookup: unlinked inode 280821991 in dir #297599203
Feb  8 06:03:05 backup kernel: EXT3-fs error (device sdb2): ext3_lookup: unlinked inode 280855537 in dir #297632751

pawprint_net · 02-09-2011, 03:56 PM

More information.

I tried re-installing with CentOS 5.5 on new hard drives - as soon as I started the backup running - (takes about 4 hours) the same problem cropped up - this confirms for me without any doubt that it's NOT the hard drives that are the problem. I believe it's either the OS or the Motherboard - Intel won't support the Mobo with Linux so I have now installed Windows 7 on the system and am running the backup that way to see if any problem crops up. Not really asking any question at this point (unless someone has an idea) just updating the thread in case anyone else has a similar problem ever.

unSpawn · 02-09-2011, 05:41 PM

Thanks, definitely interesting. Could help to post motherboard detailed version and HW specs, especially used chipset nfo (or update the http://www.linuxquestions.org/hcl/).

business_kid · 02-10-2011, 02:32 AM

I've had similar on 2 occasions
1. A mismatch of drives (Seagate & anything else) on the same ide lead produced 'ringing' so things saw logic levels that weren't there, and the fs threw errors.
2. logic levels on a bus drifting out of spec, at which point the device stopped working.