Fixing disk problems under Linux with smartmontools

Assumptions: Linux OS, ext2 or ext3 file system.

Starting with GNU coreutils release 5.3.0, dd on Linux includes options 'iflag=direct' and 'oflag=direct'. Using these with the dd commands below should be helpful, because adding these flags should avoid any interaction with the block buffering IO layer in Linux and permit direct reads/writes from the raw device. Use 'dd --help' to see if your version of dd supports these options. If not, build the latest code from fttp://alpha.gnu.org/gnu/coreutils.

In this example, the disk is failing self-tests at Logical Block Address LBA = 0x016561e9 = 23421417. The LBA counts sectors in units of 512 bytes, and starts at zero.

[root@host]# smartctl -l selftest /dev/hda:
SMART Self-test log structure revision number 1
Num Test_Description Status Remaining LifeTime(hours) LBA_of_first_error
# 1 Extended offline Completed: read failure 90% 217 0x016561e9 

Note that other signs that there is a bad sector on the disk can be
found in the non-zero value of the Current Pending Sector count:

[root@host]# smartctl -A /dev/hda
ID# ATTRIBUTE_NAME FLAG VALUE WORST THRESH TYPE UPDATED WHEN_FAILED RAW_VALUE
5 Reallocated_Sector_Ct 0x0033 100 100 005 Pre-fail Always - 0
196 Reallocated_Event_Count 0x0032 100 100 000 Old_age Always - 0
197 Current_Pending_Sector 0x0022 100 100 000 Old_age Always - 1
198 Offline_Uncorrectable 0x0008 100 100 000 Old_age Offline - 1 

First Step: We need to locate the partition on which this sector of
the disk lives:

[root@host]# fdisk -lu /dev/hda
Disk /dev/hda: 123.5 GB, 123522416640 bytes
255 heads, 63 sectors/track, 15017 cylinders, total 241254720 sectors
Units = sectors of 1 * 512 = 512 bytes

Device Boot Start End Blocks Id System
/dev/hda1 * 63 4209029 2104483+ 83 Linux
/dev/hda2 4209030 5269319 530145 82 Linux swap
/dev/hda3 5269320 238227884 116479282+ 83 Linux
/dev/hda4 238227885 241248104 1510110 83 Linux  

The partition /dev/hda3 starts at LBA 5269320 and extends past the 'problem' LBA. The 'problem' LBA is offset 23421417 - 5269320 = 18152097 sectors into the partition /dev/hda3.

To verify the type of the file system and the mount point, look in /etc/fstab:

[root@host]# grep hda3 /etc/fstab
/dev/hda3 /data ext2 defaults 1 2 

You can see that this is an ext2 file system, mounted at /data.

Second Step: we need to find the blocksize of the file system
(normally 4096 bytes for ext2):

[root@host]# tune2fs -l /dev/hda3 | grep Block
Block count: 29119820
Block size: 4096  

In this case the block size is 4096 bytes.

Third Step: we need to determine which File System Block contains this
LBA. The formula is:

b = (int)((L-S)*512/B)

where:

b = File System block number
B = File system block size in bytes
L = LBA of bad sector
S = Starting sector of partition as shown by fdisk -lu
and (int) denotes the integer part.

In our example, L=23421417, S=5269320, and B=4096. Hence the 'problem' LBA is in block number
b = (int)18152097*512/4096 = (int)2269012.125
so b=2269012.

Note: the fractional part of 0.125 indicates that this problem LBA is actually the second of the eight sectors that make up this file system block.

Fourth Step: we use debugfs to locate the inode stored in this block, and the file that contains that inode:

[root@host]# debugfs
debugfs 1.32 (09-Nov-2002)
debugfs: open /dev/hda3
debugfs: icheck 2269012
Block Inode number
2269012 41032
debugfs: ncheck 41032
Inode Pathname
41032 /S1/R/H/714197568-714203359/H-R-714202192-16.gwf  

In this example, you can see that the problematic file (with the mount point included in the path) is:

/data/S1/R/H/714197568-714203359/H-R-714202192-16.gwf 

To force the disk to reallocate this bad block we'll write zeros to the bad block, and sync the disk:

[root@host]# dd if=/dev/zero of=/dev/hda3 bs=4096 count=1 seek=2269012
[root@host]# sync  

NOTE: THIS LAST STEP HAS PERMANENTLY AND IRRETRIEVABLY DESTROYED SOME OF THE DATA THAT WAS IN THIS FILE. DON'T DO THIS UNLESS YOU DON'T NEED THE FILE OR YOU CAN REPLACE IT WITH A FRESH OR CORRECT VERSION.

Now everything is back to normal: the sector has been reallocated.
Compare the output just below to similar output near the top of this
article:

[root@host]# smartctl -A /dev/hda
ID# ATTRIBUTE_NAME FLAG VALUE WORST THRESH TYPE UPDATED WHEN_FAILED RAW_VALUE
5 Reallocated_Sector_Ct 0x0033 100 100 005 Pre-fail Always - 1
196 Reallocated_Event_Count 0x0032 100 100 000 Old_age Always - 1
197 Current_Pending_Sector 0x0022 100 100 000 Old_age Always - 0
198 Offline_Uncorrectable 0x0008 100 100 000 Old_age Offline - 1  

Note: for some disks it may be necessary to update the SMART Attribute values by using:

smartctl -t offline /dev/hda 

The disk now passes its self-tests again:

[root@host]# smartctl -t long /dev/hda [wait until test completes, then]
[root@host]# smartctl -l selftest /dev/hda
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% 239 -
# 2 Extended offline Completed: read failure 90% 217 0x016561e9
# 3 Extended offline Completed: read failure 90% 212 0x016561e9
# 4 Extended offline Completed: read failure 90% 181 0x016561e9
# 5 Extended offline Completed without error 00% 14 -
# 6 Extended offline Completed without error 00% 4 -  

and no longer shows any offline uncorrectable sectors:

[root@host]# smartctl -A /dev/hda
ID# ATTRIBUTE_NAME FLAG VALUE WORST THRESH TYPE UPDATED WHEN_FAILED RAW_VALUE
5 Reallocated_Sector_Ct 0x0033 100 100 005 Pre-fail Always - 1
196 Reallocated_Event_Count 0x0032 100 100 000 Old_age Always - 1
197 Current_Pending_Sector 0x0022 100 100 000 Old_age Always - 0
198 Offline_Uncorrectable 0x0008 100 100 000 Old_age Offline - 0 

A SECOND EXAMPLE

On this drive, the first sign of trouble was this email from smartd:

To: ballen
Subject: SMART error (selftest)
detected on host: medusa-slave166.medusa.phys.uwm.edu

This email was generated by the smartd daemon running on host:
medusa-slave166.medusa.phys.uwm.edu in the domain: master001-nis

The following warning/error was logged by the smartd daemon:
Device: /dev/hda, Self-Test Log error count increased from 0 to 1 

Running:

[root@host]# smartctl -a /dev/hda 

confirmed the problem:

Num Test_Description Status Remaining LifeTime(hours) LBA_of_first_error
# 1 Extended offline Completed: read failure 80% 682 0x021d9f44 

Note that the failing LBA reported is 0x021d9f44 (base 16) = 35495748 (base 10)

ID# ATTRIBUTE_NAME FLAG VALUE WORST THRESH TYPE UPDATED WHEN_FAILED RAW_VALUE
5 Reallocated_Sector_Ct 0x0033 100 100 005 Pre-fail Always - 0
196 Reallocated_Event_Count 0x0032 100 100 000 Old_age Always - 0
197 Current_Pending_Sector 0x0022 100 100 000 Old_age Always - 3
198 Offline_Uncorrectable 0x0008 100 100 000 Old_age Offline - 3 

and one can see above that there are 3 sectors on the list of pending sectors that the disk can't read but would like to reallocate.

The device also shows errors in the SMART error log:

Error 212 occurred at disk power-on lifetime: 690 hours
After command completion occurred, registers were:

ER ST SC SN CL CH DH
-- -- -- -- -- -- --
40 51 12 46 9f 1d e2 Error: UNC 18 sectors at LBA = 0x021d9f46 = 35495750

Commands leading to the command that caused the error were:

CR FR SC SN CL CH DH DC Timestamp Command/Feature_Name
-- -- -- -- -- -- -- -- --------- --------------------
25 00 12 46 9f 1d e0 00 2485545.000 READ DMA EXT  

Signs of trouble at this LBA may also be found in SYSLOG:

[root@host]# grep LBA /var/log/messages | awk '{print $12}' | sort | uniq
LBAsect=35495748
LBAsect=35495750 

So I decide to do a quick check to see how many bad sectors there really are. Using the bash shell I check 70 sectors around the trouble area:

[root@host]# export i=35495730
[root@host]# while [ $i -lt 35495800 ]
> do echo $i
> dd if=/dev/hda of=/dev/null bs=512 count=1 skip=$i
> let i+=1
> done

35495734
1+0 records in
1+0 records out
35495735
dd: reading `/dev/hda': Input/output error
0+0 records in
0+0 records out

35495751
dd: reading `/dev/hda': Input/output error
0+0 records in
0+0 records out
35495752
1+0 records in
1+0 records out
...  

which shows that the seventeen sectors 35495735-35495751 (inclusive) are not readable.

Next, we identify the files at those locations. The partitioning information on this disk is identical to the first example above, and as in that case the problem sectors are on the third partition /dev/hda3. So we have:

L=35495735 to 35495751
S=5269320
B=4096  

so that b=3778301 to 3778303 are the three bad blocks in the file
system.

[root@host]# debugfs
debugfs 1.32 (09-Nov-2002)
debugfs: open /dev/hda3
debugfs: icheck 3778301
Block Inode number
3778301 45192
debugfs: icheck 3778302
Block Inode number
3778302 45192
debugfs: icheck 3778303
Block Inode number
3778303 45192
debugfs: ncheck 45192
Inode Pathname
45192 /S1/R/H/714979488-714985279/H-R-714979984-16.gwf
debugfs: quit  

And finally, just to confirm that this is really the damaged file:

[root@host]# md5sum /data/S1/R/H/714979488-714985279/H-R-714979984-16.gwf
md5sum: /data/S1/R/H/714979488-714985279/H-R-714979984-16.gwf: Input/output error  

Finally we force the disk to reallocate the three bad blocks:

[root@host]# dd if=/dev/zero of=/dev/hda3 bs=4096 count=3 seek=3778301
[root@host]# sync  

We could also probably use:

[root@host]# dd if=/dev/zero of=/dev/hda bs=512 count=17 seek=35495735 

At this point we now have:

ID# ATTRIBUTE_NAME FLAG VALUE WORST THRESH TYPE UPDATED WHEN_FAILED RAW_VALUE
5 Reallocated_Sector_Ct 0x0033 100 100 005 Pre-fail Always - 0
196 Reallocated_Event_Count 0x0032 100 100 000 Old_age Always - 0
197 Current_Pending_Sector 0x0022 100 100 000 Old_age Always - 0
198 Offline_Uncorrectable 0x0008 100 100 000 Old_age Offline - 0  

which is encouraging, since the pending sectors count is now zero.
Note that the drive reallocation count has not yet increased: the drive may now have confidence in these sectors and have decided not to reallocate them..

A device self test:

[root@host]# smartctl -t long /dev/hda

(then wait about an hour) shows no unreadable sectors or errors:

Num Test_Description Status Remaining LifeTime(hours) LBA_of_first_error
# 1 Extended offline Completed without error 00% 692 -
# 2 Extended offline Completed: read failure 80% 682 0x021d9f44 

USEFUL HINTS ADDED BY OTHERS

From: Kay Diederichs

I read your badblocks-howto at http://smartmontools.sourceforge.net/BadBlockHowTo.txt and greatly benefitted from it. One thing that's (maybe) missing is that often the "smartctl -t long" scan finds a bad sector which is _not_ assigned to any file. In that case it does not help to run debugfs, or rather debugfs reports the fact that no file owns that sector. Furthermore, it is somewhat laborious to come up with the correct numbers for debugfs, and debugfs is slow ...

So what I suggest in the case of presence of Current_Pending_Sector/Offline_Uncorrectable errors is to create a huge file on that filesystem.

[root@host]# dd if=/dev/zero of=/some/mount/point bs=4k 

creates the file. Leave it running until the partition/filesystem is full. This will make the disk reallocate those sectors which do not belong to a file. Check the "smartctl -a" output after that and make sure that the sectors are reallocated. If any remain, use the debugfs method. Of course the usual caveats apply - back it up first, and so on.

From: Frederic BOITEUX

HOW TO LOCATE AND REPAIR BAD BLOCKS ON AN LVM VOLUME

* Smartd reports an error in a short test :

[root@host]# smartctl -a /dev/hdb
...
SMART Self-test log structure revision number 1
Num Test_Description Status Remaining LifeTime(hours) LBA_of_first_error
# 1 Short offline Completed: read failure 90% 66 37383668  

So the disk has a bad block located in LBA block 37383668

* In which physical partition is the bad block ?

[root@host]# sfdisk -lu /dev/hdb
Disk /dev/hdb: 9729 cylinders, 255 heads, 63 sectors/track
Units = sectors of 512 bytes, counting from 0

Device Boot Start End #sectors Id System
/dev/hdb1 63 996029 995967 82 Linux swap / Solaris
/dev/hdb2 * 996030 1188809 192780 83 Linux
/dev/hdb3 1188810 156296384 155107575 8e Linux LVM
/dev/hdb4 0 - 0 0 Empty 

It's in the /dev/hdb3 partition, a LVM2 partition.

From the LVM2 partition beginning, the bad block has an offset of
(37383668 - 1188810) = 36194858

We have to find in which LVM2 logical partition the block belongs to.

* In which logical partition is the bad block ?

*IMPORTANT* : LVM2 can use different schemes dividing its physical partitions to logical ones : linear, striped, contiguous or not... The following example assumes that allocation is linear !

The physical partition used by LVM2 is divided in PE (Physical Extent)units of the same size, starting at pe_start' 512 bytes blocks from the beginning of the physical partition.

The 'pvdisplay' command gives the size of the PE (in KB) of the LVM partition :

[root@host]# part=/dev/hdb3 ; pvdisplay -c $part | awk -F: '{print $8}' 4096  

To get its size in LBA block size (512 bytes or 0.5 KB), we multiply this number by 2 : 4096 * 2 = 8192 blocks for each PE.

To find the offset from the beginning of the physical partition is a bit more difficult : if you have a recent LVM2 version, try :

[root@host]# pvs -o+pe_start $part 

Either, you can look in /etc/lvm/backup :

[root@host]# grep pe_start $(grep -l $part /etc/lvm/backup/*) pe_start = 384 

Then, we search in which PE is the badblock, calculating the PE rank in which the faulty block of the partition is :

physical partition's bad block number / sizeof(PE) = 36194858 / 8192 = 4418.3176  

So we have to find in which LVM2 logical partition is used the PE number 4418 (count starts from 0) :

[root@host]# lvdisplay --maps |egrep 'Physical|LV Name|Type' LV Name /dev/WDC80Go/racine

Type linear
Physical volume /dev/hdb3
Physical extents 0 to 127
LV Name /dev/WDC80Go/usr

Type linear
Physical volume /dev/hdb3
Physical extents 128 to 1407
LV Name /dev/WDC80Go/var

Type linear
Physical volume /dev/hdb3
Physical extents 1408 to 1663
LV Name /dev/WDC80Go/tmp

Type linear
Physical volume /dev/hdb3
Physical extents 1664 to 1791
LV Name /dev/WDC80Go/home

Type linear
Physical volume /dev/hdb3
Physical extents 1792 to 3071
LV Name /dev/WDC80Go/ext1

Type linear
Physical volume /dev/hdb3
Physical extents 3072 to 10751
LV Name /dev/WDC80Go/ext2

Type linear
Physical volume /dev/hdb3
Physical extents 10752 to 18932  

So the PE #4418 is in the /dev/WDC80Go/ext1 LVM logical partition.

* Size of logical block of filesystem on /dev/WDC80Go/ext1 :

It's a ext3 fs, so I get it like this :

[root@host]# dumpe2fs /dev/WDC80Go/ext1 | grep 'Block size'
dumpe2fs 1.37 (21-Mar-2005)

Block size: 4096

* bad block number for the filesystem :

The logical partition begins on PE 3072 :
(# PE's start of partition * sizeof(PE)) + parttion offset[pe_start] =
(3072 * 8192) + 384 = 25166208

512b block of the physical partition, so the bad block number for the
filesystem is :

(36194858 - 25166208) / (sizeof(fs block) / 512) = 11028650 / (4096 / 512) = 1378581.25

* Test of the fs bad block :

dd if=/dev/WDC80Go/ext1 of=block1378581 bs=4096 count=1 skip=1378581 

If this dd command succeeds, without any error message in console or syslog, then the block number calculation is probably wrong ! *Don't* go further, re-check it and if you don't find the error, please renunce !

* Search / correction follows the same scheme as for simple partitions :
- find possible impacted files with debugfs (icheck ,
then ncheck ).
- reallocate bad block writing zeros in it, *using the fs block size* :

[root@host]# dd if=/dev/zero of=/dev/WDC80Go/ext1 count=1 bs=4096 seek=1378581  

3 comments:

  1. Instead of all of this you could just install and use the hdrecover program.

    ReplyDelete
  2. You sure can, this shows how things used to be done some time ago, and it's a good primer on tools and methodologies for troubleshooting disk problems.

    ReplyDelete
  3. very good article, I could learn a lot. thanks!

    ReplyDelete