Linux Troubleshooting

If you are booting a CentOS 6 system after having migrated its root filesystem to a new volume, you might get the following errors if /proc or /sys is missing:

EXT4-fs (dm-0): mounted filesystem with ordered data mode. Opts: 
mount: /dev/mapper/vg0-root already mounted or /sysroot busy
mount: according to mtab, /dev/mapper/vg0-root is already mounted on /sysroot
dracut: Remounting /dev/mapper/vg0-root with -o relatime,ro
EXT4-fs (dm-0): mounted filesystem with ordered data mode. Opts: 
mount: /dev/mapper/vg0-root already mounted or /sysroot busy
mount: according to mtab, /dev/mapper/vg0-root is already mounted on /sysroot
dracut: Remounting /dev/mapper/vg0-root with -o relatime,ro
EXT4-fs (dm-0): mounted filesystem with ordered data mode. Opts: 
dracut Warning: Can't mount root filesystem

To fix this, all you need to do is mount the root filesystem and “mkdir proc/ sys/”. You can even do this from inside of dracut if you add the “rdshell” argument to the end of your kernel command line:

dracut:/# mount -o remount,rw /sysroot
dracut:/# mkdir /sysroot/proc /sysroot/sys
dracut:/# mount -o remount,ro /sysroot
dracut:/# exit
(You may need to reboot the server)

-Eric

First, it is my opinion that you shouldst use hardware RAID of some form.  Software RAID, in my opinion, is best used to stripe volumes between multiple hardware RAID controllers which do not support spanning.

My opinion aside, will the server still boot?  Yes!  … if it is configured correctly.

The Multiple Disk (md) infrastructure in Linux is quite flexible, and there are many articles available for its use.  When configuring a server to recover from a failed disk-0 in a RAID mirror, your boot partition should be mirrored using metadata version 1.0.  Version 1.0 places metadata at the end of the device, whereas 1.1 metadata is at the front of the device.  Since metadata is at the end of the disk, GRUB (or whatever bootloader you prefer) can still read your boot images.

Lets say you have a server with (at least) three disk bays.  Disk-0 in bay1 fails,  so you add a 3rd disk in bay3 and rebuild the volume.  The process might look something like thos:

## Transfer the boot sector
# dd if=/dev/sdb count=1 of=/dev/sdc 

## Reread the partition table
# blockdev --rereadpt /dev/sdc

## Add the hot spare
# mdadm --add /dev/md0 /dev/sdc1
# mdadm --add /dev/md1 /dev/sdc2

## Fail the bad disk:
# mdadm --fail /dev/sda1
# mdadm --fail /dev/sda2

Now disk-0 (sda) is failed, and the mirror is rebuilding on sdb/sdc.  If you boot, what will happen?  Will it load the mirror correctly?  Will the kernel respect which disk is in the mirror?  We recently had a real-life scenario where a CentOS 6 server was in production and could not be rebooted, but we needed to know if the server would come up if there was a reboot.  Disk-0 was dying (but not completely dead yet).

Test to make certain

1. If disk1 may not contain the right boot sector, so when disk0 is removed, will the server boot?
2. If disk0 isn’t removed and the server is rebooted, will it boot?  If it does come up, will the kernel respect that disk0 is, indeed, failed?

The answer to both of these questions, at least in theory, is yes.

To be sure, I simulated the two failure scenarios above and everything worked without intervention.  This was the order of things, disks are named disk0, disk1, disk2:

1. Install CentOS 6 on mirrored boot and lvm partitions across two disks.
2. Add disk2, copy the bootsector over, and add as a hot spare.
3. Fail disk0, let the hot spare rebuild.
4. reboot!
5. The system loads the bootsector from disk0 because it is the first physical disk serviced by BIOS.
6. The kernel boots and auto-detects the RAID1 mirrors on disk1 and disk2, ignoring disk0 which we failed (good!)  This verifies question #1.
7. Physically remove disk0; BIOS will see disk1 as the first BIOS drive.
8. reboot.
9. The system loads the bootsector from disk1 because it is the first physical disk serviced by BIOS.
10. The kernel boots and initrd auto-configures the RAID1 mirrors on disk1 and disk2.  Thus validates question #2.

Of course you would expect the above to work—but its always best to test and understand exactly how your disk-volume software will act in various failure scenarios when working in a production environment.  “I think so” isn’t good enough to go on—you must know.

So, if you’re booting from software RAID, you can usually trust that your data is safe.   Sometimes a failed disk will hang IOs to the device.  I have seen servers completely freeze when this happens while it attempts to retry the IO over-and-over-and-over.  This is where hardware RAID can really save you; the hardware controller would have timed-out the RAID member disk, failed it, and continued with very little (if any) interruption.

Linux Raid controller tips

• Be careful of “softraid” chipsets out there, not all RAID is real-RAID.  My favorite controllers in order or preference are 3ware, Areca, and LSI.  The PERC 7xx series are ok too, but I wouldn’t trust a PERC 2xx.
• If you use LSI go with a higher-end controller for better performance and less fuss.  Generally speaking, I’ve had great success with LSI controllers that have onboard cache memory (even if you don’t use it in write-back mode).  Cacheless LSI controllers have created problems more times than I care to recall.
• Check the RAID-levels that the card supports.  If the controller supports RAID-5 or -6, it is probably a better controller even if you only use the RAID-10 functionality.
• Also of note, LSI now owns 3ware and uses LSI chips in 3ware’s hardware.  I have since used LSI-built 3ware cards and they still have the simple and robust 3ware feel.  I have a feeling that LSI will keep the 3ware brand for some time to come.

-Eric

/dev/vg/somevolume: read failed after 0 of 4096 at nnnnn: Input/output error

If you’ve ever seen the above error, this usually means you have run out of disk space on the CoW-volume of a snapshot volume.

…but there is another uses for snapshots, and that is thin provisioning for sparse data use.  If you create an LVM volume using the –virtualsize option, you can provide a logical size that is much larger than the actual underlying volume.  If you exceed the space for such a volume, you will get the same error above—and all data on the volume will be invalidated and inaccessible.

LVM silently uses the ‘zero’ devicemapper target as the underlying volume.  Thus, even though the data is invalidated nothing is lost.  By overlaying the lost data over the top of a zero device, we can resurrect the data.

We have prepared our example file with the following:

lvcreate -L 100m --virtualsize 200m -n virtual_test vg
mkfs.ext4 /dev/vg/virtual_test
 [...]
mount /dev/vg/virtual_test /mnt/tmp/

And now we fill the disk:

dd if=/dev/zero of=/mnt/tmp/overflow-file
dd: writing to `/mnt/tmp/overflow-file': Input/output error

Message from syslogd@backup at Aug 27 15:17:27 ...
 kernel:journal commit I/O error
272729+0 records in
272728+0 records out
139636736 bytes (140 MB) copied
[I had to reboot here.  The kernel still thought
 the filesystem was mounted and I could not continue.
 Obviously we are working near the kernel's limits on
 this CentOS 6.2 2.6.32-based kernel]

Now we have a 200MB volume with 100MB allocated to it, which is now full.  LVM has marked the volume as invalid and the data is no longer available.

First, resize the volume so we have room after resizing.  Otherwise, the first byte written to the volume would, again, invalidate the disk:

lvresize -L +100m /dev/vg/virtual_test
 [errors, possibly, just ignore them]
  Extending logical volume virtual_test to 200.00 MiB
  Logical volume virtual_test successfully resized

Now we edit the -cow file directly with a short perl script.  The 5th byte is the ‘valid’ flag (see http://web.archive.org/web/20200808212331/http://www.redhat.com/archives/linux-lvm/2006-September/msg00132.html) so all we need to is set it to ‘1’:

 perl -e 'open(F, ">>", "/dev/mapper/vg-virtual_test-cow"); seek(F, 4, SEEK_SET); syswrite(F,"\x01",1); close(F);'

Now have lvm re-read the CoW metadata and you’re in business:

lvchange -an /dev/backup/virtual_test
  [ignore errors]
lvchange -ay /dev/backup/virtual_test
  [shouldn't have any errors]
lvs
  LV                    VG       Attr     LSize   Pool Origin               Data% 
  virtual_test          vg   swi-a-s- 200.00m      [virtual_test_vorigin]   33.63

At this point you should probably fsck your filesystem, it may be damaged—or at least nead a journal-replay since it stopped abruptly at the end of its allocated space.  And as you can see, the “overflow” file is there up until the point of filling the disk.

[root@backup mapper]# e2fsck /dev/vg/virtual_test
e2fsck 1.41.12 (17-May-2010)
/dev/vg/virtual_test: recovering journal
/dev/vg/virtual_test: clean, 12/51200 files, 66398/204800 blocks
[root@backup mapper]# mount /dev/vg/virtual_test /mnt/tmp/
[root@backup mapper]# ls -lh /mnt/tmp/
total 54M
drwx------. 2 root root 12K Aug 27 15:16 lost+found
-rw-r--r--. 1 root root 54M Aug 27 15:17 overflow-file

-Eric