Partition table overlaps, possibly due to Super Grub Disk

[Forlornity]

Hey all, I'm having some troubles with parted.
It tells me I have overlapping partitions.

I recently installed Windows XP on a small 20GB partition outside of the extended partition in which my Ubuntu partitions reside, then I restored GRUB to the MBR using Super Grub Disk, This worked fine, Ubuntu booted without issue. I'd intended to shrink my Ubuntu partition and grow my windows one (20GB isn't enough for a full XP install along with all of the half life series :P)
I went to open gparted, but it died with the error "Cannot have overlapping partitions", I tried with parted, same error.
Here's the output of fdisk -lu

omitting empty partition (5)

Disk /dev/sda: 160.0 GB, 160041885696 bytes
255 heads, 63 sectors/track, 19457 cylinders, total 312581808 sectors
Units = sectors of 1 * 512 = 512 bytes
Disk identifier: 0x1f29c9cc

Device Boot Start End Blocks Id System
/dev/sda1 2048 14465023 7231488 27 Unknown
Partition 1 does not end on cylinder boundary.
/dev/sda2 14469840 270632879 128081520 5 Extended
Partition 2 does not end on cylinder boundary.
/dev/sda3 78457680 270632879 96087600 83 Linux
Partition 3 does not end on cylinder boundary.
/dev/sda4 * 270632880 312575759 20971440 7 HPFS/NTFS
Partition 4 does not end on cylinder boundary.
/dev/sda5 14469966 73059839 29294937 83 Linux
/dev/sda6 73059903 78457679 2698888+ 82 Linux swap / Solaris


and windows displays my partition table as such:
103621

I can boot both windows and ubuntu fine at the moment, but I'd really like to be able to resize my partitions and I feel uncomfortable with my partition table in such a state.
Many thanks in advance, Forlornity.

[caljohnsmith]

omitting empty partition (5)

Disk /dev/sda: 160.0 GB, 160041885696 bytes
255 heads, 63 sectors/track, 19457 cylinders, total 312581808 sectors
Units = sectors of 1 * 512 = 512 bytes
Disk identifier: 0x1f29c9cc

Device Boot Start End Blocks Id System
/dev/sda1 2048 14465023 7231488 27 Unknown
Partition 1 does not end on cylinder boundary.
/dev/sda2 14469840 270632879 128081520 5 Extended
Partition 2 does not end on cylinder boundary.
/dev/sda3 78457680 270632879 96087600 83 Linux
Partition 3 does not end on cylinder boundary.
/dev/sda4 * 270632880 312575759 20971440 7 HPFS/NTFS
Partition 4 does not end on cylinder boundary.
/dev/sda5 14469966 73059839 29294937 83 Linux
/dev/sda6 73059903 78457679 2698888+ 82 Linux swap / Solaris


Unfortunately your partition table is corrupt, because as parted has all ready alerted you, your sda HDD has overlapping partitions. Or to be more specific, your sda3 primary partition is inside of your sda2 extended partition, so sda3 should be a logical partition instead. If you would like some help fixing your partition table, how about posting:

sudo sfdisk -d
Also, which partition has your main Ubuntu install, sda3 or sda5?

[Forlornity]

sudo sfdisk -d:

# partition table of /dev/sda
unit: sectors

/dev/sda1 : start= 2048, size= 14462976, Id=27
/dev/sda2 : start= 14469840, size=256163040, Id= 5
/dev/sda3 : start= 78457680, size=192175200, Id=83
/dev/sda4 : start=270632880, size= 41942880, Id= 7, bootable
/dev/sda5 : start= 14469966, size= 58589874, Id=83
/dev/sda6 : start= 73059903, size= 5397777, Id=82


My main install was on two partitions inside the extended partition (or should be at least, that's how it was after install) with / being on sda5 and /home on sda3.
Here's df -h:

/dev/sda5 28G 5.7G 21G 22% /
tmpfs 1012M 0 1012M 0% /lib/init/rw
varrun 1012M 364K 1012M 1% /var/run
varlock 1012M 0 1012M 0% /var/lock
udev 1012M 2.8M 1009M 1% /dev
tmpfs 1012M 104K 1012M 1% /dev/shm
lrm 1012M 2.0M 1010M 1% /lib/modules/2.6.27-11-generic/volatile
/dev/sda3 91G 62G 24G 72% /home

[caljohnsmith]

Do you have a Live CD that you can boot? You will need that in order to carry out all the steps, because you will need to reinstall Grub to the MBR since we have to make your sda3 partition sda5, and then your sda5 partition will become sda6. So if you have a Live CD ready, how about downloading the attached "partition_table.txt" file to your Ubuntu desktop (at this point it can be your Ubuntu install on sda5 or the Live CD, it doesn't matter), and then do:

sudo sfdisk --no-reread -f /dev/sda < ~/Desktop/partition_table.txt
And please post the output. Then reboot to your Live CD, and please post the output of all the following commands:

sudo fdisk -lu
sudo parted /dev/sda print
sudo grub
grub> root (hd0,5)
grub> setup (hd0)
grub> quit
And we can work from there.

[Forlornity]

So do I run
sudo sfdisk --no-reread -f /dev/sda < ~/Desktop/partition_table.txt in the liveCD or booted?
Or does it not matter?

Just gotta be sure :)

[caljohnsmith]

So do I run
/media/Data/dotnetfx3setup.exe in the liveCD or booted?
Or does it not matter?

Just gotta be sure :)
Where did you get that command? That's not the sfdisk command I gave in my post. You can run that sfdisk from your booted Ubuntu install or the Live CD, it does not matter so long as you first download the "partition_table.txt" file to your desktop. You might as well run it from your Ubuntu install since that is where you seem to be right now.

[Forlornity]

Output for partition table rewrite:

Disk /dev/sda: 19457 cylinders, 255 heads, 63 sectors/track
Warning: extended partition does not start at a cylinder boundary.
DOS and Linux will interpret the contents differently.
Old situation:
Units = cylinders of 8225280 bytes, blocks of 1024 bytes, counting from 0

Device Boot Start End #cyls #blocks Id System
/dev/sda1 0+ 900- 901- 7231488 27 Unknown
end: (c,h,s) expected (900,103,35) found (956,163,35)
/dev/sda2 900+ 16846- 15946- 128081520 5 Extended
start: (c,h,s) expected (900,180,1) found (957,0,1)
end: (c,h,s) expected (1023,254,63) found (1023,239,63)
/dev/sda3 4883+ 16846- 11963- 96087600 83 Linux
start: (c,h,s) expected (1023,254,63) found (1023,0,1)
end: (c,h,s) expected (1023,254,63) found (1023,239,63)
/dev/sda4 * 16846+ 19456- 2611- 20971440 7 HPFS/NTFS
start: (c,h,s) expected (1023,254,63) found (1023,0,1)
end: (c,h,s) expected (1023,254,63) found (1023,239,63)
/dev/sda5 900+ 4547- 3648- 29294937 83 Linux
start: (c,h,s) expected (900,182,1) found (957,2,1)
end: (c,h,s) expected (1023,254,63) found (1023,239,63)
/dev/sda6 4547+ 4883- 336- 2698888+ 82 Linux swap / Solaris
start: (c,h,s) expected (1023,254,63) found (1023,1,1)
end: (c,h,s) expected (1023,254,63) found (1023,239,63)
New situation:
Units = sectors of 512 bytes, counting from 0

Device Boot Start End #sectors Id System
/dev/sda1 2048 14465023 14462976 27 Unknown
/dev/sda2 14469840 270632879 256163040 5 Extended
/dev/sda3 0 - 0 0 Empty
/dev/sda4 * 270632880 312575759 41942880 7 HPFS/NTFS
/dev/sda5 78457680 270632879 192175200 83 Linux
/dev/sda6 14469966 73059839 58589874 83 Linux
/dev/sda7 73059903 78457679 5397777 82 Linux swap / Solaris
Warning: partition 1 does not end at a cylinder boundary
Successfully wrote the new partition table

Re-reading the partition table ...
BLKRRPART: Device or resource busy
The command to re-read the partition table failed
Reboot your system now, before using mkfs

If you created or changed a DOS partition, /dev/foo7, say, then use dd(1)
to zero the first 512 bytes: dd if=/dev/zero of=/dev/foo7 bs=512 count=1
(See fdisk(8).)


Ran that in main booted env.
Rebooting to liveCD now.

[Forlornity]

Where did you get that command? That's not the sfdisk command I gave in my post. You can run that sfdisk from your booted Ubuntu install or the Live CD, it does not matter so long as you first download the "partition_table.txt" file to your desktop. You might as well run it from your Ubuntu install since that is where you seem to be right now.

My mistake, had the correct command copied then I went and middle clicked :P
I meant the sfdisk command.

Also, for note, I'm posting this on my desktop, while my laptop's the one with the issues, and it's all backed up so no need to worry too much, though I'd rather not have to go through the restoration process again, of course.

And thanks for the help so far :)

[Forlornity]

Here's the output of my liveCD session:

ubuntu@ubuntu:~$ sudo fdisk -lu

Disk /dev/sda: 160.0 GB, 160041885696 bytes
255 heads, 63 sectors/track, 19457 cylinders, total 312581808 sectors
Units = sectors of 1 * 512 = 512 bytes
Disk identifier: 0x1f29c9cc

Device Boot Start End Blocks Id System
/dev/sda1 2048 14465023 7231488 27 Unknown
Partition 1 does not end on cylinder boundary.
/dev/sda2 14469840 270632879 128081520 5 Extended
/dev/sda4 * 270632880 312575759 20971440 7 HPFS/NTFS
/dev/sda5 78457680 270632879 96087600 83 Linux
/dev/sda6 14469966 73059839 29294937 83 Linux
/dev/sda7 73059903 78457679 2698888+ 82 Linux swap / Solaris

Partition table entries are not in disk order
ubuntu@ubuntu:~$ sudo parted /dev/sda print
Model: ATA HITACHI HTS54251 (scsi)
Disk /dev/sda: 160GB
Sector size (logical/physical): 512B/512B
Partition Table: msdos

Number Start End Size Type File system Flags
1 1049kB 7406MB 7405MB primary ntfs
2 7409MB 139GB 131GB extended
6 7409MB 37.4GB 30.0GB logical ext3
7 37.4GB 40.2GB 2764MB logical linux-swap
5 40.2GB 139GB 98.4GB logical ext3
4 139GB 160GB 21.5GB primary ntfs boot

ubuntu@ubuntu:~$ sudo grub
Probing devices to guess BIOS drives. This may take a long time.
ubuntu@ubuntu:~$



and during the grub session:


grub> root (hd0,5)

grub> setup (hd0)
Checking if "/boot/grub/stage1" exists... yes
Checking if "/boot/grub/stage2" exists... yes
Checking if "/boot/grub/e2fs_stage1_5" exists... yes
Running "embed /boot/grub/e2fs_stage1_5 (hd0)"... 16 sectors are embedded.
succeeded
Running "install /boot/grub/stage1 (hd0) (hd0)1+16 p (hd0,5)/boot/grub/stage2
/boot/grub/menu.lst"... succeeded
Done.



Any more before I reboot?

- Forlornity

[caljohnsmith]

I forgot to ask, but are you using 8.10 or a previous Ubuntu version? If you are using 8.10, go ahead and reboot and let me know how far you get. If you are using a version prior to 8.10, you will probably have to tweak your menu.lst to account for the new partition changes. Let me know if that applies to you or not.

[Forlornity]

Intrepid, yes.
Booting now, looks promising.
I'll test it out then tell you :)

Thanks much for the help.

[Forlornity]

Ubuntu's booting fine, XP's lost its hal.dll, but I should be able to replace that fairly swiftly, all the partitions mount fine and all looks good, thanks a lot!
:)

[caljohnsmith]

You're welcome, glad you can boot into Ubuntu now at least. About getting a "missing hal.dll" error when booting Windows, I think you will find that Windows isn't missing that file; since we changed your partition table, your Windows boot.ini file is misconfigured now. If you want help correcting that, how about doing:

sudo mount /dev/sda4 /mnt
gksudo gedit /mnt/boot.ini
And then change the two instances of "partition(3)" to "partition(2)" instead like:

[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(2)\WINDOW S
[operating systems]
multi(0)disk(0)rdisk(0)partition(2)\WINDOWS="Microsoft Windows XP" /fastdetect /NoExecute=OptIn
Then try booting Windows, and if all goes well it should work OK now. Let me know how that goes or if you run into problems.

[Forlornity]

It was what I was doing anyway :P
Once I'd noticed the change in my partition table at least.

Thanks very much for your help, I would've been tearing my hair for a day or so 'til I figured it out otherwise :)

- Forlornity

[ebf.beltran]

I have a similar problem.

I resized my partitions with Partition Manager in order to grant Ubuntu with more space and I get two things:

1)
At start up I get:

grub rescue>
grub rescue>ls
(hd0) (hd0,1) (hd0,2) (hd0,3) ... (hd0,5)

I am not sure how far it goes I think it also included hd0,6

and

2)
Using a CD to but Ubuntu I get from sudo fdisk -l:

Device Boot Start End Blocks ID System
/dev/sda1 1 192 1536000 27 Unknown
Partition 1 does not end on cylinder boundary.
/dev/sda2 192 12442 98403341 7 HPFS/NTFS
/dev/sda3 12443 14594 17279987 5 Extended
/dev/sda5 12443 14550 16932478 83 Linux
/dev/sda6 14551 14594 345088 82 Linux swap / Solaris

So I was wondering if you think my problem could be resolved by fixing the partition table or if the problem is probably bigger.

[srs5694]

ebf.beltran, first, please see my Web page on this symptom. (http://www.rodsbooks.com/missing-parts/) My suspicion is that you've got this problem.

Second, if you need more help, please post the complete output of "sudo fdisk -lu" (note the "u"), and please post it between
and strings to improve legibility.

[ebf.beltran]

I read the site and thank you. I had already tried most of what was there before replying. I don't like asking questions that have already been answered but I am a bit stock since I had never before manipulated partitions... a bit back when I used Windows 3.1 but it was a long time ago.

I don't really need to fix the computer, but rather access a few files in the partition that are part of my research. I don't mind starting from scratch afterwards. Is just that half of the data was not backed up.

When I mount the windows part I can access without problem from the Ubuntu CD but when I mount the linux partition I get:



Unable to mount location

Error mounting: mount: wrong fs type, bad option, bad superblock on /dev/sda5,
missing codepage or helper program, or other error
In some cases useful info is found in syslog - try
dmesg | tail or so


Well here are the specifics I got



root@ubuntu:/home/ubuntu# fdisk -lu

Disk /dev/sda: 120.0 GB, 120034123776 bytes
255 heads, 63 sectors/track, 14593 cylinders, total 234441648 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x6bba44a8

Device Boot Start End Blocks Id System
/dev/sda1 2048 3074047 1536000 27 Unknown
Partition 1 does not end on cylinder boundary.
/dev/sda2 3074048 199880729 98403341 7 HPFS/NTFS
/dev/sda3 * 199880730 234440703 17279987 5 Extended
/dev/sda5 199880793 233745749 16932478+ 83 Linux
/dev/sda6 233750528 234440703 345088 82 Linux swap / Solaris

I also bashed a set of data from another thread that looks like this




Boot Info Script 0.55 dated February 15th, 2010

============================= Boot Info Summary: ==============================

=> Grub 2 is installed in the MBR of /dev/sda and looks on the same drive in
partition #5 for /boot/grub.

sda1: __________________________________________________ _______________________

File system: ntfs
Boot sector type: Windows Vista/7
Boot sector info: No errors found in the Boot Parameter Block.
Operating System:
Boot files/dirs:

sda2: __________________________________________________ _______________________

File system: ntfs
Boot sector type: Windows Vista/7
Boot sector info: No errors found in the Boot Parameter Block.
Operating System: Windows Vista
Boot files/dirs: /bootmgr /Boot/BCD /Windows/System32/winload.exe

sda3: __________________________________________________ _______________________

File system: Extended Partition
Boot sector type: -
Boot sector info:

sda5: __________________________________________________ _______________________

File system: ext4
Boot sector type: -
Boot sector info:
Mounting failed:
mount: /dev/sda5: can't read superblock

sda6: __________________________________________________ _______________________

File system: swap
Boot sector type: -
Boot sector info:

=========================== Drive/Partition Info: =============================

Drive: sda ___________________ __________________________________________________ ___

Disk /dev/sda: 120.0 GB, 120034123776 bytes
255 heads, 63 sectors/track, 14593 cylinders, total 234441648 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes

Partition Boot Start End Size Id System

/dev/sda1 2,048 3,074,047 3,072,000 27 Hidden HPFS/NTFS
/dev/sda2 3,074,048 199,880,729 196,806,682 7 HPFS/NTFS
/dev/sda3 * 199,880,730 234,440,703 34,559,974 5 Extended
/dev/sda5 199,880,793 233,745,749 33,864,957 83 Linux
/dev/sda6 233,750,528 234,440,703 690,176 82 Linux swap / Solaris


blkid -c /dev/null: __________________________________________________ __________

Device UUID TYPE LABEL

/dev/loop0 squashfs
/dev/sda1 84A4EC25A4EC1C04 ntfs TOSHIBA SYSTEM VOLUME
/dev/sda2 F4D6F105D6F0C93E ntfs Windows
/dev/sda3: PTTYPE="dos"
/dev/sda5 08e48988-0d05-41e0-8ce7-d106041c43fb ext4
/dev/sda6 c5bc2b4c-70b2-4bf9-b75b-f96cbdba5175 swap
/dev/sda: PTTYPE="dos"

============================ "mount | grep ^/dev output: ===========================

Device Mount_Point Type Options

aufs / aufs (rw)
/dev/sr0 /cdrom iso9660 (ro,noatime)
/dev/loop0 /rofs squashfs (ro,noatime)

[srs5694]

I don't think it's a partitioning problem; your partitions look fine to me, so unless I've missed something or there's an issue too subtle to show up in the fdisk output, it's not partitions.

Your Boot Info Script output, however, does include a clue:



mount: /dev/sda5: can't read superblock


This suggests that something has damaged the filesystem on /dev/sda5. Given that the problems began when you resized it (expanding it earlier on the disk, I presume), it's possible that it's been very badly damaged. If possible, I recommend you do a dd backup of the partition to another disk before you do anything else; that way, you can try fairly aggressive recovery procedures and restore to the current condition if you think they may have damaged the disk further. If that's not possible, I suppose you'll just have to forge ahead. I'd try fsck first, and if that doesn't work, delete the partition using fdisk and then use TestDisk; maybe it will be able to do something with it. If that fails, you may just have to re-install, perhaps using PhotoRec to recover any user files that are important to you. (That will be a tough task, though.)

Good luck!

[ebf.beltran]

So I have space in an external hard drive how can I use dd to copy the partition of interest in terms of the research data???


Already into it... sorry for asking.

[ebf.beltran]

PhotoRec did the job

I already have the data I had lost. THANK U!

I was wondering if you could point me in the right direction to at least making Windows work again if you think that is at all possible.

If you think it is a lot of work I might just go on and reformat and reinstall.

[srs5694]

You could try re-installing GRUB, or you could install a standard DOS/Windows-style boot loader in the MBR. You might look at ms-sys-free (http://sourceforge.net/projects/ms-sys-free/) for the latter.