How do I fix "Partition table entries are not in disk order" error?

[Ray Hamilton]

Hi

I am trying to install Ubuntu 7.10 and eventually 8.04, but the installer does not see the existing partitions. fdisk -l gives me the message "Partition table entries are not in disk order". I know this is the problem but even after reading through the forums entries, I do not know how to fix this. I am sure this must be a fairly common problem.

[jrusso2]

I don't know I have never seen this error. Usually it has to do with over lapping partitions.

I would delete all the partitions, you will lose your data and make new ones if this possible for you to do.

Seems like this happens when you resize partitions.

[caljohnsmith]

It's OK if the partitions are not in the same order as they are physically on the HDD, but the question is if your partition table is corrupt. How about posting the output of:

sudo fdisk -lu
sudo sfdisk -d

[Ray Hamilton]

Sorry for the delay in posting. here is the output requested

sudo fdisk -lu
Disk /dev/hda: 40.0 GB, 40007761920 bytes
16 heads, 63 sectors/track, 77520 cylinders, total 78140160 sectors
Units = sectors of 1 * 512 = 512 bytes

Device Boot Start End Blocks Id System
/dev/hda1 * 63 39070079 19535008+ 7 HPFS/NTFS
/dev/hda2 68675040 78140159 4732560 83 Linux
/dev/hda3 39070080 48516299 4723110 83 Linux
/dev/hda4 48516426 68661809 10072692 5 Extended
/dev/hda5 67392738 68661809 634536 82 Linux swap / Solaris
/dev/hda6 53143146 66734009 6795432 83 Linux
/dev/hda7 66734073 67392674 329301 82 Linux swap / Solaris
/dev/hda8 * 48516426 52869914 2176744+ 83 Linux
/dev/hda9 52869978 53143019 136521 82 Linux swap / Solaris

Partition table entries are not in disk order

sudo sfdisk -d
Warning: extended partition does not start at a cylinder boundary.
DOS and Linux will interpret the contents differently.
# partition table of /dev/hda
unit: sectors

/dev/hda1 : start= 63, size= 39070017, Id= 7, bootable
/dev/hda2 : start= 68675040, size= 9465120, Id=83
/dev/hda3 : start= 39070080, size= 9446220, Id=83
/dev/hda4 : start= 48516426, size= 20145384, Id= 5
/dev/hda5 : start= 67392738, size= 1269072, Id=82
/dev/hda6 : start= 53143146, size= 13590864, Id=83
/dev/hda7 : start= 66734073, size= 658602, Id=82
/dev/hda8 : start= 48516426, size= 4353489, Id=83, bootable
/dev/hda9 : start= 52869978, size= 273042, Id=82

I hope this will help us get to the bottom of the problem.

[caljohnsmith]

sudo fdisk -lu
Disk /dev/hda: 40.0 GB, 40007761920 bytes
16 heads, 63 sectors/track, 77520 cylinders, total 78140160 sectors
Units = sectors of 1 * 512 = 512 bytes

Device Boot Start End Blocks Id System
/dev/hda1 * 63 39070079 19535008+ 7 HPFS/NTFS
/dev/hda2 68675040 78140159 4732560 83 Linux
/dev/hda3 39070080 48516299 4723110 83 Linux
/dev/hda4 48516426 68661809 10072692 5 Extended
/dev/hda5 67392738 68661809 634536 82 Linux swap / Solaris
/dev/hda6 53143146 66734009 6795432 83 Linux
/dev/hda7 66734073 67392674 329301 82 Linux swap / Solaris
/dev/hda8 * 48516426 52869914 2176744+ 83 Linux
/dev/hda9 52869978 53143019 136521 82 Linux swap / Solaris

It looks like the problem is that your hda8 linux logical partition starts on the exact same sector as the hda4 extended partition; hda8 can start on any sector after the start of hda4 (and usually hda8 would start at least 63 sectors beyond the starting sector of hda4), so your partition table is corrupt at this point. How about first seeing if you can mount hda8:

sudo mount /dev/hda8 /mnt && ls -l /mnt
If that gives you a directory listing of hda8, then it is obvious that hda8 has the correct starting sector, and the problem is with your hda4 extended partition starting sector. So if you can see hda8's root directory with the above command, next do:

echo "48516300,20145510,5" | sudo sfdisk --no-reread -fuS /dev/hda -N4 -O ~/Desktop/hda_sectors_modified.save
And please post the output. The above command will create a backup of the few sectors being modified as a small "sda_sectors_modified.save" file on your desktop, so if for some reason anything were to go wrong, we can easily restore your original partition table with that file. Therefore, please copy that file to a different drive, or you could for instance save it to your email account or something like that. After that, reboot, and please post the new output of:

sudo fdisk -lu
sudo sfdisk -d
sudo parted /dev/hda print
And also I just wanted to mention, your multiple linux installs can share the same swap partition, so there is really no need to have three swap partitions. If you would like some help configuring your distros so they all use the same swap partition, let me know. Then you could delete two of your swap partitions and use that space as you please. Let me know if you are interested.

[Ray Hamilton]

Here is the output of the first command:
Disk /dev/hda: 77520 cylinders, 16 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 = sectors of 512 bytes, counting from 0

Device Boot Start End #sectors Id System
/dev/hda1 * 63 39070079 39070017 7 HPFS/NTFS
/dev/hda2 68675040 78140159 9465120 83 Linux
/dev/hda3 39070080 48516299 9446220 83 Linux
/dev/hda4 48516426 68661809 20145384 5 Extended
/dev/hda5 67392738 68661809 1269072 82 Linux swap / Solaris
/dev/hda6 53143146 66734009 13590864 83 Linux
/dev/hda7 66734073 67392674 658602 82 Linux swap / Solaris
/dev/hda8 * 48516426 52869914 4353489 83 Linux
/dev/hda9 52869978 53143019 273042 82 Linux swap / Solaris
New situation:
Units = sectors of 512 bytes, counting from 0

Device Boot Start End #sectors Id System
/dev/hda1 * 63 39070079 39070017 7 HPFS/NTFS
/dev/hda2 68675040 78140159 9465120 83 Linux
/dev/hda3 39070080 48516299 9446220 83 Linux
/dev/hda4 48516300 68661809 20145510 5 Extended
/dev/hda5 67392738 68661809 1269072 82 Linux swap / Solaris
/dev/hda6 53143146 66734009 13590864 83 Linux
/dev/hda7 66734073 67392674 658602 82 Linux swap / Solaris
/dev/hda8 * 48516426 52869914 4353489 83 Linux
/dev/hda9 52869978 53143019 273042 82 Linux swap / Solaris
Warning: partition 3 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).)

[Ray Hamilton]

After the above post GRUB was stuffed - cannot load stage 1.5
Currently I am using a SUPERGRUB CD that managed to find a Windows partition. (I suspect the PCLinuxOS as causing some of the problems becuase grub has never been able to use it since I tried to install it last year!) What now? Especially in view of the fact that I didn't take a copy of the file - hopefully I'll be able to "recover" this shortly.

[caljohnsmith]

You never mentioned, but were you able to successfully mount hda8 and view its root directory? To try and restore Grub, how about booting your Live CD, open a terminal (Applications > Accessories > Terminal) and do:

sudo grub
grub> find /boot/grub/stage1
grub> find /grub/stage1
One of the above commands should return the partitions that have Grub's boot files in the form of (hdX,Y) where X and Y are numbers, for example (hd0,5), but use whatever it returns as follows:


grub> root (hdX,Y)
grub> setup (hdX)
grub> quit
Please post the output of all the above commands.

[Ray Hamilton]

Yes, sorry, hda8 mounted and I was able to see the directory, that is why I went ahead with the fix of the partition table.

I am going to try fixing grub.

[Ray Hamilton]

I have tried the grub thing (actually using SuperGrub Disk) and I only have a non-working Linux partition, a Swap, a Windows and another with only lost+found. I also cannot seem to get my LiveCD to set up wireless!! I am currently using my Windows partition. HEEEELLPP!!

[caljohnsmith]

If you want help, how about giving more details of the problem and what your goal is. What happened when you tried the commands I gave? Did you get any errors? What do you mean by "one non-working linux partition"? What about the other three partitions--can you mount them and access them? Did you look in the lost+found folder of the one partition to see if it has any of your files? Can you mount your linux partitions from the Live CD and and then save your important files to some other drive or maybe to your Windows partition? If you can do that then you could at least reinstall.

[Ray Hamilton]

My goal is to put the partitions back as they were if possible, to double check if there was anything important I need to keep. Then put things into such an order that I can install Ubuntu 7.10 to learn as much as I can from a book I have about Ubuntu 7.10)

Here are the results of the last 3 commands you asked me to enter

ubuntu@ubuntu:~$ sudo fdisk -lu
Warning: ignoring extra data in partition table 6
Warning: invalid flag 0x83d0 of partition table 6 will be corrected by w(rite)

Disk /dev/sda: 40.0 GB, 40007761920 bytes
16 heads, 63 sectors/track, 77520 cylinders, total 78140160 sectors
Units = sectors of 1 * 512 = 512 bytes
Disk identifier: 0xcccdcccd

Device Boot Start End Blocks Id System
/dev/sda1 * 63 39070079 19535008+ 7 HPFS/NTFS
/dev/sda2 68675040 78140159 4732560 83 Linux
/dev/sda3 39070080 48516299 4723110 83 Linux
/dev/sda4 48516300 68661809 10072755 5 Extended
/dev/sda5 67392612 68661683 634536 82 Linux swap / Solaris
/dev/sda6 ? 1814276593 1814277213 310+ ff BBT

Partition table entries are not in disk order

Disk /dev/sdb: 65 MB, 65454080 bytes
4 heads, 32 sectors/track, 998 cylinders, total 127840 sectors
Units = sectors of 1 * 512 = 512 bytes
Disk identifier: 0xef2a8f94

Device Boot Start End Blocks Id System
/dev/sdb1 * 32 127839 63904 6 FAT16
Partition 1 has different physical/logical endings:
phys=(1023, 3, 32) logical=(998, 2, 32)

ubuntu@ubuntu:~$ sudo sfdisk -d

sfdisk: ERROR: sector 53142894 does not have an msdos signature
# partition table of /dev/sda
unit: sectors

/dev/sda1 : start= 63, size= 39070017, Id= 7, bootable
/dev/sda2 : start= 68675040, size= 9465120, Id=83
/dev/sda3 : start= 39070080, size= 9446220, Id=83
/dev/sda4 : start= 48516300, size= 20145510, Id= 5
/dev/sda5 : start= 67392612, size= 1269072, Id=82
# partition table of /dev/sdb
unit: sectors

/dev/sdb1 : start= 32, size= 127808, Id= 6, bootable
/dev/sdb2 : start= 0, size= 0, Id= 0
/dev/sdb3 : start= 0, size= 0, Id= 0
/dev/sdb4 : start= 0, size= 0, Id= 0
ubuntu@ubuntu:~$ sudo parted /dev/hda print
Error: Could not stat device /dev/hda - No such file or directory.
Retry/Cancel? r
Error: Could not stat device /dev/hda - No such file or directory.
Retry/Cancel?

[caljohnsmith]

OK, how about first doing:

sudo fdisk -lu
See if your drive is sda or hda, then do:

sudo fdisk /dev/sda
But replace sda with hda if necessary. At the fdisk prompt type "w" and enter. Next post the new output of:

sudo fdisk -lu
sudo sfdisk -d
sudo parted /dev/sda print

Replace sda with hda above if necessary.

[Ray Hamilton]

Here are the results of the commands you asked me to enter, after sudo fdisk/dev/sda and pressing enter at the prompt:

The partition table has been altered!

Calling ioctl() to re-read partition table.
Syncing disks.
ubuntu@ubuntu:~$ sudo fdisk -lu
Warning: ignoring extra data in partition table 6

Disk /dev/sda: 40.0 GB, 40007761920 bytes
16 heads, 63 sectors/track, 77520 cylinders, total 78140160 sectors
Units = sectors of 1 * 512 = 512 bytes
Disk identifier: 0xcccdcccd

Device Boot Start End Blocks Id System
/dev/sda1 * 63 39070079 19535008+ 7 HPFS/NTFS
/dev/sda2 68675040 78140159 4732560 83 Linux
/dev/sda3 39070080 48516299 4723110 83 Linux
/dev/sda4 48516300 68661809 10072755 5 Extended
/dev/sda5 67392612 68661683 634536 82 Linux swap / Solaris
/dev/sda6 ? 1814276593 1814277213 310+ ff BBT

Partition table entries are not in disk order
ubuntu@ubuntu:~$ sudo sfdisk -d
# partition table of /dev/sda
unit: sectors

/dev/sda1 : start= 63, size= 39070017, Id= 7, bootable
/dev/sda2 : start= 68675040, size= 9465120, Id=83
/dev/sda3 : start= 39070080, size= 9446220, Id=83
/dev/sda4 : start= 48516300, size= 20145510, Id= 5
/dev/sda5 : start= 67392612, size= 1269072, Id=82
/dev/sda6 : start=1814276593, size= 621, Id=ff
/dev/sda7 : start=2011916942, size=4173628185, Id=ff
/dev/sda8 : start=2264655070, size=3229946052, Id= 0
/dev/sda9 : start=1499287654, size=4285548171, Id= 0
ubuntu@ubuntu:~$ sudo parted /dev/sda print
Error: Can't have a partition outside the disk!
Information: Don't forget to update /etc/fstab, if necessary.

[Ray Hamilton]

Here are the results of the commands you asked me to enter, after sudo fdisk/dev/sda and pressing enter at the prompt:

The partition table has been altered!

Calling ioctl() to re-read partition table.
Syncing disks.
ubuntu@ubuntu:~$ sudo fdisk -lu
Warning: ignoring extra data in partition table 6

Disk /dev/sda: 40.0 GB, 40007761920 bytes
16 heads, 63 sectors/track, 77520 cylinders, total 78140160 sectors
Units = sectors of 1 * 512 = 512 bytes
Disk identifier: 0xcccdcccd

Device Boot Start End Blocks Id System
/dev/sda1 * 63 39070079 19535008+ 7 HPFS/NTFS
/dev/sda2 68675040 78140159 4732560 83 Linux
/dev/sda3 39070080 48516299 4723110 83 Linux
/dev/sda4 48516300 68661809 10072755 5 Extended
/dev/sda5 67392612 68661683 634536 82 Linux swap / Solaris
/dev/sda6 ? 1814276593 1814277213 310+ ff BBT

Partition table entries are not in disk order
ubuntu@ubuntu:~$ sudo sfdisk -d
# partition table of /dev/sda
unit: sectors

/dev/sda1 : start= 63, size= 39070017, Id= 7, bootable
/dev/sda2 : start= 68675040, size= 9465120, Id=83
/dev/sda3 : start= 39070080, size= 9446220, Id=83
/dev/sda4 : start= 48516300, size= 20145510, Id= 5
/dev/sda5 : start= 67392612, size= 1269072, Id=82
/dev/sda6 : start=1814276593, size= 621, Id=ff
/dev/sda7 : start=2011916942, size=4173628185, Id=ff
/dev/sda8 : start=2264655070, size=3229946052, Id= 0
/dev/sda9 : start=1499287654, size=4285548171, Id= 0
ubuntu@ubuntu:~$ sudo parted /dev/sda print
Error: Can't have a partition outside the disk!
Information: Don't forget to update /etc/fstab, if necessary.

[caljohnsmith]

OK, how about instead doing:

sudo fdisk /dev/sda
This time press "d", then "6" for the partition, then "w" to write the changes. Then post the output again of:

sudo fdisk -lu

[Ray Hamilton]

Hi caljohnsmith

The partition table has been altered!

Calling ioctl() to re-read partition table.
Syncing disks.
ubuntu@ubuntu:~$ sudo fdisk -lu
Warning: ignoring extra data in partition table 5

Disk /dev/sda: 40.0 GB, 40007761920 bytes
16 heads, 63 sectors/track, 77520 cylinders, total 78140160 sectors
Units = sectors of 1 * 512 = 512 bytes
Disk identifier: 0xcccdcccd

Device Boot Start End Blocks Id System
/dev/sda1 * 63 39070079 19535008+ 7 HPFS/NTFS
/dev/sda2 68675040 78140159 4732560 83 Linux
/dev/sda3 39070080 48516299 4723110 83 Linux
/dev/sda4 48516300 68661809 10072755 5 Extended
/dev/sda5 67392612 68661683 634536 82 Linux swap / Solaris

[caljohnsmith]

OK, let's try doing this differently, so first do:

sudo fdisk -lu
Make sure your HDD is still listed as sda, and if so, proceed by downloading the attached "partition_table.txt" file to your Ubuntu desktop, and then do:

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

sudo fdisk -lu; sudo sfdisk -d; sudo parted /dev/sda print

[Ray Hamilton]

Hi caljohnsmith, here is the output of the first set of commands

ubuntu@ubuntu:~$ sudo sfdisk --no-reread -f /dev/sda < ~/Desktop/partition_table.txt

Disk /dev/sda: 4864 cylinders, 255 heads, 63 sectors/track
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+ 2431 2432- 19535008+ 7 HPFS/NTFS
end: (c,h,s) expected (1023,254,63) found (1023,15,63)
/dev/sda2 4274+ 4863 590- 4732560 83 Linux
start: (c,h,s) expected (1023,254,63) found (1023,15,63)
end: (c,h,s) expected (1023,254,63) found (1023,15,63)
/dev/sda3 2432 3019 588 4723110 83 Linux
start: (c,h,s) expected (1023,254,63) found (1023,15,63)
end: (c,h,s) expected (1023,254,63) found (1023,15,63)
/dev/sda4 3020 4273 1254 10072755 5 Extended
start: (c,h,s) expected (1023,254,63) found (1023,15,63)
end: (c,h,s) expected (1023,254,63) found (1023,15,63)
/dev/sda5 4194+ 4273- 79- 634536 82 Linux swap / Solaris
start: (c,h,s) expected (1023,254,63) found (1023,15,63)
end: (c,h,s) expected (1023,254,63) found (1023,15,63)
/dev/sda6 ? 124948+ 117395- 259797- 2086814092+ ff BBT
start: (c,h,s) expected (1023,254,63) found (368,139,3)
end: (c,h,s) expected (1023,254,63) found (708,208,3)
New situation:
Units = sectors of 512 bytes, counting from 0

Device Boot Start End #sectors Id System
/dev/sda1 * 63 39070079 39070017 7 HPFS/NTFS
/dev/sda2 68675040 78140159 9465120 83 Linux
/dev/sda3 39070080 48516299 9446220 83 Linux
/dev/sda4 48516300 68661809 20145510 5 Extended
/dev/sda5 48516426 52869914 4353489 83 Linux
/dev/sda6 52869978 53143019 273042 82 Linux swap / Solaris
/dev/sda7 53143146 66734009 13590864 83 Linux
Warning: partition 2 does not start at a cylinder boundary
Successfully wrote the new partition table

Re-reading the partition table ...

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).)

[Ray Hamilton]

Hi caljohnsmith, here is the output from the second command "list":

ubuntu@ubuntu:~$ sudo fdisk -lu; sudo sfdisk -d; sudo parted /dev/sda print

Disk /dev/sda: 40.0 GB, 40007761920 bytes
255 heads, 63 sectors/track, 4864 cylinders, total 78140160 sectors
Units = sectors of 1 * 512 = 512 bytes
Disk identifier: 0xcccdcccd

Device Boot Start End Blocks Id System
/dev/sda1 * 63 39070079 19535008+ 7 HPFS/NTFS
/dev/sda2 68675040 78140159 4732560 83 Linux
/dev/sda3 39070080 48516299 4723110 83 Linux
/dev/sda4 48516300 68661809 10072755 5 Extended
/dev/sda5 48516426 52869914 2176744+ 83 Linux
/dev/sda6 52869978 53143019 136521 82 Linux swap / Solaris
/dev/sda7 53143146 66734009 6795432 83 Linux

Partition table entries are not in disk order
# partition table of /dev/sda
unit: sectors

/dev/sda1 : start= 63, size= 39070017, Id= 7, bootable
/dev/sda2 : start= 68675040, size= 9465120, Id=83
/dev/sda3 : start= 39070080, size= 9446220, Id=83
/dev/sda4 : start= 48516300, size= 20145510, Id= 5
/dev/sda5 : start= 48516426, size= 4353489, Id=83
/dev/sda6 : start= 52869978, size= 273042, Id=82
/dev/sda7 : start= 53143146, size= 13590864, Id=83

Disk /dev/sda: 40.0GB
Sector size (logical/physical): 512B/512B
Partition Table: msdos

Number Start End Size Type File system Flags
1 32.3kB 20.0GB 20.0GB primary ntfs boot
3 20.0GB 24.8GB 4836MB primary ext3
4 24.8GB 35.2GB 10.3GB extended
5 24.8GB 27.1GB 2229MB logical ext3
6 27.1GB 27.2GB 140MB logical linux-swap
7 27.2GB 34.2GB 6959MB logical ext3
2 35.2GB 40.0GB 4846MB primary ext3

Information: Don't forget to update /etc/fstab, if necessary.

[caljohnsmith]

It looks like your partition table is fine now according to the results you posted. In case you hadn't all ready noticed, we rearranged your partitions to be in the same order as they are physically on the HDD (even though that's not necessary, it was convenient to do so), and also we deleted your two extra swap partitions. So you should be able to go ahead and install Ubuntu to either of those linux partitions, or you should be able to use gparted now to make whatever partition changes you want. Good luck with your Ubuntu install.

[Ray Hamilton]

Hi caljohnsmith

I am posting this from my newly installed ubuntu 7.10 (only had a few problems!), I think everything is okay with my existing partitions.

Thanks, you have very helpful and knowledgeable. I hope I can make some contribution back to the community with the knowledge I gain.

Ray Hamilton