Can't read partition table after install f13

jonathonp · #1 27th May 2010, 05:40 AM

I have installed the fedora 13 x86_64 live cd. I updated fedora as well as installing gparted. My hard disc containing my operating systems is not being read by gparted.

unalloacted partition table.

Also i am not able to mount a ntfs parition on the same hard disc.

I did create the partition table on all hard discs with gparted live. Anybody else had this problem? A kernel crash is also reported.

EDIT:
I booted ubuntu 10.04 and opened gparted v5.1 without any problem. I booted fedora 13 again and now gparted 5.2 can read my partition table...)

jonathonp · #2 28th May 2010, 11:52 AM

Same problem again today. Looks like i will need to reinstall with a new partition table.

The situation has gone from bad to worse. I booted gparted live v.4 and found my partition table was no longer readable.

I used the gparted live cd to create a new partition scheme. I then installed fedora 13 and soon discovered my other hard drives partition tables were no longer readable.

Fortunately i had backed up most of my data except for the most recent. I feel really pissed off with the whole situation. Previously I had installed fedora 12 and Ubuntu 10.04. Fedora 13 appears to be corrupting each partition table. This is not a good way to spend a day.

I just installed Ubuntu and was able to open the previously lost partitions.

In ubuntu everything looks ok in in gparted and fdisk.

stoat · #3 28th May 2010, 01:54 PM

Hello jonathonp,

I don't know what is happening to you here. Sorry. But I do have some comments that came to mind while reading your story. Somebody should say something if only to sympathize, I guess. You're not being ignored. I think we're thinking.

One is just FYI. It's that according to Hans de Goede (an Anaconda developer and member here), Anaconda (the Fedora installer) uses parted to create partitions for Fedora. Maybe something is wrong with the current version. I don't know. GParted, the Gnome partition editor, uses the same library used by parted. Just FYI.

Another one just FYI. The partition table is a simple thing. It's only 64 bytes long and exists from the 447th byte through the 510th byte in the very first sector of a traditional hard drive (the master boot record). The 64 bytes of the partition table is divided into four 16-byte sections. Each of those contains the descriptive information for four primary partitions. The information is basically the boot status, partition type, starting sector, ending sector, size, and number of sectors before the partition. The partition table for logical partitions is scattered all over the place. It exists in the first sectors of the extended partition and each logical partition. It's a daisy-chained affair with each logical partition boot sector containing partition information about itself and the next logical partition.

Try looking closely at the fdisk report (sudo fdisk -l). I like to look at the starting and ending cylinders or sectors (sudo fdisk -lu). Find the very first one and see it's end. Then find the partition that starts next, and so on. The first cylinder in fdisk is 1, but it's normal for the first sector in the sector view of fdisk to be 63. In a fully partitioned drive, you should be able to account for every cylinder or sector (except sectors 0-62) even if their order is mixed up in the fdisk list. In the sector view of fdisk, there may be small "empty" gaps between logical partitions. But none of the primary and logical partition boundaries should overlap another partition in the fdisk list (except for the logical partitions each existing within the range of cylinders or sectors that comprise the extended partition). Check out this truly screwed up partition table...

http://fedoraforum.org/forum/showthread.php?p=1353483

Next, even if something is happening to your partition table, the data out on the disk platters should still be sitting there. Usually, a utility such as TestDisk can find and recover partitions that are lost due to partition table damage. It will simply rewrite the bytes for the recovered partition back into the partition table. Anyway, it's worth trying before re-installing things. I keep TestDisk handy at all times on a bootable floppy and a bootable CD. But it's also in the fedora repo (yum install testdisk)

I installed Fedora 13 amongst multiple other operating systems on multiple drives and partitions, and so far I haven't notice any partition abnormalities. I guess I mainly don't want you to arrive at a wrong conclusion from the assembled facts so far. If I think of anything that might actually be useful to you, then I will say it.

P.S.: Another FYI. The version of parted released with Fedora 13 is parted-2.1-8.fc13. The current update version in Fedora 12 is parted-1.9.0-17.2.fc12. I didn't see gparted listed amongst the Fedora 13 release packages. The current update version of gparted in Fedora 12 is gparted-0.5.1-1.fc12.i686.rpm. The current stable version of the GParted LiveCD is 0.5.2-9.

jonathonp · #4 28th May 2010, 05:18 PM

Hi stoat, thanks for the detailed information. I ended up reinstalling fedora again but still the partition table is not recognised. I ran testdisk and rebooted but still no luck. Here is the log output:

Code:

Analyse Disk /dev/sdb - 1500 GB / 1397 GiB - CHS 182401 255 63
Current partition structure:
No partition is bootable
Ask the user for vista mode
Allow partial last cylinder : No
search_vista_part: 0

search_part()
Disk /dev/sdb - 1500 GB / 1397 GiB - CHS 182401 255 63

recover_EXT2: s_block_group_nr=0/3906, s_mnt_count=40/27, s_blocks_per_group=32768, s_inodes_per_group=8192
recover_EXT2: s_blocksize=4096
recover_EXT2: s_blocks_count 127999887
recover_EXT2: part_size 1023999096
     Linux                    0   1  1 63740 254 57 1023999096 [DVD_1]
     EXT3 Large file Sparse superblock, 524 GB / 488 GiB

recover_EXT2: s_block_group_nr=0/3906, s_mnt_count=41/22, s_blocks_per_group=32768, s_inodes_per_group=8192
recover_EXT2: s_blocksize=4096
recover_EXT2: s_blocks_count 127999895
recover_EXT2: part_size 1023999160
     Linux                63741   0  1 127481 254 58 1023999160 [Data_1]
     EXT3 Large file Sparse superblock, 524 GB / 488 GiB

recover_EXT2: s_block_group_nr=0/781, s_mnt_count=1/26, s_blocks_per_group=32768, s_inodes_per_group=8192
recover_EXT2: s_blocksize=4096
recover_EXT2: s_blocks_count 25599569
recover_EXT2: part_size 204796552
     Linux                127482   1  1 140229 254 58  204796552 [Data_2]
     EXT3 Large file Sparse superblock, 104 GB / 97 GiB

recover_EXT2: s_block_group_nr=0/781, s_mnt_count=41/25, s_blocks_per_group=32768, s_inodes_per_group=8192
recover_EXT2: s_blocksize=4096
recover_EXT2: s_blocks_count 25599569
recover_EXT2: part_size 204796552
     Linux                140230   1  1 152977 254 58  204796552 [Data_3]
     EXT3 Large file Sparse superblock, 104 GB / 97 GiB

recover_EXT2: s_block_group_nr=0/1803, s_mnt_count=39/24, s_blocks_per_group=32768, s_inodes_per_group=8192
recover_EXT2: s_blocksize=4096
recover_EXT2: s_blocks_count 59085054
recover_EXT2: part_size 472680432
     Linux                152978   1  1 182400 254 63  472680432 [Music]
     EXT3 Large file Sparse superblock, 242 GB / 225 GiB
get_geometry_from_list_part_aux head=255 nbr=10
get_geometry_from_list_part_aux head=8 nbr=1
get_geometry_from_list_part_aux head=16 nbr=1
get_geometry_from_list_part_aux head=32 nbr=1
get_geometry_from_list_part_aux head=64 nbr=1
get_geometry_from_list_part_aux head=128 nbr=1
get_geometry_from_list_part_aux head=240 nbr=1
get_geometry_from_list_part_aux head=255 nbr=10

Results
   * Linux                    0   1  1 63740 254 63 1023999102 [DVD_1]
     EXT3 Large file Sparse superblock, 524 GB / 488 GiB
   P Linux                63741   0  1 127481 254 63 1023999165 [Data_1]
     EXT3 Large file Sparse superblock, 524 GB / 488 GiB
   L Linux                127482   1  1 140229 254 63  204796557 [Data_2]
     EXT3 Large file Sparse superblock, 104 GB / 97 GiB
   L Linux                140230   1  1 152977 254 63  204796557 [Data_3]
     EXT3 Large file Sparse superblock, 104 GB / 97 GiB
   L Linux                152978   1  1 182400 254 63  472680432 [Music]
     EXT3 Large file Sparse superblock, 242 GB / 225 GiB

interface_write()
 1 * Linux                    0   1  1 63740 254 63 1023999102 [DVD_1]
 2 P Linux                63741   0  1 127481 254 63 1023999165 [Data_1]
 3 E extended LBA         127482   0  1 182400 254 63  882273735
 5 L Linux                127482   1  1 140229 254 63  204796557 [Data_2]
 6 L Linux                140230   1  1 152977 254 63  204796557 [Data_3]
 7 L Linux                152978   1  1 182400 254 63  472680432 [Music]
write!

write_mbr_i386: starting...
write_all_log_i386: starting...
write_all_log_i386: CHS: 127482/0/1,lba=2047998330
write_all_log_i386: CHS: 140230/0/1,lba=2252794950
write_all_log_i386: CHS: 152978/0/1,lba=2457591570
You will have to reboot for the change to take effect.
3999096
     Linux                    0   1  1 63740 254 57 1023999096 [DVD_1]
     EXT3 Large file Sparse superblock, 524 GB / 488 GiB

block_group_nr 3

recover_EXT2: "e2fsck -b 98304 -B 4096 device" may be needed
recover_EXT2: s_block_group_nr=3/3906, s_mnt_count=0/27, s_blocks_per_group=32768, s_inodes_per_group=8192
recover_EXT2: s_blocksize=4096
recover_EXT2: s_blocks_count 127999887
recover_EXT2: part_size 1023999096
     Linux                    0   1  1 63740 254 57 1023999096 [DVD_1]
     EXT3 Large file Sparse superblock Backup superblock, 524 GB / 488 GiB

In device sda (taken in fedora) the 2 primary partitions are not listed either.

Code:

[root@amd-jp jonathon]# fdisk -lu

Disk /dev/sda: 319.9 GB, 319936615424 bytes
255 heads, 63 sectors/track, 38896 cylinders, total 624876202 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: 0xcc0e3584

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1   *   102462631   624864239   261200804+   5  Extended
/dev/sda5       102462633   114752294     6144831   82  Linux swap / Solaris
/dev/sda6   *   114752358   145468574    15358108+  83  Linux
/dev/sda7       145468638   186434324    20482843+  83  Linux
/dev/sda8       186434388   206917199    10241406   83  Linux
/dev/sda9       206917263   227400074    10241406   83  Linux
/dev/sda10      227400138   624864239   198732051    7  HPFS/NTFS

Disk /dev/sdb: 1500.3 GB, 1500301910016 bytes
255 heads, 63 sectors/track, 182401 cylinders, total 2930277168 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: 0xb718ba76

   Device Boot      Start         End      Blocks   Id  System

Disk /dev/sdc: 500.1 GB, 500106780160 bytes
255 heads, 63 sectors/track, 60801 cylinders, total 976771055 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: 0x42274226

   Device Boot      Start         End      Blocks   Id  System
/dev/sdc1              63   976768064   488384001    7  HPFS/NTFS

The following data was taken in ubuntu:

Code:

jonathon@amd-jp:~$ sudo fdisk -lu

Disk /dev/sda: 320.1 GB, 320072933376 bytes
255 heads, 63 sectors/track, 38913 cylinders, total 625142448 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: 0xcc0e3584

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1              63       80324       40131    b  W95 FAT32
/dev/sda2           80325   102462569    51191122+   7  HPFS/NTFS
/dev/sda3   *   102462631   624864239   261200804+   5  Extended
/dev/sda5       102462633   114752294     6144831   82  Linux swap / Solaris
/dev/sda6       114752358   145468574    15358108+  83  Linux
/dev/sda7       145468638   186434324    20482843+  83  Linux
/dev/sda8   *   186434388   206917199    10241406   83  Linux
/dev/sda9       206917263   227400074    10241406   83  Linux
/dev/sda10      227400138   624864239   198732051    7  HPFS/NTFS

Disk /dev/sdb: 1500.3 GB, 1500301910016 bytes
255 heads, 63 sectors/track, 182401 cylinders, total 2930277168 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: 0xb718ba76

   Device Boot      Start         End      Blocks   Id  System
/dev/sdb1              63  1023999164   511999551   83  Linux
/dev/sdb2      1023999165  2047998329   511999582+  83  Linux
/dev/sdb3      2047998330  2930272064   441136867+   f  W95 Ext'd (LBA)
/dev/sdb5      2047998393  2252794949   102398278+  83  Linux
/dev/sdb6      2252795013  2457591569   102398278+  83  Linux
/dev/sdb7      2457591633  2930272064   236340216   83  Linux

Disk /dev/sdc: 500.1 GB, 500107862016 bytes
255 heads, 63 sectors/track, 60801 cylinders, total 976773168 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: 0x42274226

   Device Boot      Start         End      Blocks   Id  System
/dev/sdc1              63   976768064   488384001    7  HPFS/NTFS
jonathon@amd-jp:~$

Notice the extended partition in /dev/sda is flagged to boot after installing fedora. I guess that is because the extended partitions of the primary type and the linux partitions are logical volumes.

stoat · #5 28th May 2010, 09:03 PM

So to summarize, you installed Apollo 13, oops I mean Fedora 13, to the hard drive from the 64-bit LiveCD into partitions created in advance by a GParted LiveCD. Fedora 13 boots and runs, I guess. But fdisk and gparted (installed) report the frightening partition information. Rebooting into an existing Ubuntu system reveals all is well. You then re-installed Fedora 13 again into partitions prepared in advance by a GParted LiveCD, and a similar but worse thing happened. Once again, and fortunately, Ubuntu says everything is fine. Do I understand?

If so, then to me, this is shaping up to be a Bugzilla reportable incident. First, for the record, you should confirm that you verified the ISO file used to create the LiveCD and had your burning software verify the burned data. It might also be interesting to see what difference it makes to let Anaconda create the partitions instead of the GParted LiveCD in advance. Then search Bugzilla for an existing report and add on to it, or submit a new one.

jonathonp · #6 29th May 2010, 12:45 PM

Quote:

Originally Posted by stoat

So to summarize, you installed Apollo 13, oops I mean Fedora 13, to the hard drive from the 64-bit LiveCD into partitions created in advance by a GParted LiveCD. Fedora 13 boots and runs, I guess. But fdisk and gparted (installed) report the frightening partition information. Rebooting into an existing Ubuntu system reveals all is well. You then re-installed Fedora 13 again into partitions prepared in advance by a GParted LiveCD, and a similar but worse thing happened. Once again, and fortunately, Ubuntu says everything is fine. Do I understand?.

Exactly as happened except for one point. After installing Fedora 13 and seeing my partition tables missing i booted gparted live and found /devsda/ was no longer readable. I created a new partition scheme and reinstalled fedora 13. Then i installed ubuntu and found out that my data on the other hard discs was intact.

i have used the live disc on another pc without any problems. I ran the self media check option when booting it on both occasions.

Will check the iso and burn a new copy.

Edit:

i verified the x86_64 iso:

Code:

[jonathon@amd-jp ~]$ curl https://fedoraproject.org/static/fedora.gpg | gpg --import
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  6318  100  6318    0     0   2929      0  0:00:02  0:00:02 --:--:--  3801
gpg: /home/jonathon/.gnupg/trustdb.gpg: trustdb created
gpg: key D22E77F2: public key "Fedora (11) <fedora@fedoraproject.org>" imported
gpg: key 57BBCCBA: public key "Fedora (12) <fedora@fedoraproject.org>" imported
gpg: key E8E40FDE: public key "Fedora (13) <fedora@fedoraproject.org>" imported
gpg: key 217521F6: public key "Fedora EPEL <epel@fedoraproject.org>" imported
gpg: Total number processed: 4
gpg:               imported: 4  (RSA: 3)
[jonathon@amd-jp ~]$ sha256sum -c *-CHECKSUM
Fedora-13-x86_64-Live.iso: OK

I ended up creating a new partition scheme with gparted in fedora 13. Fedora is my main operating system so it's worth the extra effort to get things working. I'm not that comfortable with the command line in Ubuntu anyway so i'm sticking with fedora. Looking on the bright side of things i gained some insight into boot sectors and partition schemes. Thanks for your help. Jonathon

PS I did look at filing a bug report but the process seems complicated to say the least.

Thanks for you help. Jonathon

stoat · #7 29th May 2010, 02:21 PM

Quote:

Originally Posted by jonathonp

I ended up creating a new partition scheme with gparted in fedora 13.

Just to clarify matters... Did you mean that you allowed the Fedora installer to create its own partitions, and now things are normal?

jonathonp · #8 29th May 2010, 03:16 PM

i installed gparted (yum install gparted) in fedora 13 and proceeded to create a new partition layout on a hard disc (Seagate SATA 1.5TB) that had been allocated for data. I also checked it with fedora's disk utility program before hand which reported no problems other than not being able to read the partition table.

Now with the new partition table the hard disc is working with fedora 13.

The first 2 primary partitions on sda (Hitachi SATA 320GB) are not being read with fedora 13 as mentioned earlier but i can read them with Ubuntu as well as with other live CDs and Windows XP as well. I'm just going to leave it that and ignore it.

The other hard disc, a Samsung SATA 500GB would not read either in fedora 13 (during the live CD installation) so i disconnected it after the installation, restarted fedora, shut-down it down again, reconnected the hard disc and it has been OK ever since.

Just to clarify, I have my operating systems on a single hard disc (Hitachi SATA 320GB) and i used gparted live 0.4.6-1 to create the partitions for this hard disc. The new partition table on my Seagate Hard disc was created by gparted 0.5.2 with fedora 13.