Partition does not end on cylinder boundary

[MadEgg]

I recently installed a new hard disk and reinstalled Ubunut (well, Kubuntu, but anway), and afterwards Windows 7.

My partition table was supposed to be:



/dev/sda1 ext2 /boot
/dev/sda2 extended partition for Linux install
/dev/sda3 NTFS Windows Boot partition
/dev/sda4 NTFS Windows Partition
/dev/sda5 ext4 /
/dev/sda6 ext4 /home
/dev/sda7 swapfs swap


Most of this worked fine; I even created the partitions for Windows using the installer partition manager.

Here comes the problem: the Windows installer does not want to change the partition type, so the only way to install was to remove the partitions for Windows from the Windows installer and have the installer recreate them.

Somehow this messed things up.

fdisk -l /dev/sda shows:



Device Boot Start End Blocks Id System
/dev/sda1 1 122 975872 83 Linux
Partition 1 does not end on cylinder boundary.
/dev/sda2 122 61640 494139393 5 Extended
/dev/sda3 * 61640 61653 102400 7 HPFS/NTFS
Partition 3 does not end on cylinder boundary.
/dev/sda4 61653 182402 969917440 7 HPFS/NTFS
Partition 4 does not end on cylinder boundary.
/dev/sda5 122 24437 195311616 83 Linux
/dev/sda6 24438 60910 292967424 83 Linux
/dev/sda7 60910 61640 5858304 82 Linux swap / Solaris


The problem is the 'does not end on cylinder boundary'. This problem also makes it impossible to start cfdisk to change the partition table.

Right now I don't have any incentive to change the partitions as both Kubuntu and Windows run fine. Still it bothers me that something apparently is wrong. Is there any way to fix the partition table without reinstalling both OS'es?

[garvinrick4]

If you notice one starts at same # other ends at, no big deal. Does all your OS's boot fine?

[MadEgg]

After some searching that seems to be the problem instead of the cylinder boundaries. The error I get when I run cfdisk is:

Bad primary partition 3: Partition ends in the final partial cylinder

Everything currently runs fine, but there is loads of space available so maybe the overlapping blocks are not currently used yet so no conflict can occur.

[garvinrick4]

After some searching that seems to be the problem instead of the cylinder boundaries. The error I get when I run cfdisk is:

Bad primary partition 3: Partition ends in the final partial cylinder

Everything currently runs fine, but there is loads of space available so maybe the overlapping blocks are not currently used yet so no conflict can occur.

When I make my partitions i give them 1 meg between each partition. Have one install

that has partition ending on same as next partition has not seemed to bother anything for
a long time.

[srs5694]

In terms of the legality of the disk structures, there is no problem, as far as I can tell from the description. If cfdisk is complaining about this, then that's a cfdisk bug. You might try a more recent version. It's part of the util-linux-ng (http://userweb.kernel.org/~kzak/util-linux-ng/) package, so check there for source code.

The problem with cfdisk probably derives from the fact that the standard for how partitions are aligned is changing. In Windows XP and previous versions of Windows, as well as most Linux partitioning tools until a matter of a few weeks or months ago, the standard was to align partitions on cylinder boundaries. This made sense a few decades ago when such alignment could improve performance for technical reasons that have long been moot; but today cylinder alignment is meaningless. Aligning partitions on cylinder boundaries has no performance benefit and is rather arbitrary anyhow, since the "cylinders" described by hard disks in their cylinder/head/sector (CHS) geometry values, as reported to the computer, are fictions. (Disks do have real cylinders, but the CHS values reported to the computer no longer correctly describe the disk's real geometry.)

Since Windows Vista, Microsoft has switched to a new partition alignment standard, and Linux partitioning tools are beginning to support this new method, too. In the new system, partitions are aligned on multiples of 1 mebibyte (1 MiB; 2048 sectors, given the usual 512-byte sector size). This alignment prevents performance degradation on the new "Advanced Format" disks that use 4096-byte physical sectors with 512-byte logical sectors, and to a lesser extent also with some types of RAID array.

Most core Linux utilities, such as the kernel, GRUB, etc., don't care about partition alignment; partitions can be aligned to the cylinder, to 1 MiB blocks, or not at all, and everything works. If cfdisk is refusing to work because of a particular alignment, it's probably trying to enforce long-obsolete partition alignment recommendations. In other words, it's broken. You should use something else, if at all possible. If that's not possible (say, if some utility is launching cfdisk and refuses to let you use something else), then you've got a problem. Upgrading cfdisk might help; or you might be able to temporarily rename cfdisk and substitute something else, such as fdisk or parted.

[MadEgg]

Thanks for the clear explanation. But your explanation only treats the cylinder boundaries. There's still the other problem of maybe overlapping partitions. Is it OK of the next partitions starts at the same block that the first partition ends?

I see in my fdisk -l output posted above that sda2 starts where sda1 ends, and sda3 starts where sda2 ends and sda4 starts where sda3 ends. But sda5, sda6 and sda7 show no such overlap. Or is this some fundamental difference between primary and extended partitions?

[srs5694]

The "fdisk -l" command only shows partition boundaries in cylinder terms. Chances are the partitions aren't actually overlapping, but you'll need to check with greater precision to be sure. Try "fdisk -lu" instead; that will show the start and end points in units of sectors rather than cylinders.

[MadEgg]

Allright, that gives me this:



Device Boot Start End Blocks Id System
/dev/sda1 2048 1953791 975872 83 Linux
Partition 1 does not end on cylinder boundary.
/dev/sda2 1955838 990234623 494139393 5 Extended
/dev/sda3 * 990234624 990439423 102400 7 HPFS/NTFS
Partition 3 does not end on cylinder boundary.
/dev/sda4 990439424 2930274303 969917440 7 HPFS/NTFS
Partition 4 does not end on cylinder boundary.
/dev/sda5 1955840 392579071 195311616 83 Linux
/dev/sda6 392581120 978515967 292967424 83 Linux
/dev/sda7 978518016 990234623 5858304 82 Linux swap / Solaris


Seems better indeed. Now there appear to be some gaps between some of the partitions but that shouldn't be a problem I suppose.

Thanks a lot. Now I just need to update cfdisk :)

[dino99]

you may need to boot with a good tool like partedmagic to check partitions errors and repair them

http://partedmagic.com/