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I've just installed ubuntu 12.04. I didn't put my data yet, I want before to make sure that the installation is fine. And I get Disk Utility warning about misaligned partition.

I have / on sda1 and sda2 is extended partition with sda5 for swap and sda6 for /home. There is no other partition on the disc. From other questions about the same problem I've understood that I should boot my computer from live USB and fix the problem with gParted. The problem is that when I boot my computer from live USB stick and enter try mode, both primary partitions are mounted, so I can't do any operation on it.

Since I don't have any data yet, I can even re-install the system, but I should know how do set the installer to align the partitions in right way. I've chosen not to use the install option without partitioning, since I'd like to have /home on separate partition. I could also try to fix it with the present installation, but I don't know how to unmount swap partition (and I'm not sure if it's reasonable).

Here is the output of 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 / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disk identifier: 0x00027dec

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1   *        2048    29999103    14998528   83  Linux
/dev/sda2        30001150   625141759   297570305    5  Extended
Partition 2 does not start on physical sector boundary.
/dev/sda5        30001152    33998847     1998848   82  Linux swap / Solaris
/dev/sda6        34000896   625141759   295570432   83  Linux

Disk is ATA ST320LT007-9ZV142


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up vote 4 down vote accepted

Actually, Frank is only partially correct. The problem is not that MiB alignment was chosen; that's actually the correct alignment. (Selecting cylinder alignment would definitely be wrong.) When using MiB alignment, partitions are aligned to 1MiB boundaries -- that is, they start on sectors whose numbers are multiples of 2048. Since 2048 is a multiple of 8, this means that all partitions begin on multiples of 8, which is required for optimum performance on Advanced Format disks. Most modern hard disks are Advanced Format models, so as a general rule you should use 1MiB (or at least 8-sector) alignment on modern disks. For further information on this, see this article I wrote on the subject for IBM developerWorks.

If you check the start sector numbers, you'll see that they all align on 2048-sector boundaries, except for one: /dev/sda2. It seems that fdisk is now providing a warning about this, with its Partition 2 does not start on physical sector boundary message. This message is a false alarm. Yes, it's true that it doesn't fit on an 8-sector boundary (30001150 / 8 = 3750143.75); but /dev/sda2 is also an exception to the rule I've just laid out. It's an extended partition, which means that it's a placeholder for logical partitions. The speed problems associated with misaligned partitions occur because filesystem data structures are read and written in 4KiB (8-sector) chunks; but the only data accessed directly through /dev/sda2 is the pointer to the first partition it contains, and that's a 512-byte data structure, so it occupies only part of a physical sector no matter what the extended partition's start point is. What's more, this data structure is read once when the computer boots and is rarely written. Thus, it doesn't matter what the alignment is on extended partitions, and any tool that complains about their misalignment is causing concern without reason.

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It's no problem. I had the same situation on my box. It works, and it didn't slow down.

It's because you can choose to align a partition to MiB or cylinder. Check with Gparted. If you choose a partition where no file system is mounted, you will see both options under resize/move.

Maybe some older OS may be unable to handle misalignment.

If you want to fix it, you can redo your installation, and take care while partitioning your harddisk. Everytime choose the option to align to cylinder.

Gparted shows option to align

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You should not align partitions to cylinders on modern hard disks. Such alignment was appropriate in the 1980s, but on a modern Advanced Format disk it will almost certainly result in serious performance problems! – Rod Smith May 8 '13 at 23:10

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