"the partition is misaligned" error in Disk Utility - should I repartition?

This answer may help you. Checkout ubuntuforums.org post at http://ubuntuforums.org/showthread.php?t=1635018. That in turn points to http://www.ibm.com/developerworks/linux/library/l-4kb-sector-disks/ for a technical discussion.

Partition is misaligned error when resizing or creating software raid

Hello, I know this is an old post but this was one of the first posts that came up on google and I have solved it. So i will share in case someone else is as Frustrated as I was.

1. The cause
   
   • The reason this happened for me is "Advanced formatting" on my WDC Green drive.
2. The Fix
   • For me, I created a new partition table (Not a new partition) I moved my files, deleted the partition, then replaced the MSDOS "Master boot record" table with a GPT "GUID Partition table" a new
3. Mind you this is how i fixed it, scouring google gave me no better answer. I will now go answer this question on the other forums I found this issue on and then save the world.

I had similar problems after I installed my new Western Digital Blue disk which is the kind of "Advanced Format", please see wdc.com/advformat. What you need to do is align the partitions to 1 MB ranges. I found a way to do that during installation of Ubuntu:

1. Boot installation CD (or usb stick) so you get the page showing HD needs, internet connection etc.
2. Press Ctrl+alt+F1 to get into "terminal mode".
3. Run sudo parted -a optimal /dev/sda (change drive name accordingly). This will startup parted with this optimal setting for this drive.
4. Create (or remove and recreate) your partitions to your needs. You will likely loose all data! Perhaps moving will work?
5. You may use the command align-check opt to see that the partitions are optimally aligned.
6. Quit and return to installation program by pressing Ctrl+Alt+F7. Continue with the installation and when you come to the partition step of the install, just choose the partitions, press Edit and set the filetypes (ext4, swap etc) and mount point. (For me, the installation actually crashed before setting up the partitions but you will be returned to the desktop and you can re-run the installation.)

Next question is how worse it will get. I did, just after installation, a read-only performance test in the disk utility and I couldn't see any major difference with partitions aligned versus misaligned. So if it seems to hard work to reinstall Ubuntu you can probably keep it as it is!