Solution for “Disk Utility” WARNING: The partition is misaligned by 1024 bytes

Recently, while I was trying to install Linux Mint 13 Maya on Western Digital 1 TB Cavier Green Hard disk, the Disk Utility displayed the warning:

WARNING: The partition is misaligned by 1024 bytes

As usual, search by Google displayed numerous curt and detailed solutions. BTW this Disk is formatted with GUID Partition format. After wasting about an hour this was the solution:

1. Leave 8 mb raw space in the beginning of the Disk.

2. Partition the disk at a size in multiple of 4096 bytes. Round figure is a complete no no.

3. If in doubt, leave 8 Mb of space between the partitions.

4. While using Gparted, make sure that the partition is aligned to “Mb.” and not to “Cylinder”

Actually the problem is caused by the conflict in communication. For technical reason the Western Digital’s large Hard Disks (now other manufacturers as well) have ‘Advanced Formatting’ which means that data is aligned in sectors sized about 4096 bytes instead of 512 bytes. But the disk communicates the system as if it is maintaining data in 512 bytes per sector which creates this anomaly.  In any case Western Digital Hard Disks have problems. While I am typing this post, another Hard Disk has crashed again just within four months of replacement.

In this case, merely three small partitions in the beginning of disk had this problem and re-partitioning these partitions solved the problem. If it required re-partitioning of large partitions of 400gb, perhaps I may have let it go. But for future, while partitioning large disks, this care has to be taken. Amazing thing was that these partitions had Ubuntu Precise installed thereon for many months and the Disk Utility never displayed any warning. Why now? Why in Linux Mint 13?

© Sandeep Bhalla

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3 thoughts on “Solution for “Disk Utility” WARNING: The partition is misaligned by 1024 bytes

  1. Yep, having the same problem right now. Not sure what to make of it, and I’m not sure what caused it, but it is giving me a headache. Nothing I do will get my brand new HDD back to “normal”.
    Ubuntu 12.04.1 was the first thing I installed on the brand new hard drive. I think the problem came into play when I tried a Windows 7 dual boot setup. After I wiped Windows 7 and stated over, nothing had been the same.

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