Filesystem config for 4k sector drive that reports 512 byte sectors [duplicate]

As I stated in my comments, as long as the actual filesystem on the partition has been set to use 4kb clusters and these clusters are aligned with with the drives 4kb sectors by ensuring that the sector start value of the partition is a multiple of 8 then the operating system itself will always write its data in 4kb clusters and thus always write to the drive in a 4kb sector block. This means you will never see the read-modify-write performance penalty.

Western Digital tells you how to ensure that your partitions are 4kb aligned at http://wdc.custhelp.com/app/answers/detail/a_id/5655

The Linux partition editor: parted, has an alignment option to ensure that Advanced Format drives are correctly configured from version 2.1:

-a alignment-type, --align alignment-type

valid alignment types are:

     none              Aligns to 512 byte sector boundaries. 

     cylinder         Align partitions to cylinders. 

     minimal          Use minimum alignment: 4KB on AF drives 

     optimal          Use optimum alignment: 1MB boundaries  

The default from parted 2.2 is to align to 1MB boundaries - optimal. Use minimal or optimal for Advanced Format drives. For example if your drive is sda:

parted -a optimal /dev/sda

will ensure that parted creates partitions on 1 MB boundaries.