Linux Not Fully Prepared for 4096-Byte Sector Hard Drives
Recently, I bought a pair of those new Western Digital Caviar Green drives. These new drives represent a transitional point from 512-byte sectors to 4096-byte sectors. A number of articles have been published recently about this, explaining the benefits and some of the challenges that we'll be facing during this transition. Reportedly, Linux should unaffected by some of the pitfalls of this transition, but my own experimentation has shown that Linux is just as vulnerable to the potential performance impact as Windows XP. Despite this issue being known about for a long time, basic Linux tools for partitioning and formatting drives have not caught up.
The problem most likely to hit you with one of these drives is very slow write performance. This is caused by improper logical-to-physical sector alignment. OS's like Linux use 4K blocks (or multiples of 4K) to store data, which matches well with the physical sector. However, nothing restricts you from creating a partition that starts on an odd-numbered 512-byte logical sector. This misalignment causes a performance hit since the drive has to read and rewrite the 4K sectors with whatever 512-byte slices changed.
