Is there a way to properly format it
for an Ubuntu 9.10 Server to take
advantage of the advanced format? Such
as with sector sizes?
The potential problem arises not from formatting the drive but from where on the drive the partitions are located. 4K sector drives need to be aligned on a logical block address that is a multiple of 8.
Supposedly the Linux tools have been updated to do the right thing when it comes to the 4K sector drives.
If you are using the most recent version of a popular Linux partition editor to create one or more new partitions on the drive you should be OK.
One warning: The WD drives can be jumpered as a kludge to work "correctly" with partitions created by Windows XP. Since you are using Linux make sure you do not have the jumper set for Windows XP. (If you did have the XP jumper set then you would get terrible performance from the drive).
OK, after Googling around a bit further, I'm confused. On the one hand, I've read the overview articles which claim Linux has no problem at all with 4K sector drives. But on the other hand, there are articles like these which claim the opposite.
Linux Not Fully Prepared for 4096-Byte Sector Hard Drives
Linux WD EARS Advanced Hard Drive Format
The second link above is probably more useful since it seems to offer suggestions on how to properly partition a 4K sector drive.
What I suggest is that you first check the alignment of your partitions by using
fdisk -lu to display their starting LBAs. If your partition(s) are already aligned on LBAs that are a multiple of 8 then you should be fine. (You could also time the transfer of a large file just as an extra sanity check.)
If you have unaligned partitions then you probably want to delete and recreate using the method in the second article to ensure they are aligned properly.
Hope this helps ...