Windows 2003 does not align MBR disks with most SAN subsystems by default. This will cause extra I/O operations, decreasing performance. To reduce extra I/O it is best to align the disk prior to using it. The following example is provided for EMC storage, but it will work for most other vendors as well.
Windows 2008 servers are aligned by default, you can skip this if you are using Server 2008.
To align the disk you need to use the “diskpart” utility.
Open a command window and run diskpart
List the disks so you can find the one you need to align. Look for the size of the disk you just mounted.
DISKPART> list disk
Select the blank disk that you need to align
DISKPART> Select disk x
If the disk will be greater than 2TB you need to make it a GPT disk. Do this in Diskpart:
DISKPART> convert gpt
Align the disk by creating a partition with an offset.
DISKPART> create partition primary align=1024
Once the disk is aligned you can format the disk. If it is a SQL drive, the best practice unit size is 64k (vs. the default of 4096 bytes)