A virtual hard disk (VHD) is partitioned with a master boot record that is used by a Linux virtual machine. It must be aligned with the underlying LUN for best performance.
If the data block boundaries of a disk partition do not align with the block boundaries of the underlying LUN, the storage system often has to complete two block reads or writes for every operating system block read or write. The additional block reads and writes caused by the misalignment can lead to serious performance problems.
The misalignment is caused by the location of the starting sector for each partition defined by the master boot record. Partitions created by Linux usually are not aligned with underlying NetApp LUNs.
A workaround for misaligned Linux guests is available at the NetApp Linux Community Program site at http://linux.netapp.com/tools/fix-alignment.