When addressing system performance issues, a key element that is often overlooked is Disk Fragmentation. Even on a brand new system with plenty of RAM and high-end processors, the performance of the hard disk may be a bottleneck causing system performance issues. It takes time to load large data files into memory - issues become particularly noticeable when dealing with movies, video clips, database files or .ISO image files which may easily be several gigabytes in size. On a freshly formatted disk, these files load fairly quickly. Over time, however you may start to notice performance degradation - caused by disk fragmentation.
We touched on disk fragmentation when we were discussing the Page File a couple of months ago, but we never really got into the nuts and bolts of it. To understand disk fragmentation though, you need to understand the basic structure of hard disks. When you format a hard disk, the formatting process divides the disk into sectors, each of which contains space for 512 bytes of data. The file system then combines groups of sectors into clusters. A cluster is the smallest unit of space available for holding a single file - or part of a file. On NTFS disks, the cluster sizes are determined based on the drive size as shown below (this information is also available in Microsoft KB 314878). When formatting disks it is possible to change the cluster size, however this may cause additional performance issues.