Fragmentation occurs on disks when portions of files are stored in areas physically remote from other parts of the files. It is caused by deletion of smaller files which then causes larger files written later to be stored in disconnected pieces. Fragmentation affects disk read and write times adversely because disks are usually read/written sequentially and sectors are laid out on the disk to optimize sequential performance. Disk operations are delayed not only by the time required to move the read write heads but by the time to wait for data areas to rotate under the read-write heads after the heads are moved.

Disk fragmentation can cause substantial problems in benchmarking especially if the operating system is buffering data to disk. For example, Windows benchmarks can vary from run to run if a temporary swap file is used and the disk is not freshly defragmented.

Most modern operating systems include defragmentation utilities. These utilities move data around on disks in order to store files in sequential order. Some files such as Windows permanent swap files can not be moved because permanent pointers are stored in the software. By custom, such files are stored as hidden files and are not moved by defragmentation utilities.

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