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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