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I am looking for a program to benchmark whole disk and show access time for different sectors on a disk. (I use HD Tune for that purpose on Microsoft Windows)
You can use hdparm, dd, bonnie++, fio, iozone or orion to benchmark your disk on Linux. All these programs are free and open source. See How can I benchmark my HDD?, I/O Performance Benchmarking Linux, and Linux File System Read Write Performance Test for information on how to use them.
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