How can I do in the nios2linux

What FPGA are you downloading to? (Stratix, Stratix II, Cyclone, etc..)

When you are changing the speed of your system, are you doing the following?

1) Changing the PLL clock ratio (or changing an external clock)

2) Modifying the clock frequency in SOPC builder

3) Rebuilding your SOPC system

If your changed clock frequency effects other systems, are you modifying those that influence the NIOS processor? (such as a piece of hardware that resides outside the NIOS system but is controlled by the NIOS).