Math functions (sine & cosine) latency

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So hardware FPU won't help any functions defined in math.h.

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That's not true. In the Tutorial "Using Nios II Floating-Point Custom Instructions", you can find :

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Table 1–2 indicates which math library functions use floating-point, and of those, which use floating-point division. If a function uses floating-point, it runs faster with floating-point hardware. If a function uses floating-point division, it runs even faster with floating-point division hardware.

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So the use of the floating point custom instruction affects the computation speed of the sine and cosine.