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Most libraries and application are written to be used on an operating system such as Linux, so porting is likely to be a lot easier if you are using one. The Nios II Linux distribution uses the same Linux kernel as your Linux desktop, but for the Nios II architecture, so porting many libraries is simple.
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Thanks for reply, ykozlov,
After installing a uclinux system on the nios II processor, will using a C2H accelerator still be possible?
I mean, the reason I use the FPGA to run my code is to get a higher speed compared to my computer. If using a system on nios II processor, will using the hardware accelerator still be possible? (If all implemeted by software, I think the computer cpu will do much better than the nios II processor. )