I know this question has been asked many times, but I did a lot of searching and followed few tutorials and still couldn't make it to work on DE0-Nano. I want to save both hardware and Nios II software in EPCS so that the system will run after power up. I know my project works, because it runs without problem if I load the hardware through USB blaster and run the Nios II software from on-chip memory. I understand in order to run Nios II SW from EPCS I first need to include an epcs_flash_controller in the Qsys project and change the CPU reset vector memory to EPCS. I've tried the following two methods to download HW/SW to EPCS, but only the HW part works, SW doesn't. Method 1: using Nios II command shell I ran the following commands in the command shell sof2flash --epcs --input=nios2_quartus2_project.sof --output=hw.flash --verbose elf2flash --input=count.elf --output=sw.flash --epcs --after=hw.flash --verbose nios2-elf-objcopy -I srec -O ihex hw.flash hw.hex nios2-elf-objcopy -I srec -O ihex sw.flash sw.hex Then I used the Quartus II Convert Programming File tool to create a JIC file with the hex files created above. And used the Quartus II programmer to program this JIC file to DE0-Nano. After power reset, the HW works but SW doesn't. Method 2: Nios II Flash Programmer In Nios II Flash Programmer I simply added SOF and ELF files to the program and press the start button. The result is the same. HW works, but SW doesn't. Can anyone tell me what I did wrong? And here is another question. From both of the methods above, the programmer first writes the HW to EPCS at address 0x00, then immediately followed by SW hex. Although the CPU's reset vector memory is set to EPCS, but how does it know where the software instructions start at? It is not at 0x00. Thank you!