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  • I think it is necessary to consider the possibility that the Arduino's bootloader is setting up the UART in some way that the Arduino Serial library assumes, and does not do itself. I believe this is plausible as IIRC the Arduino bootloader will always be run before any uploaded (Arduino) program is started. Can you put the Arduino bootloader onto your ATmega328, and then try to upload to it using your USB-UART? You might need to fiddle with the reset to your ATmega to get it into the right state as autoboot might not work (unless you can wire that up correctly too) Commented Sep 17, 2016 at 20:29
  • Definitely a question for the Arduino StackExchange. Or even Ask Ubuntu.. Commented Sep 17, 2016 at 21:36
  • @gbulmer your theory is incorrect. There is absolutely no dependency whatsoever between the bootloader and main program, and it is well known that Arduino code does not in any way require a bootloader to be present. Commented Sep 18, 2016 at 5:58
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    What is the clock source and frequency of your circuit? What was the clock source and frequency of the Arduino board configuration you used to build? If there is a mismatch all the serial baud rates will be off. If they are off by a power of two, you may be able to temporarily work around the issue by setting your computer to a baud rate that differs by the same factor, but it would be better to make the board configuration match the board. Commented Sep 18, 2016 at 6:01
  • @ChrisStratton, I tried to answer your question. I think I understand what you mean. The Arduino libraries are using some constants to deal with time dependent functionalities and those constant varies according to the board you want to program. If you compile you code with a ucontroller with 8MHz as target and run it on a 1Mhz, your 9600 baud rates will not be achieved. My guess is that either these constants are derived from the -B parameter or from another part of the avrdude configuration. Commented Sep 18, 2016 at 8:45