I am trying to burn my atmega16 with arduino as ISP. So far the codes have been uploaded to my arduino flawlessly. I have uploaded arduino as ISP codes to my arduino, I have burnt bootloader of atmega16 using arduino IDE. As I sent the core working code from arduino IDE this went flawlessly. But the atmega is not showing the response, i.e. hardware is not working. And that is my (case I) issue. Case II: Furthermore, when I tried sending hex file (core working code) with avrdude compiler, it says ser_open() ... can't find lpt1. Is this the problem of avrdude's compiler? In case II there it didn't even uploaded the code, let alone the working of hardware. Please help.
arduino as isp and to burn atmega16 using avrdude compiler
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The fact that it's trying to send it to the LPT1 parallel port suggests you haven't specified "Arduino as ISP" as your programmer. Also make sure you do a Control-Shift-U (upload via programmer) instead of Control-U (upload via the bootloader). Finally keep in mind that uploading code via an external programmer will overwrite the bootloader so you won't be able to upload via USB after that unless you reflash the bootloader or do it via the command line.