USB upload to Pro Micro (32u4)

Question

My project is based around the ATMEGA32u4 microcontroller.

I followed the Arduino Pro Micro schematic to design my own board layout and build a custom PCB, soldered on the components. Then I used the Arduino IDE to successfully upload the Arduino bootloader with SPI.

Currently I can also upload programs to my `32u4 over SPI (using "in-serial programming"). Tested that with Blink.

But I cannot upload programs with the USB, like you would normally be able to do with a Pro Micro. What things should I look for to debug this?

avrdude: Version 6.3, compiled on Jan 17 2017 at 12:00:53
 Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
 Copyright (c) 2007-2014 Joerg Wunsch
 System wide configuration file is "C:\Users\Myname\AppData\Local\Arduino15\packages\arduino\tools\avrdude6円.3.0-arduino9/etc/avrdude.conf"
 Using Port : COM12
 Using Programmer : avr109
 Overriding Baud Rate : 57600
 AVR Part : ATmega32U4
 Chip Erase delay : 9000 us
 PAGEL : PD7
 BS2 : PA0
 RESET disposition : dedicated
 RETRY pulse : SCK
 serial program mode : yes
 parallel program mode : yes
 Timeout : 200
 StabDelay : 100
 CmdexeDelay : 25
 SyncLoops : 32
 ByteDelay : 0
 PollIndex : 3
 PollValue : 0x53
 Memory Detail :
 Block Poll Page Polled
 Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
 ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
 eeprom 65 20 4 0 no 1024 4 0 9000 9000 0x00 0x00
 flash 65 6 128 0 yes 32768 128 256 4500 4500 0x00 0x00
 lfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
 hfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
 efuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
 lock 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
 calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00
 signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00
 Programmer Type : butterfly
 Description : Atmel AppNote AVR109 Boot Loader
Connecting to programmer: .avrdude: butterfly_recv(): programmer is not responding

• Gerben: When you program the blink sketch using ISP, you overwrite the bootloader!!! Did you set the correct fuses? How did you program the bootloader?
• MichaelT: Oh, I did not know that. I used an Arduino UNO as a SPI master to upload the bootloader to my 32u4. After that I uploaded a blink sketch the same way. I will try uploading the bootloader again and then the sketch via USB.
• MichaelT: Yes, that worked. Thanks, would have taken me a long time to work that out. I will post a reply.
• Gerben: It’s one of those gotchas. Glad you got it working now.

Answer 1

The answer, as kindly pointed out by Gerben, is that ISP program upload overwrites the bootloader.

Only upload the bootloader via ISP, then switch to USB for uploading Arduino sketches.