Unable to upload code to Leonardo

Question

I was using Arduino-Makefile to upload code to a Leonardo via its standard make upload. However, it became "stuck" and unresponsive, as Leonardo's sometimes do. I tried power cycling it, and unplugging the USB cable, but nothing worked. So I tried re-burning the bootloader via an AVRISP MkII programmer and the Arduino 1.8.2 IDE, but that only made things worse.

It somehow uploaded a simple "blink" program, but now the it's completely unable to be programmed via USB. When I run make upload, or use the Arduino IDE's "upload" button, the Leonoardo's status LED begins blinking rapidly and its /dev/ttyACM0 device disappears permanently. I have to power-cycle it to make the device reappear, but the upload still fails, with the error:

/usr/share/arduino/bin/ard-reset-arduino --caterina /dev/ttyACM0
make[1]: Leaving directory '/usr/local/myproject/main'
make do_upload
make[1]: Entering directory '/usr/local/myproject/main'
/usr/share/arduino/hardware/tools/avr/bin/avrdude -v -p atmega32u4 -C /usr/share/arduino/hardware/tools/avr/etc/avrdude.conf -D -c avr109 -b 57600 -P /dev/ttyACM0 \
 -U flash:w:build-leonardo/main.hex:i
avrdude: Version 6.3, compiled on Jan 17 2017 at 11:00:16
 Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
 Copyright (c) 2007-2014 Joerg Wunsch
 System wide configuration file is "/usr/share/arduino/hardware/tools/avr/etc/avrdude.conf"
 User configuration file is "/home/chris/.avrduderc"
 User configuration file does not exist or is not a regular file, skipping
 Using Port : /dev/ttyACM0
 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
avrdude: butterfly_recv(): programmer is not responding
avrdude: butterfly_recv(): programmer is not responding
avrdude: butterfly_recv(): programmer is not responding
avrdude: butterfly_recv(): programmer is not responding
avrdude: butterfly_recv(): programmer is not responding
Found programmer: Id = ""; type = 
 Software Version = .; Hardware Version = �.
avrdude: butterfly_recv(): programmer is not responding
avrdude: butterfly_recv(): programmer is not responding
avrdude: error: buffered memory access not supported. Maybe it isn't
a butterfly/AVR109 but a AVR910 device?
avrdude: initialization failed, rc=-1
 Double check connections and try again, or use -F to override
 this check.
avrdude: butterfly_recv(): programmer is not responding
avrdude: error: programmer did not respond to command: leave prog mode
avrdude: butterfly_recv(): programmer is not responding
avrdude: error: programmer did not respond to command: exit bootloader

If I manually run:

/usr/share/arduino/bin/ard-reset-arduino --caterina /dev/ttyACM0

or upload via the Arduino IDE, it makes the Leonardo disappear from USB, and blink rapidly. Pressing the reset button does nothing. I have to manually unplug its USB cable to fix it.

I can program it still using the AVRISP MkII programmer...but obviously that's a huge inconvenience since it takes about 5 minutes just to upload the sample blink sketch, and even then it requires that I first power off the Leonardo, disconnect the programmer, and then power on. For development, where I might need to make dozens of revisions, this turnout is far too slow.

Why am I unable to program the Leonardo via avrdude and USB?

• Peter Mortensen: I need to press the Leonardo's "RESET" button to get out of this state (it will always fail after the first flash failure). It works best pressing the "RESET" button when the Arduino log window shows the lines with "PORTS ..." (for example, "PORTS {/dev/ttyACM1, } / {/dev/ttyACM1, } => {}").

Answer 1

Using some examples and similar questions, such as this one and this one, I fixed udev rules for the AVRISP MkII programmer, then I manually reflashed the Leonardo's bootloader with with the MkII by running:

avrdude -c avrispmkii -p m32u4 -P usb -B 8 -u -e -U lock:w:0x3F:m -v
avrdude -c avrispmkii -p m32u4 -P usb -v
avrdude -c avrispmkii -p m32u4 -P usb -u -U efuse:w:0xcb:m -v
avrdude -c avrispmkii -p m32u4 -P usb -u -U hfuse:w:0xd8:m -v 
avrdude -c avrispmkii -p m32u4 -P usb -u -U lfuse:w:0xFF:m -v 
avrdude -c avrispmkii -p m32u4 -P usb -U flash:w:/usr/share/arduino/hardware/arduino/avr/bootloaders/caterina/Leonardo-prod-firmware-2012年12月10日.hex -v
avrdude -c avrispmkii -p m32u4 -P usb -U lock:w:0x0F:m -v

I'm not sure if the first and last command to write the lock bytes were necessary, since they returned the verification error; content mismatch error, but they didn't seem to break anything either.

Oddly, this ran in seconds, whereas the Arduino IDE took almost 5 minutes to burn the bootloader. So I suspect there's a bug in the Arduino IDE that burns an incorrect or corrupted bootloader.

After running this, ard-reset-arduino works correctly, and make upload can successfully upload a sketch again.

On a side note, I'm not 100% sure if Leonardo-prod-firmware-2012年12月10日.hex was the correct bootloader to use. Again, I just made an educated guess based on naming. I'd read that the Leonardo uses the "caterina" bootloader, and the directory /usr/share/arduino/hardware/arduino/avr/bootloaders/caterina contained several .hex files, only three of which contained "Leonardo" in the name:

Caterina-Leonardo.hex
Leonardo-prod-firmware-2012年04月26日.hex
Leonardo-prod-firmware-2012年12月10日.hex

It seemed logical to not use Leonardo-prod-firmware-2012年04月26日.hex, since that was likely an old and obsolete bootloader based on the date. That left Caterina-Leonardo.hex or Leonardo-prod-firmware-2012年12月10日.hex. Unfortunately, checking the commit logs shows they're exactly the same age. In my experience, prod tends to mean the final or production product, so I decided to try that one first and it worked. If anyone knows what Caterina-Leonardo.hex is for and how it differs from the others, please tell me. I don't want to risk breaking my Leonardo again experimenting with this.

The only issue I'm having now is that after I upload my sketch, with uses ROS and about 49% of the Arduino's memory, I again can no longer upload new sketches to it. I'm assuming the sketch's use of the Serial port is somehow stopping ard-reset-arduino from properly resetting it`. However, I the Arduino IDE is still able to upload sketches, so as a clumsy workaround, I can use that to upload the "blink" sketch, afterwhich then I can upload my own revised sketch.

• Nick Gammon: If you believe this has fixed your issue please accept your own answer. Thanks!