Using avrdude to program atmega8 and some other small avr controllers
worked fine. With the atmega2560 problems started when my program
becomes bigger than 64KB. I found out how to workaround the problem:
In the hex files exchanging addresses 0x10000 and 0x30000 helped.

I wrote a small homepage to describe the problem and the workaround:
http://www.rolfp.ch/elektronik/avr/mk3/avrdude64k-problem.html
(only in german because my english is not good enough)

Im not absolutly shure yet if it is really a bug in avrdude
and not in the programmer.

I also started to make a bootloader. This will work much faster
for programming more than 64KB.
http://www.rolfp.ch/elektronik/avr/mk3/#bootloader

When trying out reading eeprom with my bootloader and compared
with reading eeprom with avrdude I found it was wrong.
I think the bootloader is right and avrdude (version 5.11) has an other
bug here. With avrdude-5.6 on an older Mac it readed out the same as my
bootloader.

Rolf

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