Have you tried avarice?  I've had better luck with that under Linux.  It can 
program chips and it can interface to GDB for debugging.

Here is the command line I use:

avarice -j /dev/ttyS0 -2 -P atmega1281 :4242 --erase -f project.elf

To just program the chip, leave out the :4242 option.

Make sure you use stabs format for debugging, not dwarf-2.

Blake

On Thursday 13 September 2007, jmonreal wrote:
> Hi, I'm new in the field. I have just acquire an STK500 AVR Starter Kit. It
> comes with AT90S8515 micro-controller. I work only under GNU/Linux and I've
> followed the steps to install all necesary software to work with this
> "board". The thing is I keep getting the same error with avrdude
>
> $ avrdude -p 8515 -c stk500v2 -P /dev/ttyS0 -e -U flash:w:simple.hex:i
>
> avrdude: AVR device initialized and ready to accept instructions
>
> Reading | ################################################## | 100% 0.01s
>
> avrdude: Device signature = 0x1e9306
> avrdude: erasing chip
> avrdude: reading input file "simple.hex"
> avrdude: writing flash (96 bytes):

<snip>


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