First we need to download and setup the toolchain:

$ git clone https://github.com/ramangopalan/avr32-gnu-toolchain-linux_x86
$ sudo mkdir /opt/avr32
$ cd avr32-gnu-toolchain-linux_x86
$ sudo cp -a * /opt/avr32/
$ export PATH=/opt/avr32/bin:$PATH

Compile NuttX to avr32dev1 (similar uc3b-cpu board)

$ ./tools/configure.sh avr32dev1:nsh
$ export LC_ALL=C
$ make

I tried to flash using the AVR32 DFU:

$ sudo dmesg
...
[26451.339347] usb 3-5.1: new full-speed USB device number 15 using xhci_hcd
[26451.490782] usb 3-5.1: New USB device found, idVendor=03eb, idProduct=2ff6, bcdDevice=10.00
[26451.490793] usb 3-5.1: New USB device strings: Mfr=1, Product=2, SerialNumber=3
[26451.490796] usb 3-5.1: Product: AT32UC3B DFU
[26451.490799] usb 3-5.1: Manufacturer: ATMEL
[26451.490802] usb 3-5.1: SerialNumber: 1.0.2

Let to list the DFU configurations:

$ sudo dfu-util -l
dfu-util 0.9

Copyright 2005-2009 Weston Schmidt, Harald Welte and OpenMoko Inc.
Copyright 2010-2016 Tormod Volden and Stefan Schmidt
This program is Free Software and has ABSOLUTELY NO WARRANTY
Please report bugs to http://sourceforge.net/p/dfu-util/tickets/

Found DFU: [03eb:2ff6] ver=1000, devnum=15, cfg=1, intf=0, path="3-5.1", alt=0, name="UNKNOWN", serial="1.0.2"

Unfortunately the DFU flashing didn’t work:

$ sudo dfu-util -d 03eb:2ff6 -D nuttx.bin 
dfu-util 0.9

Copyright 2005-2009 Weston Schmidt, Harald Welte and OpenMoko Inc.
Copyright 2010-2016 Tormod Volden and Stefan Schmidt
This program is Free Software and has ABSOLUTELY NO WARRANTY
Please report bugs to http://sourceforge.net/p/dfu-util/tickets/

dfu-util: Invalid DFU suffix signature
dfu-util: A valid DFU suffix will be required in a future dfu-util release!!!
Opening DFU capable USB device...
ID 03eb:2ff6
Run-time device DFU version 0101
Claiming USB DFU Interface...
Setting Alternate Setting #0 ...
Determining device status: state = dfuIDLE, status = 15
dfuIDLE, continuing
WARNING: DFU Status: 'Device stalled an unexpected request'
DFU mode device DFU version 0101
Device returned transfer size 65535
Limited transfer size to 4096
Copying data from PC to DFU device
Download	[                         ]   0%            0 bytesdfu-util: Error during download