In the SAM-BA main window, select the "NandFlash" tab and in the "Scripts" dropdown menu select "Enable NandFlash", to program the on-board NandFlash device. Click Execute and SAM-BA should emit the following in the message area:

(SAM-BA v2.10) 1 % NANDFLASH::Init
-I- NANDFLASH::Init (trace level : 0)
-I- Loading applet isp-nandflash-at91sam9g45.bin at address 0x70000000
-I- Memory Size : 0x10000000 bytes
-I- Buffer address : 0x70003E34
-I- Buffer size: 0x20000 bytes
-I- Applet initialization done
(SAM-BA v2.10) 1 %

The actual options and output of SAM-BA may vary according to the version you are using. The behaviour documented here is that of SAM-BA 2.10.

Now select "Send BootFile" from the "Scripts" menu and "Execute" it. When the file open dialog appears, select the nandflash_at91sam9g45ekes.bin file and click "Open". The following output should be seen:

(SAM-BA v2.10) 1 % GENERIC::SendBootFileGUI
GENERIC::SendFile Z:/eCos/SAM-BA/nandflash_at91sam9g45ekes.bin at address 0x0
-I- File size : 0x1334 byte(s)
-I-     Writing: 0x1334 bytes at 0x0 (buffer addr : 0x70003E34)
-I-     0x1334 bytes written by applet
(SAM-BA v2.10) 1 %

Click the "Send File" button. SAM-BA will put up a dialog box while it is writing the file to the NAND Flash, and will output something similar to the following in the message area:

(SAM-BA v2.10) 1 % send_file {NandFlash} "Z:/eCos/SAM-BA/redboot_ROM.bin" 0x020000 0
-I- Send File Z:/eCos/SAM-BA/redboot_ROM.bin at address 0x020000
GENERIC::SendFile Z:/eCos/SAM-BA/redboot_ROM.bin at address 0x20000
-I- File size : 0x24658 byte(s)
-I-     Writing: 0x20000 bytes at 0x20000 (buffer addr : 0x70003E34)
-I-     0x20000 bytes written by applet
-I-     Writing: 0x4658 bytes at 0x40000 (buffer addr : 0x70003E34)
-I-     0x4658 bytes written by applet
(SAM-BA v2.10) 1 %

Shut down SAM-BA and start up Hyperterm or similar on the real COM port, not the USB port, configured for 115200 baud 8-N-1 with no flow control. Attach an ethernet cable between the board and a switch on your network. Press the reset button on the board and something similar to the following should be output on the DEBUG serial line.

Start AT91Bootstrap...
+**Warning** FLASH configuration checksum error or invalid key
Use 'fconfig -i' to [re]initialize database
Ethernet eth0: MAC address 0e:00:00:ea:18:f0
IP: 10.0.2.1/255.0.0.0, Gateway: 10.0.0.3
Default server: 0.0.0.0
DNS server IP: 10.0.0.1, DNS domain name: <null>

RedBoot(tm) bootstrap and debug environment [ROM]
Non-certified release, version UNKNOWN - built 14:54:15, Aug 20 2010

Copyright (C) 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009
Free Software Foundation, Inc.
Copyright (C) 2003, 2004, 2005, 2006, 2007, 2008 eCosCentric Limited
RedBoot is free software, covered by the eCos license, derived from the
GNU General Public License. You are welcome to change it and/or distribute
copies of it under certain conditions. Under the license terms, RedBoot's
source code and full license terms must have been made available to you.
Redboot comes with ABSOLUTELY NO WARRANTY.

Platform: AT91SAM9G45-EK (ARM9)
RAM: 0x20000000-0x28000000 [0x20035f78-0x27ffe530 available]
FLASH: 0x50000000-0x5041ffff, 8192 x 0x210 blocks
RedBoot>

The board is now running and the flash can be configured.

Use the following command to initialize RedBoot's Flash Information System (FIS):

RedBoot> fis init
About to initialize [format] FLASH image system - continue (y/n)? y
*** Initialize FLASH Image System
... Erase from 0x5041fdf0-0x5041ffff: .
... Program from 0x27fffdf0-0x28000000 to 0x5041fdf0: .
RedBoot>

Now configure RedBoot's Flash configuration with the fconfig command. Remember to substitute the appropriate MAC address for this board at the appropriate step. If a BOOTP/DHCP server is not available, then IP configuration may be set manually. The default server IP address can be set to a PC that will act as a TFTP host for future RedBoot load operations, or may be left unset. The following gives an example configuration:

RedBoot> fconfig -i
Initialize non-volatile configuration - continue (y/n)? y
Run script at boot: false
Use BOOTP for network configuration: false
Gateway IP address: 192.168.7.11
Local IP address: 192.168.7.83
Local IP address mask: 255.255.255.0
Default server IP address: 192.168.7.11
Console baud rate: 115200
DNS domain name: farm.ecoscentric.com
DNS server IP address: 192.168.7.11
Network hardware address [MAC]: 0x0E:0x00:0x00:0xEA:0x18:0xF0
GDB connection port: 9000
Force console for special debug messages: false
Update RedBoot non-volatile configuration - continue (y/n)? y
... Erase from 0x5041ef80-0x5041f7bf: ....
... Program from 0x27fff5b0-0x27fffdf0 to 0x5041ef80: ....
RedBoot>