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A sample source code to blink led for ATMEL AT91sam9260-EK board(ARM9).

This simple application maps the AT91RM9200 system controller into
  user space to access the controllers peripherals such as GPIO, etc.
  In this program the GPIO signals controlling the user LEDs are toggled
  at a fixed rate.

AT91RM9200.h was taken from u-boot tree (open-source)

If you are using the sample buildroot cross compiler tree from
  KwikByte FTP server (copied to your root at /), you can build
  with "make" command.

If not, edit the Makefile for your compiler (top lines):

BASE_TOOLS=/buildroot/build_arm_nofpu/staging_dir/bin
CC=${BASE_TOOLS}/arm-linux-gcc
LD=${BASE_TOOLS}/arm-linux-ld


By default, the application is built as a static binary so no libraries
  are required on the target.  Also, debugging information is included
  so you can debug this image.

If you want to reduce the size of the image, make sure libraries are installed
  on the target and change the Makefile (LDFLAGS) so that the image is not
  statically linked and debug information is not included

Most people will not want to do this because this program is just a simple
  example anyway.

After you transfer the image to the board, make sure the file has the correct
  permissions.  You can view the permissions with "ls -al led_app".  You can
  set permissions with "chmod 755 led_app".

Execute the program with "./led_app"

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Transferring the program to the board:

If the app is not already on the board, you can do one of the following to
  get it there:
  1) Mount NFS share and copy to local directory
  2) Copy to USB disk from PC, then copy from USB disk to board
  3) Use TFTP  <- easiest method

Make sure you set the MAC on the board first.  This is done with
  "setenv ethaddr x.x.x.x.x.x".  The 'x' characters must be replaced with a
  valid MAC.  Then, set the local IP with "setenv ipaddr y.y.y.y" where
  the 'y' values are set for your network.  You can test the setting with
  "ping z.z.z.z" where the 'z' characters represent another machine on the
  network that will respond to ping packets: e.g., a router.  This is all
  done within U-Boot.  You can save the changes with "saveenv" or just proceed.
  Boot the board now with "boot".  During the next seconds, you will see the
  boot progress displayed on the serial terminal (serial cable is included
  with the board).  The root password is empty, so just login as 'root'.
  Verify the network configuration with "ifconfig eth0".  If you did not
  set the IP, you can do so here with "ifconfig eth0 y.y.y.y".  
  Now, "tftp -g -r led_app h.h.h.h" where the 'h' characters are the IP
  address of the TFTP server: e.g., your host PC running a simple TFTP server
  program.  Now, check the file permissions (see above) and run the program.
  You will see the LEDs toggling and observe some output on the serial terminal!