The Linux kernel 2.6.30 and up includes GPIO drivers. Writing hardware registers from user space application is not safe. Please upgrade to newer kernel and use the GPIO driver as shown here,
https://www.ridgerun.com/developer/wiki/index.php/How_to_use_GPIO_signalsThe GPIO lines may require allocation in the board init code as following to ensure proper operation,
at91_set_GPIO_periph(AT91_PIN_PB0, 1);
at91_set_GPIO_periph(AT91_PIN_PB1, 1);
at91_set_GPIO_periph(AT91_PIN_PB2, 1);
at91_set_GPIO_periph(AT91_PIN_PB3, 1);
at91_set_GPIO_periph(AT91_PIN_PB8, 1);
at91_set_GPIO_periph(AT91_PIN_PB9, 1);
at91_set_GPIO_periph(AT91_PIN_PC4, 1);
at91_set_GPIO_periph(AT91_PIN_PC5, 1);
at91_set_GPIO_periph(AT91_PIN_PC6, 1);
at91_set_GPIO_periph(AT91_PIN_PC7, 1);
in file arch/arm/mach-at91/board-sam9260ek.c