Reading the RDR register with the debugger clears the RDRF bit. Thats 
why I told you not do do that: https://embdev.net/topic/383997#4382228

Yes you had mentioned the below. I have a question.

>1. Reading spi_RDR in debug window is potentially harmful: This is a
>hardware register where reading has side effects!

>2. While you are debugging SPI code, save those registers into a variable
>that you can safely read with the debugger."
   I had assigned the receive register to a variable. Even though it is 
not showing correct value. Please find the code below.

spi_read_status spi_read(Spi *p_spi,uint8_t *pcs, uint16_t *data)
{

  static uint32_t register_value;
  uint32_t timeout = SPI_READ_TIME_OUT;

  while (!(p_spi->SPI_SR & SPI_SR_RDRF)) {
    //if timer expires return timeout.
  }

  register_value = p_spi->SPI_RDR;
  if (spi_get_peripheral_select_mode(p_spi)) {
    //get the pcs value here from the spi_rdr
  }
  *data= (uint16_t) (register_value & SPI_RDR_Mask);

  return SPI_READ_OK;
}

Please clarify whether my understaning here is correct or not. Did you 
mean that I can't  debug and test in this way. Thank you.

fop wrote:

> I never used JTAG on Atmels - is there no interference between Debugger
> and SPI ? I ask because programming is done via SPI pins on AVRs.
 On atsam device there are only 2 interface to program/debug the micro 
controller i.e. jtag and swd. Is this reason why I am not able to see 
the proper values in the receive register during debugging?
 Because all other suggestions u had mentioned is working fine.