Building Embedded Debian Linux bootable SD card for SAMA5D3 Xplained

This article illustrates how to build an   Embedded  Debian Linux bootable SD card for SAMA5D3 Xplained  board.


  •  Linux PC (tested on Lubuntu 13.10 installed in VirtualBox)
  • ARM cross toolchain
  • AT91Bootstrap for SC card
  • Linux Kernel +  Device Tree
  • 4GB+ SD Card and  SAMA5D3 Xplained to test

1. Cross toolchain

You could build cross toolchain using buildroot or simply install:

$sudo apt-get install emdebian-archive-keyring
$sudo apt-get install libc6-armel-cross libc6-dev-armel-cross
$sudo apt-get install binutils-arm-linux-gnueabi
$sudo apt-get install gcc-arm-linux-gnueabi
$sudo apt-get install g++-arm-linux-gnueabi
$sudo apt-get install u-boot-tools
$sudo apt-get install libncurses5-dev

You could also use gnueabihf:

$sudo apt-get install gcc-arm-linux-gnueabihf
$sudo apt-get install g++-arm-linux-gnueabihf

2. AT91Bootstrap

more details

$git clone git://
$cd at91bootstrap/
$make mrproper
$make sama5d3_xplainedsd_linux_zimage_dt_defconfig
$#make menuconfig #if you want to change something
$make CROSS_COMPILE=arm-linux-gnueabi-
$cd ..


Get kernel source and compile details

$git clone git://
$cd linux-at91/
$ls arch/arm/configs/+(at91|sam)*
$make ARCH=arm sama5d3_xplained_defconfig
$make ARCH=arm CROSS_COMPILE=arm-linux-gnueabi- zImage
$make ARCH=arm CROSS_COMPILE=arm-linux-gnueabi- dtbs
$make modules ARCH=arm CROSS_COMPILE=arm-linux-gnueabi-
$make modules_install INSTALL_MOD_PATH=./modules ARCH=arm
$cd ..

4.Build an Embedded Debian root filesystem

Install tools:

sudo apt-get install multistrap
sudo apt-get install qemu
sudo apt-get install qemu-user-static
sudo apt-get install binfmt-support
sudo apt-get install dpkg-cross


$mkdir emdebian
$cd emdebian

Create file multistrap.conf and paste this inside:

debootstrap=Emdebian Net Utils Php Python


#Basic packages to enable the networking
packages=netbase net-tools ethtool udev iproute iputils-ping ifupdown isc-dhcp-client ssh

#General purpose utilities
packages=locales adduser nano less wget vim rsyslog dialog sudo

packages=php5-cgi lighttpd

#Python language
packages=python python-serial

then run:

$sudo multistrap -f multistrap.conf
$sudo cp /usr/bin/qemu-arm-static target-rootfs/usr/bin
$sudo LC_ALL=C LANGUAGE=C LANG=C chroot target-rootfs dpkg --configure -a

Create file


#Directories used to mount some SD card partitions
echo "Create mount directories"
mkdir $TARGET_ROOTFS_DIR/media/kernel

#Set the target board hostname
echo Creating $filename
echo SAMA5D3_Xplained > $filename

#Set the default name server
echo Creating $filename
echo nameserver > $filename
echo nameserver >> $filename

#Set the default network interfaces
echo Updating $filename
echo allow-hotplug eth0 >> $filename
echo iface eth0 inet dhcp >> $filename

#Set the eth0 interface MAC address
echo hwaddress ether 12:34:56:78:90:12 >> $filename

#Set a terminal to the debug port
echo Updating $filename
echo T0:2345:respawn:/sbin/getty -L ttyS0 115200 vt100 >> $filename

#Set how to mount the SD partitions
echo Creating $filename
echo /dev/mmcblk0p1 /media/mmc_p1 vfat noatime 0 1 > $filename
echo /dev/mmcblk0p2 / ext4 noatime 0 1 >> $filename
echo proc /proc proc defaults 0 0 >> $filename

#Add the standard Debian repositories.
echo Creating $filename
echo deb wheezy main > $filename
echo deb wheezy/updates main >> $filename

Then run and enter root password:

$sudo chmod +x
$sudo ./
$sudo chroot target-rootfs passwd

4. Format SD 

details are here

Run: System -> Administration -> Gparted

  • select sd card device /dev/sdb or similar (It is very important to select correct device!!!)
  • unmount
  • delete
  • new partition:
    • New size: 64MB
    • File system: FAT16
    • Label: kernel
  • newnev partition:
    • Leave size default
    • File system: EXT4
    • Label: rootfs
  • Apply changes
  • Close program GParted

Remove SD card from computer, wait 5 seconds and insert again.

SD card should be mounted as:


where $USER will be replaced with your user name.
Copy Kernel AT91Bootstrap and Device tree file to SD card:

cp at91bootstrap/binaries/sama5d3_xplained-sdcardboot-linux-zimage-dt-3.6.2.bin /media/$USER/kernel/BOOT.BIN
cp linux-at91/arch/arm/boot/at91-sama5d3_xplained.dtb /media/$USER/kernel/
cp linux-at91/arch/arm/boot/zImage /media/$USER/kernel/

Copy root filesystem and kernel modules to SD card:

sudo rsync -axHAX --progress embedian/target-rootfs/ /media/$USER/rootfs/
sudo rsync -avc linux-at91/modules/lib/. /media/$USER/rootfs/lib/.

Unmount SD card and remove from PC and inset into SAMA5D3 Xplained.
There ia also prebuild SD card image.



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8 thoughts on “Building Embedded Debian Linux bootable SD card for SAMA5D3 Xplained

  1. Very good information. Thank you for this!
    However: Is there some steps missing when it comes to formating the SD card?
    The reason I wonder is because I downloaded your prebuild and flashed with win32 diskimager and it worked fine. I then removed your bootstrap (BOOT.BIN) and put my own in and it worked (my bootstrap was loaded as expected). The problem comes when I setup anouther SD-card with GParted. This SD-card is not detected by the MCU (or at least the BOOT.bin isn’t).
    Note that I use GParded via a virtualbox ubuntu (client) on a windows7 (host) but I can not see why that should make a difference in this case…


    • After many hours I found out what the problem was… The housing for the SD card is bad… I have 3 SD cards I work with and when ever I did a test it didnt work… but when I tried shifting the SD card and pressing reset some times it worked. Either I have a bad example or the housing for the SD card is not very good… The future will tell….

      Liked by 1 person

    • It should work if you simple replace existing filesystem in flash with Debian filesystem (it should be minimal).
      Problem could be amount of flash memory on the board. – I just testing Debian with X11 – lxde and there is 1.2GB of files on sd card. X11 work just fine on SAMA5D3 xplained.


  2. Thank you very much. It is a great tutorial. And I have a small problem at the last step. When I run the rsync -axHAX –progress…. There is an error:
    xuez@ubuntu:~$ sudo rsync -axHAX –progress embedian/target-rootfs /media/$USER/rootfs/
    sending incremental file list
    rsync: change_dir “/home/xuez//embedian” failed: No such file or directory (2)
    rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1183) [sender=3.1.0]
    I tried to Google it and didn’t find anything that really helpful. So I came here seeking for help.
    Thank you


    • rsync is fast file copy tool. (copy files to sd-card)
      Usage: rsync [OPTION…] [destination]
      In your case you should check the location of sd card partition mount. ‘Automount’ location is different in different linux distribution.
      I usually use mount comand which print all mount devices with mount location…..
      Thank you


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