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Linux On Hydra

This document is obsolete.
Last modified August 8, 2014

Fashion Cotton Design Hawkeye Children's T-shirtIntroduction
Virtual Box
Install Virtual Box
Install Ubuntu on the virtual machine
Preparing the development tools
Environment Settings
The AT91 Bootstrap
SD Card Test
File System
Prepare the file system
Prepare SD Card parition
Copy the filesystem to the SD card
Boot to Command Prompt
Add a display (preliminary)
Hello World Blinky
If you have a Rev. 1.2 board

These pages aspire to be a “getting started” guide to boot your FEZ Hydra using Linux. We hope that this effort gets the community interested in this direction and eventually assemble a lean Linux machine for the Hydra and future boards.

You have several options. If you already have a Linux Box, you could skip these pages. However for someone foraying into the world of Linux for the very first time, these pages attempt to make the journey as easy as possible.

There is no need for a dedicated computer for Linux, you can install Linux using different methods:
– Dual Boot
– Live CD (or USB installs)
– Virtualization
– Minimalist GNU for Windows
– Search for other options on your search engine of choice

However these pages are going to take a proven path and use desktop virtualization.
These instructions are not supported. GHI Electronics will respond to any questions at its own discretion.

These instructions should be treated as general guidelines. When they were written they were briefly tested. The current version of the FEZ Hydra product and/or the version/distribution of the Linux systemmay not work at all.

There is no guarantee these intructions will work or are bug free.
Virtual Box

Virtual Box is a virtualization product that is Open Source Software under the terms of the GNU General Public License (GPL) version 2. It is feature rich and high performance. USB support for guest operating systems is very clean and will make a big difference for this project.

Visit to learn more
Download or execute the VirtualBox 4.1.6 for Windows hosts or use the following link [1]

Install Virtual Box
You could choose to ‘Run’ or ‘Save’ and then execute the installer.

The default options presented by the installer should be good enough, but go ahead and explore the options.

You will see several message pertaining to Storage, USB and Network devices. Please do install them as they will be required for the Linux guest to interact with the Host devices.

Post install the VirtualBox Manager should come up. Go ahead and close or minimize for now.
Install Ubuntu on the virtual machine

There are several Linux distros that you could use for development. Visit to see what is available.

The instructions that follow will use Ubuntu.
Head over to and grab the ISO image for 10.04 LTS 32 bit. You have the option to download the latest 11.10 32 bit image, but this could be a little bloated compared to the 10.04 version.

Create a folder called Linux and save the Ubuntu ISO image to that folder. If you have multiple physical disks, you could choose to create this on a disk other than the disk that runs your primary operating system (eg. Windows). We will create the virtual machine disks on this folder later and will enhance performance.

Once the ISO image is downloaded open up Virtual Box manager and click on the Machine->New menu item (Ctrl+N)

Click through the wizard welcome page and on the VM name and OS type page type ‘Ubuntu’. This will select Linux and Ubuntu.

Proceed to the Memeory page and allocate memory for the virtual machine. You can use the slider to atleast cover the green mark on the slider. You have to balance for performance and ensure that the Windows host is not starved either.

Proceed to the Virtual Hard Disk page, check ‘startup disk’ and ‘create new hard disk’. Proceed to the next page, select ‘VDI (VirtualBox Disk Image)’. Proceed to the next page and select ‘Dynamically allocated’, this will make you disk grow as it fills rather than allocating it upfront. For a temporary virtual machine this works great and for a more permanent one you may want to use ‘Fixed size’ to avoid running out of disk at a later date.

Proceed to the next page and click on the folder icon to choose the ‘Linux’ folder that you created earlier. Use the slider to give about 20GB disk size. On the final page review the parameters and create the virtual disk.

After the virtual disk is created, click on the create button on the ‘virtual machine’ window to create the virtual machine. The virtual machine will appear on the Virtual Box manager.

Right click and select ‘Start’ from the menu. This will launch the ‘First Run Wizard’
As the virtual machine starts you may see alerts for keyboard and mouse capture or the display color depth. Read and click on the ‘OK button’

On the First Run wizard selec the installation media by clicking on the folder icon and selecting the Ubunti ISO image that was downloaded earlier.

The installation should start, just follow the install prompts and select the default options.
Choose to “Install Ubuntu 10.04.3 LTS”

Choose to “Erase and use the entire disk”
When prompted enter your user name, password and the computer name. You can choose anything but make sure that you can remember, offcourse ‘Hydra’ is a good choice.

Continue with the installation. You will be prompted to restart and also unmount the installation media. Please read all the alerts and wait for you new virtual ‘Ubuntu’ system to boot.

Login using the user name and password you provided during installation.
At this point you have a spanking new Linux box to play with. Take some time to go through the options on both Virtual Box and Ubuntu. Try to understand the different display modes that Virtual Box supports. You can use ‘Full Screen’, ‘Scaled mode’ or even ‘Seamless mode’. The ‘Seamless’ mode is interesting and allows you to drag Linux windows to the MS Windows desktop. This means that you can have a notepad window and a Linux command shell next to each other on your desktop.

For some of these fucntions to work you need to install the “Guest Additions” from the Virtual Box menu Devices>Install Guest Additions and then restart the Virtual machine.

As a quick note, Linux has a complete command mode (shell) and the graphics interface is X windows with a Window manager. Ubuntu uses GDM (Gnome Display Manager) as the default Window manager. You can change to other like KDE. There are even Windows 7 themes available to make the Ubuntu desktop look very familiar. There are tons of free applications including office applications. Take some time to play around and discover.

Preparing the development tools
The Atmel AT91SAMRL64 processor on the Hydra has a ROM based bootloader. On startup this bootloader checks for the status of the BMS pin. If the pin state is 0 teh bootloader continues to boot from NOR Flash present on EDI0 (CS0). If the pin state is 1 then the bootloader tries to boot on a sequence of SDCard (MCI1), NAND flash on EBI0 (CS3), Dataflash on SPI0 (CS0) and finally a SAM-BA boot.

The Hydra has Dataflash on SPI0, but that is something that will be used for the NETMF environment. So an SD Card Module should be connected on the F socket.

The bootloader on ROM will load the bootloader on the SDCARD. This boot loader runs on the bare metal of the AT91 chip. Hence the bootloader has to be compiled using an ARM compiler. This compiler can be the ARM GCC for Linux. CodeSourcery provides this compiler and is also used for NETMF GCC builds.

Now open a Linux command shell on Ubuntu. Click on the Applications > Accessories > Terminal
Remember that you have logged in using your user account and will require administrative permission to complete configuration changes. The easy way to do this to elevate you shell to a super user mode.

Type: sudo bash
You can see that the shell prompt has changed to ‘root@hydra:/#’

Change the current directory to the root ‘/’ using ‘cd /’ and you can check the current directory using ‘pwd’.

From the root create a new folder named ‘hydra’. This will be the work folder for this project. To create a folder use ‘mkdir hydra’, to change to the folder user ‘cd hydra’ and to find the current directory use ‘pwd’

The Embedded Linux Development Kit (ELDK) includes the GNU cross development tools, such as the compilers, binutils, gdb, etc.and a number of pre-built target tools and libraries necessary to provide some functionality on the target system.

ELDK is maintained by the folks at DENX Software Engineering.

This download will take a while (a hour or less depending on your connection speed) about 556 MB (556,728,320)

At the end of the download you should have a file named arm-2008-11-24.iso. You need to mount this ISO to install the ELDK.

To mount the ISO first create a new folder (assuming you are still in the /hydra folder)
mkdir disk

To mount the ISO file on the new folder
mount -o loop arm-2008-11-24.iso disk

The contents of the ISO can be accessed from the folder.
cd disk

To start the install of the ELDK
./install -d /hydra/eldk arm

Do you really want to install into /hydra/eldk directory[y/n] : y
The installation will continue to run to the end. You may see messages regarding permissions etc. Ignore them.

Return to the ‘hydra’ work folder
ELDK installation is complete.

Environment Settings
A couple of environmental variables have to be set for the paths and cross compile settings.

export CROSS_COMPILE=arm-linux-

To check the installation of the tools you can use the ‘which’ command. This command prints out the full path to a command or shell script.

which arm-linux-gcc
The response should see

eval $CROSS_COMPILEgcc –version

The response should see (depending on the folder names)
arm-linux-gcc (GCC) 4.2. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

The AT91 Bootstrap
AT91Bootstrap is a first step bootloader providing a set of algorithms to manage hardware initialization (GPIO, Clock, SDRAM, etc), to download your main application from specified FLASH media to main memory and to start it.

Atmel maintains the AT91Bootstrap and provides prebuilt versions for thier development boards.
1.Downloaded boostrap code from the ftp site.

2.Once code is downloaded as an archive and can be expanded using

tar xvf AT91Bootstrap-5series_1.2.tgz
This will extract the code a a folder named ‘AT91Bootstrap-5series_1.2’

These sources are maintained by Atmel and spans all the AT91 evaluation kits. Since the Hydra uses the AT91SAMRL64 it will make sense to modidy the AT91SAMRL64-EK code.

One of the major changes between Hydra and the EK is the SDRAM. Hydra uses a 16MB SRAM (MT48LC8M16A2P). This SDRAM has a 16bit bus width 4K row addressing (A0 – A11) and 1K column addressing (A0 – A9). These parameters have to be changed in the bootstrap code.

3.Change to the correct folder
cd /hydra/AT91Bootstrap-5series_1.2/board/at91sam9rlek

4.Open the init code
gedit at91sam9rlek.c

5.On Gedit search for ‘#ifdef MCK_100’
There will be 2 block of code calling sdram_init. The ‘if’ part make a call for a 100Mhz (PC-100) SDRAM and the else for the 133Mhz (PC-133) SDRAM.

Change the 100Mhz call from

With this change the bootstap can be configured, compiled and tested. The source is buit using make files. The bootstap code has a ‘menuconfig’ option allowing configuration using a simple CUI.

6.First change to the the top folder.
cd /hydra/AT91Bootstrap-5series_1.2

To use menuconfig a dependent libraray called ‘Ncurses’ is required. To install this library use the ‘apt-get’ command. This command will download and install the required library.

apt-get install libncurses5-dev
7.At this point the AT91 bootstrap can be compiled

If there is an error like
Makefile:92: *** Environment variable “CROSS_COMPILE” must be defined!. Stop.

read the section above and set the environment variables and try again.
8.Next configure the build for the RL64 with SD Card Support

make at91sam9rlsd_defconfig
When prompted select option#4 ‘4. at91sam9rlek (CONFIG_AT91SAM9RLEK)’

The make will complete and create a configuration file named ‘.config’
9.Configure the Image Loading Strategy using the CUI

make menuconfig
This command will bring up the CUI

Press ‘i’ to move the cursor to the correct menu item and ensure that it reads ‘Image Loading Strategy (Load U-Boot into last MBYTE of SDRAM).

If not hit ‘enter’ key to bring up the options
On the menu option use the ‘l’ key to select the first option ‘Load U-Boot into the last MBYTE of SDRAM’ and use the ‘space’ bar or the ‘enter’ key to select the option and exit the menu.

Bck on the main menu options press the ‘Esc’ key twice to exit. Select ‘yes’ when prompted to save the nre at91bootstrap configuration.

10.Build the AT91 bootstrap

The build shoud display the following on success:
Size of at91sam9rlek-sdcardboot-3.1.bin is 10596 bytes
[Succeeded] It’s OK to fit into SRAM area

The SRAM is the on chip 64K SRAM and boot code should fit into it.

U-boot is a second stage bootloader. It is responsible of configuring main interfaces and launching a Linux system. Note however that it is possible to avoid this step and to directly boot Linux from AT91Bootstrap, in a production phase for instance.

U-Boot is maintained by the fold at DENX Software Engineering.
1.Change to the ‘hydra’ work folder

2.Download U-Boot sources

3.Extract the source
tar xvfj u-boot-2011.09.tar.bz2

4.Edit the board file
gedit u-boot-2011.09/board/atmel/at91sam9rlek/at91sam9rlek.c

Add the following code to the top of the file along with the other defines and before the ‘DECLARE_GLOBAL_DATA_PTR;’

Add the following SD CARD initialization code to the end of the file
5.Edit the MCI include file

gedit u-boot-2011.09/drivers/mmc/atmel_mci.h

Add the following defines

6.Edit the gen_atmel_mci driver file
gedit u-boot-2011.09/drivers/mmc/gen_atmel_mci.c

Search for
Insert the following code after the above

7.Edit the board configuration settings at91sam9rlek.h
Search for ‘/* DataFlash */’

Insert the following before the above
Search for ‘#define CONFIG_CMD_NAND’ and edit to

Search for ‘#define CONFIG_HAS_DATAFLASH’ and edit to
8.Edit the CPU initialization code

gedit u-boot-2011.09/arch/arm/cpu/arm926ejs/at91/at91sam9rl_devices.c
Add the following code to the end of the file

9.Edit the board configuration
gedit u-boot-2011.09/include/configs/at91sam9rlek.h

Search for ‘/* CONFIG_SYS_USE_NANDFLASH */’ and edit to
Scroll to the ‘#endif’ after the above and insert the configuration for a SD CARD boot as

10.Add an entry for the SD CARD configuration in the boards.cfg file
gedit u-boot-2011.09/boards.cfg

Search for ‘at91sam9rlek_dataflash’ and insert the following on the next line
11.The code is ready to compile. Change to the correct folder

cd u-boot-2011.09
12.Clean existing objects

13.Build U-Boot
make at91sam9rlek_sdcard

If the build completes with no issues the following message will be displayed
arm-linux-objcopy –gap-fill=0xff -O binary u-boot u-boot.bin
make[1]: Leaving directory `/hydra/u-boot-2011.09′

1.Change to the hydra folder

2.Get the Linux Kernel sources

3.Extract the sources
tar xvfj linux-2.6.30.tar.bz2

4.Change to the source folder
cd linux-2.6.30

5.Get the AT91 patch

6.Apply the patch
zcat 2.6.30-at91.patch.gz | patch -p1

If you see an error regarding ‘patch’ e.g. The program ‘patch’ is currently not installed. You can install it by typing: apt-get install patch

Do the above superman ripping shirt t shirt womens step and try step 6 to apply the patch.
7.Download the experimental patch for RL64.Skipping this step will break the Kernel.

8.Extract the patch

tar xvzf 2.6.30-at91-exp.4.tar.gz
9.Apply the patch

for p in 2.6.30-at91-exp.y/*; do patch -p1 < $p ; done

make mrproper
11.make config

make ARCH=arm at91sam9rlek_defconfig
12.compile the kernel

make uImage ARCH=arm
The compile should complete with the following messages

Image Name: Linux-2.6.30
Created: Sun Jan 8 14:53:36 2012
Image Type: ARM Linux Kernel Image (uncompressed)
Data Size: 1002336 Bytes = 978.84 kB = 0.96 MB
Load Address: 0x20008000
Entry Point: 0x20008000
Image arch/arm/boot/uImage is ready

SD Cards greater than 2GB can not be used for boot loading. Hydra can read and write to SD HC of any size after boot up.

SD Card Test
At this point all the assets to boot and load the Linux kernel are available. A quick test will help to ensure that everything is correct to this point.

Connect the Serial Module [2] and SD Card module [3] to the Hydra. Remove all other modules and the T35 if connected.

Open a Tera Term or other terminal and connect to the Serial Module virtual COM port using 115200 baud.

Get a 2 GB (or 1GB) SD Card and make a 50MB partition and format the partition as FAT16. This step can be done using Windows for now. Make sure to give a simple partition name like ‘BOOT’. This will make it easier to figure out the mount point under Linux

An external card reader works best. Plug in the reader and configure VirtualBox to use the device.
Use the Devices > USB Devices > You Card Reader Device

Insert the SD Card into the reader and Unix will auto mount the SD Card filesystem. Open the ‘File Browser’ application to view the card contents.

1. Change to the hydra work folder
cd /hydra

2. Copy the bootstrap to the SD Card (assumes that the SD volume name is ‘BOOT’)
cp AT91Bootstrap-5series_1.2/binaries/at91sam9rlek-sdcardboot-3.1.bin /media/BOOT/boot.bin

3. Copy u-boot to the SD Card (assumes that the SD volume name is ‘BOOT’)
cp u-boot-2011.09/u-boot.bin /media/BOOT/u-boot.bin

4. Copy Linux kernel to the SD Card (assumes that the SD volume name is ‘BOOT’)
cp linux-2.6.30/arch/arm/boot/uImage /media/BOOT/image.bin

The SD Card is ‘Linux ready’. Unmount the card by clickin on the eject icon.
5.Remove the SD Card from the reader and insert into the module. Power up Hydra by connecting the Power module.

Watch the messages output on the terminal window.
Boot Strap starts U-Boot loads Kernel loads

Kernels spews errors stating it can not find the file system.
File System

Building a complete file sytem from scratch is a bigger project than using the file system provided by Atmel. A practical first step will be to download and use the Atmel provided filesystem.

The file system is very important for a Linux system, considering that everything on Linux is a file. If something is not a file it has to be a process. Configuration, binaries, device drivers, sockets etc. exists as files on the Linux system. Directories are considered as files too. These files are organized as a tree on the partition.

Prepare the file system
1.Download the Atmel binary files

2.Extract the file

The filesystem is archived as a .jffs2

Journalling Flash File System version 2 or JFFS2 is a log-structured file system for use with flash memory devices.

To copy these files to the SD Card the file has to be mounted on a loop back device (Block Memory MTD Emulation)

3.Create the device file
mknod /tmp/mtdblock0 b 31 0

4.Load mtd block module
modprobe mtdblock

5.Load mtd ram module
modprobe mtdram total_size=65536 erase_size=256

6.Load jff2 module
modprobe jffs2

7.Use a low level operation to copy the file contents to the block device
dd if=linux4sam-angstrom-at91sam9rlek/Angstrom-x11-at91sam9-image-glibc-ipk-2009.X-stable-at91sam9rlek.rootfs.jffs2 of=/tmp/mtdblock0

8.Create a mount folder
mkdir /media/jffs2

9.Mount the media
mount -t jffs2 /tmp/mtdblock0 /media/jffs2

10.The media is mounted and to list contents
ls /media/jffs2/

11.Archive the contents for transfer to SD card
tar czf hydra-fs.tar.gz -C /media/jffs2/ .

Prepare SD Card parition
The filesystem partition required a ext2 partition.

1.Insert the SD Card into the reader. Linux will mount the SD Card and the FAT16 filesystem will be displayed.

2.Install ‘gparted’ a partition editor for graphically managing your disk partitions
apt-get install gparted

3.Start gparted

4.Once the gparted UI comes up select the correct device using GParted->Devices->/dev/sdb
5.The current partitions are displayed on the UI. Right click on the ‘unallocated’ area and select ‘New’

6.On the ‘Create new Partition’ dialog type in a label name ‘hydrafs’ and click Add.
7.Click on Edit->Apply All Operations to save changes to the disk. Click on ‘Apply’ when prompted. The operation will take a while and display the success dialog. Click ‘Close’.

The GUI will display superman ripping shirt t shirt womens the updated parition table.
Exit gparted.

8.On the Linux file browser the new filesystem ‘hydrafs’ will be displayed.
Copy the filesystem to the SD card

tar xvf hydra-fs.tar.gz -C /media/hydrafs/
Ignore messages like ‘implausibly old time stamp 1969-12-31 19:00:00’.

The command may complete pretty fast and it may appear that the copy is complete. However this is a operation that Linux will push to the background and yeild the prompt. The SD card should not be ejected to avoid corruption.

Click on the ‘eject’ icon to allow Linux to complete the operation if still pending. On umount the filesystems ‘hydrafs’ and ‘BOOT’ will not appear on the File Browser’

Boot to Command Prompt
Eject the SD Card from the reader and insert into the Hydra SD module. Ensure that the terminal is connected. Power on or reset the mainboard.

The boot process should complete and present the login: prompt. Type root and hit enter.
Feel free to try various *NIX command on the prompt ‘ls’ ‘pwd’ etc.

Do not forget that Hydra is running a full OS and has a open file system. It is best to shutdown the OS when you are done using

shutdown -f now
Wait for some time to see the ‘Power Down’ message to disconnect power. Sometimes the shutdown will hang at ‘INIT: no more processes left in this runlevel’

If you power off abruptly and face problems on the next boot up, you may have to rebuild the SD Card.

Add a display (preliminary)
Note: TouchScreen does NOT work

The T35 display [4] can be made to work using the following kernel changes. Edit the following and recompile the kernel following the appropriate steps.

1.Edit the Atmel framebuffer driver
gedit /hydra/linux-2.6.30/drivers/video/atmel_lcdfb.c

2.Edit the atmel_lcdfb_set_par function
3.Edit the RL board function

gedit /hydra/linux-2.6.30/arch/arm/mach-at91/board-sam9rlek.c
Change the fb_videomode struct to :

4.Edit the RL device function
gedit /hydra/linux-2.6.30/arch/arm/mach-at91/at91sam9rl_devices.c

Change the __init at91_add_device_lcdc to :
5.Compile the Kernel

6.Copy the uImage file to the SD Card as image.bin
7.Connect the T35 LCD to the Hydra

8.Ensure that the board is powered from a Computer USB port, powered HUB or external power.
10.Insert the SD Card

11.Power Up
12.Wait a while as the GUI comes up on the LCD

Hello World Blinky
Hydra is an embedded system, blink a LED to show that.

1.Connect a eBlock expansion module [5] to socket 7 on the Hydra
2.Ensure that the expansion module voltage is set to 3.3v

3.Plug in a LED eBlock [6] to Pin8 on the expansion module
4.Boot up Hydra using the SD Card

5.On the terminal log on as root
6.Open a new script file using ‘vi’

7.Set the execute bit for the script

chmod +x
8.Execute the script

Watch the LED blink 10 times.

If you have a Rev. 1.2 board
Please populate the RTC 32.768Khz crystal, else the board will not boot. This is a through hole part and marked as Q1 on the board.

These steps should help the begineer to get started on embedded Linux. The Atmel Linux build was made for the RL64 EK. The EK has 64MB SDRAM and will be faster. Hydra has 16MB and the SD Card is used as the storage, expect a little sluggish performance. The start up scripts can be modified not to load some of the services that is currently loaded for better performance. The kernel can be tweaked to exclude drivers and features that are not required.

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