Diamond Systems HELIX SINGLE BOARD COMPUTER User manual

Helix User Manual Revision A.02 www.diamondsystems.com Page 1
Helix Single Board Computer
PC/104 SBC with DMP Vortex86DX3 SoC
Copyright 2016
FOR TECHNICAL SUPPORT Diamond Systems Corporation
PLEASE CONTACT: 158 Commercial Street
Sunnyvale, CA 94086 USA
[e-mail] Tel [phone]
Fax [phone]
www.diamondsystems.com
Revision
Date
Comment
A.00
5/24/2016
Initial Release
A.01
6/16/2016
Data Acquisition section expanded
A.02
7/6/16
Additional information added
A.03
3/27/17
Boot Device Option note added
A.04
4/24/17
AC Adapter information updated

Helix User Manual Revision A.02 www.diamondsystems.com Page 2
CONTENTS
1. Important Safe Handling Information .............................................................................................................5
2. Introduction.......................................................................................................................................................7
2.1 Available Models............................................................................................................................................7
2.2 Features.........................................................................................................................................................7
2.3 Operating System Support ............................................................................................................................8
2.4 Mechanical, Electrical, Environmental...........................................................................................................8
2.5 Customization Options ..................................................................................................................................8
3. Functional Block Diagram ...............................................................................................................................9
3.1 Feature Descriptions .................................................................................................................................. 10
3.1.1 Processor and Memory...................................................................................................................... 10
3.1.2 Ethernet.............................................................................................................................................. 10
3.1.3 Video.................................................................................................................................................. 10
3.1.4 SATA.................................................................................................................................................. 10
3.1.5 USB.................................................................................................................................................... 10
3.1.6 PS/2 Keyboard and Mouse................................................................................................................ 11
3.1.7 Serial Ports ........................................................................................................................................ 12
3.1.8 Audio.................................................................................................................................................. 12
3.1.9 Data Acquisition (DAQ)...................................................................................................................... 12
3.1.10 Backup Battery................................................................................................................................... 12
3.1.11 PCIe MiniCard / mSATA Socket........................................................................................................ 12
3.1.12 PC/104 Expansion ............................................................................................................................. 12
3.1.13 PCIe Link Routing.............................................................................................................................. 12
3.1.14 Watchdog Timer................................................................................................................................. 13
3.1.15 LED Indicators ................................................................................................................................... 14
3.1.16 BIOS Features................................................................................................................................... 14
3.1.17 Power Supply..................................................................................................................................... 15
4. Mechanical Board Drawing........................................................................................................................... 16
5. Board Layout.................................................................................................................................................. 17
5.1 I/O Connectors, Jumpers and LED Summary............................................................................................ 18
6. I/O Connectors ............................................................................................................................................... 19
6.1 Connector Pinout and Signal Description................................................................................................... 19
6.1.1 PC/104 (J1, J2).................................................................................................................................. 19
6.1.2 Audio (J3)........................................................................................................................................... 20
6.1.3 USB 2.0 Ports (J4, J5, J6) ................................................................................................................. 20
6.1.4 Serial Ports (J7, J8) ........................................................................................................................... 20
6.1.5 LCD Backlight (J9)............................................................................................................................. 21
6.1.6 Power In (J10).................................................................................................................................... 21
6.1.7 External Battery (J11)........................................................................................................................ 21
6.1.8 PS/2 Keyboard and Mouse (J12)....................................................................................................... 22
6.1.9 VGA (J13) .......................................................................................................................................... 22
6.1.10 Ethernet (J14, J15) ............................................................................................................................ 22
6.1.11 Utility (J16)......................................................................................................................................... 23
6.1.12 Digital I/O (J17).................................................................................................................................. 23
6.1.13 Analog I/O (J18)................................................................................................................................. 24
6.1.14 SATA (J19) ........................................................................................................................................ 25
6.1.15 CAN (J20) .......................................................................................................................................... 25
6.1.16 LVDS LCD (J21) ................................................................................................................................ 25
6.1.17 PCIe MiniCard / mSATA Socket (J24)............................................................................................... 26
6.2 List Of Connectors...................................................................................................................................... 27
7. I/O CableS....................................................................................................................................................... 28
8. Jumper Description ....................................................................................................................................... 29
8.1 Digital IO (JP1) ........................................................................................................................................... 30
8.2 CAN Termination (JP2) .............................................................................................................................. 30
8.3 Miscellaneous (JP3) ................................................................................................................................... 31
8.4 RS-422/485 Termination (JP4)................................................................................................................... 32
8.5 LVDS Backlight and LVDS VDD (JP5)....................................................................................................... 33
8.6 IRQ Selection (JP6).................................................................................................................................... 33
9. BIOS Key Features......................................................................................................................................... 34
9.1 Entering the BIOS....................................................................................................................................... 34
9.2 Restoring Default BIOS Settings................................................................................................................ 34

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9.3 Upgrading BIOS using DOS Utility............................................................................................................. 34
9.4 Setting the Date and Time.......................................................................................................................... 34
9.5 Boot Priority................................................................................................................................................ 34
9.6 LED............................................................................................................................................................. 35
9.7 Watchdog Timer ......................................................................................................................................... 35
9.8 Quiet / Quick Boot / Splash Screen............................................................................................................ 35
9.9 Serial Port Configuration ............................................................................................................................ 35
10. Getting Started............................................................................................................................................... 36
10.1 Development Kit Contents.......................................................................................................................... 36
10.2 Quick Setup................................................................................................................................................ 36
10.3 Boot Device Options................................................................................................................................... 36
10.4 Installing OS and Booting........................................................................................................................... 37
11. Video Features ............................................................................................................................................... 38
11.1 VGA ............................................................................................................................................................ 38
11.2 LCD............................................................................................................................................................. 38
11.2.1 Backlight............................................................................................................................................. 38
11.3 Dual Display................................................................................................................................................ 38
11.4 Changing LCD Resolution.......................................................................................................................... 39
11.4.1 Step 1: Modify the VBIOS file ............................................................................................................ 39
11.4.2 Step 2: Integrate the VBIOS with the BIOS file ................................................................................. 41
12. Serial Ports and System Console ................................................................................................................ 43
12.1 Overview..................................................................................................................................................... 43
12.2 Configuration .............................................................................................................................................. 43
12.3 Console redirection..................................................................................................................................... 43
13. MASS STORAGE............................................................................................................................................ 44
13.1 Flashdisk Models and Capacities............................................................................................................... 44
13.2 Installation and Configuration..................................................................................................................... 44
14. Utility Connector Features............................................................................................................................ 45
14.1 I2C .............................................................................................................................................................. 45
14.2 Reset .......................................................................................................................................................... 45
14.3 Gigabit Ethernet LED Signals..................................................................................................................... 45
14.4 Power and Ground ..................................................................................................................................... 45
15. A Model Data Acquisition Circuit................................................................................................................. 46
15.1 Features...................................................................................................................................................... 46
15.2 Block Diagram ............................................................................................................................................ 47
15.3 Analog-to-Digital Circuit.............................................................................................................................. 47
15.3.1 A/D Circuit Overview.......................................................................................................................... 47
15.3.2 A/D Channel Selection, Sampling, and Timing.................................................................................. 48
15.3.3 A/D FIFO and High Speed Sampling................................................................................................. 48
15.3.4 A/D Operation .................................................................................................................................... 49
15.3.5 A/D Resolution................................................................................................................................... 49
15.3.6 Input Range Selection........................................................................................................................ 50
15.3.7 Converting A/D Readings to Volts or Engineering Units ................................................................... 50
15.3.8 Measurement Accuracy and Calibration............................................................................................ 51
15.3.9 Input Impedance ................................................................................................................................ 51
15.4 Digital-to-Analog Circuit.............................................................................................................................. 52
15.4.1 Overview............................................................................................................................................ 52
15.4.2 D/A Resolution................................................................................................................................... 52
15.4.3 Output Range Selection..................................................................................................................... 52
15.4.4 D/A Conversion Formula.................................................................................................................... 53
15.4.5 Output Accuracy and Calibration....................................................................................................... 53
15.5 Digital I/O Features..................................................................................................................................... 54
15.5.1 Overview............................................................................................................................................ 54
15.5.2 Edge Detection Circuit....................................................................................................................... 54
15.5.3 Support for Special Functions............................................................................................................ 55
15.5.4 Power Pins......................................................................................................................................... 55
15.6 Counter/Timer Features ............................................................................................................................. 55
15.6.1 Overview............................................................................................................................................ 55
15.6.2 Counter Commands........................................................................................................................... 56
15.6.3 Counter I/O Signals............................................................................................................................ 56
15.6.4 Counter Advanced Features.............................................................................................................. 56
15.7 Pulse Width Modulator Features................................................................................................................ 57

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15.7.1 Overview............................................................................................................................................ 57
15.7.2 PWM Commands............................................................................................................................... 57
15.7.3 PWM Output Signals.......................................................................................................................... 57
15.8 Interrupt Operation ..................................................................................................................................... 58
15.8.1 Overview............................................................................................................................................ 58
15.8.2 Interrupt Sources ............................................................................................................................... 58
16. “D” Model Digital I/O Circuit ......................................................................................................................... 59
16.1 Features...................................................................................................................................................... 59
16.2 Block Diagram ............................................................................................................................................ 59
16.3 Configuration and Programming................................................................................................................. 60
16.3.1 Register Map...................................................................................................................................... 60
16.3.2 Programming Instructions.................................................................................................................. 61
17. PC/104 I/O Expansion.................................................................................................................................... 61
17.1 Address Ranges Available ......................................................................................................................... 61
17.2 IRQs Available............................................................................................................................................ 61
18. Software Driver Overview ............................................................................................................................. 62
19.Specifications................................................................................................................................................. 63

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1. IMPORTANT SAFE HANDLING INFORMATION
WARNING!
ESD-Sensitive Electronic Equipment
Observe ESD-safe handling procedures when working with this product.
Always use this product in a properly grounded work area and wear appropriate
ESD-preventive clothing and/or accessories.
Always store this product in ESD-protective packaging when not in use.
Safe Handling Precautions
The Helix SBC contains a high number of I/O connectors with connection to sensitive electronic components. This
creates many opportunities for accidental damage during handling, installation and connection to other
equipment. The list here describes common causes of failure found on boards returned to Diamond Systems for
repair. This information is provided as a source of advice to help you prevent damaging your Diamond (or any
vendor’s) embedded computer boards.
ESD damage –This type of damage is usually almost impossible to detect, because there is no visual sign of
failure or damage. The symptom is that the board eventually simply stops working, because some component
becomes defective. Usually the failure can be identified and the chip can be replaced.
To prevent ESD damage, always follow proper ESD-prevention practices when handling computer boards.
Damage during handling or storage –On some boards we have noticed physical damage from mishandling. A
common observation is that a screwdriver slipped while installing the board, causing a gouge in the PCB surface
and cutting signal traces or damaging components.
Another common observation is damaged board corners, indicating the board was dropped. This may or may not
cause damage to the circuitry, depending on what is near the corner. Most of our boards are designed with at
least 25 mils clearance between the board edge and any component pad, and ground / power planes are at least
20 mils from the edge to avoid possible shorting from this type of damage. However these design rules are not
sufficient to prevent damage in all situations.
A third cause of failure is when a metal screwdriver tip slips, or a screw drops onto the board while it is powered
on, causing a short between a power pin and a signal pin on a component. This can cause overvoltage / power
supply problems described below. To avoid this type of failure, only perform assembly operations when the
system is powered off.
Sometimes boards are stored in racks with slots that grip the edge of the board. This is a common practice for
board manufacturers. However our boards are generally very dense, and if the board has components very close
to the board edge, they can be damaged or even knocked off the board when the board tilts back in the rack.
Diamond recommends that all our boards be stored only in individual ESD-safe packaging. If multiple boards are
stored together, they should be contained in bins with dividers between boards. Do not pile boards on top of each
other or cram too many boards into a small location. This can cause damage to connector pins or fragile
components.
Power supply wired backwards –Our power supplies and boards are not designed to withstand a reverse
power supply connection. This will destroy each IC that is connected to the power supply (i.e. almost all ICs). In
this case the board will most likely will be unrepairable and must be replaced. A chip destroyed by reverse power
or by excessive power will often have a visible hole on the top or show some deformation on the top surface due
to vaporization inside the package. Check twice before applying power!
Board not installed properly in PC/104 stack –A common error is to install a PC/104 board accidentally shifted
by 1 row or 1 column. If the board is installed incorrectly, it is possible for power and ground signals on the bus to
make contact with the wrong pins on the board, which can damage the board. For example, this can damage
components attached to the data bus, because it puts the 12V power supply lines directly on data bus lines.

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Overvoltage on analog input –If a voltage applied to an analog input exceeds the design specification of the
board, the input multiplexor and/or parts behind it can be damaged. Most of our boards will withstand an
erroneous connection of up to 35V on the analog inputs, even when the board is powered off, but not all boards,
and not in all conditions.
Overvoltage on analog output –If an analog output is accidentally connected to another output signal or a
power supply voltage, the output can be damaged. On most of our boards, a short circuit to ground on an analog
output will not cause trouble.
Overvoltage on digital I/O line –If a digital I/O signal is connected to a voltage above the maximum specified
voltage, the digital circuitry can be damaged. On most of our boards the acceptable range of voltages connected
to digital I/O signals is 0-5V, and they can withstand about 0.5V beyond that (-0.5 to 5.5V) before being damaged.
However logic signals at 12V and even 24V are common, and if one of these is connected to a 5V logic chip, the
chip will be damaged, and the damage could even extend past that chip to others in the circuit.
Bent connector pins –This type of problem is often only a cosmetic issue and is easily fixed by bending the pins
back to their proper shape one at a time with needle-nose pliers. The most common cause of bent connector pins
is when a PC/104 board is pulled off the stack by rocking it back and forth left to right, from one end of the
connector to the other. As the board is rocked back and forth it pulls out suddenly, and the pins at the end get
bent significantly. The same situation can occur when pulling a ribbon cable off of a pin header. If the pins are
bent too severely, bending them back can cause them to weaken unacceptably or even break, and the connector
must be replaced.

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2. INTRODUCTION
Helix is a compact, rugged single board computer that features the DMP Vortex86DX3 System on Chip (SoC)
processor in an extended PC/104 form factor. The full rectangular shape provides more coastline for I/O
connectors than other boards of its size. In this compact form factor, Helix includes a wide range of I/O plus data
acquisition functionality, meeting the majority of today’s connectivity requirements in a single board.
2.1 Available Models
Model
Processor
/ Speed
Memory
Analog
I/O
Digital
I/O
10/100
Ethernet
Port
Gigabit
Ethernet
Port
USB2.0
HLX1000-2GA
1GHz
2GB
Yes
27
1
1
6
HLX1000-1GD
1GHz
1GB
No
16
1
1
3
HLX1000-2GD *
1GHz
2GB
No
16
1
1
3
* Custom version, minimum order quantities apply
2.2 Features
1GHz DMP Vortex86DX3 dual core CPU
Up to 2GB DDR3 SDRAM soldered on board
I/O Support:
- 3 or 6 USB2.0 ports (model dependent)
- 2 RS-232/422/485 & 2 RS-232 ports
- 1 10/100Mbps Ethernet port
- 1 Gigabit Ethernet port
- 1 SATA port for disk-on-module or external drive
- 24-bit dual channel LVDS LCD display
- VGA CRT
- HD audio
- PCIe MiniCard socket shared with mSATA
- 16 digital I/O lines with programmable direction
Data Acquisition:
- 16 16-bit analog inputs
- 100KHz max sample rate
- 4 16-bit analog outputs
- 11 additional digital I/O lines with programmable direction
- 8 32-bit counter/timers
- 4 24-bit pulse width modulators
PC/104 stackable I/O expansion capability

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2.3 Operating System Support
Linux, Windows Embedded Standard 7
Both Linux and Windows Embedded 7 Software Development Kits are available with bootable images
and drivers
2.4 Mechanical, Electrical, Environmental
PC/104 extended form factor (4.0” x 4.0”)
Extremely rugged with soldered RAM and -40°C to +85°C (-40°F to +185°F) operating temperature
Power input: +5VDC +/- 5% or optional +9 to 36VDC
2.5 Customization Options
The following customization options are available for the Helix single board computer. Minimum order quantities
may apply for customization. Contact Diamond Systems sales or support for further information
2GB on-board DDR3 RAM instead of 1GB
1 CANbus 2.0 port
+9 to +36V 50W DC/DC wide voltage power input
Latching connectors instead of pin headers
Extended life backup battery
Replace configuration jumpers with 0 ohm resistors
Low profile heatsink
Conformal coating
Custom BIOS
Custom FPGA code

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3. FUNCTIONAL BLOCK DIAGRAM
Figure 1: Functional Block Diagram

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3.1 Feature Descriptions
This section describes the key subsystems of the Helix SBC.
3.1.1 Processor and Memory
Helix SBCs use the Vortex86DX3 SoC from DMP Electronics. It is a 32-bit x86 architecture dual-core 1GHz
microprocessor designed for ultra-low power consumption, combining both the North and South bridges with a
rich set of integrated features including a 32KB write through 8-way L1 cache, 512KB write through/write back 4-
way L2 cache, PCIe bus at 2.5 GHz, DDR3 controller, ISA, I2C, SPI, IPC (includes Internal Peripheral Controllers
with DMA and interrupt timer/counter), Fast Ethernet, FIFO UART, USB2.0 Host, and an IDE/SATA controller.
The SBC supports up to 2GB of DDR3 memory soldered on-board.
3.1.2 Ethernet
The Helix SBC provides two Ethernet ports. One is a 10/100 Ethernet port provisioned directly from the Vortex
SoC (System on Chip). The second is a 10/100/1000 Ethernet port realized using an Intel I210IT PCIe Gigabit
Ethernet Controller (MAC + PHY). The board also includes the necessary magnetics. Ethernet connections are
via a pin header.
On-board LEDs are provided for Link, Activity, and Speed. The LEDs are located along the board edge near the
Ethernet connector. The connector does not provide access to the LED signals.
3.1.3 Video
The SBC offers two display outputs: one VGA and one LVDS. The VGA interface comes directly from the
processor and is made available on a 2x5 header. The LVDS interface is realized from the 24-bit DVO of the
processor using a DS90C187LF chip.
The maximum display resolution is 1920 x 1080 at 60Hz. The SBC supports dual display mode. In dual display
mode, the maximum resolution supported is 1280 x 1024 at 60Hz.
The LCD backlight control is provided by a PWM circuit. LCD backlight power and control signals are terminated
on a separate latching connector.
3.1.4 SATA
The Helix SBC has one industry-standard vertical SATA connector that accepts cables with latching connectors.
The SATA port is derived directly from the processor. It is connected to a connector placed on the board in a
position that allows a miniature SATA disk-on-module (DOM) to be installed in it and attached with a mounting
spacer and screw.
The board offers an additional SATA port derived from a x1 PCIe lane. This SATA port is available over the
shared mSATA / PCIe MiniCard socket.
3.1.5 USB
The board provides seven user accessible USB 2.0 ports. Three of these comes directly from the processor, and
are available on a 2x5 header.
The fourth port from the processor is connected to a 4-port USB hub from SMSC (USB2514). Three of the four
downstream ports from the USB hub are connected to a 2x5 header and the fourth port is connected to the PCIe
MiniCard socket. The USB configurations possible are depicted in the following images. The Helix A model offers
all six USB ports. The D model offers only the three driven directly from the SoC.

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Option 1 : Six USB2.0 ports available on USB2.0 header (Helix A model)
Option 2: Three USB2.0 ports available on USB2.0 header (Helix D model)
3.1.6 PS/2 Keyboard and Mouse
Helix supports PS/2 keyboard and mouse driven directly from the Vortex SoC.

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3.1.7 Serial Ports
The SBC provides four serial ports: two with fixed RS-232 capability using SP211EHEA-L, and a second two
having RS-232/422/485 capability using a SP336. The built-in UARTs from the VortexDX3 are used. In RS-232
mode, only the signals TX, RX, RTS, and CTS are provided. Protocol selection for serial ports 3-4 is controlled
using GPIO pins from the SoC and is configurable via BIOS configuration screens as well as via application
software. Jumpers are used to enable termination resistors (121 Ohm) for RS-422 and RS-485 protocols.
Console redirection, using a serial port for keyboard input and terminal display via a link to a second computer, is
provided via the BIOS on serial port 1.
3.1.8 Audio
The SBC supports HD audio with an ALC892. Audio I/O signals include stereo line in, stereo line out and mic in.
3.1.9 Data Acquisition (DAQ)
The SBC provides an optional data acquisition circuit containing analog input, analog output, and additional digital
I/O features. This circuit is controlled by an FPGA interfaced to the processor via SPI.
The data acquisition features include 16 single-ended / 8 differential analog inputs with 16-bit resolution,
programmable input ranges, and a 100KHz maximum sample rate; 4 analog outputs with 16-bit resolution and
programmable output ranges; and 11 additional digital I/O lines with selectable 3.3V logic levels, selectable pull-
up/down resistors, programmable direction, buffered I/O, and capability for use as counter/timer and PWM
circuits.
In models with DAQ support (A models), 27 total digital I/O lines are available on the DAQ Digital I/O and Analog
I/O connectors. In models without DAQ (D models), 16 digital I/O lines from the VortexDX3 are made available on
the Digital I/O connector.
3.1.10 Backup Battery
The SBC contains an on-board RTC backup battery. On models with fixed +5VDC input, a battery is mounted on
the top side of the board. On custom models with wide voltage input, an extended life RTC battery is mounted on
the bottom side of the board.
On all models, a connector is provided to enable the use of an external battery.
The SBC can boot and function properly without a backup battery installed. A jumper is provided to disconnect the
battery during long term storage.
3.1.11 PCIe MiniCard / mSATA Socket
The Helix SBC has one full size (51mm length) shared PCIe MiniCard and mSATA socket. The socket supports
both PCIe MiniCard and mSATA modules, one module at a time. It has a PCIe/mSATA switch controlled by a pin
on the socket to select which interface is active.
A PCIe x1 lane is available on this connector directly from the Vortex86DX3 SoC. A USB port from the USB hub
(SMSC USB2514) is also connected to the socket.
The SATA lane is realized from the same PCIex1 lane that connects to the PCIe MiniCard connector. A PCIe to
SATA bridge chip ASM1061 is used as well as a mux to avoid stub on PCIe and SATA signals.
3.1.12 PC/104 Expansion
Helix provides stackable I/O expansion options over the PC/104 ISA bus. The ISA bus comes directly from the
Vortex86DX3 SoC and supports DMA access. Refer to Section18 for details on the ISA addresses and IRQs
available for the Windows 7 operating system.
3.1.13 PCIe Link Routing
Two PCIe lanes from the SoC are used to provide Gigabit Ethernet functionality and expansion card options. The
lane configurations are as listed below.
Lane 1 (from SoC): Gigabit Ethernet
Lane 2 (from SoC): PCIe MiniCard / PCIe to SATA bridge

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3.1.14 Watchdog Timer
The Helix SBC has one watchdog timer (WDT) generated from the Vortex86DX3 SOC, WDT1. The WDT can be
enabled/ disabled from BIOS or software. The timer can be triggered only from software. If the watchdog timer
times out before it is retriggered, it will cause a system reset. The watchdog timer uses a 32.768KHz clock to
count a 24-bit register. The timeout period is programmable from 30.5us to 512 seconds with a resolution of
30.5us.
Following are the registers associated with the watchdog timer, WDT1.
IO port Address (Hex)
Register
A8
Watchdog Timer 1 control register
AA
Watchdog Timer 1 Counter 0 register
AB
Watchdog Timer 1 Counter 1 register
AC
Watchdog Timer 1 Counter 2 register
AD
Watchdog Timer 1 Status register
AE
Watchdog Timer 1 Reload register
Watchdog Timer 1 Control Register (A8h)
Bit
Name
Attribute
Description
7
RSVD
-
Reserved
6
WE
RW
WDT1 Enable control (Write bit = 1 to reload the WDT1 counter)
0: WDT1 disabled (default)
1: WDT1 enabled
5-0
RSVD
-
Reserved
Watchdog Timer 1 Counter Registers (AAh - ACh)
Bit
Name
Attribute
Description
7-0
CNT0
RW
Watchdog Timer 1 Counter 0 (Resolution is 30.5us)
15-8
CNT1
RW
Watchdog Timer 1 Counter 1 (Resolution is 30.5us)
23-16
CNT2
RW
Watchdog Timer 1 Counter 2 (Resolution is 30.5us)
Watchdog Timer 1 Status Register (ADh)
Bit
Name
Attribute
Description
7
WDTF
RW
Watchdog timer 1Flag
0: WDT1 has not timed out
1: WDT1 has timed out. Write 1 to clear this flag. Writing 0 will
have no effect.
6-0
RSVD
-
Reserved

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Watchdog Timer 1 Reload Register (AEh)
Bit
Name
Attribute
Description
7-0
WDTRL
W
Write this register to reload WDT1 internal counter
Follow the below steps to setup the Watchdog timer:
1. Set Bit 6 (WE) of register A8h = 0 to disable the watchdog timer
2. Write the desired counter value (30.5us to 512 sec) to registers AAh-ACh
3. Set Bit 6 (WE) of register A8h = 1 to enable the watchdog timer
4. As the counter reaches the set value, system will reset
5. Any write to Reload register (AEh) before the counter times out will restart the counter
3.1.15 LED Indicators
The SBC provides the following LED indicators. All LEDs are located near a board edge or their respective
features. The blue LED is located along the lower edge of the board. All LEDs are labeled in silkscreen with their
function.
Power input: Green LED when input power is applied
Power on: Green LED when board is powered on
BIOS LED: Green LED connected to a GPIO line on the processor. This LED is off during
power-up and is turned on by the BIOS to indicate a successful system BIOS
startup.
Ethernet 10/100: Green LED for duplex and speed
GBE: Green LED for link, speed and activity
DAQ: Blue LED driven with reverse logic from +5V and controlled by the FPGA
DONE: Green LED driven by the FPGA. The LED comes on once the FPGA code is
downloaded successfully
PCIe MiniCard socket: 3 Green LEDs to support WWAN, WPAN, WLAN signals from the connector
3.1.16 BIOS Features
In addition to supporting all the interfaces specified in the block diagram, the BIOS provides the following key
features:
Boot from LAN (PXE only on 10/100 port) as well as USB and SATA ports
Free boot sequence configuration to allow different boot sequences as first, second and third boot
devices
Support dual display mode, VGA and LVDS can be active simultaneously
Support for various LCD configurations
LCD backlight control using PWM; LCD VDD Enable using GPIO
Console redirection to one or more COM ports
ISA_IRQ 5 or ISA_IRQ_7 can be reserved for FPGA
Quiet boot option
POST message displays “Diamond Systems Corporation” and also displays the board name and
BIOS version
FPGA ID readback in BIOS menu
Enable/disable for individual COM ports
Protocol selection for COM ports 3 and 4, default for all ports is RS-232
Enable/ disable digital I/O ports A and B (GPIO_P0 and GPIO_P1) from SoC
Direction control (Input/ Output) for digital I/O ports A and B
Ethernet MAC address read back on boot-up and in BIOS screens

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Single BIOS to support both 1GB and 2GB DDR3 memory configurations
BIOS LED to indicate successful BIOS initialization
Supports standard BIOS hotkey including DEL key to enter BIOS menu and END key to load BIOS
default settings
Password protection
Field upgradeable via a DOS utility
WDT can be configured from BIOS setup menu -- timeout and action are screen-configurable and
programmable
3.1.17 Power Supply
The Helix SBC is powered from a +5VDC input. As an optional custom feature, a 50W DC/DC wide voltage input
circuit of +9V to +36V is also available.
All required supply voltages other than +12V are derived from the input supply. The power supplies are able to
support the highest capacity on-board memory plus have enough reserve capacity to support the following add-on
features:
5V 3.3V Feature
2.0A PC/104 add-on modules
1.5A PCIe MiniCard add-on modules
0.25A SATA disk module
1.4A 0.7A LCD power
0.9A LCD backlight
0.05A DAQ connector
0.05A Utility connector
3A USB 2.0 ports

Helix User Manual Revision A.02 www.diamondsystems.com Page 16
4. MECHANICAL BOARD DRAWING
Figure 2: Mechanical Board Drawing

Helix User Manual Revision A.02 www.diamondsystems.com Page 17
5. BOARD LAYOUT
Figure 3: Board Layout
J2
J1
LED
Block 1
LED
Block 2
LED
Block 3
LED
Block 4
J19
J3
J4
J5
J6
J7
JP4
J8
J9
JP5
J10
J11
J12
J13
J14
J15
J16
J18
JP3
J17
J20
J21
J24
J22
JP1
JP2
JP6
J25

Helix User Manual Revision A.02 www.diamondsystems.com Page 18
5.1 I/O Connectors, Jumpers and LED Summary
Connector
Function
Jumper
Function
J1
PC/104 - ISA A/B
JP1
Digital VIO
J2
PC/104 - ISA C/D
JP2
CAN Termination
J3
Audio
JP3
Miscellaneous
J4
USB 2.0 Port 1,2
JP4
RS-422/485
Termination
J5
USB 2.0 Port 3,4
JP5
LVDS VCC & Backlight
J6
USB 2.0 Port 5,6
JP6
IRQ Selection
J7
Serial ports 1,2
LED Block 1
J8
Serial ports 3,4
1st LED (Topmost in
block)
GBE LINK1000
J9
LCD Backlight
2nd LED (Second
from top in block)
GBE ACT
J10
Power In
3rd LED (Third from
top in block)
GBE LINK100
J11
External Battery
4th LED (Fourth
from top in block)
10/100 LINK/ACT
J12
PS/2 Keyboard and Mouse
5th LED (bottom
most in block)
10/100 DUPLEX
J13
VGA
LED Block 2
J14
Ethernet 10/100/1000
1st LED (Leftmost in
block)
PWRIN
J15
Ethernet 10/100
2st LED (Middle one
in block)
PWRON
J16
Utility
3rd LED (Rightmost
in block)
BIOS
J17
Digital I/O
LED Block 3
J18
Analog I/O
1st LED (Leftmost in
the block)
WAN
J19
SATA
2st LED (Middle one
in the block)
LAN
J20
CAN
3rd LED (Rightmost
in the block)
PAN
J21
LVDS LCD
LED Block 4
J22
JTAG for FPGA
1st LED (Left one in
the block)
DAQ LED
J23
SATA Power Connector
2st LED (Right one
in the block)
FPGA DONE
J24
PCIe MiniCard / mSATA
J25
Processor JTAG

Helix User Manual Revision A.02 www.diamondsystems.com Page 19
6. I/O CONNECTORS
6.1 Connector Pinout and Signal Description
6.1.1 PC/104 (J1, J2)
The Helix SBC includes the non-stack through / short pin 8-bit and 16-bit PC/104 connectors on the top side in
the standard position as described by the latest revision of the PC/104 specification.
Note: On the 64-pin connector J1, the leftmost pins are numbered 1. On the 40-pin connector J2, the leftmost pins
are numbered 0.
View from Top of Board
J2: PC/104 16-bit bus connector J1: PC/104 8-bit bus connector
Ground
D0
C0
Ground
IOCHCHK-
A1
B1
Ground
MEMCS16-
D1
C1
SBHE-
SD7
A2
B2
RESET
IOCS16-
D2
C2
LA23
SD6
A3
B3
+5V
IRQ10
D3
C3
LA22
SD5
A4
B4
IRQ9
IRQ11
D4
C4
LA21
SD4
A5
B5
-5V
IRQ12
D5
C5
LA20
SD3
A6
B6
DRQ2
IRQ15
D6
C6
LA19
SD2
A7
B7
-12V
IRQ14
D7
C7
LA18
SD1
A8
B8
0WS-
DACK0-
D8
C8
LA17
SD0
A9
B9
+12V
DRQ0
D9
C9
MEMR-
IOCHRDY
A10
B10
Key
DACK5-
D10
C10
MEMW-
AEN
A11
B11
SMEMW-
DRQ5
D11
C11
SD8
SA19
A12
B12
SMEMR-
DACK6-
D12
C12
SD9
SA18
A13
B13
IOW-
DRQ6
D13
C13
SD10
SA17
A14
B14
IOR-
DACK7-
D14
C14
SD11
SA16
A15
B15
DACK3-
DRQ7
D15
C15
SD12
SA15
A16
B16
DRQ3
+5V
D16
C16
SD13
SA14
A17
B17
DACK1-
MASTER-
D17
C17
SD14
SA13
A18
B18
DRQ1
Ground
D18
C18
SD15
SA12
A19
B19
Refresh-
Ground
D19
C19
Key
SA11
A20
B20
SYSCLK
SA10
A21
B21
IRQ7
SA9
A22
B22
IRQ6
SA8
A23
B23
IRQ5
SA7
A24
B24
IRQ4
SA6
A25
B25
IRQ3
SA5
A26
B26
DACK2-
SA4
A27
B27
TC
SA3
A28
B28
BALE
SA2
A29
B29
+5V
SA1
A30
B30
OSC
SA0
A31
B31
Ground
Ground
A32
B32
Ground
Connector Type: J1 –64 pins .435” high solder tails
J2 –40 pins .435” high solder tails

Helix User Manual Revision A.02 www.diamondsystems.com Page 20
6.1.2 Audio (J3)
Audio signals are provided on connector J3 with following pinout.
LineOut-L
1
2
LineOut-R
GND_Audio
3
4
GND_Audio
LineIn-L
5
6
LineIn-R
GND_Audio
7
8
GND_Audio
MIC_L
9
10
MIC_R
Connector Type: Standard 2mm dual row straight pin header.
6.1.3 USB 2.0 Ports (J4, J5, J6)
There are three USB 2.0 connectors with identical pinouts, J4, J5 and J6. Each connector provides access to two
USB 2.0 ports for a total of six USB 2.0 ports.
Key
1
2
Shield
USB1 Pwr-
3
4
USB0 Pwr-
USB1 Data+
5
6
USB0 Data+
USB1 Data-
7
8
USB0 Data-
USB1 Pwr+
9
10
USB0 Pwr+
Connector Type: Standard 2mm dual row straight pin header.
6.1.4 Serial Ports (J7, J8)
There are two serial port connectors J7 and J8, supporting two ports per connector. Serial ports 1-2 support only
RS-232 mode. Serial ports 3-4 support RS-232/485/422 modes.
RS-232
RS-422
TX1
1
2
RTS1
RX1
3
4
CTS1
GND
5
6
GND
TX2
7
8
RTS2
RX2
9
10
CTS2
TX1+
1
2
TX1-
RX1+
3
4
RX1-
GND
5
6
GND
TX2+
7
8
TX2-
RX2+
9
10
RX2-