Aaeon GENE-APL5 User manual

Last Updated: December 14, 2016
GENE-APL5
3.5” Subcompact Board
User’s Manual 1st Ed

Preface II
3.5” Subcompact Board GENE-APL5
Copyright Notice
This document is copyrighted, 2016. All rights are reserved. The original manufacturer
reserves the right to make improvements to the products described in this manual at
any time without notice.
No part of this manual may be reproduced, copied, translated, or transmitted in any
form or by any means without the prior written permission of the original manufacturer.
Information provided in this manual is intended to be accurate and reliable. However,
the original manufacturer assumes no responsibility for its use, or for any infringements
upon the rights of third parties that may result from its use.
The material in this document is for product information only and is subject to change
without notice. While reasonable efforts have been made in the preparation of this
document to assure its accuracy, AAEON assumes no liabilities resulting from errors or
omissions in this document, or from the use of the information contained herein.
AAEON reserves the right to make changes in the product design without notice to its
users.

Preface III
3.5” Subcompact Board GENE-APL5
Acknowledgement
All other products’ name or trademarks are properties of their respective owners.
Microsoft Windows is a registered trademark of Microsoft Corp.
Intel, Pentium, Celeron, and Xeon are registered trademarks of Intel Corporation
Core, Atom are trademarks of Intel Corporation
ITE is a trademark of Integrated Technology Express, Inc.
IBM, PC/AT, PS/2, and VGA are trademarks of International Business Machines
Corporation.
All other product names or trademarks are properties of their respective owners.

Preface IV
3.5” Subcompact Board GENE-APL5
Packing List
Before setting up your product, please make sure the following items have been
shipped:
Item
Quantity
GENE-APL5 1
Product DVD with User’s Manual (in pdf) and drivers 1
If any of these items are missing or damaged, please contact your distributor or sales
representative immediately.

Preface V
3.5” Subcompact Board GENE-APL5
About this Document
This User’s Manual contains all the essential information, such as detailed descriptions
and explanations on the product’s hardware and software features (if any), its
specifications, dimensions, jumper/connector settings/definitions, and driver installation
instructions (if any), to facilitate users in setting up their product.
Users may refer to the AAEON.com for the latest version of this document.

Preface VI
3.5” Subcompact Board GENE-APL5
Safety Precautions
Please read the following safety instructions carefully. It is advised that you keep this
manual for future references
1. All cautions and warnings on the device should be noted.
2. Make sure the power source matches the power rating of the device.
3. Position the power cord so that people cannot step on it. Do not place anything
over the power cord.
4. Always completely disconnect the power before working on the system’s
hardware.
5. No connections should be made when the system is powered as a sudden rush
of power may damage sensitive electronic components.
6. If the device is not to be used for a long time, disconnect it from the power
supply to avoid damage by transient over-voltage.
7. Always disconnect this device from any AC supply before cleaning.
8. While cleaning, use a damp cloth instead of liquid or spray detergents.
9. Make sure the device is installed near a power outlet and is easily accessible.
10. Keep this device away from humidity.
11. Place the device on a solid surface during installation to prevent falls
12. Do not cover the openings on the device to ensure optimal heat dissipation.
13. Watch out for high temperatures when the system is running.
14. Do not touch the heat sink or heat spreader when the system is running
15. Never pour any liquid into the openings. This could cause fire or electric shock.
16. As most electronic components are sensitive to static electrical charge, be sure to
ground yourself to prevent static charge when installing the internal components.
Use a grounding wrist strap and contain all electronic components in any
static-shielded containers.

Preface VII
3.5” Subcompact Board GENE-APL5
17. If any of the following situations arises, please the contact our service personnel:
i. Damaged power cord or plug
ii. Liquid intrusion to the device
iii. Exposure to moisture
iv. Device is not working as expected or in a manner as described in
this manual
v. The device is dropped or damaged
vi. Any obvious signs of damage displayed on the device
18.
DO NOT LEAVE THIS DEVICE IN AN UNCONTROLLED ENVIRONMENT WITH
TEMPERATURES BEYOND THE DEVICE’S PERMITTED STORAGE TEMPERATURES
(SEE CHAPTER 1) TO PREVENT DAMAGE.

Preface VIII
3.5” Subcompact Board GENE-APL5
FCC Statement
This device complies with Part 15 FCC Rules. Operation is
subject to the following two conditions: (1) this device may not
cause harmful interference, and (2) this device must accept any
interference received including interference that may cause
undesired operation.
Caution:
There is a danger of explosion if the battery is incorrectly replaced. Replace only with
the same or equivalent type recommended by the manufacturer. Dispose of used
batteries according to the manufacturer’s instructions and your local government’s
recycling or disposal directives.
Attention:
Il y a un risque d’explosion si la batterie est remplacée de façon incorrecte.
Ne la remplacer qu’avec le même modèle ou équivalent recommandé par le
constructeur. Recycler les batteries usées en accord avec les instructions du fabricant et
les directives gouvernementales de recyclage.

Preface IX
3.5” Subcompact Board GENE-APL5
China RoHS Requirements (CN)
产品中有毒有害物质或元素名称及含量
AAEON Main Board/ Daughter Board/ Backplane
部件名称
有毒有害物质或元素
铅
(Pb)
汞
(Hg)
镉
(Cd)
六价铬
(Cr(VI))
多溴联苯
(PBB)
多溴二苯醚
(PBDE)
印刷电路板
及其电子组件
○
○
○
○
○
○
外部信号
连接器及线材
○
○
○
○
○
○
O：表示该有毒有害物质在该部件所有均质材料中的含量均在
SJ/T 11363-2006 标准规定的限量要求以下。
X：表示该有毒有害物质至少在该部件的某一均质材料中的含量超出
SJ/T 11363-2006 标准规定的限量要求。
备注：此产品所标示之环保使用期限，系指在一般正常使用状况下。

Preface X
3.5” Subcompact Board GENE-APL5
China RoHS Requirement (EN)
Poisonous or Hazardous Substances or Elements in Products
AAEON Main Board/ Daughter Board/ Backplane
Component
Poisonous or Hazardous Substances or Elements
Lead
(Pb)
Mercury
(Hg)
Cadmium
(Cd)
Hexavalent
Chromium
(Cr(VI))
Polybrominated
Biphenyls
(PBB)
Polybrominated
Diphenyl Ethers
(PBDE)
PCB & Other
Components
O O O O O ○
Wires &
Connectors
for External
Connections
O O O O O O
O
：
The quantity of poisonous or hazardous substances or elements found in each of the
component's parts is below the SJ/T 11363-2006-stipulated requirement.
X: The quantity of poisonous or hazardous substances or elements found in at least one of the
component's parts is beyond the SJ/T 11363-2006-stipulated requirement.
Note: The Environment Friendly Use Period as labeled on this product is applicable under normal
usage only

Preface XI
3.5” Subcompact Board GENE-APL5
Table of Contents
Chapter 1 - Product Specifications........................................................................................ 1
1.1 Specifications............................................................................................................2
Chapter 2 – Hardware Information ....................................................................................... 5
2.1 Dimensions ...............................................................................................................6
2.1.1 Dimensions (Optional HDMI SKU) ..................................................... 8
2.2 Jumpers and Connectors.....................................................................................10
2.2.1 Jumpers and Connectors (Optional HDMI SKU)...........................12
2.3 Block Diagram........................................................................................................14
2.4 List of Jumpers .......................................................................................................15
2.4.1 LVDS Port 1 Backlight Inverter VCC Selection (JP1).....................16
2.4.2 LVDS Port 1 Operating VDD Selection (JP1) .................................16
2.4.3 LVDS Port 1 Backlight Lightness Control Mode Selection (JP2) 16
2.4.4 COM2 Pin8 Function Selection (JP3)...............................................16
2.4.5 COM3 Pin8 Function Selection (JP4)...............................................17
2.4.6 Auto Power Button Enable/Disable Selection (JP5) .....................17
2.4.7 Front Panel Connector (JP6) .............................................................17
2.4.8 LVDS Port 2 Backlight Inverter VCC Selection (JP7).....................18
2.4.9 LVDS Port 2 Operating VDD Selection (JP7) .................................18
2.4.10 LVDS Port 2 Backlight Lightness Control Mode Selection (JP8) 18
2.4.11 Touch Screen 4, 5, 8 Wire Selection (JP9).......................................18
2.4.12 Clear CMOS Jumper (JP10)...............................................................19
2.5 List of Connectors..................................................................................................20
2.5.1 +5VSB Output w/SMBus (CN1)........................................................22
2.5.2 LVDS Port 1 Inverter / Backlight Connector (CN2) ......................22
2.5.3 +5V Output for SATA HDD (CN3)....................................................23
2.5.4 SATA Port (CN4)...................................................................................23

Preface XII
3.5” Subcompact Board GENE-APL5
2.5.5 External Power Input (CN5)...............................................................23
2.5.6 External +5VSB Input (CN6)..............................................................24
2.5.7 Audio I/O Port (CN7)..........................................................................24
2.5.8 LVDS Port 1 (CN8)...............................................................................25
2.5.9 COM Port 2 (CN9)...............................................................................26
2.5.10 LPT Port or Digital I/O Port (CN10).................................................28
2.5.11 LPC Port (CN11) ..................................................................................31
2.5.12 COM Port 3 (CN12) ............................................................................32
2.5.13 BIOS Debug Port (CN13)...................................................................34
2.5.14 COM Port 4 (CN14) ............................................................................34
2.5.15 PS/2 Keyboard/Mouse Combo Port (CN15) .................................35
2.5.16 USB 2.0 Port 2 (CN16)........................................................................36
2.5.17 USB 2.0 Port 3 (CN17)........................................................................36
2.5.18 COM Port 1 (CN18) (Wafer, Opional)..............................................37
2.5.19 USB 2.0 Port 4 (CN19)........................................................................37
2.5.20 USB 2.0 Port 5 (CN20)........................................................................38
2.5.21 LVDS Port 2 (CN21).............................................................................38
2.5.22 Touchscreen Connector (CN22) .......................................................40
2.5.23 CPU Fan (CN23, Optional).................................................................42
2.5.24 LVDS Port 2 Inverter / Backlight Connector (CN24)....................42
2.5.25 USB 3.0 Ports 0 and 1 (CN25) ..........................................................43
2.5.26 LAN (RJ-45) Port 2 (CN26)................................................................44
2.5.27 LAN (RJ-45) Port 1 (CN27) ................................................................44
2.5.28 COM Port 1 (CN28, D-SUB 9)...........................................................45
2.5.29 HDMI Port (CN29, Optional).............................................................45
2.5.30 Battery (CN30) .....................................................................................46
2.5.31 VGA Port (CN31) .................................................................................47
2.5.32 Micro SIM Card Socket (CN32).........................................................47

Preface XIII
3.5” Subcompact Board GENE-APL5
2.5.33 Mini-Card Slot (Half-Mini) (CN33)....................................................48
2.5.34 mSATA (Full-Size) (CN34)...................................................................50
Chapter 3 - AMI BIOS Setup ................................................................................................ 53
3.1 System Test and Initialization ..............................................................................54
3.2 AMI BIOS Setup .....................................................................................................55
3.3 Setup submenu: Main ..........................................................................................56
3.4 Setup submenu: Advanced .................................................................................57
3.4.1 Advanced: Trusted Computing.........................................................58
3.4.2 Advanced: CPU Management..........................................................60
3.4.3 Advanced: Hardware Monitor ..........................................................62
3.4.3.1 Hardware Monitor: CPU Smart Fan Mode
Configuration..............................................................................................63
3.4.4 Advanced: SIO Configuration...........................................................65
3.4.4.1 SIO Configuration: Serial Port 1 Configuration............66
3.4.4.2 SIO Configuration: Serial Port 2 Configuration............67
3.4.4.3 SIO Configuration: Serial Port 3 Configuration............68
3.4.4.4 SIO Configuration: Serial Port 4 Configuration............69
3.4.4.5 SIO Configuration: Parallel Port Configuration ............70
3.4.5Advanced: Power Management.......................................................71
3.4.6 Advanced: Digital IO Port Configuration .......................................73
3.5 Setup submenu: Chipset......................................................................................74
3.5.1 Chipset: North Bridge ........................................................................75
3.5.1.1 North Bridge: LVDS Panel Configuration ......................76
3.6 Setup submenu: Security .....................................................................................79
3.7 Setup submenu: Boot...........................................................................................80
3.8 Setup submenu: Save & Exit ...............................................................................81
3.9 Note for Users........................................................................................................82
Chapter 4 – Drivers Installation............................................................................................ 83

Preface XIV
3.5” Subcompact Board GENE-APL5
4.1 Product CD/DVD ...................................................................................................84
Appendix A - Watchdog Timer Programming................................................................... 86
A.1 Watchdog Timer Registers ..................................................................................87
A.2 Watchdog Sample Program................................................................................88
Appendix B - I/O Information .............................................................................................. 91
B.1 I/O Address Map ...................................................................................................92
B.2 Memory Address Map .........................................................................................94
B.3 IRQ Mapping Chart...............................................................................................95
Appendix C – Mating Connectors ..................................................................................... 100
C.1 List of Mating Connectors and Cables............................................................101
Appendix D – Digital I/O Ports .......................................................................................... 103
D.1 Digital I/O Register..............................................................................................104
D.2 Digital I/O Sample Code (4 in 4 out, 2 low 2 high)......................................106

3.5” Subcompact Board GENE-APL5
Chapter 1
Chapter 1 - Product Specifications

Chapter 1 – Product Specifications 2
3.5” Subcompact Board GENE-APL5
1.1
Specifications
System

Form Factor
3.5”

CPU
Intel®Pentium® N4200 / Celeron® N3350
Processor SoC

CPU Frequency
Up to 2.5 GHz

Chipset
Intel®Atom™ N4200/ N3350 Processor SoC

Memory Type
DDR3L 1867 Mhz SODIMM x 1

Max Memory Capacity
Up to 8 GB

BIOS
UEFI

Wake On LAN
Yes

Watchdog Timer
255 levels

Power Requirement
+12 V or 9 ~ 19 V (optional)

Power Supply Type
AT/ATX

Power Consumption (Typical)
Intel® N4200, DDR3L 1600MHz 8G,
0.8A@ +12V

Dimensions (L x W)
146 x 101.7 mm (5.75 x 4”)

Operating Temperature
0 ~ 60°C (32 ~ 140°F)

Storage Temperature
-40 ~ 81°C (-40 ~ 176°F)

Operation Humidity
10 ~ 90% relative humidity, non-condensing

MTBF
-

Chapter 1 – Product Specifications 3
3.5” Subcompact Board GENE-APL5

Certification
CE/FCC
Display

VGA/LCD Controller
Intel®Pentium® N4200 / Celeron® N3350
Processor SoC integrated

Video Output
VGA/LVDS/ LVDS2 (co-layout with HDMI,
optional)

Backlight Inverter Supply
Ye s
I/O

Ethernet
Intel® I210/I211, 10/100/1000Base-TX, RJ-45 x 2

Audio
High definition audio interface

USB
USB 3.0 x 2
USB 2.0 x 4

Serial Port
RS-232 x 2
RS-232/422/485 x 2

Parallel Port
SPP/EPP/ECP x 1 (option, share with DIO)

HDD Interface
SATA 3.0 x 1
+5V SATA power connector x 1

SSD
mSATA

Expansion Slot
Mini Card x 2 and default is
1.1. mSATA x 1 (full-size)
1.2. miniCard x 1(half-size)

DI/O
8-bit

SIM
1 (uSIM, option)

Chapter 1 – Product Specifications 4
3.5” Subcompact Board GENE-APL5

TPM
1 (option)

To u c h
option

3.5” Subcompact Board GENE-APL5
Chapter 2
Chapter 2 – Hardware Information

Chapter 2 – Hardware Information 6
3.5” Subcompact Board GENE-APL5
2.1 Dimensions
Component Side
A
A
AA
A