Aaeon GENE-APL6 User manual

Last Updated: October 27, 2021
GENE-APL6
3.5”Subcompact Board
User’s Manual 5th Ed

Preface II
3.5”Subcompact Board GENE-APL6
Copyright Notice
This document is copyrighted, 2021. 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-APL6
Acknowledgements
All other products’ name or trademarks are properties of their respective owners.
⚫Microsoft Windows is a registered trademark of Microsoft Corp.
⚫Intel®, Pentium®, and Celeron® are registered trademarks of Intel Corporation
⚫Intel Atom™is a trademark 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-APL6
Packing List
Before setting up your product, please make sure the following items have been
shipped:
Item
Quantity
⚫GENE-APL6 MB
1
⚫Heat Spreader
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-APL6
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 product page at AAEON.com for the latest version of this
document.

Preface VI
3.5”Subcompact Board GENE-APL6
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-APL6
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-APL6
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-APL6
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-APL6
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)
Me rcury
(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 substancesor 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-APL6
Table of Contents
Chapter 1 - Product Specifications.................................................................1
1.1 Specifications ..................................................................................................2
Chapter 2 –Hardware Information............................................................... 6
2.1 Dimensions .....................................................................................................7
2.1.1 Dimensions (Optional HDMI SKU) .....................................................10
2.2 Jumpers and Connectors..............................................................................13
2.2.1 Jumpers and Connectors (Optional HDMI SKU) ...............................14
2.3 Assembly Options..........................................................................................15
2.4 Block Diagram ...............................................................................................16
2.5 List of Jumpers...............................................................................................17
2.5.1 Front Panel Connector (JP1) ...............................................................18
2.5.2 COM2 Pin8 Function Selection (JP2) .................................................18
2.5.3 COM3 Pin8 Function Selection (JP3) .................................................19
2.5.4 LVDS Port2 Backlight Lightness Control Mode Selection (JP4) ........19
2.5.5 LVDS Port2 Backlight Inverter VCC Selection (JP5) ...........................19
2.5.6 LVDS Port1 Backlight Inverter VCC Selection (JP6)...........................20
2.5.7 LVDS Port1 Backlight Lightness Control Mode Selection (JP7) ........20
2.5.8 Auto Power Button Enable/Disable Selection (JP8) .........................20
2.5.9 Touch Screen 4,5,8 Wire Selection (JP9) ............................................21
2.5.10 Clear CMOS Jumper (JP10).................................................................21
2.6 List of Connectors.........................................................................................22
2.6.1 External +5VSB Input (CN1)...............................................................24
2.6.2 +5V Output for SATA HDD (CN2) .....................................................24
2.6.3 External Power Input (CN3) ...............................................................25
2.6.4 SATA Port (CN4).................................................................................25
2.6.5 CPU FAN (Optional) (CN5) ................................................................26

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3.5”Subcompact Board GENE-APL6
2.6.6 Audio I/O Port (CN6).........................................................................27
2.6.7 Mini-Card Slot (Full-Size) (CN7) ........................................................27
2.6.8 COM Port 2 (CN8) .............................................................................30
2.6.9 COM Port 3 (CN9) .............................................................................32
2.6.10 COM Port 4 (CN10)............................................................................34
2.6.11 mSATA Slot (Half-Sized) (CN11) .........................................................35
2.6.12 LPC Port (CN12) .................................................................................37
2.6.13 LVDS Port2 (CN13) .............................................................................38
2.6.14 Micro SIM Card Socket (CN14) ..........................................................40
2.6.15 BIOS Debug Port (CN15)....................................................................41
2.6.16 LPT Port or Digital I/O Port (CN16) ...................................................42
2.6.17 LVDS Port2 Inverter / Backlight Connector (CN17) ..........................45
2.6.18 LVDS Port1 (CN18)..............................................................................46
2.6.19 USB 2.0 Port 4 (CN19)........................................................................48
2.6.20 USB 2.0 Port 5 (CN20).......................................................................48
2.6.21 LVDS Port1 Inverter / Backlight Connector (CN21)...........................49
2.6.22 Touch Screen Connector (Optional) (CN22).....................................50
2.6.23 LAN (RJ-45) Port1 (CN23)..................................................................53
2.6.24 LAN (RJ-45) Port2 (CN24).................................................................53
2.6.25 COM Port 1 (Wafer, Optional) (CN25)...............................................54
2.6.26 Dual USB3.0 Connector (CN26) ........................................................55
2.6.27 COM Port 1 (D-SUB 9) (CN27) ..........................................................56
2.6.28 Battery CONN (CN28).......................................................................56
2.6.29 HDMI (CN29)......................................................................................57
2.6.30 VGA Port (CN30)................................................................................58
2.6.31 DDR3L SO-DIMM Slot (DIMM1) ........................................................58
Chapter 3 - AMI BIOS Setup..................................................................... 59
3.1 System Test and Initialization .......................................................................60

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3.5”Subcompact Board GENE-APL6
3.2 AMI BIOS Setup.............................................................................................61
3.3 Setup Submenu: Main..................................................................................62
3.4 Setup Submenu: Advanced .........................................................................63
3.4.1 Trusted Computing ............................................................................64
3.4.2 CPU Configuration.............................................................................66
3.4.3 SATA Configuration............................................................................68
3.4.4 SCC Configuration .............................................................................70
3.4.5 PCI Express Configuration ..................................................................71
3.4.5.1 PCIE Slot (CN7) ......................................................................72
3.4.6 Hardware Monitor .............................................................................73
3.4.6.1 CPU Smart Fan Mode Configuration ....................................74
3.4.7 SIO Configuration ..............................................................................76
3.4.7.1 Serial Port 1 Configuration.....................................................77
3.4.7.2 Serial Port 2 Configuration ....................................................78
3.4.7.3 Serial Port 3 Configuration ....................................................79
3.4.7.4 Serial Port 4 Configuration ....................................................80
3.4.7.5 Parallel Port Configuration .....................................................81
3.4.8 Power Management ..........................................................................82
3.4.9 Digital IO Port Configuration ............................................................83
3.5 Setup Submenu: Chipset..............................................................................84
3.5.1 North Bridge......................................................................................85
3.5.1.1 LVDS Panel Configuration .....................................................86
3.6 Setup Submenu: Security .............................................................................88
3.6.1 Secure Boot........................................................................................89
3.6.1.1 Key Management...................................................................90
3.7 Setup Submenu: Boot ...................................................................................91
3.8 Setup Submenu: Exit ....................................................................................92
Chapter 4 –Drivers Installation ................................................................. 93

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3.5”Subcompact Board GENE-APL6
4.1 Driver Download/Installation .......................................................................94
Appendix A - I/O Information................................................................... 96
A.1 I/O Address Map..........................................................................................97
A.2 Memory Address Map.................................................................................99
A.3 IRQ Mapping Chart.....................................................................................100
Appendix B –Mating Connectors ..............................................................117
B.1 List of Mating Connectors and Cables ....................................................... 118

3.5”Subcompact Board GENE-APL6
Chapter 1
Chapter 1 - Product Specifications

Chapter 1 –Product Specifications 2
3.5”Subcompact Board GENE-APL6
1.1 Specifications
System
Form Factor
3.5'' Subcompact Board
CPU
Intel® Atom™/ Celeron®/ Pentium®
Processor:
Pentium N4200 (4C/4T, 1.10 GHz, up to 2.5
GHz)
Celeron N3350 (2C/2T, 1.10 GHz, up to 2.40
GHz)
Atom E3950 (4C/4T, 1.60 GHz, up to 2.00GHz)
Atom E3940 (4C/4T, 1.60GHz, up to 1.80GHz)
Atom E3930 (2C/2T, 1.30GHz, up to 1.80GHz)
CPU TDP
6W: N4200, N3350
12W: Atom E3950
9.5W: Atom E3940
6.5W: Atom E3930
Chipset
Integrated with Intel® SoC
Memory Type
DDR3L up to 1866MHz, SODIMM x 1
BIOS
UEFI
Wake on LAN
Yes
Watchdog Timer
255 Levels
Security
TPM 2.0 (Optional)
RTC Battery
Lithium Battery 3V/240mAH
Dimensions
5.75” x 4” (146mm x 101.7mm)

Chapter 1 –Product Specifications 3
3.5”Subcompact Board GENE-APL6
Power
Power Requirement
+9-36V (Optional: +12V)
Power Supply Type
AT/ATX
Connector
Phoenix 2-pin Connector
Power Consumption Typical
2.36A at +12V with Intel® E3950, DDR3L
1866MHz 8GB
Power Consumption Max
2.41A at +12V with Intel® E3950, DDR3L
1866MHz 8GB
Display
Controller
Intel® HD Graphics 500/505
LVDS/ eDP
LVDS1 Dual Channel 18/24bit x 1
LVDS2 Dual Channel 18/24bit x 1 (Optional:
HDMI 1.4b)
Display Interface
VGA x 1
Multiple Display
Up to 3 Simultaneous Displays
Audio
Codec
Realtek ALC897/892
Audio Interface
Line In/ Line Out/ MIC
Speaker
—
External I/O
Ethernet
Intel® i210/i211, 10/100/1000Base, RJ-45 x 2
USB
USB3.2 Gen 1 x 2
Serial Port
COM1 (RS232)
Video
VGA x 1

Chapter 1 –Product Specifications 4
3.5”Subcompact Board GENE-APL6
Internal I/O
USB
USB2.0 x 2
Serial Port
COM2, COM3 (RS232/422/485, supports
5V/12V/RI)
COM4 (RS232)
Video
LVDS1 x 1
LVDS2/HDMI x 1 (Default LVDS2)
SATA
SATA III x 1
+5V SATA Power Connector x 1
Audio
Audio Header x 1
DIO/GPIO
8-bit
SMBus/I2C
I2C/SMBus x 1 (Default: I2C)
Touch
4/5/8-wire Touch Controller x 1 (optional)
Fan
DC Fan x 1 (Optional: Smart Fan)
SIM
Micro SIM x 1 (Optional)
Front Panel
HDD LED, PWR LED, Power Button, Buzzer,
Reset
Others
eMMC 16GB/ 32GB/ 64GB (optional)
Parallel Port (SPP/EPP/ECP) x 1 (optional;
function set by BIOS)
Expansion
Mini PCIe/ mSATA
Full-size mPCIe x 1
Half-size mSATA x 1
M.2
—
Others
—

Chapter 1 –Product Specifications 5
3.5”Subcompact Board GENE-APL6
Environment
Operating Temperature
32°F ~ 140°F (0°C ~ 60°C)
Storage Temperature
-40°F ~ 176°F (-40°C ~ 80°C)
Operating Humidity
0% ~ 90% relative humidity, non-condensing
MTBF (Hours)
374,567
EMC Certification
CE/FCC Class A

3.5” Subcompact Board GENE-APL6
Chapter 2
Chapter 2 –Hardware Information