Aaeon GENE-APL5 User manual

Last Updated: November 16, 2021
GENE-APL5
3.5”Subcompact Board
User’s Manual 5th Ed

Preface II
3.5”Subcompact Board GENE-APL5
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-APL5
Acknowledgements
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
Intel Core™ and Intel 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 MB
1
Heatsink
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 product page at 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
1.2 Function Block Diagram......................................................................................... 6
Chapter 2 –Hardware Information ........................................................................................7
2.1 Dimensions ............................................................................................................... 8
2.1.1 Dimensions (Optional HDMI SKU)....................................................10
2.2 Jumpers and Connectors......................................................................................13
2.2.1 Jumpers and Connectors (Optional HDMI SKU)............................15
2.3 List of Jumpers ........................................................................................................17
2.3.1 LVDS Port 1 Backlight Inverter VCC Selection (JP1) .......................17
2.3.2 LVDS Port 1 Operating VDD Selection (JP1)....................................18
2.3.3 LVDS Port 1 Backlight Lightness Control Mode Selection (JP2)..18
2.3.4 COM2 Pin8 Function Selection (JP3)................................................18
2.3.5 COM3 Pin8 Function Selection (JP4)................................................19
2.3.6 Auto Power Button Enable/Disable Selection (JP5) ......................19
2.3.7 Front Panel Connector (JP6) ..............................................................19
2.3.8 LVDS Port 2 Backlight Inverter VCC Selection (JP7).....................20
2.3.9 LVDS Port 2 Operating VDD Selection (JP7) .................................20
2.3.10 LVDS Port 2 Backlight Lightness Control Mode Selection (JP8) 20
2.3.11 Touch Screen 4, 5, 8 Wire Selection (JP9) .......................................21
2.3.12 Clear CMOS Jumper (JP10).................................................................21
2.4 List of Connectors..................................................................................................22
2.4.1 +5VSB Output w/SMBus (CN1) ........................................................23
2.4.2 LVDS Port 1 Inverter / Backlight Connector (CN2).......................24
2.4.3 +5V Output for SATA HDD (CN3)....................................................24
2.4.4 SATA Port (CN4)...................................................................................25

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3.5”Subcompact Board GENE-APL5
2.4.5 External Power Input (CN5)...............................................................25
2.4.6 External +5VSB Input (CN6) (Optional) ..........................................26
2.4.7 Audio I/O Port (CN7)..........................................................................26
2.4.8 LVDS Port 1 (CN8)................................................................................27
2.4.9 COM Port 2 (CN9)...............................................................................29
2.4.10 LPT Port or Digital I/O Port (CN10)...................................................31
2.4.11 LPC Port (CN11)....................................................................................34
2.4.12 COM Port 3 (CN12).............................................................................35
2.4.13 BIOS Debug Port (CN13)....................................................................37
2.4.14 COM Port 4 (CN14).............................................................................38
2.4.15 PS/2 Keyboard/Mouse Combo Port (CN15)..................................39
2.4.16 USB 2.0 Port 2 (CN16).........................................................................39
2.4.17 USB 2.0 Port 3 (CN17).........................................................................40
2.4.18 COM Port 1 (CN18) (Wafer, Optional)..............................................40
2.4.19 USB 2.0 Port 4 (CN19)..........................................................................41
2.4.20 USB 2.0 Port 5 (CN20)........................................................................42
2.4.21 LVDS Port 2 (CN21) .............................................................................42
2.4.22 Touchscreen Connector (CN22) .......................................................44
2.4.23 CPU Fan (CN23, Optional).................................................................46
2.4.24 LVDS Port 2 Inverter / Backlight Connector (CN24)....................47
2.4.25 USB 3.0 Ports 0 and 1 (CN25) ...........................................................47
2.4.26 LAN (RJ-45) Port 2 (CN26)................................................................48
2.4.27 LAN (RJ-45) Port 1 (CN27).................................................................49
2.4.28 COM Port 1 (CN28, D-SUB 9)...........................................................50
2.4.29 HDMI Port (CN29, Optional).............................................................50
2.4.30 Battery (CN30)......................................................................................51
2.4.31 VGA Port (CN31)..................................................................................52
2.4.32 Micro SIM Card Socket (CN32).........................................................53

Preface XIII
3.5”Subcompact Board GENE-APL5
2.4.33 Mini-Card Slot (Half-Mini) (CN33) ...................................................53
2.4.34 mSATA (Full-Size) (CN34)...................................................................55
Chapter 3 - AMI BIOS Setup ................................................................................................ 58
3.1 System Test and Initialization ..............................................................................59
3.2 AMI BIOS Setup .....................................................................................................60
3.3 Setup Submenu: Main...........................................................................................61
3.4 Setup Submenu: Advanced.................................................................................62
3.4.1 Trusted Computing .............................................................................63
3.4.2 CPU Configuration..............................................................................65
3.4.3 SATA Configuration.............................................................................67
3.4.3.1 PCI Express Configuration................................................68
3.4.4 Hardware Monitor...............................................................................70
3.4.4.1 Smart Fan Configuration ...................................................71
3.4.5 SIO Configuration ...............................................................................72
3.4.5.1 Serial Port 1 Configuration ...............................................73
3.4.5.2 Serial Port 2 Configuration...............................................74
3.4.5.3 Serial Port 3 Configuration...............................................75
3.4.5.4 Serial Port 4 Configuration...............................................76
3.4.5.5 Parallel Port Configuration ...............................................77
3.4.6 Power Management ...........................................................................78
3.4.7 Digital IO Port Configuration............................................................79
3.5 Setup Submenu: Chipset .....................................................................................80
3.5.1 North Bridge .........................................................................................81
3.5.1.1 North Bridge: LVDS Panel Configuration ......................82
3.6 Setup Submenu: Security.....................................................................................84
3.6.1 Secure Boot ..........................................................................................85
3.6.1.1 Key Management...............................................................86
3.7 Setup Submenu: Boot ..........................................................................................88

Preface XIV
3.5”Subcompact Board GENE-APL5
3.8 Setup Submenu: Save & Exit...............................................................................89
3.9 User Notes ..............................................................................................................90
Chapter 4 –Drivers Installation.............................................................................................91
4.1 Drivers Download and Installation.....................................................................92
Appendix A - I/O Information.............................................................................................. 94
A.1 I/O Address Map ...................................................................................................95
A.2 Memory Address Map .........................................................................................97
A.3 IRQ Mapping Chart...............................................................................................98
Appendix B –Mating Connectors ......................................................................................103
B.1 List of Mating Connectors and Cables............................................................ 104
Appendix C –Electrical Specifications for I/O Ports.........................................................107
C.1 Electrical Specifications for I/O Ports............................................................... 108

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'' Subcompact Board
CPU
Intel® Atom™/ Celeron®/ Pentium®
Processor:
Pentium® N4200 (4C/4T, 1.10GHz, up to
2.50GHz)
Celeron® N3350 (2C/2T, 1.10GHz, up to
2.40GHz)
Atom® E3950 (4C/4T, 1.60GHz, up to
2.00GHz)
Atom® E3940 (4C/4T, 1.60GHz, up to 1.80GHz)
Atom® E3930 (2C/2T, 1.30GH, up to 1.80GHz)
CPU TDP
Pentium® N4200, Celeron® N3350: 6W
Atom® E3950: 12W
Atom® E3940 9.5W
Atom® E3930 6.5W
Chipset
Integrated with Intel® SoC
Memory Type
DDR3L up to 1866MHz, SODIMM x 1
Max. Memory Capacity
8GB
BIOS
UEFI
Wake on LAN
Yes
Watchdog Timer
255 Levels
Security
TPM 2.0 (Optional)
RTC Battery
Lithium Battery 3V/240mAh

Chapter 1 –Product Specifications 3
3.5”Subcompact Board GENE-APL5
Power
Power Requirement
+12V (Optional: +9~19V)
Power Supply Type
AT/ATX
Connector
Phoenix 2-pin Connector
Power Consumption (Typical)
2.03A at +12V with Intel® E3950, DDR3L
1866MHz 8GB memory
Power Consumption (Max)
2.45A at +12V with Intel® E3950, DDR3L
1866MHz 8GB memory
Display
Controller
Intel® HD Graphics 500/505
LVDS/eDP
LVDS1 Dual Channel 18/24-bit x 1
LVDS2 Dual Channel 18/24-bit x 1 (Optional:
HDMI 1.4b)
Display Interface
VGA x 1
Multiple Display
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-TX, RJ-45 x 2
USB
USB3.2 Gen 1 x 2
Serial Port
COM1 (RS232, supports RI)
Video
VGA x 1
Power Input
Phoenix 2-pin Connector

Chapter 1 –Product Specifications 4
3.5”Subcompact Board GENE-APL5
Internal I/O
USB
USB2.0 x 4
Serial Port
COM2, COM3 (RS232/422/485, supports
5V/12V/RI)
COM4 (RS232, supports RI)
Video
LVDS1 Dual Channel 18/24-bit x 1
LVDS2 Dual Channel 18/24-bit x 1 (Optional:
HDMI 1.4b)
SATA
SATA III x 1
+5V SATA Power Connector x 1
Audio
Audio Header x 1
DIO/GPIO
8-bit
SMBus/ I2C
I2C x 1
SMBus x 1
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
Parallel Port(SPP/EPP/ECP) x 1 (optional, select
by BIOS)
Expansion
Mini PCIe/ mSATA
mSATA x 1 (Full-Size)
Mini Card x 1 (Half-Size)
M.2
—
BIO
—

Chapter 1 –Product Specifications 5
3.5”Subcompact Board GENE-APL5
Mechanical
Dimensions (L x W)
5.75” x 4” (146mm x 101.7mm)
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)
365,976
Certification
EMC
CE/ FCC Class A

Chapter 1 –Product Specifications 6
3.5”Subcompact Board GENE-APL5
1.2 Function Block Diagram