MSI MS-98H6 User manual

i
MS-98H6
(v1.x) Industrial Computer Board

ii
Preface MS-98H6
Copyright Notice
The material in this document is the intellectual property of MICRO-STAR
INTERNATIONAL. We take every care in the preparation of this document, but no
guarantee is given as to the correctness of its contents. Our products are under
continual improvement and we reserve the right to make changes without notice.
Trademarks
All trademarks are the properties of their respective owners.
Revision History
Revision Date
V1.0 2016/01
Technical Support
If a problem arises with your system and no solution can be obtained from
the user’s manual, please contact your place of purchase or local distributor.
Alternatively, please try the following help resources for further guidance.
Visit the MSI website for technical guide, BIOS updates, driver updates and other
information, or contact our technical sta󰘯 via http://www.msi.com/support/

iii
Preface MS-98H6
Safety Instructions
￭Always read the safety instructions carefully.
￭Keep this User’s Manual for future reference.
￭Keep this equipment away from humidity.
￭Lay this equipment on a reliable at surface before setting it up.
￭The openings on the enclosure are for air convection hence protects the
equipment from overheating. DO NOT COVER THE OPENINGS.
￭Make sure the voltage of the power source and adjust properly 110/220V
before connecting the equipment to the power inlet.
￭Place the power cord such a way that people can not step on it. Do not place
anything over the power cord.
￭Always Unplug the Power Cord before inserting any add-on card or mod-
ule.
￭All cautions and warnings on the equipment should be noted.
￭Never pour any liquid into the opening that could damage or cause electrical
shock.
￭If any of the following situations arises, get the equipment checked by ser-
vice personnel:
◯The power cord or plug is damaged.
◯Liquid has penetrated into the equipment.
◯The equipment has been exposed to moisture.
◯The equipment does not work well or you can not get it work according
to User’s Manual.
◯The equipment has dropped and damaged.
◯The equipment has obvious sign of breakage.
￭DO NOT LEAVE THIS EQUIPMENT IN AN ENVIRONMENT UNCONDI-
TIONED, STORAGE TEMPERATURE ABOVE 60oC (140oF), IT MAY DAM-
AGE THE EQUIPMENT.
警告使用者:
這是甲類資訊產品，在居住的環境中使用時，可能會造成無線電干擾，在這種情
況下，使用者會被要求採取某些適當的對策。

iv
Preface MS-98H6
Chemical Substances Information
In compliance with chemical substances regulations, such as the EU REACH
Regulation (Regulation EC No. 1907/2006 of the European Parliament and the
Council), MSI provides the information of chemical substances in products at:
http://www.msi.com/html/popup/csr/evmtprtt_pcm.html
Battery Information
European Union:
Batteries, battery packs, and accumulators should not be
disposed of as unsorted household waste. Please use the
public collection system to return, recycle, or treat them in
compliance with the local regulations.
廢電池請回收
Taiwan:
For better environmental protection, waste batteries should
be collected separately for recycling or special disposal.
California, USA:
The button cell battery may contain perchlorate material
and requires special handling when recycled or disposed
of in California.
For further information please visit:
http://www.dtsc.ca.gov/hazardouswaste/perchlorate/
Danger of explosion if battery is incorrectly replaced. Replace only with the
same or equivalent type recommended by the manufacturer.

v
Preface MS-98H6
CE Conformity
Hereby, Micro-Star International CO., LTD declares that this device
is in compliance with the essential safety requirements and other
relevant provisions set out in the European Directive.
FCC-A Radio Frequency
Interference Statement
This equipment has been tested and found to comply with
the limits for a Class A digital device, pursuant to Part 15
of the FCC Rules. These limits are designed to provide reasonable protection
against harmful interference when the equipment is operated in a commercial
environment. This equipment generates, uses and can radiate radio frequency
energy and, if not installed and used in accordance with the instruction manual,
may cause harmful interference to radio communications. Operation of this
equipment in a residential area is likely to cause harmful interference, in which
case the user will be required to correct the interference at his own expense.
Notice 1
The changes or modifications not expressly approved by the party responsible for
compliance could void the user’s authority to operate the equipment.
Notice 2
Shielded interface cables and AC power cord, if any, must be used in order to
comply with the emission limits.
VOIR LA NOTICE D’INSTALLATION AVANT DE RACCORDER AU RESEAU.
This device complies with Part 15 of the 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.
WEEE Statement
Under the European Union (“EU”) Directive on Waste Electrical and
Electronic Equipment, Directive 2002/96/EC, which takes effect on
August 13, 2005, products of “electrical and electronic equipment”
cannot be discarded as municipal waste anymore and manufacturers
of covered electronic equipment will be obligated to take back such
products at the end of their useful life. MSI will comply with the product
take back requirements at the end of life of MSI-branded products that are sold
into the EU. You can return these products to local collection points.

vi
Preface MS-98H6
Japan JIS C 0950 Material
Declaration
A Japanese regulatory requirement, defined by specification JIS C 0950,
mandates that manufacturers provide material declarations for certain categories
of electronic products offered for sale after July 1, 2006.
http://www.msi.com/html/popup/csr/cemm_jp.html
http://tw.msi.com/html/popup/csr_tw/cemm_jp.html
日本JIS C 0950材質宣言
日本工業規格JIS C 0950により、2006年7月1日以降に販売される特定分野の
電気および電子機器について、製造者による含有物質の表示が義務付けられま
す。
http://www.msi.com/html/popup/csr/cemm_jp.html
http://tw.msi.com/html/popup/csr_tw/cemm_jp.html
India RoHS
This product complies with the "India E-waste (Management and Handling) Rule
2011" and prohibits use of lead, mercury, hexavalent chromium, polybrominated
biphenyls or polybrominated diphenyl ethers in concentrations exceeding 0.1
weight % and 0.01 weight % for cadmium, except for the exemptions set in
Schedule 2 of the Rule.
Turkey EEE Regulation
Conforms to the EEE Regulations of the Republic Of Turkey
Türkiye EEE yönetmeliği
Türkiye Cumhuriyeti: EEE Yönetmeliğine Uygundur
Ukraine Restriction of Hazardous
Substances
The equipment complies with requirements of the Technical Regulation, approved
by the Resolution of Cabinet of Ministry of Ukraine as of December 3, 2008 №
1057, in terms of restrictions for the use of certain dangerous substances in
electrical and electronic equipment.
Україна обмеження на наявність небезпечних речовин
Обладнання відповідає вимогам Технічного регламенту щодо обмеження
використання деяких небезпечних речовин в електричному та електронному
обладнані, затвердженого постановою Кабінету Міністрів України від 3
грудня 2008 № 1057.

vii
Preface MS-98H6
Vietnam RoHS
As from December 1, 2012, all products manufactured by MSI comply with
Circular 30/2011/TT-BCT temporarily regulating the permitted limits for a number
of hazardous substances in electronic and electric products.
Việt Nam RoHS
Kể từ ngày 01/12/2012, tất cả các sản phẩm do công ty MSI sản xuất tuân thủ
Thông tư số 30/2011/TT-BCT quy định tạm thời về giới hạn hàm lượng cho phép
của một số hóa chất độc hại có trong các sản phẩm điện, điện tử"

viii
Preface MS-98H6
CONTENTS
Copyright Notice............................................................................................ ii
Trademarks ................................................................................................... ii
Revision History ............................................................................................ ii
Technical Support.......................................................................................... ii
Safety Instructions.........................................................................................iii
Chemical Substances Information ............................................................... iv
Battery Information....................................................................................... iv
CE Conformity............................................................................................... v
FCC-A Radio Frequency Interference Statement ......................................... v
WEEE Statement .......................................................................................... v
1. Overview.......................................................................................1-1
Motherboard Specications........................................................................1-2
Motherboard Layout...................................................................................1-4
2. Hardware Setup ...........................................................................2-1
Power Supply.............................................................................................2-3
Rear Panel I/O ...........................................................................................2-4
Connector...................................................................................................2-5
Jumper .....................................................................................................2-10
Slot...........................................................................................................2-12
3. BIOS Setup...................................................................................3-1
Entering Setup ...........................................................................................3-2
The Menu Bar ............................................................................................3-4
Main ...........................................................................................................3-5
Advanced ...................................................................................................3-6
Boot..........................................................................................................3-12
Security ....................................................................................................3-13
Chipset.....................................................................................................3-17
Power .......................................................................................................3-18
Save & Exit...............................................................................................3-20
Appendix WDT & GPIO ................................................................... A-1
WDT Sample Code ................................................................................... A-2
GPIO Sample Code .................................................................................. A-3

1-1-1
Thank you for choosing the MS-98H6, an excellent industrial computer
board.
Based on the innovative Intel® Braswell N3000 Series SoC for optimal
system efciency, the MS-98H6 supports 2 GB of onboard DDR3L
1600MHz memory and allows connection to 3 or 2 independent displays
with HDMI, DP and LVDS outputs.
With compact design and versatile I/O interfaces, the MS-98H6 provides
a low power fanless solution for a wide variety of industrial applications.
1Overview

1-2
Overview MS-98H6
Motherboard Specications
Processor (Optional)
■Intel® Pentium® Processor N3710 (QC/1.6GHz/2.56GHz for Burst/TDP-6W)
■Intel® Celeron® Processor N3160 (QC/1.6GHz/2.24GHz for Burst/TDP-6W)
■Intel® Celeron® Processor N3010 (DC/1.04GHz/2.24GHz for Burst/TDP-
4W)
Memory
■Single-channel DDR3L 1600MHz
■Onboard 2GB
LAN
■1 x Intel® I211-AT Gigabit Fast Ethernet Controller
SATA
■1 x SATA 6Gb/s Port
Audio
■Realtek® ALC887-VD2-CG HD Audio Codec
Graphics
■HD Graphics integrated in Intel®processor
■Shared system memory up to 1.7 GB SDRAM
■LVDS up to 1920 x 1080 @ 60 Hz
■HDMI1.4b up to 2560 x 1600 @ 60 Hz, 3840 x 2160 @ 30 Hz
■DP1.1a up to 2560 x 1600 @ 60 Hz, 3840 x 2160 @ 30 Hz
Rear Panel I/O
■2 x USB 3.0 Ports
■1 x RJ45 GbE LAN Port
■1 x DisplayPort
■1 x HDMI Port

1-3
Overview MS-98H6
Onboard Headers/ Connectors/ Jumpers
■1 x 4-pin DC Power Connector
■1 x 2-pin SATA Power Connector
■1 x System FAN Connector
■1 x SATA 6Gb/s Port
■1 x 8-pin USB 2.0 Header (2 ports)
■1 x LPC Connector
■1 x RS232/422/485 Serial Port Connector (2 ports)
■1 x GPIO Connector
■1 x Front Panel/Front Audio/I2C Connector
■1 x LVDS Connector
■1x LVDS Inverter Connector
■1x Clear CMOS Jumper
■1 x LVDS Power Jumper
■1x LVDS Inverter Power Jumper
■1 x COM Port Power Jumper
■1 x AT/ATX Select Jumper
Slot
■1 x Half-size Mini-PCIe Slot
■1 x Full-size mSATA Slot
Form Factor
■Pico-ITX: 100 x 72 mm
Environmental
■Operating Temperature: -10 ~ 60oC
■Storage Temperature: -20 ~ 80oC
■Humidity: 10 ~ 90% RH, non-condensing

1-4
Overview MS-98H6
Motherboard Layout
System Fan
Connector
Clear
CMOS
Jumper
AT/ATX
Jumper
COM Port
Connector
USB
Connector
SATA
Port
GPIO
Connector
COM Port
Power Jumper
Power
Connector
SATA Power
Connector
Mini PCIe
Slot
Back Panel
LVDS Power
Jumper
Inverter
Connector
Inverter
Power
Jumper
LVDS
Connector
mSATA
Slot
Front Panel/
Audio/I2C
Connector
HDMI Port
DisplayPort
USB 3.0
Port
RJ45 GbE
LAN Port

2-2-1
This chapter provides you with the information about hardware setup
procedures. While doing the installation, be careful in holding the com-
ponents and follow the installation procedures. For some components, if
you install in the wrong orientation, the components will not work prop-
erly.
Use a grounded wrist strap before handling computer components. Static
electricity may damage the components.
2Hardware Setup

2-2
Hardware Setup MS-98H6
Components Reference Guide
Power Supply....................................................................................2-3
DC-In Power Connector: JPWR1...............................................................2-3
SATA Power Connector: JPW1 ..................................................................2-3
Rear Panel I/O ...................................................................................2-4
Connector..........................................................................................2-5
Fan Power Connector: SYSFAN1 ..............................................................2-5
Serial ATA Connector: SATA1 ....................................................................2-5
GPIO Connector: JGPIO1..........................................................................2-6
Front Panel/ Audio/ I2C Connector: JFP1/JAUD1/I2C ...............................2-6
RS232/422/485 Serial Port Connector: JCOM1&JCOM2..........................2-7
LVDS Inverter Connector: JINVDD1 ..........................................................2-8
LVDS Connector: JLVDS1 .........................................................................2-8
USB 2.0 Header: JUSB1............................................................................2-9
LPC Debug Port Connector: JDP1.............................................................2-9
Jumper.............................................................................................2-10
Clear CMOS Jumper: JCMOS1 ...............................................................2-10
AT/ATX Select Jumper: JATX1.................................................................2-10
Serial Port Power Jumper: JCOMP1&JCOMP2....................................... 2-11
LVDS Power Jumper: JVDD1 .................................................................. 2-11
LVDS Inverter Power Jumper: JINV1....................................................... 2-11
Slot...................................................................................................2-12
Mini-PCIe (Peripheral Component Interconnect Express) Slot................2-12

2-3
Hardware Setup MS-98H6
Power Supply
DC-In Power Connector: JPWR1
This connector is used to provide power to the motherboard.
SATA Power Connector: JPW1
This connector is used to provide power to SATA devices.
Important
Make sure that all power connectors are connected to the power supply to ensure
stable operation of the motherboard.

2-4
Hardware Setup MS-98H6
Rear Panel I/O
HDMI Port
DisplayPort
USB 3.0
Port
RJ45 GbE
LAN Port
hUSB 3.0 Port
The USB 3.0 port is backward-compatible with USB 2.0 devices and supports
data transfer rate up to 5 Gbit/s (SuperSpeed).
hRJ45 GbE LAN Port
The standard single RJ45 LAN jack is provided for connection to the Local Area Network
(LAN). You can connect a network cable to it.
Active LED Speed
LED
LED LED Status Description
Active
LED
Off No link
Yellow Linked
Blinking Data activity
Speed
LED
Off 10 Mbps connection
Green 100 Mbps connection
Orange 1 Gbps connection
hDisplayPort
DisplayPort is a digital display interface standard. This connector is used to con-
nect a monitor with DisplayPort inputs.
hHDMI Port
The High-Denition Multimedia Interface (HDMI) is an all-digital audio/video in-
terface capable of transmitting uncompressed streams. HDMI supports all TV
format, including standard, enhanced, or high-denition video, plus multi-channel
digital audio on a single cable.

2-5
Hardware Setup MS-98H6
Connector
Fan Power Connector: SYSFAN1
The fan power connector supports system cooling fan with +12V. When con-
necting the wire to the connectors, always note that the red wire is the positive
and should be connected to the +12V; the black wire is Ground and should be
connected to GND. If the motherboard has a System Hardware Monitor chipset
onboard, you must use a specially designed fan with speed sensor to take advan-
tage of the CPU fan control.
Serial ATA Connector: SATA1
This connector is a high-speed Serial ATA interface port. Each connector can
connect to one Serial ATA device.
Important
Please do not fold the SATA cable into a 90-degree angle. Otherwise, data loss
may occur during transmission.

2-6
Hardware Setup MS-98H6
GPIO Connector: JGPIO1
This connector is provided for the General-Purpose Input/Output (GPIO) periph-
eral module.
Front Panel/ Audio/ I2C Connector: JFP1/JAUD1/I2C
This front panel connector is provided for electrical connection to the front panel
switches & LEDs.
Important
I2C is supported under Windows 7 32/64bit OS only.

2-7
Hardware Setup MS-98H6
RS232/422/485 Serial Port Connector: JCOM1&JCOM2
This connector is a 16550A high speed communications port that sends/receives
16 bytes FIFOs. You can attach serial devices to it through the optional serial
port bracket.
PIN SIGNAL DESCRIPTION
1
3
5
7
9
11
13
15
17
2
4
6
8
10
12
14
16
18
DCD
SIN
SOUT
DTR
GND
DSR
RTS
CTS
VCC_COM1
Data Carrier Detect
Signal In
Signal Out
Data Terminal Ready
Signal Ground
Data Set Ready
Request To Send
Clear To Send
Voltage select setting by jumper
RS232
PIN SIGNAL DESCRIPTION
1
3
5
7
9
11
13
15
17
2
4
6
8
10
12
14
16
18
422 TXD-
422 TXD+
422 RXD+
422 RXD-
GND
NC
NC
NC
NC
Transmit Data, Negative
Transmit Data, Positive
Receive Data, Positive
Receive Data, Negative
Signal Ground
No Connection
No Connection
No Connection
No Connection
RS422
PIN SIGNAL DESCRIPTION
1
3
5
7
9
11
13
15
17
2
4
6
8
10
12
14
16
18
485 TXD-
485 TXD+
NC
NC
GND
NC
NC
NC
NC
Transmit Data, Negative
Transmit Data, Positive
No Connection
No Connection
Signal Ground
No Connection
No Connection
No Connection
No Connection
RS485

2-8
Hardware Setup MS-98H6
LVDS Inverter Connector: JINVDD1
The connector is provided for LCD backlight options.
LVDS Connector: JLVDS1
The LVDS (Low Voltage Differential Signal) connector provides a digital interface
typically used with at panels. After connecting an LVDS interface at panel to
the JLVDS1, be sure to check the panel datasheet and set the LVDS jumper to
proper power voltage.
Important
Pin 12 is a detect pin. When using a customized LVDS cable, pin 12 should be a
signal ground with a low impedance. Otherwise, LVDS will not function.