MSI MS-98H3 User manual

i
MS-98H3
(v1.x) Industrial Computer Board

ii
Preface MS-98H3
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 2017/ 08
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 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-98H3
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-98H3
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-98H3
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 modi󰘰cations 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.
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 e󰘯ect 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-98H3
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
Overview............................................................................................1-1
Mainboard Specications...........................................................................1-2
Mainboard Layout ......................................................................................1-4
Hardware Setup ...............................................................................2-1
Memory ......................................................................................................2-3
Power Supply.............................................................................................2-4
Rear Panel I/O ...........................................................................................2-5
Connector...................................................................................................2-7
Jumper .....................................................................................................2-12
Slot...........................................................................................................2-15
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.....................................................................................................3-20
Power .......................................................................................................3-21
Save & Exit...............................................................................................3-23
Appendix WDT & GPIO ................................................................... A-1
WDT Sample Code ................................................................................... A-2
GPIO Sample Code .................................................................................. A-3

1-1-1
Thank you for choosing the MS-98H3, an excellent industrial computer
board.
With low power and low prole design, the MS-98H3 accommodates the
Intel®KBL/SKL ULT Series Processor and supports up to single channel
DDR4 2133 MHz SO-DIMM slot to provide the maximum of 16GB
memory capacity.
In the entry-level and mid-range market segment, the MS-98H3 provides
a high-performance solution for today’s front-end and general purpose
workstation, as well as in the future.
1Overview

1-2
Overview MS-98H3
Mainboard Specications
Processor
■Intel® KBL ULT i7-7600U/i5-7300U/i3-7100U/Celeron 3965U Processor
■Intel® SKL ULT i7-6600U/i5-6300U/i3-6100U/Celeron 3955U Processor
Memory
■1x DDR4 2133 MHz SO-DIMM slot
■Up to 16GB
LAN
■LAN1: Intel® I219LM GbE-PHY LAN
■LAN2: Intel® I210-AT GbE LAN
SATA
■2x SATA 6Gb/s ports
■1 x mSATA 6Gb/s slot (shared with Mini-PCIe2)
Audio
■Realtek® ALC887-VD2-CG (Co-lay ALC888S)
■1 x audio header
■1 x amplier header
Graphics
■HD Graphics integrated in Intel®processor
■LVDS up to 1920 x 1200 @60Hz
■HDMI1/HDMI2 support HDMI1.4 for up to 3840 x 2160 @24Hz
■DisplayPort 1/DisplayPort 2 up to 3840 x 2160 @60Hz
■eDP up to 3840 x 2160 @60Hz
■Supports three independent displays: LVDS/HDMI/DisplayPort/eDP
Rear Panel I/O
■2 x USB 2.0 ports
■2 x USB 3.0 ports
■2 x Gigabit LAN jacks
■2 x HDMI ports (Option 1)
■2 x DisplayPorts (Option 2)
■1 x DisplayPort + 1 x HDMI port (Standard)

1-3
Overview MS-98H3
Onboard Headers/ Connectors/ Jumpers
■1 x 4-pin DC power connector
■1x System fan connector
■2 x SATA 6Gb/s ports
■2 x SATA power connectors
■2 x USB 2.0 connectors (4 ports)
■1 x RS-232/422/485 serial port connector
■5 x RS232 serial port connectors
■3 x COM port power jumpers
■1 x Front panel connector
■1 x Audio/Amplier/SMbus Connector
■1 x GPIO connector
■1 x LVDS connector
■1 x LVDS power jumper
■1 x LVDS inverter connector
■1 x LVDS inverter power jumper
■1 x TPM 2.0 (LPC Header)
■1 x Clear CMOS jumper
■1 x AT/ATX select jumper
■1 x Intel ME jumper
Expansion Slot
■1 x eDP connector
■1 x Micro SD socket (Support Win10 64-Bit SDR50 Clock Frequency)
■1 x Mini-PCIe1 (Full -size, with Nano SIM-Holder)
■1 x Mini-PCIe2 (Full-size, with m-SATA)
Form Factor
■Form Factor: 146 mm x 102 mm (3.5-inch size)
Environmental
■Operating Temperature: -10 ~ 60oC
■Storage Temperature: -20 ~ 80oC
■Humidity: 10 ~ 90% RH, non-condensing

1-4
Overview MS-98H3
Mainboard Layout
Standard
RJ45 GbE LAN Ports
USB3.0 Ports
HDMI PortDisplayPort
Option 1
RJ45 GbE LAN Ports
USB3.0 Ports
HDMI PortHDMI Port
Option 2
RJ45 GbE LAN Ports
USB3.0 Ports
DisplayPortDisplayPort

1-5
Overview MS-98H3
Micro SD Card Slot
System Fan
Connector
Clear CMOS
Jumper
AT/ATX
Jumper
COM Port
Connectors
USB2.0
Connector
GPIO
Connector
COM Port
Power Jumpers
DC Power
Connector
SATA Port and
Power Connector
Mini-PCIe1
Back Panel
LVDS
Inverter
Connector
Front Panel
Connector
Audio/Amplier/
SMbus Connector
SO-DIMM Slot
Mini-PCIe2/
mSATA Slot
Nano SIM-Hoder
LVDS
Connector
LVDS Power
Jumper
TPM (LPC)
Connector
eDP Connector
eDP Power
Jumper
Inverter Power
Jumper
ME Jumper
RTC Battery
Connector

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-98H3
Components Reference Guide
Memory..............................................................................................2-3
Power Supply....................................................................................2-4
DC Power Connector: JPWR1 / JPWR2(By Request)...............................2-4
SATA Power Connector: JPW1 / JPW2 .....................................................2-4
Rear Panel I/O ...................................................................................2-5
Standard.....................................................................................................2-5
Option 1......................................................................................................2-5
Option 2......................................................................................................2-5
Connector..........................................................................................2-7
Fan Power Connector: SYSFAN1 ..............................................................2-7
GPIO Connector: JGPIO1..........................................................................2-7
Serial ATA Connector: SATA1, SATA2........................................................2-7
Front Panel Connector: JFP1.....................................................................2-8
LPC Debug Port Connector: JLPC1 (With TPM Support)..........................2-8
LVDS Inverter Connector: JINVDD1 ..........................................................2-8
LVDS Connector: JLVDS1 .........................................................................2-9
USB 2.0 Connector: JUSB1 / JUSB2.........................................................2-9
Serial Port Connector: COM1~6 ..............................................................2-10
Audio/Amplier/SMbus Connector: JCON1 ............................................. 2-11
eDP Connector......................................................................................... 2-11
Jumper.............................................................................................2-12
Clear CMOS Jumper: JCMOS1 ...............................................................2-12
AT/ATX Select Jumper: JATX1.................................................................2-12
Serial Port Power Jumper: JCOMP1 (for COM1 & COM2)......................2-13
Serial Port Power Jumper: JCOMP2 (for COM3 & COM4) / JCOMP3 (for
COM5 & COM6).......................................................................................2-13
LVDS Power Jumper: JVDD1 ..................................................................2-13
LVDS Inverter Power Jumper: JINV1.......................................................2-13
Intel ME Jumper: JME1............................................................................2-14
eDP Power Jumper: JEDP_VDD1 ...........................................................2-14
Slot...................................................................................................2-15
Mini-PCIe (Peripheral Component Interconnect Express) Slot................2-15
Nano SIM-Holder .....................................................................................2-15
Micro SD Card Slot ..................................................................................2-15

2-3
Hardware Setup MS-98H3
Memory
The SO-DIMM slot is intended for memory modules.
1. Locate the SO-DIMM slot. Align
the notch on the DIMM with the
key on the slot and insert the
DIMM into the slot.
2. Push the DIMM gently down-
wards until the slot levers click
and lock the DIMM in place.
3. To uninstall the DIMM, ip the slot levers outwards and the DIMM will be
released instantly.
Important
You can barely see the golden nger if the DIMM is properly inserted in the
DIMM slot.

2-4
Hardware Setup MS-98H3
Power Supply
DC Power Connector: JPWR1 / JPWR2(By Request)
This connector allows you to connect a 12V/ 19V/ 24V DC power adapter.
4.Ground
3.Ground
2.DC Power
1.DC Power
2.GND
1.DC_IN
SATA Power Connector: JPW1 / JPW2
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.

2-5
Hardware Setup MS-98H3
Rear Panel I/O
Standard
RJ45 GbE LAN Ports
USB3.0 Ports
HDMI PortDisplayPort
Option 1
RJ45 GbE LAN Ports
USB3.0 Ports
HDMI PortHDMI Port
Option 2
RJ45 GbE LAN Ports
USB3.0 Ports
DisplayPortDisplayPort

2-6
Hardware Setup MS-98H3
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).
hLAN Port
The standard RJ-45 LAN jack is for connection to the Local Area Network (LAN).
You can connect a network cable to it.
Yellow Green/ Orange
LED Color LED State Condition
Left Yellow Off LAN link is not established.
On (steady state) LAN link is established.
On (blinking) The computer is communicating with another
computer on the LAN.
Right Green Off 10 Mbit/sec data rate is selected.
On 100 Mbit/sec data rate is selected.
Orange On 1000 Mbit/sec data rate is selected.
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.
hDisplayPort
DisplayPort is a digital display interface standard. This connector is used to
connect a monitor with DisplayPort inputs.

2-7
Hardware Setup MS-98H3
Connector
Fan Power Connector: SYSFAN1
The fan power connector supports system cooling fans 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 ad-
vantage of the fan control.
GPIO Connector: JGPIO1
This connector is provided for the General-Purpose Input/Output (GPIO) periph-
eral module.
11. N_GPO4
13. N_GPO5
15. N_GPO6
17. N_GPO7
19. VCC5
1. GND
3. N_GPO0
5. N_GPO1
7. N_GPO2
9. N_GPO3
20. VCC5
18. N_GPI7
16. N_GPI6
14. N_GPI5
12. N_GPI4
10. N_GPI3
8. N_GPI2
6. N_GPI1
4. N_GPI0
2. GND
Serial ATA Connector: SATA1, SATA2
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.

2-8
Hardware Setup MS-98H3
Front Panel Connector: JFP1
This front panel connector is provided for electrical connection to the front panel
switches & LEDs and is compliant with Intel Front Panel I/O Connectivity Design
Guide.
LPC Debug Port Connector: JLPC1 (With TPM Support)
This connector works as LPC debug port and supports TPM modules through
an adapter.
LVDS Inverter Connector: JINVDD1
The connector is provided for LCD backlight options.