MSI MS-98J4 User manual

i
MS-98J4
(v1.x) Industrial Computer Board

ii
Preface MS-98J4
Copyright and Trademarks Notice
Copyright © Micro-Star Int’l Co., Ltd. All rights reserved. The MSI logo used is
a registered trademark of Micro-Star Int’l Co., Ltd. All other marks and names
mentioned may be trademarks of their respective owners. No warranty as to
accuracy or completeness is expressed or implied. MSI reserves the right to
make changes to this document without prior notice.
Revision History
Revision Date
V1.0 2018/10
Technical Support
If a problem arises with your product and no solution can be obtained from
the user’s manual, please contact your place of purchase or local distributor.
Alternatively, please visit https://www.msi.com/support/ for further guidance.

iii
Preface MS-98J4
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 module.
￭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
service 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
UNCONDITIONED, STORAGE TEMPERATURE ABOVE 60oC, IT MAY
DAMAGE THE EQUIPMENT.

iv
Preface MS-98J4
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:
https://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:
https://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-98J4
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-B Radio Frequency
Interference Statement
This equipment has been tested and found to comply with
the limits for a Class B digital device, pursuant to Part 15 of the FCC Rules.
These limits are designed to provide reasonable protection against harmful
interference in a residential installation. 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.
However, there is no guarantee that interference will not occur in a particular
installation. If this equipment does cause harmful interference to radio or
television reception, which can be determined by turning the equipment o󰘯 and
on, the user is encouraged to try to correct the interference by one or more of the
measures listed below:
￭Reorient or relocate the receiving antenna.
￭Increase the separation between the equipment and receiver.
￭Connect the equipment into an outlet on a circuit di󰘯erent from that to
which the receiver is connected.
￭Consult the dealer or an experienced radio/television technician for
help.
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.

vi
Preface MS-98J4
CONTENTS
Copyright and Trademarks Notice................................................................. ii
Revision History ............................................................................................ ii
Technical Support.......................................................................................... ii
Safety Instructions.........................................................................................iii
Chemical Substances Information ............................................................... iv
Battery Information....................................................................................... iv
CE Conformity............................................................................................... v
FCC-B Radio Frequency Interference Statement ......................................... v
WEEE Statement .......................................................................................... v
1. Overview.......................................................................................1-1
Specications.............................................................................................1-2
Layout ........................................................................................................1-6
Rear Panel I/O Options..............................................................................1-7
2. Hardware Setup ...........................................................................2-1
Memory ......................................................................................................2-3
Power Supply.............................................................................................2-4
Rear Panel I/O ...........................................................................................2-5
Connector...................................................................................................2-7
Jumper .....................................................................................................2-14
Slot...........................................................................................................2-16
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.....................................................................................................3-21
Power .......................................................................................................3-22
Save & Exit...............................................................................................3-24
Appendix GPIO WDT BKL Programming ...................................... A-1
Abstract..................................................................................................... A-3
General Purposed IO ................................................................................ A-4
Watchdog Timer ........................................................................................ A-5
LVDS Backlight Brightness Control........................................................... A-6
SMBus Access .......................................................................................... A-7

1-1-1
Thank you for choosing the MS-98J4, an excellent industrial computer
board.
Based on the innovative Intel®Kaby Lake/ Skylake Processor, the MS-
98J4 is engineered to provide reliable performance for a wide variety of
industrial applications.
1Overview

1-2
Overview MS-98J4
Specications
Processor
■Intel® Kaby Lake-U Core™ i7, Core™ i5, Core™ i3 Series Processor
■Intel® Skylake-U Core™ i7, Core™ i5, Core™ i3 Series Processor
■Intel® Kaby Lake-R Core™ i5 Series Processor
PCH
■Integrated with Processor
Memory
■2 * DDR4 SO-DIMM slots
■Dual-Channel DDR4 Non-ECC memory up to 2133 MHz
■Max 32GB
Network
■1* Intel® I219LM GbE LAN PHY
■1* Intel® I211AT GbE LAN (Co-lay I210AT)
Storage
■2* SATA 6Gb/s ports
■1 * M.2 Key M 2280 slot for SSD (Optional)
-With SATA and PCIe signal
-PCIe signal shared with PCIe x4 slot, auto switch by switch IC and PCIe
x4 as top priority
■1 * mSATA slot (shared with Mini-PCIe)
Audio
■Realtek ALC887 audio codec (Co-lay ALC888S)
■1 * Line-Out jack
■1 * Mic-In jack
■1 * Amplier header
■1 * SPDIF header

1-3
Overview MS-98J4
Graphics
■Integrated Intel® HD Graphics
■2 * LVDS 18/24 bit, Dual Channel
-LVDS1 shared with eDP
-LVDS2 shared with DP2/HDMI2.0
-Max resolution 1920x1200@60Hz
■1 * eDP
-Shared with LVDS1
-Max resolution 4096×2304@60Hz
■2 * DP
-DP1 shared with HDMI1.4
-DP2 shared with LVDS2/HDMI2.0
-Max resolution 4096x2160@60Hz, Default (Co-lay HDMI)
■2 * HDMI
-HDMI1.4 shared with DP1
-HDMI2.0 shared with DP2
-Max resolution 4096x2160@24Hz, Optional (Co-lay DP)
■3 independent displays
-LVDS1+DP1+DP2 (default)
-LVDS1+DP1+HDMI2.0
-LVDS1+LVDS2+DP1
-LVDS1+LVDS2+HDMI1.4
-LVDS1+HDMI1.4+DP2
-LVDS1+HDMI1.4+HDMI2.0
-eDP+DP1+DP2
-eDP+DP1+HDMI2.0
-eDP+LVDS2+DP1
-eDP+LVDS2+HDMI1.4
-eDP+HDMI1.4+DP2
-eDP+HDMI1.4+HDMI2.0
Expansion Slot
■1 * PCIe x4 slot
-Signal shared with M.2 Key M, auto switch by switch IC and PCIe x4 as
top priority
■2 * Mini-PCIe slots
-MPCIE/MSATA1 slot supports Mini-PCIe and mSATA cards
-MINI_PCIE1 slot supports Mini-PCIe cards
■1 * Nano SIM holder
■1 * M.2 Key E 2230 slot for Wi-Fi/BT modules
-With PCIe x1 and USB 2.0 signal
Rear Panel I/O
■1 * DC power jack (Co-lay 4-pin power connector)
■2 * DisplayPorts (Co-lay HDMI)
■2 * GbE RJ45 ports
■4 * USB3.0 ports
■1 * Mic-In jack
■1 * Line-Out jack

1-4
Overview MS-98J4
Internal I/O
■1 * DC power connector (Optional)
■1 * CPU fan header
■1 * System fan header
■2 * SATA 6Gb/s ports
■2 * SATA power box headers
■1 * Vertical USB2.0 connector (1 port) (Optional)
■2 * USB2.0 headers (4 ports)
■1 * Front panel header
■1 * SPDIF header
■1 * Amplier header
■1 * GPIO box header
■1 * TPM header
■1 * Chassis intrusion header
■1 * Keyboard/Mouse box header
■2 * RS232/422/485 serial port box headers (Optional)
■2 * RS232 serial port box headers
■2 * LVDS headers
■2 * LVDS inverter box headers
■1 * eDP connector
■1 * SMBus box header
■4 * Serial port power jumpers
■2 * LVDS power jumpers
■2 * LVDS inverter power jumpers
■1 * eDP power jumper
■1 * Clear CMOS jumper
■1 * AT/ATX jumper
■1 * LAN NVM jumper
■1 * ME jumper
Form Factor
■170 mm x 170 mm (6.7 x 6.7 inches, mini-ITX)
Environment
■Operating Temperature: -10 ~ 60oC
■Storage Temperature: -20 ~ 80oC
■Humidity: 10 ~ 90% RH, non-condensing
Accessories
■1 * DC-in power cable (Max 12A supported)
■1 * I/O shield
■1 * SATA cable
■1 * Driver CD

1-5
Overview MS-98J4
SKU Comparison
SKUs
Features SKU1 SKU2 SKU3
Processor Intel Core™ i5-8250U Intel Core™ i5-7300U Intel Core™ i3-6100U
Graphics
Display
■eDP/LVDS1
■HDMI2.0/LVDS2
■HDMI1.4
■eDP/LVDS1
■DP2/LVDS2
■DP1
■LVDS1
■LVDS2
■DP1
LVDS 222
eDP 1 1
HDMI 2
DP 2 1
Expansion
PCIe x4 1 1
M.2 Key M
2280 1 1
Rear I/O
LAN 2 (LAN1: i219,
LAN2: i210)
2 (LAN1: i219,
LAN2: i211) 1 (LAN2: i211)
Power DC jack DC jack 4-pin connector
Internal I/O
Internal
Vertical
USB2.0
1 1
COM
4
(2 x RS232/422/485,
2 x RS232)
4
(2 x RS232/422/485,
2 x RS232)
2
(2 x RS232)

1-6
Overview MS-98J4
Layout
CMOS
Jumper
AT/ATX
Jumper
LVDS1 Power
Jumper
LVDS1 Inverter
Power Jumper
LVDS1
Rear Panel
I/O eDP
LVDS2
System Fan
LVDS1
Inverter
LVDS2
Inverter USB2.0
DDR4
SO-DIMM
Nano SIM
Mini- PCIe
Mini-PCIe/
mSATA
M.2
Key E
PS/2
KB/MS
ME Jumper
Chassis
Intrusion
COM
SATA
PCIe x4
SATA
Power
Front
Panel
S/PDIF
Amplier
GPIO
TPM
(LPC)
COM
Power
Jumper
COM
Power
Jumper
USB2.0
LVDS2 Power
Jumper
LVDS2 Inverter
Power Jumper
CPU Fan
eDP Power
Jumper

1-7
Overview MS-98J4
Rear Panel I/O Options
SKU1
HDMI1.4
Port
GbE RJ45 Ports USB3.0 PortsHDMI2.0
Port
DC Jack Mic-In
Jack
Line-Out
Jack
SKU2
DisplayPort GbE RJ45 Ports USB3.0 PortsDisplayPortDC Jack Mic-In
Jack
Line-Out
Jack
SKU3
DisplayPort GbE RJ45 Port USB3.0 Ports Mic-In
Jack
Line-Out
Jack
DC-In
Connector

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

2-2
Hardware Setup MS-98J4
Components Reference Guide
Memory..............................................................................................2-3
Power Supply....................................................................................2-4
DC Power Connector: JPWR2...................................................................2-4
SATA Power Connector: JSATAPWR1, JSATAPWR2................................2-4
Rear Panel I/O ...................................................................................2-5
Connector..........................................................................................2-7
CPU Fan Power Connector: CPUFAN1 .....................................................2-7
System Fan Power Connector: SYSFAN1 .................................................2-7
SMBus Connector: JSMB1 ........................................................................2-7
USB2.0 Connector: JUSB1, JUSB2, USB2 ...............................................2-8
Serial ATA Connector: SATA1, SATA2........................................................2-8
Front Panel Connector: JFP1.....................................................................2-9
LPC Debug Port Connector: JTPM1..........................................................2-9
LVDS Inverter Connector: JINV1, JINV2..................................................2-10
LVDS Connector: JLVDS1, JLVDS2.........................................................2-10
COM Port Connector: JCOM1 ~ JCOM6 ................................................. 2-11
Audio Amplier Header: JAMP1...............................................................2-12
S/PDIF Header: JSPD1............................................................................2-12
Chassis Intrusion Header: JCASE1 .........................................................2-12
PS/2 Keyboard/Mouse Connector: JKB/MS1...........................................2-12
GPIO (DIO) Connector: JGPIO1..............................................................2-13
eDP Connector: EDP1 .............................................................................2-13
Jumper.............................................................................................2-14
Clear CMOS Jumper: JCMOS1 ...............................................................2-14
AT/ATX Jumper: JAT1..............................................................................2-14
ME Jumper: JME1....................................................................................2-14
eDP Power Jumper: JEDP_VDD1 ...........................................................2-14
JCOM1~JCOM2 Power Jumper: JCOMP1, JCOMP2 .............................2-15
JCOM3~JCOM6 Power Jumper: JCOMP3 ~ JCOMP6 ...........................2-15
LVDS Power Jumper: JVDD1, JVDD2 .....................................................2-15
LVDS Inverter Power Jumper: JINVDD1, JINVDD2.................................2-15
Slot...................................................................................................2-16
PCIe (Peripheral Component Interconnect Express) Slot........................2-16
M2_M1: M.2 Slot (Key M, 2280) for SSD.................................................2-16
M2_E1: M.2 Slot (Key E, 2230) for WiFi/BT.............................................2-16
Mini-PCIe (Peripheral Component Interconnect Express) Slot................2-17
Nano SIM Holder......................................................................................2-17

2-3
Hardware Setup MS-98J4
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
downwards 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-98J4
Power Supply
DC Power Connector: JPWR2
This connector allows you to connect a DC-in power cable.
SATA Power Connector: JSATAPWR1, JSATAPWR2
This connector is used to provide power to SATA devices.
Important
• Make sure all power connectors are connected to the power supply to ensure
stable operation of the motherboard.
• Make sure that you hold the onboard power connector rmly before
disconnecting the power cable.

2-5
Hardware Setup MS-98J4
Rear Panel I/O
SKU1
HDMI1.4
Port
GbE RJ45 Ports USB3.0 PortsHDMI2.0
Port
DC Jack Mic-In
Jack
Line-Out
Jack
SKU2
DisplayPort GbE RJ45 Ports USB3.0 PortsDisplayPortDC Jack Mic-In
Jack
Line-Out
Jack
SKU3
DisplayPort GbE RJ45 Port USB3.0 Ports Mic-In
Jack
Line-Out
Jack
DC-In
Connector
hDC Jack
This jack is used to provide power to the motherboard.
hHDMI Port
The High-Denition Multimedia Interface (HDMI) is an all-digital audio/video
interface 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.

2-6
Hardware Setup MS-98J4
hGbE RJ45 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.
Speed LED Active
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
hUSB3.0 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).
hMic-In Jack
For microphones.
hLine-Out Jack
For speakers or headphones.