MSI MS-98J0 User manual

i
MS-98J0
(v1.x) Industrial Computer Board

ii iii
Preface MS-98J0
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
V1.1 2020/07
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.

ii iii
Preface MS-98J0
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 v
Preface MS-98J0
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.

iv v
Preface MS-98J0
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 2012/19/EU, 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 PB
Preface MS-98J0
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 ........................................................................................................1-5
Rear Panel I/O Options..............................................................................1-6
2. Hardware Setup ...........................................................................2-1
Memory ......................................................................................................2-3
Power Supply.............................................................................................2-4
Rear Panel I/O ...........................................................................................2-5
Connector...................................................................................................2-7
Jumper .....................................................................................................2-13
Slot...........................................................................................................2-15
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 GPIO WDT BKL Programming ...................................... A-1
Abstract..................................................................................................... A-2
General Purposed IO - GPIO/DIO............................................................. A-2
Watchdog Timer ........................................................................................ A-3
LVDS Backlight Brightness Control........................................................... A-4
SMBus Access .......................................................................................... A-5

1-1-1
Thank you for choosing the MS-98J0, an excellent industrial computer
board.
Based on the innovative Intel®Apollo Lake processor for optimal
system e󰘲ciency, the MS-98J0 accommodates versatile I/O interfaces
and supports up to 2 DDR3L 1866MHz SO-DIMM slots to provide the
maximum of 8GB memory capacity.
Designed to withstand harsh industrial conditions, the MS-98J0 is
engineered to provide reliable performance for a wide variety of industrial
applications.
1Overview

1-2
Overview MS-98J0
Specications
Processor
￭Intel® Celeron® J3455 QC 1.5GHz/2.3GHz (Burst)
￭Intel® Celeron® N3350 DC 1.1GHz/2.4GHz (Burst)
￭Intel® Atom™ x5-E3940 QC 1.6/1.8GHz (Burst)
Memory
￭2 x SO-DIMM slots
￭Dual-channel Non-ECC DDR3L, up to 1866MHz
￭Up to 8GB
Network
￭2 x Realtek® RTL8111H GbE LAN
Storage
￭1 x SATA 6Gb/s port
Expansion Slot
￭1 x PCIe x1 slot
￭1 x M.2 M Key (SATA3.0), 2242 slot
￭1 x M.2 E Key (PCIe x1 & USB 2.0), 2230 slot

1-3
Overview MS-98J0
Internal I/O
￭1 x 4-pin DC power connector (12V)
￭1 x SATA power connector
￭1 x System FAN connector
￭1 x 10-pin USB 2.0 box header (2 ports)
￭1 x USB 2.0 connector (1 port)
￭1 x RS232/422/485 COM port connector
￭5 x RS232 COM port connectors
￭1 x GPIO header (4 x GPI, 4 x GPO; 5V)
￭1 x Front panel header
￭1 x Front audio header
￭1 x S/PDIF header
￭1 x Audio amplier header
￭1 x SMBus connector
￭1 x keyboard/mouse connector
￭1 x LPC header
￭1 x LVDS connector
￭1 x LVDS backlight header & power jumper
￭1 x eDP connector (Optional)
￭1 x eDP power jumper (Optional)
￭1x Clear CMOS jumper
￭1 x RTC jumper
￭1 x AT/ATX jumper
￭1 x COM port power jumper
￭1 x SMBus power jumper
￭1 x TXE F/W jumper
Rear I/O
￭1 x DC-In jack
￭4 x USB 3.2 Gen 1 ports (5V/0.9A)
￭1 x DisplayPort (N3350/E3940 SKU)
￭1 x VGA port (J3455 SKU)
￭1 x HDMI port
￭2 x RJ45 GbE LAN ports
￭1 x Line-Out jack

1-4
Overview MS-98J0
Graphics
￭HD Graphics integrated in Intel®processor
￭VGA up to 1920 x 1200 @ 60 Hz
￭LVDS up to 1920 x 1200 @ 60 Hz
￭HDMI up to 3840 x 2160 @ 30 Hz
￭DisplayPort up to 4096 x 2160 @ 60 Hz
￭eDP up to 4096 x 2160 @ 60 Hz
￭Supporting three independent displays: (eDP or LVDS) + (DP2 or VGA)
+ (DP1 or HDMI)
Audio
￭Realtek® ALC887 HD Audio Codec
￭1 x Audio amplier connector
￭1 x S/PDIF header
￭1 x Line-Out jack
Power
￭DC 12V
￭1 x 4-pin power connector
￭1x DC-In jack
Environment
￭Operating temperature: -10 ~ 60oC
￭Storage temperature: -20 ~ 80oC
￭Humidity: 10 ~ 90% RH, non-condensing
Form Factor
￭Mini-ITX: 170 mm x 170 mm
Certication
￭EMC: CE, FCC, RCM, VCCI, BSMI /ClassB

1-5
Overview MS-98J0
Layout
Rear Panel I/O
System Fan
Connector
Clear CMOS
Jumper
AT/ATX
Jumper
USB 2.0
Connectors
SATA
Port
GPIO
Header
Power
Connector
PCIe Slot
Audio
Amplier
Header
LPC
Header
Front Panel
Header
COM Port
Connectors
SO-DIMM
Slot
M.2 E Key
Slot
LVDS
Connector
S/PDIF
Header
Keyboard/
Mouse
Connector
Front Audio
Header
eDP Connector
(Optional)
SMBus
Connector
SATA
Power
Connector
TXE F/W
Jumper
LVDS
Backlight
Header
& Power
Jumper eDP Power
Jumper
(Optional)
SO-DIMM
Slot
COM Port
Power Jumper
SMBus Power
Jumper
M.2 M Key
Slot
RTC
Jumper

1-6
Overview MS-98J0
Rear Panel I/O Options
HDMI Port GbE RJ45 PortsUSB 3.2 Gen 1
Ports
DisplayPortDC-In
Jack
Line-Out
Jack
N3350/E3940 SKU
J3455 SKU
HDMI Port GbE RJ45 PortsVGA PortDC-In
Jack
Line-Out
Jack
USB 3.2 Gen 1
Ports

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-98J0
Components Reference Guide
Memory..............................................................................................2-3
Power Supply....................................................................................2-4
System Power Connector: JPWR2 ............................................................2-4
SATA Power Connector: JPW1 ..................................................................2-4
Rear Panel I/O ...................................................................................2-5
Connector..........................................................................................2-7
Fan Power Connector: SYSFAN1 ..............................................................2-7
Serial ATA Connector: SATA1 ....................................................................2-7
GPIO Header: JGPIO1...............................................................................2-8
Audio Amplier Header: JAMP1.................................................................2-8
S/PDIF Header: JSPD1..............................................................................2-8
Front Audio Header: JAUD1.......................................................................2-8
Front Panel Header: JFP1 .........................................................................2-9
Keyboard/Mouse Connector: JKB/MS1 .....................................................2-9
USB 2.0 Connector: JUSB1, JUSB2..........................................................2-9
SMBus Connector: JSMB1 ......................................................................2-10
LVDS Connector: LVDS1 ........................................................................2-10
COM Port Connector: COM1 ~ COM6..................................................... 2-11
eDP Connector: EDP1 (Optional) ............................................................2-12
LPC Debug Port Header: JLPC1 (With TPM Support).............................2-12
Jumper.............................................................................................2-13
Clear CMOS Jumper: JCMOS1 ...............................................................2-13
AT/ATX Jumper: JATX1............................................................................2-13
TXE F/W Jumper: JTXE1.........................................................................2-13
RTC Jumper: JRTC1................................................................................2-13
SMBus Power Jumper: JSMBP1 .............................................................2-14
eDP Power Jumper: JEDP1 (Optional)....................................................2-14
Serial Port Power Jumper: JCOMP1........................................................2-14
LVDS Backlight Header & Power Jumper: JLCD1 ..................................2-14
Slot...................................................................................................2-15
PCIe (Peripheral Component Interconnect Express) Slot........................2-15
M2_M1: M.2 Slot (Key M, 2242) ..............................................................2-15
M2_E1: M.2 Slot (Key E, 2230)................................................................2-15

2-3
Hardware Setup MS-98J0
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.
Important
You can barely see the golden nger
if the DIMM is properly inserted in the
DIMM slot.
3. To uninstall the DIMM, 󰘱ip the slot levers outwards and the DIMM will
be released instantly.

2-4
Hardware Setup MS-98J0
Power Supply
System Power Connector: JPWR2
This connector is used to provide power to the system.
4.+12V
2
.Ground
3.+12V
1
.Ground
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.

2-5
Hardware Setup MS-98J0
Rear Panel I/O
HDMI Port GbE RJ45 PortsUSB 3.2 Gen 1
Ports
DisplayPortDC-In
Jack
Line-Out
Jack
N3350/E3940 SKU
J3455 SKU
HDMI Port GbE RJ45 PortsVGA PortDC-In
Jack
Line-Out
Jack
USB 3.2 Gen 1
Ports
hDC-In Jack
This jack is used to provide power to the motherboard.
hUSB 3.2 Gen 1 Port
The USB 3.2 Gen 1 port is backward-compatible with USB 2.0 devices and supports
data transfer rate up to 5 Gbit/s (SuperSpeed).
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.
hVGA Port
The DB15-pin female connector is provided for monitor.

2-6
Hardware Setup MS-98J0
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
hLine-Out Jack
For speakers or headphones.

2-7
Hardware Setup MS-98J0
Connector
Fan Power Connector: SYSFAN1
The fan power connectors support system cooling fan with +12V. When connecting
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 advantage of the
CPU fan control.
Important
Fan cooler sets with 3- or 4-pin power connector are both available.
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.

2-8
Hardware Setup MS-98J0
GPIO Header: JGPIO1
This connector is provided for the General-Purpose Input/Output (GPIO)
peripheral module.
Audio Amplier Header: JAMP1
The connector is used to connect audio ampli󰘰ers to enhance audio performance.
S/PDIF Header: JSPD1
This header is used to connect S/PDIF (Sony & Philips Digital Interconnect
Format) interface for digital audio transmission.
Front Audio Header: JAUD1
This connector allows you to connect the front panel audio.