MSI MS-98N1 User manual

MS-98N1
Industrial Computer Board
User Guide

2Contents
Revision
V1.0, 2023/05
Contents
Regulatory Notices....................................................................................................... 4
Safety Information........................................................................................................ 7
Specifications ............................................................................................................... 8
Motherboard Overview............................................................................................... 11
Rear I/O Panel............................................................................................................. 12
Power Jack ............................................................................................................ 12
DisplayPort ............................................................................................................ 12
Connector ....................................................................................... 12
VGA Port................................................................................................................. 12
RJ-45 LAN Jack ..................................................................................................... 13
USB 3.2 Gen 1 Port ................................................................................................ 13
USB 2.0 Port .......................................................................................................... 13
Line-Out Jack ........................................................................................................ 13
ME Overview................................................................................................................ 14
Board Dimension................................................................................................... 14
DP + HDMI SKU ................................................................................................................................. 14
VGA + HDMI SKU ...............................................................................................................................15
Suggested Chassis I/O Gap Dimension................................................................. 16
Memory ....................................................................................................................... 18
DIMM1~2: DDR4 SO DIMM Slots.......................................................................................................18
Storage........................................................................................................................ 19
JSATA1: SATA 3.0 6Gb/s Port............................................................................................................19
M2_M1: M.2 Slot (M Key, 2242)......................................................................................................... 20
Installing M.2 SSD............................................................................................................................. 20
Expansion Slots .......................................................................................................... 21
JUSIM1: Nano SIM Holder................................................................................................................21
M2_E1: M.2 Slot (E Key, 2230)........................................................................................................... 22
M2_B1: M.2 Slot (B Key, 2242/ 3042) ................................................................................................22
Connectors.................................................................................................................. 23
Power Connectors ................................................................................................. 23

3
Contents
JPWR1: DC-In Power Connector (Optional)......................................................................................23
JSATA_PWR1: SATA Power Connector ............................................................................................23
Graphics Connectors............................................................................................. 24
JINV1: LVDS Inverter Box Header.................................................................................................... 24
JLVDS1: LVDS+eDP Wafer Connector .............................................................................................. 25
Other Connectors .................................................................................................. 28
SYSFAN1: System Fan Box Header .................................................................................................28
JKBMS1: PS/2® Keyboard & Mouse Box Header.............................................................................28
JFP1: Front Panel Connector...........................................................................................................29
JTPM1: SPI TPM Module Header......................................................................................................29
JAUD1: Front Audio Header ............................................................................................................30
JAMP1: Audio Amplifier Header ....................................................................................................... 30
JGPIO1: GPIO (DIO) Box Header........................................................................................................ 30
JCOM1~6: COM Port Box Headers....................................................................................................31
JUSB1~2: USB 2.0 Box Headers ......................................................................................................33
JSMB1: SMBus Box Header............................................................................................................. 33
JBAT1: CMOS Battery Header...........................................................................................................34
Replacing CMOS battery ...................................................................................................................34
Jumpers ...................................................................................................................... 35
BIOS Setup .................................................................................................................. 37
Entering Setup....................................................................................................... 37
The Menu Bar ............................................................................................................. 41
Main ............................................................................................................................. 42
Advanced..................................................................................................................... 43
Boot.............................................................................................................................. 50
Security........................................................................................................................ 51
Chipset......................................................................................................................... 61
Power .......................................................................................................................... 62
Save & Exit .................................................................................................................. 63
GPIO WDT SMBus Access Programming................................................................. 64
Abstract ................................................................................................................. 64
General Purpose IO ............................................................................................... 65
Watchdog Timer .................................................................................................... 66
SMBus Access ....................................................................................................... 67

4Regulatory Notices
Regulatory Notices
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 radiates radio frequency energy, and, if not installed and
used in accordance with the instructions, 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 off and on, the
user is encouraged to try to correct the interference by one or more of the following
measures:
∙Reorient or relocate the receiving antenna.
∙Increase the separation between the equipment and receiver.
∙Connect the equipment into an outlet on a circuit different from that to which the
receiver is connected.
NOTE
∙The changes or modifications not expressly approved by the party responsible for
compliance could void the user’s authority to operate the equipment.
∙Shield interface cables and AC power cord, if any, must be used in order to comply
with the emission limits.
FCC Conditions
This device complies with part 15 of the FCC Rules. Operation is subject to the
following two conditions:
∙This device may not cause harmful interference.
∙This device must accept any interference received, including interference that may
cause undesired operation.
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.
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.

5
Regulatory Notices
Battery Information
Please take special precautions if this product comes with a battery.
∙Danger of explosion if battery is incorrectly replaced. Replace only with the same or
equivalent type recommended by the manufacturer.
∙Avoid disposal of a battery into fire or a hot oven, or mechanically crushing or
cutting of a battery, which can result in an explosion.
∙Avoid leaving a battery in an extremely high temperature or extremely low air
pressure environment that can result in an explosion or the leakage of flammable
liquid or gas.
∙Do not ingest battery. If the coin/button cell battery is swallowed, it can cause
severe internal burns and can lead to death. Keep new and used batteries away
from children.
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.
BSMI:
廢電池請回收
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/
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://csr.msi.com/global/index
Environmental Policy
∙The product has been designed to enable proper reuse of parts and
recycling and should not be thrown away at its end of life.
∙Users should contact the local authorized point of collection for recycling
and disposing of their end-of-life products.
∙Visit the MSI website and locate a nearby distributor for further recycling
information.
∙Users may also reach us at [email protected] for information regarding proper
Disposal, Take-back, Recycling, and Disassembly of MSI products.

6Regulatory Notices
Green Product Features
∙Reduced energy consumption during use and stand-by
∙Limited use of substances harmful to the environment and health
∙Easily dismantled and recycled
∙Reduced use of natural resources by encouraging recycling
∙Extended product lifetime through easy upgrades
∙Reduced solid waste production through take-back policy
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.
The terms HDMI™, HDMI™ High-Definition Multimedia Interface, HDMI™ Trade dress
and the HDMI™ Logos are trademarks or registered trademarks of HDMI™ Licensing
Administrator, Inc.
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.

7
Safety Information
Safety Information
∙The components included in this package are prone to damage from electrostatic
discharge (ESD). Please adhere to the following instructions to ensure successful
computer assembly.
∙Ensure that all components are securely connected. Loose connections may cause
the computer to not recognize a component or fail to start.
∙Hold the motherboard by the edges to avoid touching sensitive components.
∙It is recommended to wear an electrostatic discharge (ESD) wrist strap when
handling the motherboard to prevent electrostatic damage. If an ESD wrist strap
is not available, discharge yourself of static electricity by touching another metal
object before handling the motherboard.
∙Store the motherboard in an electrostatic shielding container or on an anti-static
pad whenever the motherboard is not installed.
∙Before turning on the computer, ensure that there are no loose screws or metal
components on the motherboard or anywhere within the computer case.
∙Do not boot the computer before installation is completed. This could cause
permanent damage to the components as well as injury to the user.
∙If you need help during any installation step, please consult a certified computer
technician.
∙Always turn off the power supply and unplug the power cord from the power outlet
before installing or removing any computer component.
∙Keep this user guide for future reference.
∙Keep this motherboard away from humidity.
∙Make sure that your electrical outlet provides the same voltage as is indicated on
the PSU, before connecting the PSU to the electrical outlet.
∙Place the power cord such a way that people can not step on it. Do not place
anything over the power cord.
∙All cautions and warnings on the motherboard should be noted.
∙If any of the following situations arises, get the motherboard checked by service
personnel:
• Liquid has penetrated into the computer.
• The motherboard has been exposed to moisture.
• The motherboard does not work well or you can not get it work according to user
guide.
• The motherboard has been dropped and damaged.
• The motherboard has obvious sign of breakage.
∙Do not leave this motherboard in an environment above 60°C (140°F), it may damage
the motherboard.

Specifications
Model MS-98N1
Form factor Mini-ITX
Dimensions 170 x 170mm (6.7 x 6.7 inches)
Processor
∙PC Client SKUs
-Intel® Elkhart Lake J6412/ N6210 SoC
4.5W up to 12W (Burst)
∙Embedded SKUs
-Intel® Atom® x6211E Processor
4.5W up to 12W (Burst)
Chipset Within processor
Memory
∙2 x DDR4 SO-DIMM slots (260-pin, horizontal)
-Dual Channel for DDR4, Non-ECC
-Up to 3200 MT/s
-Up to 32 GB
Network ∙2 x Intel® I225V PCIe 2.5 GbE LAN (for PC client SKUs)
∙2 x Intel® I225-IT PCIe 2.5 GbE LAN (for embedded SKUs)
Storage
∙1 x SATA 3.0 6Gb/s port
∙1 x M.2 M Key slot (2242)
-SATA 3.0
Expansion
Slots
∙1 x M.2 B Key slot (2242/ 3042)
-With PCIe x1, USB3.2 Gen 1 & USB 2.0 signal
-Support Nano SIM holder
-Support 5G modules
∙1 x M.2 E Key slot (2230)
-With PCIe x1 & USB 2.0 signal
∙1 x Nano SIM Holder
-Supported by M.2 B key (SIM) slot
Graphics
∙1 x LVDS up to 1920x1200 @60Hz (Co-lay eDP)
∙1 x eDP up to 4096×2160 @60 Hz (Co-lay LVDS)
∙1 x DP 1.4a up to 4096×2160 @60Hz
(Co-lay VGA, option by SKU)
∙1 x HDMI™ 1.4b up to 4096x2160 @24Hz
∙3 independent display modes supported
-LVDS or eDP
-HDMI™
-DP/ VGA
Continued on next column
8Specifications

Model MS-98N1
Audio
∙Realtek® ALC897 High Definition Audio Codec
-Co-lay ALC888S-VD2
∙3 x Connectors for audio
-1 x Line-out Jack (Rear I/O)
-2 x 5-pin headers for front audio (Headphone & Mic-in)
Rear Panel I/O
∙1 x VGA port
∙1 x DisplayPort (default, VGA by SKU option)
∙1 x HDMI™ connector
∙3 x USB 3.2 Gen 1 Type-A ports (5 Gbps)
∙1 x USB 2.0 Type-A ports (480 Mbps)
∙2 x 2.5 GbE RJ-45 LAN ports
∙1 x Line-out jack
Onboard I/O
∙1 x SATA power connector
∙1 x LVDS Inverter box header
∙1 x LVDS + eDP Wafer Connector
∙1 x System fan box header
∙1 x PS/2® keyboard & mouse box header
∙1 x Front panel connector
∙1 x SPI TPM module header
∙1 x Front audio header
∙1 x Audio amplifier header
∙1 x GPIO (DIO) connector
∙1 x COM port box header
∙2 x USB 2.0 box headers
∙1 x CMOS battery header
∙2 x COM power jumpers
∙1 x Clear CMOS jumper
∙1 x ME jumper
∙1 x AT/ ATX mode select jumper
∙1 x SMBus power jumper (for JSMB1)
∙1 x Clear RTC battery jumper
∙1 x LVDS power jumper
∙1 x Chassis Intrusion jumper
Power 12V/ 19V/ 24V DC-in
Continued on next column
9
Specifications

Model MS-98N1
Environment
∙Operating Temperature
-PC Client SKUs: 0 ~ 60°C with 0.7m/s air flow
-Embedded SKUs: -20 ~ 70°C with 0.7m/s air flow
∙Storage Temperature: -20 ~ 80°C
∙Humidity: 10 ~ 90%, non-condensing
10 Specifications

Motherboard Overview
JUSB1
JCOM2
JCOM1
JCOM3
JCOM4
JCOM5
JUSB2
JGPIO1
VGA + HDMI SKU
JME_DIS1
JCASE1
JCOMP2
JATX1
JSMBP1
JCOMP1
M2_M1
JFP1
JKBMS1
JSBM1
JCOM6
JSATA1
JAMP1
JAUD1
Rear I/O Panel
JUSIM1
JRTC1
M2_E1 M2_B1
JTPM1 DIMM2
DIMM1
JINV1
SYSFAN1
JCOMS1
JLVDS1
JVDD1
JBAT1
JPWR1
(Optional)
1
4
1
2
4
5
6
2
3
5
6
3
DP + HDMI SKU
JSATA_PWR1
11
Motherboard Overview

Rear I/O Panel
VGA + HDMI SKU
DP + HDMI SKU
RJ-45
LAN Jacks
DisplayPort
Power
Jack
Line-Out
Jack
USB
3.2 Gen 1 Ports
USB 2.0 Port
VGA Port USB 2.0 Port
Power Jack
Power supplied through this jack supplies power to your system.
DisplayPort
DisplayPort is a digital display interface standard. This connector is used to connect a
monitor with DisplayPort inputs.
Connector
The High-Definition 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-definition video, plus multi-channel
digital audio on a single cable.
VGA Port
The DB15-pin female connector is provided for monitors.
12 Rear I/O Panel

RJ-45 LAN Jack
The standard single RJ45 LAN jack is provided for connection to the Local Area
Network (LAN). You can connect a network cable to it.
Link/ Activity LED
Status Description
Off No link
Yellow Linked
Blinking Data activity
Speed LED
Status Description
Off 10/100 Mbps
Green 1000 Mbps
Orange 2.5 Gbps
USB 3.2 Gen 1 Port
This connector is provided for USB peripheral devices. (Speed up to 5 Gbps)
USB 2.0 Port
This connector is provided for USB peripheral devices. (Speed up to 480 Mbps)
⚠
Important
High-speed devices are recommended for USB 3.2 ports whereas low-speed devices,
such as mouse or keyboard, are suggested to be plugged into the USB 2.0 ports.
Line-Out Jack
This connector is provided for headphones or speakers.
13
Rear I/O Panel

ME Overview
Board Dimension
DP + HDMI SKU
14,45 18,50 18,95 17,00 18,05 29,18 25,32 1,15
170,00
132,08
157,48
170,00
Unit of measurement: mm
14 ME Overview

Unit of measurement: mm
15
ME Overview
VGA + HDMI SKU
14,45 18,50 18,9517,00 18,05 29,43 25,07 1,15
170,00
132,08
157,48
170,00

Suggested Chassis I/O Gap Dimension
Chassis
PCB
Gap: 1.5mm (min)
16 ME Overview

Component Contents
Component Page
Memory 18
DIMM1~2: DDR4 SO DIMM Slots 18
Storage 19
JSATA1: SATA 3.0 6Gb/s Port 19
M2_M1: M.2 Slot (M Key, 2242) 20
Installing M.2 SSD 20
Expansion Slots 21
JUSIM1: Nano SIM Holder 21
M2_E1: M.2 Slot (E Key, 2230) 22
M2_B1: M.2 Slot (B Key, 2242/ 3042) 22
Connectors 23
Power Connectors 23
JPWR1: DC-In Power Connector (Optional) 23
JSATA_PWR1: SATA Power Connector 23
Graphics Connectors 24
JINV1: LVDS Inverter Box Header 24
JLVDS1: LVDS+eDP Wafer Connector 25
Other Connectors 28
SYSFAN1: System Fan Box Header 28
JKBMS1: PS/2® Keyboard & Mouse Box Header 28
JFP1: Front Panel Connector 29
JTPM1: SPI TPM Module Header 29
JAUD1: Front Audio Header 30
JAMP1: Audio Amplifier Header 30
JGPIO1: GPIO (DIO) Box Header 30
JCOM1~6: COM Port Box Headers 31
JUSB1~2: USB 2.0 Box Headers 33
JSMB1: SMBus Box Header 33
JBAT1: CMOS Battery Header 34
Replacing CMOS battery 34
Jumpers 35
17
Component Contents

Memory
DIMM1~2: DDR4 SO DIMM Slots
The SO-DIMM slots is intended for memory modules.
Installing SO DIMM Slot
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, flip the slot levers outwards and the DIMM will be
released instantly.
⚠
Important
∙ Always insert memory modules in the DIMM1 slot first.
∙ You can barely see the golden finger if the DIMM is properly inserted in the DIMM slot.
∙ To ensure system stability for Dual channel mode, memory modules must be of the
same type, number and density.
DIMM1
DIMM2
18 Memory

Storage
JSATA1: SATA 3.0 6Gb/s Port
This connector is SATA 6Gb/s interface port, it can connect to one SATA device.
JSATA1
⚠
Important
∙ This SATA port supports hot plug.
∙ Please do not fold the SATA cable at a 90-degree angle. Data loss may result during
transmission otherwise.
∙ SATA cables have identical plugs on either sides of the cable. However, it is
recommended that the flat connector be connected to the motherboard for space
saving purposes.
JSATA1
19
Storage

M2_M1: M.2 Slot (M Key, 2242)
Please install the M.2 solid-state drive (SSD) into the M.2 slot as shown below.
M2_M1
Installing M.2 SSD
2. Secure the M.2 SSD in
place with the supplied
M.2 screw.
1. Insert your M.2 SSD
into the M.2 slot at a
30-degree angle.
30°
Supplied M.2 screw
Feature
Supports SATA 3.0 signal.
⚽
Video Demonstration
Watch the video to learn how to
Install M.2 SSD.
20 Storage