MSI MS-98N9 User manual

i
MS-98N9 V1.0
Industrial Computer Board

ii
Preface MS-98N9 V1.0
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 2021/05
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-98N9 V1.0
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-98N9 V1.0
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-98N9 V1.0
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
Preface MS-98N9 V1.0
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 - W480E SKU.................................................................................1-7
Layout - Q470E SKU..................................................................................1-8
2 Hardware Setup ...........................................................................2-1
CPU (Central Processing Unit) ..................................................................2-3
Memory ......................................................................................................2-6
Power Supply.............................................................................................2-8
Rear Panel I/O ...........................................................................................2-9
Connector.................................................................................................2-12
Jumper .....................................................................................................2-20
Slot...........................................................................................................2-21
3 BIOS Setup...................................................................................3-1
Entering Setup ...........................................................................................3-2
The Menu Bar ............................................................................................3-4
Main ...........................................................................................................3-5
Advanced ...................................................................................................3-6
Boot..........................................................................................................3-14
Security ....................................................................................................3-15
Chipset .....................................................................................................3-22
Power.......................................................................................................3-23
Save & Exit...............................................................................................3-25
Appendix GPIO WDT Programming............................................... A-1
Abstract..................................................................................................... A-2
General Purposed IO ................................................................................ A-3
Watchdog Timer ........................................................................................ A-4
SMBus Access .......................................................................................... A-5

1-1-1
Thank you for choosing the MS-98N9 V1.0, an excellent industrial
computer board.
Based on the innovative 10th Gen Intel® Comet Lake Processor, the
MS-98N9 V1.0 is engineered to provide reliable performance for a wide
variety of industrial applications.
1Overview

1-2
Overview MS-98N9 V1.0
Specications
Processor
■10th Gen Intel® Comet Lake Processors
■W480E SKU:
• Intel®Xeon® Series
-Xeon W-1290E(95W)/W-1290TE(35W)
-Xeon W-1270E(80W)/W-1290TE(35W)
-Xeon W-1250E(80W)/W-1250TE(35W)
• Intel® Core™ Series
-Core i9-10900K (125W)
-Core i9-10900E (65W)/i9-10900TE (35W)
-Core i7-10700E (65W)/i7-10700TE (35W)
-Core i5-10500E (65W)/i5-10500TE (35W)
-Core i3-10100E (65W)/i3-10100TE (35W)
• Intel® Pentium® Series
-G6400E (58W)/G6400TE (35W)
• Intel® Celeron® Series
-G5900E (58W)/G5900TE (35W)
■Q470E SKU:
• Intel® Core™ Series
-Core i9-10900K (125W)
-Core i9-10900E (65W)/i9-10900TE (35W)
-Core i7-10700E (65W)/i7-10700TE (35W)
-Core i5-10500E (65W)/i5-10500TE (35W)
-Core i3-10100E (65W)/i3-10100TE (35W)
• Intel® Pentium® Series
-G6400E (58W)/G6400TE (35W)
• Intel® Celeron® Series
-G5900E (58W)/G5900TE (35W)
PCH
■W480E SKU: Intel® W480E Express Chipset
■Q470E SKU: Intel® Q470E Express Chipset

1-3
Overview MS-98N9 V1.0
Memory
■Dual Channel DDR4 Memory Running at 2933/2666/2400 MHz
■4 * UDIMM slots, up to 128GB
■Q470E SKU: Non-ECC Supported;
■W480E SKU: ECC/Non ECC supported, ECC single-bit supported only
■Memory Speed (Depends on CPU):
• Intel®Xeon® Series
-Xeon W-1290E(95W)/W-1290TE(35W): Up to 2933 MT/s
-Xeon W-1270E(80W)/W-1290TE(35W): Up to 2933 MT/s
-Xeon W-1250E(80W)/W-1250TE(35W): Up to 2933 MT/s
• Intel® Core™ Series
-Core i9-10900K (125W): Up to 2933 MT/s
-Core i9-10900E (65W)/i9-10900TE (35W): Up to 2933 MT/s
-Core i7-10700E (65W)/i7-10700TE (35W): Up to 2933 MT/s
-Core i5-10500E (65W)/i5-10500TE (35W): Up to 2666 MT/s
-Core i3-10100E (65W)/i3-10100TE (35W): Up to 2666 MT/s
• Intel® Pentium® Series
-G6400E (58W)/G6400TE (35W): Up to 2400 MT/s
• Intel® Celeron® Series
-G5900E (58W)/G5900TE (35W): Up to 2400 MT/s
Network
■LAN1: Intel® I219LM GbE LAN PHY (Supports iAMT 14.0)
■LAN2: Intel® I210-AT GbE LAN
■LAN3: Intel® I210-AT GbE LAN (for W480E SKU only)
■LAN4: Intel® I210-AT GbE LAN (for W480E SKU only)
Storage
■Intel W480E/Q470E Express Chipset
■4 * SATA 6Gb/s ports
• RAID 0, 1, 5, 10 supported
• AHCI Mode supported
■3 * M.2 slots
• M2_M1: 2242/2260/2280
-With PCIe x4/x2/x1 Signal: PCIe Signal Shared by PCIe Slot1
-Supports PCIe x4 NVMe SSD
-Supports B+M Key Module
• M2_M2: 2242/2260/2280
-With PCIe x4/x2/x1 Signal: PCIe x4 Signal Shared by PCIe Slot3
-Supports PCIe x4 NVMe SSD
-Supports B+M Key Module
• M2_M3: 2242/2260/2280/22110
• With PCIe x4/x2/x1 Signal: PCIe x4 Signal Shared by PCIe Slot5
• Supports PCIe x4 NVMe SSD
• Supports B+M Key Module

1-4
Overview MS-98N9 V1.0
Audio
■Realtek® ALC888S/ ALC897 High Denition Audio codec
■1 * Line-Out jack
■1 * Mic-In jack
■1 * Front audio box header
■1 * S/PDIF box header
Graphics
■Integrated Intel® HD Graphics (DirectX12 supported)
■1 * HDMI 1.4b
• Max Resolution 4096 x 2160 @30Hz
■1 * Display Port 1.4 (DP++ Support)
• Max Resolution 4096 x 2304 @60Hz
■1 * VGA
• Max resolution 1920 x 1200 @60Hz
■1 * eDP 1.4
• Max resolution 4096x2304 @ 60Hz
Expansion Slots
■2 * PCIe x16 slots
• Each slot supports Max. 75W
• Support Signal Matrix Listed:
-If “PCIe x16 Slot CFG Jumper” is 1-2 pin shorted, PCIE2 slot is PCIe
x16 Gen3, PCIE4 slot is no signal.
-If “PCIe x16 Slot CFG Jumper” is 2-3 pin shorted, PCIE2 & PCIE4 slots
are PCIe x8 Gen3.
■3 * PCIe x4 slots
• Support Multiple PCIe Gen3 & NVMe SSD
• PCIE1 slot supports Thunderbolt™ 3 (By request)
• Each slot supports Max. 25W
■2 * PCI slots
• Support 3.3V/5V (IOPWR)
■1 * Mini-PCIe slot
• Supports Full-size/Half-size, with PCIe x1 & USB 2.0 Signal
COM Ports
■COM1~2
• Support RS-232/422/485 with Ring/0V/5V/12V Auto-ow Control (Default
set to Ring)
■COM3~6
• Support RS-232/422/485 with 0V/5V/12V Auto-ow Control
■COM7~10 (for W480E SKU only)
• Support RS-232, 0V/5V/12V (Default set to 5V)

1-5
Overview MS-98N9 V1.0
USB Ports
■Intel W480E/Q470E Express Chipset
■6 * USB 3.2 Gen 2 ports (6 x Rear)
■2 * USB 3.2 Gen 1 ports (2 x Internal)
■5 * USB 2.0 ports (2 x Rear, 3 x Internal with one Vertical Type-A Connector)
Rear Panel I/O
■1 * HDMI port
■1 * DisplayPort
■1 * COM port
■1 * D-SUB (VGA) port
■4 * RJ45 LAN ports (W480E SKU), 2 * RJ45 LAN ports (Q470E SKU)
■6 * USB 3.2 Gen 2 ports
■2 * USB 2.0 ports
■1 * Line-Out jack
■1 * Mic-In jack
Internal I/O
■1 * eDP connector
■1 * eDP Power Select jumper
■1 * USB 3.2 Gen1 header (supports two USB 3.2 Gen1 ports)
■1 * USB 2.0 header (supports two USB 2.0 ports)
■1 * USB 2.0 vertical Type-A connector
■1 * Front LAN LED header for LAN1~LAN4 active LED
■1 * Parallel port header
■1 * AT/ATX jumper
■1 * Clear CMOS jumper
■5 * 2x5-pin serial port headers (COM2~6)
■1 * 2x20-pin serial port header (COM7~10)
■2 * 2x3-pin jumpers (Select Ring/0V/5V/12V for COM1~2)
■8 * 1x3-pin jumpers (Select 0V/5V/12V for COM3~10)
■2 * Digital I/O headers for 16-bit 8 x GPI & 8 x GPO
■1 * PMBus connector
■1 * SMBus connector
■1 * I2C connector
■1 * ME jumper for iAMT BIOS Flash
■1 * PCIe x16 slot CFG jumper (for select single PCIe x16 slot or 2 PCIe x8
slots)
■1 * S/PDIF header
■2 * Thunderbolt™ 3 Control connectors
■1 * Front audio header
■1 * Front panel header
■1 * CPU fan connector
■3 * System fan connectors
■1 * Chassis Intrusion header
■1 * LPC debug port header
■1 * SPI ash debug port header
■1 * PS/2 header

1-6
Overview MS-98N9 V1.0
Form Factor
■ATX Size: 305mm (L) x 244mm (W) x 1.6mm (H)
Environment
■Operating Temperature: -10 ~ 60oC
■Storage Temperature: -20 ~ 80oC
■Humidity: 10 ~ 90% RH, non-condensing
Accessories
■2 * SATA3.0 cables
■1 * Dual USB 2.0 cable with bracket
■1 * I/O shield
Certication
■CE, FCC Class B, BSMI, RCM, VCCI
OS Support
■Windows 10 Enterprise 2019 SAC (RS5) 64bits
■Linux Kernel 5.4
■Noted : All driver base on Intel & chip vendor supported

1-7
Overview MS-98N9 V1.0
Layout - W480E SKU
Rear Panel
S/PDIF
Header
PS/2
Header
PMBus Header
Clear CMOS
Jumper
AT/ATX
Jumper
DIMM Slots
SATA
Ports
M.2 Slots
Mini-PCIe
Slot
CPU Fan
Connector
System Fan
Connector
eDP
Connector
eDP Power
Select Jumper
System Fan
Connector
SMBus
Box Header
CPU Power
Connector
System
Power
Connector
PCIe Slots
PCI Slots
Front Panel
Header
LPC Debug
Port Header
ME Jumper
SPI Header
Front LAN
LED Header
System Fan
Connector
Program BIOS
debug Jumper
USB 2.0
Headers
USB 3.2 Gen1
Header
USB 2.0 Vertical
Type-A Connector
GPI
Header
GPO
Header
Parallel
Port Header
COM Port Box Headers &
Power Jumpers
Front Audio
Header
Chassis
Intrusion
Header
PCIe Congure
Jumper
I2C Box
Header
COM1 Power
Jumper
D-SUB (VGA)
GbE
RJ45
LAN
GbE
RJ45
LAN
GbE
RJ45
LAN
GbE
RJ45
LAN
USB 3.2
Gen 2
USB 3.2
Gen 2
USB 3.2
Gen 2
USB 2.0
DisplayPort Line-Out
Mic-InHDMI
COM1

Layout - Q470E SKU
Rear Panel
S/PDIF
Header
PS/2
Header
PMBus Header
Clear CMOS
Jumper
AT/ATX
Jumper
DIMM Slots
SATA
Ports
M.2 Slots
Mini-PCIe
Slot
CPU Fan
Connector
System Fan
Connector
eDP
Connector
eDP Power
Select Jumper
System Fan
Connector
SMBus
Box Header
CPU Power
Connector
System
Power
Connector
PCIe Slots
PCI Slots
Front Panel
Header
ME Jumper
LPC Debug
Port Header
SPI Header
Front LAN
LED Header
System Fan
Connector
Program BIOS
debug Jumper
USB 2.0
Headers
USB 3.2 Gen1
Header
USB 2.0 Vertical
Type-A Connector
GPIO1
Header
GPIO2
Header
Parallel
Port Header
COM Port Box Headers &
Power Jumpers
Front Audio
Header
Chassis
Intrusion
Header
PCIe Congure
Jumper
I2C Box
Header
COM1 Power
Jumper
D-SUB (VGA)
GbE
RJ45
LAN
GbE
RJ45
LAN
USB 3.2
Gen 2
USB 3.2
Gen 2
USB 3.2
Gen 2
USB 2.0
DisplayPort Line-Out
Mic-InHDMI
COM1

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
Quick Component Guide
CPU (Central Processing Unit)........................................................2-3
Introduction to LGA 115x CPU ...................................................................2-3
CPU Installation .........................................................................................2-4
Memory..............................................................................................2-6
Dual-Channel Mode ...................................................................................2-6
Recommended Memory Population...........................................................2-6
Installing Memory Modules ........................................................................2-7
Power Supply....................................................................................2-8
System Power Connector: JPWR1 ............................................................2-8
CPU Power Connector: JPWR2.................................................................2-8
Rear Panel I/O ...................................................................................2-9
Connector........................................................................................2-11
CPU/System Fan Header: CPUFAN1, SYSFAN1~3................................ 2-11
SMBus Box Header: JSMB1.................................................................... 2-11
I2C Box Header: JI2C1 ............................................................................. 2-11
GPI Box Header: JGPIO1 ........................................................................2-12
GPO Box Header: JGPIO2 ......................................................................2-12
Dual Stacked SATA Connector: SATA1_2, SATA3_4...............................2-12
USB 2.0 Box Header: JUSB1, JUSB2, ...................................................2-13
USB 2.0 Port: USB1.................................................................................2-13
Front Panel Box Header: JFP1 ................................................................2-13
Chassis Intrusion Header: JCASE1 .........................................................2-14
TPM Box Header: JTPM1 ........................................................................2-14
Front Audio Box Header: JAUD1 .............................................................2-15
S/PDIF Box Header: JSPDIF1 .................................................................2-15
Parallel Port Box Header: JLPT1 .............................................................2-15
RS232/422/485 COM Port Box Header: JCOM1, JCOM2.......................2-16
RS232 COM Port Box Header: JCOM3, JCOM4, JCOM5, JCOM6 ........2-16
Jumper.............................................................................................2-18
Slot...................................................................................................2-19
PCIe (Peripheral Component Interconnect Express) Slot........................2-19
PCI (Peripheral Component Interconnect) Slot........................................2-19
M2_M1: M.2 Key M 2242/2260/2280 Slot for SSD ..................................2-19

2-3
MS-98N9 V1.0
CPU (Central Processing Unit)
When installing the CPU, make sure that you install the cooler to prevent
overheating. If you do not have the CPU cooler, consult your dealer before
turning on the computer.
Important
Overheating
Overheating will seriously damage the CPU and system. Always make sure the
cooling fan can work properly to protect the CPU from overheating. Make sure
that you apply an even layer of thermal paste (or thermal tape) between the CPU
and the heatsink to enhance heat dissipation.
Replacing the CPU
While replacing the CPU, always turn o the power supply or unplug the power
supply’s power cord from the grounded outlet rst to ensure the safety of CPU.
Introduction to LGA 115x CPU
The surface of LGA 115x CPU. Remember to apply some thermal paste on it for
better heat dispersion.
Alignment Key
Yellow triangle is the
Pin 1 indicator
Alignment Key

2-4
Hardware Setup
CPU Installation
When you are installing the CPU, make sure the CPU has a cooler attached on
the top to prevent overheating. Meanwhile, do not forget to apply some thermal
paste on CPU before installing the heat sink/cooler fan for better heat dispersion.
1. Open the load lever and remove the
plastic cap.
2. Lift the load lever up to fully open
position.
3. After con󰘰rming the CPU direction for
correct mating, put down the CPU in
the socket housing frame. Be sure to
grasp on the edge of the CPU base.
Note that the alignment keys are
matched.
4. Engage the load lever while pressing
down lightly onto the load plate.
Alignment Key
Important
Visually inspect if the CPU is seated well into the socket. If not, take out the CPU with
pure vertical motion and reinstall.

2-5
MS-98N9 V1.0
5. Secure the load lever with the hook
under the retention tab.
6. Make sure the four hooks are in proper
position before you install the cooler.
Align the holes on the motherboard
with the cooler. Push down the cooler
until its four clips get wedged into the
holes of the motherboard.
7. Press the four hooks down to fasten
the cooler. Turn over the motherboard
to con󰘰rm that the clip-ends are
correctly inserted.
8. Finally, attach the CPU Fan cable
to the CPU fan connector on the
motherboard.
Important
• Conrm if your CPU cooler is rmly installed before turning on your system.
• Do not touch the CPU socket pins to avoid damage.
• Whenever CPU is not installed, always protect your CPU socket pins with the plastic
cap covered.
• Please refer to the documentation in the CPU cooler package for more details about
the CPU cooler installation.
• Read the CPU status in BIOS.

2-6
Hardware Setup
Memory
Dual-Channel Mode
In Dual-Channel mode, make sure that you install memory modules of the same
type and density in di󰀨erent channel DIMM slots.
DIMMA1 DIMMB1
Channel A Channel B
DIMMA2 DIMMB2
Recommended Memory Population
DIMMB2 DIMMB2
DIMMB1
DIMMA2 DIMMA2 DIMMA2
DIMMA1
Important
• Always insert memory modules in the DIMMA2 slot rst.
• Due to chipset resource allocation, the available capacity of memory will be a
little less than the amount installed.
• Please note that the maximum capacity of addressable memory is 4GB or less
for 32-bit Windows OS due to the memory address limitation. Therefore, we
recommend that you install 64-bit Windows OS if you want to install more than
4GB memory on the motherboard.
• Paired memory installation for Max performance.
• Populate the same DIMM type in each channel, specically: 1. Use the same
DIMM size; 2. Use the same number of ranks per DIMM.