MSI MS-98K9 User manual

i
MS-98K9
(v1.x) Industrial Computer Board

ii iii
Preface MS-98K9
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
V1.2 2020/09
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-98K9
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-98K9
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-98K9
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-98K9
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
CPU (Central Processing Unit) ..................................................................2-3
Memory ......................................................................................................2-6
Power Supply.............................................................................................2-8
Rear Panel I/O ...........................................................................................2-9
Connector................................................................................................. 2-11
Jumper .....................................................................................................2-18
Slot...........................................................................................................2-20
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 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-98K9, an excellent industrial computer
board.
Based on the innovative Intel®Co󰀨ee Lake-S Processor, the MS-98K9 is
engineered to provide reliable performance for a wide variety of industrial
applications.
1Overview

1-2
Overview MS-98K9
Specications
Processor
■8th Gen Intel® Co󰀨ee Lake-S Xeon®, Core™ i7/i5/i3, Pentium®, Celeron®
Processor, Max 95W
PCH
■Intel® C246/Q370 Express
Memory
■Dual Channel DDR4, up to 2666MHz
■4* UDIMM slots, up to 128GB
■C246 SKU: ECC, Non ECC supported
■Q370 SKU: Non ECC supported
Network
■LAN1: Intel® I219LM GbE LAN PHY (Supports iAMT 12.0)
■LAN2: Intel® I210-AT GbE LAN (Co-lay I211-AT)
■LAN3: Intel® I210-AT GbE LAN (Co-lay I211-AT, SKU1 & SKU2)
Storage
■6* SATA 6Gb/s ports
-SATA signal of SATA6 port shared with M.2 Key M slot
-RAID 0, 1, 5, 10 supported
-AHCI Mode supported
■1 * M.2 Key M 2242/2260/2280 slot for SSD
-With PCIe x4 & SATA signal
-SATA signal shared with SATA6 port
Audio
■Realtek® ALC887 High Denition Audio codec (Co-lay ALC888S)
■1 * Line-In jack
■1 * Line-Out jack
■1 * Mic-In jack
■1 * Front audio box header
■1 * S/PDIF box header

1-3
Overview MS-98K9
Graphics
■Integrated Intel® HD Graphics (DirectX12 supported)
■1 * VGA (SKU1, SKU2)
-Max resolution 1920 x 1200 @60Hz
■1 * HDMI 1.4
-Max resolution 4096 x 2160 @24Hz
■2 * DisplayPort 1.2
-Max resolution 4096 x 2304 @60Hz
■3 independent displays
-DP1+DP2+HDMI
-DP1+DP2+VGA
-DP1+HDMI+VGA
-DP2+HDMI+VGA
Expansion Slots
■3 * PCIe x16 slots (PCIE1, PCIE2, PCIE3)
Jumper
Setting
Slot
J_PCIECFG1
1 x8 PCIe
2 x4 PCIe
1
2
5
6
2 x8 PCIe
1
2
5
6
1 x16 PCIe
1
2
5
6
PCIE1 PCIe x8 Gen3 PCIe x8 Gen3 PCIe x16 Gen3
PCIE2 PCIe x4 Gen3 PCIe x8 Gen3 No Signal
PCIE3 PCIe x4 Gen3 No Signal No Signal
■2 * PCIe x1 slots (PCIE4, PCIE6)
■2 * PCIe x16 slots with PCIe x4 signal (PCIE5, PCIE7)
■1 * M.2 Key E 2230 slot for Wi-Fi/Bluetooth modules
-With PCIe x1 and USB 2.0 signal
Rear Panel I/O
SKU1, SKU2 SKU3
■1 * Mouse/Keyboard combo port
■1 * D-Sub VGA port
■1 * HDMI port
■2 * DisplayPorts
■3 * GbE RJ45 ports
■2 * USB 2.0 ports
■6 * USB 3.1 Gen 2 ports
■1 * Line-In jack
■1 * Line-Out jack
■1 * Mic-In jack
■1 * Mouse/Keyboard combo port
■1 * HDMI port
■2 * DisplayPorts
■2 * GbE RJ45 ports
■2 * USB 2.0 ports
■4 * USB 3.1 Gen 2 ports
■1 * Line-In jack
■1 * Line-Out jack
■1 * Mic-In jack

1-4
Overview MS-98K9
Internal I/O
■1 * System power connector
■1 * CPU power connector
■1 * CPU fan header
■3 * System fan headers
■6 * SATA 6Gb/s ports
■1 * Vertical USB 2.0 port
■2 * USB 2.0 box headers (4 ports)
■1 * Front panel box header
■1 * TPM box header
■2 * GPIO box headers
■1 * Chassis intrusion header
■1 * Parallel port box header
■2 * 10-pin RS232/422/485 serial port box headers
■2 * 40-pin RS232 serial port headers (SKU1, SKU2)
■1 * 40-pin RS232 serial port header (SKU3)
■1 * Front audio box header
■1 * S/PDIF box header
■1 * SMBus box header
■1 * I2C box header
■1 * Clear CMOS jumper
■1 * AT/ATX jumper
■2 * NVM LAN jumpers (SKU1, SKU2)
■1 * NVM LAN jumper (SKU3)
■1 * PCIe option jumper
■2 * 6-pin COM port jumpers
■2 * 3-pin COM port jumpers (SKU1, SKU2)
■1 * 3-pin COM port jumper (SKU3)
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
Important
The product doesn’t support ErP standard (S5 Power consumption under 1W).
Accessories
■2 * SATA3.0 cables
■1 * Dual COM port cable with bracket
■1 * Dual USB 2.0 cable with bracket
■1 * Parallel port cable with bracket
■1 * Driver & user manual CD
■1 * I/O shield

1-5
Overview MS-98K9
SKU Comparison
SKUs
Features SKU1 SKU2 SKU3
PCH Intel® C246 Intel® Q370
Network
LAN1 Intel® I219LM
LAN2 Intel® I210-AT Intel® I210-AT
LAN3 Intel® I210-AT
USB3.1 Gen2 6 * USB3.1 Gen2 4 * USB3.1 Gen2
COM 2 * RS232/422/485
8 * RS232
2 * RS232/422/485
4 * RS232
Onboard TPM 2.0 Yes
VGA Yes

1-6
Overview MS-98K9
Layout
Rear Panel
S/PDIF Box
Header
System Fan Header
Clear CMOS
Jumper
AT/ATX
Jumper
DIMM Slots
SATA
Ports
CPU Fan
Header
System Fan
Header
SMBus
Box Header
NVM LAN
Jumpers
CPU Power
Connector
System
Power
Connector
PCIe Slots
M.2 Key E
Slot
USB 2.0 Port
Front Panel
Box Header
TPM Box
Header
System Fan
Header
USB 2.0 Box
Headers
GPIO Box
Headers
Parallel
Port Box
Header
COM Port Headers/ Box
Headers/ Jumpers
Front Audio
Box Header
M.2 Key M
Slot
Chassis
Intrusion
Header
PCIe Option Jumper
I2C Box
Header

1-7
Overview MS-98K9
Rear Panel I/O Options
SKU1, SKU2
D-Sub Port
GbE
RJ45
Ports
USB 3.1
Gen 2
Ports
Line-In
Mic-In
Mouse/Keyboard
Combo Port
USB 2.0
Ports
DisplayPorts Line-Out HDMI Port
GbE
RJ45
Ports
USB 3.1
Gen 2
Ports
GbE
RJ45
Ports
USB 3.1
Gen 2
Ports
SKU3
GbE
RJ45
Ports
USB 3.1
Gen 2
Ports
Line-In
Mic-In
Mouse/Keyboard
Combo Port
USB 2.0
Ports
DisplayPorts Line-Out HDMI Port
GbE
RJ45
Ports
USB 3.1
Gen 2
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
Quick Component Guide
CPU (Central Processing Unit)........................................................2-3
Memory..............................................................................................2-6
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: JIIC1 .............................................................................. 2-11
GPI Box Header: JGPIO1 ........................................................................2-12
GPO Box Header: JGPIO2 ......................................................................2-12
Dual Stacked SATA Connector: SATA1_2, SATA3_4, SATA5_6..............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: JSPDI1 ...................................................................2-15
Parallel Port Box Header: JPARA1 ..........................................................2-15
RS232/422/485 COM Port Box Header: JCOM1, JCOM2.......................2-16
RS232 COM Port Header: JCOM3 (COM3~COM6 )...............................2-17
RS232 COM Port Header: JCOM4 (COM7~COM10 for SKU1, SKU2)...2-17
Jumper.............................................................................................2-18
Clear CMOS Jumper: JCMOS1 ...............................................................2-18
AT/ATX Jumper: JAT1..............................................................................2-18
PCIe Option Jumper: J_PCIECFG1.........................................................2-18
NVM LAN Jumper: JNVM2 ......................................................................2-19
NVM LAN Jumper: JNVM3 (SKU1, SKU2) ..............................................2-19
JCOM1~JCOM2 Jumper: JCOMP1, JCOMP2 ........................................2-19
JCOM3 Jumper: JCOMP3 .......................................................................2-19
JCOM4 Jumper: JCOMP4 (SKU1, SKU2) ...............................................2-19
Slot...................................................................................................2-20
PCIe (Peripheral Component Interconnect Express) Slot........................2-20
M2_M1: M.2 Key M 2242/2260/2280 Slot for SSD ..................................2-20
M2_E1: M.2 Key E 2230 Slot for WiFi/BT................................................2-21

2-3
MS-98K9
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-98K9
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.