MSI MS-98M9 User manual

i
MS-98M9
(v1.x) Industrial Computer Board

ii
Preface MS-98M9
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 2020/01
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-98M9
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-98M9
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-98M9
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-98M9
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
2 Hardware Setup ...........................................................................2-1
CPU Installation .........................................................................................2-3
Memory ......................................................................................................2-6
Power Supply.............................................................................................2-8
Rear Panel I/O ...........................................................................................2-9
Connector................................................................................................. 2-11
Jumper .....................................................................................................2-17
Slot...........................................................................................................2-18
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
Power .......................................................................................................3-21
Save & Exit...............................................................................................3-23
ME Conguration .....................................................................................3-24
Appendix GPIO WDT Programming............................................... A-1
Abstract..................................................................................................... A-2
General Purposed IO ................................................................................ A-3
Watchdog Timer ........................................................................................ A-5
SMBus Access .......................................................................................... A-6
Appendix How to rename the network adapter ............................ B-1

1-1-1
Thank you for choosing the MS-98M9, an excellent industrial computer
board.
Based on the innovative Intel®Skylake-SP & Cascade Lake-SP
Processor, the MS-98M9 is engineered to provide reliable performance
for a wide variety of industrial applications.
1Overview

1-2
Overview MS-98M9
Specications
Processor
■1st / 2nd Gen Intel® Skylake-SP & Cascade Lake-SP Xeon® Processor, Max
205W
PCH
■SKU1: Intel® C622 Express
■SKU2: Intel® C621 Express
Memory
■6 * 288-pin DDR4 RDIMMs
■DDR4 ECC RDIMMs memory up to 2666MHz
■Max 192GB
Network
■Full SKU
-LAN1 / LAN2: Intel® I210-AT GbE LAN
-LAN3 / LAN4: Intel® X557-AT2 10GbE LAN (10GBASE-T transmissions
requests thecable grade of Cat 6/Cat 6a or above)
■Basic SKU
-LAN1 / LAN2: Intel® I210-AT GbE LAN
Storage
■8* SATA 6Gb/s ports
-RAID 0, 1, 5, 10 supported
-AHCI Mode supported
■1 * mSATA Slot (Full-size/Half-size, Shared with Mini-PCIe)
Audio
■Realtek® ALC887 High Denition Audio codec (Co-lay ALC888S)

1-3
Overview MS-98M9
Expansion Slots
■2 * PCIe x 16 slots
-PCIE2, PCIE4 (Graphics Card Supported)
■3 * PCIe x 8 slots
-PCIE1
-PCIE3, PCIE5 (Graphics Card Supported)
■2 * PCIe x 4 slots
-PCIE6, PCIE7
■1 * Mini-PCIe Slot (Full-size/Half-size, Shared with mSATA)
Important
• PCIE1~5 with the latest Intel RSTe it provides a compelling RAID solution
for NVMe SSDs via Intel VROC HW key.
Rear Panel I/O
■2 * COM ports
■2 * 10GbE RJ45 ports (Full SKU)
■2 * GbE RJ45 ports
■6 * USB 3.2 Gen 1 ports (5V/0.9A)
■1 * Mouse/Keyboard combo port
Internal I/O
■1 * System power connector
■1 * CPU power connector
■8 * SATA 6Gb/s ports
■1 * Vertical USB 2.0 port
■3 * USB 2.0 box headers (6 ports)
■1 * VROC box header
■1 * TPM pin header
■4 * RS232 serial port box headers (COM3~COM6)
■6 * Serial port power jumpers
■1 * SMBus box header
■1 * PMBus box header
■1 * ME jumper
■2 * PCIe congure jumper
■1 * S/PDIF box header
■1 x 2*6-pin 2.54-pitch Pin-header for Audio (Line-in/Line-Out/Mic-in)
■1 * Front panel box header
■1 * Front audio box header
■1 * CPU fan header
■6 * System fan headers
■1 * Chassis intrusion header
■1 * AT/ATX jumper
■1 * Clear CMOS jumper
■1 * LAN LED header
■2 * GPIO box headers (8 x GPI, 8 x GPO; 5V)

1-4
Overview MS-98M9
Form Factor
■ATX Size: 305mm (L) x 244mm (W) x 1.6mm (H)
Environment
■Operating Temperature: 0 ~ 60oC
■Storage Temperature: -20 ~ 80oC
■Humidity: 10 ~ 90% RH, non-condensing
Important
• The product doesn’t support ErP standard (S5 Power consumption under
1W).
• Please use a power supply which minimum output should be at least 850
W.
Accessories
■2 * SATA3.0 cables
■1 * Dual USB 2.0 cable with bracket
■1 * Driver & user manual CD
■1 * I/O shield
Certication
■CE, FCC Class B, BSMI, RCM, VCCI
OS Support
■Skylake-SP
-Windows Server 2012 R2 (64-bit)
-Windows Server 2016 (64-bit)
-Linux Kernel 4.14, Ubuntu 18.04 LTS, Fedora 29
-Windows 10 IoT Enterprise LTSC/SAC 1809 (64-bit, RS5, Pre-test only)
■Cascade Lake-SP
-Windows Server 2016 (64-bit)
-Windows Server 2019 (64-bit)
-Linux Kernel 4.14, Ubuntu 18.04 LTS, Fedora 29
-Windows 10 IoT Enterprise LTSC/SAC 1809 (64-bit, RS5, Pre-test only)

1-5
Overview MS-98M9
Layout
USB 3.2
Gen 1
Ports
Mouse/Keyboard
Combo Port
COM Port
GbE
RJ45
Port
USB 3.2
Gen 1
Ports
10GbE
RJ45 Port
(Full SKU)
USB 3.2
Gen 1
Ports
GbE
RJ45
Port
10GbE
RJ45 Port
(Full SKU)
COM Port
Rear Panel
S/PDIF Box
Header
Clear CMOS
Jumper
AT/ATX
Jumper
RDIMM Slots
SATA
Ports
SMBus
Box Header
System
Power
Connector
PCIe Slots
USB 2.0 Port
Front Panel
Box Header
TPM Header
System Fan
Header
USB 2.0
Box Headers
GPIO Box
Headers
COM Port Box Headers &
Power Jumpers
Front Audio
Box Header
Chassis
Intrusion
Header
PCIe
Congure
Jumper
LED LAN Header
System Fan
Header
System
Fan
Header
CPU Fan
Header
COM Port
Power
Jumper
CPU
Power
Connector
PMBus
Box Header
Mini PCIe Slot
System Fan
Header
VROC
Box Header
COM Port
Power
Jumper
ME Header

1-6
Overview MS-98M9
2 Slot thickness PCIe Graphics Card Supported
thickness Max 40 mm
PCIE1
PCIE2
PCIE3
PCIE4
PCIE5
PCIE6
PCIE7

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 Installation................................................................................2-3
Memory..............................................................................................2-6
Hexa-Channel Mode ..................................................................................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, SYSFAN1~6................................ 2-11
SMBus Box Header: JSMB1.................................................................... 2-11
PMBus Box Header: JPMBUS1............................................................... 2-11
GPI Box Header: JGPIO1 ........................................................................2-12
GPO Box Header: JGPIO2 ......................................................................2-12
Dual Stacked SATA Connector: SATA1_2, SATA3_4, SATA5_6, SATA7_8
.................................................................................................................2-12
USB 2.0 Box Header: JUSB1, JUSB2, JUSB3 ........................................2-13
USB 2.0 Port: USB1.................................................................................2-13
Front Panel Box Header: JFP1 ................................................................2-13
Chassis Intrusion Header: JCASE1 .........................................................2-14
TPM Pin Header: JTPM1 .........................................................................2-14
Audio Box Header: JAUD1.......................................................................2-14
Front Audio Box Header: JAUD2 .............................................................2-15
S/PDIF Box Header: JSPDIF1 .................................................................2-15
VROC Box Header: JVROC.....................................................................2-15
RS232 COM Port Box Header: JCOM3, JCOM4, JCOM5, JCOM6 ........2-16
LAN LED Header: LAN_LED ...................................................................2-16
Jumper.............................................................................................2-17
Slot...................................................................................................2-18
PCIe (Peripheral Component Interconnect Express) Slot........................2-18
Mini-PCIe (Peripheral Component Interconnect Express) Slot................2-19

2-3
MS-98M9
CPU Installation
Use appropriate ground straps, gloves and ESD mats to protect yourself from
electrostatic discharge (ESD) while installing the CPU.
Check out Intel’s website at https://www.intel.com/content/www/us/en/
support/topics/desktop-server-processor-installation.html for detailed LGA
3647 CPU installation instructions.
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.
1. Check the CPU and the processor carrier for their Pin 1 Alignment
Marks.
Triangle is the Pin 1
Alignment Mark.

2-4
Hardware Setup
2. Align their Pin 1 Alignment
Marks before inserting the CPU
into the processor carrier. If in-
stalled properly, the CPU will
snap into the clips located on
the inside ends of the processor
carrier.
3. Check the heatsink for #1 clip. Flip the heatsink over and align the
CPU’s Pin 1 Alignment Mark with the heatsink’s #1 clip. Gently en-
gage the CPU and carrier package down. Make sure the attach clips
on the carrier grab onto the heatsink and 󰘰rmly secure the carrier,
CPU and heatsink as one Processor Heatsink Module.

2-5
MS-98M9
4. Place the Processor Heatsink Module on top of the CPU socket with
Pin 1 indicators aligned. Finally, secure the Processor Heatsink Mod-
ule screws in the assigned diagonal sequences.
1
2
3
4
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
Hexa-Channel Mode
Make sure that you install memory modules of the same type and density in
di󰀨erent channel DIMM slots.
DIMM6 (Channel F)
DIMM5 (Channel E)
DIMM4 (Channel D)
DIMM1 (Channel A)
DIMM2 (Channel B)
DIMM3 (Channel C)
Important
• 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.

2-7
MS-98M9
Installing Memory Modules
1. The memory module has only one notch on the center and will only 󰘰t in the
right orientation.
2. Insert the memory module vertically into the DIMM slot. Then push it in until
the golden 󰘰nger on the memory module is deeply inserted in the DIMM slot.
The plastic clip at each side of the DIMM slot will automatically close when
the memory module is properly seated.
3. Manually check if the memory module has been locked in place by the DIMM
slot clips at the sides.
Notch
Volt
Important
• You can barely see the golden nger if the memory module is properly inserted
in the DIMM slot.
• To enable successful system bootup, always insert the memory module into
the DIMM1 rst.

2-8
Hardware Setup
Power Supply
System Power Connector: JPWR1
This connector allows you to connect a power supply. To connect to the power
supply, make sure the plug of the power supply is inserted in the proper
orientation and the pins are aligned. Then push down the power supply rmly
into the connector.
13.+3.3V
1.+3.3
V
14.-12V
2.+3.3V
15.GND
3.GND
16.PS-ON#
4.+5V 17.GND
5.GND
18.GND
6.+5V
19.GND
7.GND
22.+5V
10.+12V
20.NA
8.PWR OK
23.+5V
11.+12V
21.+5V
9.5VSB
24.GND
1
2.+3.3V
CPU Power Connector: JPWR2
This connector is used to provide power to the CPU.
7.+12V
3.GND
5.+12V
1.
GND
8.+12V
4.GND
6.+12V
2.GND
Important
• Make sure that all power connectors are connected to the power supply to
ensure stable operation of the motherboard.
• To avoid some issues like system instability, reset and shutdown caused by
energy-insucient power supply, we suggest you should follow Intel Power
Supply Design Guide Rev 1.4 list and Intel Document Number 595284 to
choose your power supply unit.