MSI MS-98L2 User manual

i
MS-98L2
(v1.x) Industrial Computer Board

ii
Preface MS-98L2
Copyright 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 ac-
curacy or completeness is expressed or implied. MSI reserves the right to make
changes to this document without prior notice.
Trademarks
All trademarks are the properties of their respective owners.
Revision History
Revision Date
V1.0 2019/03
Technical Support
If a problem arises with your system and no solution can be obtained from the
user’s manual, please contact your place of purchase or local distributor. Alter-
natively, please visit the MSI website for technical guide, BIOS updates, driver
updates and other information, or contact our technical staff via http://www.msi.
com/support/

iii
Preface MS-98L2
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 flat surface before setting it up.
• The openings on the enclosure are for air convection hence protects the equip-
ment 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 (140oF), IT MAY DAMAGE THE EQUIP-
MENT.

iv
Preface MS-98L2
Chemical Substances Information
In compliance with chemical substances regulations, such as the EU REACH Reg-
ulation (Regulation EC No. 1907/2006 of the European Parliament and the Coun-
cil), MSI provides the information of chemical substances in products at:
http://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:
http://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.
WEEE Statement
Under the European Union (“EU”) Directive on Waste Electrical and
Electronic Equipment, Directive 2002/96/EC, which takes effect on
August 13, 2005, 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.

v
Preface MS-98L2
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 reason-
able protection against harmful interference in a residential
installation. This equipment generates, uses and can radi-
ate 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 tele-
vision 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
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 different from that to
which the receiver is connected.
• Consult the dealer or an experienced radio/television technician for
help.
Notice 1
The changes or modifications 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.

vi
Preface MS-98L2
CONTENTS
Copyright Notice...............................................................................................ii
Trademarks ......................................................................................................ii
Revision History................................................................................................ii
Technical Support.............................................................................................ii
Safety Instructions .......................................................................................... iii
Chemical Substances Information.................................................................. iv
Battery Information......................................................................................... iv
WEEE Statement ............................................................................................. iv
CE Conformity .................................................................................................. v
FCC-B Radio Frequency Interference Statement............................................ v
1 Overview �������������������������������������������������������������������������������������1-1
Motherboard Specifications ......................................................................... 1-2
Motherboard Layout..................................................................................... 1-5
2 Hardware Setup ��������������������������������������������������������������������������2-1
CPU (Central Processing Unit)..................................................................... 2-4
Memory......................................................................................................... 2-7
Power Supply................................................................................................ 2-8
Rear Panel I/O .............................................................................................. 2-9
Connector................................................................................................... 2-12
Jumper ....................................................................................................... 2-19
Slot.............................................................................................................. 2-21
3 BIOS Setup ����������������������������������������������������������������������������������3-1
Entering Setup.............................................................................................. 3-2
The Menu Bar............................................................................................... 3-4
Main.............................................................................................................. 3-5
Advanced ...................................................................................................... 3-6
Boot ............................................................................................................ 3-11
Security....................................................................................................... 3-12
Chipset........................................................................................................ 3-18
Power.......................................................................................................... 3-19
Save & Exit.................................................................................................. 3-20
Appendix GPIO WDT Programming ������������������������������������������������ A-1
General Purposed IO – GPIO/DIO.................................................................A-2
Set output value of GPO ............................................................................... A-2
Watchdog Timer – WDT................................................................................A-3
SMBus Access .............................................................................................. A-4

Thank you for choosing the MS-98L2, an excellent industrial
computer board.
Based on the innovative Intel®C246 / Q370 chipset for optimal
system efficiency, the MS-98L2 accommodates the Intel®Desk-
top Coffee Lake-S processor and supports up to 4 DDR4 2666MHz
U-DIMM slots to provide the maximum of 64 GB memory capacity.
Designed to withstand harsh industrial conditions, the MS-98L2
is engineered to provide reliable performance for a wide variety of
industrial applications.
1Overview

1-2
Overview MS-98L2
Motherboard Specifications
Processor
• 8th Gen Intel®Desktop Coffee Lake-S Core™ /Pentium®/Celeron®Series
Processor, Max 95W
Chipset
• SKU1: Intel®C246
• SKU2 & SKU3: Intel®Q370
Memory
• Dual channel DDR4, up to 2666MHz
• 4 x U-DIMM slots, up to 64GB
• SKU1: ECC, Non ECC supported
• SKU2 & SKU3: Non ECC supported
Network
• SKU1 & SKU2: 4 x LAN ports
»1 x Intel®I219-LM GbE LAN PHY
»3 x Intel®I210-AT GbE LAN (Co-lay I211-AT)
• SKU3: 2 x LAN ports
»1 x Intel®I219-LM GbE LAN PHY
»1 x Intel®I210-AT GbE LAN (Co-lay I211-AT)
Storage
• 4 x SATA 6Gb/s ports
• 1 x M.2 M Key slot
»Supports up to PCIe 3.0 x4 and SATA 6Gb/s
»PCIe x4 signal switchable with PCIe x4 slot2 (Either PCIe x4 (PCIE2)
signal or M.2 M Key (SATA & PCIe) signal is supported when both slots
are occupied.
»Supports 2242/ 2260 /22800 modules
• Supports SATA RAID 0, 1, 5, 10
Expansion Slot
• 1 x PCIe 3.0 x16 slot
• 3 x PCIe x4 slots
»PCIE2 slot signal switchable with M.2 M Key slot
»Only PCIE2 & PCIE4 support NVMe
• 1 x full-size Mini-PCIe slot
»Supports PCIe x1, USB2.0
»Supports Wi-Fi/Bluetooth modules

1-3
Overview MS-98L2
Internal I/O
• 1 x 8-pin power connector
• 1 x 24-pin power connector
• 3 x 4-pin System fan connectors
• 1 x 4-pin CPU fan connector
• 2 x USB 2.0 box headers (4 ports)
• 1 x USB 2.0 Vertical Type-A port
• 5 x RS-232 COM port connectors (COM2~COM6)
»SKU1 & SKU2: COM2 supports RS-232/422/485 with 0V/5V/12V Auto-flow
Control, COM3~6 RS-232, 0V/5V/12V
»SKU3: COM2~6 RS-232, 0V/5V/12V
»RS-485 support TR 1000 Meter
• 6 x COM port power jumpers
• 1 x Parallel port header
• 2 x GPIO headers
• 1 x Front panel header
• 1 x S/PDIF box header
• 1 x TPM header
• 1 x Front audio box header
• 1 x Keyboard/Mouse box header
• 1 x Chassis intrusion header
• 1 x Clear CMOS jumper
• 1 x AT/ATX select jumper
• 1 x PCIe option jumper
• 1 x ME jumper
• 1 x SMBus box header
• 1 x I2C box header
Rear I/O
• 1 x COM port (COM1)
»Supports RS-232/422/485 with Ring/0V/5V/12V Auto-flow Control
»RS-485 support TR 1000 Meter
• 1 x VGA port
• 1 x DisplayPort port
• 1 x HDMI port
• 4 or 2 x RJ45 LAN ports (SKU1 & SKU2: 4 x LAN ports, SKU3: 2 x LAN ports)
• 4 x USB 3.1 Gen2 Type-A ports
• 4 x USB 3.1 Gen1 Type-A ports
• 3 x Audio jacks (Line-In, Line-Out, Mic-In)

1-4
Overview MS-98L2
Graphics
• Integrated Intel®HD Graphics
»1 x VGA (Max resolution 1920 x 1200 @ 60Hz)
»1 x DisplayPort (Max resolution 4096 x 2304 @ 60Hz)
»1 x HDMI (Max resolution 4096 x 2160 @ 24Hz)
Audio
• Realtek®ALC887/888S HD Audio Codec
»1 x Front audio header
»1 x S/PDIF connector
»3 x Audio jacks (Line-In, Line-Out, Mic-In)
Environment
• Operating Temperature: -10 ~ 60oC
• Storage Temperature: -20 ~ 80oC
• Humidity: 10 ~ 90%, non-condensing
• RoHS: Compliant
Form Factor
• Micro-ATX: 244mmx244mm
Certification
• CE, FCC Class B, BSMI, RCM, VCCI
SKU Comparison
Features SKU1 SKU2 SKU3
PCH C246 Q370
LAN3 I210-AT N/A
LAN4 I210-AT N/A
COM 2 x RS-232/422/485
4 x RS-232
1 x RS-232/422/485
5 x RS-232
Memory ECC non-ECC

1-5
Overview MS-98L2
Motherboard Layout
System Fan
Connector
System Fan
Connector
System Fan
Connector
CPU Fan
Connector
Clear CMOS
Jumper
AT/ATX
Jumper
Chassis Intrusion
Header
SATA
Ports
LPT
Connector
GPIO Box
Headers
COM 2~6
Jumpers
USB 2�0
Box Headers
PCIe Slot
M�2 M KEY slot
TPM box
header
Front Panel
Box Header
COM3~6
Connector
COM2
Box Header
U-DIMM
Slots
Mini-PCIe
Slot
ME
Jumper
S/PDIF
Connector
Power
Connector
Power
Connector
SPI
Connector
SMBus Box
Header
I2C Box
Header
Rear I/O
USB 2�0
Connector
Front Audio
Box Header
COM1
Jumper

1-6
Overview MS-98L2
VGA Port
VGA Port
HDMI Port
HDMI Port
COM Port
COM Port
DisplayPort
DisplayPort
USB 3�1 Gen 2 Ports
USB 3�1 Gen 2 Ports
USB 3�1 Gen 1 Ports
USB 3�1 Gen 1 Ports
Line-In
Line-Out
Mic-In
Line-In
Line-Out
Mic-In
RJ45 GbE LAN Ports
RJ45 GbE LAN Ports
SKU1 & SKU2 Rear I/O
SKU3 Rear I/O

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 compo-
nents. Static electricity may damage the components.
2Hardware Setup

2-2
Hardware Setup MS-98L2
Components Reference Guide
CPU (Central Processing Unit)���������������������������������������������������������2-4
Introduction to LGA 115x CPU...................................................................... 2-4
CPU Installation ........................................................................................... 2-5
Memory �������������������������������������������������������������������������������������������2-7
Dual-Channel Mode ..................................................................................... 2-7
Recommended Memory Population............................................................. 2-7
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 ��������������������������������������������������������������������������������������2-12
Fan Power Connector: CPUFAN1, SYSFAN1~3.......................................... 2-12
Dual Stacked SATA Connector: SATA1_2, SATA3_4 ................................... 2-12
Chassis Intrusion Header: JCASE4............................................................ 2-13
GPI Box Header: JGPIO1 ............................................................................ 2-13
GPO Box Header: JGPIO2 ........................................................................... 2-13
Front Panel Box Header: JFP1................................................................... 2-14
SMBus Box Header: JSMB1 ....................................................................... 2-14
I2C Box Header: JI2C1 ................................................................................ 2-14
RS232/422/485 COM Port Box Header: JCOM2 ......................................... 2-15
RS232 COM Port Header: JCOM3 (COM3~COM6 ) ..................................... 2-16
Parallel Port Box Header: JLPT1............................................................... 2-16
TPM Box Header: JTPM1............................................................................ 2-17
Front Audio Box Header: JAUD1 ................................................................ 2-17
S/PDIF Box Header: JSPDI1....................................................................... 2-17
USB 2.0 Box Header: JUSB1, JUSB2, ....................................................... 2-18
USB 2.0 Port: USB1.................................................................................... 2-18
PS/2 Keyboard/Mouse Connector: JKBMS1 .............................................. 2-18
Jumper ������������������������������������������������������������������������������������������2-19
COM1 Power Jumper: JCOMP1.................................................................. 2-19
JCOM2~JCOM6 Power Jumper: JCOMP2 ~ JCOMP6 ................................ 2-19
Clear CMOS Jumper: JCMOS1................................................................... 2-19
AT/ATX Jumper: JAT1 ................................................................................. 2-20
PCIe Option Jumper: J_CFG1..................................................................... 2-20
ME Jumper: ME_DIS1 ................................................................................ 2-20

2-3
Hardware Setup MS-98L2
Slot ������������������������������������������������������������������������������������������������2-21
PCIe (Peripheral Component Interconnect Express) Slot ......................... 2-21
M2_M1: M.2 Slot (Key M, 2280) for SSD..................................................... 2-21
MINIPCIE1: Mini-PCIe Slot......................................................................... 2-22

2-4
Hardware Setup MS-98L2
CPU (Central Processing Unit)
When installing the CPU, make sure that you install the cooler to prevent over-
heating. 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 cool-
ing 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 heat-
sink to enhance heat dissipation.
Replacing the CPU
While replacing the CPU, always turn off the power supply or unplug the power sup-
ply’s power cord from the grounded outlet first 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

2-5
Hardware Setup MS-98L2
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 confirming the CPU direc-
tion 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.

2-6
Hardware Setup MS-98L2
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 confirm that the
clip-ends are correctly inserted.
8. Finally, attach the CPU Fan cable
to the CPU fan connector on the
motherboard.
Important
•Confirm if your CPU cooler is firmly 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.

2-7
Hardware Setup MS-98L2
Memory
Dual-Channel Mode
In Dual-Channel mode, make sure that you install memory modules of the same
type and density in different channel slots.
Recommended Memory Population
Number of U-DIMMs installed 1 2 3 4
DIMM1 (ch A) V V V V
DIMM2 (ch A) V V
DIMM3 (ch B) V V V
DIMM4 (ch B) V
Important
•"V" indicates a populated DIMM slot.
•Paired memory installation for Max performance.
•Populate the same DIMM type in each channel, specifically: 1. Use the same DIMM
size; 2. Use the same number of ranks per DIMM.
Installing Memory Modules
1. Unlock the DIMM slot by flipping open its side clips.
2. Vertically insert the DIMM into the slot. The DIMM has an off-center notch at
the bottom that will only allow it to fit one way into the slot. Push the DIMM
deeply into the slot. The side clips of the slot will automatically close when the
DIMM is properly seated and an audible click should be heard.
3. Manually check if the DIMM has been locked in place by the slot’s side clips.
Important
You can barely see the golden finger if the DIMM is properly inserted in the DIMM slot.

2-8
Hardware Setup MS-98L2
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 orien-
tation and the pins are aligned. Then push down the power supply firmly into the
connector.
CPU Power Connector: JPWR2
This connector is used to provide power to the CPU.
7.+12V
3.Ground
5.+12V
1.
Ground
8.+12V
4
.Ground
6.+12V
2.Ground
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 en-
ergy-insufficient 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.