MSI MS-98E2 User manual

i
MS-98E2
(v1.x) Industrial Computer Board

ii
Preface MS-98E2
Copyright Notice
The material in this document is the intellectual property of MICRO-STAR
INTERNATIONAL. We take every care in the preparation of this document, but no
guarantee is given as to the correctness of its contents. Our products are under
continual improvement and we reserve the right to make changes without notice.
Trademarks
All trademarks are the properties of their respective owners.
Revision History
Revision Date
V1.0 2017/03
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.
Alternatively, please visit the MSI website for technical guide, BIOS updates,
driver updates and other information, or contact our technical sta󰘯 via http://www.
msi.com/support/

iii
Preface MS-98E2
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 mod-
ule.
￭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 ser-
vice 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 UNCONDI-
TIONED, STORAGE TEMPERATURE ABOVE 60oC (140oF), IT MAY DAM-
AGE THE EQUIPMENT.

iv
Preface MS-98E2
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:
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.

v
Preface MS-98E2
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 2002/96/EC, which takes e󰘯ect 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.

vi
Preface MS-98E2
CONTENTS
Copyright Notice............................................................................................ ii
Trademarks ................................................................................................... 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
Motherboard Specications........................................................................1-2
Motherboard Layout...................................................................................1-5
2 Hardware Setup ...........................................................................2-1
CPU (Central Processing Unit) ..................................................................2-4
Memory ......................................................................................................2-6
Power Supply.............................................................................................2-7
Rear Panel I/O ...........................................................................................2-8
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 ...................................................................................................3-7
Boot..........................................................................................................3-12
Security ....................................................................................................3-13
Chipset.....................................................................................................3-19
Power .......................................................................................................3-21
Save & Exit...............................................................................................3-22
Appendix WDT & GPIO ................................................................... A-1
WDT Sample Code ................................................................................... A-2
GPIO Sample Code .................................................................................. A-3

1-1-1
Thank you for choosing the MS-98E2, an excellent industrial computer
board.
Based on the innovative Intel® C236 / H110 chipset for optimal system
e󰀩ciency, the MS-98E2 accommodates the Intel® Desktop Kaby Lake-S/
Skylake-S processor and supports up to 4 / 2 DDR4 2133MHz / 2400MHz
(7th Gen) U-DIMM slots to provide the maximum of 64 / 32GB memory
capacity.
Designed to withstand harsh industrial conditions, the MS-98E2 is
engineered to provide reliable performance for a wide variety of industrial
applications.
1Overview

1-2
Overview MS-98E2
Motherboard Specications
Processor
■7th/6th Gen Intel® Desktop Kaby Lake-S/Skylake-S Core™ i7/i5/i3/Penti-
um®/Celeron® Series Processor, Max 95W
Chipset
■SKU1: Intel®C236
■SKU2: Intel®H110
Memory
■Dual channel DDR4, up to 2133MHz / 2400MHz (7th Gen)
■SKU1: 4 x U-DIMM slots, up to 64GB, ECC
■SKU2: 2 x U-DIMM slots, up to 32GB, Non ECC
Network
■1 x Intel® I210-AT GbE LAN (Co-lay I211-AT)
■1 x Intel® I219-LM GbE LAN PHY
Storage
■SKU1:C236
-6 x SATA 6Gb/s (RAID 0, 1, 5, 10)
-1 x mSATA
-1 x M.2
■SKU2:H110
-3 x SATA 6Gb/s
-1 x mSATA
Expansion Slot
■SKU1:C236
-1 x PCIe x16 slot
-1 x PCIe x1 slot
-1 x PCIe x8 slot (signal x4)
-1 x PCI slot
-1 x M.2 slot (M Key, PCIe x4, SATA 6Gb/s)
-1 x full-size Mini-PCIe slot (Support PCIe, SATA 6Gb/s, USB2.0)
■SKU2:H110
-1 x PCIe x16 slot
-1 x PCIe x1 slot
-1 x PCIe x8 slot (signal x1)
-1 x PCI slot
-1 x full-size Mini-PCIe slot (SATA 6Gb/s)

1-3
Overview MS-98E2
Internal I/O
■1 x 8-pin power connector
■1 x 24-pin power connector
■3 x System fan connectors
■1 x CPU fan connector
■2 x USB2.0 connectors (4 ports)
■1 x USB3.0 port (2 ports) (SKU1:C236)
■5 x RS-232 COM port connectors (0V/5V/12V)(COM2~COM6)
■1 x RS-232 COM port header (COM7~COM10) (SKU1:C236)
■5 x COM port jumpers
■1 x GPIO header
■1 x Front panel header
■1 x S/PDIF connector
■1 x Amplier header
■1 x TPM header
■1 x LVDS connector (SKU1:C236)
■1 x LVDS inverter connector (SKU1:C236)
■1 x LVDS power jumpers (SKU1:C236)
■1 x PCI power jumper
■1 x Front audio header
■1 x Chassis intrusion header
■1 x Clear CMOS jumper
■1 x AT/ATX select jumper
■1 x ME jumper
■1 x LAN congure jumper
■1 x SMBus connector
■1 x Buzzer header
Rear I/O
■1 x PS/2 mouse/keyboard combo port
■2 x USB2.0 ports
■1 x RS-232/422/485 serial port (0V/5V/12V)
■1 x DisplayPort
■1 x VGA port
■1 x DVI-D port
■2 x RJ45 GbE LAN ports
■4 x USB3.0 ports
■3 x Audio jacks (Line-In, Line-Out, Mic-In)

1-4
Overview MS-98E2
Graphics
■Integrated Intel® HD Graphics
-1 x VGA (Max resolution 1920 x 1200)
-1 x DVI-D (Max resolution 1920 x 1200)
-1 x DisplayPort (Max resolution 3840 x 2160)
-1 x LVDS (18/24 bit, Dual Channel)(SKU1:C236)
■SKU1 C236: Up to 3 independent displays (VGA+DVI-D+DP, VGA+D-
VI-D+LVDS, DVI-D+DP+LVDS)
■SKU2 H110: Up to 2 independent displays (VGA+DVI-D, VGA+DP, DVI-
D+DP)
Audio
■Realtek® ALC887/888S HD Audio Codec
■1 x Amplier header
■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: 5 ~ 95% RH, non-condensing
Form Factor
■Micro-ATX: 244mmx244mm
Certication
■CE, FCC, BSMI, VCCI, RCM
SKU Comparison
SKUs
Features SKU1:C236 SKU2:H110
PCH C236 H110
Memory DDR4, support ECC DDR4, non-ECC
SATA 6 x SATA 6Gb/s 3 x SATA 6Gb/s
M.2 Yes No

1-5
Overview MS-98E2
Motherboard Layout
SKU1:C236
System Fan
Connector
Clear CMOS
Jumper
AT/ATX
Jumper
Chassis
Intrusion Header
USB 3.0
Connector
SATA
Ports
GPIO
Header
COM Port
Connector/
Jumper
PCIe Slot
Amplier
Header
TPM Header
Front Panel
Header
COM Port
Header
U-DIMM
Slots
Mini-PCIe
Slot
M.2 Slot
LVDS
Connector
ME
Jumper
LVDS Inverter
Connector
COM Port
Power Jumper
S/PDIF
Connector
CPU Power
Connector
Power
Connector
System Fan
Connector
SMBus
Connector
CPU Fan
Connector
Rear I/O
PCI Slot
System Fan
Connector
USB 2.0
Connector
NVM LAN
Jumper
Front Audio
Connector
LVDS Inverter
Jumper
PCI Slot
Jumper
Serial Port
Mouse/
Keyboard
Combo
Port
USB2.0
Port DisplayPort
VGA Port
USB3.0
Port
RJ45 GbE
LAN Port
DVI-D Port
Line-In
Line-Out
Mic-In
RJ45 GbE
LAN Port
USB3.0
Port

1-6
Overview MS-98E2
SKU2:H110
System Fan
Connector
Clear CMOS
Jumper
AT/ATX
Jumper
Chassis
Intrusion Header
SATA
Ports
GPIO
Header
COM Port
Connector/
Jumper
PCIe Slot
Amplier
Header
TPM Header
Front Panel
Header
U-DIMM
Slots
Mini-PCIe
Slot
ME
Jumper
COM Port
Power Jumper
S/PDIF
Connector
CPU Power
Connector
Power
Connector
System Fan
Connector
SMBus
Connector
CPU Fan
Connector
Rear I/O
PCI Slot
System Fan
Connector
USB 2.0
Connector
NVM LAN
Jumper
Front Audio
Connector
PCI Slot
Jumper
Serial Port
Mouse/
Keyboard
Combo
Port
USB2.0
Port DisplayPort
VGA Port
USB3.0
Port
RJ45 GbE
LAN Port
DVI-D Port
Line-In
Line-Out
Mic-In
RJ45 GbE
LAN Port
USB3.0
Port

2-2-1
This chapter provides you with the information about hardware setup
procedures. While doing the installation, be careful in holding the com-
ponents and follow the installation procedures. For some components, if
you install in the wrong orientation, the components will not work prop-
erly.
Use a grounded wrist strap before handling computer components. Static
electricity may damage the components.
2Hardware Setup

2-2
Hardware Setup MS-98E2
Components Reference Guide
CPU (Central Processing Unit)........................................................2-4
Introduction to LGA 115x CPU ...................................................................2-4
CPU Installation .........................................................................................2-5
Memory..............................................................................................2-6
Dual-Channel Mode ...................................................................................2-6
Recommended Memory Population...........................................................2-6
Installing Memory Modules ........................................................................2-6
Power Supply....................................................................................2-7
System Power Connector: PWRCONN1 ...................................................2-7
CPU Power Connector: JPWR1.................................................................2-7
Rear Panel I/O ...................................................................................2-8
Connector........................................................................................2-11
Fan Power Connector: CPUFAN1, SYSFAN1~3 ..................................... 2-11
Serial ATA Connector: SATA1~6 (SATA 6Gb/s for SKU1:C236) .............. 2-11
Serial ATA Connector: SATA1~3 (SATA 6Gb/s for SKU2:H110)............... 2-11
Chassis Intrusion Header: J4...................................................................2-12
GPIO Connector: JGPIO1........................................................................2-12
USB2.0 Connector: JUSB1, JUSB4 (SKU1:C236) ..................................2-12
USB2.0 Connector: JUSB6, JUSB7 (SKU2:H110)...................................2-12
Audio Amplier Connector: JAMP1 ..........................................................2-13
Front Panel Header: JFP1 .......................................................................2-13
I2C Bus Connector: JSMB1 .....................................................................2-13
LVDS Inverter Connector: JINVT1 (SKU1:C236).....................................2-14
LVDS Connector: JLVDS1 (SKU1:C236) .................................................2-14
RS-232 COM Port Header: COM7~COM10 (SKU1:C236)......................2-15
LPC Debug Port Connector: JTPM1 (With TPM Support) .....................2-15
RS232 Serial Port Connector: JCOM2~JCOM6 ......................................2-16
USB 3.0 Connector: JUSB3 (SKU1:C236)...............................................2-16
Front Audio Connector: JAUD1................................................................2-17
S/PDIF Pinheader: JSPDI1......................................................................2-17

2-3
Hardware Setup MS-98E2
Jumper.............................................................................................2-18
NVM LAN Jumper: JNVM1 ......................................................................2-18
Clear CMOS Jumper: J_CMOS1 .............................................................2-18
AT/ATX Select Jumper: JAT1...................................................................2-18
COM Port Power Jumper: JCOMP7 (for JCOM1), JCOMP3~6 (for JCOM3~6)
�����������������������������������������������������������������������������������������������������������������2-19
LVDS Power Jumper: JVDD1 (SKU1:C236) ............................................2-19
PCI Slot Power Jumper: JVDD2 ..............................................................2-19
ME Jumper: ME_DIS1 .............................................................................2-19
Slot...................................................................................................2-20
PCIe (Peripheral Component Interconnect Express) Slot........................2-20
Mini-PCIe (Peripheral Component Interconnect Express) Slot................2-20
M.2 Slot (SKU1:C236)..............................................................................2-20
PCI (Peripheral Component Interconnect) Slot........................................2-21

2-4
Hardware Setup MS-98E2
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
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

2-5
Hardware Setup MS-98E2
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�

2-6
Hardware Setup MS-98E2
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.
Recommended Memory Population
SKU1:C236
Number of 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
SKU2:H110
Number of DIMMs installed 1 2
DIMM1 (ch A) V V
DIMM3 (ch B) V
Important
• "V" indicates a populated DIMM slot�
• 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�
Installing Memory Modules
1. Unlock the DIMM slot by ipping open its side clips.
2. Vertically insert the DIMM into the slot. The DIMM has an o󰀨-center notch at
the bottom that will only allow it to t 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 󰘰nger if the DIMM is properly inserted in the DIMM
slot.

2-7
Hardware Setup MS-98E2
Power Supply
System Power Connector: PWRCONN1
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 orienta-
tion and the pins are aligned. Then push down the power supply rmly into the
connector.
CPU Power Connector: JPWR1
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�

2-8
Hardware Setup MS-98E2
Rear Panel I/O
Serial Port
Mouse/
Keyboard
Combo Port
USB2.0
Port DisplayPort
VGA Port
USB3.0
Port
RJ45 GbE
LAN Port
DVI-D Port
Line-In
Line-Out
Mic-In
RJ45 GbE
LAN Port
USB3.0
Port
hMouse / Keyboard Combo Port
The standard PS/2® mouse/keyboard DIN connector is for a PS/2® mouse/key-
board.
hUSB2.0 Port
The USB (Universal Serial Bus) port is for attaching USB devices such as key-
board, mouse, or other USB-compatible devices.
hVGA Port
The DB15-pin female connector is provided for monitor.
hDVI-D Port
The DVI-D (Digital Visual Interface-Digital) connector allows you to connect an
LCD monitor. It provides a high-speed digital interconnection between the com-
puter and its display device. To connect an LCD monitor, simply plug your monitor
cable into the DVI connector, and make sure that the other end of the cable is
properly connected to your monitor (refer to your monitor manual for more infor-
mation.)
hRS-232/422/485 Serial Port: JCOM1 (0V/5V/12V)
The serial port is a 16550A high speed communications port that sends/receives
16 bytes FIFOs. With Auto-Flow Control and RI Function Support, it supports
barcode scanners, barcode printers, bill printers, credit card machine, etc.
15
69