MSI MS-98H5 User manual

i
MS-98H5
(v1.x) Industrial Computer Board

ii
Preface MS-98H5
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
V1.2 2019/ 09
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-98H5
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.
警告使用者:
這是甲類資訊產品，在居住的環境中使用時，可能會造成無線電干擾，在這種情
況下，使用者會被要求採取某些適當的對策。

iv
Preface MS-98H5
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-98H5
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-A Radio Frequency
Interference Statement
This equipment has been tested and found to comply with
the limits for a Class A digital device, pursuant to Part 15
of the FCC Rules. These limits are designed to provide reasonable protection
against harmful interference when the equipment is operated in a commercial
environment. 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. Operation of this
equipment in a residential area is likely to cause harmful interference, in which
case the user will be required to correct the interference at his own expense.
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. MSI will comply with the product take back
requirements at the end of life of MSI-branded products that are sold into the EU.
You can return these products to local collection points.

vi
Preface MS-98H5
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-A Radio Frequency Interference Statement ......................................... v
WEEE Statement .......................................................................................... v
1 Overview.......................................................................................1-1
Mainboard Specications...........................................................................1-2
Mainboard Layout ......................................................................................1-4
2 Hardware Setup ...........................................................................2-1
Power Supply.............................................................................................2-3
Rear Panel I/O ...........................................................................................2-4
Connector...................................................................................................2-6
Jumper .....................................................................................................2-12
Slot...........................................................................................................2-14
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.....................................................................................................3-15
Power .......................................................................................................3-16
Save & Exit...............................................................................................3-18
Appendix GPIO WDT BKL Programming ..................................... A-1
Abstract..................................................................................................... A-2
GPIO Sample Code .................................................................................. A-3
Watchdog Timer – WDT............................................................................ A-5
LVDS Backlight Brightness Control........................................................... A-7
SMBus Access .......................................................................................... A-8

1-1-1
Thank you for choosing the MS-98H5, an excellent industrial computer
board.
With low power and low prole design, the MS-98H5 accommodates the
Intel®Apollo Lake-I / Apollo LakeSeries SoC and supports onboard 4GB
LPDDR4 Memory (Max. 8GB by option).
In the entry-level and mid-range market segment, the MS-98H5 provides
a high-performance solution for today’s front-end and general purpose
workstation, as well as in the future.
1Overview

1-2
Overview MS-98H5
Mainboard Specications
Processor (Optional)
■Apollo Lake-I Series
- Intel®Atom® Processor X5-E3950 (QC 1.6/2.0GHz for Burst/TDP-12W)
- Intel®Atom® Processor X5-E3940 (QC 1.6/1.8GHz for Burst/TDP-9W)
- Intel®Atom® Processor X5-E3930 (DC 1.3/1.8GHz for Burst/TDP-6W)
■Apollo Lake Series
- Intel®Celeron®Processor J3455 (DC 1.1/2.3GHz for Burst/TDP-10W)
Memory
■Onboard 4GB LPDDR4 Memory (8GB by option)
■2133 MT/s
LAN
■Apollo Lake-I Series
- 2 x Intel®I210-IT Gigabit Fast Ethernet Controller (With PoE IEEE 802.3af)
■Apollo Lake Series
- 2 x Intel®I211-AT Gigabit Fast Ethernet Controller
SATA
■1x SATA 6Gb/s port
Audio
■Realtek® ALC887-VD2-CG (Co-lay ALC888S)
■1 x audio header
■1 x amplier header (6W)
Graphics
■HD Graphics integrated in Intel®processor
■LVDS up to 1920 x 1200 @60Hz
■HDMI port up to 3840 x 2160 @30Hz / DisplayPort up to 4096 x 2160 @60Hz (Op-
tion)
■DVI-D port up to 1920 x 1200 @60Hz
■Supports displays:
-Standard: DVI-D or (HDMI or DisplayPort) or LVDS
-Two independent: DVI-D + (HDMI or DisplayPort) or LVDS+ (HDMI or DisplayPort)
or DVI-D + LVDS
-Three independent: DVI-D + (HDMI or DisplayPort) + LVDS
Rear Panel I/O
■4 x USB 3.1 Gen 1 ports
■2 x Gigabit LAN jacks
■1 x HDMI port (Standard) or DisplayPort (Option)
■1 x DVI-D port

1-3
Overview MS-98H5
Onboard Headers/ Connectors/ Jumpers
■1 x 2-pin DC power connector (For Apollo Lake-I Series)
■1 x 4-pin DC power connector (For Apollo Lake Series)
■1x System fan connector
■1 x SATA 6Gb/s port
■1 x SATA power connector
■2 x USB 2.0 connectors (4 ports)
■1 x RS-232/422/485 serial port connector (COM1~COM2)
■2 x RS232 serial port connectors (COM3~COM6)
■3 x COM port power jumpers
■1 x Front panel connector
■1 x Audio connector
■1 x Amplier connector
■1 x SMbus connector
■1 x GPIO connector
■1 x LVDS connector
■1 x LVDS power jumper
■1 x LVDS inverter connector
■1 x LVDS inverter power jumper
■1 x LAN LED connector
■2 x CANBus 2.0 connectors (For Apollo Lake-I Series)
■2 x NANO SIM-Holders
■1 x TPM 2.0 (LPC Header)
■1 x Clear CMOS jumper
■1 x AT/ATX select jumper
■1 x ME jumper
■1 x RTC battery connector
Expansion Slot
■1 x Mini-PCIe (Full-size, with Nano SIM-Holder)
■1 x M.2 M Key 2242 (SATA-3.0 Signal)
■1 x M.2 B Key 2242/3042(PCIe x1 & USB 2.0 Signal)
Form Factor
■Form Factor: 165(L) mm x 115(W) mm
Environmental
■Operating
- Temperature: -40 ~ 85°C (For Apollo Lake-I Series)
- Temperature: -10 ~ 60°C (For Apollo Lake Series)
- Humidity: 10 ~ 90%, non-condensing
■Storage
- Temperature: -40 ~ 85°C (For Apollo Lake-I Series)
- Temperature: -20 ~ 80°C (For Apollo Lake Series)
- Humidity: 10 ~ 90%, non-condensing

1-4
Overview MS-98H5
Mainboard Layout
Standard
RJ45 GbE LAN Ports
(PoE supported for
Apollo Lake-I Series) USB3.1 Gen 1 Ports
HDMI Port
DVI-D Port
Option
RJ45 GbE LAN Ports
(PoE supported for
Apollo Lake-I Series) USB3.1 Gen 1 Ports
DisplayPort
DVI-D Port

1-5
Overview MS-98H5
Apollo Lake Series
System Fan
Connector
Clear CMOS
Jumper
AT/ATX Jumper
COM Port
Connectors
USB2.0
Connectors
GPIO
Connector
COM Port
Power Jumpers
SATA Power
Connector
Mini-PCIe1
Back Panel
LVDS
Inverter
Connector
Front Panel
Connector
Amplier
Connector
Nano SIM-Hoders
LVDS
Connector
LVDS
Power
Jumper DC Power Connector
Inverter
Power
Jumper
ME Jumper
RTC Battery
Connector
SATA Port
LAN LED
Connector
SMbus
Connector
Audio
Connector
M.2 B Key Slot
M.2 M Key Slot
TPM Connector
(Back side)

1-6
Overview MS-98H5
Apollo Lake-I Series
System Fan
Connector
Clear CMOS
Jumper
AT/ATX Jumper
COM Port
Connectors
USB2.0
Connectors
GPIO
Connector
COM Port
Power Jumpers
SATA Power
Connector
Mini-PCIe1
Back Panel
LVDS
Inverter
Connector
Front Panel
Connector
Amplier
Connector
Nano SIM-Hoders
LVDS
Connector
LVDS
Power
Jumper DC Power Connector
Inverter
Power
Jumper
ME Jumper
RTC Battery
Connector
SATA Port
LAN LED
Connector
SMbus
Connector
Audio
Connector CANBus 2.0
Connectors
M.2 B Key Slot
M.2 M Key Slot
TPM Connector
(Back side)

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-98H5
Components Reference Guide
Power Supply....................................................................................2-3
DC-In Power Connector: JPWR1 (For Apollo Lake-I) ...............................2-3
DC-In Power Connector: JPWR2 (For Apollo Lake) ..................................2-3
SATA Power Connector: JSATAPWR1.......................................................2-3
Rear Panel I/O ...................................................................................2-4
Standard.....................................................................................................2-4
Option.........................................................................................................2-4
Connector..........................................................................................2-6
Fan Power Connector: SYSFAN1 ..............................................................2-6
GPIO Connector: JGPIO1..........................................................................2-6
Serial ATA Connector: JSATA1...................................................................2-6
Front Panel Connector: JFP1.....................................................................2-7
LPC Debug Port Connector: JTPM1..........................................................2-7
LVDS Inverter Connector: JINV1 ...............................................................2-7
LVDS Connector: JLVDS1 .........................................................................2-8
USB 2.0 Connector: JUSB1 / JUSB2.........................................................2-8
Serial Port Connector: JCOM1/JCOM2/JCOM3 ........................................2-9
Front Audio Connector: JAUD1................................................................2-10
Audio Amplier Connector: JAMP1 ..........................................................2-10
SMBus Connector: JSMB1 ...................................................................... 2-11
CANBus 2.0 Connector: JCAN1/JCAN2 (For Apollo Lake-I Series) ....... 2-11
LAN LED Connector: JLANLED1............................................................. 2-11
Jumper.............................................................................................2-12
Clear CMOS Jumper: JCMOS1 ...............................................................2-12
AT/ATX Select Jumper: JAT1...................................................................2-12
Serial Port Power Jumper: JCOMP1 (for COM1 & COM2)......................2-12
Serial Port Power Jumper: JCOMP2 (for COM3 & COM4)/ JCOMP3 (for
COM5 & COM6).......................................................................................2-13
LVDS Power Jumper: JVDD1 ..................................................................2-13
LVDS Inverter Power Jumper: JINVDD1..................................................2-13
Intel ME Jumper: JTXE1 ..........................................................................2-13
Slot...................................................................................................2-14
Mini-PCIe (Peripheral Component Interconnect Express) Slot................2-14
M2_M1: M.2 Slot (Key M, 2242) for SSD.................................................2-14
M2_B1: M.2 Slot (Key B, 2242/3042) for WiFi/BT....................................2-14
Nano SIM Holder......................................................................................2-15

2-3
Hardware Setup MS-98H5
Power Supply
DC-In Power Connector: JPWR1 (For Apollo Lake-I)
This connector is used to provide power to the motherboard.
2.GND
1.DC_IN (12V~48V)
DC-In Power Connector: JPWR2 (For Apollo Lake)
This connector is used to provide power to the motherboard.
4.GND
3.GND
2.DC-IN (12V~48V)
1.DC-IN (12V~48V)
SATA Power Connector: JSATAPWR1
This connector is used to provide power to SATA devices.
2.GND
3.GND
1.VCC5
4.+12V
Important
Make sure that all power connectors are connected to the power supply to ensure
stable operation of the motherboard.

2-4
Hardware Setup MS-98H5
Rear Panel I/O
Standard
RJ45 GbE LAN Ports
(PoE supported for
Apollo Lake-I Series) USB3.1 Gen 1 Ports
HDMI Port
DVI-D Port
Option
RJ45 GbE LAN Ports
(PoE supported for
Apollo Lake-I Series) USB3.1 Gen 1 Ports
DisplayPort
DVI-D Port

2-5
Hardware Setup MS-98H5
hDVI-D Port
The DVI-D (Digital Visual Interface- Digital) connector can be connected to a LCD
monitor, or a CRT monitor with an adapter. To connect a monitor, please refer to
the monitor’s manual for more information.
hHDMI Port
The High-Denition Multimedia Interface (HDMI) is an all-digital audio/video in-
terface capable of transmitting uncompressed streams. HDMI supports all TV
format, including standard, enhanced, or high-denition video, plus multi-channel
digital audio on a single cable.
hDisplayPort
DisplayPort is a digital display interface standard. This connector is used to
connect a monitor with DisplayPort inputs.
hLAN Port
The standard RJ-45 LAN jack is for connection to the Local Area Network (LAN).
You can connect a network cable to it.
Yellow Green/ Orange
LED Color LED State Condition
Left Yellow Lighting LAN link is established.
Blinking The computer is communicating with another
computer on the LAN.
Right Green O󰀨 10 Mbit/sec data rate is selected.
On 100 Mbit/sec data rate is selected.
Orange On 1000 Mbit/sec data rate is selected.
hUSB 3.1 Gen 1 Port
The USB 3.1 Gen 1 port is backward-compatible with USB 2.0 devices and sup-
ports data transfer rate up to 5 Gbit/s (SuperSpeed).

2-6
Hardware Setup MS-98H5
Connector
Fan Power Connector: SYSFAN1
The fan power connector supports system cooling fans with +12V. When con-
necting the wire to the connectors, always note that the red wire is the positive
and should be connected to the +12V; the black wire is Ground and should be
connected to GND. If the motherboard has a System Hardware Monitor chipset
onboard, you must use a specially designed fan with speed sensor to take ad-
vantage of the fan control.
GPIO Connector: JGPIO1
This connector is provided for the General-Purpose Input/Output (GPIO) periph-
eral module.
11. N_GPO4
13. N_GPO5
15. N_GPO6
17. N_GPO7
19. VCC5
1. GND
3. N_GPO0
5. N_GPO1
7. N_GPO2
9. N_GPO3
20. VCC5
18. N_GPI7
16. N_GPI6
14. N_GPI5
12. N_GPI4
10. N_GPI3
8. N_GPI2
6. N_GPI1
4. N_GPI0
2. GND
Serial ATA Connector: JSATA1
This connector is a high-speed Serial ATA interface port. Each connector can
connect to one Serial ATA device.
Important
Please do not fold the SATA cable into a 90-degree angle. Otherwise, data loss
may occur during transmission.

2-7
Hardware Setup MS-98H5
Front Panel Connector: JFP1
This front panel connector is provided for electrical connection to the front panel
switches & LEDs and is compliant with Intel Front Panel I/O Connectivity Design
Guide.
8.POWER SWITCH
3.HDD LED-
1.HDD LED+
6.POWER SWITCH
5.RESET SWITCH
4.POWER LED-
7.RESET SWITCH
2.POWER LED+
9.NC
LED(+) Voltage(V) Current(mA)
Power 5 10
HDD 5 10
LPC Debug Port Connector: JTPM1
This connector works as LPC debug port.
1. LPC_FRAME#
14. GND
2. LPC_AD3
3. LPC_AD2
5. LPC_AD0
4. LPC_AD1
6. L_LDRQ0#
7. CLK
8. SEIRQ
10. VCC5
9. PLTRST#
11. VCC3
12. GND
13. NA
LVDS Inverter Connector: JINV1
The connector is provided for LCD backlight options.

2-8
Hardware Setup MS-98H5
LVDS Connector: JLVDS1
The LVDS (Low Voltage Di󰀨erential Signal) connector provides a digital interface
typically used with at panels. After connecting an LVDS interface at panel to
the JLVDS1, be sure to check the panel datasheet and set the LVDS jumper to
proper power voltage.
39.LVDSB_CLK
#
27.LVDSB_DATA#1
25.LVDSB_DATA1
23.GND
21.LVDSA_DATA#3
19.LVDSA_DATA3
17.GND
15.LVDSA_DATA#1
13.LVDSA_DATA1
11.LVDS_BLON
9.L_BKLT_CTRL#
7.LVDS_DDC_CLK
5.LCD_VDD
3.LCD_VDD
1.+12V
40.
LVDSA_CLK#
28.LVDSB_DATA#0
26.
LVDSB_DATA0
24.GND
22.LVDSA_DATA#2
20.LVDSA_DATA2
18.GND
16.LVDSA_DATA#0
14.LVDSA_DATA0
12.LVDS_DETECT#_C
10.LVDS_VDD_EN
8.
LVDS_DDC_DATA
6.LCD_VDD
4.+12V
2.+12V
37.LVDSB_CLK
35.GND
33.LVDSB_DATA#3
31.LVDSB_DATA3
29.GND
38.LVDSA_CLK
36.GND
34.LVDSB_DATA#2
32.LVDSB_DATA2
30.GND
Important
Pin 12 is a detect pin. When using a customized LVDS cable, pin 12 should be a
signal ground with a low impedance. Otherwise, LVDS will not function.
USB 2.0 Connector: JUSB1 / JUSB2
This connector, compliant with Intel I/O Connectivity Design Guide, is ideal for
connecting high-speed USB interface peripherals such as USB HDD, digital cam-
eras, MP3 players, printers, modems and the like.
8.Power
3.USB-
1.Power
6.USB-
5.USB+
4.USB+
7.GND
2.GND
Important
Note that the pins of VCC and GND must be connected correctly to avoid possible
damage.