MSI MS-98D2 User manual

i
MS-98D2
(v1.x) Industrial Computer Board

ii
Preface MS-98D2
Preface MS-98D2
Copyright Notice
The material in this document is the intellectual property of MICRO-STAR INTER-
NATIONAL. We take every care in the preparation of this document, but no guar-
antee is given as to the correctness of its contents. Our products are under con-
tinual improvement and we reserve the right to make changes without notice.
Trademarks
All trademarks are the properties of their respective owners.
MSI®is a registered trademark of Micro-Star Int’l Co.,Ltd.
NVIDIA®is a registered trademark of NVIDIA Corporation.
AMD®is a registered trademark of AMD Corporation.
Intel®is a registered trademark of Intel Corporation.
Windows®is a registered trademark of Microsoft Corporation.
AMI®is a registered trademark of Advanced Micro Devices, Inc.
Award®is a registered trademark of Phoenix Technologies Ltd.
Realtek®is a registered trademark of Realtek Semiconductor Corporation.
Revision History
Revision Date
V1.1 2013/10
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. Alterna-
tively, please try the following help resources for further guidance.
Visit the MSI website for technical guide, BIOS
updates, driver updates, and other information:
http://www.msi.com/service/download/
Contact our technical sta󰘯 at:
http://support.msi.com/
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Preface MS-98D2
iii
Preface MS-98D2
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.
CAUTION: Danger of explosion if battery is incorrectly replaced. Replace only
with the same or equivalent type recommended by the manufacturer.
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。
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iv
Preface MS-98D2
Preface MS-98D2
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.
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.

Preface MS-98D2
v
Preface MS-98D2
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.
VOIR LA NOTICE D’INSTALLATION AVANT DE RACCORDER AU RESEAU.
This device complies with Part 15 of the FCC Rules. Operation is subject to the
following two conditions:
this device may not cause harmful interference, and
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 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. MSI will comply with the product take back require-
ments at the end of life of MSI-branded products that are sold into the EU. You
can return these products to local collection points.
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2)

vi
Preface MS-98D2
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
Quick Component Guide............................................................................2-2
Memory ......................................................................................................2-3
Power Supply.............................................................................................2-4
Rear Panel I/O ...........................................................................................2-5
Connector...................................................................................................2-6
Jumper .....................................................................................................2-14
Slot...........................................................................................................2-16
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.....................................................................................................3-16
Power .......................................................................................................3-17
Save & Exit...............................................................................................3-19
Appendix A. WDT & GPIO.............................................................. A-1
WDT Sample Code ................................................................................... A-2
GPIO Sample Code .................................................................................. A-3

1-1-1
Thank you for choosing the MS-98D2, an excellent industrial computer
board.
Based on the innovative Intel® NM10 chipset for optimal system efciency,
the MS-98D2 accommodates the Intel®Atom™ Processor D2550 and
supports one DDR3 1067 SO-DIMM slot to provide the maximum of 4GB
memory capacity.
The MS-98D2 is durable under extreme environments and suitable to be
applied in every industrial eld, such as digital signage, kiosk, gaming,
industrial control automation and POS.
1Overview

1-2
Overview MS-98D2
Overview MS-98D2
Mainboard Specications
Processor
Intel®Atom™ Processor D2550■
Chipset
Intel®NM10 chipset■
Memory
1 unbuffered non-ECC DDR3 1067 SO-DIMM slot
Supports the maximum of 4GB
■
■
LAN
Realtek®RTL8111E Gigabit Fast Ethernet controller■
Audio
Realtek® ALC887 High Denition Audio codec
1 audio pinheader
1 amplier pinheader
■
■
■
Storage
2 SATA 3Gb/s ports■
Graphics
Integrated Graphic Engine Intel®HD 3650 Graphics
1 internal vertical type HDMI connector
1 LVDS connector
1 VGA port
■
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Rear Panel I/O
1 DC-in 12V power jack
1 PS/2 mouse/keyboard combo port
1 VGA port
4 USB 2.0 ports
1 RJ45 Gigabit LAN jack
1 RJ11 jack (12/24V, MAX 2A)
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Overview MS-98D2
1-3
Overview MS-98D2
Onboard Pinheaders/ Connectors/ Jumpers
2 SATA 3Gb/s connectors
1 SATA power connector
2 USB 2.0 pinheaders (3 ports)
6 serial port connectors
1 CPU fan connector
1 system fan connector
1 front panel pinheader
1 LVDS connector
1 inverter connector
2 DC power connectors
1 parallel port pinheader
1 front audio pinheader
1 amplier pinheader
1 GPIO pinheader
1 HDMI connector
1 VGA connector
1 TPM pinheader
1 keyboard/mouse connector
1 chassis intrusion pinheader
1 clear CMOS jumper
1 LVDS power jumper
2 serial port jumpers
1 RJ11 power select jumper
1 ATX/AT select jumper
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Slot
1 Mini-PCIe slot■
Form Factor
Mini-ITX: 17.0cm x 17.0cm■
Environmental
Operating Temperature: 0oC ~ 60oC
Storage Temperature: -20oC ~ 80oC
Humidity: 5% ~ 90% RH, Non-Condensing
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1-4
Overview MS-98D2
Mainboard Layout
Back Panel
Front Panel
Pinheader
LVDS Connector
Fan Connector
Mini-PCIe Slot
Clear CMOS
Jumper
AT/ATX Jumper
SO-DIMM Slot
DC Power
Connector
COM Port
Connector
USB 2.0
Pinheader
COM Port
Jumper
Chassis
Intrusion
Pinheader
SATA Port
TPM
Connector
Amplier
Pinheader
Inverter
Connector
GPIO
Pinheader
Parallel Port
Pinheader
VGA Connector
Front Audio
Phineader
LVDS Power
Jumper
RJ11 Power
Jumper
SATA Power
Connector
COM Port
Jumper
HDMI Connector
KB/MS Connector
RJ11
Jack
USB 2.0
Port
Mouse/
Keyboard
Combo
Port VGA Port
USB 2.0
Port LAN
Port
DC
Power
Jack

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-98D2
Hardware Setup MS-98D2
Quick Component Guide
Back Panel,
p. 2-5
JFP1, p. 2-8
JLVDS1, p. 2-11
CPUFAN1,
SYSFAN1, p. 2-6
MINI_PCIE1,
p. 2-16
JCMOS1, p. 2-14
JATX1, p. 2-14
DIMM1, p. 2-3
JPWR1, PJ1,
p. 2-4
COM1~COM6,
p. 2-9
JUSB2,
JUSB1, p. 2-13
COM2_SEL1,
p. 2-15
JCASE1, p. 2-10
SATA2,
SATA1, p. 2-7
JTPM1,
p. 2-10
JAMP1, p. 2-8
JINV1, p. 2-11
JGPIO1,
p. 2-7
JLPT1, p. 2-13
VGA2, p. 2-12
JAUD1, p. 2-8
JVDD1, p. 2-15
JVDD2, p. 2-15
JHDDPWR1,
p. 2-4
HDMI1, p. 2-12
JKB_MS1, p. 2-12
COM1_SEL1,
p. 2-15

Hardware Setup MS-98D2
2-3
Hardware Setup MS-98D2
Memory
The SO-DIMM slot is intended for memory modules.
1. Locate the SO-DIMM slot. Align
the notch on the DIMM with the
key on the slot and insert the
DIMM into the slot.
2. Push the DIMM gently down-
wards until the slot levers click
and lock the DIMM in place.
3. To uninstall the DIMM, ip the slot levers outwards and the DIMM will be
released instantly.
Important
You can barely see the golden nger if the DIMM is properly inserted in the
DIMM slot.

2-4
Hardware Setup MS-98D2
Hardware Setup MS-98D2
Power Supply
DC Power Connector: JPWR1
This connector is used to provide power to the motherboard.
4.+12V
2.Ground
3.+12V
1.Ground
SATA Power Connector: JHDDPWR1
This connector is used to provide power to SATA devices.
2.GND
3.GND
1.VCC5
4.+12V
DC Out Power Connector: PJ1
The connector provides 12V DC out.
2.12V
1.Ground
Important
Make sure that all power connectors are connected to the power supply to ensure
stable operation of the motherboard.

Hardware Setup MS-98D2
2-5
Hardware Setup MS-98D2
Rear Panel I/O
RJ11
Jack
USB 2.0
Port
Mouse/
Keyboard
Combo
Port VGA Port
USB 2.0
Port LAN
Port
DC
Power
Jack
DC Power Jack
This DC jack provides 12V power for the system.
Keyboard / Mouse Combo Port
The standard PS/2®mouse/keyboard DIN connector is for a PS/2®mouse/key-
board.
VGA Port
The DB15-pin female connector is provided for monitor.
USB 2.0 Port
The USB (Universal Serial Bus) port is for attaching USB devices such as key-
board, mouse, or other USB-compatible devices.
LAN 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 Off LAN link is not established.
On (steady state) LAN link is established.
On (blinking) The computer is communicating with another
computer on the LAN.
Right Green Off 10 Mbit/sec data rate is selected.
On 100 Mbit/sec data rate is selected.
Orange On 1000 Mbit/sec data rate is selected.
RJ11 Jack
The standard RJ11 jack is provided for cash drawers.
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2-6
Hardware Setup MS-98D2
Hardware Setup MS-98D2
Connector
Fan Power Connector: CPUFAN1, SYSFAN1
The fan power connectors support system cooling fan 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 advan-
tage of the CPU fan control.
3.+12V
1.GND
2.FAN_CTRL
Important
Please refer to your processor’s o󰘲cial website or consult your vendor to 󰘰nd
recommended CPU cooling fans.
If there are not enough ports on the mainboard to connect all system fans,
adapters are available to connect a fan directly to a power supply.
Before 󰘰rst boot up, ensure that there are no cables impeding any fan blades.
•
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•

Hardware Setup MS-98D2
2-7
Hardware Setup MS-98D2
Serial ATA Connector: SATA1, SATA2
This connector is a high-speed Serial ATA interface port. Each connector can
connect to one Serial ATA device.
Speed
Chipset SATA 3 Gb/s
Intel NM10 SATA1, SATA2
Important
Please do not fold the SATA cable into a 90-degree angle. Otherwise, data loss
may occur during transmission.
GPIO Pinheader: JGPIO1
This connector is provided for the General-Purpose Input/Output (GPIO) periph-
eral module.
8.GPIO Output 2
6.GPIO Output 1
4.GPIO Output 0
1.VCC3
3.GPIO Input 0
10.GPIO Output 3
5.GPIO Input 1
7.GPIO Input 2
9.GPIO Input 3
2.VCC5
12.KEY 11.GND

2-8
Hardware Setup MS-98D2
Hardware Setup MS-98D2
Audio Amplier Pinheader: JAMP1
The JAMP1 is used to connect audio ampliers to enhance audio performance.
2.AMP_L+
1.AMP_L-
4.AMP_R+
3.AMP_R-
Front Audio Pinheader: JAUD1
This connector allows you to connect the front audio panel located on your
computer case.
1.MICR
3.MICL
10.Line Out Jack Detect
5.Line Out R
7.NC
9.Line Out L
8.Key
6.MICJackDetect
4.NC
2.GND
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.
1.+
3.-
10.No Pin
5.-Reset Switch
HDD LED
Power Switch
Power LED
7.+
9.Reserved
8.-
6.+
4.-
2.+

Hardware Setup MS-98D2
2-9
Hardware Setup MS-98D2
Serial Port Connector: COM1 (RS-232/-422/-485)
Serial Port Connector: COM2~6 (RS-232)
This connector is a 16550A high speed communications port that sends/receives
16 bytes FIFOs. You can attach a serial device to it through an optional serial port
bracket.
8.CTS
3.TXD
1.DCD
6.DSR
5.GND
4.DTR
7.RTS
2.RXD
9.VCC_COM
RS-232
PIN SIGNAL DESCRIPTION
1
2
3
4
5
6
7
8
9
DCD
RXD
TXD
DTR
GND
DSR
RTS
CTS
VCC_COM
Data Carrier Detect
Receive Data
Transmit Data
Data Terminal Ready
Signal Ground
Data Set Ready
Request To Send
Clear To Send
Power Source
RS-232
RS-422
8.NC
3.TX+
1.TX-
6.NC
5.GND
4.RX-
7.NC
2.RX+
9.NC
PIN SIGNAL DESCRIPTION
1
2
3
4
5
6
7
8
9
422 TXD-
422 RXD+
422 TXD+
422 RXD-
GND
NC
NC
NC
NC
Transmit Data, Negative
Receive Data, Positive
Transmit Data, Positive
Receive Data, Negative
Signal Ground
No Connection
No Connection
No Connection
No Connection
RS-422
RS-485
8.NC
3.DATA+
1.DATA-
6.NC
5.GND
4.NC
7.NC
2.NC
9.NC
PIN SIGNAL DESCRIPTION
1
2
3
4
5
6
7
8
9
485 TXD-
NC
485 TXD+
NC
GND
NC
NC
NC
NC
Transmit Data, Negative
No Connection
Transmit Data, Positive
No Connection
Signal Ground
No Connection
No Connection
No Connection
No Connection
RS-485

2-10
Hardware Setup MS-98D2
Hardware Setup MS-98D2
Chassis Intrusion Pinheader: JCASE1
This connector connects to the chassis intrusion switch cable. If the computer
case is opened, the chassis intrusion mechanism will be activated. The system
will record this intrusion and a warning message will ash on screen. To clear the
warning, you must enter the BIOS utility and clear the record.
1.CINTRU
2.Ground
TPM Module Connector: JTPM1
This connector connects to a TPM (Trusted Platform Module) module (optional).
Please refer to the TPM security platform manual for more details.
10.No Pin
14.Ground
8.5V Power
12.Ground
6.Serial IRQ
4.3.3V Power
2.3V Standby power 1.LPC Clock
3.LPC Reset
5.LPC address&data pin0
7.LPC address&data pin1
9.LPC address&data pin2
11.LPC address&data pin3
13.LPC Frame