MSI MS-98D3 User manual

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MS-98D3
(v1.x) Industrial Computer Board

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Preface MS-98D3
Preface MS-98D3
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
V1.0 2013/09
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. 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-98D3
iii
Preface MS-98D3
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
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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Preface MS-98D3
Preface MS-98D3
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-98D3
v
Preface MS-98D3
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 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.
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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vi
Preface MS-98D3
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 Specifications...........................................................................1-2
Mainboard Layout ......................................................................................1-4
2 Hardware Setup ...........................................................................2-1
Quick Component Guide............................................................................2-2
CPU (Central Processing Unit) ..................................................................2-3
Memory ......................................................................................................2-6
Power Supply.............................................................................................2-7
Rear Panel I/O ...........................................................................................2-8
Connector...................................................................................................2-9
Jumper .....................................................................................................2-16
Slot...........................................................................................................2-18
3 BIOS Setup...................................................................................3-1
Entering Setup ...........................................................................................3-2
The Menu Bar ............................................................................................3-4
Main ...........................................................................................................3-5
Advanced ...................................................................................................3-6
Boot..........................................................................................................3-12
Security ....................................................................................................3-13
Chipset.....................................................................................................3-17
Power .......................................................................................................3-18
Save & Exit...............................................................................................3-20

1-1-1
Thank you for choosing the MS-98D3, an excellent industrial computer
board.
Based on the innovative Intel®H81 chipset for optimal system efficiency,
the MS-98D3 accommodates the Intel®Haswell processor and supports
2 DDR3 1333/1600 SO-DIMM slots to provide the maximum of 16GB
memory capacity.
The MS-98D3 is durable under extreme environments and suitable to be
applied in every industrial field, such as digital signage, kiosk, gaming,
industrial control automation and POS.
1Overview

1-2
Overview MS-98D3
Overview MS-98D3
Mainboard Specications
Processor
Intel Haswell processor (LGA1150)￭
Chipset
Intel H81 chipset￭
Memory
2 unbuffered non-ECC DDR3 1333/1600 SO-DIMM slots
Supports Low Voltage Memory (DDR3L)
Supports the maximum of 16GB
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LAN
RTL8111E Gigabit Fast Ethernet controller￭
Audio
Realtek ALC887 audio codec￭
SATA
2 SATA 6Gb/s ports (SATA1, SATA2)￭
Graphics
Graphics integrated in Intel processor￭
Rear Panel I/O
1 PS/2 mouse/keyboard combo port
1 VGA port
2 USB 2.0 ports
2 USB 3.0 ports
1 RJ45 Gigabit LAN jack
1 RJ11 jack
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Overview MS-98D3
1-3
Overview MS-98D3
Onboard Pinheaders/ Connectors/ Jumpers
2 SATA 6Gb/s connectors
1 SATA power connectors
2 USB 2.0 pinheaders
6 serial port connectors
1 CPU fan connector
1 system fan connector
1 front panel pinheader
1 LVDS connector
1 LVDS power jumper
2 DC power connectors
1 parallel port pinheader
1 amplifier connector
1 GPIO pinheader
1 VGA connector
1 TPM pinheader
1 chassis intrusion pinheader
1 clear CMOS jumper
2 serial port power jumpers
1 RJ11 power select pinheader
1 ME enable select pinheader
1 ATX/AT switch pinheader
1 DC out connector
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Slot
1 mini PCI-E colay mSATA￭
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-98D3
Mainboard Layout
CPU Socket
Front Audio
Phineader
LVDS Power
Jumper
Battery Connector
VGA Connector
DC Out Power Connector
ME Jumper
RJ11 Power
Jumper
Back Panel
Front Panel
Pinheader
LVDS Connector
Fan Connector
Mini-PCIe Slot
Clear CMOS
Jumper
AT/ATX Jumper
SO-DIMM Slots
DC-in Power
Connector
COM Port Connector
USB 2.0
Pinheader
Chassis Intrusion
Pinheader
SATA Port
TPM Module
Connector
Amplier
Pinheader
LVDS Inverter
Connector
SATA Power
Connector
GPIO
Pinheader
Parallel Port
Pinheader
Fan Connector
COM1 Port
Power Jumper
COM2 Port
Power Jumper
RJ11
Jack
USB 2.0
Port
Mouse/
Keyboard
Combo
Port
VGA Port USB 3.0
Port LAN
Port
MS-98D3 v1.0

Overview MS-98D3
NOTE

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-98D3
Hardware Setup MS-98D3
Quick Component Guide
Back Panel,
p. 2-8
JFP1, p. 2-11
CPU Socket, p. 2-3
MINI_PCIE1,
p. 2-18
JAUD1, p. 2-11
JCMOS1, p. 2-16
COM1_SEL1,
p. 2-17
DIMM1~2,p. 2-6
JPWR1, p. 2-7
COM1~6, p. 2-12
JUSB1~2,
p. 2-15
JVDD1, p. 2-17
JCASE1, p. 2-13
SATA1~2,
p. 2-10
JTPM1, p. 2-13
JSPK1, p. 2-11
JINV1, p. 2-14
JRTC1, p. 2-10
JLPT1, p. 2-15
SYSFAN, p. 2-9
JVGA2, p. 2-14
PWR1, p. 2-7
JATX1, p. 2-16
COM2_SEL1,
p. 2-17
J1, p. 2-7
JME1, p. 2-16
JGPIO1, p. 2-10
CPUFAN, p. 2-9
JVDD2, p. 2-17
PWR2, p. 2-7
JLVDS1, p. 2-14

Hardware Setup MS-98D3
2-3
Hardware Setup MS-98D3
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 off the power supply or unplug the power
supply’s power cord from the grounded outlet first to ensure the safety of CPU.
INTRODUCTION TO LGA 115X
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

2-4
Hardware Setup MS-98D3
Hardware Setup MS-98D3
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 disper-
sion.
Open the load lever and remove the
plastic cap.
1. Lift the load lever up to fully open
position.
2.
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.
3. Engage the load lever while pressing
down lightly onto the load plate.
4.
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.
Secure the load lever with the hook
under the retention tab.
5. 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.
6.
Press the four hooks down to fasten
the cooler. Turn over the motherboard
to con󰘰rm that the clip-ends are
correctly inserted.
7. Finally, attach the CPU Fan cable
to the CPU fan connector on the
motherboard.
8.
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.
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Hardware Setup MS-98D3
2-5
Hardware Setup MS-98D3
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 disper-
sion.
Open the load lever and remove the
plastic cap.
1. Lift the load lever up to fully open
position.
2.
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.
3. Engage the load lever while pressing
down lightly onto the load plate.
4.
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.
Secure the load lever with the hook
under the retention tab.
5. 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.
6.
Press the four hooks down to fasten
the cooler. Turn over the motherboard
to con󰘰rm that the clip-ends are
correctly inserted.
7. Finally, attach the CPU Fan cable
to the CPU fan connector on the
motherboard.
8.
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.
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2-6
Hardware Setup MS-98D3
Hardware Setup MS-98D3
Memory
These DIMM slots are intended for memory modules.
1. Unlock the DIMM slot by flip-
ping open its side clips.
2. Vertically insert the DIMM into
the DIMM slot. The DIMM
has an off-center notch at the
bottom that will only allow it to
fit one way into the DIMM slot.
Push the DIMM deeply into the
DIMM 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
DIMM slot’s side clips.
Important
Motherboard photos shown in
this section are for demonstra-
tion only and may differ from the
actual look of your motherboard.
You can barely see the golden
finger if the DIMM is properly in-
serted in the DIMM slot.
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Hardware Setup MS-98D3
2-7
Hardware Setup MS-98D3
Power Supply
ATX POWER CONNECTOR: PWR1, PWR2
This connector is used to provide power to the motherboard.
4.+12V/19V
2.Ground
3.+12V/19V
1.Ground
Important
Make sure that all power connectors are connected to the power supply to ensure
stable operation of the motherboard.
SATA Power Connector: JPWR1
The connector provides power to the SATA device.
2.GND
3.GND
1.VCC5
4.+12V
DC Out Power Connector: J1
The connector provides 12V DC out.
2.12V
1.Ground

2-8
Hardware Setup MS-98D3
Hardware Setup MS-98D3
Rear Panel I/O
RJ11
Jack
USB 2.0
Port
Mouse/
Keyboard
Combo
Port
VGA Port USB 3.0
Port LAN
Port
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.
USB 3.0 Port
The USB 3.0 port is backward-compatible with USB 2.0 devices and supports
data transfer rate up to 5 Gbit/s (SuperSpeed).
LAN Jack
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 RJ-11 jack is used for cash drawer.
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Hardware Setup MS-98D3
2-9
Hardware Setup MS-98D3
Connector
FAN POWER CONNECTOR: CPUFAN, SYSFAN
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 with Sensor
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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