MSI MS-98B5 User manual

i
MS-98B5
(v1.x) Industrial Computer Board

ii
Preface MS-98B5
Preface MS-98B5
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 2014/02
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-98B5
iii
Preface MS-98B5
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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iv
Preface MS-98B5
Preface MS-98B5
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-98B5
v
Preface MS-98B5
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-98B5
Preface MS-98B5
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 ......................................................................................1-5
2. Hardware Setup...........................................................................2-1
CPU (Central Processing Unit) ..................................................................2-3
Memory ......................................................................................................2-6
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
MS-98B5 Q87 SKU....................................................................................3-4
The Menu Bar ............................................................................................3-4
Main ...........................................................................................................3-5
Advanced ...................................................................................................3-6
Boot..........................................................................................................3-12
Security ....................................................................................................3-13
Chipset.....................................................................................................3-18
Power .......................................................................................................3-19
Save & Exit...............................................................................................3-21

Preface MS-98B5
vii
Preface MS-98B5
MS-98B5 H81 SKU ..................................................................................3-22
The Menu Bar ..........................................................................................3-22
Main .........................................................................................................3-23
Advanced .................................................................................................3-24
Boot..........................................................................................................3-30
Security ....................................................................................................3-31
Chipset.....................................................................................................3-35
Power .......................................................................................................3-36
Save & Exit...............................................................................................3-38
Appendix WDT & GPIO ...................................................................A-1
WDT Sample Code ................................................................................... A-2
GPIO Sample Code .................................................................................. A-3

1-1-1
Thank you for choosing the MS-98B5, an excellent industrial computer
board.
Based on the innovative Intel®H81/ Q87 chipset for optimal system
efficiency, the MS-98B5 accommodates the Intel®Haswell processor and
supports up to 4 DDR3/DDR3L 1333/1600 UDIMM slots to provide the
maximum of 32GB memory capacity.
In the advanced-level and mid-range market segment, MS-98B5 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-98B5
Overview MS-98B5
Mainboard Specications
Processor
4th generation Intel Core i3/ i5/ i7 processor (LGA1150)■
Chipset
Q87 SKU
Intel Q87 chipset
H81 SKU
Intel H81 chipset
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■
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Memory
Q87 SKU
4 DDR3/DDR3L 1333/1600 UDIMM slots
Supports the maximum of 32GB
Supports dual-channel mode
H81 SKU
2 DDR3/DDR3L 1333/1600 UDIMM slots
Supports the maximum of 16GB
Supports dual-channel mode
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LAN
Intel I217-LM Gigabit Fast Ethernet controller (LAN1)
Intel I210-AT Gigabit Fast Ethernet controller (LAN2)
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SATA
Q87 SKU
6 SATA 6Gb/s ports (SATA1, SATA2, SATA3, SATA4, SATA5_3,
SATA6_4)
H81 SKU
2 SATA 6Gb/s ports (SATA1, SATA2)
2 SATA 3Gb/s ports (SATA5_3, SATA6_4)
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Audio
Realtek ALC887 audio codec
3 audio jacks
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Graphics
Graphics integrated in Intel processor■

Overview MS-98B5
1-3
Overview MS-98B5
Rear Panel I/O
Q87 SKU
1 PS/2 mouse/keyboard combo port
2 RS-232/422/485 serial ports
2 Gigabit LAN jacks
4 USB 3.0 ports
2 USB 2.0 ports
1 DVI-I port
1 DisplayPort
3 flexible audio ports
H81 SKU
1 PS/2 mouse/keyboard combo port
2 RS-232/422/485 serial ports
2 Gigabit LAN jacks
2 USB 3.0 ports
4 USB 2.0 ports
1 DVI-I port
1 DisplayPort
3 flexible audio ports
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Onboard Pin Headers/ Connectors/ Jumpers
Q87 SKU
6 SATA 6Gb/s ports
3 USB 2.0 connectors (6 ports)
4 RS-232 serial port connectors
1 TPM connector
1 parallel port connector
1 front panel connector
1 front audio connector
1 GPIO pin header
1 SMBus connector
1 DisplayPort connector
1 chassis intrusion pin header
1 clear CMOS jumper
6 serial port power jumpers
1 AT/ATX select jumper
1 non-volatile memory jumper
H81 SKU
2 SATA 6Gb/s ports
2 SATA 3Gb/s ports
2 USB 2.0 connectors (4 ports)
4 RS-232 serial port connectors
1 TPM connector
1 parallel port connector
1 front panel connector
1 front audio connector
1 GPIO pin header
1 SMBus connector
1 DisplayPort connector
1 chassis intrusion pin header
1 clear CMOS jumper
6 serial port power jumpers
1 AT/ATX select jumper
1 non-volatile memory jumper
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1-4
Overview MS-98B5
Overview MS-98B5
Slot
Q87 SKU
1 PCIe x16 slot (Gen 3)
3 PCIe x1 slots
2 full-size Mini-PCIe slots
3 PCI slots
H81 SKU
1 PCIe x16 slot (Gen 2)
3 PCIe x1 slots
3 PCI slots
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Form Factor
ATX form factor: 12” x 9.6”■
Environmental
Operating Temperature: 0oC ~ 60oC
Storage Temperature: -20oC ~ 80oC
Humidity: 5% ~ 90% RH, Non-Condensing
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SKU Comparison
SKUs
Features Q87 SKU H81 SKU
PCH Q87 H81
DIMM slot 4 2
SATA 6 G/bs qty 6 2
SATA 3 G/bs qty 0 2
Rear panel USB 4 USB 3.0
2 USB 2.0
2 USB 3.0
4 USB 2.0
Onboard USB pin header 3 USB 2.0 (6 Ports) 2 USB 2.0 (4 Ports)
Mini-PCIe slot 2 0

Overview MS-98B5
1-5
Overview MS-98B5
Mainboard Layout
MS-98B5 Q87 SKU
Serial Port LAN
Port
USB 3.0
Port
Line-In
Mic-In
Mouse/
Keyboard
Combo
Port
USB 2.0
Port
DisplayPort
Line-Out
Serial Port USB 3.0
Port
LAN
Port DVI-I Port
Front Audio
Connector
System Fan Connector
CPU Socket
Mini-PCIe Slot
Clear CMOS
Jumper
AT/ATX Jumper
DIMM Slots
COM Port Con-
nector/Jumper
USB 2.0 Pin
Header
Chassis Intru-
sion Pin Header
SATA
Port
TPM
Connector
GPIO Pin Header
Parallel Port
Connector
Back Panel
System Fan
Connector
CPU Fan Connector
System Fan
Connector
DisplayPort
Connector
COM Port
Jumper
NVM Jumper
Power
Connector
Power
Connector
SMBus
Connector
Front Panel
Connector
PCI Slot
PCIe Slot
PCIe Slot

1-6
Overview MS-98B5
Serial Port LAN
Port
USB 3.0
Port
Line-In
Mic-In
Mouse/
Keyboard
Combo
Port
USB 2.0
Port
DisplayPort
Line-Out
Serial Port USB 2.0
Port
LAN
Port DVI-I Port
MS-98B5 H81 SKU
Front Audio
Connector
CPU Socket
Clear CMOS
Jumper
AT/ATX Jumper
DIMM Slots
COM Port Con-
nector/Jumper
USB 2.0 Pin
Header
Chassis Intru-
sion Pin Header
SATA
Port
TPM
Connector
GPIO Pin Header
Parallel Port
Connector
Back Panel
DisplayPort
Connector
COM Port
Jumper
NVM Jumper
Power
Connector
Power
Connector
SMBus
Connector
Front Panel
Connector
PCI Slot
PCIe Slot
PCIe Slot
System Fan
Connector
System Fan ConnectorCPU Fan Connector
System Fan
Connector

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-98B5
Hardware Setup MS-98B5
Components Reference Guide
CPU (Central Processing Unit)........................................................2-3
Memory..............................................................................................2-6
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 ~ SYSFAN3 .....................2-12
GPIO Pin Header: JGPIO1 ......................................................................2-13
Serial ATA Connector: SATA1 ~ SATA6 ...................................................2-13
I2C Bus Connector: JSMB1 .....................................................................2-14
Front Panel Connector: JFP1...................................................................2-14
USB 2.0 Connector: JUSB1, JUSB2, JUSB3...........................................2-15
RS-232 Serial Port Connector: JCOM3 ~ JCOM6 ...................................2-15
TPM Module Connector: JTPM1..............................................................2-16
Front Audio Connector: JAUD1................................................................2-17
DisplayPort Connector: JDP1 ..................................................................2-17
Chassis Intrusion Pin Header: JCI1 .........................................................2-18
Parallel Port Connector: JLPT1................................................................2-18
Jumper.............................................................................................2-19
Clear CMOS Jumper: JBAT1 ...................................................................2-19
AT/ATX Select Jumper: JAT1 ...................................................................2-19
Serial Port Power Jumper: JCOMP1 ~ JCOMP6.....................................2-20
Non-Volatile Memory Jumper: JNVM1 .....................................................2-20
Slot...................................................................................................2-21
PCIe (Peripheral Component Interconnect Express) Slot........................2-21
Mini-PCIe (Peripheral Component Interconnect Express) Slot................2-21
PCI (Peripheral Component Interconnect) Slot........................................2-21

Hardware Setup MS-98B5
2-3
Hardware Setup MS-98B5
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 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

2-4
Hardware Setup MS-98B5
Hardware Setup MS-98B5
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-98B5
2-5
Hardware Setup MS-98B5
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-98B5
Hardware Setup MS-98B5
Memory
Dual-Channel Mode
In Dual-Channel mode, make sure that you install memory modules of the same
type and density in different channel DIMM slots.
Q87 SKU
DIMM1 (Channel A)
DIMM2 (Channel A)
DIMM3 (Channel B)
DIMM4 (Channel B)
H81 SKU
DIMM1 (Channel A)
DIMM3 (Channel B)
Recommended Memory Population
Q87 SKU
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
H81 SKU
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, specifically: 1. Use the same
DIMM size; 2. Use the same number of ranks per DIMM.
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