MSI MS-98F3 User manual

i
MS-98F3
Industrial Computer Board

ii
Preface MS-98F3
Copyright and Trademarks Notice
Copyright © Micro-Star Int’l Co., Ltd. All rights reserved. The MSI logo used is
a registered trademark of Micro-Star Int’l Co., Ltd. All other marks and names
mentioned may be trademarks of their respective owners. No warranty as to
accuracy or completeness is expressed or implied. MSI reserves the right to
make changes to this document without prior notice.
Revision History
Revision Date
V2.1 2018/08
Technical Support
If a problem arises with your product and no solution can be obtained from
the user’s manual, please contact your place of purchase or local distributor.
Alternatively, please visit https://www.msi.com/support/ for further guidance.

iii
Preface MS-98F3
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:
此為甲類資訊技術設備，於居住環境中使用時，可能會造成射頻擾動，在此種情
況下，使用者會被要求採取某些適當的對策。

iv
Preface MS-98F3
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:
https://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:
https://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-98F3
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.

vi
Preface MS-98F3
CONTENTS
Copyright and Trademarks Notice................................................................. 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
Specications.............................................................................................1-2
Layout ........................................................................................................1-4
2. Hardware Setup ...........................................................................2-1
Memory ......................................................................................................2-3
Power Supply.............................................................................................2-4
Rear Panel I/O ...........................................................................................2-5
Connector...................................................................................................2-6
Jumper ..................................................................................................... 2-11
Slot...........................................................................................................2-14
3. BIOS Setup...................................................................................3-1
Entering Setup ...........................................................................................3-2
The Menu Bar ............................................................................................3-4
Main ...........................................................................................................3-5
Advanced ...................................................................................................3-6
Boot..........................................................................................................3-12
Security ....................................................................................................3-13
Chipset.....................................................................................................3-18
Power .......................................................................................................3-19
Save & Exit...............................................................................................3-21
Appendix GPIO WDT BKL Programming ...................................... A-1
Abstract..................................................................................................... A-3
General Purposed IO ................................................................................ A-4
Watchdog Timer ........................................................................................ A-5
LVDS Backlight Brightness Control........................................................... A-6
SMBus Access .......................................................................................... A-7

1-1-1
Thank you for choosing the MS-98F3, an excellent industrial computer
board.
Based on the innovative Intel®Broadwell ULT i3-5010U processor, the
MS-98F3 is engineered to provide reliable performance for a wide variety
of industrial applications.
1Overview

1-2
Overview MS-98F3
Specications
Processor
■Intel Broadwell ULT i3-5010U processor
Memory
■1x DDR3L 1600 MHz SO-DIMM slot
■Up to 8GB
Network
■LAN1: Intel I218LM Gigabit Fast Ethernet PHY controller (with iAMT support)
■LAN2: Intel I210-AT Gigabit Fast Ethernet controller (Co-Lay I211-AT)
Storage
■2x SATA 6Gb/s ports
■1x mSATA slot (shared with Mini-PCIe slot)
Audio
■Realtek ALC887 audio codec
■1 x front audio header
■1 x amplier header
Graphics
■Graphics integrated in Intel processor
-VGA port / DisplayPort, HDMI, LVDS
Expansion Slot
■1 x Mini-PCIe slot (shared with mSATA )
■1 x M.2 slot
- 1 x E key (PCIe & USB2.0), 2230 slot
Rear Panel I/O
■2 x USB 2.0 ports
■2 x USB 3.0 ports
■2 x RJ45 GbE LAN ports
■1 x HDMI port
■1 x VGA port

1-3
Overview MS-98F3
Internal I/O
■1x DC power connector
■1x system fan connector
■2 x SATA 6Gb/s ports
■1 x SATA power connector
■1 x USB 2.0 connector
■1 x front panel connector
■1 x front audio connector
■1 x amplier connector
■1 x GPIO connector
■1 x keyboard/mouse connector
■1 x SMBus connector
■4 x serial port connectors
■1 x LVDS connector
■1 x LVDS inverter connector
■1 x LVDS power jumper
■1 x LVDS inverter jumper
■1x clear CMOS jumper
■2 x serial port power jumpers
■1 x AT/ATX select jumper
■1 x Intel ME jumper
Form Factor
■Form Factor: 102mm x 146mm
Environmental
■Operating Temperature: -10 ~ 60oC
■Storage Temperature: -20 ~ 80oC
■Humidity: 10 ~ 90% RH, non-condensing

1-4
Overview MS-98F3
Layout
Front Audio
Connector
Mini-PCIe/
mSATA Slot
Clear CMOS
Jumper
AT/ATX Jumper
SO-DIMM Slot
COM Port
Connector
USB 2.0
Connector
LVDS Inverter
Connector
SATA 3.0
Connector
GPIO Connector
System Fan
Connector
LVDS
Connector
COM Port
Power Jumper
LPC Debug
Port Connector
Front Panel
Connector
SATA Power
Connector
Amplier
Connector
LVDS Power
Jumper
Keyboard/Mouse
Connector
M.2 Slot
LVDS Inverter
Jumper
LAN2 Jumper
SMBus Connector
DC-In 12V/19V/24V
Power Connector
COM Port
Power Jumper
Back Panel
Intel ME
Jumper

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-98F3
Component Reference Guide
Memory..............................................................................................2-3
Power Supply....................................................................................2-4
DC Power Connector: JPWR2...................................................................2-4
SATA Power Connector: JPW1 ..................................................................2-4
Rear Panel I/O ...................................................................................2-5
Connector..........................................................................................2-6
Fan Power Connector: SYSFAN1 ..............................................................2-6
GPIO Connector: JGPIO1..........................................................................2-6
Serial ATA Connector: SATA1, SATA2........................................................2-6
Front Panel Connector: JFP1.....................................................................2-7
LPC Debug Port Connector: JDP1.............................................................2-7
USB 2.0 Connector: JUSB1.......................................................................2-7
LVDS Inverter Connector: JINVDD1 ..........................................................2-8
LVDS Connector: JLVDS1 .........................................................................2-8
Serial Port Connector: COM1 ~ COM4......................................................2-9
Audio Amplier Pinheader: JAMP1 ..........................................................2-10
Front Audio Connector: JAUDIO1 ............................................................2-10
PS/2 Keyboard/Mouse Connector: JKBMS1............................................2-10
SMBus Connector: JSMB1 ......................................................................2-10
Jumper.............................................................................................2-11
Clear CMOS Jumper: JCMOS1 ............................................................... 2-11
AT/ATX Select Jumper: JATX1................................................................. 2-11
Serial Port Power Jumper: JCOMP1, JCOMP2.......................................2-12
LAN Congure Jumper: JLAN2................................................................2-12
LVDS Power Jumper: JVDD1 ..................................................................2-13
LVDS Inverter Power Jumper: JINV1.......................................................2-13
Intel ME Jumper: JME1............................................................................2-13
Slot...................................................................................................2-14
Mini-PCIe (Peripheral Component Interconnect Express) Slot................2-14
M.2 Slot (Key E, 2230).............................................................................2-14

2-3
Hardware Setup MS-98F3
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-98F3
Power Supply
DC Power Connector: JPWR2
This connector allows you to connect a 12V/ 19V/ 24V DC power adapter.
4.Ground
3.Ground
2.DC Power
1.DC P
ower
SATA Power Connector: JPW1
This connector is used to provide power to SATA devices.
Important
Make sure that all power connectors are connected to the power supply to ensure
stable operation of the motherboard.

2-5
Hardware Setup MS-98F3
Rear Panel I/O
USB 3.0
Port VGA Port
USB 2.0
Port GbE RJ45 Port HDMI Port
hUSB 2.0 Port
The USB (Universal Serial Bus) port is for attaching USB devices such as key-
board, mouse, or other USB-compatible devices.
hUSB 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).
hGbE RJ45 Port
The standard single RJ45 LAN jack is provided for connection to the Local Area
Network (LAN). You can connect a network cable to it.
Speed LED Active
LED
LED LED Status Description
Active
LED
Off No link
Yellow Linked
Blinking Data activity
Speed
LED
Off 10 Mbps connection
Green 100 Mbps connection
Orange 1 Gbps connection
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.
hVGA Port
The DB15-pin female connector is provided for monitors.

2-6
Hardware Setup MS-98F3
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.
9.N_GPO0
8.N_GPI1
3.N_GPO
3
1.GND
6.N_GPI2
5.N_GPO2
4.N_GPI3
7.N_GPO1
2.VCC5
10.N_GPI0
Serial ATA Connector: SATA1, SATA2
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-98F3
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.GND
3.HD_LED
1.HDD+
6.PWSW+
5.GND
4.SUS_LED
7.RESET+
2.PWR_LED
9.NC
LPC Debug Port Connector: JDP1
This connectoris LPC debug port.
1.LPC_FRAME#
2.LPC_AD3
3.LPC_AD2
4.LPC_AD1
5.LPC_AD0
6.L_LDRQ0#
7.TPM_CLK
8.SERIRQ_R
9.PLTRST_TPM#
10.VCC5
11.VCC3
12.GND
13.NA
14.GND
USB 2.0 Connector: JUSB1
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.

2-8
Hardware Setup MS-98F3
LVDS Inverter Connector: JINVDD1
The connector is provided for LCD backlight options.
6.Ground
4.VDIM
2.
INV_VDD(5V/12V DC)
5.Ground
3.Von/ off
1.INV_VDD(5V/12V DC)
LVDS Connector: JLVDS1
The LVDS (Low Voltage Differential 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.

2-9
Hardware Setup MS-98F3
Serial Port Connector: COM1 ~ COM4
This connector is a 16550A high speed communications port that sends/receives
16 bytes FIFOs. You can attach a serial device to it. COM1 supports RS-232/
422/ 485. COM2~4 support RS-232.
hCOM1
RS-232
PIN SIGNAL DESCRIPTION
1
2
3
4
5
6
7
8
9
10
NDCD
NSIN
NSOUT
NDTR
GND
NDSR
NRTS
NCTS
VCC
NC
Data Carrier Detect
Signal In
Signal Out
Data Terminal Ready
Signal Ground
Data Set Ready
Request To Send
Clear To Send
5V or 12V selected by jumper
No Connection
RS-422
PIN SIGNAL DESCRIPTION
1
2
3
4
5
6
7
8
9
10
422 TXD-
422 RXD+
422 TXD+
422 RXD-
GND
NC
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
No Connection
RS-485
PIN SIGNAL DESCRIPTION
1
2
3
4
5
6
7
8
9
10
485 TXD-
NC
485 TXD+
NC
GND
NC
NC
NC
NC
NC
Transmit Data, Negative
No Connection
Transmit Data, Positive
No Connection
Signal Ground
No Connection
No Connection
No Connection
No Connection
No Connection
hCOM2, COM3, COM4
RS-232
PIN SIGNAL DESCRIPTION
1
2
3
4
5
6
7
8
9
10
NDCD
NSIN
NSOUT
NDTR
GND
NDSR
NRTS
NCTS
VCC
NC
Data Carrier Detect
Signal In
Signal Out
Data Terminal Ready
Signal Ground
Data Set Ready
Request To Send
Clear To Send
5V or 12V selected by jumper
No Connection

2-10
Hardware Setup MS-98F3
Audio Amplier Pinheader: JAMP1
The JAMP1 is used to connect audio ampliers to enhance audio performance.
1.AMP_L-
2.AMP_L+
3.AMP_R-
4.AMP_R+
Front Audio Connector: JAUDIO1
This connector allows you to connect the front panel audio and is compliant with
Intel Front Panel I/O Connectivity Design Guide.
1.LINE1_1R_J
8.LINE1_JD
10.GND
3.LINE1_1L_J
6.MIC1_JD
5.LINE_FOUTR_J
4.MIC1_L_J
7.LINE_FOUTL_J
2.MIC1_R_J
12.GND
9.FRONT_JD
11.GND
PS/2 Keyboard/Mouse Connector: JKBMS1
This connector is provided to connect a keyboard and a mouse.
6.MS_CLK
4.KB_CLK
5.5VSB
3.MS_DAT
1.KB_DAT
2.GND
SMBus Connector: JSMB1
This connector is provided for users to connect System Management Bus
(SMBus) interface.
2.SMBCLK
3.SMBDAT
A
1.3VSB
4.GND