MSI MS-99A1 User manual

i
MS-99A1
Qseven Carrier Board

ii
Preface MS-99A1
Copyright Notice
The material in this document is the intellectual property of MICRO-STAR IN-
TERNATIONAL. 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
V1.0 2015/11
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, or contact our technical sta󰘯 via http://www.msi.com/support/

iii
Preface MS-99A1
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 module.
￭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.

iv
Preface MS-99A1
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-99A1
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 environ-
ment. 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:
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 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
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-99A1
Japan JIS C 0950 Material
Declaration
A Japanese regulatory requirement, de󰘰ned by speci󰘰cation JIS C 0950, man-
dates that manufacturers provide material declarations for certain categories of
electronic products o󰘯ered for sale after July 1, 2006.
http://www.msi.com/html/popup/csr/cemm_jp.html
http://tw.msi.com/html/popup/csr_tw/cemm_jp.html
日本JIS C 0950材質宣言
日本工業規格JIS C 0950により、2006年7月1日以降に販売される特定分野の
電気および電子機器について、製造者による含有物質の表示が義務付けられま
す。
http://www.msi.com/html/popup/csr/cemm_jp.html
http://tw.msi.com/html/popup/csr_tw/cemm_jp.html
India RoHS
This product complies with the "India E-waste (Management and Handling) Rule
2011" and prohibits use of lead, mercury, hexavalent chromium, polybrominat-
ed biphenyls or polybrominated diphenyl ethers in concentrations exceeding
0.1 weight % and 0.01 weight % for cadmium, except for the exemptions set in
Schedule 2 of the Rule.
Turkey EEE Regulation
Conforms to the EEE Regulations of the Republic Of Turkey
Türkiye EEE yönetmeliği
Türkiye Cumhuriyeti: EEE Yönetmeliğine Uygundur
Ukraine Restriction of Hazardous
Substances
The equipment complies with requirements of the Technical Regulation, ap-
proved by the Resolution of Cabinet of Ministry of Ukraine as of December 3,
2008 № 1057, in terms of restrictions for the use of certain dangerous substances
in electrical and electronic equipment.
Україна обмеження на наявність небезпечних речовин
Обладнання відповідає вимогам Технічного регламенту щодо обмеження
використання деяких небезпечних речовин в електричному та електронному
обладнані, затвердженого постановою Кабінету Міністрів України від 3
грудня 2008 № 1057.

vii
Preface MS-99A1
Vietnam RoHS
As from December 1, 2012, all products manufactured by MSI comply with
Circular 30/2011/TT-BCT temporarily regulating the permitted limits for a number
of hazardous substances in electronic and electric products.
Việt Nam RoHS
Kể từ ngày 01/12/2012, tất cả các sản phẩm do công ty MSI sản xuất tuân thủ
Thông tư số 30/2011/TT-BCT quy định tạm thời về giới hạn hàm lượng cho phép
của một số hóa chất độc hại có trong các sản phẩm điện, điện tử"

viii
Preface MS-99A1
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
Board Specications ..................................................................................1-2
Board Layout..............................................................................................1-4
2. Hardware Setup ...........................................................................2-1
Power Supply.............................................................................................2-3
Rear Panel I/O ...........................................................................................2-4
Connector...................................................................................................2-7
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.......................................................................................................... 3-11
Security ....................................................................................................3-12
Chipset.....................................................................................................3-16
Power .......................................................................................................3-17
Save & Exit...............................................................................................3-19
Appendix WDT & GPIO ................................................................... A-1
WDT Sample Code ................................................................................... A-2
GPIO Sample Code .................................................................................. A-3

1-1-1
Thank you for choosing the MS-99A1, an excellent Qseven Carrier
Board. It is a highly advanced, feature-rich carrier that offers PCIe and
Mini-PCIe expansion. This carrier board also features USB 3.0/USB 2.0
ports, an HDMI port, a DisplayPort, LVDS interface, serial port connec-
tors, audio connectors, a SATA port, Gigabit LAN jacks, etc.
1Overview

1-2
Overview MS-99A1
Board Specications
Storage
■1 x SATA 6Gb/s Port
■1 x SD Card Slot
Network
■LAN1: Based on CPU Module Board
■LAN2 ~ LAN6: Intel I211-AT GbE LAN
Audio
■Realtek ALC887 Audio Codec
■1 x Front Audio Connector
■1 x Amplier Connector
Graphics
■HDMI, DisplayPort, LVDS Interfaces
Onboard Headers/ Connectors/ Jumpers
■1 x 4-pin DC Power Connector
■1 x 4-pin SATA Power Connector
■1 x System FAN Connector
■1 x CPU FAN Connector
■1 x SATA 6Gb/s Port
■1 x Front Panel Connector
■1 x Front Audio Connector
■1 x Amplier Connector
■4 x RS232 Serial Port Connectors
■1 x UART Connector
■1 x GPIO Connector
■1 x SMBus Connector
■1 x CAN Bus Connector (Depending on CPU Module Board)
■1 x USB 2.0 Connector (1 port)
■1 x LVDS Connector
■1 x Inverter Connector
■1 x Keyboard/Mouse Connector
■1 x Chassis Intrusion Header
■1 x BIOS Select Jumper
■1 x Inverter Power Jumper
■1 x LVDS Power Jumper
■1 x I2C Power Jumper
■ 1 x AT/ATX Select Jumper
■3 x COM Port Power Jumpers
■ 5 x LAN NVM Jumpers

1-3
Overview MS-99A1
Rear Panel I/O
■2 x RS232/422/485 Serial Ports
■1 x HDMI Port
■1 x DisplayPort
■6 x Gigabit LAN Jacks
■2 x USB 3.0 Ports
■2 x USB 2.0 Ports
Expansion Slots
■1 x MXM Slot
■1 x PCIe x1 Slot
■2 x Mini-PCIe Slots
-MINI_PCIE1 supports full-size mSATA, WiFi and Bluetooth modules with
USB 2.0 signal.
-MINI_PCIE2 supports full-size WiFi/Bluetooth/3G modules with USB 2.0
signal. (Optional by SKU)
■1 x SIM Card Slot (Optional by SKU)
Form Factor
■Mini-ITX: 170mm x 170mm
Environmental
■Operating Temperature: -10 ~ 60oC
■Storage Temperature: -20 ~ 80oC
■Humidity: 10 ~ 90% RH, non-condensing
Regulatory Compliance
■ EMC: CE, FCC, BSMI, RCM, VCCI
■ RoHS compliant

1-4
Overview MS-99A1
Board Layout
USB 2.0
Port
DisplayPort USB 3.0
Port
HDMI Port
Serial Port Serial Port
RJ45 GbE LAN Port
RJ45 GbE LAN Port
RJ45 GbE LAN Port
Front Audio
Connector
AT/ATX Jumper COM Port
Connector
USB 2.0
Connector
SATA
Port
GPIO
Connector
LPC
Connector
Back Panel I/O
System Fan
Connector
KB/MS
Connector
COM Port Power
Jumper
Power
Connector
SMBus
Connector
Front Panel
Connector
PCIe Slot
Inverter
Connector
Inverter Power
Jumper LVDS Power
Jumper
BIOS Select
Jumper
LVDS Connector
CPU Fan
Connector
MXM Slot
UART Connector
COM Port Power
Jumper
CAN Bus
Connector
I2C Connector
I2C Power
Jumper
Amplier
Connector
Chassis Intrusion
Header
COM Port
Power Jumper
LAN NVM
Jumper
Mini PCIe Slot SIM Card
Slot
SD Card
Slot
SATA Power
Connector

2-2-1
This chapter provides you with the information about hardware
setup procedures. While doing the installation, be careful in holding
the components and follow the installation procedures. For some
components, if you install in the wrong orientation, the components will
not work properly.
Use a grounded wrist strap before handling computer components. Static
electricity may damage the components.
2Hardware Setup

2-2
Hardware Setup MS-99A1
Components Reference Guide
Power Supply....................................................................................2-3
DC-In Power Connector: JPWR1...............................................................2-3
SATA Power Connector: JSATA_PWR1.....................................................2-3
Rear Panel I/O ...................................................................................2-4
Connector..........................................................................................2-7
Fan Power Connector: CPUFAN1, SYSFAN1 ...........................................2-7
SMBus/I2C Bus Connector: JSMB1, JI2C2 �����������������������������������������������2-7
CAN Bus Connector: JCANBUS1��������������������������������������������������������������2-7
GPIO Pin Header: JGPIO1 ........................................................................2-8
Serial ATA Connector: SATA1 ....................................................................2-8
Keyboard/Mouse Connector: JKBMS1 ......................................................2-9
Front Panel Connector: JFP1.....................................................................2-9
UART Connector: JUART1 ����������������������������������������������������������������������2-10
Serial Port Connector: JCOM3, JCOM4, JCOM5, JCOM6......................2-10
LVDS Inverter Connector: JINVDD1 ........................................................ 2-11
LVDS Connector: JLVDS1 ....................................................................... 2-11
Audio Amplier Header: JAMP1...............................................................2-12
Front Audio Connector: JAUDIO1 ............................................................2-12
USB 2.0 Connector: JUSB1.....................................................................2-12
Chassis Intrusion Header: JCASE1 .........................................................2-13
LPC Debug Port Connector: JLPC1.........................................................2-13
Jumper.............................................................................................2-14
NVM LAN Jumper: JNVM1, JNVM2, JNVM3, JNVM4, JNVM5 ...............2-14
AT/ATX Select Jumper: JATATX1 ............................................................2-14
I2C Power Jumper: JI2C1........................................................................2-14
COM Port Power Jumper: JCOMP1, JCOMP2, JCOMP3 .......................2-15
BIOS Select Jumper: JBIOS1 ..................................................................2-15
LVDS Power Jumper: JVDD1 ..................................................................2-15
Inverter Power Jumper: JINV1.................................................................2-15
Slot...................................................................................................2-16
Qseven Connector Slot............................................................................2-16
PCIe (Peripheral Component Interconnect Express) Slot........................2-16
Mini-PCIe (Peripheral Component Interconnect Express) Slot................2-16

2-3
Hardware Setup MS-99A1
Power Supply
DC-In Power Connector: JPWR1
This connector is used to provide power to the motherboard.
SATA Power Connector: JSATA_PWR1
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-99A1
Rear Panel I/O
USB 2.0
Port
DisplayPort USB 3.0
Port
HDMI Port
Serial Port Serial Port
RJ45 GbE LAN Port
RJ45 GbE LAN Port
RJ45 GbE LAN Port
USB 2.0
Port
DisplayPort USB 3.0
Port
HDMI Port
Serial Port Serial Port RJ45 GbE LAN Port
hRS232/422/485 Serial Port
The serial port is a 16550A high speed communications port that sends/ receives
16 bytes FIFOs. You can attach a serial mouse or other serial devices directly to
the connector.
PIN SIGNAL DESCRIPTION
1
2
3
4
5
6
7
8
9
DCD
RXD
TXD
DTR
GND
DSR
RTS
CTS
VCC_COM1
Data Carrier Detect
Receive Data
Transmit Data
Data Terminal Ready
Signal Ground
Data Set Ready
Request To Send
Clear To Send
Voltage select setting by jumper
RS232

2-5
Hardware Setup MS-99A1
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
RS422
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
RS485
hHDMI Port
The High-Denition Multimedia Interface (HDMI) is an all-digital audio/video
interface 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.
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).
hUSB 2.0 Port
The USB (Universal Serial Bus) port is for attaching USB devices such as
keyboard, mouse, or other USB-compatible devices.

2-6
Hardware Setup MS-99A1
hRJ45 GbE 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.

2-7
Hardware Setup MS-99A1
Connector
Fan Power Connector: CPUFAN1, SYSFAN1
The fan power connectors support system cooling fan with +12V. When
connecting 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.
SMBus/I2C Bus Connector: JSMB1, JI2C2 (This function de-
pends on CPU module board)
This connector, known as I2C, is for users to connect System Management Bus
(SMBus) interface.
CAN Bus Connector: JCANBUS1 (This function depends on
CPU module board)
Controller Area Network (CAN or CAN-bus) is a message based protocol
designed specically for automotive applications but now is also used in other
areas such as industrial automation and medical equipment. The bus connector
for the CAN Bus is used to connect a CAN Bus participant to the CAN Bus line.

2-8
Hardware Setup MS-99A1
GPIO Pin Header: JGPIO1
This connector is provided for the General-Purpose Input/Output (GPIO)
peripheral module.
Serial ATA Connector: SATA1
This connector is a high-speed Serial ATA Gen3 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�