Advantech MIC-3399 User manual

User Manual
MIC-3399
6U CompactPCI Blade SBC with
6th Gen. Intel® Core™ i3/i5/i7
Processor and Optional ECC
Memory

MIC-3399 User Manual ii
Copyright
The documentation and the software included with this product are copyrighted 2020
by Advantech Co., Ltd. All rights are reserved. Advantech Co., Ltd. reserves the right
to improve the products described in this manual at any time without notice. No part
of this manual may be reproduced, copied, translated, or transmitted in any form or
by any means without the prior written permission of Advantech Co., Ltd. The infor-
mation provided in this manual is intended to be accurate and reliable. However,
Advantech Co., Ltd. assumes no responsibility for its use, nor for any infringements
of the rights of third parties that may result from its use.
Acknowledgments
Intel® and Core™ i are trademarks of Intel Corporation.
All other product names or trademarks are properties of their respective owners.
Product Warranty (2 years)
Advantech warrants the original purchaser that each of its products will be free from
defects in materials and workmanship for two years from the date of purchase.
This warranty does not apply to any products that have been repaired or altered by
persons other than repair personnel authorized by Advantech, or products that have
been subject to misuse, abuse, accident, or improper installation. Advantech
assumes no liability under the terms of this warranty as a consequence of such
events.
Because of Advantech’s high quality-control standards and rigorous testing, most
customers never need to use our repair service. If an Advantech product is defective,
it will be repaired or replaced free of charge during the warranty period. For out-of-
warranty repairs, customers will be billed according to the cost of replacement mate-
rials, service time, and freight. Please consult your dealer for more details.
If you believe your product is defective, follow the steps outlined below.
1. Collect all the information about the problem encountered. (For example, CPU
speed, Advantech products used, other hardware and software used, etc.) Note
anything abnormal and list any onscreen messages displayed when the prob-
lem occurs.
2. Call your dealer and describe the problem. Please have your manual, product,
and any helpful information readily available.
3. If your product is diagnosed as defective, obtain a return merchandize authori-
zation (RMA) number from your dealer. This allows us to process your return
more quickly.
4. Carefully pack the defective product, a completed Repair and Replacement
Order Card, and a proof of purchase date (such as a photocopy of your sales
receipt) into a shippable container. Products returned without a proof of pur-
chase date are not eligible for warranty service.
5. Write the RMA number clearly on the outside of the package and ship the pack-
age prepaid to your dealer.
Part No. 2002339900 Edition 1
Printed in China September 2020

iii MIC-3399 User Manual
Declaration of Conformity
CE
This product has passed the CE test for environmental specifications when shielded
cables are used for external wiring. We recommend the use of shielded cables.
FCC Class A
This equipment has been tested and found to comply with the limits for a Class A dig-
ital device, pursuant to part 15 of the FCC Rules. These limits are designed to pro-
vide 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. Opera-
tion of this equipment in a residential area is likely to cause harmful interference. In
this event, users are required to correct the interference at their own expense.
FM
This equipment has passed the FM certification. According to the National Fire Pro-
tection Association, work sites are categorized into different classes, divisions, and
groups based on hazard considerations. This equipment is compliant with the specifi-
cations for Class I, Division 2, Groups A, B, C, and D indoor hazards.
Technical Support and Assistance
1. Visit the Advantech website at http://support.advantech.com to obtain the latest
product information.
2. Contact your distributor, sales representative, or Advantech’s customer service
center for technical support if you need additional assistance. Please have the
following information ready before calling:
–Product name and serial number
–Description of your peripheral attachments
–Description of your software (operating system, version, application software,
etc.)
–A complete description of the problem
–The exact wording of any error messages

MIC-3399 User Manual iv
Warnings, Cautions, and Notes
Document Feedback
To assist us with improving this manual, we welcome all comments and constructive
criticism. Please send all such feedback in writing to [email protected].
Packing List
Before system installation, check that the items listed below are included and in good
condition.
1 x MIC-3399 all-in-one single-board computer (CPU heatsink and PCH heat-
sink included)
1 x Daughter board for SATA HDD (assembled)
1 x HDD tray and screw package
1 x Solder-side cover (assembled)
1 x RJ45-to-DB9 cable
1 x Warranty certificate
If any of the above items are missing or damaged, contact your distributor or sales
representative immediately.
Warning! Warnings indicate conditions that if not observed can cause personal
injury!
Caution! Cautions are included to help prevent hardware damage and data
losses. For example,
“Batteries are at risk of exploding if incorrectly installed. Do not attempt
to recharge, force open, or heat the battery. Replace the battery only
with the same or equivalent type as recommended by the manufacturer.
Discard used batteries according to the manufacturer's instructions.”
Note! Notes provide additional optional information.

v MIC-3399 User Manual
Safety Instructions
1. Read these safety instructions carefully.
2. Retain this user manual for future reference.
3. Disconnect the equipment from all power outlets before cleaning. Use only a
damp cloth for cleaning. Do not use liquid or spray detergents.
4. For pluggable equipment, the power outlet socket must be located near the
equipment and easily accessible.
5. Protect the equipment from humidity.
6. Place the equipment on a reliable surface during installation. Dropping or letting
the equipment fall may cause damage.
7. The openings on the enclosure are for air convection. Protect the equipment
from overheating. Do not cover the openings.
8. Ensure that the voltage of the power source is correct before connecting the
equipment to a power outlet.
9. Position the power cord away from high-traffic areas. Do not place anything over
the power cord.
10. All cautions and warnings on the equipment should be noted.
11. If the equipment is not used for a long time, disconnect it from the power source
to avoid damage from transient overvoltage.
12. Never pour liquid into an opening. This may cause fire or electrical shock.
13. Never open the equipment. For safety reasons, the equipment should be
opened only by qualified service personnel.
14. If any of the following occurs, have the equipment checked by service person-
nel:
The power cord or plug is damaged.
Liquid has penetrated the equipment.
The equipment has been exposed to moisture.
The equipment is malfunctioning, or does not operate according to the user
manual.
The equipment has been dropped and damaged.
The equipment shows obvious signs of breakage.
15. Do not leave the equipment in an environment with a storage temperature of
below -20 °C (-4 °F) or above 60 °C (140 °F) as this may damage the compo-
nents. The equipment should be kept in a controlled environment.
16. Batteries are at risk of exploding if incorrectly installed. Replace only with the
same or equivalent type as recommended by the manufacturer. Discard used
batteries according to the manufacturer’s instructions.
17. In accordance with the IEC 704-1:1982 specifications, the sound pressure level
at the operator’s position does not exceed 70 dB (A).
DISCLAIMER: These instructions are provided according to IEC 704-1 standards.
Advantech disclaims all responsibility for the accuracy of any statements contained
herein.

MIC-3399 User Manual vi
Safety Precautions - Static Electricity
Follow these simple precautions to protect yourself from harm and the products from
damage:
To avoid electrical shock, always disconnect the power from the PC chassis
before manual handling. Do not touch any components on the CPU card or
other cards while the PC is powered on.
Disconnect the power before making any configuration changes. A sudden rush
of power after connecting a jumper or installing a card may damage sensitive
electronic components.
We Appreciate Your Input
Please let us know of any aspect of the product could use improvement or correction.
We appreciate your valuable input in helping to make our products better.

vii MIC-3399 User Manual
Glossary
ACPI Advanced configuration and power interface
API Application programming interface
BIOS Basic input/output system
BMC Baseboard management controller
CLI Command line interface
CPU Central processing unit
DDR4 Double data rate 4
DIMM Dual in-line memory module
DIP Dual in-line package
ECC Error checking and correction
FCBGA Flip chip BGA
Flash Flash memory
FPGA Field-programmable gate array
FRU Field replaceable unit
GbE Gigabit Ethernet
GPIO General purpose input/output
HDD Hard disk drive
HPM.1 Hardware PlatformManagement.1
HW Hardware
I/O Input/output
IC Integrated circuit
I2C Inter-integrated circuit
IPMB Intelligent platform management bus
IPMI Intelligent platform management interface
KCS Keyboard controller style
LPC Low pin count
MAC Medium access control
NCSI Network controller sideband interface
NVRAM Non-volatile random access memory
PCI Peripheral component interconnect
PCIe Peripheral component interconnect express
RIO Rear input/output
RMCP Remote management communication protocol
RS-232 Recommended standard 232
RTC Real-time clock
RTM Rear transition module
SATA Serial advanced technology attachment
SDR Sensor data record
SEL System event log
SPD Serial presence detect
SPI Serial peripheral interface
SW Software
UART Universal asynchronus receiver transmitter
USB Universal serial bus

MIC-3399 User Manual viii

ix MIC-3399 User Manual
Contents
Chapter 1 Hardware Configuration.....................1
1.1 Introduction ............................................................................................... 2
1.2 Specifications............................................................................................ 2
1.2.1 CompactPCI Bridge ...................................................................... 2
1.2.2 Processor...................................................................................... 3
Table 1.1: Processor Type .......................................................... 3
1.2.3 Chipset.......................................................................................... 3
1.2.4 Memory ......................................................................................... 4
Table 1.2: Memory Type.............................................................. 4
1.2.5 Ethernet ........................................................................................ 4
1.2.6 Storage Interface .......................................................................... 4
1.2.7 Serial ports.................................................................................... 5
1.2.8 USB Port ....................................................................................... 5
1.2.9 System Reset and BMC Reset Button.......................................... 5
1.2.10 XMC IEEE1386.1 Compliant......................................................... 5
1.2.11 Watchdog Timer............................................................................ 5
1.2.12 BIOS ............................................................................................. 5
1.2.13 I/O Connectivity............................................................................. 6
1.2.14 Optional Rear I/O Modules ........................................................... 6
Table 1.3: RIO-3316 Configuration.............................................. 6
1.2.15 Mechanical and Environmental Specifications.............................. 7
1.2.16 Compact Mechanical Design ........................................................ 7
1.2.17 Hardware Monitor ......................................................................... 7
1.2.18 Super I/O....................................................................................... 7
1.2.19 RTC and Battery ........................................................................... 7
1.2.20 IPMI............................................................................................... 7
1.3 Functional Block Diagram ......................................................................... 8
Figure 1.1 MIC-3399 Functional Block Diagram.......................... 8
1.4 Jumpers and Switches .............................................................................. 8
Table 1.4: Jumper Descriptions................................................... 8
Table 1.5: Switch Descriptions .................................................... 8
1.4.1 Jumper Settings ............................................................................ 9
Table 1.6: JCMOS1 Clear RTC ................................................... 9
Table 1.7: JLVDS1 Settings ........................................................ 9
1.4.2 Switch Settings ........................................................................... 10
Table 1.8: SW2-1 Switch VGA Output....................................... 10
Table 1.9: SW2-2 Switch LAN2 Output ..................................... 10
Table 1.10:SW2-3 Switch PCI Bridge Mode............................... 10
Table 1.11:SW2-4 Drone Mode Settings.................................... 11
Table 1.12:SW4 PCIE Mode Settings ........................................ 11
1.4.3 RIO-3316-C1E DIP Switch Settings............................................ 12
Table 1.13:SW3 and SW4 for Internal COM1 ............................ 12
Table 1.14:SW5 and SW6 for COM2 ......................................... 12
1.5 Connector Definitions.............................................................................. 13
Table 1.15:Onboard Connector Descriptions ............................. 13
Figure 1.2 MIC-3399 Front Panel Ports, Indicators, and Buttons ..
..................................................................................13
Figure 1.3 RIO-3316-C1E Front Panel Ports and Indicators ..... 13
1.6 Safety Precautions.................................................................................. 13
1.7 Hardware Installation .............................................................................. 14
1.7.1 HDD Installation .......................................................................... 14
Figure 1.4 MIC-3399 Assembly with 2.5” HDD.......................... 14
Figure 1.5 Attach the SATA HDD to the HDD brackets............. 15
Figure 1.6 Installing the SATA HDD into the Chassis................ 15

MIC-3399 User Manual x
1.8 Battery Replacement .............................................................................. 16
1.9 Software Support .................................................................................... 16
Chapter 2 AMI BIOS Setup................................. 17
2.1 Introduction ............................................................................................. 18
Figure 2.1 BIOS Setup Utility Main Menu.................................. 18
2.2 BIOS Setup Utility ................................................................................... 19
2.3 Entering the BIOS ................................................................................... 19
Figure 2.2 BIOS POST Screen.................................................. 19
2.3.1 Main Screen................................................................................ 20
Figure 2.3 Main BIOS Setup Page ........................................... 20
2.3.2 Platform Settings ........................................................................ 21
Figure 2.4 Platform BIOS Setup Page....................................... 21
Figure 2.5 Serial Console Setting.............................................. 22
Figure 2.6 Firmware Update...................................................... 23
Figure 2.7 USB Configuration.................................................... 24
Figure 2.8 Trusted Computing................................................... 25
Figure 2.9 Virtualization............................................................. 26
Figure 2.10Platform Management .............................................. 27
2.3.3 Hardware Settings ...................................................................... 28
Figure 2.11Hardware BIOS Setup Page .................................... 28
Figure 2.12CPU Configuration ................................................... 29
Figure 2.13Northbridge............................................................... 30
Figure 2.14Memory Configuration .............................................. 30
Figure 2.15PEG Port Configuration............................................ 31
Figure 2.16PCI Subsystem......................................................... 32
Figure 2.17Graphics Configuration............................................. 33
Figure 2.18LCD Control.............................................................. 34
Figure 2.19Southbridge .............................................................. 35
Figure 2.20SATA Configuration.................................................. 36
Figure 2.21NCT6126D Super I/O Configuration......................... 37
Figure 2.22SIO Uart1 to RJ45 .................................................... 37
Figure 2.23SIO UART1 to BMC UART2..................................... 38
Figure 2.24Serial Port Mode....................................................... 39
Figure 2.25Serial Port1 Configuration ........................................ 40
Figure 2.26Serial Port 2 Configuration ....................................... 41
Figure 2.27Serial Port 3 Configuration ....................................... 42
Figure 2.28Serial Port 4 Configuration ....................................... 43
Figure 2.29H/W Monitor configuration........................................ 44
2.3.4 Server Management ................................................................... 45
Figure 2.30Server Mgmt BIOS Setup Page ............................... 45
2.3.5 Post & Boot................................................................................. 46
Figure 2.31Post & Boot BIOS Setup Page ................................. 46
Figure 2.32CSM16 Parameters.................................................. 47
Figure 2.33CSM Parameters...................................................... 48
2.3.6 Security....................................................................................... 49
Figure 2.34Security Settings ...................................................... 49
2.3.7 Save & Exit ................................................................................. 50
Figure 2.35Save & Exit............................................................... 50
Chapter 3 IPMI Configuration ............................ 51
3.1 Introduction ............................................................................................. 52
3.2 Terms and Definitions ............................................................................. 53
3.3 IPMI Interfaces........................................................................................ 54
Figure 3.1 Management Block Diagram .................................... 54
3.3.1 IPMB-0........................................................................................ 54
3.3.2 KCS ............................................................................................ 54

xi MIC-3399 User Manual
3.3.3 LAN ............................................................................................. 55
Table 3.1: Supported Network Protocols................................... 55
3.4 Command Line Interface......................................................................... 56
Table 3.2: Standard CLI Commands ......................................... 56
3.5 BMC Watchdog....................................................................................... 57
3.5.1 BIOS Boot Watchdog.................................................................. 57
3.6 System Event Log (SEL)......................................................................... 57
3.7 Sensors ................................................................................................... 58
3.7.1 Sensor List .................................................................................. 58
Table 3.3: BMC Sensor List....................................................... 58
3.7.2 Threshold-Based Sensors .......................................................... 59
Table 3.4: Sensor Threshold Description .................................. 59
3.7.3 Voltage Sensors.......................................................................... 59
Table 3.5: Voltage Sensor List .................................................. 59
3.7.4 Temperature Sensors ................................................................. 60
Table 3.6: Temperature Sensor List .......................................... 60
3.7.5 Integrity Sensor........................................................................... 60
Table 3.7: Integrity Sensor Event Data Table............................ 60
3.8 OEM IPMI Commands ............................................................................ 61
Table 3.8: OEM Command List ................................................. 61
3.8.1 Set Multiplexer Command........................................................... 61
Table 3.9: Set Multiplexer Command ........................................ 61
3.8.2 Get Multiplexer Command .......................................................... 62
Table 3.10:Get Multiplexer Command........................................ 62
3.8.3 SEL Mode Configuration Command ........................................... 62
Table 3.11:SEL Mode Configuration Command......................... 62
3.8.4 Reload NVRAM Defaults Command........................................... 62
Table 3.12:Reload NVRAM Defaults Command ........................ 62
3.8.5 Write MAC Address Command................................................... 63
Table 3.13:Write MAC Address Command ................................ 63
3.8.6 Store Configuration Command ................................................... 64
Table 3.14:Store Configuration Command ................................. 64
3.8.7 Read Configuration Command ................................................... 66
Table 3.15:Read Configuration Settings Command ................... 66
3.8.8 Read Port 80 Command ............................................................. 67
Table 3.16:Read Port 80 Command (BIOS POST Code) .......... 67
3.8.9 Read MAC Address Command................................................... 68
Table 3.17:Read MAC Address Command ................................ 68
3.8.10 Reload BMC Default Configuration Command ........................... 68
Table 3.18:Reload BMC Default Configuration Command......... 68
3.9 HPM.1 Upgrade Support......................................................................... 69
Table 3.19:Supported HPM.1 Components................................ 69
3.9.1 Bootloader Update ...................................................................... 69
3.9.2 Firmware Upgrade ...................................................................... 69
3.9.3 FPGA Upgrade ........................................................................... 69
3.9.4 BIOS Upgrade............................................................................. 69
3.10 Board Information.................................................................................... 70
Table 3.20:Board Info Area-SKU1.............................................. 70
Table 3.21:Board Info Area-SKU2.............................................. 71
Table 3.22:Board Info Area-SKU3.............................................. 71
3.10.1 Product Information..................................................................... 72
Table 3.23:Product Info Area...................................................... 72
Appendix A Pin Assignments ...............................73
A.1 J1 Connector........................................................................................... 74
Table A.1: J1 CompactPCI I/O................................................... 74
A.2 J2 Connector........................................................................................... 75
Table A.2: J2 CompactPCI I/O................................................... 75

MIC-3399 User Manual xii
A.3 J3 Connector........................................................................................... 76
Table A.3: J3 CompactPCI I/O (PICMG 2.16) ........................... 76
A.4 J4 Connector........................................................................................... 77
Table A.4: J4 CompactPCI I/O port ........................................... 77
A.5 J5 Connector........................................................................................... 78
Table A.5: J5 CompactPCI I/O Port........................................... 78
A.6 On-Board Connector............................................................................... 79
Table A.6: SATA1 Daughter Board Connector .......................... 79
Table A.7: XMC1 Connector...................................................... 79
A.7 Front I/O Connector ................................................................................ 80
Table A.8: VGA1 Connector ...................................................... 80
Table A.9: RJ45 LAN1/LAN2 Connector ................................... 80
Table A.10:USB3CN1, USB3CN2, USB3CN3............................ 80
Table A.11:COM1 (RJ45) Connector.......................................... 80
Table A.12:BH1 CMOS Battery .................................................. 80
A.8 M/D, PWR, BMC, HDD, and Hot-Swappable LEDs................................ 81
Table A.13:Front Panel LED Indicators ...................................... 81
Appendix B Programming the Watchdog Timer . 83
Appendix C FPGA Specifications......................... 85
C.1 Overview ................................................................................................. 86
C.2 Features.................................................................................................. 86
C.3 FPGA I/O Registers ................................................................................ 86
Table C.1: LPC I/O Registers Address ...................................... 86

Chapter 1
1Hardware
Configuration
This chapter describes how to
configure the MIC-3399 hardware.

MIC-3399 User Manual 2
1.1 Introduction
Advantech’s MIC-3399 series are 6U CompactPCI blade single-board computers
(SBCs) with a 6th gen. Intel® Core™ i3/i5/i7/ Xeon®E3 processor and Intel® CM236
chipset. The processor uses Intel® 14 nm process technology, with a clock speed of
up to 2.8 GHz and 8 MB smart cache, and supports dual-channel memory (ECC
optional) of up to 32 GB DDR4 at 2133 MHz, with 16 GB onboard and one 16 GB
SODIMM.
The front panel features up to six SATA in various 2.5”SATA/M.2/NAND flash form
factors, five Gigabit Ethernet (including two PICMG 2.16 GbE), eleven USB, three
COM, and one PS/2 interfaces that can be reserved for RTM J3/J4/J5. One PCIe x8
interface is reserved for J3 using a high-speed UHM connector with certain configu-
rations.
Designed for harsh environments, MIC-3399 can be installed via a standard Com-
pactPCI system slot and is ideal for datacom, telecom, military, medical, defense, and
other vertical segment applications. Compliant with PICMG 2.1/2.16/2.9/2.0 Rev 3.0
specifications, MIC-3399 supports 64-bit PCI bus extensions (66/33 MHz) for up to
six CompactPCI slots at +3.3 V or +5 V VIO.
1.2 Specifications
1.2.1 CompactPCI Bridge
MIC-3399 uses a Pericom PI7C9X130 universal bridge as a gateway to intelligent
subsystems. When configured as a system controller, the bridge acts as a standard
transparent PCIe-to-PCI/PCI-X bridge. As a peripheral controller, the local MIC-3399
processor can be used to configure and control the onboard local subsystem inde-
pendently from the CompactPCI bus host processor. When MIC-3399 is in drone
mode, the Pericom PI7C9X130 bridge is electrically isolated from the CompactPCI
bus, receives power from the backplane, and supports the rear I/O only. The Pericom
PI7C9X130 PCI bridge offers the following features:
PCI interface
–Full compliance with the PCI Local Bus Specification, Revision 3.0
–Supports 3.3V PCI signaling with 5V I/O tolerance
Supports transparent mode operations
Supports forward bridging
64-bit, 66 MHz asynchronous operation
Provides two-level arbitration support for 7 PCI bus masters
16-bit address decode for VGA
Can be installed via a CompactPCI slot
For additional details, refer to the Pericom PI7C9X130 datasheet.

3 MIC-3399 User Manual
Chapter 1 Hardware Configuration
1.2.2 Processor
MIC-3399 supports a 6th gen. Intel® Core™ i3/i5/i7/Xeon® E3 processor with clock
frequencies of up to 2.8 GHz and a Direct Media Interface (DMI) of up to 8 GT/s.
Contact your local distributor or sales representative for more informations regarding
processor configurations.
1.2.3 Chipset
The mobile Intel® CM236 chipset provides excellent flexibility for developers of
embedded applications by offering improved graphics and increased I/O bandwidth
compared to previous Intel chipsets. The Intel® CM236 chipset offers up to 8 GT/s for
fast access to peripheral devices and supports high-bandwidth interfaces such as
PCI Express Gen III, Serial ATA Gen III, and Hi-Speed USB 2.0 and USB 3.0.
Table 1.1: Processor Type
Intel Model
Number
CPU
Archite
cture
#
Cores
#
Threads Freq. Cache DMI CPU TDP Package Required Airflow
i3-6100E
Sky-
lake
(14 nm)
2 4 2.7 GHz 3 MB 8 GT/s 35 W FCBGA 30 CFM
I7-6822EQ
Sky-
lake
(14 nm)
4 8 2.0 GHz 8 MB 8 GT/s 25 W FCBGA 30 CFM
I7-6820EQ
Sky-
lake
(14 nm)
4 8 2.8 GHz 8 MB 8 GT/s 45 W FCBGA 30 CFM
Note! Because power consumption and thermal restrictions vary between dif-
ferent CompactPCI systems, double check these specifications before
installing a higher speed CPU not listed in the table above.

MIC-3399 User Manual 4
1.2.4 Memory
MIC-3399 features up to 16 GB onboard DDR4 memory with the Intel® Core™/
Xeon® processor offering support for optional ECC memory. The system also has
one 260-pin SODIMM socket that can accommodate an additional 4 GB SODIMM(up
to 16 GB max.). The following table lists the SODIMM modules that have been tested
with MIC-3399.
.
1.2.5 Ethernet
MIC-3399 is equipped with five high-performance PCIe-based network interface con-
trollers that are fully compliant with IEEE802.3 10/100/1000BASE-TX Ethernet. The
front panel features two GbE ports (LAN1 and LAN2) and three panel-to-RTM J3/J5
connectors. One port can be switched between front panel LAN2 and RTM J5. Fur-
thermore, MIC-3399 supports the PICMG 2.16 Packet Switching Backplane (cPSB)
architecture via the J3 connector.
Front I/O (RJ45)
Rear I/O (rear transition module)
PICMG 2.16
1.2.6 Storage Interface
MIC-3399 provides up to six SATA III interfaces with RAID 0/1/5/10 support. Two
SATA interfaces are routed to the onboard 2.5” SATA daughter board (only one 2.5”
SATA daughter board is reserved as a default); one to a SATA M.2 connector with
2242/2280 form factor; one to optional onboard NAND flash; and two to the rear I/O
module.
Advantech’s RIO-3316C rear transition board is compatible with MIC-3399 and can
support SATA II devices as a default and SATA III devices with the inclusion of a
UHM connector upon request. Contact your local sales representative for more
details.
Table 1.2: Memory Type
Brand Size Speed Vendor Part
Number ECC Pin Count Memory Chip
Advantech
16 GB DDR4 2600 AQD-
SD4U16GE26-SE Yes 260 pin Samsung
16 GB DDR4 2600 AQD-
SD4U16N26-SE No 260 pin Samsung
8 GB DDR4 2600 AQD-
SD4U8GN26-SE No 260 pin Samsung
Kingston 4 GB DDR4 2400 KVR24S17S6/4-
SP No 260 pin Samsung
Note! ECC support is optional. Please contact your local sales team if you
require ECC memory.

5 MIC-3399 User Manual
Chapter 1 Hardware Configuration
1.2.7 Serial ports
One RJ45 COM1 port (RS-232/422/485) is provided on the front panel with one
RJ45-to-DB9 adapter cable provided as an accessory. Two COM ports are routed to
the rear I/O module via the J5 connector. If you encounter problems with a serial
device, check the pin assignments listed in Appendix A. The IRQ and address range
for these ports are fixed. If a disabled port or parameter modification is required, refer
to Chapter 2.
1.2.8 USB Port
MIC-3399 provides three USB 3.0 type-A ports on the front panel and up to six USB
2.0 and three USB 3.0 interfaces via a J3/J5-to-CompactPCI connector. The MIC-
3399 USB interfaces comply with USB, R2.0 and 3.0, specifications and are fuse pro-
tected (5 V @ 1.1 A).
1.2.9 System Reset and BMC Reset Button
MIC-3399 provides a system reset button located on the front panel. The system
reset button resets all payload and application-related circuitry. However, it does not
reset the system management (IPMI)-related circuitry. A separate BMC reset button
on the front panel is provided for BMC and related hardware control.
1.2.10 XMC IEEE1386.1 Compliant
Additional I/O or co-processing functionality is supported with the inclusion of add-on
XMC modules. MIC-3399 supports one single-width XMC that is fully compliant with
VITA 42.0-2005 and 42.3-2006. XMC supports PCIe x8 Gen3 at 3.3V, 5V, and 12V
depending on usage.
The two-layer front panel design complies with IEEE 1101.10 standard specifications.
Connectors are firmly screwed into the front panel, and a shielding gasket is attached
to the panel edge. This reduces emissions and increases protection from external
interference.
1.2.11 Watchdog Timer
An onboard watchdog timer provides system reset capabilities via software control.
The programmable time interval ranges from 1 to 255 seconds.
1.2.12 BIOS
MIC-3399 features dual 16 MB SPI flash containing specific AMI BIOS firmware with
a fail-over mechanism, satisfying industrial and embedded system requirements.

MIC-3399 User Manual 6
1.2.13 I/O Connectivity
The MIC-3399 front panel I/O includes two RJ45 Gigabit Ethernet, one RJ45 COM,
three USB 3.0, one VGA, and one XMC knockout. Rear I/O connectivity is available
via CompactPCI connectors as listed below.
Different J3 connector types can be configured as HM or uHM to enable different
SATA/PCIe extension speeds. For user-designed RTM boards, refer to the J3/J4/J5
pin definition information in Appendix A.
1.2.14 Optional Rear I/O Modules
The optional rear transition module (also known as rear I/O module) designed for
MIC-3399 is Advantech’s RIO-3316 module. RIO-3316 offers a wide variety of I/O,
including four RJ45 LAN, one RJ45 COM, two DVI, one USB 3.0, one USB 2.0, one
P/S2 in the rear panel, one COM pin header, four USB 2.0 pin headers, and two
SATA connectors. RIO-3316 modules are available with various I/O as shown below.
RTM Connector Connector Type Reserved Interface
J3 HM or uHM
(optional)
Two SATA 3.0
One PCIex8
Two GbE LAN (PICMG 2.16)
Two USB 3.0
J4 HM
One LVDS
One DVI
One Audio/Mic
J5 HM
Two GbE (one port is switchable with front
LAN2)
Two COM
Two USB 2.0
One PS/2
One DVI
Table 1.3: RIO-3316 Configuration
RTM
Model
Number
Rear Panel Onboard Pin Header/Connector
LAN
(RJ45)
COM
(RJ45)
DVI
-I
DVI
-D PS/2 USB 2.0
USB
3.0
USB
2.0 SATA COM*Audio Conn.
RIO-
3316-
C1E
4 1 1 1 1 1 1 4 2 1 1 J3, J4,
J5
Note! *The onboard COM pin header is switchable with the front panel RJ45
COM port.

7 MIC-3399 User Manual
Chapter 1 Hardware Configuration
1.2.15 Mechanical and Environmental Specifications
Operating Temperature: 0 ~ 55 °C/-32 ~ 131 °F
Storage Temperature: -40 ~ 85 °C/-40 ~ 185 °F
Humidity: 95% @ 40 °C/104 °F (non-condensing)
Humidity (non-operating): 95% @ 60 °C/140 °F (non-condensing)
Vibration: 5~100 Hz, 2 Grms (without onboard 2.5” SATA HDD)
Shock: 10 G (without onboard 2.5” SATA HDD)
Board Size: 233.35 x 160 mm/9.18 x 6.29 in (6U size), 1-slot (4 TE) wide
Weight: 0.8 kg (1.76 lb)
1.2.16 Compact Mechanical Design
Forced air cooling in the chassis is recommended for MIC-3399 to optimize the sys-
tem stability and reliability although a special Cu-designed heatsink is included in the
unit.
1.2.17 Hardware Monitor
MIC-3399 features two types of HWM management systems. In order to monitor the
processor temperature and core voltage information, NCT7904D is connected to the
BMC and NCT6776D is connected to the X86 payload.
1.2.18 Super I/O
The MIC-3399 super I/O device provides the following legacy PC features:
Serial port COM1 and COM2 are connected to J5 and can be accessed via the
rear I/O module. The rear COM1 can be switched with the front panel COM via
multiplexer in the FPGA.
PS2 (keyboard/mouse) is routed to J5 and can be accessed via the rear I/O
module.
1.2.19 RTC and Battery
The RTC module retains the system date and time. The MIC-3399 RTC circuitry is
connected to the battery source (CR2032, 3V).
1.2.20 IPMI
MIC-3399 uses the Intelligent Platform Management Interface (IPMI) to monitor the
system health. An LPC1768 microcontroller provides BMC functionality to interface
between the system management software and platform hardware. MIC-3399 offers
fully compliant IPMI 2.0 functionality and conforms to the PICMG 2.9 R1.0 specifica-
tion. The IPMI firmware is based on proven technology from Advantech. Full IPMI
details are provided in Chapter 3.
Note! The operating temperature range of the MIC-3399 depends on the
installed processor and the airflow through the chassis.

MIC-3399 User Manual 8
1.3 Functional Block Diagram
Figure 1.1 MIC-3399 Functional Block Diagram
1.4 Jumpers and Switches
The jumper and switch functions are listed in Tables 1.4 and 1.5. Read this section
carefully before modifying the jumper and switch settings on the MIC-3399 board.
Table 1.4: Jumper Descriptions
Number Function Note
JCMOS1 Clear CMOS
JLVDS1 Rear LVDS power voltage setting
Table 1.5: Switch Descriptions
Number Function Note
SW1-1 PCI bridge clock frequency selection
SW2-1 Switch VGA output to front panel or to rear
SW2-2 Switch LAN output to front panel or to rear
SW2-3 PCI bridge master/drone mode
SW2-4 Drone mode PCI bus reset
SW4 PEG bus configuration setting