TYAN GT62B-B5539 Quick start guide

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GT62B-B5539
Service Engineer’s Manual

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PREFACE
Copyright
This publication, including all photographs, illustrations, and software, is protected
under international copyright laws, with all rights reserved.
Neither this manual, nor any material contained herein, may be reproduced without
written consent of manufacturer.
Copyright 2017 MITAC COMPUTING TECHNOLOGY CORPORATION. All rights
reserved. TYAN®is a registered trademark of MITAC COMPUTING TECHNOLOGY
CORPORATION.
Version 1.0c
Disclaimer
Information contained in this document is furnished by MITAC COMPUTING
TECHNOLOGY CORPORATION and has been reviewed for accuracy and reliability
prior to printing. MiTAC assumes no liability whatsoever, and disclaims any express
or implied warranty, relating to sale and/or use of TYAN®products including liability
or warranties relating to fitness for a particular purpose or merchantability. MiTAC
retains the right to make changes to produce descriptions and/or specifications at
any time, without notice. In no event will MiTAC be held liable for any direct or
indirect, incidental or consequential damage, loss of use, loss of data or other
malady resulting from errors or inaccuracies of information contained in this
document.
Trademark Recognition
All registered and unregistered trademarks and company names contained in this
manual are property of their respective owners including, but not limited to the
following.
TYAN®is a trademark of MITAC COMPUTING TECHNOLOGY CORPORATION.
Intel®is a trademark of Intel®Corporation.
AMI®, AMIBIOS® and combinations thereof are trademarks of AMI Technologies.
Microsoft®, Windows®are trademarks of Microsoft Corporation.
IBM®, PC®, AT®and PS/2®are trademarks of IBM Corporation.
Winbond®is a trademark of Winbond Electronics Corporation.

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● FCC Declaration
Notice for the USA
Compliance Information Statement (Declaration of Conformity Procedure) DoC FCC
Part 15: This device complies with part 15 of the FCC Rules.
This device complies with Part 15 of the FCC Rules. Operation is subject to the
following conditions:
‧This device may not cause harmful interference.
‧This device must accept any interference received, including interference that may
cause undesired operation.
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 for Canada
This Class A digital apparatus complies with Canadian ICES-003. Cet appareil
numérique de la Classe A est conforme à la norme NMB-003 du Canada.
● Notice for Europe (CE Mark)
This product is in conformity with the Council Directive 2014/30/EU.

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Warning
This equipment is compliant with Class A of CISPR 32. In a residential environment
this equipment may cause radio interference.
CAUTION
Lithium battery included with this board. Do not puncture, mutilate, or dispose of
battery in fire. There will be danger of explosion if battery is incorrectly replaced.
Replace only with the same or equivalent type recommended by manufacturer.
Dispose of used battery according to manufacturer instructions and in accordance
with your local regulations.
● VCCI-A
この装置は、クラスＡ情報技術装置です。この装置を家庭環境で使用すると電波妨
害を引き起こすことがあります。この場合には使用者が適切な対策を講ずるよう要
求されることがあります。
● Safety: EN/IEC 60950-1
This equipment is compliant with CB/LVD of Safety: EN/IEC 60950-1.

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About this Manual
This manual is intended for trained service technician/personnel with hardware
knowledge of computers. Components inside the compartments should be serviced
only by a trained service technician/personnel. This manual is aimed to provide you
with instructions on installing your TYAN GT62B-B5539.
How this guide is organized
This guide contains the following parts:
Chapter 1: Overview
This chapter provides an introduction to the TYAN GT62B-B5539 barebones and
standard parts list, describes the external components, gives an overview of the
product from different angles.
Chapter 2: Setting Up
This chapter covers procedures on installing the memory modules, hard drivers and
other optional parts.
Chapter 3: Replacing the Pre-installed Components
This chapter covers the removal and replacement procedures for pre-installed
components.
Appendix:
This chapter provides the cable connection table, the FRU parts list for reference of
system setup, and technical support in case a problem arises with your system.

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Safety and Compliance Information
Before installing and using TYAN GT62B-B5539, take note of the following
precautions:
·Read all instructions carefully.
·Do not place the unit on an unstable surface, cart, or stand.
·Do not block the slots and opening on the unit, which are provided for
ventilation.
·Only use the power source indicated on the marking label. If you are not
sure, contact the power company.
·The unit uses a three-wire ground cable, which is equipped with a third pin to
ground the unit and prevent electric shock. Do not defeat the purpose of this
pin. If your outlet does not support this kind of plug, contact your electrician
to replace your obsolete outlet.
·Do not place anything on the power cord. Place the power cord where it will
not be in the way of foot traffic.
·Follow all warnings and cautions in this manual and on the unit case.
·Do not push objects in the ventilation slots as they may touch high voltage
components and result in shock and damage to the components.
·When replacing parts, ensure that you use parts specified by the
manufacturer.
·When service or repairs have been done, perform routine safety checks to
verify that the system is operating correctly.
·Avoid using the system near water, in direct sunlight, or near a heating
device.
·Cover the unit when not in use.

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Safety Information
Retain and follow all product safety and operating instructions provided
with your equipment. In the event of a conflict between the instructions in
this guide and the instructions in equipment documentation, follow the
guidelines in the equipment documentation.
Observe all warnings on the product and in the operating instructions. To
reduce the risk of bodily injury, electric shock, fire and damage to the
equipment, observe all precautions included in this guide.
You must become familiar with the safety information in this guide before
you install, operate, or service TYAN products.
Symbols on Equipment
Caution. This symbol indicates a potential hazard.
The potential for injury exists if cautions are not
observed. Consult equipment documentation for
specific details.
Caution. Slide-mounted equipment is not to be
used as a shelf or a work space.
Warning. This symbol indicates the presence of
hazardous energy circuits or electric shock
hazards. Refer all servicing to qualified personnel.
Warning. This symbol indicates the presence of a
hot surface or hot component. If this surface is
contacted, the potential for injury exists.
To reduce risk of injury from a hot component,
allow the surface to cool before touching.
General Precautions
· Follow all caution and warning instructions marked on the equipment and
explained in the accompanying equipment documentation.
Machine Room Environment
· This device is for use only in a machine room or IT room.
 · Make sure that the area in which you install the system is properly
ventilated and climate-controlled.

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· Ensure that the voltage and frequency of your power source match the
voltage and frequency inscribed on the electrical rating label of the
equipment.
·Do not install the system in or near a plenum, air duct, radiator, or heat
register.
·Never use the product in a wet location.
Equipment Chassis
· Do not block or cover the openings to the system.
·Never push objects of any kind through openings in the equipment.
Dangerous voltages might be present.
·Conductive foreign objects can produce a short circuit and cause fire,
electric shock, or damage to your equipment.
·Lift equipment using both hands and with your knees bent.
Equipment Racks
To avoid injury or damage to the equipment:
·Observe local occupational health and safety requirements and guidelines
for manual materials handling.
·Do not attempt to move a rack by yourself; a minimum of two people are
needed to move a rack.
·Do not attempt to move a fully loaded rack. Remove equipment from the
rack before moving it.
·Do not attempt to move a rack on an incline that is greater than 10 degrees
from the horizontal.
·Make sure the rack is properly secured to the floor or ceiling.
·Make sure the stabilizing feet are attached to the rack if it is a single-rack
installation.
·Make sure racks are coupled together if it is a multiple-rack installation.
·Make sure the rack is level and stable before installing an appliance in the
rack.
·Make sure the leveling jacks are extended to the floor.
·Make sure the full weight of the rack rests on the leveling jacks.

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·Always load the rack from the bottom up. Load the heaviest component in
the rack first.
·Make sure the rack is level and stable before pulling a component out of the
rack.
·Make sure only one component is extended at a time. A rack might become
unstable if more than one component is extended.
To avoid damage to the equipment:
· The rack width and depth must allow for proper serviceability and cable
management.
· Ensure that there is adequate airflow in the rack. Improper installation or
restricted airflow can damage the equipment.
·The rack cannot have solid or restricted airflow doors. You must use a
mesh door on the front and back of the rack or remove the doors to ensure
adequate air flow to the system.
·If you install the Model in a rack, do not place equipment on top of the unit.
It will cause restricted airflow and might cause damage to the equipment.
·Make sure the product is properly matted with the rails. Products that are
improperly matted with the rails might be unstable.
·Verify that the AC power supply branch circuit that provides power to the
rack is not overloaded. This will reduce the risk of personal injury, fire, or
damage to the equipment. The total rack load should not exceed 80 percent
of the branch circuit rating. Consult the electrical authority having jurisdiction
over your facility wiring and installation requirements.
Equipment Power Cords
· Use only the power cords and power supply units provided with your
system. The system might have one or more power cords.
·Plug the power cord into a grounded (earthed) electrical outlet that is easily
accessible at all times.
·In all European electrical environments, you must ground the Green/Yellow
tab on the power cord. If you do not ground the Green/Yellow tab, it can
cause an electrical shock due to high leakage currents.
·
Do not place objects on AC power cords or cables. Arrange them so that no
one might accidentally step on or trip over them.

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·Do not pull on a cord or cable. When unplugging from the electrical outlet,
grasp the cord by the plug.
·To reduce the risk of electrical shock, disconnect all power cords before
servicing the appliance.
Equipment Batteries
· The system battery contains lithium manganese dioxide. If the battery pack
is not handled properly, there is risk of fire and burns.
·Do not disassemble, crush, puncture, short external contacts, or dispose of
the battery in fire or water.
·Do not expose the battery to temperatures higher than 60°C (140°F).
·The system battery is not replaceable. If the battery is replaced by an
incorrect type, there is danger of explosion. Replace the battery only with a
spare designated for your product.
·Do not attempt to recharge the battery.
·Dispose of used batteries according to the instructions of the manufacturer.
Do not dispose of batteries with the general household waste. To forward
them to recycling or proper disposal, use the public collection system or return
them to TYAN, your authorized TYAN partner, or their agents.
Equipment Modifications
· Do not make mechanical modifications to the system. TYAN is not
responsible for the regulatory compliance of TYAN equipment that has been
modified.

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Equipment Repairs and Servicing
· The installation of internal options and routine maintenance and service of
this product should be performed by trained service technicians/personnel
who are knowledgeable about the procedures, precautions, and hazards
associated with equipment containing hazardous energy levels.
·Do not exceed the level of repair specified in the procedures in the product
documentation. Improper repairs can create a safety hazard.
·Allow the product to cool before removing covers and touching internal
components.
·Remove all watches, rings, or loose jewelry when working before removing
covers and touching internal components.
·Do not use conductive tools that could bridge live parts.
·Use gloves when you remove or replace system components; they can
become hot to the touch.
·If the product sustains damage requiring service, disconnect the product
from the AC electrical outlet and refer servicing to an authorized service
provider. Examples of damage requiring service include:
– The power cord, extension cord, or plug has been damaged.
– Liquid has been spilled on the product or an object has fallen into the
product.
–The product has been exposed to rain or water.
– The product has been dropped or damaged.
– The product does not operate normally when you follow the operating
instructions.

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Table of Contents
Chapter 1: Overview....................................................................... 17
1.1 About the TYAN GT62B-B5539 ............................................. 17
1.2 Product SKUs......................................................................... 17
1.3 Features.................................................................................. 18
1.4 Standard Parts List................................................................. 27
1.4.1 Box Contents and Accessories........................................ 27
1.5 About the Product................................................................... 28
1.5.1 System Front View .......................................................... 28
1.5.2 LED Definitions................................................................ 29
1.5.3 System Rear View........................................................... 30
1.5.4 System Top View............................................................. 32
1.5.5 Motherboard (S5539) Layout........................................... 34
1.5.6 LED Definitions................................................................ 37
Chapter 2: Setting Up..................................................................... 39
2.0.1 Before you Begin............................................................. 39
2.0.2 Work Area........................................................................ 39
2.0.3 Tools................................................................................ 39
2.0.4 Precautions...................................................................... 40
2.1 Installing Motherboard Components ...................................... 41
2.1.1 Removing the Chassis Cover.......................................... 41
2.1.2 Installing the Memory ...................................................... 42
2.1.3 Installing Hard Drives ...................................................... 43
2.2 Rack Mounting........................................................................ 45
2.2.1 Installing the inner Rails to the Chassis .......................... 46
2.2.2 Installing the Outer Rails to the Rack.............................. 47
2.2.3 Rack mounting the Server............................................... 49
Chapter 3: Replacing Pre-Installed Components ........................ 51
3.0.1 Introduction...................................................................... 51
3.0.2 Disassembly Flowchart.................................................... 51
3.1 Removing the Cover............................................................... 52
3.2 Replacing the M2091 and M2092 Cards................................ 52
3.3 Replacing the M5539-2E MEZZ Card.................................... 54
3.4 Replacing the Front Panel Board ...........................................55
3.4.1 Front Panel Board Features............................................ 57
3.4.2 Front Panel Board Connector Pin Definition ................... 57
3.5 Replacing the System Fan ..................................................... 58
3.6 Replacing the HDD Backplane Board.................................... 60
3.6.1 HDD Backplane Board Specifications............................. 61
3.6.2 HDD BP Board LED Definitions ...................................... 63
3.7 Removing the Motherboard.................................................... 64

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3.8 Replacing the Power Distribution Board (optional) ................ 65
3.8.1 M7016-B7066-PDB Power Distribution Board Feature... 66
3.8.2 Power Distribution Board Pin Definitions......................... 67
3.9 Replacing the Power Supply .................................................. 69
Appendix I: Cable Connection Tables .......................................... 73
Appendix II: Fan and Temp Sensors ............................................ 75
Appendix: FRU Parts Table ........................................................... 77
Appendix IV: Technical Support ................................................... 79

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NOTE

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Chapter 1: Overview
1.1 About the TYAN GT62B-B5539
Congratulations on your purchase of the TYAN®GT62B-B5539, a highly optimized
rack-mountable barebone system. The GT62B-B5539 is designed to support single
Intel®Xeon Processor D-1541 SoC (8 cores) processor and up to 64GB/128GB
UDIMM/RDIMM DDR4 2400 memory, providing a rich feature set and incredible
performance. Leveraging advanced technology from Intel®, the GT62B-B5539
server system is capable of offering scalable 32 and 64-bit computing, high
bandwidth memory design, and lightning-fast PCI-E bus implementation. The
GT62B-B5539 not only empowers your company in nowadays IT demand but also
offers a smooth path for future application usage.
TYAN®also offers the GT62B-B5539 in a version that can support up to six 2.5”
hot-swap SATA/SAS and four 2.5” NVMe SSD hard drives. The GT62B-B5539 uses
TYAN’s latest chassis featuring a robust structure and a solid mechanical enclosure.
All of this provides GT62B-B5539 the power and flexibility to meet the needs of
nowadays server application.
1.2 Product SKUs
The system boards within the Tyan Barebones contain different features and
chipsets, which are defined by the following SKUs:
Model SKU LAN Ports Power Supply
GT62B-B5539
B5539G62BV6E4HR-D41-2T (2) 10GbE (2) GbE
(1) PHY 3Y YM2651M
(1+1) Redundant
PSU
B5539G62BV6E4HR-D41 (2) GbE
(1) PHY
B5539G62BV6E4H-D41-2T (2) 10GbE (2) GbE
(1) PHY Delta
DPS-500AB-5 C
Single PSU
B5539G62BV6E4H-D41 (2) GbE
(1) PHY

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1.3 Features
TYAN GT62B-B5539 (B5539G62BV6E4HR-D41-2T (BTO))
System
Form Factor 1U Rackmount
Gross Weight 16 kg
Chassis Model GT62B
Dimension (D x W x
H) 24.6" x 17.2" x 1.72" (625.4 x 436 x 43.6mm)
Motherboard S5539GM4NR-D41-2T
Board Dimension Micro ATX, 9.6"x9.6" (243.8x243.8mm)
Front Panel
Buttons (1) PWR / (1) RST / (1) ID
LEDs (1) PWR / (1) HDD / (2) LAN / (1) ID / (1) Warning
I/O Ports (2) USB ports
External Drive
Bay
HDD backplane
support (6) SATA 6Gb/s + (4) mini-SAS HD for NVMe devices
Supported HDD
Interface (6) SATA 6Gb/s + (4) NVMe
System Cooling
Configuration FAN (4) 4cm fans
Power Supply
Type RPSU
Efficiency 80 plus Platinum
Redundancy 1+1
Input Range AC 100-240V, 10-5A
Frequency 50-60 Hz
Output Watts 650 Watts
Processor
Supported CPU
Series Intel Xeon processor D-1541 SoC, 8 cores
Thermal Design
Power (TDP) wattage 45W
Memory
Supported DIMM Qty (4) DIMM slots
DIMM Type / Speed UDIMM/RDIMM DDR4 2400 (by Intel CPU type)
Capacity Up to 64GB/128GB UDIMM/RDIMM
Memory channel 2 Channels
Memory voltage 1.2V
Expansion Slots
PCI-E (1) PCI-E Gen3 x8 slot
Pre-install TYAN
Riser Card M2091, PCI-E x16 1U riser card
Pre-install TYAN
MEZZ Card
M5539-2E MEZZ card, (2) mini-SAS HD
connectors, PCI-E Gen3 x8 link;
M2092 half height NVMe MEZZ card, (2) mini-SAS
HD connectors, PCI-e Gen3 x8 link
LAN Port Q'ty (2) 10GbE ports, (2) GbE ports, (1) PHY dedicated
for IPMI
Controller Intel I210 / Intel X557-AT2

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PHY Realtek RTL8211E
Storage
NVMe (4) Internal mini-SAS HD connectors (SFF-8643)
from M2092 & M5539-2E
SATA
Connector (6) SATA
Controller Intel Xeon processor D-1541 SoC CPU
Speed 6.0 Gb/s
Graphic
Connector type D-Sub 15-pin
Resolution Up to 1920x1200
Chipset Aspeed AST2400
I/O Ports
USB (2) USB3.0 ports (2 at rear)/ (2) USB2.0 ports (2 at
front)
COM (1) DB-9 COM port
VGA (1) D-Sub 15-pin port
RJ-45 (2) 10GbE ports, (2) GbE ports, (1) PHY dedicated
for IPMI
Button ID Button
System
Monitoring
Chipset Aspeed AST2400
Voltage Monitors voltage for CPU, memory, chipset &
power supply
Temperature Monitors temperature for CPU & memory & system
environment
LED Over temperature warning indicator / Fan & PSU
fail LED indicator
Others Watchdog timer support
Server
Management
Onboard Chipset Onboard Aspeed AST2400
AST2400 IPMI
Feature
IPMI 2.0 compliant baseboard management
controller (BMC) / Supports storage over IP and
remote platform-flash / USB 2.0 virtual hub
AST2400 iKVM
Feature 24-bit high quality video compression / 10/100 Mb/s MAC interface
BIOS
Brand / ROM size AMI / 16MB
Feature Hardware Monitor / SMBIOS 2.7/PnP/Wake on LAN / PXE boot support / ACPI 3.0/ACPI sleeping
states S4,S5
Operating
System OS supported list Please refer to our Intel OS supported list.
Regulation
FCC (DoC) Class A
CE (DoC) Class A
VCCI Class A
CB/LVD Yes
RCM Class A
Operating
Environment
Operating Temp. 10° C ~ 35° C (50° F~ 95° F)
Non-operating Temp. - 40° C ~ 70° C (-40° F ~ 158° F)
In/Non-operating 90%, non-condensing at 35° C

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Humidity
RoHS RoHS 6/6 Compliant Yes
Package
Contains
Barebone (1) GT62B-B5539 Barebone
Manual (1) Quick Installation Guide
Installation CD (1) TYAN installation CD
TYAN GT62B-B5539 (B5539G62BV6E4HR-D41 (BTO))
System
Form Factor 1U Rackmount
Gross Weight 16 kg
Chassis Model GT62B
Dimension (D x W x H) 24.6" x 17.2" x 1.72" (625.4 x 436 x 43.6mm)
Motherboard S5539GM2NR-D41
Board Dimension Micro ATX, 9.6"x9.6" (243.8x243.8mm)
Front Panel
Buttons (1) PWR / (1) RST / (1) ID
LEDs (1) PWR / (1) HDD / (2) LAN / (1) ID / (1) Warning
I/O Ports (2) USB ports
External Drive
Bay
HDD backplane
support (6) SATA 6Gb/s + (4) mini-SAS HD for NVMe devices
Supported HDD
Interface (6) SATA 6Gb/s + (4) NVMe
System Cooling
Configuration FAN (4) 4cm fans
Power Supply
Type RPSU
Efficiency 80 plus Platinum
Redundancy 1+1
Input Range AC 100-240V, 10-5A
Frequency 50-60 Hz
Output Watts 650 Watts
Processor
Supported CPU
Series Intel Xeon processor D-1541 SoC, 8 cores
Thermal Design
Power (TDP) wattage 45W
Memory
Supported DIMM Qty (4) DIMM slots
DIMM Type / Speed UDIMM/RDIMM DDR4 2400 (by intel CPU type)
Capacity Up to 64GB/128GB UDIMM/RDIMM
Memory channel 2 Channels
Memory voltage 1.2V
Expansion Slots
PCI-E (1) PCI-E Gen3 x8 slot
Pre-install TYAN
Riser Card M2091, PCI-E x16 1U riser card
Pre-install TYAN M5539-2E MEZZ card, (2) mini-SAS HD