Fujitsu HX2560 M1 User manual

User's Manual
CA92344-0331-02
FUJITSU HX2560 M1 /
FUJITSU HX2560 M2

The information in this User’s Manual has been carefully reviewed and is believed to be accurate. The
vendor assumes no responsibility for any inaccuracies that may be contained in this document, makes
no commitment to update or to keep current the information in this manual, or to notify any person or
organization of the updates.
FUJITSU LIMITED reserves the right to make changes to the product described in this manual at any time
and without notice. This product, including software and documentation, is the property of FUJITSU LIMITED
and/or its licensors, and is supplied only under a license. Any use or reproduction of this product is not
allowed, except as expressly permitted by the terms of said license.
IN NO EVENT WILL FUJITSU LIMITED BE LIABLE FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, SPECULATIVE OR
CONSEQUENTIAL DAMAGES ARISING FROM THE USE OR INABILITY TO USE THIS PRODUCT OR DOCUMENTA-
TION, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. IN PARTICULAR, FUJITSU LIMITED SHALL NOT
HAVE LIABILITY FOR ANY HARDWARE, SOFTWARE, OR DATA STORED OR USED WITH THE PRODUCT, INCLUD-
ING THE COSTS OF REPAIRING, REPLACING, INTEGRATING, INSTALLING OR RECOVERING SUCH HARDWARE,
SOFTWARE, OR DATA.
FCC 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 equip-
ment generates, uses, and can radiate radio frequency energy and, if not installed and used in accordance
with the manufacturer’s instruction manual, may cause harmful interference with radio communications.
Operation of this equipment in a residential area is likely to cause harmful interference, in which case you
will be required to correct the interference at your own expense.
Manual Revision 2.0
Release Date: September 4, 2013
Unless you request and receive written permission from FUJITSU LIMITED, you may not copy any part of
this document.
Information in this document is subject to change without notice. Other products and companies re-
ferred to herein are trademarks or registered trademarks of their respective companies or mark holders.
Copyright 2013 FUJITSU LIMITED

Preface
About This Manual
This manual is written for professional system integrators and PC technicians. It pro-
vides information for the installation and use of the server. Installation and mainte-
nance should be performed by experienced technicians only.
The server is based on the 2U rackmount server chassis and the serverboard.
Before reading this manual
For your safety
This manual contains important information for safely and correctly using this product.
Carefully read the manual before using this product. Pay particular attention to the ac-
companying manual "Safety Notes and Regulations" and ensure these safety notes are
understood before using the product. Keep this manual and the manual "Safety Notes
and Regulations" in a safe place for easy reference while using this product.
Aluminum electrolytic capacitors
The aluminum electrolytic capacitors used in the product's printed circuit board as-
semblies and in the mouse and keyboard are limited-life components. Use of these
components beyond their operating life may result in electrolyte leakage or depletion,
potentially causing emission of foul odor or smoke.
As a guideline, in a normal ofce environment (25°C) operating life is not expected to
be reached within the maintenance support period (5 years). However, operating life
may be reached more quickly if, for example, the product is used in a hot environment.
The customer shall bear the cost of replacing replaceable components which have ex-
ceeded their operating life. Note that these are only guidelines, and do not constitute
a guarantee of trouble-free operation during the maintenance support period.
High safety use
This product is designed and manufactured to be used in commercial and/or industrial
areas as a server.
When used as visual display workplace it must not be placed in the direct eld of view
to avoid incommoding reections. The device has not been designed or manufactured
for uses which demand extremely high level of safety and carry a direct and serious
risk of life or body if such safety cannot be assured.
These uses include control of nuclear reactions in nuclear power plants, automatic air-
plane ight control, air trafc control, trafc control in mass transport systems, medical
devices for life support, and missile guidance control in weapons systems (hereafter,
iii
Preface

HX2560 M1/HX2560 M2 User's Manual
iv
"high safety use"). Customers should not use this product for high safety use unless
measures are in place for ensuring the level of safety demanded of such use. Please
consult the sales staff of Fujitsu if intending to use this product for high safety use.
Measures against momentary voltage drop
This product may be affected by a momentary voltage drop in the power supply caused
by lightning. To prevent a momentary voltage drop, use of an AC uninterruptible power
supply is recommended.
(This notice follows the guidelines of Voltage Dip Immunity of Personal Computer
issued by JEITA, the Japan Electronics and Information Technology Industries Associa-
tion.)
Technology controlled by the Foreign Exchange and Foreign Trade Control Law of Japan
Documents produced by Fujitsu may contain technology controlled by the Foreign
Exchange and Foreign Trade Control Law of Japan. Documents which contain such
technology should not be exported from Japan or transferred to non-residents of Japan
without rst obtaining authorization in accordance with the above law.
外国為替及び外国貿易法に基づく特定技術について
当社のドキュメントには「外国為替及び外国貿易法」に基づく特定技術が含まれているこ
とがあります。特定技術が含まれている場合は、当該ドキュメントを輸出または非居住者に
提供するとき、同法に基づく許可が必要となります。
電波障害対策について
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。 VCCI-A
高調波電流規格について
本製品は、高調波電流規格 JIS C 61000-3-2 適合品です。
Only for the Japanese market:
SATA ハードディスクドライブについて
このサーバの SATA バージョンは、BC-SATA ストレージインタフェースを搭載したハードディ
スクドライブをサポートしています。ご使用のハードディスクドライブのタイプによって使用
方法と動作条件が異なりますので、ご注意ください。
使用できるタイプのハードディスクドライブの使用方法と動作条件の詳細は、以下の Web
サイトを参照してください。
http://jp.fujitsu.com/platform/server/primergy/harddisk/
(使用方法と動作条件はPRIMERGYと同様になります。）

v
Preface
Manual Organization
Chapter 1: Introduction
The rst chapter provides a checklist of the main components included with the server
system and describes the main features of the serverboard and the 2U rackmount server
chassis.
Chapter 2: Server Installation
This chapter describes the steps necessary to install the system into a rack and check
out the server conguration prior to powering up the system. If your server was ordered
without the processor and memory components, this chapter will refer you to the ap-
propriate sections of the manual for their installation.
Chapter 3: System Interface
Refer to this chapter for details on the system interface, which includes the functions and
information provided by the control panel on the chassis as well as other LEDs located
throughout the system.
Chapter 4: System Safety
You should thoroughly familiarize yourself with this chapter for a general overview of
safety precautions that should be followed when installing and servicing the system.
Chapter 5: Advanced Serverboard Setup
Chapter 5 provides detailed information on the serverboard, including the locations and
functions of connectors, headers and jumpers. Refer to this chapter when adding or
removing processors or main memory and when reconguring the serverboard.
Chapter 6: Advanced Chassis Setup
Refer to Chapter 6 for detailed information on the 2U rackmount server chassis. You should
follow the procedures given in this chapter when installing, removing or reconguring
SATA or peripheral drives and when replacing system power supply units and cooling fans.
Chapter 7: BIOS
The BIOS chapter includes an introduction to BIOS and provides detailed information on
running the BIOS Setup Utility.
Appendix A: Cabling
Appendix B: BIOS POST Error Codes
Appendix C: System Specications

HX2560 M1/HX2560 M2 User's Manual
vi
Notes

Table of Contents
viii
Table of Contents
Preface
About This Manual................................................................................................................iii
Before reading this manual ..................................................................................................iii
Manual Organization ............................................................................................................. v
Chapter 1 Introduction
1-1 Overview ................................................................................................................ 1-1
1-2 Serverboard Features.............................................................................................. 1-2
Processors .............................................................................................................. 1-2
Memory.................................................................................................................. 1-2
Serial ATA .............................................................................................................. 1-2
PCI Expansion Slots ................................................................................................ 1-2
Onboard Controllers/Ports....................................................................................... 1-2
IPMI........................................................................................................................ 1-2
1-3 Server Chassis Features .......................................................................................... 1-3
System Power ......................................................................................................... 1-3
SATA Subsystem...................................................................................................... 1-3
Front Control Panel................................................................................................. 1-3
Cooling System....................................................................................................... 1-3
1-4 GPU Subsystem....................................................................................................... 1-4
Chapter 2 Server Installation
2-1 Overview ................................................................................................................ 2-1
2-2 Unpacking the System............................................................................................ 2-1
2-3 Preparing for Setup ................................................................................................ 2-1
Choosing a Setup Location..................................................................................... 2-1
Rack Precautions .................................................................................................... 2-2
Server Precautions.................................................................................................. 2-2
Rack Mounting Considerations............................................................................... 2-2
Ambient Operating Temperature....................................................................... 2-2
Reduced Airow ................................................................................................ 2-3
Mechanical Loading .......................................................................................... 2-3
Circuit Overloading............................................................................................ 2-3
Reliable Ground................................................................................................. 2-3
2-4 Installing the System into a Rack........................................................................... 2-4
Identifying the Sections of the Rack Rails .............................................................. 2-4

ix
Locking Tabs........................................................................................................... 2-5
Releasing the Inner Rail......................................................................................... 2-5
Installing The Inner Rails on the Chassis................................................................ 2-6
Installing the Outer Rails on the Rack.................................................................... 2-7
Standard Chassis Installation ................................................................................. 2-8
Optional Quick Installation Method........................................................................ 2-9
Chapter 3 System Interface
3-1 Overview ................................................................................................................ 3-1
3-2 Control Panel Buttons ............................................................................................ 3-2
Reset ...................................................................................................................... 3-2
Power ..................................................................................................................... 3-2
3-3 Control Panel LEDs ................................................................................................. 3-2
Power ..................................................................................................................... 3-2
HDD........................................................................................................................ 3-3
NIC1........................................................................................................................ 3-3
NIC2........................................................................................................................ 3-3
Overheat/Fan Fail/UID LED ..................................................................................... 3-3
Power Failure.......................................................................................................... 3-4
3-4 Drive Carrier LEDs................................................................................................... 3-4
Chapter 4 System Safety
4-1 Electrical Safety Precautions................................................................................... 4-1
4-2 General Safety Precautions..................................................................................... 4-2
4-3 ESD Precautions ..................................................................................................... 4-3
4-4 Operating Precautions............................................................................................ 4-4
Chapter 5 Advanced Serverboard Setup
5-1 Handling the Serverboard ...................................................................................... 5-1
Precautions ............................................................................................................ 5-1
Unpacking .............................................................................................................. 5-1
5-2 Serverboard Installation......................................................................................... 5-2
5-3 Connecting Cables.................................................................................................. 5-3
Connecting Data Cables ......................................................................................... 5-3
Connecting Power Cables ....................................................................................... 5-3
Connecting the Control Panel................................................................................. 5-3
5-4 I/O Ports ................................................................................................................. 5-4
5-5 Memory.................................................................................................................. 5-5
Memory Support..................................................................................................... 5-5
HX2560 M1/HX2560 M2 User's Manual

x
Processor/DIMM Population Congurations............................................................ 5-5
5-6 Expansion Cards ..................................................................................................... 5-6
5-7 Serverboard Details ................................................................................................ 5-7
Serverboard Quick Reference.................................................................................. 5-8
5-8 Connector Denitions ...........................................................................................5-10
5-9 Jumper Settings.....................................................................................................5-16
5-10 Onboard Indicators................................................................................................5-17
5-11 SATA Ports .............................................................................................................5-19
Chapter 6 Advanced Chassis Setup
6-1 Static-Sensitive Devices.......................................................................................... 6-1
Precautions ............................................................................................................ 6-1
6-2 Control Panel.......................................................................................................... 6-2
6-3 Chassis Cover Installation/Removal ........................................................................ 6-2
6-4 System Cooling....................................................................................................... 6-3
System Fan Failure ................................................................................................. 6-3
6-5 Drive Bay Installation/Removal .............................................................................. 6-4
6-6 Expansion Card Setup............................................................................................. 6-5
Low-Prole Expansion Card Setup.........................................................................6-10
Installing Graphics (GPU) Cards.............................................................................6-12
Installing Graphics Cards for Left Side GPU Bracket (PCI slot 1,2) ....................6-13
Installing Graphics Cards for Right Side GPU Bracket (PCI slot 3,4)..................6-18
6-7 Power Supply.........................................................................................................6-25
Installing the redundant Power Supply .................................................................6-25
Power Supply Replacement ...................................................................................6-25
Chapter 7 BIOS
7-1 Introduction............................................................................................................ 7-1
Starting BIOS Setup Utility...................................................................................... 7-1
How To Change the Conguration Data ................................................................. 7-2
Starting the Setup Utility........................................................................................ 7-2
7-2 Main Setup............................................................................................................. 7-2
7-3 Advanced Setup Congurations.............................................................................. 7-3
7-4 Event Logs ............................................................................................................7-23
7-5 IPMI.......................................................................................................................7-25
7-6 Boot ......................................................................................................................7-27
7-7 Security .................................................................................................................7-28
7-8 Save & Exit............................................................................................................7-29
Table of Contents

HX2560 M1/HX2560 M2 User's Manual
xi
Appendix A Cabling
Appendix B BIOS POST Error Codes
Appendix C System Specications

Chapter 1
Introduction
1-1 Overview
The HX2560 M1/HX2560 M2 is a GPU-optimized server comprised of two main subsystems:
the 2U rackmount server chassis and the serverboard.
• Five 8-cm chassis fans
• One air shroud
• One passive 1U CPU heatsink
• One passive 2U CPU heatsink
• Riser Cards:
One RSC-R2UG-2E16-X9 for two PCI-E x16 cards, left front side
One RSC-R2UG-2E16R-X9 for two PCI-E x16 cards, right front side
One RSC-R2UG-E8G-X9 for onene PCI-E x4 card, left rear side
One RSC-R2UG-E16R-X9 for one low-prole PCI-E x8 card
• Four power cables for GPU cards
• One GPU bracket
• SATA Accessories:
One HDD backplane
Ten SATA drive carriers
Two iPass to 4 SATA cables (for onbaord SATA controller)
Two SATA cables (for onbaord SATA controller)
One SGPIO cable (for onbaord SATA controller)
• One rail set
Chapter 1: Introduction
1-1

1-2
HX2560 M1/HX2560 M2 User's Manual
1-2 Serverboard Features
At the heart of the HX2560 M1/HX2560 M2 is the serverboard, a dual processor
serverboard based on the Intel® C602 chipset. Below are the main features of the
serverboard. (See Figure 1-1 for a serverboard block diagram).
Processors
The serverboard supports two Intel® Xeon® Processor E5-2600 / E5-2600 v2 Series in LGA
2011 sockets (Socket R).
Memory
The serverboard has eight DIMM slots that can support up to 128 GB of registered ECC
DDR3-1866/1600/1333/1066/800 MHz RDIMMs. Modules of the same size and speed are
recommended. See Chapter 5 for details.
Serial ATA
A SATA controller is integrated into the chipset to provide a 10-port SATA subsystem.
Two of these are SATA 3.0 ports and eight are SATA 2.0 ports. The SATA drives are
hot-swappable units.
PCI Expansion Slots
The serverboard has four PCI-Express 3.0 x16 slots to support four double-width GPU
cards. Additional slots support one PCI-Express 3.0 x8 low-prole card and one PCI-E 2.0
x4 standard card.
Onboard Controllers/Ports
The color-coded I/O ports include a VGA (monitor) port, two USB 2.0 ports, two 1Gb
Ethernet LAN ports and one dedicated IPMI LAN port.
IPMI
IPMI (Intelligent Platform Management Interface) is a hardware-level interface speci-
cation that provides remote access, monitoring and administration. IPMI allows server
administrators to view a server’s hardware status remotely, receive an alarm automatically
if a failure occurs, and power cycle a system that is non-responsive.

1-3
Chapter 1: Introduction
1-3 Server Chassis Features
System Power
The HX2560 M1/HX2560 M2 features a high-efciency, redundant 1800W power supply
composed of two separate power modules. This power redundancy feature allows you to
replace a failed power supply without shutting down the system. See Chapter 6 for details.
SATA Subsystem
The HX2560 M1/HX2560 M2 includes ten 2.5" drive bays, which may be used to house
hot-swap SATA drives.
Note: If you use RAID 0, 1, 1E, 1+0, 5, 5+0, 6 or 6+0, a RAID controller card is
required. When the RAID controller card is installed, SATA drives can be
installed in Bay 0-7
To provide power for the HDD backplane, connect the JPW11 header on the
serverboard to both 4-pin connectors on the HDD backplane using SATA cables.
Front Control Panel
The control panel provides a system monitoring and control interface. LEDs indicate
system power, HDD activity, network activity, and a system overheat/fan fail/ UID LED. A
main power button and a system reset button are also included.
Cooling System
The HX2560 M1/HX2560 M2 has an innovative cooling design that includes ve 8-cm
heavy-duty fans. The power supply modules also include a cooling fan. All chassis and
power supply fans operate continuously.

1-4
HX2560 M1/HX2560 M2 User's Manual
1-4 GPU Subsystem
HX2560 M1/HX2560 M2 supports a maximum of four GPU cards or coprocessor cards
which suit the forefront of the technical computing. Supported cards are as follows.
• NVIDIA® Tesla® K20
• NVIDIA® Tesla® K20X
• Intel® Xeon Phi™ Coprocessor 3120P
• Intel® Xeon Phi™ Coprocessor 5110P
• Intel® Xeon Phi™ Coprocessor 7120P
Note
For the latest information on optional products provided for the HX2560 M1/HX2560
M2 see the congurator of the server:
http://jp.fujitsu.com/solutions/hpc/products/pcserver/ (for the Japanese market)
Power Notes
To provide power for the GPU cards, connect the GPU power cable from each of the
GPUs to the serverboard (JPW3, 4, 5, 6, 7, 8, and 11) and the PDB (CN602 and CN603)
(one cable for each card).
When installing Xeon Phi coprocessor 7120P/3120P, connect two GPU power cables for
each card.

1-5
Chapter 1: Introduction
Figure 1-1. Serverboard Block Diagram
Note: This is a general block diagram. Please see Chapter 5 for details.
CPU1
E5-2600 Series /
E5-2600v2 Series
P0
P1
#2 #3 #1 DMI2
CPU2
E5-2600 Series /
E5-2600v2 Series
P0
P1
#1 #2 #3 DMI2
QPI
8G
QPI
8G
DDR3 800/1066/1333/1600/1866
#0-1
#0-2
#0-3
#0-4
DDR3 800/1066/1333/1600/1866
#1-1
#1-2
#1-3
#1-4
PCI-E X16
PCI-E X16
PCI-E X16
PCI-E X16
SLOT 4
SLOT 3
SLOT 2
SLOT 1
PCI-E X8
SLOT 5
LAN
I350
PCI-E X16 G3
PCI-E X16 G3
PCI-E X16 G3
PCI-E X16 G3
PCI-E X8 G3
PCI-E X8 G3
DMI2
LANE1/2/3/4
PCH
C602
SAS/SATA
Ports #0-3
SATA
Ports #0-5
PCI
LANE5
LANE6
#2-3,8-9
#0-1
#4-7
SPI
S-SATA2
I-SATA
I-SATA
SATA2/
SAS1
3.0 Gb/s
SATA2
3.0 Gb/s
SATA3
6.0 Gb/s
USB
#0-1
USB 2.0
2 in Rear
Panel
BMC
WPCM450
VGA
PCI
Internal
COM Port
Header
PCI-E X4
SLOT 6
PCI-E X4 Gen2
VGA Port
Dedicated LAN
DMI2
4GB/s

1-6
HX2560 M1/HX2560 M2 User's Manual
Notes

Chapter 2: Server Installation
2-1
Chapter 2
Server Installation
2-1 Overview
This chapter provides a quick setup checklist to get your system up and running. Following
these steps in the order given should enable you to have the system operational within
a minimum amount of time. This quick setup assumes that your system has come to you
with the processors and memory preinstalled. If your system is not already fully integrated
with a serverboard, processors, system memory etc., please turn to the chapter or section
noted in each step for details on installing specic components.
2-2 Unpacking the System
You should inspect the box the system was shipped in and note if it was damaged in any
way. If the server itself shows damage you should le a damage claim with the carrier
who delivered it.
Decide on a suitable location for the rack unit that will hold the server. It should be
situated in a clean, dust-free area that is well ventilated. Avoid areas where heat, elec-
trical noise and electromagnetic elds are generated. You will also need it placed near
a grounded power outlet. Read the Rack and Server Precautions in the next section.
2-3 Preparing for Setup
The box the server was shipped in should include two sets of rail assemblies, two rail
mounting brackets and the mounting screws you will need to install the system into the
rack. Follow the steps in the order given to complete the installation process in a minimum
amount of time. Please read this section in its entirety before you begin the installation
procedure outlined in the sections that follow.
Choosing a Setup Location
• Leave enough clearance in front of the rack to enable you to open the front door
completely (~25 inches) and approximately 30 inches of clearance in the back of the
rack to allow for sufcient airow and ease in servicing.This product is for installa-
tion only in a Restricted Access Location (dedicated equipment rooms, service closets
and the like).
• This product is not suitable for use with visual display work place devices acccording
to §2 of the the German Ordinance for Work with Visual Display Units.

2-2
HX2560 M1/HX2560 M2 User's Manual
Warnings and Precautions!
Rack Precautions
• Ensure that the leveling jacks on the bottom of the rack are fully extended to the
oor with the full weight of the rack resting on them.
• In single rack installation, stabilizers should be attached to the rack. In multiple rack
installations, the racks should be coupled together.
• Always make sure the rack is stable before extending a component from the rack.
• You should extend only one component at a time - extending two or more simultane-
ously may cause the rack to become unstable.
• Rack-mounted equipment should not be used as a shelf or work space.
Server Precautions
• Review the electrical and general safety precautions in Chapter 4.
• Determine the placement of each component in the rack before you install the rails.
• Install the heaviest server components on the bottom of the rack rst, and then
work up.
• Use a regulating uninterruptible power supply (UPS) to protect the server from power
surges, voltage spikes and to keep your system operating in case of a power failure.
• Allow the hot plug SATA drives and power supply modules to cool before touching
them.
• Always keep the rack's front door and all panels and components on the servers closed
when not servicing to maintain proper cooling.
Rack Mounting Considerations
Ambient Operating Temperature
If installed in a closed or multi-unit rack assembly, the ambient operating temperature
of the rack environment may be greater than the ambient temperature of the room.
Therefore, consideration should be given to installing the equipment in an environment
compatible with the manufacturer’s maximum rated ambient temperature (Tmra).

Chapter 2: Server Installation
2-3
Reduced Airow
Equipment should be mounted into a rack so that the amount of airow required for safe
operation is not compromised.
Mechanical Loading
Equipment should be mounted into a rack so that a hazardous condition does not arise
due to uneven mechanical loading.
Circuit Overloading
Consideration should be given to the connection of the equipment to the power supply
circuitry and the effect that any possible overloading of circuits might have on overcurrent
protection and power supply wiring. Appropriate consideration of equipment nameplate
ratings should be used when addressing this concern.
Reliable Ground
A reliable ground must be maintained at all times. To ensure this, the rack itself should
be grounded. Particular attention should be given to power supply connections other than
the direct connections to the branch circuit (i.e. the use of power strips, etc.).

2-4
HX2560 M1/HX2560 M2 User's Manual
2-4 Installing the System into a Rack
This section provides information on installing the chassis into a rack unit with the rails
provided. There are a variety of rack units on the market, which may mean that the as-
sembly procedure will differ slightly from the instructions provided. You should also refer
to the installation instructions that came with the rack unit you are using.
Note: This rail will t a rack between 675mm and 927mm deep.
Identifying the Sections of the Rack Rails
The chassis package includes two rail assemblies in the rack mounting kit. Each assembly
consists of three sections: an inner chassis rail that secures directly to the chassis, an
outer rail that secures to the rack, and a middle rail that extends from the outer rail.
These assemblies are left/right specic.
Figure 2-1. Identifying the Sections of the Rack Rails
(Left Rail Assembly Shown)
Inner Rail
Rail Assembly
(Shown with Rails
Retracted)
This Side Faces Outward
Locking Tab
Middle Rail
Outer Rail