Bull Novascale R423-E2 User manual

NOVASCALE
R423-E2
Installation and User's Guide
REFERENCE
86 A1 52FA 00

NOVASCALE
R423-E2
Installation and User's Guide
Hardware
May 2009
BULL CEDOC
357 AVENUE PATTON
B.P.20845
49008 ANGERS CEDEX 01
FRANCE
REFERENCE
86 A1 52FA 00

The following copyright notice protects this book under Copyright laws which prohibit such actions as, but not limited
to, copying, distributing, modifying, and making derivative works.
Copyright © Bull SAS 2009
Copyright © Super Micro Computer, Inc., 2009
Printed in France
Suggestions and criticisms concerning the form, content, and presentation of this book are
invited. A form is provided at the end of this book for this purpose.
To order additional copies of this book or other Bull Technical Publications, you are invited
to use the Ordering Form also provided at the end of this book.
Trademarks and Acknowledgements
We acknowledge the rights of the proprietors of the trademarks mentioned in this manual.
All brand names and software and hardware product names are subject to trademark and/or patent protection.
Quoting of brand and product names is for information purposes only and does not represent trademark misuse.
Intel® and Xeon® are registered trademarks of Intel Corporation.
Windows® and Microsoft® software are registered trademarks of Microsoft Corporation.
Linux® is a registered trademark of Linus Torwalds.
Phoenix® is a registered trademark of Phoenix Technologies.
The information in this document is subject to change without notice. Bull will not be liable for errors
contained herein, or for incidental or consequential damages in connection with the use of this material.

iii
Preface
Preface
About This Manual
This manual is written for professional system integrators and PC technicians. It
provides information for the installation and use of the NovaScale R423-E2. Instal-
lation and maintainance should be performed by experienced technicians only.
The NovaScale R423-E2 is a high-end server based on a rackmount chassis and
the NovaScale R423-E2 serverboard. The R423-E2 supports the Intel® 5500 Series
3URFHVVRUSODWIRUPWKH¿UVWGXDOSURFHVVLQJSODWIRUPWKDWVXSSRUWVWKH,QWHO4XLFN-
3DWK ,QWHUFRQQHFW 43, 7HFKQRORJ\ SURYLGLQJ WKH QH[W JHQHUDWLRQ SRLQWWRSRLQW
system interface to replace the current Front Side Bus. With the Intel 5520 chipset
built in, the R423-E2 substantially enhances system performance with increased
bandwidth and unprecedented scalability optimized for HPC/Cluster systems and
intensive applications.
Manual Organization
Chapter 1: Introduction
7KH¿UVWFKDSWHUSURYLGHVDFKHFNOLVWRIWKHPDLQFRPSRQHQWVLQFOXGHGZLWKWKHVHUY-
er system and describes the main features of the NovaScale R423-E2 serverboard
and the chassis, which comprise the NovaScale R423-E2.
Chapter 2: Server Installation
This chapter describes the steps necessary to install the NovaScale R423-E2 into
DUDFNDQGFKHFNRXWWKHVHUYHUFRQ¿JXUDWLRQSULRUWRSRZHULQJXSWKHV\VWHP,I
your server was ordered without processor and memory components, this chapter
will refer you to the appropriate sections of the manual for their installation.
Chapter 3: System Interface
Refer here 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.

NovaScale R423-E2 Installation and User's Guide
iv
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
NovaScale R423-E2.
Chapter 5: Advanced Serverboard Setup
Chapter 5 provides detailed information on the NovaScale R423-E2 serverboard,
including the locations and functions of connections, headers and jumpers. Refer
to this chapter when adding or removing processors or main memory and when
UHFRQ¿JXULQJWKHVHUYHUERDUG
Chapter 6: Advanced Chassis Setup
Refer to Chapter 6 for detailed information on the NovaScale R423-E2 server chas-
sis. You should follow the procedures given in this chapter when installing, removing
RUUHFRQ¿JXULQJ6$7$RUSHULSKHUDOGULYHVDQGZKHQUHSODFLQJV\VWHPSRZHUVXSSO\
units and cooling fans.
Chapter 7: BIOS
The BIOS chapter includes an introduction to BIOS and provides detailed informa-
tion on running the CMOS Setup Utility.
Appendix A: BIOS Beep Error Codes
Appendix B: Intel HostRaid Setup Guidelines
Appendix C: Adaptec HostRaid Setup Guidelines
Appendix D: System Specications

v
Preface
Table of Contents
Chapter 1. Introduction
1-1 Overview ......................................................................................................... 1-1
1-2 Serverboard Features ..................................................................................... 1-2
CPU................................................................................................................. 1-2
Chipset ............................................................................................................ 1-2
Memory ........................................................................................................... 1-2
6HULDO$7$ ....................................................................................................... 1-2
PCI Expansion Slots ....................................................................................... 1-3
UIO.................................................................................................................. 1-3
Onboard Controllers/Ports .............................................................................. 1-3
$7,*UDSKLFV&RQWUROOHU................................................................................... 1-3
Other Features ................................................................................................ 1-3
1-3 Server Chassis Features ................................................................................ 1-4
System Power ................................................................................................. 1-4
6HULDO$7$6XEV\VWHP ..................................................................................... 1-4
Front Control Panel......................................................................................... 1-4
I/O Backplane.................................................................................................. 1-4
Cooling System ............................................................................................... 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............................................................................. 2-2
Rack Precautions ............................................................................................ 2-2
Server Precautions.......................................................................................... 2-2
Rack Mounting Considerations ....................................................................... 2-3
$PELHQW2SHUDWLQJ7HPSHUDWXUH ................................................................ 2-3
5HGXFHG$LUÀRZ ......................................................................................... 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
Installing the Chassis Rails............................................................................. 2-4
Installing the Rack Rails: ................................................................................ 2-6
Installing the Server into the Rack.................................................................. 2-6

vi
NovaScale R423-E2 Installation and User's Guide
2-5 Checking the Serverboard Setup.................................................................... 2-8
2-6 Checking the Drive Bay Setup...................................................................... 2-10
Chapter 3. System Interface
3-1 Overview ......................................................................................................... 3-1
3-2 Control Panel Buttons ..................................................................................... 3-1
Reset............................................................................................................... 3-1
Power .............................................................................................................. 3-1
3-3 Control Panel LEDs ........................................................................................ 3-2
Power Fail ....................................................................................................... 3-2
Overheat/Fan Fail: .......................................................................................... 3-2
NIC1 ................................................................................................................ 3-2
NIC2 ................................................................................................................ 3-2
HDD................................................................................................................. 3-3
Power .............................................................................................................. 3-3
3-4 Drive Carrier LEDs.......................................................................................... 3-3
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 Motherboard Setup
5-1 Handling the Motherboard .............................................................................. 5-1
Precautions ..................................................................................................... 5-1
Unpacking ....................................................................................................... 5-2
5-2 Motherboard Installation.................................................................................. 5-2
5-3 Connecting the Motherboard .......................................................................... 5-3
Connecting Data Cables ................................................................................. 5-3
Connecting Power Cables .............................................................................. 5-3
Connecting the Control Panel......................................................................... 5-3
5-4 Back Panel Connectors/IO Ports .................................................................... 5-4
5-5 Installing the Processors and Heat Sinks....................................................... 5-6
,QVWDOOLQJDQ/*$3URFHVVRU ................................................................. 5-6
Installing a CPU Heatsink .............................................................................. 5-8
Removing the Heatsink ............................................................................. 5-9
5-6 Installing Memory .......................................................................................... 5-10
Memory Support............................................................................................ 5-10
 $GGLQJ3&,$GG2Q&DUGV............................................................................ 5-12
5-8 Motherboard Details...................................................................................... 5-13

vii
Table of Contents
1RYD6FDOH5(0RWKHUERDUG4XLFN5HIHUHQFH .................................... 5-14
 %DFN3DQHO&RQQHFWRU3LQ'H¿QLWLRQV.......................................................... 5-15
5-10 Front Control Panel....................................................................................... 5-20
5-11 Connecting Cables ....................................................................................... 5-25
5-12 Jumper Settings ............................................................................................ 5-30
5-13 Onboard LED Indicators ............................................................................... 5-34
 )ORSS\6HULDO$7$DQG6$6&RQQHFWLRQV..................................................... 5-36
Chapter 6. Advanced Chassis Setup
6-1 Static-Sensitive Devices.................................................................................. 6-1
Precautions ..................................................................................................... 6-1
Unpacking ....................................................................................................... 6-1
6-2 Control Panel .................................................................................................. 6-2
6-3 System Fans ................................................................................................... 6-3
System Fan Failure......................................................................................... 6-3
Replacing System Fans .................................................................................. 6-3
6-4 Drive Bay Installation/Removal ....................................................................... 6-4
$FFHVVLQJWKH'ULYH%D\V ............................................................................... 6-4
6$7$'ULYH,QVWDOODWLRQ.................................................................................... 6-5
Hard Drive Backplane ..................................................................................... 6-6
DVD-ROM and Floppy Drive Installation ........................................................ 6-7
6-5 Power Supply .................................................................................................. 6-8
Power Supply Failure...................................................................................... 6-8
Removing/Replacing the Power Supply.......................................................... 6-8
Chapter 7. BIOS
7-1 Introduction...................................................................................................... 7-1
7-2 Main Setup ...................................................................................................... 7-2
 $GYDQFHG6HWXS&RQ¿JXUDWLRQV...................................................................... 7-4
7-4 Security Settings ........................................................................................... 7-26
 %RRW&RQ¿JXUDWLRQ ........................................................................................ 7-27
7-6 Exit Options................................................................................................... 7-29
Appendix A. BIOS Error Beep Codes
$ %,26(UURU%HHS&RGHV .................................................................................$1
Appendix B. Intel HostRAID Setup Guidelines
Appendix C. Adaptec HostRAID Setup Guidelines
Appendix D. System Specications

Notes
viii
NovaScale R423-E2 Installation and User's Guide

Chapter 1. Introduction
1-1 Overview
The NovaScale R423-E2 is a high-end server that is comprised of two main subsys-
tems: a 2U server chassis and the NovaScale R423-E2 dual Intel® Xeon® processor
serverboard. Please refer to our web site for information on operating systems that
have been certied for use with the NovaScale R423-E2 (http://www.bull.com).
In addition to the serverboard and chassis, various hardware components have
been included with the NovaScale R423-E2, as listed below:
One (1) SAS/SATA backplane (BPN-SAS-825TQ)•
Two (2) 8-pin to 8-pin Ribbon Cables for SGPIO (Supports Up to 4 Drives •
CBL-0157L)
Two (2) SATA Cable Sets (CBL-0180L-01)•
Three (3) 2U, 8cm 6300 RPM Fans (FAN-0094L)•
Eight (8) SATA hot-swap drive carriers (MCP-220-00001-01)•
(The chassis has eight carriers but only six SATA drives are supported.)
One (1) rail set (MCP-290-00002-00)•
One (1) DVD-Rom Drive Dummy Cover Black (MSP-290-00007-01)•
One (1) air shroud (MCP-310-82502-0N)•
Two (2) 700W 2U power supplies (PWS-702A-1R)•
One (1) Power distributor (PDB-PT825-N24)•
Two (2) CPU passive heatsinks (SNK-P0025P)•
Chapter 1: Introduction
1-1

1-2
NovaScale R423-E2 Installation and User's Guide
1-2 Serverboard Features
At the heart of the NovaScale R423-E2 lies the NovaScale R423-E2 serverboard,
a dual processor serverboard based on the Intel 5520 chipset and designed to
provide maximum performance. Below are the main features of the NovaScale
R423-E2 serverboard. (See Figure 1-1 for a block diagram of the 5520 chipset).
CPU
The NovaScale R423-E2 serverboard supports two Intel® 5500 Series (LGA
1366) processors. Each processor supports two full-width Intel QuickPath Inter-
connect (QPI) @6.4 GT/s with a total of up to 51.2 GB/s Data Transfer Rate (6.4
GB/s per direction).
Chipset
Intel 5520 chipset, including: two 5520 I/O Hubs (North Bridge), and one ICH10R
(South Bridge) Memory
Memory
The NovaScale R423-E2 serverboard has eighteen (18) 240-pin DIMM sockets.
It supports up to 144 GB of DDR3 Reg. ECC 1333/1066/800 MHz Memory mo-
dules (see section 5-6 in Chapter 5 for memory population).
Serial ATA
A SATA controller is integrated into the ESB2 (South Bridge) portion of the 5520
chipset to provide a six-port 3 Gb/s Serial ATA subsystem, which is RAID 0, 1, 10
and 5 supported. The Serial ATA drives are hot-swappable units.
Note: The operating system you use must have RAID support to enable the
hot-swap capability and RAID function of the Serial ATA drives.

1-3
Chapter 1: Introduction
PCI Expansion Slots
The NovaScale R423-E2 serverboard has:
Three PCI-E x8 slots (Slot 1/Slot 3/Slot 7),•
Two PCI-E 2.0 x16 slots (Slot 2/Slot 6),•
One PCI-E 2.0 x4 (in x8) slot (Slot 5),•
One PCI-E 2.0 x8 (in x16) slot (Slot 4).•
UIO
The NovaScale R423-E2 serverboard is a specially-designed serverboard that
features UIO (Universal I/O) technology. UIO serverboards have a PCI-Express
x8 connector that can support any one of several types of UIO card types (low-
prole only) to add SAS ports, additional LAN ports, etc. to the serverboard.
This allows the user to tailor the serverboard to their own needs.
Note: the NovaScale R423-E2 does not come with a UIO card pre-installed.
Onboard Controllers/Ports
One oppy drive connector and two onboard ATA/100 connectors (one reserved
for the use of a compact ash card) are provided to support IDE hard drives or
ATAPI devices. The color-coded I/O ports include one COM port (an additional
COM header is located on the serverboard), a VGA (monitor) port, two USB
2.0 ports (three additional USB headers are included on the serverboard), PS/2
mouse and keyboard ports and two gigabit Ethernet ports.
ATI Graphics Controller
The NovaScale R423-E2 serverboard features an integrated ATI video controller
based on the ES1000 32 MB graphics chip. The ES1000 was designed speci-
cally for servers, featuring low power consumption, high reliability and superior
longevity.
Other Features
Other onboard features that promote system health include onboard voltage
monitors, a chassis intrusion header, auto-switching voltage regulators, chassis
and CPU overheat sensors, virus protection and BIOS rescue.

1-4
NovaScale R423-E2 Installation and User's Guide
1-3 Server Chassis Features
The following is a general outline of the main features of the NovaScale R423-E2
server chassis.
System Power
The NovaScale R423-E2 server chassis features a redundant 700W power sup-
ply composed of two separate power modules. This power redundancy feature
allows you to replace a failed power supply without shutting down the system.
Serial ATA Subsystem
The NovaScale R423-E2 server chassis supports up to six 3 Gb/s Serial ATA
drives. The Serial ATA drives are hot-swappable units and are connected to a
backplane that provides power and control.
Note: The operating system you use must have RAID support to enable the hot-
swap capability of the Serial ATA drives.
Front Control Panel
The control panel on the NovaScale R423-E2 provides you with system monito-
ring and control. LEDs indicate system power, HDD activity, network activity, sys-
tem overheat and power supply failure. A main power button and a system reset
button are also included. In addition, two USB ports have been incorporated into
the control panel to provide front side USB access.
I/O Backplane
The NovaScale R423-E2 server chassis is an ATX form factor chassis designed
to be used in a 2U rackmount conguration. The I/O backplane provides seven
low-prole PCI expansion slots, one COM port, a parallel port, a VGA port, two
USB 2.0 ports, PS/2 mouse and keyboard ports and two gigabit Ethernet ports.
Cooling System
The NovaScale R423-E2 server chassis has an innovative cooling design that
includes three 8-cm hot-plug system cooling fans located in the middle section of
the chassis. An air shroud channels the airow from the system fans to efciently
cool the processor area of the system. The power supply module also includes a
cooling fan.

1-5
Chapter 1: Introduction
Figure 1-1. Intel 5520 Chipset: System Block Diagram
Note: This is a general block diagram. Please see Chapter 5 for details.

1-6
NovaScale R423-E2 Installation and User's Guide
Notes

Chapter 2: Server Installation
2-1
Chapter 2. Server Installation
2-1 Overview
This chapter provides a quick setup checklist to get your NovaScale R423-E2 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 NovaScale R423-E2 was shipped in and note if it
was damaged in any way. If the server itself shows damage you should le a dam-
age claim with the carrier who delivered it.
Decide on a suitable location for the rack unit that will hold the NovaScale R423-E2.
It should be situated in a clean, dust-free area that is well ventilated. Avoid areas
where heat, electrical noise and electromagnetic elds are generated. You will also
need it placed near a grounded power outlet. Read the Rack and Server Precau-
tions in the next section.
2-3 Preparing for Setup
The box the NovaScale R423-E2 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.

2-2
NovaScale R423-E2 Installation and User's Guide
Choosing a Setup Location
Leave enough clearance in front of the rack to enable you to open the front•
door completely (about 65 cm / 25 inches) and approximately 75 cm / 30 inches
of clearance in the back of the rack to allow for sufcient airow and ease in
servicing.
!
!
Warnings and Precautions!
This product is for installation 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.
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 si-•
multaneously may cause the rack to become unstable.
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 touch-•
ing them.
Always keep the rack's front door and all panels and components on the servers•
closed when not servicing to maintain proper cooling.

Chapter 2: Server Installation
2-3
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 environ-
ment compatible with the manufacturer’s maximum rated ambient temperature
(Tmra): 10° to 35° C (50° to 95° F).
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 connec-
tions other than the direct connections to the branch circuit (i.e. the use of power
strips, etc.).

2-4
NovaScale R423-E2 Installation and User's Guide
2-4 Installing the System into a Rack
This section provides information on installing the NovaScale R423-E2 into a rack
unit. If the NovaScale R423-E2 has already been mounted into a rack, you can skip
ahead to Sections 2-5 and 2-6. There are a variety of rack units on the market, which
may mean the assembly procedure will differ slightly. The following is a guideline for
installing the system into a rack with the rack rails provided. You should also refer
to the installation instructions that came with the rack unit you are using.
Identifying the Sections of the Rack Rails
You should have received a total of six rack rail sections with the NovaScale
R423-E2. Two of these sections secure directly to the NovaScale R423-E2 and
the third (which actually consists of two joined sections) secures directly to the
rack itself. All screws and hardware mentioned in the installation steps should be
included in the hardware kit.
Refer to Figure 2-1 to determine which rail section gets attached to the front of the
chassis and which gets attached to the rear of the chassis. (The longer of the two
is the front section. The third rail section attaches to the rack.)
Installing the Chassis Rails
Position the front and rear chassis rail sections along the side of the NovaScale
R423-E2 making sure the screw holes line up. Note that these two rails are left/
right specic.Screw the front chassis rail (the long piece) securely to the side of
the chassis (see Figure 2-1, step 1). There should be two screws for each side.
Repeat this procedure for the other rail on the opposite side of the chassis. Then
attach the two rear chassis rails to the chassis in the same manner, again keep-
ing in mind that the rails are left/right specic. (You will also need to attach the rail
brackets when installing into a rack.)
Locking Tabs: Both front chassis rails and the rack rails have a locking tab, which
serves two functions. The rst is to lock the server into place when installed and
pushed fully into the rack, which is its normal position. Secondly, these tabs also
lock the server in place when fully extended from the rack. This prevents the server
from coming completely out of the rack when you pull it out for servicing.