Supero SuperServer 1025C-M3 User manual

SUPER
USER’S MANUAL
Revision 1.0
®
SUPERSERVER 1025C-M3

Manual Revision 1.0
Release Date: November 4, 2008
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. Please Note: For the most up-to-date version of this
manual, please see our web site at www.supermicro.com.
Super Micro Computer, Inc. ("Supermicro") reserves the right to make changes to the product
described in this manual at any time and without notice. This product, including software, if any,
and documentation may not, in whole or in part, be copied, photocopied, reproduced, translated or
reduced to any medium or machine without prior written consent.
IN NO EVENT WILLSUPERMICRO BE LIABLE FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL,
SPECULATIVE OR CONSEQUENTIAL DAMAGES ARISING FROM THE USE OR INABILITY TO
USE THIS PRODUCT OR DOCUMENTATION, EVEN IF ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES. IN PARTICULAR, SUPERMICRO SHALL NOT HAVE LIABILITY FOR ANY
HARDWARE, SOFTWARE, OR DATASTORED OR USED WITH THE PRODUCT, INCLUDINGTHE
COSTS OF REPAIRING, REPLACING, INTEGRATING, INSTALLING OR RECOVERING SUCH
HARDWARE, SOFTWARE, OR DATA.
Any disputes arising between manufacturer and customer shall be governed by the laws of Santa
Clara County in the State of California, USA. The State of California, County of Santa Clara shall
be the exclusive venue for the resolution of any such disputes. Super Micro's total liability for
all claims will not exceed the price paid for the hardware product.
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 equipment 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.
California Best Management Practices Regulations for Perchlorate Materials: This Perchlorate
warning applies only to products containing CR (Manganese Dioxide) Lithium coin cells. “Perchlorate
Material-special handling may apply. See www.dtsc.ca.gov/hazardouswaste/perchlorate”
WARNING: Handling of lead solder materials used in this
product may expose you to lead, a chemical known to
the State of California to cause birth defects and other
reproductive harm.
Unless you request and receive written permission from Super Micro Computer, Inc., you may not
copy any part of this document.
Information in this document is subject to change without notice. Other products and companies
referred to herein are trademarks or registered trademarks of their respective companies or mark
holders.
Copyright © 2008 by Super Micro Computer, Inc.
All rights reserved.
Printed in the United States of America

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 SuperServer 1025C-M3. In-
stallation and maintenance should be performed by experienced technicians only.
The SuperServer 1025C-M3 is a high-end dual processor rackmount server
based on the SC113MTQ-560CB 1U server chassis and the Super X7DCL-3
serverboard.
Manual Organization
Chapter 1: Introduction
The first chapter provides a checklist of the main components included with the
server system and describes the main features of the Super X7DCL-3 serverboard
and the SC113MTQ-560CB chassis.
Chapter 2: Server Installation
This chapter describes the steps necessary to install the SuperServer 1025C-M3
into a rack and check out the server configuration prior to powering up the system. If
your server was ordered without the processor and memory components, this chap-
ter will refer you to the appropriate 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
SuperServer 1025C-M3.
iii
Preface

SUPERSERVER 1025C-M3 User's Manual
iv
Chapter 5: Advanced Serverboard Setup
Chapter 5 provides detailed information on the X7DCL-3 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 reconfiguring the
serverboard.
Chapter 6: Advanced Chassis Setup
Refer to Chapter 6 for detailed information on the SC113MTQ-560CB 1U rackmount
server chassis. You should follow the procedures given in this chapter when install-
ing, removing or reconfiguring hot-swap or peripheral drives and when replacing
system power supply 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 POST Messages
Appendix B: BIOS POST Codes
Appendix C:

v
Preface
Notes

vi
SUPERSERVER 1025C-M3 User's Manual
Table of Contents
Chapter 1 Introduction
1-1 Overview .........................................................................................................1-1
1-2 Serverboard Features..................................................................................... 1-2
Processors ......................................................................................................1-2
Memory ...........................................................................................................1-2
Onboard SAS..................................................................................................1-2
Serial ATA........................................................................................................1-2
PCI Expansion Slots....................................................................................... 1-3
Ethernet Ports................................................................................................. 1-3
Onboard Controllers/Ports .............................................................................. 1-3
Other Features................................................................................................1-3
1-3 Server Chassis Features ................................................................................ 1-5
System Power.................................................................................................1-5
Control Panel .................................................................................................. 1-5
I/O Backplane.................................................................................................. 1-5
Cooling System...............................................................................................1-5
1-4 Contacting Supermicro....................................................................................1-6
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.......................................................................2-3
Ambient Operating Temperature................................................................ 2-3
Reduced Airflow .........................................................................................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
Inner Rails.......................................................................................................2-5
Outer Rails......................................................................................................2-6
Installing the Server into a Telco Rack...........................................................2-9
2-5 Checking the Serverboard Setup.................................................................. 2-10

vii
2-6 Checking the Drive Bay Setup.......................................................................2-11
Chapter 3 System Interface
3-1 Overview .........................................................................................................3-1
3-2 Control Panel Buttons..................................................................................... 3-1
Reset...............................................................................................................3-1
Power..............................................................................................................3-1
UID..................................................................................................................3-1
3-3 Control Panel LEDs ........................................................................................3-2
NIC2................................................................................................................3-2
NIC1................................................................................................................3-2
HDD................................................................................................................. 3-2
Power..............................................................................................................3-2
3-4 Hard 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 Serverboard Setup
5-1 Handling the Serverboard............................................................................... 5-1
Precautions .....................................................................................................5-1
Unpacking .......................................................................................................5-2
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......................................................................... 5-4
5-4 I/O Ports..........................................................................................................5-4
5-5 Processor and Heatsink Installation................................................................5-5
5-6 Installing Memory............................................................................................5-8
5-7 Adding PCI Cards........................................................................................... 5-9
5-8 Serverboard Details ...................................................................................... 5-10
Motherboard Layout...................................................................................... 5-10
X7DCL-3 Quick Reference.............................................................................5-11
5-9 Connector Definitions ...................................................................................5-12
ATX Power Connector..............................................................................5-12
Processor Power Connector ...................................................................5-12
PW_ON Connector...................................................................................5-12

viii
SUPERSERVER 1025C-M3 User's Manual
Reset Connector ...................................................................................... 5-12
Overheat LED (OH)..................................................................................5-13
NIC2 (LAN2) LED.....................................................................................5-13
NIC1 (LAN1) LED.....................................................................................5-13
HDD LED.................................................................................................. 5-13
Power On LED......................................................................................... 5-13
NMI Button ............................................................................................... 5-14
Fan Headers............................................................................................. 5-14
ATX PS/2 Keyboard and PS/2 Mouse Ports............................................ 5-14
Chassis Intrusion......................................................................................5-14
LAN1/2 (Ethernet Ports)........................................................................... 5-14
Universal Serial Bus (USB)...................................................................... 5-15
Wake-On-LAN .......................................................................................... 5-15
Wake-On-Ring..........................................................................................5-15
Power Supply Fail Detect......................................................................... 5-16
Alarm Reset.............................................................................................. 5-16
PWR I2C................................................................................................... 5-16
BPI2C........................................................................................................5-16
Serial Ports...............................................................................................5-17
SGPIO Headers ....................................................................................... 5-17
Power LED/Speaker................................................................................. 5-17
Keylock.....................................................................................................5-17
5-10 Jumper Settings............................................................................................ 5-18
Explanation of Jumpers ................................................................................5-18
CMOS Clear.............................................................................................5-18
VGA Enable/Disable................................................................................. 5-18
LAN1/LAN2 Enable/Disable.....................................................................5-19
SAS Enable/Disable................................................................................. 5-19
SAS RAID Select ..................................................................................... 5-19
Watch Dog................................................................................................ 5-19
I2C Bus to PCI/PCI-Exp. Slots................................................................. 5-20
5-11 Onboard Indicators........................................................................................5-20
LAN1/LAN2 LEDs.....................................................................................5-20
Onboard Power LED (LED3)....................................................................5-20
System Status LED (LED4)......................................................................5-20
CPU_VRM Overheat LED Indicators (LED5/LED6)................................. 5-21
5-12 Floppy and IDE Drive Connections...............................................................5-21
Floppy Connector.....................................................................................5-21
IDE Connector..........................................................................................5-22

ix
SAS Ports.................................................................................................5-23
SATA Ports ............................................................................................... 5-23
5-13 Installing Software.........................................................................................5-24
Supero Doctor III...........................................................................................5-25
Chapter 6 Advanced Chassis Setup
6-1 Static-Sensitive Devices..................................................................................6-1
Precautions .....................................................................................................6-1
6-2 Control Panel .................................................................................................. 6-2
6-3 System Cooling...............................................................................................6-2
System Fan Failure......................................................................................... 6-3
6-4 Drive Bay Installation/Removal....................................................................... 6-4
Accessing the Drive Bays............................................................................... 6-4
Hard Drive Installation.....................................................................................6-4
DVD Drive Installation..................................................................................... 6-6
6-5 Power Supply..................................................................................................6-8
Power Supply Failure...................................................................................... 6-8
Chapter 7 BIOS
7-1 Introduction...................................................................................................... 7-1
7-2 Running Setup ................................................................................................ 7-2
7-3 Main BIOS Setup............................................................................................ 7-2
7-4 Advanced Setup..............................................................................................7-7
7-5 Security ......................................................................................................... 7-20
7-6 Boot...............................................................................................................7-21
7-7 Exit ................................................................................................................ 7-22
Appendix A BIOS POST Messages
Appendix B BIOS POST Codes
Appendix C System Specifications
Table of Contents

SUPERSERVER 1025C-M3 User's Manual
x
Notes

Chapter 1
Introduction
1-1 Overview
The SuperServer 1025C-M3 is a dual processor server comprised of two main
subsystems: the SC113MTQ-560CB 1U rackmount chassis and the X7DCL-3
serverboard. Please refer to our web site for information on operating systems that
have been certified for use with the 1025C-M3 (www.supermicro.com).
In addition to the serverboard and chassis, various hardware components may have
been included with the 1025C-M3, as listed below.
Two (2) CPU heatsinks (SNK-P0017)
•
One (1) slim DVD-ROM drive (DVM-TEAC-824B)•
SAS/SATA Accessories:•
Eight (8) SAS/SATA hard drive carriers (MCP-220-00047-0B)
One (1) internal SAS/SATA backplane (BPN-SAS-113TQ)
Two (2) SAS/SATA cable sets (CBL-0186L)
Two (2) SGPIO cables (CBL-0157L)
•
One (1) PCI-E x8 riser card (CSE-RR1U-E8)•
One (1) front side USB/COM port tray [(CSE-PT-40(B)]•
Four (4) 4-cm high-performance fans (FAN-0061L4)•
Rackmount hardware with screws (CSE-PT51L)•
One (1) CD containing drivers and utilities•
SuperServer 1025C-M3 User's Manual•
Note: "B" indicates part is available in black.
Chapter 1: Introduction
1-1

1-2
SUPERSERVER 1025C-M3 User's Manual
1-2 Serverboard Features
At the heart of the SuperServer 1025C-M3 lies the X7DCL-3, a single processor
serverboard based on Intel's 5100 chipset and designed to provide maximum per-
formance. Below are the main features of the X7DCL-3.
Processors
The X7DCL-3 supports dual Intel®5400, 5300, 5200 or 5100 Series processors in
LGA771 sockets. Please refer to our web site for a complete listing of supported
processors (www.supermicro.com).
Memory
The X7DCL-3 has six 240-pin DIMM sockets that can support up to 48 GB of reg-
istered ECC DDR2-667/533 SDRAM. Memory must be installed in an interleaved
(dual-channel) configuration. All memory modules used to populate the system
should be the same size, type and speed. See Chapter 5 for details.
Onboard SAS
An onboard LSI 1068E SAS controller in integrated into the X7DCL-3. The hot-swap
SAS drives are connected to a backplane that provides power, bus termination and
configuration settings.
Note: The operating system you use must have RAID support to enable
the hot-swap capability and RAID function of the SAS drives. RAID 0, 1,
5 and 10 are supported. Refer to the following ftp site for setup guidelines
<ftp://ftp.supermicro.com/driver/SAS/LSI/LSI_SAS_EmbMRAID_SWUG.pdf>.
Serial ATA
The South Bridge (ICH9R) of the 5100 chipset includes a Serial ATA controller.
The hot-swap SATA drives are connected to a backplane that provides power, bus
termination and configuration settings.
Note: The operating system you use must have RAID support to enable the
hot-swap capability and RAID function of the SAS drives. RAID 0, 1, and 10
are supported. Refer to the following link on our web site for setup guidelines:
<http://www.supermicro.com/support/manuals/ for setup guidelines>.

Chapter 1: Introduction
1-3
PCI Expansion Slots
The X7DCL-3 has two PCI-Express x8 slots, one PCI-Express x4 slot (in a x8 slot)
and three 32-bit, 33 MHz (5V) PCI slots. In the 1025C-M3 server configuration, a
PCI-E riser card (CSE-RR1U-E8) has been installed to support a single PCI-Ex-
press add-on card.
Ethernet Ports
The X7DCL-3 has two network controllers integrated into the chipset to support two
Gigabit LAN ports (100/1000Base-T/1000BaseTX, RJ45 output).
Onboard Controllers/Ports
An onboard IDE controller supports Ultra ATA 100 hard drives or ATAPI devices.
Onboard I/O backpanel ports include one COM port, a VGA port, two USB ports,
PS/2 mouse and keyboard ports and two Gigabit LAN (NIC) ports.
Other Features
Other onboard features that promote system health include voltage monitors, a
chassis intrusion header, auto-switching voltage regulators, chassis and CPU
overheat sensors, virus protection and BIOS rescue.

1-4
SUPERSERVER 1025C-M3 User's Manual
Figure 1-1. Intel 5100 Chipset:
System Block Diagram
Note: This is a general block diagram. Please see Chapter 5 for details.
USB 2.0
PORT
PORT
PORT
#0
MCH
Intel 5100
PROCESSOR#2
ICH9R
PCI-EXP x8
FWH
RJ45
LPC
COM1
External
SIO
W83627HG
VGA
PCI 33MHz
VGA
CONN
KB
MS
ISL6312A
#2,3
#4,5
ISL6312A
PROCESSOR#1
1067/1333 MT/S
1067/1333
MT/S
USB
#0
#1
#2
#3
#4
PCIE X4
#0-2
#0-1
DDR2 667
PORT
#6,7
PCI-EXP x8
#1-2
#1-1
DDR2 667
IDE
IT8213F
DMI
LANE5
LANE1/2/3/4
PCI-EXP x1
PCI-E x8
LSI 1068E
COM2
INTERNAL/SOL
PCI-EXP x8
PCI-E x8
#0-3
#1-3
82573V
GDDR2 SDRAM 32MB
#4
#5
SAS
#0
#1
#2
#3
3.0 Gb/S
#6
#7
LANE6
PCI-33
PCI-33
PCI-33
#4
#5
3.0 Gb/S
SATA
#0
#1
#2
#3
#5
#6
PCI-EXP x1
RJ45 82573V
Volari Z9S
PCI-E x8 Slot
PCI-E x4Signal

Chapter 1: Introduction
1-5
1-3 Server Chassis Features
The SC113MTQ-560CB is a short depth (20") 1U chassis that features eight 2.5"
hard drive bays and a high-efficiency power supply. The following is a general outline
of the main features of the SC113MTQ-560CB chassis.
System Power
When configured as a SuperServer 1025C-M3, the SC113MTQ-560CB chassis
includes a single 560W power supply. This is a high-efficiency power supply that
operates at 80% efficiency or better.
Control Panel
The control panel on the SC113MTQ-560CB provides important system monitoring
and control information. LEDs indicate power on, network activity, hard disk drive
activity and a UID (Universal Information) LED. Also present are a main power
button, a system reset button and a UID button.
I/O Backplane
The SC113MTQ-560CB is a 1U rackmount chassis. Its I/O backplane provides three
PCI slots, one COM port (the other is internal), one VGA port, two USB ports, PS/2
mouse and keyboard ports, two Ethernet (LAN) ports and a UID LED.
Cooling System
The SC113MTQ-560CB chassis' revolutionary cooling design has been optimized
to provide sufficient cooling for dual CPU configurations. The chassis includes four
4-cm PWM (Pulse Width Modulated) fans located in the middle of the chassis.
There is a "Fan Speed Control Mode" in BIOS that allows chassis fan speed to be
determined by system temperature.

1-6
SUPERSERVER 1025C-M3 User's Manual
1-4 Contacting Supermicro
Headquarters
Address: Super Micro Computer, Inc.
980 Rock Ave.
San Jose, CA 95131 U.S.A.
Tel: [phone]
Fax: [phone]
Email: [email protected] (General Information)
[email protected] (Technical Support)
Web Site: www.supermicro.com
Europe
Address: Super Micro Computer B.V.
Het Sterrenbeeld 28, 5215 ML
's-Hertogenbosch, The Netherlands
Tel: [phone]
Fax: [phone]
Email: [email protected] (General Information)
[email protected] (Technical Support)
[email protected] (Customer Support)
Asia-Pacific
Address: Super Micro Computer, Inc.
4F, No. 232-1, Liancheng Rd.
Chung-Ho 235, Taipei County
Taiwan, R.O.C.
Tel: [phone]
Fax: [phone]
Web Site: www.supermicro.com.tw
Technical Support:
Email: [email protected]
Tel: [phone], ext.132 or 139

Chapter 2: Server Installation
2-1
Chapter 2
Server Installation
2-1 Overview
This chapter provides a quick setup checklist to get your SuperServer 1025C-M3
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 SuperServer 1025C-M3 system has come to you with the proces-
sors 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 specific components.
2-2 Unpacking the System
You should inspect the box the SuperServer 1025C-M3 was shipped in and note
if it was damaged in any way. If the server itself shows damage you should file a
damage claim with the carrier who delivered it.
Decide on a suitable location for the rack unit that will hold the SuperServer 1025C-
M3. It should be situated in a clean, dust-free area that is well ventilated. Avoid
areas where heat, electrical noise and electromagnetic fields 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 SuperServer 1025C-M3 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 sufficient airflow and ease in servicing.This product is for

2-2
SUPERSERVER 1025C-M3 Manual
!
!
Warnings and Precautions!
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 floor 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 first, 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 SATAdrives 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 tempera-
ture 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 tempera-
ture (Tmra).
Reduced Airflow
Equipment should be mounted into a rack so that the amount of airflow 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
SUPERSERVER 1025C-M3 Manual
2-4 Installing the System into a Rack
This section provides information on installing the SuperServer 1025C-M3 into a
rack. If the 1025C-M3 has already been mounted into a rack, you can skip ahead to
Sections 2-5 and 2-6. Note: The rails will fit a rack between 26" and 33.5" deep.
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 1025C-
M3 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
Each assembly consists of two sections: an inner fixed chassis rail that secures
directly to the server chassis and an outer fixed rack rail that secures directly to
the rack itself.
Figure 2-1. Identifying the Sections of the Rack Rails
Inner Rails
Inner Rail
Extensions