TYAN Thunder n3600QE S4980 User manual

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Thunder n3600QE /// S4980
Version1.0
Copyright
Copyright © TYAN Computer Corporation, 2007. All rights reserved. No part of
this manual may be reproduced or translated without prior written consent from
TYAN Computer Corp.
Trademark
All registered and unregistered trademarks and company names contained in
this manual are property of their respective owners including, but not limited to
the following.
TYAN, Thunder n3600QEare trademarks of TYAN Computer Corporation.
AMD, Opteron, and combinations thereof are trademarks ofAMD Corporation.
AMI, AMIBIOS are trademarks of AMI Software Incorporated.
Microsoft, Windows are trademarks of Microsoft Corporation.
Nvidia and nForce are trademarks of Nvidia Corporation
Microsoft, Windows are trademarksof Microsoft Corporation.
SuSE,is a trademark ofSuSE AG.
Linux is a trademark of Linus Torvalds
IBM, PC, AT, and PS/2 are trademarks of IBM Corporation.
Winbond is a trademark of Winbond Electronics Corporation.
Notice
Information contained in this document is furnished by TYAN Computer
Corporation and has been reviewed for accuracy and reliability prior to printing.
TYAN assumes no liability whatsoever, and disclaims any express or implied
warranty, relating to sale and/or use of TYAN products includingliability or
warranties relating to fitness for a particular purpose or merchantability. TYAN
retains the right to make changes to product descriptions and/or specifications
at any time, without notice. In no event will TYAN be held liable for any direct or
indirect, incidental or consequential damage, loss of use, loss of data or other
malady resulting from errors or inaccuracies of information contained in this
document.

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Table of Contents
Check the box contents! 3
Chapter 1: Introduction
1.1 Congratulations 5
1.2 Hardware Specifications 5
Chapter 2: Board Installation
2.1 Board Image 8
2.2 Block Diagram 9
2.3 Board Parts, Jumpers and Connectors 10
2.4 Tips on Installing Motherboard in Chassis 18
2.5 Installing the Processor(s) 19
2.6 Installing the Memory 24
2.7 Attaching Drive Cables 26
2.8 Installing Add-in Cards 28
2.9 Connecting External Devices 29
2.10Installing the Power Supply 30
2.11Finishing up31
Chapter 3: BIOS Setup
3.1 About the BIOS 33
3.2 BIOS Menu Bar 33
3.3 Setup Basics 34
3.4 Getting Help 34
3.5 In Case of Problems 34
3.6 BIOS Main Menu 35
3.7 Advanced Menu 36
3.8 PCI/PnP Menu 57
3.9 Boot Menu 59
3.10 Security Menu 64
3.11 Chipset Menu 65
3.11 Exit Menu 73
Chapter 4: Diagnostics
4.1 Beep Codes 75
4.2 Flash Utility 75
4.3 BIOS Post Code 76
Appendix I: SMDC Information 78
Appendix II: How to Make a Driver Diskette 80
Glossary 82
Technical Support 89

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Check the box contents!
1x Thunder n3600QEmotherboard
1x Ultra-DMA-133/100/66/33 IDE cable
3x Serial ATA power cable
6x Serial ATA Cable
1x USB2.0 cable
1 x COM Port Cable
1x Thunder n3600QE user’s manual
1x Thunder n3600QE Quick Reference guide
1x TYAN driver CD
1x I/O shield
4x CPU Retention Frame and Back Plate (pre-installed)
If any of these items are missing, please contact your vendor/dealer for
replacement before continuing with the installation process.

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NOTE

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Chapter 1: Introduction
1.1 -Congratulations
You have purchased the high performanceserver with four processors (can
expand to eight). The Thunder n3600QE (S4980) is a flexible AMD®platform
for multiple applications, based on NVIDIA®NFP3600 and SMSC SCH5017
chipsets.
Designed to support four AMD®Rev. F OpteronTM 8000 series processors and
max 64GB DDR2-667/533/400 memory, and featured with integrated RJ-45
LANconnectors, one PCI-Express x16 slotplus six serial ATA ports, the S4980
offers exceptional performance and versatile solution for your server platform.
Remember to visit TYAN’s Website at http://www.TYAN.com. There you can
find information on all of TYAN’s products with FAQs, online manuals and BIOS
upgrades.
1.2 -Hardware Specifications
Processors
•Quad 1207-pin ZIF sockets
•Supports up to four AMD®Rev. F
OpteronTM 8000 series CPU
•Up to 1.0GHz Hyper-Thansport
link support
Chipset
•NVIDIA NFP3600 (MCP55 Pro)
•SMSC SCH5017
Memory
•Dual memory channels
•Supports up to sixteen DDR2
667/533/400 DIMMs
•Supports up to 64GB of registered,
ECC memory
•Supports 4-rank memory
Integrated PCI IDE
•Single channel master mode
supports up to two IDE devices
•Supports for ATA-133/100/66/33
IDE drives and ATAPI compliant
devices
Integrated 2D/3D PCI Graphics
•XGI Volari Z7 (XG20)
16MB frame buffer memory
Integrated LANControllers
•Two(2) NFP3600 integrated MA C
with two Marvell 88E1116 single
port Gigabit Ethernet PHY
-Integrated TCP offload Engine
(TOE)
-IEEE802.3 compliant, WOL/PXE
support
-Front panel LAN LED support
(TYFP2 header)
Server Management
•M3291, IPMI 2.0 Remote System
Mgmt card
•Renesas H8S2167 BMC
controller
•BT, KCS, Logging support
•IPMI-over-LAN
•Remote power on/off and reset
•2-pin warning LED

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Integrated Serial ATA II
•Three Serial ATA II Host
controllers embedded
•Supports up to six serial ports
running at 3.0Gb/s per direction
per channel
•Serial ATA II specification
compliant
•nVIDIA MediaShieldTM supports
for RAID 0, 1,0+1, 5, JBOD
•HDD LED support (TYFP header)
Back Panel I/O Ports
•Stacked PS/2 Mouse & Keyboard
ports
•One double-decked USB 2.0 port
•COM1 connector
•One 15-pin VGA port
•Two side-by-side RJ45
10/100/1000 Base-T port with
link/activity LED
Integrated I/O Interfaces
•One IDE connector
•TwoUSB 2.0 ports (via cable)
•One COM port (via cable)
•Tyan 2x9pinfan header (for Tyan
barebone)
•Tyan 2x6 pin front panel header
•Tyan 2x25 pin SMDC header
•ID LED
•SMDC Warning LED header
BIOS
•AMI BIOS 8Mbit Flash
•Supports ACPI 2.0
•PnP, DMI2.0, WfM2.0 Power
Management
•ACPI S1, S4, S5 supported
Power
•EPS 12V power with 24+8+8/4
power connectors
•One extra 2x2 power connector to
support next-generation SSI
PSU
•On board 5-phase digital VRD
Form Factor
•E-ATX footprint, 12”x13”
(304.8mm x 330.2mm)
Regulatory
•FCC Class B (Declaration of
Conformity)
•CE (Declaration of conformity)

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Chapter 2: Board Installation
You are now ready to install your motherboard. The mounting hole pattern of
the Thunder n3600QE S4980matches the E-ATX specification. Before
continuing with installation, confirm that your chassis supports anE-ATX
motherboard.
How to install our products right… the first time
The first thing you should do is reading this user’s manual. It contains important
information that will make configuration and setup much easier. Here are some
precautions you should take when installing your motherboard:
(1) Ground yourself properly before removing your motherboard from the
antistatic bag. Unplug the power from your computer power supply and
then touch a safely grounded object to release static charge (i.e. power
supply case). For the safest conditions, TYAN recommends wearing a
static safety wrist strap.
(2) Hold the motherboard by its edges and do not touch the bottom of the
board, or flex the board in any way.
(3) Avoid touching the motherboard components, IC chips, connectors,
memory modules, and leads.
(4) Place the motherboard on a grounded antistatic surface or on the
antistatic bag that the board was shipped in.
(5) Inspect the board for damage.
The following pages include details on how to install your motherboard into your
chassis, as well asinstalling the processor, memory, disk drives and cables.
NOTE
DO NOT APPLY POWER TO THE BOARD IF IT HAS BEEN
DAMAGED

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2.1-Board Image
This picture is representative of the latest board revision available at
the time of publishing. The board you receive may or may not look
exactly like the above picture.

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2.2 -Block Diagram
Thunder n3600QE S4980Block Diagram

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2.3 -Board Parts, Jumpers and Connectors
This diagram is representative of the latest board revision available at the time of
publishing. The board you receive may not look exactly like the above diagram.
Jumper Legend
©© OPEN -Jumper OFF, without jumper cover
©© CLOSED –Jumper ON, with jumper cover

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Jumper/Connector Function
J4/J5/J6/J13/J16/J18/J25/J26
Fan connector with speed control
J12 COM Port Pin Header
J17 USB Front Panel Pin Header
J14 Front Panel Pin Header
J11 IPMB Pin Header
J10 SMDC Connector
J9 LCM Pin Header
J8 SGPIO Pin Header
IDE1 Hard Drive Connector
JP2 SMDC Warning LED Header(for M3291)
JP1 Clear CMOS Jumper
SATA0/1/2/3/4/5 Serial ATA RAID Connectors
J3/J15 Reserved for Barebone only

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J15
J9
J12
J17
J3

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J15: FAN Tachometer Pin Header (for TYAN barebone use only)
1
2
17
18
Use these pin definitions to connect to the
barebone fans.
Pin 1 F1_TACH Pin 2 F6_TACH
Pin 3 F2_TACH Pin 4 F7_TACH
Pin 5 F3_TACH Pin 6 F8_TACH
Pin 7 F4_TACH Pin 8 F9_TACH
Pin 9 F5_TACH Pin 10
F10_TACH
Pin 11
GND Pin 12
KEY
Pin 13
PWM2 Pin 14
PWM1
Pin 15
F13_TACH
Pin 16
F11_TACH
Pin 17
F14_TACH
Pin 18
F12_TACH
J3: TYAN FP2 Connector (forTYAN barebone use only)
1
12
11
2
Pin 1 LAN1 LED+ Pin 2 LAN1 LED-
Pin 3 LAN2 LED+ Pin 4 LAN2 LED-
Pin 5 NC Pin 6 GND
Pin 7 ID LED+ Pin 8 ID LED1-
Pin 9 ID_LED S/W+
Pin 10
ID_LED S/W-
Pin 11
KEY Pin 12
NC
J17: USB Front Panel Connector
10 2
9 1
Pin 1
USBPWR
Pin 2 USBPWR
Pin 3
USB 4-Pin 4 USB 2-
Pin 5
USB 4+ Pin 6 USB 2+
Pin 7
GND Pin 8 GND
Pin 9
KEY Pin 10
GND
J12: COM2 Header
1 9
2 10
Pin 1
DCD
Pin 2 DSR
Pin 3
RXD
Pin 4 RTS
Pin 5
TXD
Pin 6 CTS
Pin 7
DTR
Pin 8 RI
Pin 9
GND
Pin 10
KEY
J9: LCM Pin Header
5 1
6 2
Pin 1
VCC Pin 2
RXD2
Pin 3
KEY Pin 4
GND
Pin 5
5VSB
Pin 6
TXD2

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J14
J8
SATA3/SATA4/SATA5
SATA0/SATA1/SATA2
J11

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J14: Front Panel Header
The Front Panel Header is used to connect some control or signal wires from
motherboard to chassis, such as HDD LED, power LED, power button, and
reset button.
J8: SGPIO Pin Header
8 2
7 1
Pin 1
SDATA TX0
Pin 2
SDATA RX0
Pin 3
SCLOCK Pin 4
SLOAD
Pin 5
SDATA TX1
Pin 6
SDATA RX1
Pin 7
GND Pin 8
NC
SATA0/1/2/3/4/5: Serial ATA RAID Connector
7GND
6RXP
5RXN
4GND
3TXN
2TXP
7
1
1GND
Connects to the Serial ATA ready drives via
the Serial ATA cable.
J11: IPMB Pin Header
1
Pin 1
IPMB DATA
Pin 2
GND
Pin 3
IPMB CLK Pin 4
NC
SMBUS Clock
SMBUSData
5VSB
Non-mask
Interrupt (NMI)
RESET
HLED-
HLED+
17
15
13
11
9 7 5 3 1
18
16
14
12
10
8642
Intruder
GND
Key
Warning LED-
Warning LED+
POWER
S / W
PLED-
PLED+

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JP2: Warning LED Pin Header for M3291
1
Pin 1
WLED_CTL
Pin 2
NC
J4
JP1
J5
J13
J26
J25
J18
J6
J16
J10
JP2

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J4/J5/J6/J13/J16/J18/J25/J26:4-pin Fan Connector with speed control
+12V
SpeedControl
GND
Tachometer
1
+12V
Speed Control
GND
Tachometer
1
Use this header to connect thecooling fan to
your motherboard to keep the systemat
optimum performance levels.
J4: FAN2 (CPU2 fan)
J5: FAN3 (system fan3)
J6: FAN4 (system fan4)
J13: FAN5 (CPU4 fan)
J16: FAN7 (system fan7)
J18: FAN8 (system fan8)
J25: FAN1 (CPU1 fan)
J26: FAN6 (CPU3 fan)
J10: SMDC Connector
J32
CON25X2_SVM_A
LAD0
1
LAD2
3
GND1
5GND2
7
GND3
9
GND4
11 I2C1DA
13
I2C4CLK
15
GND6
17 I2C3DA
19
I2C2CLK
21
5VSB2
23 PWRBTN#
25
RSTBTN#
27
SLPBTN#
29 EXTSMI#
31
CPUNMI
33
GPIO1
35 GND9
37
GND10
41 RSVD3
43
RSVD5
45
GND12
47 SMALERTB#
49
LAD1 2
LAD3 4
LFRAME# 6
PCI_CLK 8
PCIRST# 10
I2C1CLK 12
GND5 14
I2C4DA 16
I2C3CLK 18
5VSB1 20
I2C2DA 22
GND7 24
PCIPME# 26
SVM_IRQ# 28
SVM_WOL# 30
SVM_THERM# 32
GND8 34
GPIO2 36
GPIO4 38
PS_PWRGD 40
GND11 44
RSVD6 46
SMALERTA# 48
GND13 50
For connection with Tyan Server Management
Daughter Card (SMDC).
The SMDC connector isonly compatible with
Tyan M3291 (SMDC).
JP1: Clear CMOS Jumper
1
3
Normal
(default)
3
1
Clear CMOS
Use this jumper when you forgot your system/setup
password or need to clear system BIOS setting.
How to clear the CMOS data
-Power off system and disconnect power
supply from AC source
-Use jumper cap to close Pin_2 and 3 for
several seconds to Clear CMOS
-Replace jumper cap to close Pin_1 and 2
Reconnect power supply to AC source
Power on system

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2.4-Tips on Installing Motherboard in Chassis
Before installing your motherboard, make sure your chassis has the
necessary motherboard support studs installed. These studs are usually
metal and are gold in color. Usually, the chassis manufacturer will pre-install
the support studs. If you are unsure of stud placement, simply lay the
motherboard inside the chassis and align the screw holes of the
motherboard to the studs inside the case. If there are any studs missing,
you will know right away since the motherboard will not be able to be
securely installed.
Some chassis’ include plastic studs instead of metal. Although the plastic
studs are usable, TYAN recommends using metal studs with screws that will
fasten the motherboard more securely in place.
Below is a chart detailing what the most common motherboard studs look
like and how they should be installed.

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2.5-Installing the Processor(s)
Your S4980 ports the latest processor technologies from AMD. Check the
TYAN website for latest processor support:
http://www.tyan.com
Figure 1. Exploded View of Thermal Solution AMD PIB Platforms based on AMD
Socket F Processor
p
re
-
installed

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Back plate Assembly
The back plate is mounted on the backside of the motherboard and enhances
local stiffness to support shock and vibration loads acting on the heat sink. The
back plate assembly prevents excessive motherboard warpage in the area near
the processor. Without a back plate, excessive warpage could cause serious
damage to electrical connections of the processor socket and integrated circuit
packages surrounding the processor. The back plate also serves as a stiffener
plate for the LGA socket.
While doing the installation, be careful in holding the components. Follow these
instructions to install your backplate:
1. Remove the release liner from the back plate.
2. Align the PEM nuts on the back plate to the holes on the reverse side
of the PCB.
3. First, insert the taller upper & lower middle PEM nuts through the
holes of the PCB. The remaining four shorter PEM nuts should
automatically fit the 4 holes on the PCB as shown in the following
pictures.
Let 2 upper &
lower-middle
PEM nuts pass
through the
holes.
4 PEM nuts
should fit 4
holes.