TYAN S5642 User manual

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1
S5642
Version 1.0
Copyright
Copyright © 2021 MiTAC International Corporation. All rights reserved. No part of
this manual may be reproduced or translated without prior written consent from
MiTAC International Corporation.
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®is a trademark of MiTAC International Corporation.
Intel®is a trademark of Intel®Corporation.
AMI, AMI BIOS are trademarks of AMI Technologies.
Microsoft®, Windows®are trademarks of Microsoft Corporation.
Winbond®is a trademark of Winbond Electronics Corporation.
Notice
Information contained in this document is furnished by MiTAC International
Corporation and has been reviewed for accuracy and reliability prior to printing.
MiTAC assumes no liability whatsoever, and disclaims any express or implied
warranty, relating to sale and/or use of TYAN®products including liability or
warranties relating to fitness for a particular purpose or merchantability. MiTAC
retains the right to make changes to product descriptions and/or specifications at
any time, without notice. In no event will MiTAC be held liable for any direct or
indirect, incidental or consequential damage, loss of use, loss of data or other
malady resulting from errors or inaccuracies of information contained in this
document.

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Contents
S5642............................................................................................................1
Before you begin…....................................................................................3
Chapter 1: Instruction ................................................................................4
1.1 Congratulations .................................................................................4
1.2 Hardware Specifications....................................................................4
1.3 Software Specifications...................................................................11
Chapter 2: Board Installation...................................................................12
2.1 Board Image....................................................................................13
2.2 Block Diagram.................................................................................14
2.3 Motherboard Mechanical Drawing...................................................15
2.4Board Parts, Jumpers and Connectors ...........................................16
2.5 LED Definitions................................................................................28
2.6Installing the Processor and Heatsink.............................................31
2.7Thermal Interface Material...............................................................34
2.8Tips on Installing Motherboard in Chassis ......................................35
2.9Installing the Memory ......................................................................37
2.10 Attaching Drive Cables..................................................................41
2.11 Installing Add-In Cards..................................................................42
2.12 Connecting External Devices ........................................................43
2.13 Installing the Power Supply...........................................................45
2.14 Finishing Up...................................................................................45
Chapter 3: BIOS Setup .............................................................................46
3.1 About the BIOS................................................................................46
3.2 Main Menu.......................................................................................48
3.3 Advanced Menu...............................................................................50
3.4 Server Management......................................................................140
3.5 Security..........................................................................................144
3.6 Boot ...............................................................................................149
3.7 Save & Exit....................................................................................151
Chapter 4: Diagnostics...........................................................................153
4.1 Flash Utility....................................................................................153
4.2 AMIBIOS Post Code (Aptio)..........................................................154
Appendix I: How to recover UEFI BIOS ................................................161
Appendix II: M.2 Latch Installation .......................................................163
Glossary...................................................................................................170
Technical Support ..................................................................................176

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Before you begin…
Check the box contents!
The retail motherboard package should contain the following:
S5642 Motherboard x 1
Whitley CPU Clip x1
SATA Single Cable x 2
Rear IO shielding x 1
S5642 Quick Installation Guide x 1
M.2 latch x2
IMPORTANT NOTE:
Sales samples may not come with any of the accessories listed above.
If you have ordered a sales sample and you are missing any of the above items,
please contact your sales representative to help order accessories.

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Chapter 1: Instruction
1.1 Congratulations
You have purchased the powerful TYAN® S5642 motherboard, based on the Intel®
C621A chipset. The S5642 is designed to support Single 3rd Gen Intel®Xeon®
Scalable family series Processor, and Up to 512GB RDIMM/1,024GB LRDIMM/
2,048GB RDIMM 3DS 3200 DDR4 memory. Leveraging advanced technology from
Intel®, the S5642 is capable of offering scalable 64-bit computing, high-bandwidth
memory design, and lightning-fast PCI-E bus implementation.
The S5642 not only empowers you in today’s demanding IT environment but also
offers a smooth path for future application upgradeability. All of these rich feature
sets provide the S5642 with the power and flexibility to meet demanding
requirements for today’s IT environments.
Remember to visit the TYAN® website at http://www.tyan.com. There you can find
all the information on all TYAN®products as well as all the supporting documentation,
FAQs, Drivers and BIOS upgrades.
1.2 Hardware Specifications
S5642AGM3NRE-2T Specifications
Processor
Q'ty / Socket
Type
(1) LGA4189
Supported CPU
Series
3rd Gen Intel Xeon Scalable Processor
Thermal Design
Power (TDP)
Wattage
Max up to 270W
Chipset
PCH
Intel C621A
Memory
Supported DIMM
Qty
(8) DIMM slots
DIMM Type /
Speed
DDR4 ECC RDIMM /LRDIMM 3200
Capacity
512GB RDIMM/ 1,024GB LRDIMM/
2,048GB RDIMM 3DS *Follow latest
Intel DDR4 Memory POR
Memory channel
8 Channels per CPU

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Memory voltage
1.2V
Expansion
Slots
PCIe
(1) PCIe Gen.4 x8 slot (#4 w/x4 link) /
(1) PCIe Gen.4 x8 slot (#2 via MUX) /
(1) PCIe Gen.4 x16 slot (#3 w/x8 link) /
(2) PCIe Gen.4 x16 slots (#5,#6)
LAN
Q'ty / Port
(2) 10GbE ports + (1) GbE ports +
(1) GbE dedicated for IPMI
Controller
Intel I210 / Intel X550-AT2
PHY
Realtek RTL8211E
Storage sSATA
Connector
(2) Mini-SAS HD (8 ports)
Controller
Intel C621A
Speed
6Gb/s
RAID
RAID 0/1/10/5 (Intel RSTe)
Storage SATA
Connector
(1) Mini-SAS HD (4-ports) /
(2) 7-pin SATA for (2) SATA ports
Controller
Intel C621A
Speed
6Gb/s
RAID
RAID 0/1/10/5 (Intel RSTe)
Storage NVMe
Connector (M.2)
(2) 22110/2280 (by PCIe Gen.3 interface)
Connector (U.2)
(1) SFF-8654 for (2) NVMe ports
Storage
(Optional)
VROC Support
Yes
Graphic VGA
Connector type
D-Sub 15-pin
Resolution
Up to 1920x1200
Chipset
Aspeed AST2500
Input /Output
USB
(2) USB2.0 ports (@ rear) /
(2) USB3.2 Gen1 ports (@ rear) /
(2) USB3.2 Gen1 ports (via cable)
COM
(1) DB-9 COM Connector
VGA
(1) D-Sub 15-pin VGA port (@ rear)
RJ-45
(2) 10GbE ports + (1) GbE ports +
(1) GbE dedicated for IPMI

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Front Panel
(1) 2x12-pin SSI front panel header
Audio
(1) 2x5-pin header /
(1) 3 holes Audio Jack connector
SATA
(14) SATA-III ports
Power
2x12-pin power connector
2x4-pin power connector
2x2-pin power connector
Others
(1) UID button
TPM
(Optional)
TPM Support
Please refer to our TPM supported list.
System
Monitoring
Chipset
Aspeed AST2500
Fan
Total (5) 4-pin headers
Temperature
Monitors temperature for CPU, memory
& system environment
Voltage
Monitors voltage for CPU, memory,
chipset & power supply
LED
Over temperature warning indicator /
Fan & PSU fail LED indicator
Others
Watchdog timer support
Audio
Chipset
Realtek ALC888S-VD2-GR
Feature
2.0 ch
Server
Management
Onboard Chipset
Onboard Aspeed AST2500
AST2500 iKVM
Feature
24-bit high quality video compression /
Supports storage over IP and remote
platform-flash / USB 2.0 virtual hub
AST2500 IPMI
Feature
IPMI 2.0 compliant baseboard
management controller (BMC) /
10/100/1000 Mb/s MAC interface
BIOS
Brand / ROM size
AMI / 32MB
Feature
Hardware Monitor / Boot from USB
device/PXE via LAN/Storage / Console
Redirection / User Configurable FAN
PWM Duty Cycle / SMBIOS

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3.3/PnP/Wake on LAN / ACPI 6.2 /
ACPI sleeping states S5
Physical
Dimension
Form Factor
SSI CEB compatible
Board Dimension
12” x 10.5” (305 x 267mm)
Regulation
FCC (SDoC)
Class B
CE (DoC)
Class B
RCM
Class B
VCCI
Class B
Operating
Environment
Operating Temp.
0°C ~ 40°C (32°F~ 104°F)
Non-operating
Temp.
- 40°C ~ 70°C (-40°F ~ 158°F)
In/Non-
operating
Humidity
90%, non-condensing at 35°C
RoHS
RoHS 6/6
Compliant
Yes
Operating
System
OS supported list
Please refer to our AVL support lists.
Package
Contains
Motherboard
(1) S5642 Motherboard
Manual
(1) Quick Installation Guide
I/O Shield
(1) I/O Shield
Cable SATA
(2) SATA signal cables

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S5642AGMNRE Specifications
Processor
Q'ty / Socket
Type
(1) LGA4189
Supported CPU
Series
3rd Gen Intel Xeon Scalable Processor
Thermal Design
Power (TDP)
Wattage
Max up to 270W
Chipset
PCH
Intel C621A
Memory
Supported
DIMM Qty
(8) DIMM slots
DIMM Type /
Speed
DDR4 ECC RDIMM /LRDIMM 3200
Capacity
512GB RDIMM/ 1,024GB LRDIMM/
2,048GB RDIMM 3DS *Follow latest Intel
DDR4 Memory POR
Memory channel
8 Channels per CPU
Memory voltage
1.2V
Expansion
Slots
PCIe
(1) PCIe Gen.4 x8 slot (#4 w/x4 link) /
(1) PCIe Gen.4 x8 slot (#2 via MUX) /
(1) PCIe Gen.4 x16 slot (#3 w/x8 link) /
(2) PCIe Gen.4 x16 slots (#5,#6)
LAN
Q'ty / Port
(1) GbE port + (1) GbE dedicated for IPMI
Controller
Intel I210
PHY
Realtek RTL8211E
Storage sSATA
Connector
(1) Mini-SAS HD for (4) SATA ports /
(2) 7-pin SATA for (2) SATA ports
Controller
Intel C621A
Speed
6Gb/s
RAID
RAID 0/1/10/5 (Intel RSTe)
Storage SATA
Connector
(2) Mini-SAS HD (8-ports)
Controller
Intel C621A
Speed
6Gb/s

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RAID
RAID 0/1/10/5 (Intel RSTe)
Storage NVMe
Connector (M.2)
(2) 22110/2280 (by PCIe Gen.3 interface)
Connector (U.2)
(1) SFF-8654 for (2) NVMe ports
Storage
(Optional)
VROC Support
Yes
Graphic VGA
Connector type
D-Sub 15-pin
Resolution
Up to 1920x1200
Chipset
Aspeed AST2500
Input /Output
USB
(2) USB2.0 ports (@ rear) /
(2) USB3.2 Gen 1 ports (@ rear) /
(2) USB3.2 Gen 1 ports (via cable)
COM
(1) DB-9 COM Connector
VGA
(1) D-Sub 15-pin VGA port (@ rear)
RJ-45
(1) GbE ports +
(1) GbE dedicated for IPMI
Front Panel
(1) 2x12-pin SSI front panel header
Audio
(1) 2x5-pin header /
(1) 3 holes Audio Jack connector
SATA
(14) SATA-III ports from AHCI
Power
2x12-pin power connector
2x4-pin power connector
2x2-pin power connector
Others
(1) UID button
TPM
(Optional)
TPM Support
Please refer to our TPM supported list.
System
Monitoring
Chipset
Aspeed AST2500
Fan
Total (5) 4-pin headers
Temperature
Monitors temperature for CPU, memory
& system environment
Voltage
Monitors voltage for CPU, memory,
chipset & power supply
LED
Over temperature warning indicator /
Fan & PSU fail LED indicator

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Others
Watchdog timer support
Audio
Chipset
Realtek ALC888S-VD2-GR
Feature
2.0 ch
Server
Management
Onboard Chipset
Onboard Aspeed AST2500
AST2500 iKVM
Feature
24-bit high quality video compression /
Supports storage over IP and remote
platform-flash / USB 2.0 virtual hub
AST2500 IPMI
Feature
IPMI 2.0 compliant baseboard
management controller (BMC) /
10/100/1000 Mb/s MAC interface
BIOS
Brand / ROM
size
AMI / 32MB
Feature
Hardware Monitor / Boot from USB
device/PXE via LAN/Storage / Console
Redirection / User Configurable FAN
PWM Duty Cycle / SMBIOS
3.3/PnP/Wake on LAN / ACPI 6.2 / ACPI
sleeping states S5
Physical
Dimension
Form Factor
SSI CEB compatible
Board
Dimension
12” x 10.5” (305 x 267mm)
Regulation
FCC (SDoC)
Class B
CE (DoC)
Class B
RCM
Class B
VCCI
Class B
Operating
Environment
Operating Temp.
0°C ~ 40°C (32°F~ 104°F)
Non-operating
Temp.
- 40°C ~ 70°C (-40°F ~ 158°F)
In/Non-
operating
Humidity
90%, non-condensing at 35°C
RoHS
RoHS 6/6
Compliant
Yes

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Operating
System
OS supported
list
Please refer to our AVL support lists.
Package
Contains
Motherboard
(1) S5642 Motherboard
Manual
(1) Quick Installation Guide
I/O Shield
(1) I/O Shield
Cable SATA
(2) SATA signal cables
1.3 Software Specifications
For the latest AST2500 User’s Guide and OS (operation system) support, please
visit the Tyan’s Web site at http://www.tyan.com for the latest information

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Chapter 2: Board Installation
You are now ready to install your motherboard.
How to install our products right… the first time
The first thing you should do is read 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, MiTAC 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 as installing the processor, memory, disk drives and cables.
Caution!
1. To avoid damaging the motherboard and associated
components, do not use torque force greater than
5~7kgf/cm (4.35~6.09 lb/in) on each mounting screw
for motherboard installation.
2. Do not apply power to the board if it has been
damaged.

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2.1 Board Image
S5642AGM3NRE-2T
This picture is representative of the latest board revision available at the time of
publishing. The board you receive may not look exactly like the above picture.

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2.2 Block Diagram
S5642 Block Diagram

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2.3 Motherboard Mechanical Drawing

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2.4 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. The
DIMM slot numbers shown above can be used as a reference when reviewing the
DIMM population guidelines shown later in the manual. For the latest board revision,
please visit our web site at http://www.tyan.com.

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Motherboard Components
Connectors
1.Audio Jack(J4)
20. SATA Connector for SSATA
(SSATA5)
2. VGA+ COM PORT (VGA_COM1)
21. SATA Connector for SSATA
(SSATA4)
3. 4-Pin Fan Connector(CPU0_FAN)
22. Mini-SAS HD 4i connector for 4ports
SSATA (SSATA0_3)
4. RJ45 LAN Port(LAN4)&USB2.0x2
23. Mini-SAS HD 8i connector for 8ports
SATA (SATA0_7)
5. RJ45 LAN Port(LAN3)
Dedicated IPMI &USB3.2 Gen1 x2
24. 4-pin FAN Connector (SYS_FAN_6)
6. RJ45 LAN Ports (LAN1&LAN2)
25. TYAN Module Header (DBG_HD1)
7. Power Button(Power_BTN1)
26. M.2 Connector (NGFF2)
8. ID LED Button (IDLED_BTN1)
27. 8-Pin Power Connector (PWR2)
9. Reset Button (RST_BTN1)
28. IPMB Connector (IPMB_HD1)
10. M.2 Connector (NGFF1)
29.Vertical SLIMSAS
connector(SLIMSAS1)
11. Front Panel Header (FPIO1)
30. RTC Reset Button for Clear CMOS
(CLEAR_BTN1)
12. Intruder Header (J121)
31. 24-Pin Power Connector (PWR1)
13. Intel VROC RAID Key (J51)
32. 4-pin FAN Connector (SYS_FAN_5)
14. Fan Connector for BB
(FAN_HD1)
33. 4-pin FAN Connector (SYS_FAN_4)
15. COM Port Header(HD_COM2)
34. 4-pin FAN Connector (SYS_FAN_3)
16.SMBus Header(HDR_3)
35. 4-pin FAN Connector (SYS_FAN_2)
17.Vertical Type A USB3.2 Gen1
Connector (TYPEA_USB3)
36. 4-pin FAN Connector (SYS_FAN_1)
18. SATA SGPIO Header for SSATA
Port0~5 (SGPIO1)
37. 4-Pin Power Connector (PWR3)
19. Front USB3.2 Gen1 Header
(USB3_ FPIO1)
38. PSMI Connector (PSMI_HD1)
Jumpers/ Headers
a. PECI Jumper (J133_12)
d. COM Port Jumper (J118_23)
b. ME Recovery Jumper (J113_12)
e. System Buzzer Jumper (J120_34)
c. COM Port Jumper (J119_23)
f. PSU Throttling Function Jumper
(J125_12)
PCIE Slots
A. Standard PCIE 16X slot,
support PCIE GEN4 16 lanes
(PCIE5)
D. Standard PCIE 16X slot, support
PCIE GEN4 16 or 8 lanes (switch by
PCIE1) (PCIE2)
B. Standard PCIE 16X slot,
support PCIE GEN4 16 lanes
E. Standard PCIE 8X slot, support PCIE
GEN4 8 lanes(switch by PCIE2) (PCIE1)

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(PCIE4)
C. Standard PCIE 8X slot, support
PCIE GEN4 4 lanes (PCIE3)
LEDs
i CPU Power Good LED
(P0_PG_LED1)
viii CPU CAT ERROR LED (CAT_LED1)
ii PCH SLP_S5 LED
(SYS_SLP5_LED )
ix CPU ERROR LED (ERR_LED2)
iii CPU ERROR LED(ERR_LED0)
x ID LED (ID_LED1)
iv CPU ERROR LED(ERR_LED1)
xi BMC Heart Beat LED (BMC_LED4)
v NGFF2 LED(D9)
xii System Reset LED
(SYS_RST_LED1)
vi NGFF1 LED(LED75)
xiii BMC DEBUG LED (BMC_LED1)
vii Onboard PSMI ALERT LED
(PSMI_LED1)
xiv On board HDD active
LED(HDD_LED1)

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IPMB_HD1: IPMB Connector
Signal
Pin
Pin
Signal
IPMB_DAT
1
2
GND
IPMB_CLK
3
4
VCC3_AUX
HD_COM2: COM2 Header
Signal
Pin
Pin
Signal
COM2_DCD
1
2
COM2_DSR
COM2_RXD
3
4
COM2_RTS
COM2_TXD
5
6
COM2_CTS
COM2_DTR
7
8
COM2_NRI
GND
9
10
KEY
CPU0 FAN/ SYS FAN1~6: 4-pin CPU Fan Connector
Pin
1
2
3
4
Signal
GND
P12V
FAN_TACH
FAN_PWM
Use this header to connect the cooling fan to your motherboard to
keep the system stable and reliable.
Note: A 4-pin fan is required for fan support 4pin Control
DBG_HD1: TYAN Module Header
Signal
Pin
Pin
Signal
VCC3
1
2
FRAME
LAD0
3
4
KEY
LAD1
5
6
RESET#
LAD2
7
8
GND
LAD3
9
10
CLK
SERIRQ
11
12
GND
PRSNT#
13
14
3VSB
GPIO1
15
16
GPIO2
INTRUDER Header: Chassis Intrusion Header
Signal
Pin
Pin
Signal
INTRUDER#
1
2
GND
J51: SATA RAID KEY (VROC Header)
Pin
1
2
3
4
Signal
GND
2.21K to VCC3_Aux
GND
2.21K to VCC3_Aux

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FPIO1: Front Panel Connector
Signal
Pin
Pin
Signal
PWRLED+
1
2
VCC3_AUX
KEY
3
4
IDLED+
PWRLED-
5
6
IDLED-
HDDLED+
7
8
BMC_HW_FAULT_N
HDDLED-
9
10
BMC_SYS_FAULT_N
PWR_SW#
11
12
LAN0_LED+
GND
13
14
LAN0_LED-
RESET_SW#
15
16
SMBDATA
GND
17
18
SMBCLK
IDLED_SW#
19
20
INTRUSION#
SYS_Air_Inlet
21
22
LAN1_LED+
NMI_SW#
23
24
LAN1_LED-
PSMI_HD1: PSMI Connector
Pin
Signal
1
SMB_CLK
2
SMB_DAT
3
PSU_SMBALERT_N
4
GND
5
V3.3
USB3_FPIO1: Front USB3.2 Gen1 Header
Signal
Pin
Pin
Signal
+5V
1
2
P0_RX_N
P0_RX_P
3
4
GND
P0_TX_N
5
6
P0_TX_P
GND
7
8
P0_N
P0_P
9
10
OC_N
P1_P
11
12
P1_N
GND
13
14
P1_TX_P
P1_TX_N
15
16
GND
P1_RX_P
17
18
P1_RX_N
+5V
19
20
NC