MSI S1206 User manual

S1206 (1U12)
MS-S311
Server System
User Guide

2Contents
Revision
V1.0, 2023/04
Contents
Regulatory Notices....................................................................................................... 4
Copyright and Trademarks Notice.............................................................................. 5
Technical Support......................................................................................................... 5
Safety Information........................................................................................................ 6
System Specifications .................................................................................................. 7
System Overview .......................................................................................................... 8
System LED Indicators............................................................................................... 11
Motherboard Overview............................................................................................... 12
Motherboard Connector ............................................................................................ 13
Power Connector.................................................................................................. 13
Storage Connector................................................................................................ 15
FPC Connector...................................................................................................... 17
Box Header ........................................................................................................... 19
Motherboard Jumper................................................................................................. 24
Motherboard Expansion Slot..................................................................................... 25
Getting Started............................................................................................................ 26
Necessary Tools ................................................................................................... 26
Safety Precautions................................................................................................ 26
System Setup.............................................................................................................. 27
Drive Bay ..................................................................................................................... 27
Installing 2.5" HDD/ SSD ...................................................................................... 27
System Cover.............................................................................................................. 28
Removing System Cover....................................................................................... 28

3
Contents
CPU & Heatsink.......................................................................................................... 29
Installing CPU & Heatsink.................................................................................... 30
Memory ....................................................................................................................... 33
Recommended Memory Population..................................................................... 34
Installing Memory Modules.................................................................................. 35
M.2 M Key.................................................................................................................... 36
Installing M.2 M Key ............................................................................................. 36
PCIe Add-in Card........................................................................................................ 37
Installing PCIe Add-in Card.................................................................................. 37
Installing Riser Card Assembly............................................................................ 38
System Fan ................................................................................................................. 39
Installing 1U Fan................................................................................................... 39
Power Supply Unit (PSU) ........................................................................................... 40
Installing PSU....................................................................................................... 40

4Regulatory Notices
Regulatory Notices
WEEE Statement
Under the European Union (“EU”) Directive on Waste Electrical and
Electronic Equipment, Directive 2012/19/EU, products of “electrical and
electronic equipment” cannot be discarded as municipal waste anymore
and manufacturers of covered electronic equipment will be obligated to
take back such products at the end of their useful life.
Chemical Substances Information
In compliance with chemical substances regulations, such as the EU REACH
Regulation (Regulation EC No. 1907/2006 of the European Parliament and the
Council), MSI provides the information of chemical substances in products at:
https://csr.msi.com/global/index
CE Conformity
Hereby, Micro-Star International CO., LTD declares that this device is in
compliance with the essential safety requirements and other relevant
provisions set out in the European Directive.
FCC-A Radio Frequency Interference 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 instruction
manual, may cause harmful interference to radio communications. Operation of this
equipment in a residential area is likely to cause harmful interference, in which case
the user will be required to correct the interference at his own expense.
Notice 1
The changes or modifications not expressly approved by the party responsible for
compliance could void the user’s authority to operate the equipment.
Notice 2
Shielded interface cables and AC power cord, if any, must be used in order to comply
with the emission limits.
This device complies with Part 15 of the FCC Rules. Operation is subject to the
following two conditions:
∙This device may not cause harmful interference, and
∙This device must accept any interference received, including interference that may
cause undesired operation.

5
Copyright and Trademarks Notice
Battery Information
Please take special precautions if this product comes with a battery.
∙Danger of explosion if battery is incorrectly replaced. Replace only with the same or
equivalent type recommended by the manufacturer.
∙Avoid disposal of a battery into fire or a hot oven, or mechanically crushing or
cutting of a battery, which can result in an explosion.
∙Avoid leaving a battery in an extremely high temperature or extremely low air
pressure environment that can result in an explosion or the leakage of flammable
liquid or gas.
∙Do not ingest battery. If the coin/button cell battery is swallowed, it can cause
severe internal burns and can lead to death. Keep new and used batteries away
from children.
European Union:
Batteries, battery packs, and accumulators should not be disposed of as
unsorted household waste. Please use the public collection system to
return, recycle, or treat them in compliance with the local regulations.
BSMI:
廢電池請回收
For better environmental protection, waste batteries should be collected
separately for recycling or special disposal.
California, USA:
The button cell battery may contain perchlorate material and requires
special handling when recycled or disposed of in California.
For further information please visit:
http://www.dtsc.ca.gov/hazardouswaste/perchlorate/
Copyright and Trademarks Notice
Copyright © Micro-Star Int’l Co., Ltd. All rights reserved. The MSI logo used is
a registered trademark of Micro-Star Int’l Co., Ltd. All other marks and names
mentioned may be trademarks of their respective owners. No warranty as to accuracy
or completeness is expressed or implied. MSI reserves the right to make changes to
this document without prior notice.
Technical Support
If a problem arises with your product and no solution can be obtained from the user’s
manual, please contact your place of purchase or local distributor. Alternatively,
please visit https://www.msi.com/support/ for further guidance.

6Safety Information
Safety Information
∙Always read the safety instructions carefully.
∙Keep this User’s Manual for future reference.
∙Keep this equipment away from humidity.
∙Lay this equipment on a reliable flat surface before setting it up.
∙The openings on the enclosure are for air convection hence protects the equipment
from overheating. Do not cover the openings.
∙Make sure the voltage of the power source and adjust properly before connecting
the equipment to the power inlet.
∙Place the power cord such a way that people can not step on it. Do not place
anything over the power cord.
∙Always unplug the power cord before inserting any add-on card or module.
∙All cautions and warnings on the equipment should be noted.
∙Never pour any liquid into the opening that could damage or cause electrical shock.
∙If any of the following situations arises, get the equipment checked by service
personnel:
∙The power cord or plug is damaged.
∙Liquid has penetrated into the equipment.
∙The equipment has been exposed to moisture.
∙The equipment does not work well or you can not get it work according to User’s
Manual.
∙The equipment has dropped and damaged.
∙The equipment has obvious sign of breakage.
∙Do not leave this equipment in an environment unconditioned, storage
temperature above 60°C (140°F), it may damage the equipment.

7
System Specifications
System Specifications
Model S1206-01
Form Factor 1U
Dimensions 17.2”W (438mm) x 1.7”H (43.2mm) x 30.3”D (770mm)
Processor ∙2 x AMD® EPYC™ Genoa SP5 9004 Series Processors
-Up to 96C, cTDP max 400W
Memory ∙24 x DDR5 4800MT/s, RDIMM/ 3DS, w/ ECC
-12 x Channels DDR5 per CPU
Internal
Storage
∙2 x M.2 M-key (2280)
∙2 x MicroSD (Internal)
Drive Bays 12 x 2.5” Hot-swap drive bays
(12x NVMe/ SATA/ SAS)
Expansion
Slots
∙3 x PCIe slots
-Riser1: 1 x LP Gen 5 (x16)
-Riser2: 1 x LP Gen 5 (x16)
-Riser4: 1 x LP Gen 3 (x16)
∙1 x OCP 3.0 Mezzanine card slot
Security ∙TPM 2.0
∙Case intrusion switch
Server
Management
∙Aspeed AST2600 IPMI 2.0 with iKVM support
∙1 x GbE RJ45 Mgmt. (Realtek® RTL8211FD-CG PHY)
Cooling 2 x Passive CPU heatsink @210W
Environmental ∙System Operating Temperature: 0°C ~ 35°C
∙Non-operating Temperature: -20°C ~ 70°C
∙Non-operating Relative Humidity: 5% ~ 85% (non-condensing)
Certications CE, FCC (Class A)

8System Overview
System Overview
12 x 2.5” NVMe
Hot-Swap Drive Bays
22
11
44
55
66
77
8822991010 1111 331212
Riser #2Riser #2
Riser #4Riser #4
Riser #1Riser #1
1313

9
System Overview
11
USB 2.0 Port
This connector is provided for USB peripheral devices. (Speed up to 480 Mbps)
⚠
Important
High-speed devices are recommended for USB 3.2 ports whereas low-speed
devices, such as mouse or keyboard, are suggested to be plugged into the
USB 2.0 ports.
22USB 3.2 Gen 1 Port
This connector is provided for USB peripheral devices. (Speed up to 5 Gbps)
33VGA Port
44System Power Button/ LED
55UID Button/ LED
66System Reset Button
77
!
System Status LED
1
NIC Link LEDs
M.2 Activity LED
88UID LED Button (or BMC Reset Button, via jumper: JUID_SEL1)
99RJ45 Serial Console Port
1010
GbE RJ45 Port
The standard RJ45 LAN jack is provided for connection to the Local Area
Network (LAN). You can connect a network cable to it.
LINK/ACT
LED
SPEED
LED
LED Status Description
Link/ Activity
LED
Off No link
Green Linked
Blinking Data activity
Speed LED
Off 10 Mbps/
No LAN linked
Orange 100 Mbps
Green 1 Gbps

10 System Overview
1111
GbE RJ45 Port (for Mgmt.)
The standard RJ45 LAN jack is provided for connection to the Local Area
Network (LAN). You can connect a network cable to it.
LINK/ACT
LED
SPEED
LED
LED Status Description
Link/ Activity
LED
Off No link
Green Linked
Blinking Data activity
Speed LED
Off 10 Mbps
Orange 100 Mbps
Green 1 Gbps
1212 Power Supply Unit
1313 PCIe Add-in Card Area

11
System LED Indicators
System LED Indicators
System Power Button/ LED
System Reset Button
UID Button/ LED
!
System Status LED M.2 Activity LED
1
NIC Link LED
LED LED State Description
Power LED Blue System power is on
System power is on ACPI S0 state
Blinking System is sleeping
Off System power is off
System power is on ACPI S4, S5 state
UID LED Blue Identify active via command or button
Off No identification
!
System Status LED Red System has failed
Off System power is not present
1
NIC Link LED Green NIC link is established
Blinking NIC activity is occurring
Off NIC link is not established
M.2 Activity LED Green M.2 present, no activity
Blinking M.2 accessing
Off No M.2 activity

12 Motherboard Overview
Motherboard Overview
CPU_FAN1
CPU_FAN2
JUSB1
PSU_PWR1 PSU_PWR2
JBIOS_LOC1
JSATA_NVME_SW1
JBIOS_SYS1
JTPM1
JUSB2
GPU_PWR2
GPU_PWR1
GPU_PWR6
HDD_PWR2
HDD_PWR1
FBP_I2C_1
RBP_I2C_1
RBP_I2C_2
HDD_PWR3
GPU_PWR3
M2_2
M2_1
MSD1 MSD2
RISER3
RISER4
RISER1
RISER2
JMCIO1
JMCIO2
JMCIO3
JSLIM4X_1
JMCIO4
JMCIO6
JMCIO5
GPU_PWR4
GPU_PWR5
JFP_VGA1
JSPI_MUX1
JRTC_CLR1
JUID_SEL1
JSGPIO_PCH
JFP1
CPU1 CPU0
BMC_F1 BMC_F2
LAN1
COM1
ID_BTN1
USB2 USB1
LAN2MLAN1
JVGA1
OCP1
BAT1
JCHASSIS1
BMC_JTAG1
JSEL_BMC1
JIPMB1
F1U-8F1U-7
F1U-6
F1U-5
F1U-4F1U-3
F1U-2F1U-1
F2U-6
F2U-5
F2U-4
F2U-2 F2U-3
F2U-1
1 2 3
1
2
3
CPU1_DIMM_G1 CPU1_DIMM_H1 CPU1_DIMM_I1 CPU1_DIMM_J1 CPU1_DIMM_K1 CPU1_DIMM_L1 CPU1_DIMM_F1 CPU1_DIMM_E1 CPU1_DIMM_D1 CPU1_DIMM_C1 CPU1_DIMM_B1 CPU1_DIMM_A1 CPU0_DIMM_G1 CPU0_DIMM_H1 CPU0_DIMM_I1 CPU0_DIMM_J1 CPU0_DIMM_K1 CPU0_DIMM_L1 CPU0_DIMM_F1 CPU0_DIMM_E1 CPU0_DIMM_D1 CPU0_DIMM_C1 CPU0_DIMM_B1 CPU0_DIMM_A1

13
Motherboard Connector
Motherboard Connector
Power Connector
PSU_PWR1~2: CRPS Power Connector
These CRPS (Common Redundant Power Supplies) connectors allow you to connect
a power supply. To connect the power supply, ensure that the plug is inserted in the
proper orientation and that the pins are aligned. Then firmly push down the power
supply into the connector.
GPU_PWR1~6: GPU Power Connector
These connectors provide power output to GPUs.
HDD_PWR1~2: HDD BP Power Connector
These connectors provide power output to HDDs.
1
4
85
GPU_PWR1
GPU_PWR2
GPU_PWR3
GPU_PWR4
GPU_PWR5
GPU_PWR6
HDD_PWR1
HDD_PWR2
1 GND 2 GND
3 GND 4 GND
5 P12V 6 P12V
7 P12V 8 P12V
PSU_PWR1
GPU_PWR1
GPU_PWR2
GPU_PWR3
GPU_PWR4
GPU_PWR5
GPU_PWR6
HDD_PWR2 HDD_PWR1
HDD_PWR3
PSU_PWR2

14 Motherboard Connector
HDD_PWR3: Rear HDD BP Power Connector
This connector provides power output to HDDs on rear side.
HDD_PWR3
12
4 3
1 GND 2 GND
3P12V 4P5V
⚠
Important
Make sure that all power connectors are securely connected to the power supply to
ensure stable operation of the motherboard.

15
Motherboard Connector
Storage Connector
Slot Speed
JSLIM4X_1 PCIe®3.0 x4 8GT/s
JMCIO1~4 PCIe®4.0 x4 16GT/s (Default)
SATA 3.0 6Gb/s
JMCIO5, JMCIO6 PCIe®4.0 x8 16GT/s
M2_1, M2_2 PCIe®3.0 x2 8GT/s
JMCIO1~4: MCIO 4i Connector
These are right-angle 38-pin Mini Cool Edge IO (MCIO) connectors,
which support PCIe 4.0 x4 16GT/s and SATA 3.0 6Gb/s interfaces.
A JSATA_NVME_SW1 jumper can be used to switch signals between
SATA and PCIe NVMe (Default).
JMCIO5, JMCIO6: MCIO 8i Connector
These are vertical 74-pin Mini Cool Edge IO (MCIO) connectors, which
support PCIe 4.0 x8 16GT/s interface.
JSLIM4X_1: Slimline SAS 4i Connector
This is 38-pin Slimline SAS 4i connector, which support PCIe 3.0 x4 8GT/s interface.
M2_2
M2_1
MSD1 MSD2
JMCIO1
JMCIO2
JMCIO3
JSLIM4X_1
JMCIO4
JMCIO6
JMCIO5

16 Motherboard Connector
M2_1, M2_2: M.2 Slot (M Key, PCIe 3.0 x2, 2280)
The M.2 slot supports solid-state drive (SSD). For Installation procedure, please refer
to “System Setup > M.2 M Key".
MSD1, MSD2: Micro SD Card Slot
This slot is for inseriting the micro SD card.

17
Motherboard Connector
FPC Connector
A Flexible Printed Circuit (FPC) connector connects a flexible printed circuit or flat
ribbon cable to a PCB. FPC connectors are also referred to as flat flexible cable (FFC)
connectors or ribbon connectors. Their slim and lightweight design makes them ideal
for electronic devices and equipment that require space-saving solutions.
JFP1
JUSB2
JFP1: Front Panel FPC Connector
The front panel connector is provided for electrical connection to the front panel
switches and LEDs.
JFP1
1 26
1P3V3_AUX 2P3V3_AUX
3N/A 4FP ID LED+
5PWR_LED- 6FP ID LED-
7P3V3 8SYS_FLT_LED-
9SYS_ERR_LED- 10 M.2 SSD_ACT_LED-
11 PWR_ON_BTN- 12 NIC1_LED+
13 GND 14 NIC1_LED-
15 SYS_RST_BTN- 16 SMB_DAT
17 SMB_CLK 18 GND
19 FP_ID_BTN- 20 N/A
21 N/A 22 N/A
23 NIC2_LED+ 24 NIC2_LED-
25 GND 26 GND

18 Motherboard Connector
JUSB2: USB FPC Connector
This port is backward-compatible with USB 2.0 devices and supports data transfer
rate up to 5 Gbit/s (SuperSpeed).
JUSB2
1 26
1FUSB_VCC 2FUSB_VCC
3FUSB_VCC 4FUSB_VCC
5FUSB_VCC 6FUSB_VCC
7GND 8GND
9GND 10 GND
11 GND 12 GND
13 GND 14 GND
15 USB3_F_RXN 16 USB3_F_RXP
17 GND 18 USB3_F_TXN
19 USB3_F_TXP 20 GND
21 USB2_F1_DN 22 USB2_F1_DP
23 GND 24 USB2_F2_DN
25 USB2_F2_DP 26 GND

19
Motherboard Connector
Box Header
F2U-1~6: 2U System Fan Power Connector
The fan power connectors support 2U system cooling fans.
F2U-1~6
1 2
65
1 GND 2 P12V
3 FAN_TACH 4 FAN_PWM
5 NC 6 FAN_FAULT
F1U-1~8: 1U System Fan Power Connector
The fan power connectors support 1U system cooling fans.
1
7
2
8
F1U1~8
1 FAN_TACH 2 FAN_PWM
3 P12V 4 P12V
5 FAN_TACH 6 GND
7 GND 8 NC
CPU_FAN1, 2: CPU Fan Power Connector
The fan power connectors support CPU cooling fans.
41
CPU_FAN1, 2
1 GND 3 FAN_TACH
2P12V 4FAN_PWM
F2U-1 F2U-2 F2U-3 F2U-4 F2-U5 F2U-6
F1U-1 F1U-2 F1U-3 F1U-4 F1U-5 F1U-6 F1U-7 F1U-8
CPU_FAN2
CPU_FAN1

20 Motherboard Connector
JCHASSIS1: Chassis Intrusion Header
This connector connects to the chassis intrusion switch cable. If the chassis is opened,
the chassis intrusion mechanism will be activated. The system will record this status
and show a warning message on the screen. To clear the warning, you must enter the
BIOS utility and clear the record.
Normal
(default)
JCHASSIS1
Trigger the
chassis intrusion
event
JUSB1: USB 3.2 Gen 1 Type-A Connector
The USB (Universal Serial Bus) port is for attaching USB devices such as
keyboard, mouse, or other USB-compatible devices. It supports up to
5 Gbit/s (SuperSpeed) data transfer rate.
JIPMB1: IPMB Box Header
This connector is used to connect the IPMB (Intelligent Platform Management Bus).
JIPMB1 1
31SMB_IPMB_DAT 3SMB_IPMB_CLK
2GND
JCHASSIS1
JIPMB1
JUSB1
JUSB1