msi S3361 Server Motherboard User Manual

D3051 MS-S3361
Server Motherboard
User Guide
Revision
V1.3, 2024/02

S3361 Server Motherboard

Regulatory Notic

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  ccordance 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.

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:
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://eps.msi.com/support for further guidance.

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.

Specifications

– Processor socket AM5
Memory| ∙ 4 x DDR5 memory slots, supporting up to 128GB
–   Supports UDIMM 5200MT/s (2DPC), ECC/ non-ECC
Networking| ∙ 2 x 1GbE RJ45 ports
–    Intel® Ethernet controller I210-AT
–    JLANCONN1 (L) support shared NIC
∙ 2 x 10GbE RJ45 ports
–    Intel® Ethernet controller X710-AT2
–    JLAN1 support shared NIC| ∙ 2 x 10GbE RJ45 ports
–    Intel® Ethernet controller X710-AT2
–    JLAN1 support shared NIC| ∙ 2 x 1GbE RJ45 ports
–    Intel® Ethernet controller I210-AT
–    JLANCONN1 (L) support shared NIC
Only one NIC LAN port can be enabled at a time, either JLAN1 or JLANCONN1 (Lower).
Server Management| ∙ Aspeed AST2600 IPMI 2.0 with iKVM support
∙ 1 x GbE RJ45 port for Mgmt. (Realtek® RTL8211FD-CG-HF)
Storage| ∙ 4 x SATA 3.0 ports (SATA1~4, w/ 1 x VCC)
∙ 2 x SATA 2.0 ports (SATA3_1)
∙ 2 x M.2 M-Key (PCIe 4.0 x4, 22110/ 2280)
–    M2_1: Choose either M2_1 or PCIE_2 for the desired function.
–    M2_2: Supports PCIe 4.0 x4
The M2_1 and PCIE_2 slots cannot operate simultaneously. You can use the JSEL_M1 jumper to select which one to enable.
Internal I/O| ∙ 1 x Front panel connector
∙ 1 x Chassis intrusion header
∙ 1 x USB 2.0 Type-A connector
∙ 1 x USB 3.2 port box connector
∙ 1 x SPI TPM module box header
∙ 1 x GPIO connector
∙ 3 x I2C box headers
∙ 1 x IPMB box header
∙ 1x PMbus box header
∙ 1 x COM port box header
Rear I/O| ∙ 4 x USB 3.2 Gen 1 Type-A ports
(USB 3.2 Gen 1/ USB 2.0)
∙ 2 x 1GbE RJ45 ports
∙ 2 x 10 GbE RJ45 ports
∙ 1 x GbE RJ45 ports (Mgmt.)
∙ 1 x COM port
∙ 1 x VGA port
∙ 1 x UID LED button| ∙ 4 x USB 3.2 Gen 1 Type-A ports
(USB 3.2 Gen 1/ USB 2.0)
∙ 2 x 10 GbE RJ45 ports
∙ 1 x GbE RJ45 ports (Mgmt.)
∙ 1 x COM port
∙ 1 x VGA port
∙ 1 x UID LED button| ∙ 4 x USB 3.2 Gen 1 Type-A ports (USB 3.2 Gen 1/ USB 2.0)
∙ 2 x 1GbE RJ45 ports
∙ 1 x GbE RJ45 ports (Mgmt.)
∙ 1 x COM port
∙ 1 x VGA port
∙ 1 x UID LED button
---|---|---|---
Expansion Slot| ∙ 1 x PCIe 5.0 x 16 slot (Gen 5 x 16 signal from CPU) (PCIE_1)
∙ 1 x PCIe 4.0 x 8 slot (Gen 4 x 4 signal from CPU) (PCIE_2)
*The PCIE_2 and M2_1 slots cannot operate simultaneously. You can use the JSEL_M1 jumper to select which one to enable.
Security| 1 x TPM header
Cooling| 9 x 4-pin fan headers (1 x for liquid cooling, PUMP1)
Power Supply| ∙ 1 x 24-pin ATX power connector
∙ 1x 8-pin 12V power connector
∙ 1 x 4-pin SATA power connector
∙ 1 x 2-pin SATA DOM power connector
Environmental| ∙ Operating Temperature: 0°C to 45°C
∙ Operating Humidity: 0% to 85% (non-condensing)
Certifications| CE, FCC (Class A)

Overview of Components

LAN ports in the red dashed area vary with SKUs; please refer to the Specifications for more details.

Rear I/O Panel

UID LED Button

The UID (Unit Identification) button help users identify and locate a system, especially in high-density rack environments.

COM Port
A COM port, also called a serial port or DB9 connector, is a communication interface for transferring data between a computer and external devices such as barcode scanners, printers, and credit card machines. It’s commonly used for initial system configuration and diagnostics on server boards and for connecting legacy devices that lack modern interfaces. Users can connect a specially configured serial cable to establish a serial connection.
VGA Port
The DB15-pin female connector is provided for monitors.
USB 3.2 Gen 1 Port (USB 3.2 Gen 1/ USB 2.0)
The USB (Universal Serial Bus) port is for attaching USB devices such as keyboards, mouse, or other USB-compatible devices. USB 3.2 Gen 1 supports data transfer rates up to 5 Gbps while USB 2.0 supports data transfer rates up to 480 Mbps.

GbE RJ45 Port (for mgmt.)
Connect a specially configured RJ45 console cable to this jack for network routers/ switches to communicate with the system through a serial connection.

GbE RJ45 Port

The standard RJ-45 LAN jack is for connection to the Local Area Network (LAN). You can connect a network cable to it.

10 GbE RJ45 Port
The standard RJ-45 LAN jack is for connection to the Local Area Network (LAN). You can connect a network cable to it.

Block Diagram

CPU Socket

Introduction to the AM5 CPU The surface of the AM5 CPU has two notches and a golden triangle to assist in correctly lining up the CPU for motherboard placement. The golden triangle is the Pin 1 indicator.

Important

• Overheating will seriously damage the CPU and system. Always make sure the cooling fan can work properly to protect the CPU from overheating. Make sure that you apply an even layer of thermal paste (or thermal tape) between the CPU and the heatsink to enhance heat dissipation.
• While replacing the CPU, always turn off the power supply or unplug the power supply’s power cord from the grounded outlet first to ensure the safety of CPU.
• Confirm if your CPU cooler is firmly installed before turning on your system.
• Do not touch the CPU socket pins to avoid damage.
• Whenever CPU is not installed, always protect your CPU socket pins with the plastic cap covered.
• Please refer to the documentation in the CPU cooler package for more details about the CPU cooler installation.
• Read the CPU status in BIOS.

CPU & Heatsink Installation
Use appropriate ground straps, gloves and ESD mats to protect yourself from electrostatic discharge (ESD) while installing the processor.

**** Important
Images are for demonstration purposes only; actual parts may vary.

Memory

DIMMA1~2, DIMMB1~2: DDR5 DIMM Slots

Recommended Memory Population

Important

• Only support UDIMM.
• There should be at least 1 DDR5 DIMM populated.
• Paired memory installation for Max performance.
• If only 1 DIMM is populated in a channel, then populate it in the DIMMA2 slot.
• Populate the same DIMM type in each channel, specifically: 1. Use the same DIMM size; 2. Use the same number of ranks per DIMM.
• We don’t suggest other memory installation.

Installing Memory Modules

1. Open the side clips to unlock the DIMM slot.
2. Insert the DIMM vertically into the slot, ensuring that the off-center notch at the bottom aligns with the slot.
3. Push the DIMM firmly into the slot until it clicks and the side clips automatically close.
4. Verify that the side clips have securely locked the DIMM in place.

Important
You can barely see the golden finger if the memory module is properly inserted in the DIMM slot.

Storage

SATA1~4: SATA 3.0 6Gb/s Ports
These connectors are SATA 6Gb/s interface ports, it can connect to SATA devices.
SATA3_1: SATA 2.0 3Gb/s Ports
These connectors are SATA 3Gb/s interface ports, it can connect to SATA devices.

Important

• Please do not fold the SATA cable at a 90-degree angle. Data loss may result during transmission otherwise.
• SATA cables have identical plugs on either sides of the cable. However, it is recommended that the flat connector be connected to the motherboard for space saving purposes.

M2_1~2: M.2 Slots (M Key, PCIe 4.0, 22110/ 2280)
Please install the M.2 solid-state drive (SSD) into the M.2 slot as shown below.

*M2_1: The M2_1 and PCIE_2 slots cannot operate simultaneously. You can use the JSEL_M1 jumper to select which one to enable.

Video Demonstration
Watch the video to learn how to Install M.2 SSD.

http://youtu.be/JCTFABytrYA

Installing M.2 SSD

1. Loosen the M.2 riser screw from the motherboard.
2. Set the M.2 riser screw at the appropriate location based on the length of your M.2 SSD.
3. Insert your M.2 SSD into the M.2 slot at a 30-degree angle.
4. Secure the M.2 SSD in place with the supplied M.2 screw.

Expansion Slots

*PCIE_2: The PCIE_2 and M2_1 slots cannot operate simultaneously. You can use the JSEL_M1 jumper to select which one to enable.

PCIE_1~2: PCIe Expansion Slots
The PCI Express(Peripheral Component Interconnect Express) slots support PCIe interface expansion cards.
Important
When adding or removing expansion cards, make sure that you unplug the power supply first. Meanwhile, read the documentation for the expansion card to configure any necessary hardware or software settings for the expansion card, such as jumpers, switches or BIOS configuration.

Connectors

Power Connectors

SATAPWR1: SATA Power Connector
This connector is used to provide power to SATA devices.

JPWR1: 12V Power Connector
This connector allows you to connect an ATX power supply.

JPWR2: Main Power Connector
This connector allows you to connect an ATX power supply.

JSDOMPWR1: SATA DOM Power Connector
This connector is used to provide power to SATA DOM devices.

Important
Make sure that all power connectors are securely connected to the power supply to ensure stable operation of the motherboard.

Cooling Connectors
FAN1~8, PUMP1: Fan Power Connectors
The fan power connector supports system cooling fans with +12V. When connecting the wire to the connectors, always note that the red wire is the positive and should be connected to the +12V; the black wire is Ground and should be connected to GND.

FAN1~8| 1| GND|

3

| FAN_TACH
---|---|---|---|---
2| P12V| 4| BMC_PWM
PUMP1| 1| GND| 3| N/A
---|---|---|---|---
2| P12V| 4| BMC_PWM

Other Connectors
JFP1: Front Panel Connector
The front panel connector is provided for electrical connection to the front panel switches and LEDs.

JTPM1: SPI TPM Module Box Header
This connector connects to a TPM (Trusted Platform Module) (optional). Please refer to the TPM security platform manual for more details.

JGPIO1: GPIO Header
This connector is provided for the General-Purpose Input/Output (GPIO) peripheral module.

JPMBUS1: PMBus Box Header
Power Management Bus (PMBus) is a variant of the System Management Bus (SMBus) which is targeted at digital management of power supplies.

JCHASSIS: 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.

JIPMB1: IPMB Box Header
Intelligent Platform Management Bus (IPMB) box header is used to connect various management components, such as Baseboard Management Controller (BMC).

JIPMB1
| 1| SMB_IPMB_DAT| 2| GND
---|---|---|---|---
3| SMB_IPMB_CLK|

JUSB1: USB 3.2 Port Box Header
This port is backward-compatible with USB 2.0 devices and supports data transfer rate up to 5 Gbps.

JUSB2: USB 2.0 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 480 Mbps data transfer rate.

FP_I2C_1, RBP_I2C_1~2: I2C Box Headers
I2C connectors are used to connect to the System Management Bus (SMBus).
FBP_I2C_1 is for front HDD backplane, and RBP_I2C_1, RBP_I2C_2 are for rear HDD backplanes.

RBP_I2C_1
FP_I2C_1
RBP_I2C_2| 1| NC| 2| I2C_CLK
---|---|---|---|---
2| I2C_DAT| 4| GND

JCOM1: COM Port Box Header
This connector is a 16550A high speed communications port that sends/receives 16 bytes FIFOs. You can attach a serial device to it.

Jumpers

Important
Avoid adjusting jumpers when the system is on; it will damage the motherboard.

2-3: PCIE_2 enabled, M.2_1 disabled
JSEL_BMC1| | 1-2: Using CPU (Default)

2-3: Using BMC

JRTC_CLR1| | 1-2: Normal (Default)
2-3: Clear CMOS

Onboard LEDs

BMC_LED1: BMC Heartbeat LED
This LED indicates the BMC (Baseboard Management Controller) status.

LED_H1, LED_L1: Port 80 Debug LEDs
The Port 80 Debug LEDs display progress and error codes during and after POST (Power-On Self Test).

MSI.COM

|

EPS.MSI.COM

---|---
http://www.msi.com| https://me-qr.com/kImxnwSe

References

• MSI: Empowering the Future as a Leading Global Server Solutions Provider
• MSI - Redirect
• dtsc.ca.gov/hazardouswaste/perchlorate/
• csr
• MSI: Empowering the Future as a Leading Global Server Solutions Provider

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