MSI MS-S3361 User manual

D3051
MS-S3361
Server Motherboard
User Guide

2Contents
Revision
V1.1, 2023/07
Contents
Regulatory Notices....................................................................................................... 4
Safety Information ......................................................................................................... 6
Specifications................................................................................................................ 7
Overview of Components ............................................................................................. 9
Rear I/O Panel............................................................................................................. 10
UID LED Button..................................................................................................... 10
COM Port............................................................................................................... 10
VGA Port................................................................................................................ 10
USB 3.2 Gen 1 Port (USB 3.2 Gen 1/ USB 2.0)...................................................... 10
GbE RJ45 Port (for mgmt.) ................................................................................... 11
GbE RJ45 Port....................................................................................................... 11
10 GbE RJ45 Port.................................................................................................. 11
CPU Socket ................................................................................................................. 13
Introduction to the AM5 CPU......................................................................... 13
CPU & Heatsink Installation................................................................................. 14
Memory ....................................................................................................................... 15
DIMMA1~2, DIMMB1~2: DDR5 DIMM Slots................................................... 15
Recommended Memory Population.............................................................. 15
Installing Memory Modules.................................................................................. 16
Storage........................................................................................................................ 17
SATA3_1, SATA1~4: SATA 3.0 6Gb/s Ports................................................... 17
M2_1~2: M.2 Slots (M Key, PCIe 4.0, 22110/ 2280) ....................................... 18
Installing M.2 SSD ......................................................................................... 18
Expansion Slots .......................................................................................................... 19
PCIE_1~2: PCIe Expansion Slots .................................................................. 19

3
Contents
Connectors.................................................................................................................. 20
Power Connectors ................................................................................................ 20
SATAPWR1: SATA Power Connector............................................................ 20
JPWR1: 12V Power Connector ...................................................................... 20
JPWR2: Main Power Connector .................................................................... 21
JSDOMPWR1: SATA DOM Power Connector................................................. 21
Cooling Connectors .............................................................................................. 22
FAN1~8, PUMP1: Fan Power Connectors..................................................... 22
Other Connectors ................................................................................................. 23
JFP1: Front Panel Connector........................................................................ 23
JTPM1: SPI TPM Module Box Header ........................................................... 24
JGPIO1: GPIO Header .................................................................................... 25
JPMBUS1: PMBUS Box Header .................................................................... 25
JCHASSIS: Chassis Intrusion Header ........................................................... 26
JIPMB1: IPMB Box Header........................................................................... 26
JUSB1: USB 3.2 Port Box Header ................................................................. 27
JUSB2: USB 2.0 Type-A Connector ............................................................... 27
FP_I2C_1, RBP_I2C_1~2: I2C Box Headers ................................................. 28
JCOM1: COM Port Box Header...................................................................... 28
Jumpers ...................................................................................................................... 29
Onboard LEDs............................................................................................................. 30
BMC_LED1: BMC Heartbeat LED.................................................................. 30
LED_H1, LED_L1: Port 80 Debug LEDs ........................................................ 30

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
Regulatory Notices
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://eps.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
Specifications
Specifications
Model MS-S3361
Form factor Micro-ATX
Dimensions 243.84mm (9.6”) x 243.84mm (9.6”)
Processor ∙1 x AMD® Ryzen™ 7000 series Processors, TDP 170W
-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*
* 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 ∙6 x SATA 3.0 ports (w/ 1 x VCC)
∙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

8Specifications
Model MS-S3361
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
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)

9
Overview of Components
Overview of Components
JCHASSIS JIPMB1
JSEL_M1
JSEL_BMC1
M2_2
PCIE_1
PCIE_2
JCOM1
JLAN1 JLAN2
BZ1
M2_1
BAT1
JGPIO1
JFP1
JUSB1
JUSB2
RBP_I2C_2 RBP_I2C_1
SATA1
SATA3_1
SATA4
JTPM1
FAN1 FAN2 FAN3 FAN4 FAN5 FAN6 FAN7
SATAPWR1
JPWR2
JPWR1
DIMMA1 DIMMA2 DIMMB1 DIMMB2
SATA3
JSDOMPWR1
SATA2
FP_I2C_1
FAN8 PUMP1
JPMBUS1 ID_BTN1
JVGA1 (L)
COM1 (U)
JLANCONN1(U)
JLANCONN1(L)
MLAN_USB1
REAR_USB1
LED_L1
BMC_LED1
LED_H1

10 Rear I/O Panel
Rear I/O Panel
UID LED Button
GbE RJ45 Port
(for mgmt.)
VGA Port
COM Port
GbE RJ45 Port
10 GbE RJ45 Port
USB 3.2 Gen 1 Port
(USB 3.2 Gen 1/ 2.0)
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 Gbit/s (SuperSpeed), while USB 2.0 supports data transfer rates up to
480Mbit/s (Hi-Speed).

11
Rear I/O Panel
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.
Link/ Activity LED
Status Description
Off No link
Green Linked
Blinking Data activity
Speed LED
Status Description
Off 10M
Orange 100M
Green 1GbE
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.
Link/ Activity LED
Status Description
Off No link
Green Linked
Blinking Data activity
Speed LED
Status Description
Off 10M
Orange 100M
Green 1GbE
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.
Link/ Activity LED
Status Description
Off No link
Green Linked
Blinking Data activity
Speed LED
Status Description
Off 100M
Orange 1GbE
Green 10GbE

12 Rear I/O Panel
Component Contents
Component Page
CPU Socket 13
Memory 15
DIMMA1~2, DIMMB1~2: DDR5 DIMM Slots 15
Storage 17
SATA3_1, SATA1~4: SATA 3.0 6Gb/s Ports 17
M2_1~2: M.2 Slots (M Key, PCIe 4.0, 22110/ 2280) 18
Expansion Slots 19
PCIE_1~2: PCIe Expansion Slots 19
Connectors 20
Power Connectors 20
SATAPWR1: SATA Power Connector 20
JPWR1: 12V Power Connector 20
JPWR2: Main Power Connector 21
JSDOMPWR1: SATA DOM Power Connector 21
Cooling Connectors 22
FAN1~8, PUMP1: Fan Power Connectors 22
Other Connectors 23
JFP1: Front Panel Connector 23
JTPM1: SPI TPM Module Box Header 24
JGPIO1: GPIO Header 25
JPMBUS1: PMBUS Box Header 25
JCHASSIS: Chassis Intrusion Header 26
JIPMB1: IPMB Box Header 26
JUSB1: USB 3.2 Port Box Header 27
JUSB2: USB 2.0 Type-A Connector 27
FP_I2C_1, RBP_I2C_1~2: I2C Box Headers 28
JCOM1: COM Port Box Header 28
Jumpers 29
Onboard LEDs 30
BMC_LED1: BMC Heartbeat LED 30
LED_H1, LED_L1: Port 80 Debug LEDs 30

13
CPU Socket
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.

14 CPU Socket
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 illustration purposes only; actual parts may vary.
11
22
33
6644
55
77
88
99

15
Memory
Memory
DIMMA1~2, DIMMB1~2: DDR5 DIMM Slots
Recommended Memory Population
Quantity of DIMMs 1 2 3 4
Channel A DIMMA1 V V V
DIMMA2 V V V V V V
Channel B DIMMB1 V V V
DIMMB2 V V V V V
**“V” indicates a populated DIMM slot. **
⚠
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.
DIMMA1 DIMMB1
Channel A Channel B
DIMMA2 DIMMB2

16 Memory
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.

17
Storage
Storage
SATA3_1, SATA1~4: SATA 3.0 6Gb/s Ports
These connectors are SATA 6Gb/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.
SATA1 SATA2
SATA3
SATA4
SATA3_1

18 Storage
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* M2_2
Installing M.2 SSD
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.
1. Loosen the M.2
riser screw from the
motherboard.
30°
Supplied M.2 screw
⚽
Video Demonstration
Watch the video to learn how to
Install M.2 SSD.
*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.

19
Expansion Slots
Expansion Slots
PCIE_2*: PCIe 4.0 x 8 slot (Gen 4 x 4 signal from CPU)
PCIE_1: PCIe 5.0 x 16 slot (Gen 5 x 16 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.
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.

20 Connectors
Connectors
Power Connectors
JPWR1
JPWR2
SATAPWR1JSDOMPWR1
SATAPWR1: SATA Power Connector
This connector is used to provide power to SATA devices.
SATAPWR1 3
4
21
1 GND 2 GND
3P12V 4P5V
JPWR1: 12V Power Connector
This connector allows you to connect an ATX power supply.
1
48
5
JPWR1
1 GND 2 GND
3 GND 4 GND
5 P12V 6 P12V
7 P12V 8 P12V