Supermicro SuperServer SYS-521R-T User manual

USER’S MANUAL
Revision 1.0
®
SYS-521R-T

The information in this User’s Manual has been carefully reviewed and is believed to be accurate. The vendor assumes
no responsibility for any inaccuracies that may be contained in this document, and makes no commitment to update
or to keep current the information in this manual, or to notify any person or organization of the updates. Please Note:
For the most up-to-date version of this manual, please see our website at www.supermicro.com.
Super Micro Computer, Inc. ("Supermicro") reserves the right to make changes to the product described in this manual
at any time and without notice. This product, including software and documentation, is the property of Supermicro and/
or its licensors, and is supplied only under a license. Any use or reproduction of this product is not allowed, except
as expressly permitted by the terms of said license.
IN NO EVENT WILL Super Micro Computer, Inc. BE LIABLE FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL,
SPECULATIVE OR CONSEQUENTIAL DAMAGESARISING FROM THE USE OR INABILITYTO USE THIS PRODUCT
OR DOCUMENTATION, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. IN PARTICULAR, SUPER
MICRO COMPUTER, INC. SHALL NOT HAVE LIABILITY FOR ANY HARDWARE, SOFTWARE, OR DATA STORED
OR USED WITH THE PRODUCT, INCLUDING THE COSTS OF REPAIRING, REPLACING, INTEGRATING,
INSTALLING OR RECOVERING SUCH HARDWARE, SOFTWARE, OR DATA.
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State of California, USA. The State of California, County of Santa Clara shall be the exclusive venue for the resolution
of any such disputes. Supermicro's total liability for all claims will not exceed the price paid for the hardware product.
FCC Statement: This equipment has been tested and found to comply with the limits for a Class A or Class B 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 industrial environment for Class A device or in residential
environment for Class B device. This equipment generates, uses, and can radiate radio frequency energy and, if not
installed and used in accordance with the manufacturer’s instruction manual, may cause harmful interference with
radio communications. Operation of this equipment in a residential area is likely to cause harmful interference, in
which case you will be required to correct the interference at your own expense.
California Best Management Practices Regulations for Perchlorate Materials: This Perchlorate warning applies only
to products containing CR (Manganese Dioxide) Lithium coin cells. “Perchlorate Material-special handling may apply.
See www.dtsc.ca.gov/hazardouswaste/perchlorate”.
WARNING: This product can expose you to chemicals including
lead, known to the State of California to cause cancer and birth
defects or other reproductive harm. For more information, go
to www.P65Warnings.ca.gov.
!
The products sold by Supermicro are not intended for and will not be used in life support systems, medical equipment,
nuclear facilities or systems, aircraft, aircraft devices, aircraft/emergency communication devices or other critical

property damage. Accordingly, Supermicro disclaims any and all liability, and should buyer use or sell such products
for use in such ultra-hazardous applications, it does so entirely at its own risk. Furthermore, buyer agrees to fully
indemnify, defend and hold Supermicro harmless for and against any and all claims, demands, actions, litigation, and
proceedings of any kind arising out of or related to such ultra-hazardous use or sale.
Manual Revision 1.0
Release Date: December 15, 2023
Unless you request and receive written permission from Super Micro Computer, Inc., you may not copy any part of this

to herein are trademarks or registered trademarks of their respective companies or mark holders.
Copyright © 2023 by Super Micro Computer, Inc.
All rights reserved.
Printed in the United States of America

3
Preface
3
Warning! Indicates high voltage may be encountered when performing a procedure.
Warning! Indicates important information given to prevent equipment/property damage

Preface
About this Manual
This manual is written for professional system integrators and PC technicians. It provides
information for the installation and use of the SYS-521R-T server system. Installation and

  
supported memory, processors and operating systems (http://www.supermicro.com).
Notes
For your system to work properly, please follow the links below to download all necessary
drivers/utilities and the user’s manual for your server.
• Supermicro product manuals: http://www.supermicro.com/support/manuals/
• Product drivers and utilities: https://www.supermicro.com/wdl
• Product safety info: http://www.supermicro.com/about/policies/safety_information.cfm
If you have any questions, please contact our support team at:
[email protected]m
This manual may be periodically updated without notice. Please check the Supermicro website
for possible updates to the manual revision level.
Secure Data Deletion
A secure data deletion tool designed to fully erase all data from storage devices can be found
on our website: https://www.supermicro.com/about/policies/disclaimer.cfm?url=/wdl/utility/
Lot9_Secure_Data_Deletion_Utility/
Warnings
Special attention should be given to the following symbols used in this manual.

4
Preface
Contents
Contacting Supermicro........................................................................................................7
Chapter 1 Introduction
1.1 Overview...............................................................................................................................8
1.2 System Features ..................................................................................................................9
System: Front View.............................................................................................................9
Control Panel ....................................................................................................................10
System: Rear View............................................................................................................11
1.3 Motherboard Layout ...........................................................................................................12
Quick Reference Table......................................................................................................13
Block Diagram...................................................................................................................14
Chapter 2 Maintenance and Component Installation
2.1 Removing Power ................................................................................................................15
2.2 Hardware Security..............................................................................................................15
Front Bezel Lock ...............................................................................................................15
Rear Chassis Hasp ...........................................................................................................16
Kensington Cable Slot (K-Slot) .........................................................................................16
2.3 Accessing the System........................................................................................................17
2.4 Motherboard Components..................................................................................................18
Processor ..........................................................................................................................18
Installing an LGA1700 CPU .............................................................................................18
Heatsink ............................................................................................................................21
Installing the CPU Heatsink...........................................................................................21
Memory Support and Installation ......................................................................................22
Memory Support................................................................................................................22
General Guidelines for Optimizing Memory Performance.............................................22
DIMM Installation...........................................................................................................23
DIMM Removal..............................................................................................................23
Battery Removal and Installation ......................................................................................24
Battery Removal ............................................................................................................24
Proper Battery Disposal.................................................................................................24
Battery Installation .........................................................................................................24
2.5 Chassis Components ..........................................................................................................25
Installing Expansion Cards................................................................................................25

5
Preface
Front-Mounted Hot-Swap Drives .....................................................................................27
Installing the Internal Fixed Drives ..................................................................................29
Adding an M.2 Storage Card ............................................................................................31
Installing a Fan..................................................................................................................32
Replacing the Power Supply.............................................................................................33
Chapter 3 Motherboard Connections
3.1 Power Connections ............................................................................................................34
3.2 Headers and Connectors ...................................................................................................35
Front Control Panel...........................................................................................................37
3.3 Rear I/O Ports ....................................................................................................................40
3.4 Jumper Settings .................................................................................................................43
How Jumpers Work...........................................................................................................43
3.5 LED Indicators....................................................................................................................45
Chapter 4 Software
4.1 Microsoft Windows OS Installation.....................................................................................47
4.2 Driver Installation................................................................................................................49
4.3 SuperDoctor®5....................................................................................................................50
4.4 IPMI ....................................................................................................................................51
BMC ADMIN User Password ............................................................................................51
Chapter 5 Optional Components
5.1 Optional Parts List...............................................................................................................52
Chapter 6 Troubleshooting and Support
6.1 Information Resources ........................................................................................................53
Website .............................................................................................................................53
Direct Links for the SYS-521R-T System......................................................................53
Direct Links for General Support and Information .......................................................53
6.2 Baseboard Management Controller Interface.....................................................................54
6.3 Troubleshooting Procedures .............................................................................................55
No Power ..........................................................................................................................55
No Video ...........................................................................................................................56
System Boot Failure .........................................................................................................56
Memory Errors ..................................................................................................................56
.........................................................................56
When the System Becomes Unstable ..............................................................................56
6.4 Crash Dump Using BMC.....................................................................................................58

6
Preface
6.5 UEFI BIOS Recovery .........................................................................................................59
Overview ...........................................................................................................................59
Recovering the UEFI BIOS Image....................................................................................59
Recovering the Main BIOS Block with a USB Device......................................................59
6.6 CMOS Clear .......................................................................................................................64
6.7 Where to Get Replacement Components..........................................................................65
6.8 Reporting an Issue .............................................................................................................65
Technical Support Procedures ..........................................................................................65
Returning Merchandise for Service...................................................................................65
Vendor Support Filing System ..........................................................................................66
6.9 Feedback............................................................................................................................66
6.10 Contacting Supermicro......................................................................................................67
Appendix A Standardized Warning Statements for AC Systems
Appendix B System Specications

7
Preface
Contacting Supermicro
Headquarters
Address: Super Micro Computer, Inc.
980 Rock Ave.
San Jose, CA 95131 U.S.A.
Tel: [phone]
Fax: [phone]
Email: [email protected] (General Information)
[email protected] (Sales Inquiries)
[email protected] (Gov. Sales Inquiries)
[email protected] (Technical Support)
[email protected] (RMA Support)
[email protected] (Webmaster)
Website: www.supermicro.com
Europe
Address: Super Micro Computer B.V.
Het Sterrenbeeld 28, 5215 ML
's-Hertogenbosch, The Netherlands
Tel: [phone]
Fax: [phone]
Email: [email protected] (Sales Inquiries)
[email protected] (Technical Support)
[email protected] (RMA Support)
Website: www.supermicro.nl
Asia-Pacic
Address: Super Micro Computer, Inc.
3F, No. 150, Jian 1st Rd.
Zhonghe Dist., New Taipei City 235
Taiwan (R.O.C)
Tel: [phone]
Fax: [phone]
Email: [email protected] (Sales Inquiries)
[email protected] (Technical Support)
[email protected] (RMA Support)
Website: www.supermicro.com.tw

8
Chapter 1: Introduction
System Overview
Motherboard X13SCL-iF
Chassis CSE-721TQ-350B2
Processor Intel Xeon E-2400 and 12th Generation Pentium (V0 - LGA1700) processor with up to
eight cores
Memory Up to 64 GB of DDR5 ECC UDIMM memory with speeds of up to 4800 MT/s in two
DIMM slots
Drive Support
Four front hot-swappable 3.5" drive bays

Two SlimSAS x4 connectors (2x PCIe 4.0 x4 or 1x PCIe 4.0 x4 + 4x SATA 6 Gb/s)
One M.2 socket (M-key 2280 PCIe 4.0 x4)
Expansion Slots 
I/O Ports
One VGA port
One COM port
Two 1 GbE LAN ports (Intel i210)
One Dedicated IPMI LAN port
Two USB 3.2 Gen1 (5 Gbps) Type A ports (front)
Two USB 3.2 Gen1 (5 Gbps) Type A ports (rear)
Two USB 2.0 ports (rear)
System Cooling One 12-cm rear exhaust fan
Power One 350 Watt (80+ Gold Level) power supply module
Form Factor Compact Mini-Tower, 9.45 x 8.27 x 11 in. / 240 x 210 x 279 mm (H x W x D)
Notes: A Quick Reference Guide can be found on the product page of the Supermicro website.

with UL or CSA: 721-S3X13, 721-3.
Chapter 1
Introduction
1.1 Overview
This chapter provides a brief outline of the functions and features of the SuperServer
SYS-521R-T. This system is based on the X13SCL-iF motherboard and the CSE-721TQ-350B2
chassis.


9
Chapter 1: Introduction
1.2 System Features
System: Front View
The CSE-721TQ is a compact mini-tower chassis. Refer to Appendix B for additional
󰀨
node, four pullout service tags, and two thumbscrews.
Figure 1-1. System Front View
Front Chassis Features
Feature Description
Fixed Drive Area Space for two internal 2.5" drives and one slim DVD drive
Control Panel Control panel buttons and LEDs, see next page for details
USB Ports Two USB 3.2 Gen1 (5 Gbps) ports
Hot-swap Drive Bays Four hot-swappable drive bays for SATA3/SAS2 drives
Lock Locking mechanism for front bezel
Control Panel
Hot-swap Drive Bays
Fixed Drive Area
USB Ports
Lock

10
Chapter 1: Introduction
Figure 1-2. Control Panel
Control Panel
Power switches and status LEDs are located on the control panel on the front of the chassis.
Control Panel Features
Feature Description
Power Button The main power button applies or removes primary power from the power supply to the
server but maintains standby power.
Reset Button Resets the system
Power LED Indicates main system power is on
Drive Activity LED Indicates activity on any of the hot-swap drives
NIC LED 
Information LED Universal information LED (see table below for details).
Information LED
Color, Status Description
Red, solid An overheat condition has occurred.
Red, blinking at 1 Hz Fan failure, check for an inoperative fan.
Red, blinking at 0.25 Hz Power failure, check for a non-operational power supply
Red, solid, with Power LED blinking green Fault detected
Blue and red, blinking at 10 Hz Recovery mode
Blue, solid UID has been activated locally to locate the server in a
rack environment.
Blue, blinking at 1 Hz UID has been activated using the BMC to locate the
server in a rack environment.
Blue, blinking at 2 Hz BMC is resetting
Blue, blinking at 4 Hz BMC is setting factory defaults
Blue, blinking at 10 Hz with Power LED blinking
green 
Power Button
Reset Button
NIC LED
Information LED
Power LED
Drive Activity LED

11
Chapter 1: Introduction
Figure 1-3. System Rear View
System: Rear View
The illustration below shows the rear view of the chassis. The various I/O ports are located
below the power supply.
Rear Chassis Features
Feature Description
Power Supply One 350 Watt 80+ Gold Level power supply module
COM Serial (COM ) port
IPMI LAN Dedicated IPMI LAN port
USB 2.0 Two USB 2.0 ports
USB 3.2 Two USB 3.2 Gen1 (5 Gbps) ports
LAN Two 1GbE LAN ports
VGA VGA port
COM
IPMI LAN LAN
VGA
USB 2.0 USB 3.2
Power Supply

12
Chapter 1: Introduction
1.3 Motherboard Layout

the table on the following page for descriptions. For detailed descriptions, pinout information
Chapter 4.
Figure 1-4. Motherboard Layout
DESIGNED IN USA
X13SCL-IF
REV:1.01
BAR CODE
BIOS LICENSE
JL1
JSMB1
JTPM1
I-SATA4 I-SATA5
BT1
JSLIM2 JSLIM1
C262
JPCIE1
JCPLD1
JD1
LED3
LEDM1
JPI2C1
JMD1_SRW1
JPW2
FANA
FAN3
FAN2
FAN1
JF1
JPW1
JMD1
JBT1
JPME2
JNS1
JRF1
JPL1
JPL2
JWD1
JPG1
JVRM1
MH4
MH3
MH2
MH1 JUIDB1
LED1
LED2
PCIe 4.0 x4
PCIe 4.0 x4 / SATA x4
CMOS CLEAR
2-3: NVMe
1-2: SATAJNS1:
LEDPWR
LEDBMC
USB4/5 (3.2(5Gb))
USB2/3 (3.2(5Gb))
COM1
PCIe 4.0 x4
JMD1:M.2-C
VGA
LAN1/2
JL1: CHASSIS INTRUSION
BMC_LAN
USB0/1
:SMBus1
:PWR I2C
1-4:SPEAKER
1-2:ENABLE
2-3:DISABLE
JPL2:LAN2
2-3:DISABLE
1-2:ENABLE
JPL1:LAN1
ON
PWR RST
JF1:
NIC2
FF OH
XNIC1 LED
PWR
LED HDD
CPU SLOT7 PCIe 5.0 x16 (IN x16)
DIMMA1
DIMMB1
2-3:ME MANUFACTURING MODE
JWD1:WATCH DOG
1-2:RST
2-3:NMI
1-2:ENABLE
2-3:DISABLE
JPG1:VGA
JPME2:
1-2:NORMAL
CPU
JTPM1:TPM/PORT80
BMC
Controller
COM1
BMC_LAN
USB0/1
JBT1
FAN2
DIMMA1
DIMMB1
JF1
JPL1
JSMB1
USB4/5
JL1
JWD1
JMD1_SRW1
JPW2
SLOT7
FAN3
JRF1
JNS1
FAN1
JPME2 BT1
JSLIM1
I-SATA5
LED2
JUIDB1 LAN1/2 USB 2/3
JPW1
JPI²C1
LED3
FANA
JPG1
VGA
LED1
LEDM1
JPL2
JMD1
JD1
JSLIM2 I-SATA4
MH1
MH3 MH4
MH2
JTPM1
Notes:
• " " indicates the location of Pin 1.
• Jumpers/LED indicators not indicated are used for testing only.
• 
avoid possible explosion, do not install the onboard battery upside down.

13
Chapter 1: Introduction
Note: Table continues on the next page.
Quick Reference Table
Jumper Description Default Setting
JBT1 CMOS Clear Open (Normal)
JNS1 SATA 3.0 or PCIe 4.0 Selection Pins 1–2 (4x SATA)
Pins 2–3 (PCIe x4)
JPG1 VGA Enable/Disable Pins 1–2 (Enabled)
JPL1 LAN1 Enable/Disable Pins 1–2 (Enabled)
JPL2 LAN2 Enable/Disable Pins 1–2 (Enabled)
JPME2 Manufacturing Mode Pins 1–2 (Normal)
JRF1 CPU PCIe Bifurcation Pins 1–2 (JPCIE x16)
JWD1 Watch Dog Timer Pins 1–2 (Reset)
LED Description Status
LED1 Overheat/Power Fail/Fan Fail LED Solid Red: System Overheat
Blinking Red: Power Fail or Fan Fail
LED2 UID LED 
LED3 Onboard Power LED Solid Green: Power On
LEDM1 BMC Heartbeat LED Blinking Green: Device Working
Connector Description
BMC_LAN Dedicated BMC LAN Port
BT1 Onboard Battery
COM1 COM Port
FAN1–FAN3, FANA System Fan Headers (FAN1: CPU Fan)
I-SATA4, I-SATA5 Intel PCH SATA 3.0 Ports (RAID 0, 1, 5, 10)
JD1 Speaker
JF1 Front Control Panel Header
JL1 Chassis Intrusion Header
JMD1 M.2 PCIe 4.0 x4 Slot (supports 2280 form factor)
JMD1_SRW1 M.2 Holding Screw
JPI²C1 Power I2C System Management Bus (Power SMB) Header
JPW1 24-pin ATX Power Connector
JPW2 4-pin Power Connector
JSMB1 System Management Bus Header
JTPM1 Trusted Platform Module/Port 80 Connector
JUIDB1 UID Switch
LAN1/2 Gigabit Ethernet RJ45 Ports
MH1–MH4 Mounting Holes
SLOT7 PCIe 5.0 x16 Slot (IN x16)

14
Chapter 1: Introduction
Note: This is a general block diagram and may not exactly represent the features on your

Figure 1-5. Chipset Block Diagram
Block Diagram
Connector Description
USB0/1 Back Panel USB 2.0 Ports
USB2/3 Back Panel USB 3.2 Gen 1 Ports
USB4/5 Front Panel 3.2 Gen 1 Header
VGA VGA Port
INTEL LGA1700 DDR5 (CHA)
DDR5 (CHB)
Intel
PCH-S
C262
DMI4.0 x8
Up to 128 GB ECC UDIMM (2933 MT/s)
eSPI
SPI
PCIE[28:25]
PCIe 3.0 x1
USB 2.0[5:6]
DIMMA1
(Socket-V)
PCIe 5.0 x16
JPCIe1 PCIe 5.0 x16
I210
PCIe 3.0 x1
RGMII
RTL8211F
CPLD
PCIe[3]
PCIE[16:13] /
SATA[3:0]
4800 MT/s support islimited to 1R1R configurations. (64 GB)
DIMMB1
USB 3.2[4:3]
SPITPM2.0 HDR
2x USB 3.2 Gen 1
2x USB 3.2 Gen 1
USB3 HDR
2x USB 2.0
JUSBRJ1
eSPI
AST2600
USB3 REAR
I210
COM
COM
USB 3.2 Gen 1
+
3rd LAN
1G LAN
VGA
USB 3.0
JMD1 M.2 M-key PCIe 4.0 x4
SlimSAS 1
1x PCIe 4.0 x4 or 4x SATA 3.0
1x PCIe 4.0 x4
SlimSAS 2
USB 3.2[2:1]
PCIe[1]
PCIe[2]
1x SATA 3.0
SATA Conn.
SATA Conn.
1x SATA 3.0
SATA[4]
SATA[5]
USB 2.0[8:9]
REAR IO
VGA
MUX BIOS FLASH
DDR4

15
Chapter 2: Maintenance and Component Installation
Chapter 2
Maintenance and Component Installation
This chapter provides instructions on installing and replacing main system components. To

numbers given.
  
the system. Please follow the procedures given in each section.
2.1 Removing Power
Use the following procedure to ensure that power has been removed from the system. This
step is necessary when removing or installing non hot-swap components or when replacing
a non-redundant power supply.
1. Use the operating system to power down the system.
2. After the system has completely shut-down, disconnect the AC power cord from the
power source.
3. Disconnect the power cord from the chassis.
2.2 Hardware Security
The chassis features multiple locking devices to help deter hardware theft and protect user
data. While no lock is infallible, it is recommended that users keep their systems locked when
not in use.
Front Bezel Lock
The locking front bezel protects against unauthorized removal of the storage drives. Use the
key to lock or unlock the bezel. Always remove the key from the lock and store it in a secure
place.

16
Chapter 2: Maintenance and Component Installation
Rear Chassis Hasp
Unauthorized entry through the rear of the chassis may be discouraged by placing a lock
on the rear of the chassis. The chassis is equipped with a rear chassis hasp that can
accommodate a variety of commonly available locks (not included).
Figure 2-1. Front Bezel Lock
Figure 2-2. Rear Chassis Hasp
Figure 2-3. Inserting a Kensington Cable Device (not included)
Kensington Cable Slot (K-Slot)
The chassis features a Kensington cable slot or K-slot. This slot accepts a standard Kensington

insert the device into the K-slot as illustrated below.

17
Chapter 2: Maintenance and Component Installation
2.3 Accessing the System
The CSE-721TQ-350B2 features a removable top cover to access to the inside of the chassis.
Removing the Top Cover
1. Power down the system as described in section 2.1.
2. Lift the release lever located on the right side rear of the chassis.
3. 󰀨
Caution: Except for short periods of time, do not operate the server without the cover in place.
.
Figure 2-4. Removing the Chassis Cover
3
2

18
Chapter 2: Maintenance and Component Installation
2.4 Motherboard Components
Processor
The SYS-521R-T supports a single Intel Xeon E-2400 or Pentium series processor.
Notes:
• Use ESD protection.
• Unplug the AC power cord from all power supplies after shutting down the system.
• Check that the plastic protective cover is on the CPU socket and none of the socket pins
are bent. If they are, contact your retailer.
• When handling the processor, avoid touching or placing direct pressure on the LGA lands
(gold contacts). Improper installation or socket misalignment can cause serious damage
to the processor or CPU socket, which may require manufacturer repairs.
• When installing the processor and heatsink, ensure a torque driver set to the correct force
is used for each screw.
•              
heatsink only.
• Refer to the Supermicro website for updates on processor support.
• 󰀨
Installing an LGA1700 CPU
Load Lever Load Plate
Plastic
protective cover

19
Chapter 2: Maintenance and Component Installation
1. Remove the plastic protective cover from the load plate.
2. Gently push down the load lever to release and lift it, then lift the load plate to open it
completely.
Lever lock
3. 
and notches on the CPU to the corresponding triangle maker and notches on the CPU
load bracket. Once aligned, carefully lower the CPU straight down into the socket. (Do
not drop the CPU on the socket, or move it horizontally or vertically.)
CPU notch
CPU load
bracket notch
Pin 1
4. Do not rub the CPU against the surface or against any pins of the socket to avoid
damaging the CPU or the socket.

20
Chapter 2: Maintenance and Component Installation
5. With the CPU inside the socket, inspect all the corners to make sure it is properly
installed.
6. Close the load plate with the CPU inside the socket. Gently push the load lever down
until it locks under the Lever Lock latch.
Lever lock
Attention! You can only install the CPU in the socket in one direction. Make sure that it
is properly inserted into the CPU socket before closing the load plate. If it doesn't close
properly, do not force it as it may damage your CPU. Instead, open the load plate again
and double-check that the CPU is aligned properly.