Supermicro SuperServer 5039MS-H12TRF User Manual

SuperServer

®

5039MS-H12TRF

USER’S MANUAL

Revision 1.0

SuperServer 5039MS-H12TRF User's Manual

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 DAMAGES ARISING FROM THE USE OR INABILITY TO 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.

Any disputes arising between manufacturer and customer shall be governed by the laws of Santa Clara County in the
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 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 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: Handling of lead solder materials used in this product may expose you to lead, a
chemical known to the State of California to cause birth defects and other reproductive harm.

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

systems whose failure to perform be reasonably expected to result in signicant injury or loss of life or catastrophic

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: March 10, 2016 mk

Unless you request and receive written permission from Super Micro Computer, Inc., you may not copy any part of this

document. Information in this document is subject to change without notice. Other products and companies referred

to herein are trademarks or registered trademarks of their respective companies or mark holders.

Copyright © 2016 by Super Micro Computer, Inc.
All rights reserved.

Printed in the United States of America

Preface

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 SuperServer Installation and maintainance
should be performed by experienced technicians only.

Please refer to the server specications page on our website for updates on 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: ftp://ftp.supermicro.com

• Product safety info: http://www.supermicro.com/about/policies/safety_information.cfm

If you have any questions, please contact our support team at:

[e-mail]

This manual may be periodically updated without notice. Please check the Supermicro website
for possible updates to the manual revision level.

Warnings

Special attention should be given to the following symbols used in this manual.

Warning! Indicates important information given to prevent equipment/property damage

or personal injury.

Warning! Indicates high voltage may be encountered when performing a procedure.

3

3

SuperServer 5039MS-H12TRF User's Manual

Contents

Chapter 1 Introduction

1.1 Overview ...............................................................................................................................7

1.2 Unpacking the System .........................................................................................................7

1.3 System Features ..................................................................................................................8

1.4 Chassis Features .................................................................................................................9

Power Button/LED ...............................................................................................................9

Front Features ...................................................................................................................10

Rear Features ...................................................................................................................11

1.5 Motherboard Layout ...........................................................................................................12

Motherboard Jumpers, Connectors, and LEDs ................................................................13

Chapter 2 Installation in a Rack

2.1 Preparing for Setup ............................................................................................................15

Choosing a Setup Location ...............................................................................................15

Rack Precautions ..............................................................................................................15

Server Precautions ............................................................................................................16

Rack Mounting Considerations .........................................................................................16

2.2 Installing the Rails ............................................................................................................18

Chapter 3 Maintenance and Component Installation

3.1 Removing Power ................................................................................................................19

3.2 Accessing the System ........................................................................................................20

Top Cover ..........................................................................................................................20

Removing and Installing Motherboard Nodes ...................................................................21

Connecting to a Node .......................................................................................................22

3.3 Motherboard Components ..................................................................................................23

Processor and Heatsink Installation ..................................................................................23

Memory Installation ..........................................................................................................27

Memory Support ............................................................................................................27

DIMM Module Population Conguration ........................................................................27

DIMM Module Population Sequence .............................................................................28

Install Procedure ............................................................................................................29

Removal Procedure .......................................................................................................29

Expansion Module .............................................................................................................30

Motherboard Battery .........................................................................................................31

4

Preface

3.4 Chassis Components .........................................................................................................32

Hard Drives .......................................................................................................................32

System Cooling .................................................................................................................34

Corresponding Nodes and Fans ...................................................................................34

Replacing Fans ..............................................................................................................35

Air Shroud ......................................................................................................................36

Power Supply ...................................................................................................................37

Chapter 4 Motherboard Connections

4.1 Node Front Panel Controls.................................................................................................38

4.2 Headers and Connectors ....................................................................................................38

4.3 Ports ...................................................................................................................................40

4.4 Jumpers ..............................................................................................................................41

4.5 LED Indicators ....................................................................................................................43

Chapter 5 Software

5.1 OS Installation ..................................................................................................................44

Installing the Windows OS for a RAID System ................................................................44

Installing Windows to a Non-RAID System ......................................................................44

5.2 Driver Installation ................................................................................................................45

5.3 SuperDoctor® 5 ...................................................................................................................46

5.4 IPMI ....................................................................................................................................46

Chapter 6 BIOS

6.1 Introduction .........................................................................................................................47

Starting the Setup Utility ...................................................................................................47

6.2 Main Menu ..........................................................................................................................48

6.3 Advanced Setup Congurations .........................................................................................49

6.4 Event Logs .........................................................................................................................69

6.5 IPMI ....................................................................................................................................71

6.6 Security ...............................................................................................................................73

6.7 Boot ....................................................................................................................................76

6.8 Save & Exit .........................................................................................................................78

Appendix A BIOS Error Codes

Appendix B Standardized Warning Statements for AC Systems

Appendix C UEFI BIOS Recovery Instructions

Appendix D System Specications

5

SuperServer 5039MS-H12TRF User's Manual

SuperServer 5039MS-H12TRF User's Manual

Contacting Supermicro

Headquarters

Address: Super Micro Computer, Inc.

980 Rock Ave.

San Jose, CA 95131 U.S.A.
Tel: [phone]
Fax: [phone]
Email: [e-mail] (General Information)

[e-mail] (Technical Support)
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: [e-mail] (General Information)

[e-mail] (Technical Support)

[e-mail] (Customer 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: [e-mail]
Website: www.supermicro.com.tw

6

Chapter 1: Introduction

Chapter 1

Introduction

1.1 Overview

The SuperServer 5039MS-H12TRF is a MicroCloud server system in the SC939HS-R2K04BP
chassis, featuring twelve separate computing nodes each containing an X11SSE-F
motherboard.

In additon to the motherboards and chassis, several included parts are listed below.

Main Parts List

Description Part Number Quantity

Backplane BPN-SAS-939HS One

Fans FAN-0145L4 Four

CPU passisve heatsink SNK-P0047PSR One per node

Air ow shroud MCP-310-93903-0N One per node

MicroLP module AOM-CGP-I2M One per node

Rail kit MCP-290-41803-0N One set

1.2 Unpacking the System

Inspect the box in which the server was shipped and note if it was damaged. If any equipment

appears damaged, le a damage claim with the carrier who delivered it.

7

SuperServer 5039MS-H12TRF User's Manual

1.3 System Features

The following table provides you with an overview of the main features of the 5039MS-H12TRF.

Refer to Appendix C for additional specications.

System Features

Motherboard

X11SSE-F

Chassis

SC939HS-R2K04BP

CPU

Intel Xeon E3-1200 v5 (Skylake-S)

Socket Type

H4 LGA1151

Memory

Four DIMM ECC UDIMM VLP memory up to 64 GB

Chipset

Intel PCH C236 chipset

Expansion Slots

One MicroLP expansion module per node

Hard Drives

Internal, two 3.5" drives or four 2.5" drives, SATA3 or NVMe

Power

Dual 2000 W modules, 80+ Titanium level

Cooling

Four 9-cm exhaust fans; one airow shroud per node

Form Factor

3U rackmount

Dimensions

(WxHxD) 17.5 x 5.21 x 29.5 in. (444.5 x 132 x 749.3 mm)

8

Chapter 1: Introduction

1.4 Chassis Features

Power Button/LED

The main power button on each of the nodes functions as both an on/off switch and as a
status LED. Pressing the button will alternately power on or remove power from the node.
See the table below for the LED indications.

Node Power Button LED

LED Appearance Description

Green The node is powered on and operating normally

Solid Red The node is detecting an overheat condition

1Hz Blinking Red The node is detecting a fan failure

.25Hz Blinking Red The node is detecting a power failure

No Illumination The node is powered down

Node LED

Figure 1-1. Power Button/LED Indicator

(single node, front view)

9

SuperServer 5039MS-H12TRF User's Manual

Front Features

The SC939HS-R2K04BP is a 3U chassis holding 12 discreet computing nodes. The chassis
front offers access to the dual power modules. It also includes two dedicated LAN ports to
provide IPMI management capabilitites for all nodes.

Note: The IPMI connections can be used in two ways.

• Cascade: Connect one to a managment device and the other to another server.

• Redundancy: For redundant IPMI managment, connect each port to a different subnetwork,

that is, each to a different switch.

Six Nodes Six Nodes

Two IPMI LAN Ports

Two Power Modules

Figure 1-2. Chassis Front View

1

32

4

Item Feature Description

1 UID button Unit identier button and LED

2 Power button Power button and LED

3 KVM port

4 LAN

Figure 1-3. Single Node Front View

Node Features

Connect the adapter to this port to provide two USB2 ports, one COM
port, and one serial port

Two LAN ports, by means of the MicroLP expansion module

10

Chapter 1: Introduction

Rear Features

The illustration below shows the features included on the rear of the chassis.

Power Plugs (2)

Exhaust Fans (4)

Figure 1-4. Chassis Rear View

11

SuperServer 5039MS-H12TRF User's Manual

CPU MICRO-LP PCI-E 3.0 X8

1.5 Motherboard Layout

Below is a layout of the X11SSE-F with jumper, connector and LED locations shown. See

the table on the following page for descriptions. For detailed descriptions, pinout information

and jumper settings, refer to Chapter 4.

JKVM1/VGA

J21

DIMMB1

DIMMB2

J21
MICRO-LP

JPG1

DIMMA1DIMMA2

BAR CODE

JPO1

JPG1

BMC

JBT1

JPO1

JBT1

LICENSE

BIOS

USB0/1

JKVM1/VGA
USB0/1

BT1

BT1

LED6

LED6

Intel PCH

JPME1

SW2

SW2

JTPM1

USB2 (3.0)

MAC CODE

LED5

JUIDB1

JTPM1

JWD1

JPME2

JPME1

I-SATA6

JSD1

LED5

JUIDB1

JPME2

JWD1

USB2

I-SATA6

JSD1

DIMMB2

DIMMB1

DIMMA2

Figure 1-4. Motherboard Layout

Notes:

• " " indicates the location of pin 1.

Rev. 1.01

DIMMA1

CPU

X11SSE-F

I-SATA0

I-SATA0

• Jumpers/LED indicators not indicated are used for testing only.

12

Chapter 1: Introduction

Motherboard Jumpers, Connectors, and LEDs

Jumper Description Default Setting

JBT1 CMOS Clear Open (Normal)

JPG1 VGA Enable/Disable Pins 1-2 (Enabled)

JPME1 ME Recovery Pins 1-2 (Normal)

JPME2 ME Manufacturing Mode Pins 1-2 (Normal)

JPO1 Power Fail Override Pins 2-3 (Disabled)

JWD1 Watch Dog Pins 1-2 (Reset)

Connector Description

BT1 Onboard Battery

I-SATA0 & I-SATA6 SATA 3.0 Connectors

J21 CPU Micro-LP PCI-E 3.0 x8 Slot

JKVM1/VGA

JSD1 SATA Disk On Module (DOM) Power Connector

JTPM1 Trusted Platform Module (TPM)/Port 80 Connector

JUIDB1 UID (Unit Identication) Switch

SW2 Power Switch/LED Indicator

USB0/1 Back panel USB 2.0 ports via KVM

USB2 USB 3.0 internal connector

KVM/VGA (Monitor) (UART) Connector for Remote Console Redirection or Remote
Network Interface

LED Description State: Status

LED5 Rear UID LED Blue: On; Unit Identied

LED6 BMC Heartbeat LED Green: Blinking; BMC Normal

13

SuperServer 5039MS-H12TRF User's Manual

PCIe x8 MLP SLOT

DIMMA1

DIMMA2

DIMMB1

DIMMB2

1 X SATA-III DOM

1 X USB A-type

2 X USB 2.0 Rear

2 X USB 2.0 MLP

PCIe3.0_x8

8.0GT/s

DDR4 (CHA)

2133/1866/1600MHz

DDR4 (CHB)

2133/1866/1600MHz

SATA-III

6Gb/s

USB3.0
5Gbps

USB2.0

480Mbps

USB2.0

480Mbps

Port [19]

USB3[5] USB2[5]

USB2[1/2]

USB2(3/4]

LGA1151

(Socket-H4)

PCH-H

C236

FLASH
SPI 128Mb

x4 DMI
8GT/s

IMVP8

Port [10,15-18]

Port [9]

Port [14]

SPI

LPC

SVID

SATA-III

6Gb/s

SGPIO

PCIe3.0_x1

8.0GT/s

IMVP8

PCIe3.0_x8

8.0GT/s

5 x SATA-III

6Gb/s

SGPIO
Decoder

SMBUS

AST2400

TPM1.2 Header

I-SATA0

RGMII

RTL8211FS

VGA

AOM-BPN-MC12S

1000BASE-X

1000BASE-X

1Gb/s

SATA-III

6Gb/s

PCIe3.0 x4

8.0GT/s

SATA

6Gb/s

PCIe3.0 x4

8.0GT/s

SATA-III

6Gb/s

SATA-III

6Gb/s

SATA-III

6Gb/s

1Gb/s

-III

I-SATA[2]/NVMe1

I-SATA[3]/NVMe2

I-SATA[4]

I-SATA[5]

SATA-III

6Gb/s

1000BASE-X

1Gb/s

AOM-PDB-MC12S

I-SATA[1]

BPN-SAS-939HS

Figure 1-5. Intel PCH C236 Chipset: System Block Diagram

Note: This is a general block diagram and may not exactly represent the features on your

motherboard. See the System Specications appendix for the actual specications of your

motherboard.

14

Chapter 2 Installation in a Rack

Chapter 2

Installation in a Rack

This chapter provides advice and instructions for mounting your system in a rack.

2.1 Preparing for Setup

The box in which the system was shipped should include the hardware needed to install it
into the rack. Please note the precautions in this chapter and Appendix B

Choosing a Setup Location

• The system should be situated in a clean, dust-free area that is well ventilated. Avoid areas

where heat, electrical noise and electromagnetic elds are generated. It will also require

a grounded AC power outlet nearby.

• Leave enough clearance in front of the rack so that you can open the front door completely

(~25 inches) and approximately 30 inches of clearance in the back of the rack to allow

sufcient space for airow and access when servicing.

• This product should be installed only in a Restricted Access Location (dedicated equipment

rooms, service closets, etc.).

• This product is not suitable for use with visual display workplace devices acccording to §2

of the the German Ordinance for Work with Visual Display Units.

Rack Precautions

• Ensure that the leveling jacks on the bottom of the rack are extended to the oor so that

the full weight of the rack rests on them.

• In single rack installations, stabilizers should be attached to the rack. In multiple rack in-

stallations, the racks should be coupled together.

• Always make sure the rack is stable before extending a server or other component from

the rack.

• Extend only one server or component at a time - extending two or more simultaneously

may cause the rack to become unstable.

15

SuperServer 5039MS-H12TRF User's Manual

Server Precautions

• Review the electrical and general safety precautions in Chapter 3.

• Determine the placement of each component in the rack before you install the rails.

• Install the heaviest server components at the bottom of the rack rst and then work your

way up.

• Use a regulating uninterruptible power supply (UPS) to protect the server from power

surges and voltage spikes and to keep your system operating in case of a power failure.

• Allow any drives and power supply modules to cool before touching them.

• When not servicing, always keep the front door of the rack and all covers/panels on the

servers closed to maintain proper cooling.

Rack Mounting Considerations

Ambient Operating Temperature

If installed in a closed or multi-unit rack assembly, the ambient operating temperature of
the rack environment may be greater than the room's ambient temperature. Therefore,
consideration should be given to installing the equipment in an environment compatible with
the manufacturer’s maximum rated ambient temperature (Tmra).

Airow

Equipment should be mounted into a rack so that the amount of airow required for safe

operation is not compromised.

Mechanical Loading

Equipment should be mounted into a rack so that a hazardous condition does not arise due
to uneven mechanical loading.

Circuit Overloading

Consideration should be given to the connection of the equipment to the power supply circuitry
and the effect that any possible overloading of circuits might have on overcurrent protection
and power supply wiring. Appropriate consideration of equipment nameplate ratings should
be used when addressing this concern.

16

Chapter 2 Installation in a Rack

Reliable Ground

A reliable ground must be maintained at all times. To ensure this, the rack itself should be
grounded. Particular attention should be given to power supply connections other than the
direct connections to the branch circuit (i.e. the use of power strips, etc.).

To prevent bodily injury when mounting or servicing this unit in a rack, you must take

special precautions to ensure that the system remains stable. The following guidelines
are provided to ensure your safety:

• This unit should be mounted at the bottom of the rack if it is the only unit in the rack.

• When mounting this unit in a partially lled rack, load the rack from the bottom to the top

with the heaviest component at the bottom of the rack.

• If the rack is provided with stabilizing devices, install the stabilizers before mounting or

servicing the unit in the rack.

• Slide rail mounted equipment is not to be used as a shelf or a work space.

Stability hazard. The rack stabilizing mechanism must be in place, or the rack must

be bolted to the oor before you slide the unit out for servicing. Failure to stabilize the

rack can cause the rack to tip over.

17

SuperServer 5039MS-H12TRF User's Manual

2.2 Installing the Rails

There are a variety of rack units on the market, which may require a slightly different assembly
procedure. The following is a basic guideline for installing the system into a rack. Also refer
to the installation instructions that came with the rack.

This rail set ts a rack between 28" and 33.5" deep. Do not use a two post "telco" type rack.

1. Identify the left rail set and right rail set, as they are different.

2. In each rail set, the two sections are screwed together to keep them immobile during

shipping. Release these screws just enough to allow the rail sections to slide apart. Note

the arrow on the rail, which indicates the end that attaches to the front of the rack.

3. Slide the rail sections apart far enough to match the depth of the rack. Hang the hooks
on the rear end of the rail onto the square holes in the rear of the rack.

4. Push the two square pegs on the front of the rail through the square holes in the front
of the rack. Be sure the rail is level, front to back. Secure the front of the rail to the rack

with one athead screw.

5. Tighten the screws that keep the two rail sections from sliding.

6. Install the other rail set. Be sure it is even with the rst.

7. With one person on either side, lift the system and slide it onto the installed rails.

8. After pushing the enclosure all the way into the rack, use the thumbscrew on each side
of the server to lock it into place.

Figure 2-1. Installing the Left Rail

18

Chapter 3: Maintenance and Component Installation

Chapter 3

Maintenance and Component Installation

This chapter provides instructions on installing and replacing main system components. To

prevent compatibility issues, only use components that match the specications and/or part

numbers given.

Installation or replacement of most components require that power rst be removed from the

system. Please follow the procedures given in each section.

3.1 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(s) from the
power strip or outlet. (If your system has more than one power supply, remove the AC
power cords from all power supply modules.)

3. Disconnect the power cord(s) from the power supply module(s).

19

SuperServer 5039MS-H12TRF User's Manual

3.2 Accessing the System

Top Cover

A portion of the chassis top is removable to allow access to the system fans and backplane.

Removing the Top Cover

1. Remove power from the system as described in Section 3.1.

2. Remove the screws securing the cover to the chassis--four on top and two on each
side. See Figure 3-1.

3. Lift the cover from the chassis.

Caution: Except for short periods of time, do not operate the server without the cover in place.

The chassis cover must be in place to allow for proper airow and to prevent overheating.

Figure 3-1. Removing the Chassis Cover

20

Chapter 3: Maintenance and Component Installation

Removing and Installing Motherboard Nodes

The system comes features twelve removable nodes. Each node contains an individual
motherboard and hard drives mounted on a sled, which allows it to easily be installed and
removed from the chassis.

Release Tab

Handle

Figure 3-2. Removing/Installing a Node

Removing Nodes from the System

1. Power-down the individual node by pressing that node's power button.

2. Press and hold down the release tab on the front of the node.

3. Use the node's handle to pull the node from the system.

Caution: Except for short periods of time while swapping nodes, do not operate the server
with the node bays empty. In the unlikely event of a node failure, remove the failed node and
replace it with the dummy node that was included with the system.

21

SuperServer 5039MS-H12TRF User's Manual

Connecting to a Node

USB, COM, and serial port capabilties can be added to any node through the KVM port on
the front. Plug in the adapter (dongle).

Figure 3-3. Adapter to Provide USB, COM, and Serial Ports

22

Chapter 3: Maintenance and Component Installation

3.3 Motherboard Components

Processor and Heatsink Installation

Follow the procedures in this section to install a processor (CPU) and heatsink onto the
motherboard.

Notes:

• Be sure to use an Intel-certied multi-directional heatsink.

• When receiving a motherboard without a processor pre-installed, make sure that the plastic

protective socket cover is in place and none of the socket pins are bent; otherwise, contact
your retailer immediately.

• Refer to the Supermicro website for updates on CPU support.

Installing the Processor

1. Remove power from the system as described in Section 3.1.

2. Press the locking lever down and outward to release it, then lift it fully open. The load
plate slides loose from the retaining post.

Plastic Protective

Load Plate

Retaining Post

Cover

Locking Lever

Figure 3-2. Releasing the Locking Lever

23

SuperServer 5039MS-H12TRF User's Manual

3. Lift open the load plate.

Load Plate Open

Socket Key

Processor Notches

Figure 3-3. Placing the Processor into the Socket

4. Use your thumb and your index nger to hold the edges of the processor. Do not touch
the socket contacts or the bottom of the processor. Align the notches (the semi-circle
cutouts) on the processor with the socket keys.

5. Once aligned, carefully place the processor into the socket. Do not drop the processor
on the socket, move or rub the processor against the socket or against any socket pins,
as this may damage the components. Make sure the processor is properly aligned and
seated in the socket, checking all corners.

Figure 3-4. Seating the Processor

24

Chapter 3: Maintenance and Component Installation

6. Gently close the load plate onto the processor. The plastic protective cover on the load
plate will pop off. Save the cover to protect the socket if the processor is ever removed.

7. Making sure the slot in the load plate slides under the retaining post, close and latch the
locking lever.

Load Plate slot under

Retaining Post

Locking Lever

latched into place

Figure 3-5. Securing the Processor with the Socket Lever

25

SuperServer 5039MS-H12TRF User's Manual

Installing a Heatsink

A passive type heatsink is used on the X11SSE-F motherboard.
Note: Do not apply any thermal grease to the heatsink or the CPU; the required amount has

already been applied.

1. Place the heatsink on top of the CPU so that the four mounting holes are aligned with
those on the heatsink retention mechanism.

2. Screw in two diagonal screws (i.e. the #1 and the #2 screws) until they are just snug.
Do not fully tighten the screws or you may damage the CPU.

3. Add the two remaining screws then nish the installation by fully tightening all four
screws (be careful not to overtighten).

Screw#1

Screw#2

Figure 3-5. Installing/Removing the Heatsink

26

Chapter 3: Maintenance and Component Installation

Removing a Heatsink

We do not recommend removing the heatsink. If necessary, please follow the instructions
below to prevent damage to the CPU or the CPU socket.

1. Unscrew and remove the heatsink screws from the motherboard in the sequence as

show in the gure above.

2. Hold and gently pivot the heatsink back and forth to loosen it from the CPU. (Do not use
excessive force when dislodging the heatsink!)

3. Once the heatsink is loose, remove it from the CPU.

4. Clean the surface of the CPU and the heatsink to get rid of the old thermal grease.
Reapply the proper amount of thermal grease to the surface before you re-install the
heatsink.

Memory Installation

Memory Support

The X11SSE-F supports up to 64GB of ECC DDR4-2133/1866/1600/1333 unbuffered

(UDIMM) memory in four memory slots. Populating two adjacent slots at a time with memory

modules of the same size and type will result in interleaved (128-bit) memory, which is faster
than non-interleaved (64-bit) memory.

Check the Supermicro website for possible updates to memory support.

DIMM Module Population Conguration

For optimal memory performance, follow the table below when populating memory.

Memory Module Population for Optimal Performance

Number of
DIMMs

2 DIMMs DIMMB2/DIMMA2

4 DIMMs DIMMB2/DIMMA2, DIMMB1/DIMMA1

Memory Population Conguration Table

(For memory to work properly, please follow the instructions below.)

DIMM Slots
per Channel

2

DIMM
Type

Unbuffered
DDR4 VLP

Memory Module Population

POR Speeds
(MHz)

2133,1866,
1600

Ranks per
DIMM

SR, DR 6 SPS 1.2V1

27

Layer
Count

FW Base

Supported
Voltage

SuperServer 5039MS-H12TRF User's Manual

Memory Module Population

Max Memory
Possible

Single Rank
UDIMM

Dual Rank
UDIMMs

4GB DRAM
Technology

16GB
(4x 4GB DIMMs)

32GB
(4x 8GB DIMMs)

8GB DRAM
Technology

32GB
(4x 8GB DIMMs)

64GB
(4x 16GB DIMMs)

DIMM Module Population Sequence

When installing memory modules, the DIMM slots must be populated in the following order:

DIMMB2, DIMMA2, then DIMMB1, DIMMA1. The blue slots must be populated rst.

Towards the CPU

DIMMA1

DIMMA2 (Blue Slot)

DIMMB1

DIMMB2 (Blue Slot)

Towards the edge of the motherboard

Note: Be sure to use memory modules of the same type and speed on the motherboard.
Mixing of memory modules of different types and speeds is not allowed.

28

Chapter 3: Maintenance and Component Installation

Install Procedure

Installing Memory

1. Remove power from the system as described in Section 3.1.

2. Starting with P1-DIMMA1, push the
release tabs outwards on both ends of
the DIMM slot to unlock it.

3. Align the key of the DIMM with the
receptive point on the memory slot and
with your thumbs on both ends of the
module, press it straight down into the
slot until the module snaps into place.

Notches

Release Tabs

Press both notches straight

down into the memory slot.

4. Press the release tabs to the locked position to secure the DIMM module into the slot.

5. Repeat the procedure for the remaining DIMM modules in the order detailed in the
previous section.

Caution: Exercise extreme caution when installing or removing memory modules to prevent
damage to the DIMMs or slots.

Note: Visit the product page on the Supermicro website for possible updates to memory
support (www.supermicro.com).

Removal Procedure

To remove a DIMM module, unlock the release tabs then pull the module from the slot.

29

SuperServer 5039MS-H12TRF User's Manual

Expansion Module

Each of the twelve nodes includes a single MicroLP expansion module providing two LAN
connections. Currently, there are four supported for the 5039MS-H12TRF system.

Two LAN ports (standard), AOM-CGP-i2M
Two QSFP + USB ports (optional), AOM-CIBF-M1M
One SFP+ USB ports (optional), AOM-CTG-i1SM
Two 10G baseT ports (optional), AOM-CTGS-i2T

The MicroLP expansion module is inserted into a riser card and secured to two brackets as
shown below. This assembly is inserted into the expansion slot on the motherboard and the
rear bracket is secured to the rear of the node chassis.

Expansion Card

Riser Card

Bracket

Note: This exploded view of the expansion

module is for information only. The
expansion card, riser card and mounting
bracket come pre-assembled and installed

Figure 3-4. MicroLP Expansion Module Assembly

30