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USER’S MANUAL 

Revision 1.0

SuperWorkstation

®

5039D-I

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 significant 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: December 02, 2015

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 © 2015 by Super Micro Computer, Inc. 
All rights reserved. 

Printed in the United States of America

Summary of Contents for SuperWorkstation 5039D-I

Page 1: ...rence 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...

Page 2: ...hout 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 Indica...

Page 3: ...Dist New Taipei City 235 Taiwan R O C Tel 886 2 8226 3990 Fax 886 2 8226 3992 Email support supermicro com tw Website www supermicro com tw Chapter 4 Motherboard Connections 4 1 Power Connections 33 4...

Page 4: ...x the SuperWorkstation 5039D I was shipped in and note if it was damaged in any way If any equipment appears damaged please file a damage claim with the carrier who delivered it The system should be s...

Page 5: ...may be caused by cable congestion Blinking red 1Hz Fan failure check for an inoperative fan Solid blue Local UID has been activated Use this function to locate the server in a rackmount environment Bl...

Page 6: ...e illustration below shows the features included on the rear of the chassis 1 3 2 Front Chassis Features Item Feature Description 1 Fixed Drive Area Supports two fixed 5 25 drives such as a DVD ROM or...

Page 7: ...entifier Switch LAN1 LAN2 Gigabit RJ45 Ports PCI E CPU Slot 7 PCI Express 3 0 x8 Slot PCI E CPU Slot 6 PCI Express 3 0 x8 in x16 Slot Table continued on next page Figure 1 4 Motherboard Layout 1 5 Mot...

Page 8: ...3 0 USB 2 0 USB3 0 USB2 0 TPM Header Debug Card BIOS MUX LPC SPI SPI SPI FRONT PANEL FAN SPEED CTRL SYSTEM POWER VGA CONN COM1 Connector COM2 Header BMC AST2400 BMC Boot Flash DDR3 RJ45 Temp Sensor EM...

Page 9: ...ted circuit boards it is important to use a grounded wrist strap handle all PCBs by their edges and keep them in anti static bags when not in use 2 2 Preparing for Setup Precautions Review the electri...

Page 10: ...dant 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 strip or outlet 3 Disconnect the power cor...

Page 11: ...to install a processor CPU and heatsink to the motherboard Notes The motherboard should be installed into the chassis first and the processor should be installed into the CPU socket before you instal...

Page 12: ...ative purposes only A different heatsink may be used in the 5039D I 5 With the processor inserted into the socket inspect the four corners of the CPU to make sure that it is properly installed and flu...

Page 13: ...he module snaps into place 4 Press the release tabs to the locked positions to secure the DIMM module into the slot Repeat for other DIMM slots as needed See next page for population sequence 5 To rem...

Page 14: ...tery may release hazardous materials into the environment Do not discard a used battery in the garbage or a public landfill Please comply with the regulations set up by your local hazardous waste mana...

Page 15: ...talled or removed Installing a Hard Drive Begin by removing power from the system as described in section 3 1 and remove the chassis cover as described in section 3 2 1 To rotate the hard drive cage l...

Page 16: ...rill aligning the mounting holes of the fan grill with the mounting holes of the system fan 4 Pull the rubber pins through the mounting holes of the system fan to secure the fan to the chassis 4 Optio...

Page 17: ...ion 3 1 and access the inside of the system as described in section 3 2 1 Remove the screws securing the power supply to the chassis These are located on the rear of the chassis Set these screws aside...

Page 18: ...ction ATX Power 24 pin Connector Pin Definitions Pin Definition Pin Definition 13 3 3V 1 3 3V 14 12V 2 3 3V 15 Ground 3 Ground 16 PS_ON 4 5V 17 Ground 5 Ground 18 Ground 6 5V 19 Ground 7 Ground 20 Res...

Page 19: ...o power connectors for SATA DOM Disk_On_Module devices are located at JSD1 JSD2 Connect appropriate cables here to provide power support for your Serial Link DOM devices DOM Power Pin Definitions Pin...

Page 20: ...of a chassis intrusion when the chassis is opened Chassis Intrusion Pin Definitions Pin Definition 1 Intrusion Input 2 Ground Unit Identifier Switch UID LED Indicator A rear Unit Identifier UID switch...

Page 21: ...rn off the power when the system is in suspend mode press the button for 4 seconds or longer Power Button OH Fan Fail LED 1 NIC1 Link Active LED Reset Button 2 Power Fail LED HDD LED FP PWRLED Reset P...

Page 22: ...rive activity status Attach a cable to Pin 13 to use UID switch Refer to the table below for pin definitions HDD LED Pin Definitions JF1 Pin Definition 13 3 3V Standby UID Switch 14 HDD Active Power L...

Page 23: ...2 0 Pin Definitions Pin Definition Pin Definition 1 5V 5 5V 2 USB_N 6 USB_N 3 USB_P 7 USB_P 4 Ground 8 Ground Universal Serial Bus USB Ports There are two USB 2 0 ports USB 0 1 and two USB 3 0 ports...

Page 24: ...t is located above the USB 0 1 ports All of these ports accept RJ45 cables Please refer to the LED Indicator section for LAN LED information CMOS Clear JBT1 is used to clear CMOS which will also clear...

Page 25: ...r JPME2 to bypass SPI flash security and force the system to operate in the manufacturer mode which will allow the user to flash the system firmware from a host server for system setting modifications...

Page 26: ...ated on the rear I O panel The LED on the right indicates activity while the LED on the left indicates the speed of the connection IPMI LAN LEDs LED Color State Definition Link left Green Solid Amber...

Page 27: ...he Windows OS Setup screen will display 3 From the Windows OS Setup screen press the Enter key The OS Setup will automatically load all device files and then continue with the Windows installation 4 A...

Page 28: ...With SuperDoctor 5 Management Server SSM Server you can remotely control power on off and reset chassis intrusion for multiple systems with SuperDoctor 5 or IPMI SuperDoctor 5 Management Server monit...

Page 29: ...es built in We retain the option to include omit or change any of these text messages Settings printed in Bold are the default values A indicates a submenu Highlighting such an item and pressing the E...

Page 30: ...revert to the default to the manufacture default settings Boot Feature Quiet Boot Use this feature to select the screen display between the POST messages and the OEM logo upon bootup Select Disabled...

Page 31: ...for more than 5 minutes The options are Enabled and Disabled Power Button Function This feature controls how the system shuts down when the power button is pressed Select 4_Seconds_Override for the u...

Page 32: ...y to reduce power consumption and heat dissipation The options are Disabled and Enabled Turbo Mode Select Enabled for processor cores to run faster than the frequency specified by the manufacturer The...

Page 33: ...m to reduce power consumption The options are Enabled and Disabled Chipset Configuration Warning Setting the wrong values in the following features may cause the system to malfunc tion System Agent SA...

Page 34: ...board to change this value The default setting is 75 SLOT6 Slot Power Limit Scale Use this feature to select the scale used for the slot power limit value The options are 1 0x 0 1x 0 01x and 0 001x CP...

Page 35: ...PCH SKU Name Intel PCH Rev ID PCI Express Configuration DMI Link ASPM Control Use this feature to set the ASPM Active State Power Management state on the SA System Agent side of the DMI Link The optio...

Page 36: ...ive on the particular SATA port Model number of drive and capacity Software Preserve Support Port 0 Port 7 Spin Up Device Port 6 and Port 7 on X11SSM F only On an edge detect from 0 to 1 set this item...

Page 37: ...abled PXE boot wait time Use this option to specify the wait time to press the ESC key to abort the PXE boot Press or on your keyboard to change the value The default setting is 0 Media detect count U...

Page 38: ...ey support Select ANSI to use the Extended ASCII Character Set Select VT UTF8 to use UTF8 encoding to map Unicode characters into one or more bytes The options are VT100 VT100 VT UTF8 and ANSI COM1 Bi...

Page 39: ...set the transmission speed for a serial port used in Console Redirection Make sure that the same speed is used in the host computer and the client computer A lower transmission speed may be required f...

Page 40: ...usy lines The options are 9600 19200 57600 and 115200 bits per second Flow Control Use this item to set the flow control for Console Redirection to prevent data loss caused by buffer overflow Send a S...

Page 41: ...tect against software based attacks and ensures protection confidentiality and integrity of data stored or created on the system Use this feature to enable or disable TXT Support The options are Disab...

Page 42: ...will allow the system to wake up when an onboard device receives an incoming signal The options are Disabled and Enabled Blink LEDs Use this feature to identify the physical network port by blinking t...

Page 43: ...tely for all messages to be automatically erased from the event log when the event log memory is full The options are Do Nothing and Erase Immediately SMBIOS Event Long Standard Settings Log System Bo...

Page 44: ...take effect BMC Network Configuration BMC Network Configuration IPMI LAN Selection This item displays the IPMI LAN setting The default setting is Failover IPMI Network Link Status This item displays t...

Page 45: ...configure the following security settings for the system Password Check Select Setup for the system to check for a password at Setup Select Always for the system to check for a password at bootup or...

Page 46: ...are Yes and No Key Exchange Key Set New Key Select Yes to load the KEK from the manufacturer s defaults Select No to load the KEK from a file The options are Yes and No Append Key Select Yes to add t...

Page 47: ...r 6 Legacy UEFI Dual Boot Order 7 Legacy UEFI Dual Boot Order 8 Legacy UEFI Dual Boot Order 9 Legacy UEFI Dual Boot Order 10 Legacy UEFI Dual Boot Order 11 Legacy UEFI Dual Boot Order 12 Legacy UEFI D...

Page 48: ...changes you have made This will not reset reboot the system Discard Changes Select this option and press Enter to discard all the changes and return to the AMI BIOS utility Program Default Options Res...

Page 49: ...or Beep POST Codes Beep Code Error Message Description 1 beep Refresh Circuits have been reset Ready to power up 5 short 1 long Memory error No memory detected in system 5 beeps No con in or con out d...

Page 50: ...mit den Gefahren elektrischer Schaltungen und den blichen Verfahren zur Vorbeugung vor Unf llen vertraut Suchen Sie mit der am Ende jeder Warnung angegebenen Anweisungsnummer nach der jeweiligen bers...

Page 51: ...R DEZE INSTRUCTIES Installation Instructions Warning Read the installation instructions before connecting the system to the power source Warnung Vor dem Anschlie en des Systems an die Stromquelle die...

Page 52: ...sche installatie Controleer of het beveiligde aparaat niet groter gedimensioneerd is dan 250V 20A Power Disconnection Warning Warnung Das System muss von allen Quellen der Energie und vom Netzanschlus...

Page 53: ...n dieser Ausr stung sollte nur geschultem qualifiziertem Personal gestattet werden Advertencia Solamente el personal calificado debe instalar reemplazar o utilizar este equipo Restricted Area Waarschu...

Page 54: ...n alleen verkregen worden door gebruik te maken van speciaal gereedschap slot en sleutel of andere veiligheidsmaatregelen Battery Handling Warnung Bei Einsetzen einer falschen Batterie besteht Explosi...

Page 55: ...the unit Warnung Dieses Ger t kann mehr als eine Stromzufuhr haben Um sicherzustellen dass der Einheit kein trom zugef hrt wird m ssen alle Verbindungen entfernt werden Waarschuwing Deze eenheid kan m...

Page 56: ...ntenance Warning Hazardous voltage or energy is present on the backplane when the system is operating Use caution when servicing Comply with Local and National Electrical Codes Warnung Die Installatio...

Page 57: ...vertencia Al deshacerse por completo de este producto debe seguir todas las leyes y reglamentos nacionales Waarschuwing De uiteindelijke verwijdering van dit product dient te geschieden in overeenstem...

Page 58: ...Anschlusskabel Stromkabel und Netzteile Verwendung anderer Kabel und Adapter kann zu einer Fehlfunktion oder ein Brand entstehen Elektrische Ger te und Material Safety Law verbietet die Verwendung vo...

Page 59: ...es appareils lectriques que les produits d sign s par Supermicro seulement AC AC UL CSA UL CSA UL CSA Supermicro UL CSA AC Electrical Appliance and Material Safety Law UL CSA UL CSA Waarschuwing Bij h...

Page 60: ...2 x 1 7 x 20 in 437 x 43 x 508 mm W x H x D System Cooling Two 4 cm high performance fans Power Supply Model PWS 305 PQ AC Input Voltages 100 240 VAC Rated Input Current 5A maximum Rated Input Frequen...

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