Supermicro SuperWorkstation 5039A-IL User Manual Download Page 40

40

Chapter 4: Motherboard Connections

Reset Button

Pin Definitions (JF1)

Pin#

Definition

3

Reset

4

Ground

OH/Fan Fail

Pin Definitions (JF1)

Pin#

Definition

7

+3.3V

8

OH/Fan Fail LED

LAN LED

Pin Definitions (JF1)

Pin#

Definition

9/11

+3.3V Standby

10/12

NIC1/NIC2 Activity

Reset Button 

The Reset Button connection is located on pins 3 and 4 of JF1. Attach it to a hardware 
reset switch on the computer case to reset the system. Refer to the table on the right for pin 

definitions.

NIC1/NIC2 (LAN1/LAN2)

The NIC (Network Interface Controller) LED connection for LAN port 2 and LAN port 1 are 
located on pins 9/10 and 11/12 of JF1 respectively.  Attach an LED indicator to this header 
to display network activity.

Overheat (OH)/Fan Fail

Connect an LED cable to OH/Fan Fail connections on pins 7 and 8 of JF1 to  provide warnings 
for chassis overheat/fan failure.

OH/Fan Fail

Indicator Status

State

Definition

Off

Normal

On

Overheat

Flashing Fan Fail

Note: 

pinout information for the reset button is included for reference purposes only; there 

is no reset button on the SC732D4-500B chassis.

Summary of Contents for SuperWorkstation 5039A-IL

Page 1: ...USER S MANUAL Revision 1 0a SuperWorkstation 5039A IL...

Page 2: ...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...

Page 3: ...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...

Page 4: ...6 Choosing a Setup Location 16 General Precautions 16 Chapter 3 Maintenance and Component Installation 3 1 Removing Power 18 3 2 Accessing the System 18 3 3 Motherboard Components 19 Processor and Hea...

Page 5: ...icators 48 Chapter 5 Software 5 1 OS Installation 49 Installing the Windows OS for a RAID System 49 Installing Windows to a Non RAID System 49 5 2 Driver Installation 50 5 3 SuperDoctor 5 51 Chapter 6...

Page 6: ...Super Micro Computer B V Het Sterrenbeeld 28 5215 ML s Hertogenbosch The Netherlands Tel 31 0 73 6400390 Fax 31 0 73 6416525 Email sales supermicro nl General Information support supermicro nl Technic...

Page 7: ...ipped 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 Decide on a suitable location for the rack unit that will h...

Page 8: ...Gen Core i7 i5 i3 Pentium and Celeron processors Socket Type LGA 1151 H4 Memory Four 288 pin DIMM slots to support up to 64 GB of unbuffered ECC non ECC DDR4 2133MHz SDRAM Chipset C236 Express chipset...

Page 9: ...o perform many maintenance tasks you must also unplug system before servicing 7 Line Out Line out jack 8 Mic Microphone jack Figure 1 1 Control Panel View 1 4 Server Chassis Features Control Panel The...

Page 10: ...es such as a DVD ROM or HDD 2 Control Panel Front control panel see preceding page 3 Internal HDD Cage behind bezel Supports four 3 5 hard drives in a rotatable cage Figure 1 2 Chassis Front View Fron...

Page 11: ...80Plus Bronze Level power supply p n PWS 502 PQ 2 I O Backpanel Rear I O ports see Section 4 3 3 PCI Slots Supports seven full height full length PCI expansion cards Figure 1 3 Chassis Rear View Rear...

Page 12: ...JTPM1 JL1 JHD_AC1 JSTBY1 COM1 COM2 I SATA7 I SATA6 I SATA5 I SATA3 I SATA1 I SATA4 I SATA2 I SATA0 I SGPIO2 I SGPIO1 J23 XDP1 LEDM1 LED4 LED1 LED3 FAN5 FAN4 FAN2 FAN1 FAN3 JI2C1 JI2C2 JPAC1 JPL2 JPG1...

Page 13: ...OM1 Serial Port Header Fan1 Fan4 FanA System CPU Fan Headers I SATA0 I SATA5 Intel PCH SATA Serial ATA 3 0 Ports I SGPIO 1 2 Serial Link General Purpose I O Headers JD1 Speaker Power LED Indicator JF1...

Page 14: ...E PCH Slot 5 PCI Express 3 0 x4 in x8 Slot SP1 Internal Speaker Buzzer USB 0 1 Back Panel USB 2 0 Ports USB 2 3 USB 4 5 Front Accessible USB 2 0 Headers USB 6 7 Back Panel USB 3 0 Ports USB 8 9 Front...

Page 15: ...GA1151 PCH DDR4 DMI3 DDR4 2133 2133 B 1 B 2 A 2 A 1 PCIe3 0 x4 in x8 PCIe 3 0 x4 in x8 PCI E x4 Gen3 PCI E x4 Gen3 SATA 6 0 Gb S USB 3 0 USB 2 0 USB3 0 USB2 0 TPM Header Debug Card BIOS MUX LPC SPI SP...

Page 16: ...on 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 fields are generated Leave enou...

Page 17: ...tation Setup 17 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...

Page 18: ...n 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 cord from the power supply module 3 2 Accessing the System T...

Page 19: ...n Intel certified multi directional heatsink only When receiving a motherboard without a processor pre installed make sure that the plastic CPU socket cap is in place and none of the socket pins are b...

Page 20: ...r into the Socket Load Lever Load Plate Bottom Edge Top Edge 3 Use your thumb and your index finger to hold the edges of the processor Align the CPU key the semi circle cutouts with the socket keys 4...

Page 21: ...the X11SAE Note You should apply thermal grease to the heatsink if it has not already been pre applied 1 Place the heatsink on top of the CPU so that the four mounting holes are aligned with those on...

Page 22: ...the heatsink screws from the motherboard in the sequence as show in the figure above 2 Hold and gently pivot the heatsink back and forth to loosen it from the CPU Do not use excessive force when disl...

Page 23: ...nk Bracket Figure 3 7 Removing the Heatsink Note Wait for the heatsink to cool down before removing it 4 Clean the surface of the CPU and the heatsink to get rid of the old thermal grease Reapply the...

Page 24: ...he receptive point on the memory slot and the notches on both ends of the module with the receptive points on the slot 3 With your thumbs on both ends of the module press it straight down into the slo...

Page 25: ...DIMMB1 Possible System Memory Allocation Availability System Device Size Physical Memory Remaining with 4GB System Memory Firmware Hub flash memory System BIOS 1 MB 3 99 Local APIC 4 KB 3 99 Area Res...

Page 26: ...board Replacing the Battery Begin by removing power from the system as described in section 3 1 1 Push aside the small clamp that covers the edge of the battery When the battery is released lift it ou...

Page 27: ...escribed in section 3 2 1 To rotate the hard drive cage lift the release tab A as shown in Figure 3 11 2 Rotate the hard disk drive cage B outward Installing Hard Drives to the Hard Drive Cage 1 Press...

Page 28: ...SuperWorkstation 5039A IL User s Manual 28 Figure 3 12 Installing Drives in the Hard Drive Cage Figure 3 11 Rotating the Hard Drive Cage Release Tabs 2 3 1 3 Release Tab A HDD Cage B 2...

Page 29: ...each hard drive carrier may be secured to the exterior of the hard drive cage using one optional screw 6 Rotate the hard drive cage 90 degrees inward returning it to the closed operational position i...

Page 30: ...move the hard drive from the hard drive carrier 7 Insert the new hard drive into the hard drive carrier 8 Insert the hard drive carrier into the hard drive cage sliding it towards the back of the the...

Page 31: ...evice 1 Remove the front bezel from the chassis by lifting it upwards from the bottom and pulling off the front of the chassis 2 Remove the cover plate from the 3 5 device slot on the front of the cha...

Page 32: ...er supply fan fails the power supply itself must be replaced Installing the Rear Exhaust Fan Begin by removing power from the system as described in section 3 1 and remove the chassis cover as describ...

Page 33: ...ough the front fan bracket and into the mounting holes in the front fan 2 Pull the rubber pins through the mounting holes of the system fan to secure the fan to the chassis 3 Lower the fan into the ch...

Page 34: ...cribed in section 3 2 1 Disconnect the cables from the serverboard to the power supply 2 Remove the screws securing the power supply to the chassis which are located on the rear of the chassis Set the...

Page 35: ...included with the power supply 24 pin Primary ATX Power JPW1 8 pin Processor Power JPW2 Main ATX Power Connector The primary power connector JPW1 meets the ATX SSI EPS 12V specification You must also...

Page 36: ...finition 1 4 Ground 5 8 12V Processor Power Connector JPW2 must also be connected to the power supply This connector is used to power the processor Fan Header Pin Definitions Pin Definition 1 Ground B...

Page 37: ...nicate with the enclosure management chip in the system SGPIO Header Pin Definitions Pin Definition Pin Definition 1 NC 2 NC 3 Ground 4 Data 5 Load 6 Ground 7 Clock 8 NC Disk On Module Power Connector...

Page 38: ...le TPM Port 80 header is located at JTPM1 to provide TPM support and Port 80 connection Use this header to enhance system performance and data security Onboard Power LED JLED1 An onboard Power LED hea...

Page 39: ...on The Power Button connection is located on pins 1 and 2 of JF1 Momentarily contacting both pins will power on off the system This button can also be configured to function as a suspend button with a...

Page 40: ...le on the right for pin definitions NIC1 NIC2 LAN1 LAN2 The NIC Network Interface Controller LED connection for LAN port 2 and LAN port 1 are located on pins 9 10 and 11 12 of JF1 respectively Attach...

Page 41: ...ons JF1 Pin Definition 13 3 3V Standby 14 HDD Active Data Cables The data cables in the system have been carefully routed to maintain airflow efficiency If you disconnect any of these cables take care...

Page 42: ...includes a total of eight SATA 3 0 ports I SATA0 7 are supported by the Intel C236 Express PCH chip These SATA ports support RAID 0 1 5 and 10 Rear I O Ports Description Description Description 1 USB1...

Page 43: ...HDMI capable display using a single HDMI cable not included DVI D Port A DVI D port is located on the I O backpanel Use this port to connect to a compatible DVI Digital Visual Interface display VESA...

Page 44: ...da_SSRX 14 SuperSpeed Receiver 6 Stda_SSRX 15 Differential Pair 7 GND_DRAIN 16 Ground for Signal Return 8 Stda_SSTX 17 SuperSpeed Transmitter 9 Stda_SSTX 18 Differential Pair Type A USB 10 USB 3 0 Pin...

Page 45: ...ed Connector Pins Jumper Setting 3 2 1 3 2 1 CMOS Clear JBT1 is used to clear CMOS which will also clear any passwords Instead of pins this jumper consists of contact pads to prevent accidentally clea...

Page 46: ...llows you to enable or disable the onboard High Definition audio support The default setting is Enabled LAN1 2 Enable Disable Change the setting of jumper JPL1 and JPL2 to enable or disable the LAN1 a...

Page 47: ...re to disable it Watch Dog Jumper Settings Jumper Setting Definition Pins 1 2 Reset Pins 2 3 NMI Manufacturer Mode Select Close pins 2 and 3 of jumper JPME2 to bypass SPI flash security and force the...

Page 48: ...Onboard Power LED Indicator LED State LED Color Definition Off System off On System on Onboard Standby Power LED Indicator LED State LED Color Definition Off Power supply is off hard switch On Power s...

Page 49: ...SB port on the system Note for older legacy OS s please use a method to slipstream the drivers 3 Select the partition on the drive in which to install Windows 4 Browse the USB folder for the proper dr...

Page 50: ...er option is to go to the Supermicro website at http www supermicro com products Find the product page for your motherboard here where you may download individual drivers and utilities to your hard dr...

Page 51: ...es in local and remote management versions and can be used with Nagios to maximize your system monitoring needs With SuperDoctor 5 Management Server SSM Server you can remotely control power on off an...

Page 52: ...uch as F1 F2 etc Each main BIOS menu option is described in this manual The Main BIOS screen has two main frames The left frame displays all the options that can be configured Grayed out options canno...

Page 53: ...ighlight System Date or System Time using the arrow keys Enter new values using the keyboard Press the Tab key or the arrow keys to move between fields The date must be entered in Day MM DD YYYY forma...

Page 54: ...g may make the system unstable When this occurs revert to the default to the manufacture default settings Boot Feature Quiet Boot Use this feature to select the screen display between the POST message...

Page 55: ...reboot the system from a specified boot device after its initial boot failure The options are Disabled Legacy Boot and EFI Boot Power Configuration Watch Dog Function If enabled the Watch Dog Timer wi...

Page 56: ...cessor Cores Hyper Threading Technology Intel VT x Technology Intel SMX Technology 64 bit EIST Technology CPU C3 State CPU C6 State CPU C7 State L1 Data Cache L1 Code Cache L2 Cache L3 Cache L4 Cache...

Page 57: ...main memory to the L2 cache to improve CPU performance The options are Disabled and Enabled Adjacent Cache Line Prefetch Available when supported by the CPU The CPU prefetches the cache line for 64 by...

Page 58: ...e Ratio Limit Override This increases multiplies 1 clock speed in the CPU core in relation to the bus speed when one CPU core is active Press or on your keyboard to change the value Enter 0 to use the...

Page 59: ...e C State Un Demotion Use this feature to enable or disable the Package C State un demotion The options are Disabled and Enabled C State Pre Wake This feature allows the user to enable or disable the...

Page 60: ...and availability in networking and data sharing The options are Enabled and Disabled Gaussian Mixture Model This feature is to enable or disable the System Agent Gaussian Mixture Model device The opi...

Page 61: ...ocated Dynamic Video Memory Technology DVMT allows dynamic allocation of system memory to be used for video devices to ensure best use of available system memory based on the DVMT 5 0 platform The opt...

Page 62: ...ble or disable the DMI extended synchronization The options are Enabled and Disabled DMI De Emphasis Control Use this feature to configure the De emphasis control on DMI The options are 6dB and 3 5dB...

Page 63: ...ance The options are Auto 128 TLP and 256 TLP SLOT4 Slot Power Limit Value Use this feature to set the upper limit on the power supplied by the PCIE slot Press or on your keyboard to change this value...

Page 64: ...ions are Disabled and Enabled Memory Scrambler Select Enabled to enable memory scrambler support The options are Disabled and Enabled Fast Boot Use this feature to enable or disable fast path through...

Page 65: ...wer Management ASPM level for a PCI E device Select Auto for the system BIOS to automatically set the ASPM level based on the system configuration Select Disabled to disable ASPM support The options a...

Page 66: ...vice that is not compliant with the PCI E standards The options are Disabled and Enabled Port 61h bit 4 Emulation Select Enabled to enable the emulation of Port 61h bit 4 toggling in SMM System Manage...

Page 67: ...ort Model number of drive and capacity Software Preserve Support Information Port 0 Port 7 Spin Up Device On an edge detect from 0 to 1 set this item to allow the PCH to initialize the device The opti...

Page 68: ...t The options are Disabled Legacy and EFI CPU SLOT4 PCI E 3 0 X8 IN X16 OPROM Use this feature to select which firmware type to be loaded for the add on card in this slot The options are Disabled Lega...

Page 69: ...tion 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 Use this option to specify the number...

Page 70: ...ons are Enabled and Disabled Logical Device Settings This item displays the status of a serial part specified by the user Serial Port 2 Change Settings This feature specifies the base I O port address...

Page 71: ...rmware Type Information ME FW SKU Information ME FW Image Re Flash Use this feature to enable or disable the ME Firmware image re flash capability The options are Disabled and Enabled AMT Configuratio...

Page 72: ...e 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 for lon...

Page 73: ...and Enabled COM1 Legacy OS Redirection Resolution Use this feature to select the number of rows and columns used in Console Redirection for legacy OS support The options are 80x24 and 80x25 COM1 Putt...

Page 74: ...its and 8 Bits COM2 Parity A parity bit can be sent along with regular data bits to detect data transmission errors Select Even if the parity bit is set to 0 and the number of 1 s in data bits is even...

Page 75: ...to Bootloader legacy Console Redirection is disabled before booting the OS When set to Always Enable legacy Console Redirection remains enabled when booting the OS The options are Always Enable and Bo...

Page 76: ...ith your data bits The options are None Even Odd Mark and Space COM3 Stop Bits A stop bit indicates the end of a serial data packet Select 1 Stop Bit for standard serial data communication Select 2 St...

Page 77: ...his feature allows the user to specify how the host computer will exchange data with the client computer which is the remote computer used by the user Out of Band Management Port The feature selects a...

Page 78: ...synchronizing multimedia streams providing smooth playback and reducing the dependency on other timestamp calculation devices such as an x86 RDTSC Instruction embedded in the CPU The High Performance...

Page 79: ...Support Intel TXT Trusted Execution Technology helps protect against software based attacks and ensures protection confidentiality and integrity of data stored or created on the system Use this featur...

Page 80: ...number The PBA number is a nine digit number i e 010B00 000 located near the serial number Device Name This item displays the adapter device name Chip Type This item displays the network adapter chips...

Page 81: ...aord to select a value UEFI Driver This item displays the UEFI driver version Adapter PBA This item displays the Processor Bus Adapter PBA model number The PBA number is a nine digit number i e 010B00...

Page 82: ...bled Erasing Settings Erase Event Log If No is selected data stored in the event log will not be erased Select Yes Next Reset data in the event log will be erased upon next system reboot Select Yes Ev...

Page 83: ...plicate event must happen before the MECI counter is incremented This is a numeric value The default value is 1 METW The Multiple Event Time Window METW defines number of minutes must pass between dup...

Page 84: ...s for the system to check for a password at bootup or upon entering the BIOS Setup utility The options are Setup and Always Administrator Password Press Enter to create a new or change an existing Adm...

Page 85: ...ns are Yes and No Save All Secure Boot Variables This feature allows the user to decide if all secure boot variables should be saved Platform Key PK This feature allows the user to configure the setti...

Page 86: ...option prioritizes the order of bootable devices that the system to boot from Press Enter on each entry from top to bottom to select devices If the item above set to Legacy UEFI Dual the following it...

Page 87: ...I devices are boot devices UEFI Boot Order 1 6 7 Save Exit Select the Exit tab from the BIOS setup utility screen to enter the Exit BIOS Setup screen Discard Changes and Exit Select this option to qui...

Page 88: ...t for maximum performance Save As User Defaults To set this feature select Save as User Defaults from the Exit menu and press Enter This enables the user to save any changes to the BIOS setup for futu...

Page 89: ...continue the boot up procedure If a fatal error occurs you should consult with your system manufacturer for possible repairs These fatal errors are usually communicated through a series of audible be...

Page 90: ...support manuals AMI BIOS POST Codes User s Guide When BIOS performs the Power On Self Test it writes checkpoint codes to I O port 0080h If the computer cannot complete the boot process a diagnostic c...

Page 91: ...or assistance Only certified technicians should attempt to install or configure components Read this appendix in its entirety before installing or configuring components in the Supermicro chassis Thes...

Page 92: ...o considere los riesgos de la corriente el ctrica y familiar cese con los procedimientos est ndar de prevenci n de accidentes Al final de cada advertencia encontrar el n mero que le ayudar a encontrar...

Page 93: ...n dient u zich bewust te zijn van de bij een elektrische installatie betrokken risico s en dient u op de hoogte te zijn van de standaard procedures om ongelukken te voorkomen Gebruik de nummers aan he...

Page 94: ...mentaci n Attention Avant de brancher le syst me sur la source d alimentation consulter les directives d installation Circuit Breaker Waarschuwing Raadpleeg de installatie instructies voordat u het sy...

Page 95: ...del edificio Aseg rese de que el dispositivo de protecci n no sea superior a 250 V 20 A Attention Pour ce qui est de la protection contre les courts circuits surtension ce produit d pend de l install...

Page 96: ...e energ a y del cable el ctrico quitado de los m dulos de fuente de alimentaci n antes de tener acceso el interior del chasis para instalar o para quitar componentes de sistema Attention Le syst me do...

Page 97: ...els aangesloten op de voeding en van de behuizing te verwijderen Equipment Installation Warning Only trained and qualified personnel should be allowed to install replace or service this equipment Warn...

Page 98: ...tention Il est vivement recommand de confier l installation le remplacement et la maintenance de ces quipements des personnels qualifi s et exp riment s Warning This unit is intended for installation...

Page 99: ...una de estas reas mediante la utilizaci n de una herramienta especial cerradura con llave u otro medio de seguridad Attention Cet appareil doit tre install e dans des zones d acc s r serv s L acc s u...

Page 100: ...emblable ou quivalent recommand e par le fabricant Jeter les piles usag es conform ment aux instructions du fabricant Advertencia Existe peligro de explosi n si la bater a se reemplaza de manera incor...

Page 101: ...anbevolen wordt Gebruikte batterijen dienen overeenkomstig fabrieksvoorschriften afgevoerd te worden Redundant Power Supplies Warning This unit might have more than one power supply connection All con...

Page 102: ...omloos te maken Advertencia Puede que esta unidad tenga m s de una conexi n para fuentes de alimentaci n Para cortar por completo el suministro de energ a deben desconectarse todas las conexiones Atte...

Page 103: ...ertencia Cuando el sistema est en funcionamiento el voltaje del plano trasero es peligroso Tenga cuidado cuando lo revise Attention Lorsque le syst me est en fonctionnement des tensions lectriques cir...

Page 104: ...cumplir con las normas de electricidad locales y nacionales Backplane Waarschuwing Een gevaarlijke spanning of energie is aanwezig op de backplane wanneer het systeem in gebruik is Voorzichtigheid is...

Page 105: ...e elektriciteitsvoorschriften Warnung Die Entsorgung dieses Produkts sollte gem allen Bestimmungen und Gesetzen des Landes erfolgen Warning Ultimate disposal of this product should be handled accordin...

Page 106: ...recyclage de ce produit sont g n ralement soumis des lois et ou directives de respect de l environnement Renseignez vous aupr s de l organisme comp tent Hot Swap Fan Warning Warning Hazardous moving...

Page 107: ...tornilladores y todos los objetos lejos de las aberturas del ventilador Attention Pieces mobiles dangereuses Se tenir a l ecart des lames du ventilateur Il est possible que les ventilateurs soient tou...

Page 108: ...nnzeichnet an Ger ten oder Produkten die nicht mit Supermicro gekennzeichnet sind AC AC UL CSA UL CSE Supermicro Supermicro UL CSA UL CSA Supermicro UL CSA UL CSA Warning When installing the product u...

Page 109: ...le code pour tous les autres appareils lectriques sauf les produits d sign s par Supermicro seulement AC AC UL CSA UL CSA Supermicro UL CSA UL CSA Supermicro Advertencia Cuando instale el producto uti...

Page 110: ...Aansluitmethode deze moet altijd voldoen aan de lokale voorschriften en veiligheidsnormen inclusief de juiste kabeldikte en stekker Het gebruik van niet geschikte Kabels en of Adapters kan een storin...

Page 111: ...s for 3 5 SATA drives PCI Expansion Slots One PCI Express 3 0 x16 slot may support two PCI E 3 0 x8 cards Three PCI Express 3 0 x1 slots Two PCI 33MHz slots One M 2 slot 32Mb s Motherboard X11SAE ATX...

Page 112: ...N 61000 4 5 EN 61000 4 6 EN 61000 4 8 EN 61000 4 11 Safety CSA EN IEC UL 60950 1 Compliant UL or CSA Listed USA and Canada CE Marking Europe Perchlorate Warning California Best Management Practices Re...

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