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27

Chapter 3: Maintenance and Component Installation

3.4 Chassis Components

Storage Drives

Primary data storage capability is provided by up to four 3.5" drives that can be installed in 
the chassis. To replace or install them, the drive cage must be rotated. 

Rotating the Drive Cage

1. Remove power from the system as described in section 3.1 and remove the chassis 

cover.

2. Lift the release tab (A) as shown below.

3. Rotate the drive cage outward.

Note:

 Enterprise level drives are recommended for use in Supermicro servers. For information 

on recommended drives, visit the Supermicro website at 

http://www.supermicro.com/products/

nfo/storage.cfm

.

Figure 3-5. Rotating the Drive Cage

3

Release Tab (A)

Drive Cage

2

Summary of Contents for SuperWorkstation 5039C-T

Page 1: ...USER S MANUAL Revision 1 0 SuperWorkstation 5039C T...

Page 2: ...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...

Page 3: ...lities 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 superm...

Page 4: ...Setup 16 Choosing a Setup Location 16 General Precautions 16 Chapter 3 Maintenance and Component Installation 3 1 Removing Power 17 3 2 Accessing the System 17 3 3 Motherboard Components 19 Processor...

Page 5: ...ar I O Ports 44 4 4 Jumpers 46 4 5 LED Indicators 48 4 6 Storage Ports 48 Chapter 5 Software 5 1 OS Installation 49 5 2 Driver Installation 50 5 3 SuperDoctor 5 51 Chapter 6 BIOS 6 1 Introduction 52 S...

Page 6: ...Europe Address 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 superm...

Page 7: ...ed below Main Parts List Description Part Number Quantity Power supply PWS 502 PQ 1 Fans FAN 0124L4 1 standard 1 optional Optional Active CPU heatsink SNK P0051AP4 1 Optional 2 5 to 3 5 SSD HDD adapte...

Page 8: ...vertical socket for WIFI Bluetooth Storage Drives Four 3 5 internal drive bays Optional Four 2 5 internal drive bays One U 2 connector shared with M 2 M key 2 via PCH Two M 2 M key 2260 2280 22110 Pow...

Page 9: ...power on or off to the workstation from the power supply but maintains standby power 2 NIC LED Indicates network activity on the LAN port when flashing 3 HDD LED Indicates activity on a hard drive whe...

Page 10: ...peripheral 5 25 drives such as a DVD 2 Control Panel Front control panel see preceding page 3 USB Two USB 2 0 ports 4 USB Two USB 3 1 Gen 1 ports 5 Line Out Headphone jack 6 Mic Microphone jack 7 Int...

Page 11: ...scription 1 Power Supply Fixed module 2 I O Backpanel Rear input output ports see Section 4 3 and figure below 3 PCI E Slots Supports four full height full length PCI E expansion cards Figure 1 3 Chas...

Page 12: ...X16 PCH SLOT2 PCI E 3 0 X4 PCH SLOT7 PCI E 3 0 X1 SLOT1 PCI 33MHZ JWD1 JTBT1 CPU PCI E_M 2 M2 PCI E_M 2 M1 I SATA5 I SATA3 I SATA1 CMOS CLEAR I SATA4 I SATA2 I SATA0 I SATA7 I SATA6 U 2 1 USB4 5 3 0 U...

Page 13: ...rt DVI Digital Video Interface CPU_FAN1 2 CPU Fan Headers SYS_FAN1 3 System Fan Headers HD AUDIO Back Panel HD Audio Connectors HDMI Back Panel HDMI port I SATA0 I SATA7 SATA 3 0 Connectors via Intel...

Page 14: ...Ports USB 4 5 Front Accessible USB 2 0 Header USB 6 7 Back Panel USB 3 1 Gen 2 Ports USB6 Type C USB7 Type A USB 8 Front Accessible USB 3 1 Gen 2 Type C Header USB 9 Front Accessible USB 3 1 Gen 2 Ty...

Page 15: ...HDMI 2 0a DVI D Digital port 1 PCIe x1 SLOT 7 RJ45 GLAN1 I219LM RJ45 GLAN2 I210 AT ASM1480 PCHPE3 P21 P24 PCIe x4 SLOT 2 ASM1480 U 2 connector M 2 M KEY 2 M 2 M KEY 1 PERICOM PI3EQX1004 ASM1543 USB3...

Page 16: ...e situated in a clean dust free area that is well ventilated Avoid areas where heat electrical noise and electromagnetic fields are generated Leave enough clearance in front and back of the system to...

Page 17: ...ot 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...

Page 18: ...18 Figure 3 1 Removing the Chassis Covers Caution Except for short periods of time do not operate the workstation without the cover in place The chassis cover must be in place to allow for proper airf...

Page 19: ...oard 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 Install the the p...

Page 20: ...ap 3 Use your thumb and your index finger to hold the CPU at the North center edge and the South center edge of the CPU 4 Align the CPU key that is the semi circle cutouts against the socket keys Once...

Page 21: ...t may damage your CPU Instead open the load plate again and double check that the CPU is aligned properly CPU properly installed Load lever locked into place 5 Do not rub the CPU against the surface o...

Page 22: ...om the system 2 Place the heatsink on top of the CPU so that the four mounting screws on the heatsink are aligned with holes on the socket 3 Tighten the screws in the order noted below evenly and grad...

Page 23: ...ever if you must remove the heatsink follow the instructions below to avoid damage 1 Remove power from the system as described in Section 3 1 2 Disconnect the heatsink fan wires from the CPU fan heade...

Page 24: ...delines Regarding Mixing DIMMs Populating slots with a pair of DIMM modules of the same type and size results in inter leaved memory which improves memory performance Use memory modules of the same ty...

Page 25: ...3 Align one end of the DIMM module to the receptive point on the stationary end of the slot and the other end of the DIMM to the locking end of the slot 4 Press down on the stationary end of the slot...

Page 26: ...1 Remove power from the system as described in section 3 1 and remove the left cover from the chassis 2 Push aside the small clamp that covers the edge of the battery When the battery is released lif...

Page 27: ...tated Rotating the Drive Cage 1 Remove power from the system as described in section 3 1 and remove the chassis cover 2 Lift the release tab A as shown below 3 Rotate the drive cage outward Note Enter...

Page 28: ...he drive carrier and slide the carrier out of the drive cage Figure 3 6 Installing Drives in the Primary Drive Cage 2 3 3 3 If you are replacing a drive remove the drive from the carrier by pulling th...

Page 29: ...3 1 and remove the chassis cover 2 Loosen the thumb screw securing the drive cage to the chassis 3 Slide the drive cage out of the chassis If you are replacing a drive unplug the power and data cables...

Page 30: ...ing a drive remove the drive from the carrier by pulling the sides of the carrier outwards 6 Insert a new drive into a drive carrier by snapping it in 7 Slide the drive assembly into the drive cage un...

Page 31: ...e the following figure for that location COM1 JBT1 B3 USB0 1 2 0 JPAC1 JPME2 JF1 JLED1 CPU SLOT6 PCI E 3 0 X16 PCH SLOT2 PCI E 3 0 X4 PCH SLOT7 PCI E 3 0 X1 SLOT1 PCI 33MHZ JWD1 JTBT1 CPU PCI E_M 2 M2...

Page 32: ...tion Components 1 Remove power from the system as described in section 3 1 and remove the chassis cover 2 The black plastic holder section A should be snapped into the motherboard Prepare the holder I...

Page 33: ...ection 3 1 2 Remove the front bezel from the chassis by lifting it upwards from the bottom and pulling off the front of the chassis 3 Remove the cover plate from the bezel 4 Install the bracket rail A...

Page 34: ...are required for installation Installing the Rear Fan 1 Remove power from the system as described in section 3 1 and remove the left chassis cover 2 Insert the four rubber pins into the four mounting...

Page 35: ...he fan 3 Pull the rubber pins through the mounting holes of the fan to secure the fan to the bracket 4 Lower the fan into the chassis aligning the tabs on the bottom of the bracket with tabs in the ch...

Page 36: ...ther devices to the power supply 3 Remove the screws securing the power supply to the chassis which are located on the rear of the chassis Save the screws for later use 4 Lift the power supply out of...

Page 37: ...nstalling PCI E Expansion Cards Begin by removing power from the system as described in section 3 1 1 Remove power from the system as described in section 3 1 and remove the left chassis cover 2 Remov...

Page 38: ...ower connections supply the motherboard and several more supply for onboard devices Main Power Connector The primary power supply connector JPW1 meets the ATX SSI EPS 12V specification Important To pr...

Page 39: ...JPW2 must also be connected to the power supply This connector is used to power the processor s 12V 8 pin Power Pin Definitions Pin Definition 1 4 Ground 5 8 12V Required Connection Speaker Buzzer Hea...

Page 40: ...ns Pin Definition Pin Definition 1 NC 2 NC 3 GND 4 Data 5 Load 6 GND 7 Clock 8 NC NC No Connection I SGPIO 1 2 I SGPIO1 I SATA 3 0 Ports 0 3 I SGPIO2 I SATA 3 0 Ports 4 7 Standby Power The 5V Standby...

Page 41: ...wo M 2 solid state drives M 2 replaces mini PCI E and mSATA It allows for a greater variety of card sizes increased functionality and spatial efficiency The M 2 sockets support 3 0 x4 32 Gb s card in...

Page 42: ...ound Key Power On LED Control signal HDD LED Activity signal NIC1 LED Ground NIC2 LED Ground OH Fan Fail LED Ground Power Fail LED Ground Ground Ground 2 1 20 19 Power Button Pin Definitions JF1 Pin D...

Page 43: ...LED 8 OH Fan Fail LED LAN1 LAN2 LED Pin Definitions JF1 Pin Definition 9 NIC2 Activity LED 10 NIC2 Link LED 11 NIC1 Activity LED 12 NIC1 Link LED NIC1 NIC2 LAN1 LAN2 The NIC Network Interface Control...

Page 44: ...and 20 of JF1 NMI Button Pin Definitions JF1 Pin Definition 19 Control 20 Ground 4 3 Input Output Ports Rear I O Ports Figure 4 2 Rear I O Ports Rear I O Ports Description Description Description Desc...

Page 45: ...bit Ethernet ports each with two LEDs showing activity and speed See Section 4 5 for details USB Ports There are two USB 3 1 Gen 1 ports USB2 3 and two USB 3 1 Gen 2 ports USB6 7 CEN LFE Out and Surro...

Page 46: ...d 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 clear...

Page 47: ...ngs Jumping pins 2 3 will generate a non maskable interrupt signal for the application that hangs Watch Dog must also be enabled in BIOS The default setting is Reset Note When Watch Dog is enabled the...

Page 48: ...ported by the Intel C246 PCH chip are located on the motherboard They support RAID 0 1 5 and 10 Note For more information on the SATA HostRAID configuration refer to the Intel SATA HostRAID user s gui...

Page 49: ...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 driver files...

Page 50: ...pear Another 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 yo...

Page 51: ...ent Protocol SNMP SuperDoctor 5 comes 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 c...

Page 52: ...eft frame displays options can be configured by the user These are blue When an option is selected it is highlighted in white Settings printed in Bold are the default values In the left frame a indica...

Page 53: ...n to change the system date and time Highlight 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 m...

Page 54: ...ure default settings Boot Feature Fast Boot This feature enables the system to boot with a minimal set of required devices to launch This has no effect on BBS boot options The options are Disabled or...

Page 55: ...w the system to resume its last power state before a power loss The options are Stay Off Power On and Last State Power Button Function This feature controls how the system shuts down when the power bu...

Page 56: ...he L2 cache to improve CPU performance The options are Disabled or Enabled Adjacent Cache Line Prefetch Select Enabled for the CPU to prefetch both cache lines for 128 bytes as comprised Select Disabl...

Page 57: ...EMTTM is also enabled The options are Disabled or Enabled Package Power Limit MSR Lock This feature enables Package Power Limit locking If this is enabled a reset will be required to unlock the regist...

Page 58: ...When this feature is enabled the CPU will conditionally undemote from demoted Packaged Package C State Un Demotion The options are Disabled or Enabled CState Pre Wake Use this feature to enable the C...

Page 59: ...led 1 Enabled WARM HOT and 2 Enabled HOT Closed Loop Therm Manage This feature enables Closed Loop Thermal management The options are Disabled or Enabled Graphics Configuration Primary Display This fe...

Page 60: ...Disabled or Enabled PAVP Enable This feature enables PAVP support The options are Disabled or Enabled Cdynmax Clamping Enable This feature enables Cdynmax Clamping The options are Disabled or Enabled...

Page 61: ...range is 0 255 The default is 75 SLOT4 Power Limit Scale This feature controls the slot power limit scale The options are 1 0x 0 1x 0 01x and 0 001x Program PCIe ASPM after OpROM This feature enables...

Page 62: ...he options are Disabled or Enabled PCH IO Configuration PCI Express Configuration DMI Link ASPM Control This feature enables the control of Active State Power Management ASPM on the SA side of the DMI...

Page 63: ...C This feature enables Downstream Port Containment DPC The options are Disabled or Enabled EDPC This feature enables rootport Extension for Downstream Port Containment The options are Disabled or Enab...

Page 64: ...d 0 0 2 0 in 0 1 increments NCT6796D Super IO Configuration Serial Port 1 Configuration Serial Port 1 This feature will enable Serial Port 1 COM1 Click to check the box to enable Serial Port 1 The def...

Page 65: ...A lower transmission speed may be required for long and busy lines The options are 9600 19200 38400 57600 and 115200 bits per second COM1 Data Bits Use this feature to set the data transmission size...

Page 66: ...which is a terminal emulator designed for the Windows OS The options are VT100 LINUX XTERMR6 SCO ESCN and VT400 COM1 Redirection After BIOS POST Use this feature to enable or disable legacy Console R...

Page 67: ...mark as a parity bit to be sent along with the data bits Select Space to add a Space as a parity bit to be sent with your data bits The options are None Even Odd Mark and Space SOL Stop Bits A stop b...

Page 68: ...d Checked Enabled If the item above set to Enabled the following items will become available for configuration AMT SOL Console Redirection Settings AMT SOL Terminal Type This feature allows the user t...

Page 69: ...ed Disabled or Checked Enabled AMT SOL Recorder Mode Select Enabled to capture the data displayed on a terminal and send it as text messages to a remote server The options are Unchecked Disabled or Ch...

Page 70: ...d ASCII Character Set Select VT UTF8 to use UTF8 encoding to map Unicode characters into one or more bytes The options are ANSI VT100 VT100 and VT UTF8 EMS Bits per second Use this feature to set the...

Page 71: ...s option is enabled it will perform Staggered Spin Up on any drive this option is activated The settings are Disabled or Enabled SATA Device Type Use this feature to identify the type of HDD that is c...

Page 72: ...ts in order to provide advanced warning of possible system failures The options are Disabled or Enabled WatchDog This feature enables the WatchDog Timer The options are Disabled or Enabled OS Timer If...

Page 73: ...sets the MEBx password to its default The options are Unchecked Disabled or Checked Enabled MEBx Resolution Settings Non UI Mode Resolution This feature controls the resolution for non UI text mode Th...

Page 74: ...led PCIe PCI PnP Configuration Video This feature controls which option ROM to execute for the Video device The options are Do Not Launch UEFI and Legacy PCI PERR SERR Support This feature enables PCI...

Page 75: ...Disabled or Enabled If this feature is enabled the two features below are available Ipv4 PXE Support Select Enabled to enable Ipv4 PXE Preboot Execution Environment for boot support If this feature is...

Page 76: ...e Changing the setting will reboot the computer The options are Disabled or Enabled Pending operation This feature schedules an operation for an installed security device Changing the setting will reb...

Page 77: ...elect Yes Next Reset data in the event log will be erased upon next system reboot Select Yes Every Reset data in the event log will be erased upon every system reboot The options are No Yes Next reset...

Page 78: ...a numeric value The default value is 1 METW The Multiple Event Time Window METW defines the number of minutes that must pass between duplicate log events before MECI is incremented This is in minutes...

Page 79: ...ge to configure Security settings Create Administrator and User passwords Using ONLY an Administrator password limits access to BIOS setup Using ONLY a User password will lock unauthorized users from...

Page 80: ...ot mode The options are LEGACY UEFI and DUAL FIXED BOOT ORDER Priorities Use this feature to set the boot order priority The number of boot options shown is dependent on the boot mode selected above D...

Page 81: ...system Save Changes This option will save the changes but will remain in setup mode Discard Changes This option will discard the changes but will remain in setup mode Restore Defaults This option will...

Page 82: ...on 5039C T User s Manual 82 Boot Override IBA CL Slot 00FE v0113 This feature force boots IBA CL Slot 00FE v0113 This will restart the system UEFI Built in EFI Shell This feature force boots the Built...

Page 83: ...orresponding beep codes encountered by users BIOS Error Beep POST Codes Beep Code Error Message Description 1 short Refresh Circuits have been reset Ready to power up 5 short 1 long Memory error No me...

Page 84: ...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 85: ...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 86: ...ken 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...

Page 87: ...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 88: ...tes 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 inst...

Page 89: ...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 90: ...abels 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 Wa...

Page 91: ...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 92: ...a 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...

Page 93: ...mblable 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 incorr...

Page 94: ...aanbevolen wordt Gebruikte batterijen dienen overeenkomstig fabrieksvoorschriften afgevoerd te worden Redundant Power Supplies Warning This unit might have more than one power supply connection All co...

Page 95: ...mloos 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 Atten...

Page 96: ...dvertencia 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 c...

Page 97: ...umplir 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 g...

Page 98: ...ale elektriciteitsvoorschriften Warnung Die Entsorgung dieses Produkts sollte gem allen Bestimmungen und Gesetzen des Landes erfolgen Warning Ultimate disposal of this product should be handled accord...

Page 99: ...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 100: ...estornilladores 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 t...

Page 101: ...UL oder CAS zertifizierten Kabeln mit UL CSA gekennzeichnet an Ger ten oder Produkten die nicht mit Supermicro gekennzeichnet sind AC AC UL CSA UL CSE Supermicro Supermicro UL CSA UL CSA Supermicro U...

Page 102: ...r 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 u...

Page 103: ...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 104: ...2 M key 1 via PCH One PCI E 3 0 x1 via PCH One PCI 32bit 5V One M 2 E key vertical socket for WIFI Bluetooth Motherboard X11SCA ATX form factor 12 x 9 6 30 5cm x 24 4cm Chassis SC732D4 500B Mid size t...

Page 105: ...1 Other VCCI CISPR 32 and AS NZS CISPR 32 Environmental Directive 2011 65 EU and Directive 2012 19 EU Safety CSA EN IEC UL 60950 1 Compliant UL or CSA Listed USA and Canada CE Marking Europe Perchlora...

Page 106: ...p consists of a recovery BIOS block and a main BIOS block a main BIOS image The boot block contains critical BIOS codes including memory detection and recovery codes for the user to flash a new BIOS i...

Page 107: ...large because it contains too many folders and files To perform UEFI BIOS recovery using a USB attached device follow the instructions below 1 Using a different machine copy the Super ROM binary imag...

Page 108: ...e to proceed with BIOS recovery follow the procedures below 4 When the screen shown above displays use the arrow keys to select the item Proceed with flash update and press the Enter key You will see...

Page 109: ...Appendix D UEFI BIOS Recovery 109 5 After the BIOS recovery process is completed press any key to reboot the system...

Page 110: ...sence Condition of the Restricted Substances Marking Equipment name Type designation Type Restricted substances and its chemical symbols Note 1 Exceeding 0 1 wt and exceeding 0 01 wt indicate that the...

Page 111: ...Appendix E 111 100 240VAC 60 50Hz 7 3 5A 150 3...

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