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Chapter 3: Maintenance and Component Installation

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) to use these ports.

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

Summary of Contents for SUPERSERVER 5039MC-H12TRF

Page 1: ...USER S MANUAL Revision 1 0 SuperServer 5039MC H12TRF...

Page 2: ...pment 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 manua...

Page 3: ...user s manual for your server Supermicro product manuals http www supermicro com support manuals Product drivers and utilities https www supermicro com wftp driver Product safety info http www superm...

Page 4: ...ng a Setup Location 16 Rack Precautions 16 Server Precautions 17 Rack Mounting Considerations 17 Ambient Operating Temperature 17 Airflow 17 Mechanical Loading 17 Circuit Overloading 17 Reliable Groun...

Page 5: ...ud 39 Power Supply 40 Chapter 4 Motherboard Connections 4 1 Node Front Panel Controls 41 4 2 Headers and Connectors 41 4 3 Ports 42 4 4 Jumpers 43 4 5 LED Indicators 46 Chapter 5 Software 5 1 Microsof...

Page 6: ...ver 5039MC H12TRF User s Manual Appendix A Standardized Warning Statements for AC Systems A 1 About Standardized Warning Statements 85 Appendix B UEFI BIOS Recovery Instructions Appendix C System Spec...

Page 7: ...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 Technical Support rma supermicr...

Page 8: ...d chassis several included parts are listed below Main Parts List Description Part Number Quantity Backplane BPN SAS 939HS 1 Fans FAN 0149L4 4 CPU passisve heatsink SNK P0047PSR 1 per node Air shroud...

Page 9: ...der stress simultaneously The thermal throttle is normal when Intel Turbo Boost Technology is active Socket Type LGA1151 Memory Up to 128GB of unbuffered ECC Very Low Profile VLP DIMM with speeds of u...

Page 10: ...ng the button will alternately power on or remove power from the node See the table below for the LED indications Node LED Power Button LEDs LED Description Status Power Button LED Power LED Solid Gre...

Page 11: ...res The SC939HC 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 managemen...

Page 12: ...12 SuperServer 5039MC H12TRF User s Manual Figure 1 4 Chassis Rear View Rear Features The illustration below shows the features included on the rear of the chassis Exhaust Fans 4 Power Plugs 2...

Page 13: ...for testing only Use only the correct type of onboard CMOS battery as specified by the manufacturer Do not install the onboard battery upside down to avoid possible explosion J25 BMC_HB_LED1 A C JTPM1...

Page 14: ...ve SATA 3 0 ports via the backplane one SATA 3 0 port via the right angle receptor connector J22 Connector for AOM BPN MC12S Backplane J25 M 2 PCI E 3 0 x4 slot M Key 2280 22110 with SATA3 support JKV...

Page 15: ...8211FS VGA AST2500 PCIe3 0_x1 8 0GT s PCIe x8 MLP SLOT 1 X SATA III DOM Port 19 USB3 5 2 X USB 2 0 MLP USB2 0 480Mbps USB2 5 Port 13 Port 14 2666MHz DDR4 CHA DDR4 CHB 2666MHz DIMMA0 DIMMB0 DIMMA1 DIMM...

Page 16: ...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 sufficient space for airflow and access when servicing This...

Page 17: ...ature 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 b...

Page 18: ...s 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 fil...

Page 19: ...ich indicates the end that attaches to the front of the rack 4 Slide the rails apart far enough to match the depth of the rack Position the rails with the template and secure the front of each to the...

Page 20: ...e of each handle Note These handles need only be installed when mounting the system into a short rack When mounting into a deep rack they are unnecessary and regular screws should be used instead of t...

Page 21: ...rd The rack stabilizing mechanism must be in place or the rack must be bolted to the floor before you slide the unit out for servicing Failure to stabilize the rack can cause the rack to tip over Note...

Page 22: ...e 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 no...

Page 23: ...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 cha...

Page 24: ...alling 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 handl...

Page 25: ...nent Installation 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 to use these ports Figure 3 3 Adapter t...

Page 26: ...alled 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...

Page 27: ...essor 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 t...

Page 28: ...e 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 u...

Page 29: ...ired 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...

Page 30: ...he proper amount of thermal grease to the surface before you re install the heatsink Memory Installation Memory Support The X11SCE F supports up to 128GB of ECC Very Low Profile VLP DIMM with speeds o...

Page 31: ...in the following order DIMMB2 DIMMA2 then DIMMB1 DIMMA1 The blue slots must be populated first Note Be sure to use memory modules of the same type and speed on the motherboard Mixing of memory module...

Page 32: ...h ends of the module press it straight down into the slot until the module snaps into place 4 Press the release tabs to the locked position to secure the DIMM module into the slot 5 Repeat the procedu...

Page 33: ...110 Two NVMe U 2 PCI E x4 slots via the backplane 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 slo...

Page 34: ...tery 1 Remove power from the system as described in section 3 1 and remove the node from the chassis 2 Push aside the small clamp that covers the edge of the battery When the battery is released lift...

Page 35: ...ch node tray Installing Hard Drives 1 Power down the node and remove it from the chassis following the procedure in Section 3 2 2 Insert the hard drive with the printed circuit board side facing downw...

Page 36: ...se level hard disk drives are recommended for use in Supermicro chassis and servers For information on recommended HDDs visit the Supermicro website at http www supermicro com products nfo storage cfm...

Page 37: ...w By default there is one fan zone for the entire system This may be changed to two fan zones by opening jumper JP37 on the BPN SAS 939HS The figure below shows the two fan zone configuration Correspo...

Page 38: ...ed and no need to remove any other parts inside the chassis Replacing a Fan 1 Visually inspect the fans to see which one has failed 2 Push both release tabs on the fan inward 3 Remove the fan from the...

Page 39: ...roud does not require screws to set up Installing the Air Shroud 1 Remove the node from the chassis onto a flat non conductive surface 2 If necessary move any cables that interfere with the air shroud...

Page 40: ...120v or 180 240v An amber light will be illuminated on the power supply when the power is off An illuminated green light indicates that the power supply is operating Changing the Power Supply 1 With t...

Page 41: ...cated next to the UID switch When you press the UID switch the UID LED will be turned on Press the UID switch again to turn off the LED indicator The UID Indicator provides easy identification of a sy...

Page 42: ...d 4 3 Ports I SATA 3 0 Ports The X11SCE F has five I SATA 3 0 ports via the backplane one on the motherboard to support M 2 connector These SATA ports are supported by the Intel C246 PCH chipset I SAT...

Page 43: ...a system unit that may be in need of service Note UID can also be triggered via IPMI on the motherboard For more information on IPMI please refer to the IPMI User s Guide posted on our website at http...

Page 44: ...Do not use the PW_ON connector to clear CMOS JBT1 contact pads Management Engine ME Recovery Use jumper JPME1 to select ME Firmware Recovery mode which will limit resource allocation for essential sys...

Page 45: ...Dog is a monitor that can reboot the system when a software application hangs Jumping pins 1 2 will cause Watch Dog to reset the system if an application hangs Jumping pins 2 3 will generate a non mas...

Page 46: ...nctioning normal Refer to the table below for more information BMC Heartbeat LED Indicator LED Color Definition Green Blinking BMC Normal Overheat Fan Fail LED An Overheat and Fan Fail LED is located...

Page 47: ...upermicro com support manuals Installing the OS 1 Create a method to access the MS Windows installation ISO file That might be a DVD perhaps using an external USB SATA DVD drive or a USB flash drive o...

Page 48: ...load the driver browse the USB flash drive for the proper driver files For RAID choose the SATA sSATA RAID driver indicated then choose the storage drive on which you want to install it For non RAID c...

Page 49: ...Another option is to go to the Supermicro website at http www supermicro com products Find the product page for your motherboard and Download the Latest Drivers and Utilities Insert the flash drive or...

Page 50: ...anagement 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...

Page 51: ...Multi node information and the system information can be displayed at the same time In IPMI Web GUI view information can be displayed by clicking the Multi Node tab under the Server Health drop down...

Page 52: ...d such 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 ca...

Page 53: ...tem Time System Date You can edit this field to change the system time and date Highlight System Time or System Date using the Arrow keys Enter new values through the keyboard Press the Tab key or the...

Page 54: ...gs Use the arrow keys to select Boot Setup and press Enter to access the submenu items Boot Feature Quiet Boot Use this feature to select the screen display between the POST messages and the OEM logo...

Page 55: ...as bootable devices at bootup The options are Immediate and Postponed Re try Boot If this item is enabled the BIOS will automatically reboot the system from a specified boot device after its initial...

Page 56: ...Select Last State to allow the system to resume its last power state before a power loss The options are Power On Stay Off and Last State CPU Configuration The following CPU information will display...

Page 57: ...to Enabled the hardware prefetcher will prefetch streams of data and instructions from the main memory to the L2 cache to improve CPU performance The options are Disabled and Enabled Adjacent Cache Li...

Page 58: ...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 manufacture default setting 2 Core Ratio Limit Override...

Page 59: ...allows the user to enable or disable the C State Pre Wake The options are Disabled and Enabled Package C State Limit Use this feature to set the Package C State limit The options are C0 C1 C2 C3 C6 C...

Page 60: ...ns SGX EPOCH mode Each mode has different values which can be entered manually The options are No Change in Owner EPOCHs Change to New Random Owner EPOCHs and Manual User Defined Owner EPOCHs PRMRR Si...

Page 61: ...form factor SFF computer The options are Enabled and Disabled PM Support Use this item to enable the IGFX Power Management function The options are Enabled and Disabled PAVP Enable Use this feature to...

Page 62: ...d 256 TLP PEG0 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 The default setting is 75 PEG0 Slot...

Page 63: ...25 GB and 3 5 GB Energy Performance Gain Use this feature to enable or disable the energy performance gain The options are Disabled and Enabled Memory Scrambler Select Enabled to enable memory scrambl...

Page 64: ...Enabled and Disabled SATA Mode Selection Use this item to select the mode for the installed SATA drives The options are AHCI and RAID SATA Frozen Use this item to enable the HDD Security Frozen Mode T...

Page 65: ...ding Select Enabled to decode a PCI device that supports 64 bit in the space above 4G Address The options are Enabled and Disabled SR IOV Support Use this feature to enable or disable Single Root IO V...

Page 66: ...nboard serial port The options are Enabled and Disabled Logical Device Settings This item displays the status of a serial part specified by the user Serial Port 1 Change Settings This feature specifie...

Page 67: ...4 5 6 7 9 10 11 12 Intel Server Platform Services The following Intel Server Platform Services information will display ME BIOS Interface Version SPS Version ME FW Status Value ME FW State ME FW Oper...

Page 68: ...ions are 7 Bits and 8 Bits COM1 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...

Page 69: ...lways Enable legacy console redirection remains enabled when booting the OS The options are Always Enable and Bootloader SOL Console Redirection Select Enabled to use the SOL port for Console Redirect...

Page 70: ...top Bits if slower devices are used The options are 1 and 2 SOL Flow Control Use this feature to set the flow control for Console Redirection to prevent data loss caused by buffer overflow Send a Stop...

Page 71: ...ment Services EMS to communicate with a remote host server The options are COM1 and SOL COM2 Terminal Type Use this feature to select the target terminal emulation type for Console Redirection Select...

Page 72: ...nd Enabled Trusted Computing Configuration Security Device Support If this feature and the TPM jumper on the motherboard are both set to Enabled onbaord security devices will be enabled for TPM Truste...

Page 73: ...supported by all operating systems The options are Sha 1 and Sha256 Device Select Use this feature to select the TPM version TPM 1 2 will restrict support to TPM 1 2 devices TPM 2 0 will restrict sup...

Page 74: ...s item to enable or disable all features of the SMBIOS Event Logging during system boot The options are Enabled and Disabled Erasing Settings Erase Event Log If No is selected data stored in the event...

Page 75: ...d MECI The Multiple Event Count Increment MECI counter counts the number of occurences that a duplicate event must happen before the MECI counter is incremented This is a numeric value The default val...

Page 76: ...the IPMI firmware installed in your system System Event Log Enabling Disabling Options SEL Components Select Enabled for all system event logging at bootup The options are Enabled and Disabled Erasing...

Page 77: ...r to select the source of the IP address for this computer If Static is selected you will need to know the IP address of this computer and enter it to the system manually in the field If DHCP is selec...

Page 78: ...ion The options are Disable and Enable 6 6 Security This menu allows the user to configure the following security settings for the system Password Check Select Setup for the system to check for a pass...

Page 79: ...nagement This submenu allows the user to configure the following Key Management settings Provision Factory Default Keys Select Enabled to install the default Secure Boot keys set by the manufacturer T...

Page 80: ...atabase from the manufacturer s defaults to the existing DB Select No to load the DB from a file The options are Yes and No Forbiden Signatures Set New Key Select Yes to load the DBX from the manufact...

Page 81: ...s 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 i...

Page 82: ...oot device from which the system will boot during startup The settings are any pre defined boot device Hard Disk Drive BBS Priorities This feature allows the user to specify which hard disk drive devi...

Page 83: ...ave Changes and Reset When you have completed the system configuration changes select this option to leave the BIOS setup utility and reboot the computer so the new system configuration parameters can...

Page 84: ...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 future use Restore User Defaults To set this feature select Rest...

Page 85: ...for 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 Th...

Page 86: ...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 87: ...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 88: ...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 89: ...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 90: ...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 91: ...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 92: ...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 93: ...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 94: ...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 95: ...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 c...

Page 96: ...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 97: ...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 98: ...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 99: ...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 100: ...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 101: ...destornilladores 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...

Page 102: ...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 103: ...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 104: ...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 105: ...off control to a computer system at bootup B 2 How to Recover the UEFI BIOS Image the Main BIOS Block A UEFI BIOS flash chip consists of a recovery BIOS block and a main BIOS block a main BIOS image T...

Page 106: ...our website at www supermicro com to download the BIOS image into a USB flash device and rename it Super ROM for BIOS recovery use 2 Insert the USB device that contains the new BIOS image Super ROM in...

Page 107: ...want to start with BIOS recovery If you decide to proceed with BIOS recovery follow the procedures below 5 When the screen as shown above displays using the arrow key select the item Proceed with flas...

Page 108: ...prompt Note Do not interrupt this process until BIOS flashing is completed 9 After seeing the message that BIOS update is completed unplug the AC power cable from the power supply to clear the CMOS a...

Page 109: ...Intel PCH C246 chipset BIOS 128 Mb UEFI Memory Four DIMM slots that can support up to 128 GB of ECC Very Low Profile VLP 2666 MHz SATA Controller On chip Intel PCH C246 controller Drive Bays Internal...

Page 110: ...ve Humidity 8 to 90 non condensing Non operating Relative Humidity 5 to 95 non condensing Regulatory Compliance Electromagnetic Emissions FCC Class A EN 55022 Class A EN 61000 3 2 3 3 CISPR 22 Class A...

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