Introduction to Cluster Computing

Transcription

1 Introduction to Cluster Computing

2 Why we need High Performance Computer? Hypothesis Experiment The change in scientific discovery process Hypothesis Experiment Simulation and Modeling

3 Compute-Intensive Applications Simulation and Modeling problems: Based on successive approximations. More calculations, better results Optimization problems Problems that dependent on computations and manipulations of large amounts of data Example Weather Prediction Image and Signal Processing, Graphics Database and Data Mining

4 CFD for Clean room Analyzing behaviour of air flow in clean room for electronics industry Collaboration project Suranaree University of Technology Kasetsart University Funded by NECTEC

5 CFD Software CAMETA version 3.0 (SUT) Time-independent (steady-state) solution Three-dimensional domain Cartesian coordinate system Physical quantities of interest: Temperature distribution Relative humidity distribution Particle concentration distribution

6 Molecular Dynamic Simulation Drug Discovery using molecular docking Avian Flu HIV Analyzing property of Chemical compound

7 SWAP Model Parameter identification - Data Assimilation using RS and GA (KU/AIT) SWAP Input Parameters RS Observation sowing date, soil property, Water management, and etc. SWAP Crop Growth Model Evapotranspiration LAI LAI, Evapotranspiration Day Of Year Assimilation by finding Optimized parameters By GA Eavpotranspiration LAI LAI, Evapotranspiration Fitting Day Of Year RS Model

8 Challenges The calculation time for identify SWAP parameters only for 1 pixel (1 sq.km) takes several minutes to 30 minutes. Thus, a RS image of 1000 x 1000 sq.km of 1000x1000 pixels will take more than 50 years (30min x 1000 x 1000) is not acceptable. Solutions Parallel Computing Longitude: Latitude:

9 Graphics Rendering and Special Effect Rendering Generating 3D image from Model Problem Rendering is a time consuming process especially for complex and realistic scene Massive number of rendering job needed to be done to create a movie 22/08/49 TAM2005 9

10 Top500 Fastest Installed Computers List the top 500 supercomputer at sites worldwide. Provides a snapshot of the SC installed around the world. Began in 1993, published every 6 months. Measures the performance for the TPP Linpack Benchmark Provides a way to measure trends

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14 Parallel Processing Solving large problem by breaking it in to a number of small problems, then solve them on multiple processors at the same time Real life example building a house using many workers working on separate part Assembly line in factory

15 Parallel Processing LARGE SCALE PROBLEM SUB TASK SUB TASK SUB TASK SUB TASK SUB TASK PROCESSOR PROCESSOR PROCESSOR PROCESSOR

16 Parallel Computer Parallel computer is a special computer that is designed for parallel processing Multiple processors High-speed Interconnection network that link these processors together Hardware and software that help coordinate the computing tasks Sometime this tyep of computer are called MPP (Massively Parallel Processor) Computer

17 Compare with SMP

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19 Introduction Cluster computing is a technology related to the building of high performance scalable computing system from a collection of small computing system and high speed interconnection network

20 Applications Scientific computing CAD/CAM Bioinformatics Large scale financial analysis Simulation Drug Design Automobile Design ( Crash Simulation) IT infrastructure Scalable web server, Search engine (Google use more than node servers) Entertainment Rendering On-line Gaming

21 Why? Price Performance!

22 Beowulf Clustering Clustering technology originated from Beowulf Project at NASA Project started by Thomas Sterling and Donald Becker Characteristics of Beowulf Cluster Use PC based hardware and commodity components to gain high performance at low cost Based on Linux OS, and open source software Very popular in high performance scientific computing world, moving quickly toward enterprise uses.

23 Beowulfs!

24 Beowulf Software Architecture HPTC HTC HPC

25 How to use cluster system for your work High Throughput Computing Use cluster as a collection of processors Run sequential applications Using job scheduler to control the execution High Performance Computing Use cluster as a parallel machine Develop parallel application to harness the computing power from the cluster

26 What is needed? Interconnection Network Software Nodes

27 Cluster System Structure Compute Node Interconnection Network Frontend

28 Component Node CPU Memory Motherboard Harddisk Display card Chassis Network Others Accessories KVM Switch UPS

29 CPU Various architecture x86 or x86-64 x86/ia32 Pentium 4, Xeon, Xeon MP, Athlon XP x86-64 Athlon 64, Athlon 64 FX IA64 Itanium 2 Effect to chassis, heat sink, and power supply

30 Heat Sink 2 Types of CPU Box and Tray Box equips with heat sink and fan Tray has only CPU Box is recommended

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32 CPU Performance

33 Memory Speed and bandwidth must be compatible with CPU Pentium 4 - DDR Athlon XP DDR Athlon Opteron Dual Channel DDR Athlon 64 Dual Channel DDR Athlon 64 FX Dual Channel DDR

34 Memory Performance

35 Motherboard Must be compatible with CPU Bus speed Compute node may be use full option motherboard, for example, LAN and VGA on board Advantage for rack system

36 Selected Motherboard Features Wake-on-LAN RAID PXE PCI Slot Onboard VGA Onboard Gigabit Network

37 Network boot Pre-boot Execution Environment Network must provide DHCP and TFTP service After POST, node use DHCP to request IP and boot server After node get its IP, it download OS from boot server via TFTP Advantage: installation via PXE is very convenient or diskless cluster

38 PCI Peripheral Component Interconnect Internal data path Data rate depends on clock speed and number of bits Currently, 33 and 66 MHz with 32 and 64 bit wide 2 Voltage lever 3.3 and 5 V

39 PCI-X Next generation PCI Compatible with PCI 3.3 V 66 MHz PCI-X version 2.0 operates at 266 to 1066 MHz. The data rate is about 2.6 to 8.5 Gb/s

40 Harddisk Store system and user data Various interface IDE or ATA SATA SCSI

41 IDE (Integrated Drive Electronics) So call ATA (AT Attachment) Low cost Ease of installation because very motherboard support 1 Interface can connect up to 2 drive: master and slave Maximum speed 133 MB/s by 80 line connector by Ultra ATA/133 standard Rotation speed: 7,200 RPM, Seek time: 9 ms Size GB (Seagate)

42 SATA Serial ATA A bit more expensive that ATA Higher speed than ATA by 1-5% Transfer speed: 150 MB/s Rotation Speed: 7200 RPM, Seek time about 9 ms Size GB Need new kernel 2.6.2

43 SCSI (Small Computer System Interface) Intelligent device: Can connect various device, for example, Harddisk Scanner CD-ROM/RW Tape drive High cost for high-end system Only server s motherboard supports SCSI, Low cost motherboard needs SCSI adapter 1 Intecface can connect up to 15 devices

44 SCSI (cont d) Rotation speed: RPM, Seek time is about 4.5 ms Various speed. Currently available speed are between 20 MB/s (UltraSCSI) to 320 MB/s (Ultra 320 หร อ Ultra4 SCSI) Capacity GB (Seagate)

45 Harddisk Performance

46 RAID Redundance Array of Independent Disk Increase capacity, speed, and reliable of data Logically merge many hard disk to a big one Both software and hardware Normally, RAID is built over SCSI hard disks RAID various level. The popular is 0, 1 and 5

47 RAID Level Level 0 Stripping Increase capacity and speed. None of the space is wasted as long as the hard drives used are identical Level 1 Mirror increase data reliable via redundancy Level 5 Block level striping and distributed parity. Increase capacity and data reliability

48 RAID Implementation Hardware RAID adapter, for example, Adaptec. Some motherboard has build-in RAID controller Linux supports many hardware RAID vendor, especially Adaptec There is only and logical RAID drive at boot time Software Linux can emulate RAID 0, 1, and 5 Can be done by creating partition with RAID type, then use RAID utility to create RAID drive. The RAID drives are mapped to /dev/md0, /dev/md1, etc.

49 RAID Performance

50 Display Monitor Resolution at least May be LCD or CRT Display Adapter Linux supports most display adapter On-board display adapter is recommended for ease of installation

51 Chassis 3 main types Tower Rack-mount Blade

52 Tower Chassis The most popular 2 size Tower and mini-tower Advantage Low cost, ease of maintenance, installation, and air flow Disadvantage big size and wiring problem in large cluster

53 Rock-Mount Smaller suitable for large cluster Advantage design for rack Disadvantage the smaller, the problem with air flow

54 Blade Rack 1U is small but wiring is still a problem Blade-server is a case that contain one or more hot-swappable device called blade Each blade is a computer that share some equipment such as power supply, network connection

55 System Interconnect Interconnection among nodes is the key to cluster performance Consideration Cost Bandwidth and Latency Scalability of the interconnection Technology used Fast Ethernet (Switch) SCI (Scalable Coherent Interface) Gigabit Ethernet Myrinet Infiniband

56 Performance of MPICH-GM High Performance Linpack HPL Runtime Run time (sec) Myrinet Ethernet Problem Size

57 Interconnection Network At least 1 GB/s Various vendor and standard Gigabit Ethernet Myrinet Infiband

58 Gigabit Ethernet IEEE Gb/s Commodity hardware Connect by switch IEEE 802.3z using Fiber or STP IEEE 802.3ab using CAT 5 UTP PCI 64 internal bus is recommended

59 Gigabit Ethernet Switch Support both layer 2 or layer 3 switch Cluster can use layer 2 switch because routing function is not required For future upgrade, stackable switch is recommended

60 Myrinet Proprietary network Operate at 2+2 Gb/s High scalability On-board communication processor reduce main CPU utilization Support both PCI-X both PCI 64 Fiber

61 Infiniband Infiniband is technology for connecting remote storage and network Create IPC cluster Operate at 2.5 Gb/s with copper or fiber cable

62 Network Performance Data from NetPIPE 3.6

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64 KVM Switch Keyboard Video Mouse Connect multiple nodes to single KVM Very convenient

65 UPS Uninterruptable Power Supply Emergency power source Filter surge current from AC out let, telephone line, and LAN Should be able to notify CPU to shut down the system Load is in VA unit Capacity is specified at batteries

66 Basic Clustering Software Linux (Redhat, Mandrake, Fedora, etc.) Cluster Distribution ROCKS, SCE, OSCAR Management tools and environment SCMS, Ganglia Programming Compilers : PGI, Intel, gcc Parallel Programming PVM, MPI Library PGAPack, Scalapack, PetSC, Linpack Load Scheduler OpenPBS, SGE, SQMS, LSF Package NWCHEM, GAMESS, Fluent, Oracle 10G

67 Cluster Distribution Custom made Linux distribution that can be used to build a cluster Pre-selected set of software Automatic Installation tool or Builder Easy to use but user must follow some guide line Example: Scyld, Oscar, Rocks and SCE

68 NPACI ROCKS National Partnership for Advanced Computational Infrastructure A scalable, complete and fully automated cluster deployment solution with out of the box rational default settings. Developed by San Diego Supercomputer Centre - Grid & Cluster Computing Group UC Berkeley Millennium Project SCS Linux Competency Centre

69 Rocks Philosophy NPACI ROCKS is an entire cluster-aware distribution Full Red Hat release (tracks closely) NPACI ROCKS packages Installation, configuration & management tools Integrated de-facto standard cluster packages PBS/MAUI, MPICH, ATLAS, ScaLAPack, HPL... SGE, PVFS (added by SCS-LCC) Integrated, easy to manage cluster system!

70 Rocks Philosophy Integrated, easy to manage cluster system. Excellent scaling to large number of nodes. Single consistent cluster management methodology. Avoid version skew and maintains consistent image across cluster! Highly skilled and dedicated development team in SDCS, UC Berkeley and SCS- LCC. SUPPORT!

71 Every node is behind main node or frontend Pros Close Cluster Suitable for parallel program because external traffic does not interfere cluster communication within cluster Ease of security Cons If frontend is failure, user cannot access all nodes

72 Summary Cluster is a new dominant platform for HPC Powerful Cost effective A combination of software/hardware is needed to build a cluster Application is the key to harness the power of cluster

73 How to measure your performance standard open-source benchmarking tools HPL (High Performance Linpack) Linpack Stream - memory benchmark Bonnie++ - I/O benchmark IOZone - Intensive I/O benchmark IPerf - network performance snapshot NetPipe - intensive bandwidth test

74 HPL (High Performance Linpack) and Linpack HPL a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. a standard benchmark tool for Cluster computer, used at top500.org Performance reported in Flops (Floating-point operation per second) Rely on MPI (Message-Passing Interface) More info. on Linpack Old implementation of Linpack, used to determined single node performance

75 Stream Sustainable Memory Bandwidth in High Performance Computers Used to measure memory bandwidth using various method Performance reported in Mbytes/sec More info. on

76 Bonnie++ and IOZone Bonnie++ a benchmark suite that is aimed at performing a number of simple tests of hard drive and file system performance tests database type access to a single file Performance reported in I/O rate and Kbytes/sec More info. on IOZone a file system benchmark tool. The benchmark generates and measures a variety of file operations Performance intensive I/O benchmark on various file size and record size More info. on

77 Iperf and Netpipe Iperf a tool to measure maximum TCP bandwidth, allowing the tuning of various parameters and UDP characteristics. Report data as Kbps or Mbps More info. Netpipe a protocol independent performance tool that visually represents the network performance under a variety of conditions More info. on

78 Thank you Thank you