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Introduction of Cluster and (KBRIN) Computational Cluster Facilities

Introduction of Cluster and (KBRIN) Computational Cluster Facilities. Xiaohui Cui CECS Department University of Louisville X0cui001@uofl.edu 09/03/2003. Introduction to Cluster Technology What is a Beowulf ? Kentucky Biomedical Research Infrastructure Network

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Introduction of Cluster and (KBRIN) Computational Cluster Facilities

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  1. Introduction of Cluster and (KBRIN) Computational Cluster Facilities Xiaohui Cui CECS Department University of Louisville X0cui001@uofl.edu 09/03/2003

  2. Introduction to Cluster Technology What is a Beowulf ? Kentucky Biomedical Research Infrastructure Network MPI Programming on KBRIN cluster

  3. People always wants to have faster computer • Normal users • Play game faster • Play music better, watch movies better • Science and Engineer • Solving larger and more complex science and engineering problems using computer modeling, simulation and analysis

  4. How to make a computer faster? • Make a faster chip! • reduce feature size • better architecture, better memory subsystem • VLIW , Super scalar, vector support, DSP instruction (MMX, 3DNow) • SDRAM, NVRAM • Uni-processor speed is still limited by speed of light • Alternate technologies • Optical • Bio • Molecular

  5. How to make a computer faster? • Using multiple processors to solve a single problem • Divide problem into many small pieces • Distributed these small problems to be solved by multiple processors simultaneously • This technique is called Parallel Processing

  6. CPU CPU CPU CPU High Speed Network Parallel computer • Parallel computer is a special computer with • High Speed I/O , Large memory, multiple processing units, fast communication network • Every modern supercomputer is also a parallel computer

  7. Fastest Supercomputer in the world • Intel ASCI Red at Sandia National Laboratory • 9216 Pentium Pro Processors • 2.3 Teraflops performance

  8. But Supercomputer will cost you 100 millions, how to get enough money to buy one? • Using PC Cluster is a low cost solution to this problem

  9. Introduction to Cluster Technology • A Cluster system is • Parallel multi-computer built from high-end PCs and conventional high-speed network.

  10. Why cluster computing? • Scalability • Build small system first, grow it later. • Low-cost • Hardware based on COTS model (Component off-the-shelf) • Software based on freeware from research community • Easier to maintain • Vendor independent

  11. Different kinds of PC cluster • High Performance Computing Cluster • Load Balancing • High Availability

  12. The Beginning • Thomas Sterling and Donald Becker CESDIS, Goddard Space Flight Center, Greenbelt, MD • Summer 1994: built an experimental cluster • Called their cluster Beowulf • 16 x 486DX4, 100MHz processors • 16MB of RAM each, 256MB in total • Channel bonded Ethernet (2 x 10Mbps) • Not that different from our Beowulf

  13. Current Beowulfs • Faster processors, faster interconnect, but the idea remains the same • Cluster database: http://clusters.top500.org/ • Super cluster: 2300 processors, 11 TFLOPS peak

  14. What is a Beowulf ? • Runs a free operating system (not Wolfpack, MSCS) • Connected by high speed interconnect • Compute nodes are dedicated (not Network of Workstations)

  15. Why Beowulf? • It’s cheap! • Our Beowulf, 32 processors, 32GB RAM: $50,000 • The IBM SP2 cluster cost many millions • Everything in a Beowulf is open-source and open standard - easier to manage/upgrade

  16. Essential Components of a Beowulf • Processors • AMD and Intel • Memory • DDR RAM • RDRAM • Interconnect • Fast Ethernet • Gigabit Ethernet • Myrinet • Software

  17. Free cluster OS and management software • OS • Linux • FreeBSD • Cluster Management • Oscar: http://oscar.sourceforge.net/ • Rocks: http://rocks.npaci.edu • MOSIX: http://www.mosix.org/

  18. DIY Cluster

  19. White Box Desktop • Cheap • 2.8 GHz Pentium 4 for $1000 • Very low margins • Expandable • 4-6 PCI slots • 3-5 disk drives • Low density • 16 processor in on rack (on shelves) • Quality • 90 - 365 day warrantees

  20. Commercial designed Cluster

  21. Brand Name Servers • Expensive • Up to double equivalent desktop hardware • High density • Rack mountable • 64 processors in one rack • Blades • Quality • 3 year warrantee • Throw away machine when out of warrantee • Good thermal design

  22. Minimum Components Local Hard Drive Power Ethernet x86 server

  23. Cluster Advantages • Error isolation: separate address space limits contamination of error • Repair: Easier to replace a machine without bringing down the system than in an shared memory multiprocessor • Scale: easier to expand the system without bringing down the application that runs on top of the cluster • Cost: Large scale machine has low volume => fewer machines to spread development costs vs. leverage high volume off-the-shelf switches and computers • Amazon, AOL, Google, Hotmail, Inktomi, WebTV, and Yahoo rely on clusters of PCs to provide services used by millions of people every day

  24. Cluster Drawbacks • Cost of administering a cluster of N machines ~ administering N independent machines vs. cost of administering a shared address space N processors multiprocessor ~ administering 1 big machine • Clusters usually connected using I/O bus, whereas multiprocessors usually connected on memory bus • Cluster of N machines has N independent memories and N copies of OS, but a shared address multi-processor allows 1 program to use almost all memory

  25. Google company 2001 cluster reliability statistic • For 6000 PCs, 12000 HD, 200 EN switches • ~ 20 PCs will need to be rebooted/day • ~ 2 PCs/day hardware failure, or 2%-3% / year • 5% due to problems with motherboard, power supply, and connectors • 30% DRAM: bits change + errors in transmission (100 MHz) • 30% Disks fail • 30% Disks go very slow (10%-3% expected BW) • 200 EN switches, 2-3 fail in 2 years

  26. Kentucky Biomedical Research Infrastructure Network (KBRIN) Computational Cluster Facilities CECS DepartmentBioinformatics Laboratory KBRIN Computational ClusterDahlem Supercomputer Laboratory KBRIN Project Office KBRIN Supercomputer (16) Compute Nodes Dual AMD 2400 2 GB memory40 GB hard drive1 gb NIC Master Backup System Dual AMD 2400 Workstation2 GB memory(4) 70GB hard drives100 mb NIC Dual AMD 2400 Workstation2 GB memory80 GB hard drive100 mb and 1 gb NIC Dual AMD 2400 Workstation2 GB memory80 GB hard drive100 mb and 1 gb NIC Web Srvr / Bkp masterDual AMD 2400 2 GB memory CD RW drive(4) 70 GB hard drives100 mb and 1 gb NIC Dual AMD 2400 Workstation2 GB memory80 GB hard drive100 mb and 1 gb NIC Gigabit Ethernet 100 mb Ethernet KVM Switch Monitor, Keyboard Dual AMD 2400 Workstation2 GB memory80 GB hard drive100 mb and 1 gb NIC Master NodeDual AMD 2400 2 GB memory CD RW drive(4) 70 GB hard drives100 mb and 1 gb NIC HPLaser Printer 24 Port Gb Ethernet Switch 100 mb Ethernet Campus Ethernet Network Elb 4/1/2003

  27. Programming a Cluster • Cluster power comes from parallel processing • Large task is decomposed to a set of small tasks • These tasks are executed by a set of processes on multiple nodes • Programming model based on Message Passing • These process communicate by exchanging message which consists of data and synchronization information

  28. Programming environments • Threads (PCs, SMPs, NOW..) • POSIX Threads • Java Threads • MPI • http://www-unix.mcs.anl.gov/mpi/mpich/ • PVM • http://www.epm.ornl.gov/pvm/

  29. MPI • Message Passing Interface v1.1, v2.0 • Standard for high performance message passing on parallel machines • http://www-unix.mcs.anl.gov/mpi/ • Supports • GNU C, Fortran 77 • Intel C, Fortran 77, Fortran 90 • Portland Group C, C++, Fortran 77, Fortran 90 • Requires site license

  30. PVM • Parallel Virtual Machines v3.4.3 • Message passing interface for heterogeneous architectures • Supports over 60 variants of UNIX • Supports Windows NT • Resource control and meta computing • Fault tolerance • http://www.csm.ornl.gov/pvm/

  31. MPI Programming A Sum(A)=?

  32. MPI Programming A2 A1 Sum(A1,A2,A3,A4)=? A4 A3

  33. MPI Programming Slaves Request Master Output Master

  34. MPI Programming /* Algorithm for the master program */ initialize the array `items'. /* send data to the slaves */ for i = 0 to 3 Send items[25*i] to items[25*(i+1)-1] to slave Pi end for /* collect the results from the slaves */ for i = 0 to 3 Receive the result from slave Pi in result[i] end for /* calculate the final result */ sum = 0 for i = 0 to 3 sum = sum + result[i] end for print sum

  35. MPI Programming /* Algorithm for the slave program */ Receive 25 elements from the master in some array say `items' /* calculate intermediate result */ sum = 0 for i = 0 to 24 sum = sum + items[i] end for send `sum' as the intermediate result to the master

  36. Run MPI Program on the Cluster • MPI C compiler: mpicc • MPI job submit software: PBS • The PBS command used for submit MPI job: • Mkpbs • Qsub • Rps

  37. Portable Batch System • Three standard components to PBS • MOM • Daemon on every node • Used for job launching and health reporting • Server • On the frontend only • Queue definition, and aggregation of node information • Scheduler • Policies for what job to run out of which queue at what time

  38. Connect cluster from your computer

  39. Free X-windows Server on windows http://www.cygwin.com/

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