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Parallel computing

Parallel computing. Petr Štětka Jakub Vlášek Department of Applied Electronics and Telecommunications , Faculty of electrical engineering , University of West Bohemia , Czech Republic. About the project. Laboratory of Information Technology of JINR Project supervisor

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Parallel computing

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  1. Parallel computing Petr Štětka Jakub Vlášek Department of Applied Electronics and Telecommunications, Faculty of electrical engineering, University of West Bohemia, Czech Republic

  2. About the project • Laboratory of Information Technology of JINR • Project supervisor • Sergey Mitsyn, Alexander Ayriyan • Topics • Grids - gLite • MPI • NVIDIA CUDA

  3. Grids – introduction

  4. Grids II • Loose federation of shared resources • More efficient usage • Security • Grid provides • Computational resources (Computing Elements) • Storage resources (Storage Elements) • Resource broker (Workload Management System)

  5. gLite framework • Middleware • EGEE (EnablingGridsforE-sciencE) • User Management (security) • Users, Groups, Sites • Certificate based • Data Management • Replication • Workload Management • Matching requirements against resources

  6. gLite – User management • Users • Each user needs a certificate • Accepts AUP • Membership in a Virtual Organization • Proxy certificates • Applications use it on user’s behalf • Proxy certificate initializationvoms-proxy-init –voms edu

  7. gLite - jobs • Write job in Job Description Language • Submit jobglite-wms-job-submit –a myjob.jdl • Check statusglite-wms-job-status <job_id> • Retrieve Outputglite-wms-job-output<job_id> Executable = “myapp"; StdOutput = “output.txt"; StdError = "stderr.txt"; InputSandbox = {“myapp", "input.txt"}; OutputSandbox = {"output.txt","stderr.txt"};Requirements = …

  8. Algorithmic parallelization • Embarrassingly parallel • Set of independent data • Hard to parallelize • Interdependent data, performance depends on interconnect • Amdahl'slaw- example • Program takes 100 hours • Particular portion of 5 hours cannot be parallelized • Remaining portion of 95 hours(%) can be parallelized • => Execution can not be shorter than 5 hours, no matter how many resources we allocate. • Speedup is limited up to 20×

  9. Message Passing Interface • API (Application Programming Interface) • De facto standard for parallel programming • Multi processor systems • Clusters • Supercomputers • Abstracts away the complexity of writing parallel programs • Available bindings • C • C++ • Fortran • Python • Java

  10. Message Passing Interface II • Process communication • Master slave model • Broadcast • Point to point • Blocking or non-blocking • Process communication topology • Cartesian • Graph • Requires specification of data type • Provides interface to shared file system • Every process has a “view” of a file • Locking primitives

  11. MPI – Test program Someone@vps101:~/mpi# mpirun -np 4 ./mex 1 200 10000000 Partial integration ( 2 of 4) (from 1.000000000000e+00 to 1.000000000000e+02 in 2500000 steps) = 1.061737467015e+01 Partial integration ( 3 of 4) (from 2.575000000000e+01 to 1.000000000000e+02 in 2500000 steps) = 2.439332078942e-15 Partial integration ( 1 of 4) (from 7.525000000000e+01 to 1.000000000000e+02 in 2500000 steps) = 0.000000000000e+00 Partial integration ( 4 of 4) (from 5.050000000000e+01 to 1.000000000000e+02 in 2500000 steps) = 0.000000000000e+00 Numerical Integration result: 1.061737467015e+01 in 0.79086 seconds Numerical integration by one process: 1.061737467015e+01 • Numerical integration - Rectangle method top-left • Input parameters: beginning, end, step. • Function compiled in into the program • gLite script • Runs on grid

  12. Test program evaluation – 4 core CPU

  13. CUDA • Programmed in C++ language • Gridable • GPGPU • Parallel architecture • Proprietary technology • GeForce 8000+ • FP precision • PFLOPS range (Tesla)

  14. CUDA II • An enormous part of the GPU is dedicated to execution, unlike the CPU • Blocks * threads representthe total number of threadsthat will be processed by the kernel

  15. CUDA Test program CUDA CLI Output Integration (CUDA) = 10.621515274048 in 1297.801025 ms (SINGLE) Integration (CUDA) = 10.617374518106 in 1679.833374 ms (DOUBLE) Integration (CUDA) = 10.617374518106 in 1501.769043 ms (DOUBLE, GLOBAL) Integration (CPU) = 10.564660072327 in 30408.316406 ms (SINGLE) Integration (CPU) = 10.617374670093 in 30827.710938 ms (DOUBLE) Press any key to continue . . . • Numerical integration - Rectangle method top-left • Ported version of MPI Test program • 23 times faster on a notebook NVIDIA NVS4200M than one core of Sandy Bridge i5 CPU@2.5GHz • 160 times faster on a desktop GeForce GTX 480 than one core of AMD 1055T CPU@2.7GHz

  16. Conclusion • Familiarized with parallel computing technologies • Grid with gLite middleware • MPI API • CUDA technology • Written program for numerical integration • Running on grid • With MPI support • Also ported to Graphic card using CUDA technology • It works!

  17. Thankyouforyourattention

  18. Distributed Computing • CPU scavenging • 1997 ditstributed.net – RC5 cipher cracking • Proof of concept • 1999 SETI • BOINC • Clusters • Cloud computing • Grids • LHC

  19. MPI - functions • Initialization • Data type creation • Data exchange – all process to all process MPI_Init(&argc, &argv); MPI_Comm_rank(MPI_COMM_WORLD, &procnum); MPI_Comm_size(MPI_COMM_WORLD, &numprocs); MPI_Type_contiguous(intcount, MPI_Datatypeoldtype, MPI_Datatype *newtype) MPI_Type_commit(MPI_Datatype*datatype) MPI_Gather(void *sendbuf, intsendcount, MPI_Datatypesendtype, void *recvbuf, intrecvcount, MPI_Datatyperecvtype, int root, MPI_Commcomm) MPI_Send(void *buf, int count, MPI_Datatypedatatype, intdest, int tag, MPI_Commcomm) … MPI_Finalize();

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