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Presenter imran patel

Supporting Efficient Execution in Heterogeneous Distributed Computing Environments with Cactus and GlobusGabrielle Allen, Thomas Dramlitsch, Ian Foster, Nick Karonis, Matei Ripeanu, Ed Seidel, Brian ToonenProceedings of Supercomputing 2001 (Winning Paper for Gordon Bell Prize - Special Category)


Imran Patel

Outline Computing Environments with Cactus and Globus

  • Introduction

  • Computational Grids

  • Grid-enabled Cactus Toolkit

  • Experimental Results

  • Ghostzones and Compression

  • Adaptive Strategies

  • Conclusion

Introduction Computing Environments with Cactus and Globus

  • Widespread use of numerical simulation techniques has led to a high demand for traditional high-performance computing resources (supercomputers).

  • Low-end computers are becoming increasingly powerful and are connected with high-speed networks.

  • “Computational Grids” aim to tie these scattered resources into an integrated infrastructure.

  • Applications for the grid include large-scale simulations which require high resources for increased throughput.

Introduction the problem
Introduction: The Problem Computing Environments with Cactus and Globus

  • Heterogeneous and dynamically behaving resources makes development of grid-enabled applications extremely difficult.

  • One approach is to develop computational frameworks which hide this complexity from the programmer.

  • Cactus-G: a simulation framework which uses grid-aware components and message passing library (MPICH-G2)

Computational grids
Computational Grids Computing Environments with Cactus and Globus

  • Computational Grids differ from other parallel computing environments:

  • A grid may have nodes with different processor speeds, memory, etc

  • Grids may have widely different network interconnects and topologies.

  • Resource availability varies in a grid.

  • Nodes in a grid may have different software configurations.

Computational grids programming techniques
Computational Grids – Programming Techniques Computing Environments with Cactus and Globus

  • To overcome these problems, some generic techniques have been devised:

  • Irregular Data Distributions: use application/network/node information.

  • Grid-aware Communication schedules: overlapping/grouping, dedicated nodes

  • Redundant Computation: at the expense of reduced communication.

  • Protocol Tuning: TCP tweaks,compression

Cactus g
Cactus-G Computing Environments with Cactus and Globus

  • Cactus is a modular and parallel simulation environment used by scientists and engineers in the fields of numerical relativity, astrophysics, climate modeling, etc.

  • Cactus design consists of a core (flesh) which connects to application modules (thorns).

  • Various thorns exist for services such as Globus Toolkit, PETSc library, visualization, etc.

  • Cactus is highly portable and parallel since it uses abstraction APIs which themselves are implemented as thorns.

  • MPICH-G2 exploits Globus services and provides faster communication and QOS.

Cactus g architecture
Cactus-G: Architecture Computing Environments with Cactus and Globus

  • Applications thorns need not be grid-aware.

  • Example of a grid-aware Cactus thorn is PUGH, which provides MPI-based parallelism.

  • The DUROC library handles process management.

Experimental results setup
Experimental Results: Setup Computing Environments with Cactus and Globus

  • An application in Fortran for solving numerical relativity problems

  • 57 3-d variables, 780 flops per gridpoint per iteration.

  • N x N x 6 x ghostzone_size x 8 variables need to be sync’ed at each processor.

  • Total 1500 CPUs organized in a 5 x 12 x 25 3-d mesh

Experimental results setup1
Experimental Results: Setup Computing Environments with Cactus and Globus

  • 4 supercomputers at SDSC and NCSA

  • 1024-CPU IBM Power-SP (306 MFlops/s).

  • One 256 CPU and two 128-CPU SGI Origin2000 systems. (168 MFlops/s).

  • Intramachine: 200 MB/s

  • Intermachine: 100 MB/s

  • SDSC<->NCSA: 3 MB/s on 622 Mb/s

Communication optimizations
Communication Optimizations Computing Environments with Cactus and Globus

  • Communication/Computation Overlap: Processors across WANs were given few grid points so that they could overlap their communication with computations.

  • Compression: A cactus thorn which exploits the regularity of data for compression using the libz library.

  • Ghostzones: Larger ghostzones were used for efficient communication at the expense of redundant computations.

Performance metrics
Performance Metrics Computing Environments with Cactus and Globus

  • Flop/s rate and efficiency are used as metrics.

  • Total execution time (ttot): Measured using MPI_Wtime()

  • Expected Communication Time (tcomp): Ideal time calculated from single node.

  • Flop Count F: Calculated using hardware counters 780 Flops per gridpoint per iteration.

  • Flop/s Rate =

    F * num_gridpts * num_iterations / ttot

  • E = tcomp/ttot

Performance figures
Performance Figures Computing Environments with Cactus and Globus

  • 4 supercomputers: 42 GFlop/s, 14%

  • Compression + 10 Ghostzones: 249 GFlop/s, 63.3%

  • Smaller run on 120+1120=1140 processors: 292 GFlop/s, 88%

Ghostzones Computing Environments with Cactus and Globus

  • Increasing ghostzone size can reduce latency overhead by transferring fewer messages with same amount of total data.

  • Increasing the ghostzone size beyond a certain point does not give any benefits and wastes memory.

Compression Computing Environments with Cactus and Globus

  • For increased throughput across WANs.

  • Compression found to be highly useful since data is regular/smooth.

  • Since smoothness of data changes over time, compression effects can change. So, we need adaptive compression.

Adaptive strategies compression
Adaptive Strategies - Compression Computing Environments with Cactus and Globus

  • Predicting optimal values of ghostzone/compression parameters might be good.

  • Don’t want to use detailed network characteristics.

  • For ex: change the compression state based on efficiency, which is averaged over N iterations.

Adaptive ghostzone sizes
Adaptive Ghostzone Sizes Computing Environments with Cactus and Globus

  • Adapting Ghostzone size is challenging: Many ghostsize values possible, memory re-allocations, ripple effects, need to get extra data from neighbors.

  • Start with a size of 1 and increase/decrease in accordance with the efficiency.

Adaptive ghostzone sizes1
Adaptive Ghostzone Sizes Computing Environments with Cactus and Globus

Further information
Further Information Computing Environments with Cactus and Globus

  • The Cactus Framework and Toolkit: Design and Applications Tom Goodale, et al.

    Vector and Parallel Processing - VECPAR'2002

  • Grid Aware Parallelizing Algorithms Thomas Dramlitsch, Gabrielle Allen, Edward Seidel

    Journal of Parallel and Distributed Computing