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HPC Bedtime Reading

HPC Bedtime Reading. Myron Ginsberg, Ph.D. ACM Fellow and HPC Consultant HPC Research & Education Farmington Hills, Michigan 48335-1222 E-mail: m.ginsberg@ieee.org. HPC Benchmarking.

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HPC Bedtime Reading

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  1. HPC Bedtime Reading Myron Ginsberg, Ph.D. ACM Fellow and HPC Consultant HPC Research & Education Farmington Hills, Michigan 48335-1222 E-mail: m.ginsberg@ieee.org

  2. HPC Benchmarking • Oak Ridge National Laboratory, Papers and Presentations on Cray X1/X1E Evaluation, http://www.csm.ornl.gov/evaluation/PHOENIX/index.html • R. S. Studham et al., “Leadership Computing at Oak Ridge National Laboratory,” Proceedings of the 47th Cray User Group Conference, Albuquerque, NM, May 16-19, 2005, http://www.studham.com/scott/files/Leadership_CUG.pdf • L. Oliker et al., “Scientific Computations on Modern Parallel Vector systems,” SC2004: High Performance Computing, Networking and Storage Conference, Nov. 6-12, 2004, http://www.crd.lbl.gov/~oliker/papers/SC04.pdf • L. Oliker et al., “Leading Computational Methods on Scalar and Vector HEC Platforms,” Proceedings of Supercomputing 2005, Seattle, WA, Nov. 12-18, 2005, http://www.crd.lbl.gov/~oliker/papers/SC05_eval.pdf • J. S. Vetter et al., “Early Evaluation of the Cray XT3 at ORNL,”Proceedings of the 47th Cray User Group Conference, Albuquerque, NM, May 16-19, 2005, http://www.csm.ornl.gov/~vetter/xt3-2005-06-13/2005-05-17_cug-ornl-xt3-2005-06-13/2005-05-17_cug-ornl-xt3_eval.pdf • T. H. Dunigan, Jr., J. S. Vetter, and P. H. Worley, “Performance Evaluation of the SGI Altix 3700,” Proceedings, 2005 Intl. Conference on Parallel Processing, http://www.csm.ornl.gov/~worley/papers/2005-06-16_icpp_sgi-altix-evaluation.pdf, 2005.

  3. HPC Benchmarking • ICL, HPCC Challenge Benchmark Results, http://icl.cs.utk.edu/hpcc/hpcc_results.cgi • A complete listing of the environment for each HPCC benchmark run can be found at http://icl.cs.utk.edu/hpcc/export/hpcc.xls • Top 500 Supercomputer Sites, http://www.top500.org • Standard Performance Evaluation Corporation, SPEC Benchmark, http://www.specbench.org • NAS Parallel Benchmarks, http://www.nas.nasa.gov/Software/NPB/ • PMaC HPC Benchmark Suite, http://www.sdsc.edu/PMaC/Benchmark • IDC Balanced HPC Benchmark Ratings, http://www.hpcuseforum.com/benchmark/ • C. Lazou, “Sending out an SOS: HPCC Rescue Coming” HPCWIRE, Article 464623, Sept. 2, 2005, http://news.taborcommunicastions.com/msgget.jsp?mid=464623&xsl

  4. Supercomputing Issues • D. H. Bailey, “Twelve Ways to Fool the Masses: 10 years Later,” paper, ISC2004, Heidelberg, Germany, June 23-25, 2004, http://crd.lbl.gov/~dhbailey/dhbtalks/dhb-12ways.pdf • D. H. Bailey, “Performance of Future High-End Computers,” http://crd.lbl.gov/~dhbailey/dhbtalks/dhb-future-perf.pdf • S. L. Graham, M. Snir, and C. A. Patterson, eds., “Getting Up to Speed: The Future of Supercomputing,” U.S. National Academy of Sciences CSTB Report, 2004, http://www.cstb.org/project_supercomputing.html prepublication on-line version at http://books.nap.edu/catalog/11148.html executive summary, http://www.nap.edu/catalog/11148.html • HECRTF, Federal Plan for High-End Computing: Report of the High-End computing Revitalization Task Force (HECTRF), Executive Office of the President, Office of Science and Technology Policy, Washington, D.C., May 10, 2004 (second printing – July 2004); available at http://www.itrd.gov/pubs/2004_hecrtf/20040702_hecrtf.pdf • The Council on Competitiveness, “2004 HPC Users Conference: Supercharging U.S. Innovation & Competitiveness,” Report and DVD available, The Council on Competitiveness, Washington, D.C., 2005, http://www.compete.org/hpc/hpc_conf_report.asp • The Council on Competitiveness, “Accelerating Innovation for Competitive Advantage: The Need for HPC Application Software Solutions,”High Performance Computing Software Workshop Report, Council on Competitiveness, Washington, D.C.20005, January 2006. • The Council on Competitiveness, Second Annual High Performance Computing Users Conference Report: Accelerating Innovation for Prosperity, report and DVD entitled, “High Performance Computing: Accelerating Innovation to Enhance Everyday Life,” DreamWorks Animation SKG, Council on Competitiveness, Washington D.C. 2005, March 2006 • S. Ulfelder, “Supercomputer Architectures Battle for Hearts and Minds of Users,” Computerworld, March 6, 2006, http://computerworld.com/hardwaretopics/hardware/story/0,10801,109177,00.html

  5. Supercomputing Issues • President’s Information Technology Advisory Committee, “Computational Science: Ensuring America’s Competitiveness,” PITAC, Office of the President, Washington, D.C., June 2005, http://www.nitrd.gov/pitac/reports/20050609_computational/computational.pdf • E. Joseph, A. Snell, and C. G. Willard, Council on Competitiveness Study of U.S. Industrial HPCUsers, White Paper, IDC, Framingham, MA, July 2004, http://www.compete.org/pdf/HPC_Users_Survey.pdf • E. Joseph et al., Study of ISVs Serving the High Performance Computing Market: The Need for Better Application Software, Council on Competitiveness Initiative, White Paper, IDC, Framingham, MA, July 2005, http://www.compete.org/pdf/HPC_Software_Survey.pdf • M. Ginsberg, “Influences on the Solution Process for Large, Numeric-Intensive Automotive Simulations,”Lecture Notes in Computer Science Series, Vol. 2073, Springer, New York, 2001, pp. 1189-1198. • M. Ginsberg, “Impediments to Future Use of Petaflop Class Computers for Large-Scale Scientific/Engineering Applications in U.S. Private Industry,” Lecture Notes in Computer Science, Vol. 3514, May 2005, pp. 1059-1066. • M. Ginsberg, “Bibliographic Snapshots of High Performance/High Productivity Computing,” Chapter in Advances in Computers, edited by M. Zelkowitz, Vol. 72, Elsevier Publishing, New York, 2008 • National Coordination Office for Information Technology and Development (NITRD), http://www.itrd.gov

  6. Supercomputing Architectures • A. Gara et al., “Overview of the Blue Gene/L System Architecture,” IBM J. Res. & Dev., Vol. 49, No. 2/3 March/May 2005, http://www.research.ibm.com/journal/rd/492/gara.pdf • D. A. Bader (ed.), Petascale Computing: Algorithms and Applications, Chapman & Hall/CRC, Atlanta, GA, Dec. 2008. • G. Haff, “Blue Gene’s Teraflop Attack,” Illuminata, Inc., Nashua, NH, August 22, 2005, http://www-03.ibm.com/servers/deepcomputing/pdf/teraflopattackilluminata.pdf • ASCI Purple Benchmark Page, http://www.llnl.gov/asci/platforms/purple • Earth Simulator Homepage, http://www.es.jamstec.go.jp/esc/eng/index.html • E. Joseph et al., “NEC Launches Next-Generation Vector Supercomputer: The SX-8,” IDC White Paper #4290, IDC, Framingham, MA, October 2004. • T. Curns, “Japan: Poised for a Supercomputing Comeback?,” HPCWIRE, June 3, 2005, http://news.taborcommunications.com/msgget.jsp?mid=391555&xsl=story.xsl • Cray Inc., “Cray XT3 Supercomputer Overview,” http://www.cray.com/products/xt3/index.html • D. H. Brown Associates, Inc., Cray XT3 MPP Delivers Scalable Performance, White Paper, D. H. Brown Associates, Inc., January 19, 2005, http://www.cray.com/downloads/05.01.19.CrayXT3.pdf

  7. Supercomputing Architectures • N. Wichmann and J. Levesque, ”Computer Comparisons Using HPCC,” http://www.cray.com/downloads/sc2004/LevesqueSC04HPCCboothtalk2.pdf SC2004, Pittsburgh, PA, November 2004 • D. Abts, “Achieving a Balanced System Design,” http://www.cray.com/downloads/sc2004/SC2004_dabts_balance.pdf SC2004, Pittsburgh, PA, November 2004. • Crsy, Inc., “System Balance – An HPC Performance Metric,” http://www.cray.com/products/xd1/balance.html • Cray Inc., “CAE Strategy: The XD1 Supercomputer,” http://www.cray.com/downloads/sc2004/SC2004-CAE_nov4_pp.pdf SC2004, Pittsburgh, PA, November 2004 • A. Shan, “Cray XD1-FPGA,” http://www.cray.com/downloads/sc2004/SC-FPGABoothTheatre_pp_nov4.pdf, SC2004, Pittsburgh, PA, November 2004. • D. H. Brown Associates, Inc., “Cray XD1 Brings High-Bandwidth Supercomputing to the Mid-Market,” White Paper, D. H. Brown Associates, Inc., Oct. 2004, http://www.cray.com/downloads/dhbrown_crayxd1_oct2004.pdf • Cray, Inc., “The Cray XD1 High Performance Computer: Closing the Gap between Peak and Achievable Performance in High-Performance Computing,” White Paper, WP-0020404, Cray Inc., Seattle, WA, 2004, http://www.cray.com/downloads/whitepaper_closing_the_gap.pdf • J.L. Gustafson, “Understanding the Different Acceleration Technologies,” HPCWIRE, Vol. 13, No. 2, Nov. 14, 2006, http://www.hpcwire.com/hpc/1091512.html

  8. Supercomputing Architectures • Cray Inc., “Cray X1E Supercomputer,” http://www.cray.com/products/x1e/index.html • Cray Inc., “Cray X1E System Architecture,” http://www.cray.com/products/x1e/architecture.html • L. G. Harbaugh,”Building High-performance Linux Clusters,” (sponsored by Appro), White Paper, June 2004, http://www.appro.com/whitepaper/whitepaper.pdf • D. A. Patterson, “Latency Lags Bandwidth,” Comm. ACM, Vol. 47, No. 10, Oct. 2004, pp. 71-75. • J. Hennessy and D. A. Patterson, Computer Architecture: A Quantitative Approach, 4th Edition, Morgan Kauffman, San Francisco, CA, 2007. • D. A. Patterson and J. Hennessy, Computer Organization and Design: The Hardware/Software Interface, Morgan Kauffman, San Francisco, CA, 2004. • M. B. Gokhale and P. S. Graham, Reconfigurable Computing: Accelerating Computation with Field-Programmable Gate Arrays, Spring-Verlag, 2005. • J. D.Owens et al., “A Survey of General-Purpose Computation on Graphics Hardware,” Proceedings, Eurographics 2005, August 29-September 2, 2005, Dublin, Ireland, pp. 21-51, http://graphics.idav.ucdavis.edu/graphics/publications/func/return_pdf?pub_id=844 • H. Simon, “Progress in Supercomputing: The Top Three Breakthroughs of the Last Twenty Years and the Top Three Challenges for the Next Twenty Years,” ISC 2005, Heidelberg, June 22, 2005, video at mms://netshow01.eecs.berkeley.edu/Horst_Simon • S. K. Moore, “Winner: Multimedia Monster,” http://www.spectrum.ieee.org/jan06/2609 • S. Holland, “Taming the Wild Supercomputer,” Tom’s Hardware Guide, March 20, 2007, http://www.tomshardware.com/2007/03/20/taming_the_wild_supercomputer/index.html

  9. DARPA HPCS, Phase 2 • M. Elnozahy, “IBM Has Its PERCS,” HPCWIRE, April 7, 2006, http://www.hpcwire.com/hpc/614724.html • IBM, Inc., “The X10 Programming Language,”March 17, 2006, http://domino.research.ibm.com/comm/research_projects.nsf/pages/x10.index.html • IBM, Inc., “Report on the Experimental Language X10,”Draft v 0.41, February 7, 2006, http://domino.research.ibm.com/comm/research_projects.nsf/pages/x10.index.html/$FILE/ATTH4YZ5.pdf • V. Saraswat, “X10 Overview,” http://crd.lbl.gov/~parry/hpcs_resources.html • V. Saraswat, “X10: An Object-Oriented Approach to Non-Uniform Cluster Computing,” http://crd.lbl.gov/~parry/hpcs_resources.html

  10. DARPA HPCS, Phase 2 • M. Vildibill, “Sun’s Hero Program: Changing the Productivity Game,” HPCWIRE, April 7, 2006, http://www.hpcwire.com/hpc/614805.html • G. L. Steele, Jr., “Programming Language Research: Exploration of Programming Languages Constructs and Principles,” http://research.sun.com/projects/plrg/ • G. L. Steele, Jr., “Parallel Programming and Parallel Abstractions in Fortress,” FLOPS 2006, April 24, 2006, http://research.sun.com/projects/plrg/FLOPS2006public.pdf • G. L. Steele, Jr. and J-W Maessen, “Fortress Programming Language Tutorial,” PLDI’06, June 11, 2006, http://research.sun.com/projects/plrg/PLDITutorialSlides9Jun2006.pdf

  11. DARPA HPCS, Phase 2 • A. Snell and C. G. Willard, “Bridging the Capability Gap: Cray Pursues ‘Adaptive Supercomputing’ Vision,” White Paper No. 200808, IDC, Framingham, MA, March 2006, http://www.cray.com/downloads/IDC-AdaptiveSC.pdf • S. Scott, “In Cray’s ‘Cascade’ The Computer Will Adapt to the Codes,” HPCWIRE, April 7, 2006, http://www.hpcwire.com/hpc/614695.html • B. Chamberlain, “An Introduction to Chapel – Cray Cascade’s High-Productivity Language,” AHPCRC/DARPA PGAS Conference, September 14, 2005, http://chapel.cs.washington.edu/ChapelForAHPCRC.pdf • S. Deitz, “Chapel: Compiler Challenges,” LCPC, October 21, 2005, http://chapel.cs.washington.edu/ChapelForLCPC.pdf • Cray, Inc., “Chapel – The Cascade High-Productivity Language,” Chapel Programming Language Homepage, http://chapel.cs.washington.edu/

  12. DARPA Phase 3 • HPCWIRE, “Cray Advances to Phase III of DARPA HPCS,” HPCWIRE, November 22, 2006, http://www.hpcwire.com/hpc/1115742.html • HPCWIRE, “DARPA Selects IBM for HPCS Phase III,” HPCWIRE November 22, 2006, http://www.hpcwire.com/hpc/1115743.html • M. Feldman, “DARPA Selects Cray and IBM for Final Phase of HPCS,”Vol. 15, No. 46, November 24, 2006, http://www.hpcwire/hpc/1119092.html • M. Feldman, “High Productivity Computing for the Rest of Us,” Vol. 15, No. 46, November 24, 2006, http://www.hpcwire.com/hpc/1119786.html • M. Feldman, “Is it Time for Heterogeneous Supercomputing,” HPCWIRE, Vol. 15, No. 28, July 14, 2006, http://www.hpcwire.com/hpc/726342.html • K. Yelick, “The Software Challenges of Petascale Computing,” HPCWIRE, Vol. 15, No. 45, November 10, 2006, http://www.hpcwire.com/hpc/1071362.html

  13. Supercomputing Issues • R. W. Hockney, The Science of Computer Benchmarking, SIAM, Philadelphia, 1996. • M. Overton, Numerical Computing with IEEE Floating Point Arithmetic, SIAM, Philadelphia, 2001. • S. Goedecker and A. Hoisie, Performance Optimization of Numerically Intensive Codes, SIAM, Philadelphia, 2001. • M. Wolfe, High-Performance Compilers for Parallel Computing, Addison-Wesley, Reading, MA, 2000. • A. M. Bruaset and A. Tveito (eds.), Numerical Solutions of Partial Differential Equations on ParallelComputers, Lecture Notes in Computational Science and Engineering Series, Vol. 51, Springer-Verlag, 2006. • M. Ginsberg, “Challenges and Opportunities for U.S. Private Industry Utilization of HPC Technology,” International Conference on Scientific Computing (CSC’07), 2007 World Congress in Computer Science, Computer Engineering, and Applied Computing (WORLDCOMP07), Monte Carlo Resort Hotel, Las Vegas, NV, June 25-28, 2007.

  14. Supercomputing Issues • D. J. Lilja, Measuring Computer Performance: A Practitioner’s Guide, Cambridge University Press, UK, 2000. • B. Einarsson, Accuracy and Reliability in Scientific Computing, SIAM, 2005. • R. P. Garg and I. Sharapov, Techniques for Optimizing Applications: High Performance Computing, Prentice Hall PTR Series, Englewood Cliffs, NJ, 2002. • T. McDonald, “Designers Look to Take Computer Chips Off the Clock,” NewsFactor Network, Sept. 16, 2001, http://www.newsfactor.com/perl/printer/13584/ • A. Snell and C. G. Williard, “Bridging the Capability Gap: Cray Pursues ‘Adaptive Supercomputing’ Vision,” White Paper No. 200808, IDC, Framingham, MA, March 2006, http://www.cray.com/downloads/IDC-AdaptiveSC.pdf • S. Scott, “In Cray’s ‘Cascade’ The Computer Will Adapt to the Codes,” HPCWIRE, April 7, 2006, http://www.hpcwire.com/hpc/614695.html

  15. Supercomputing Issues • J. Dongarra, Guest Editior, “The Promise and the Perils of the Coming Multicore Revolution and its Impact,”CTWatch Quarterly, Vol. 3, No. 1, February 2007, http://ctwatch.org/quarterly/pdf/ctwatchquarterly-10.pdf • D. A. Patterson et al., “The Landscape of Parallel Computing Research: A View from Berkeley,”Tech Report No. UCB/EECS-2006-183, Dec. 18, 2006, http://www.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-183.html • E. A. Lee, “The Problem with Threads,” IEEE Computer, Vol. 39, No. 5, May 2006, pp. 33-42 or at http://www.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-1.html • D. A. Patterson et al., “RAMP: A Research Accelerator for Multiple Processors,” UCB, EECS, Nov. 24, 2006, http://www.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-158.html • D. A. Bader (ed.), Petascale Computing: Algorithms and Applications, CRC Press, Atlanta, GA, December 2007.

  16. Supercomputing Issues • IDC, “IDC’s HPC Market Categories,”IDC Analyst Briefing Breakfast at Supercomputing SC06, Tampa FL, November 15, 2006. • ISC, “The Star-P Platform: Delivering Interactive Parallel Computing Power to the Desktop,” White Paper, ISC, Waltham. MA, 2006, http://www.interactivesupercomputing.com/downloads/ISCwhitepaper.pdf

  17. Computational Science Programs • C. D. Swanson, “Computational Science Education,”Krell Institute, November 2003, http://www.krellinst.org/services/technology/CSE_survey/index.html • SIAM Working Group on CSE Undergraduate Education, “Undergraduate Computational Science and Engineering Education,” SIAM, Philadelphia, PA, September 20, 2006, http://www.siam.org/about/pdf/CSE_Report.pdf • SIAM Working Group on CSE Education, “Graduate Education in Computational Science and Engineering,” SIAM Rev., Vol. 43, No. 1, March 2001, pp. 163-177 or at http://www.siam.org/journals/sirev/43-1/37974.html • SIAM Working Group on CSE Education, “Graduate Education for Computational Science and Engineering,”2007 http://www.siam.org/students/resources/report.php

  18. Computational Science • M. T. Heath, Scientific Computing: An Introductory Survey, second edition, McGraw-hill, New York, 2001. http://www.cse.uiuc.edu/heath/scicomp. • L. R. Scott, T. Clark, and B. Bagheri, Scientific Parallel Computing, Princeton University Press, Princeton, NJ, 2005, http://amrit.ittc.ku.edu/spc/ • R. H. Landau, A First Course in Scientific Computing – Symbolic, Graphic, and Numeric Modeling using Maple, Java, Mathematica, and Fortran90, Princeton University Press, Princeton, NJ, 2005. • A. B. Shiflet and G. W. Shiflet, Introduction to Computational Science: Modeling and Simulation for the Sciences, Princeton University Press, Princeton, NJ, 2006. • H. El-Rewini and M. Abd-El-Barr, Advanced Computer Architecture and Parallel Processing, J. Wiley & Sons, Hoboken, NJ, 2005. • R. Eigenmann (ed.), Performance Evaluation and Benchmarking with Realistic Applications, MIT Press, Cambridge, MA, Jan. 2001, http://www.mitpress.mit.edu • D. T. Nguyen, Parallel-Vector Equation Solvers for Finite Element Engineering Applications, Kluwer Academic Publisher, Hingham, MA, Sept. 2001. • L. Komzsik, What Every Engineer Should Know about Computational Techniques of Finite Element Analysis, CRC Press, Boca Raton, FL, 2005

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