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Listing 50 entries

"Performance Characterization of Global Address Space Applications: A Case Study with NWChem." J. R. Hammond, S. Krishnamoorthy, S. Shende, N. A. Romero, A. D. Malony. To appear in Concurrency and Computation: Practice and Experience 2010
Keywords: NWChem, TAU, Global Address Space, PGAS

A. Nataraj, A. Malony, A. Morris, D. Arnold, B. Miller, "A Framework for Scalable, Parallel Performance Monitoring" published in Concurrency and Computation: Practice and Experience, Special Issue from STHEC'08 Workshop.
Keywords: performance, monitoring, tree-based, overlay, TAU, MRNet

V. Bui, B. Norris, K. Huck, L. C. McInnes, L. Li, O. Hernandez, and B. Chapman, "A Component Infrastructure for Performance and Power Modeling of Parallel Scientific Applications", in Component-Based High Performance Computing (CBHPC 2008), 2008.
Keywords: power modeling, performance modeling, Common Component Architecture, CCA

A. Malony, S. Shende, N. Trebon, J. Ray, R. Armstrong, C. Rasmussen, and M. Sottile, "Performance Technology for Parallel and Distributed Component Software," Concurrency and Computation: Practice and Experience, Vol. 17, Issue 2-4, pp. 117-141, John Wiley & Sons, Ltd., Feb - Apr, 2005.
Keywords: component software, performance, parallel, distributed, optimization, CCA, TAU

Aroon Nataraj, Allen D. Malony, Alan Morris, Dorian C. Arnold, Barton P. Miller: A framework for scalable, parallel performance monitoring. Concurrency and Computation: Practice and Experience 22(6): 720-735 (2010)

J. Hammond, S. Krishnamoorthy, S. Shende, N. A. Romero, A. D. Malony, "Performance Characterization of Global Address Space Applications: A Case Study with NWChem", Concurrency and Computation: Practice and Experience 24(2): 135-154, John Wiley and Sons, DOI:10.1002/cpe.1881, 2012.
Keywords: performance characterization, global address space, computational chemistry, NWChem

N. A. Romero, C. Glinsvad, A. H. Larsen, J. Enkovaara, S. Shende, V. A. Morozov, and J. J. Mortensen, "Design and performance characterization of electronic structure calculations on massively parallel supercomputers: a case study of GPAW on the Blue Gene/P architecture", Concurrency and Computation: Practice and Experience, Dec. 2013, DOI: 10.1002/cpe.3199, John Wiley and Sons.
Keywords: GPAW, electronic structure, DFT, Blue Gene, massive parallelization, high-performance computing, TAU

Salman, A., Malony, A., Turovets, S., Volkov, V., Ozog, D., & Tucker, D. (2015). Concurrency in electrical neuroinformatics: parallel computation for studying the volume conduction of brain electrical fields in human head tissues. Concurrency and Computation: Practice and Experience.

N. Trebon, A. Morris, J. Ray, S. Shende, and A. D. Malony, "Performance Modeling of Component Assemblies," Concurrency and Computation: Practice and Experience, CPE 1076, Special issue Compframe 2005, John Wiley, 2006.
Keywords: component, performance, TAU

S. Shende, A. D. Malony, A. Morris, S. Parker, J. de St. Germain, "Performance Evaluation of Adaptive Scientific Applications using TAU," chapter, Parallel Computational Fluid Dynamics - Theory and Applications, (eds - A. Deane et. al.), pp. 421-428, Elsevier B.V., 2006.
Keywords: CFD, Uintah, Phases, TAU, performance evaluation

C. E. Rasmussen, M. J. Sottile, S. S. Shende, and A. D. Malony, "Bridging the language gap in scientific computing: the Chasm approach," Concurrency and Computation: Practice and Experience,Volume 18, Issue 2 (February 2006), pp. 151-162, John Wiley & Sons, 2006.
Keywords: Fortran 95, C, C++, language interoperability, XML, compilers, PDT

A. Nataraj, A.Malony, S. Shende, A. Morris, "Integrated Parallel Performance Views." Appears in Cluster Computing published by Springer Netherlands
Keywords: Parallel performance, Kernel, Linux, Instrumentation, Measurement, Integrated

P. Beckman, K. Iskra, K. Yoshii, S. Coghlan and A. Nataraj, "Benchmarking the effects of operating system interference on extreme-scale parallel machines", Appears in Cluster Computing 2008 (pg 3-16) published by Springer Netherlands 1386-7857 (Print) 1573-7543 (Online) Volume 11, Number 1 / March, 2008
Keywords: Microbenchmark, Noise, Petascale, Synchronicity

Michael T. Heath, Allen D. Malony, Diane T. Rover, "The Visual Display of Parallel Performance Data," IEEE Computer, 28(11), Nov. 1995, pp. 21-28, 1995.
Keywords: data visualization, tracing

S. Shende, and A. D. Malony, "Integration and Application of TAU in Parallel Java Environments," Concurrency and Computation: Practice and Experience, Volume 15 (3-5), Mar-Apr 2003, Wiley, pp. 501-519, 2003.
Keywords: TAU, Parallel, Java, Performance Tools

L. Li, and A. D. Malony, "Knowledge Engineering for Automatic Parallel Performance Diagnosis," (submitted to) Concurrency and Computation: Practice and Experience, John Wiley & Sons, 2005.
Keywords: Performance, Diagnosis, Knowledge Engineering, Parallel, TAU

Allen D. Malony, B. Robert Helm, "A theory and architecture for automating performance diagnosis," Future Generation Computer Systems, Vol 18, Issue 1, Elsevier Science Publishers, Amsterdam, pg. 189-200, Sept. 2001.
Keywords: Performance, Diagnosis, Parallel

Alois Ferscha, Allen D. Malony: Performance data mining: Automated diagnosis, adaption, and optimization. Future Generation Comp. Syst. 18(1): 127-130 (2001)
Keywords: Performance data mining; Parallel; Diagnosis; Adaption; Optimization

A. D. Malony, "Tools for Parallel Computing: A Performance Evaluation Perspective," in J. Blazewicz et. al. (Editors), Handbook on Parallel and Distributed Processing, Springer Verlag, pp. 342-363, 2000.
Keywords: parallel performance environments, performance evaluation, performance diagnosis, perturbation, observability, measurement, prediction, parallel tools

Steven T. Hackstadt and Allen D. Malony, Visualizing Parallel Programs and Performance, IEEE Computer Graphics and Applications, Vol. 15, No. 4, July 1995, pp. 12-14.
Keywords: parallel performance visualization, scientific visualization, data explorer

Michael T. Heath, Allen D. Malony, and Diane T. Rover, The Visual Display of Parallel Performance Data, IEEE Computer, Vol. 28, No. 11, November 1995, pp. 21-28.
Keywords: parallel performance visualization, models, concepts, principles, scientific visualization, case studies

Michael T. Heath, Allen D. Malony, and Diane T. Rover, Parallel Performance Visualization: From Practice To Theory, IEEE Parallel and Distributed Technology, Vol. 3, No. 4, Winter 1995, pp. 44-60.
Keywords: parallel performance visualization, models, concepts, principles, scientific visualization, case studies

Allen D. Malony, "Multiprocessor Instrumentation: Approaches for Cedar," Chapter, Instrumentation for Future Parallel Computing Systems (Eds: M. Simmons, R. Koskela, I. Bucher), ACM Press, NY, pp 1-33, 1989.
Keywords: Cedar, measurement techniques, modeling techniques, parallel processors, Complexity hierarchies

David E. Bernholdt, Benjamin A. Allan, Robert Armstrong, Felipe Bertrand, Kenneth Chiu, Tamara L. Dahlgren, Kostadin Damevski, Wael R. Elwasif, Thomas G. W. Epperly, Madhusudhan Govindaraju, Daniel S. Katz, James A. Kohl, Manoj Krishnan, Gary Kumfert, J. Walter Larson, Sophia Lefantzi, Michael J. Lewis, Allen D. Malony, Lois C. McInnes, Jarek Nieplocha, Boyana Norris, Steven G. Parker, Jaideep Ray, Sameer Shende, Theresa L. Windus, and Shujia Zhou, "A Component Architecture for High-Performance Scientific Computing," International Journal of High Performance Computing Applications, ACTS Collection Special Issue, SAGE Publications, 20(2):163 -- 202, Summer 2006.
Keywords: CCA

S. Shende and A. D. Malony, "The TAU Parallel Performance System," International Journal of High Performance Computing Applications, SAGE Publications, 20(2):287-331, Summer 2006
Keywords: TAU, Profiling, Tracing, PerfDMF, performance evaluation, instrumentation, measurement, analysis, Paraprof

A. D. Malony, S. Shende, A. Morris, and F. Wolf, "Compensation of Measurement Overhead in Parallel Performance Profiling," in International Journal of High Performance Computing Applications (IJHPCA), Vol 21, No. 2, pp. 174--194, Summer 2007.
Keywords: Performance measurement and analysis, parallel computing, profiling,intrusion, overhead compensation, TAU

Allen D. Malony and Steven T. Hackstadt, Performance of a System for Interacting with Parallel Applications, International Journal of Parallel and Distributed Systems and Networks, special issue on Measurement of Program and System Performance, M. H. Mickle, ed., Vol. 2, No. 3, 1999, Acta Press, Anaheim, CA, pp. 155-170.
Keywords: distributed data, program interaction, performance analysis, parallel tool, computational steering

J. Davison de St. Germain, Alan Morris, Steven G. Parker, Allen D. Malony, Sameer Shende: Performance Analysis Integration in the Uintah Software Development Cycle. International Journal of Parallel Programming 31(1): 35-53 (2003)
Keywords: Uintah, TAU, XPARE, Performance Mapping, SEAA

Janice Cuny, Robert Dunn, Steven T. Hackstadt, Christopher Harrop, Harold H. Hersey, Allen D. Malony, and Douglas Toomey, Building Domain-Specific Environments for Computational Science: A Case Study in Seismic Tomography, International Journal of Supercomputing Applications and High Performance Computing, Vol. 11, No. 3, Fall 1997. Also appearing in the Proceedings of the Workshop on Environments and Tools For Parallel Scientific Computing, Lyon, France, August 1996.
Keywords: computational science, domain-specific environments, seismic tomography, visualization, distributed data access

A. Morris, A. D. Malony, S. Shende, "Supporting Nested OpenMP Parallelism in the TAU Performance System," (to appear) International Journal of Parallel Programming, Springer, LNCS, 2007.
Keywords: OpenMP, nested parallelism, TAU

David Ozog, Jay McCarty, Grant Gossett, Allen D. Malony, Marina Guenza: Fast equilibration of coarse-grained polymeric liquids. J. Comput. Science 9: 33-38 (2015)

D. Gunter, K. Huck, K. Karavanic, J. May, A. Malony, K. Mohror, S. Moore, A. Morris, S. Shende, V. Taylor, X. Wu, and Y. Zhang, "Performance database technology for SciDAC applications", Journal of Physics: Conference Series, vol. 78, June 2007.

P. Worley, J. Candy, L. Carrington, K. Huck, T. Kaiser, G. Mahinthakumar, A. Malony, S. Moore, D. Reed, P. Roth, H. Shan, S. Shende, A. Snavely, S. Sreepathi, F. Wolf, and Y. Zhang, "Performance analysis of GYRO: a tool evaluation", Journal of Physics: Conference Series 16 (2005) pp. 551-555, SciDAC 2005, Institute of Physics Publishing Ltd., 2005.
Keywords: IPM, KOJAK, TAU, SvPablo, PMaC, Gyro, Performance evaluation

Sergei Turovets, Vasily Volkov, Aleksei Zherdetsky, Alena Prakonina, Allen D. Malony: A 3D Finite-Difference BiCG Iterative Solver with the Fourier-Jacobi Preconditioner for the Anisotropic EIT/EEG Forward Problem. Comp. Math. Methods in Medicine 2014: 426902:1-426902:12 (2014)

M.S. Mueller, B. Chapman, B.R.d. Supinski, A.D. Malony, M. Voss (Eds), "OpenMP Shared Memory Parallel Programming". Proceedings of the International Workshop, IWOMP 2005 and IWOMP 2006.
Keywords: MPI, cluster, computing, collaborative, compiler, optimization, computational, science, data, clustering, distributed, systems, embedded, systems, grid, computing, hierarchical, thread, scheduling, high, performance, computing, hybrid, parallelization, memory, bandwidth, modeling, multi-core, multi-threaded, computing, nested, parallelism, numerical, computation, openMP, parallel, programming, parallelization, performance, evaluation, performance, optimizations, program, analysis, scalability, shared, memory, simulation

A. D. Malony, S. Shende, R. Bell, K. Li, L. Li, N. Trebon, "Advances in the TAU Performance System," Chapter, "Performance Analysis and Grid Computing," (Eds. V. Getov, M. Gerndt, A. Hoisie, A. Malony, B. Miller), Kluwer, Norwell, MA, pp. 129-144, 2003.
Keywords: Performance, tools, parallel, distributed, TAU

Allen D. Malony, Sameer Shende, "Performance Technology for Complex Parallel and Distributed Systems," in "Quality of Parallel and Distributed Programs and Systems," (Eds. Peter Kacsuk and Gabriele Kotsis), Nova Science Publishers, Inc., New York, pp. 25-41, 2003.
Keywords: Performance tools, complex systems, instrumentation, measurement, analysis, TAU

K.A. Gallivan, W. Jalby, A.D. Malony and P.C. Yew, "Performance Analysis on the Cedar System", Chapter, Performance Evaluation of Supercomputers, Edited by J. Martin, Elsevier Science Publishers B.V. (North-Holland), pp. 109-142, 1987.
Keywords: Cedar, performance measurement.

Allen D. Malony, "JED: Just an Event Display," Chapter, Performance Instrumentation and Visualization, (Eds: M. Simmons, R. Koskela), ACM Press, NY, pp. 99-115, 1990.
Keywords: JED, interconnection architectures, performance attributes, performance measurement

L. McInness, T. Dahlgren, J. Nieplocha, D. Bernholdt, B. Allan, R. Armstrong, D. Chavarria, W. Elwasif, I. Gorton, J. Kenny, M. Krishnan, A. Malony, B. Norris, J. Ray, and S. Shende, "Research Initiatives for Plug-and-play Scientific Computing", J. Physics: Conference Series Vol. 78 No. 012046, doi:10.1088/1742-6596/78/1/012046, Proc. SciDAC Conference, 2007.
Keywords: CCA, TAU, Component software, CQoS

Y. Zhang, R. Fowler, K. Huck, A. Malony, A. Porterfield, D. Reed, S. Shende, V. Taylor, and X. Wu, "US QCD Computational Performance Studies with PERI," J. Physics: Conference Series Vol. 78, No. 012083 doi:10.1088/1742-6596/78/1/012083, Proc. of SciDAC 2007 conference, 2007.
Keywords: QCD, USQCD, PERI, TAU, PerfDMF, PerfExplorer

Kyle Gallivan, Dennis Gannon, William Jalby, Allen D. Malony, Harry A. G. Wijshoff, "Behavioral Characterization of Multiprocessor Memory Systems: a Case Study," ACM SIGMETRICS Performance Evaluation Review, Vol. 17, Issue 1, pp. 79-88, May 1989.
Keywords: cache memories, software engineering, array and vector processors, supercomputers, main memory

Vincent A. Guarna, Jr., Dennis Gannon, David Jablonowski, Allen D. Malony, Yogesh Gaur, "Faust: An Integrated Environment for Parallel Programming," IEEE Software Vol. 6, No. 4, July/August 1989, pp. 20-27, 1989.
Keywords: Faust, parallel programming, project-management tool, context editor, program database, performance-evaluation tools, functional integration, common data sets, Sigma, application code, dynamic call-graph tool, multiprocessor performance analysis, parallel programming, programming environments, project support environments

Allen D. Malony, David H. Hammerslag, David J. Jablonowski, "Traceview: A Trace Visualization Tool," IEEE Software, 8(5), pp 19-28, 1991.
Keywords: Traceview, I/O features, computer graphics, trace-management, trace-data analysis, trace visualization tool, trace-analysis systems

K. A. Huck, A. D. Malony, S. Shende, and A. Morris, "Knowledge Support and Automation for Performance Analysis with PerfExplorer 2.0", Large-Scale Programming Tools and Environments, special issue of Scientific Programming, vol. 16, no. 2-3, pp. 123--134. 2008.
Keywords: TAU, parallel performance analysis, data mining, scalability, scripting, metadata, knowledge supported analysis

Steven T. Hackstadt and Allen D. Malony, DAQV: Distributed Array Query and Visualization Framework, Journal of Theoretical Computer Science, special issue on Parallel Computing, Vol. 196, No. 1-2, April 1998, pp. 289-317.
Keywords: visualization, distributed data access, hpf, parallel tool

B. Mohr, A. Malony, S. Shende, F.Wolf, "Design and Prototype of a Performance Tool Interface for OpenMP," The Journal of Supercomputing, 23, 105-128,2002 Kluwer Academic Publishers.

A. D. Malony, D. A. Reed, H. A. G. Wijshoff, "Performance Measurement Intrusion and Perturbation Analysis," IEEE Transactions on Parallel and Distributed Systems," 3(4) July 1992, pp. 433-450, 1992.
Keywords: perturbation compensation, performance measurement

Daniel A. Reed, Allen D. Malony, Bradley McCredie, "Parallel Discrete Event Simulation Using Shared Memory," IEEE Transactions on Software Engineering, 14(4), April 1988, pp. 541-553, 1988
Keywords: Chandy-Misra algorithm, deadlock recovery, discrete event simulation, distributed simulation, parallel processing

K. Gallivan, D. Gannon, W. Jalby, A. Malony, H. Wijshoff , "Experimentally Characterizing the Behavior of Multiprocessor Memory Systems: A Case Study," IEEE Transactions on Software Engineering, 16(2), pp 216-223, 1990
Keywords: Characterization, memory systems, multiprocessor, performance

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