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Leonid Oliker

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Lenny Oliker
Computer Senior Scientist
Phone: +1 510 486 6625
Fax: +1 510 486 6900

Research Interests:
  • Optimization of scientific methods on emerging multi-core systems
  • Ultra-efficient designs of domain-optimized computational platforms
  • Large-scale de novo genome assembly and genetic mapping
  • Compiler-driven autotuning for stencil computations
  • Performance evaluation of extreme-scale applications on leading supercomputers

Journal Articles

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Aydin Buluc, John Gilbert, Leonid Oliker, "Special Issue: Graph Analysis for Scientific Discovery", Parallel Computing Journal Special Issue Editors, August 1, 2015,

J. Chapman, M. Mascher, A. Buluç, K. Barry, E. Georganas, A. Session, V. Strnadova, J. Jenkins, S. Sehgal, L. Oliker, J Schmutz, K. Yelick, U. Scholz, R. Waugh, J. Poland, G. Muehlbauer, N. Stein, D. Rokhsar, "A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome", Genome biology, 2015,

Adam Lugowski, Shoaib Kamil, Aydın Buluç, Samuel Williams, Erika Duriakova, Leonid Oliker, Armando Fox, John R. Gilbert,, "Parallel processing of filtered queries in attributed semantic graphs", Journal of Parallel and Distributed Computing (JPDC), September 2014, doi: 10.1016/j.jpdc.2014.08.010

L. Oliker and R. Vuduc, "Introduction for Special Issue on Autotuning", International Journal of High Performance Computing Applications (IJHPCA), 2013,

Khaled Z Ibrahim, Kamesh Madduri, Samuel Williams, Bei Wang, Stephane Ethier, Leonid Oliker, "Analysis and optimization of gyrokinetic toroidal simulations on homogenous and heterogenous platforms", International Journal of High Performance Computing Applications (IJHPCA), July 2013, doi: 10.1177/1094342013492446

K. Madduri, J. Su, S. Williams, L. Oliker, S. Ethier, K. Yelick, "Optimization of Parallel Particle-to-Grid Interpolation on Leading Multicore Platforms", Transactions on Parallel and Distributed Systems (TPDS), October 1, 2012, doi: 10.1109/TPDS.2012.28

M. Wehner, L. Oliker, J. Shalf, D. Donofrio, L. Drummond, et al., "Hardware/Software Co-design of Global Cloud System Resolving Models", Journal of Advances in Modeling Earth Systems (JAMES), 2011, 3, M1000:22, doi: 10.1029/2011MS000073

"Emerging Programming Paradigms for Large-Scale Scientific Computing", Guest editors, Parallel Computing special issue,'Emerging Programming Paradigms for Large-Scale Scientific Computing", 2011,

Kamesh Madduri, Eun-Jin Im, Khaled Z. Ibrahim, Samuel Williams, Stephane Ethier, Leonid Oliker, "Gyrokinetic Particle-in-cell Optimization on Emerging Multi- and Manycore Platforms", Parallel Computing Journal, January 2011, 37:501 - 520, doi: 10.1016/j.parco.2011.02.001

Shoaib Kamil, Oliker, Pinar, John Shalf, "Communication Requirements and Interconnect Optimization for High-End Scientific Applications", IEEE Transactions on Parallel and Distributed Systems, Volume (TPDS), January 1, 2010, 21:188-202,

M. Wehner, L. Oliker., and J. Shalf, "Low Power Supercomputers", IEEE Spectrum, October 2009,

High-performance computing for such things as climate modeling is not going to advance at anything like the pace it has during the last two decades unless we apply fundamentally new ideas. Here we describe one possible approach. Rather than constructing supercomputers from the kinds of microprocessors found in fast desktop computers or servers, we propose adopting designs and design principles drawn, oddly enough, from the portable-electronics marketplace.

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David Donofrio, Oliker, Shalf, F. Wehner, Rowen, Krueger, Kamil, Marghoob Mohiyuddin, "Energy-Efficient Computing for Extreme-Scale Science", IEEE Computer, January 2009, 42:62-71, doi: 10.1109/MC.2009.35

 

 

S. Kamil, L. Oliker, A. Pinar, J. Shalf, "Communication Requirements and Interconnect Optimization for High-End Scientific Applications", IEEE Transactions on Parallel and Distributed Systems (TPDS), 2009,

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Kaushik Datta, Kamil, Williams, Oliker, Shalf, Katherine A. Yelick, "Optimization and Performance Modeling of Stencil Computations on Modern Microprocessors", SIAM Review, 2009, 51:129-159, doi: 10.1137/070693199

R. Biswas, J. Vetter, L. Oliker, "Revolutionary Technologies for Acceleration of Emerging Petascale Applications", Guest Editors, Parallel Computing Journal, 2009,

Samuel Williams, Carter, Oliker, Shalf, Katherine A. Yelick, "Optimization of a lattice Boltzmann computation on state-of-the-art multicore platforms", Journal of Parallel Distributed Computing (JPDC), 2009, 69:762-777, doi: 10.1016/j.jpdc.2009.04.002

J. Borrill, L. Oliker, J. Shalf, H. Shan, A. Uselton, "HPC global file system performance analysis using a scientific-application derived benchmark", Parallel Computing, 2009, 35:358-373, doi: 10.1016/j.parco.2009.02.002

S. Kamil, L. Oliker, A. Pinar, J. Shalf, "Communication Requirements and Interconnect Optimization for High-End Scientific Applications\", IEEE Transactions on Parallel and Distributed Systems (TPDS), 2009,

S. Williams, K. Datta, J. Carter, L. Oliker, J. Shalf, K. Yelick, D. Bailey, "PERI: Auto-tuning Memory Intensive Kernels for Multicore", SciDAC PI Meeting, Journal of Physics: Conference Series, 125 012038, July 2008, doi: 10.1088/1742-6596/125/1/012038

M. Wehner, L. Oliker, J. Shalf, "Performance Characterization of the World's Most Powerful Supercomputers", Internation Journal of High Performance Computing Applications (IJHPCA), April 2008,

Michael F. Wehner, L. Oliker, John Shalf, "Towards Ultra-High Resolution Models of Climate and Weather", Internation Journal of High Performance Computing Applications (IJHPCA), January 2008, 22:149-165,

S. Ethier, W. M. Tang, R. Walkup, L. Oliker, "Large-Scale Gyrokenetic particle simulation of Microturbulence in Magnetically Confined Fusion Plasmas", IBM Journal of Research and Development, 2008,

Samuel Williams, Oliker, W. Vuduc, Shalf, A. Yelick, James Demmel, "Optimization of sparse matrix-vector multiplication on emerging multicore platforms", Parallel Computing, 2008, 35:38, doi: 10.1016/j.parco.2008.12.006

Leonid Oliker, Canning, Carter, Shalf, St\ ephane Ethier, "Scientific Application Performance On Leading Scalar and Vector Supercomputering Platforms", Internation Journal of High Performance Computing Applications (IJHPCA), 2008, 22:5-20, doi: 10.1177/1094342006085020

Samuel Williams, Shalf, Oliker, Kamil, Husbands, Katherine A. Yelick, "Scientific Computing Kernels on the Cell Processor", International Journal of Parallel Programming, January 2007, 35:263-298, doi: 10.1007/s10766-007-0034-5

L. Oliker, J. Carter, M. Wehner, A. Canning, S. Ethier, A. Mirin, G. Bala, D. Parks, P. Worley, S. Kitawaki, Y. Tsuda, "Scientific Application Performance on Leading Scalar and Vector Supercomputing Platforms", International Journal of High Performance Computing Applications (IJHPCA), 2006,

H. Simon, W. Kramer, W. Saphir, J. Shalf, D. Bailey, L. Oliker, et al, "Science Driven System Architecture: A New Process for Leadsership Class Computing", Journal of the Earth Simulator, 2005,

L. Oliker, A. Canning, J. Carter, J. Shalf, H. Simon, S. Ethier, D. Parks, S. Kitawaki, Y. Tsuda, T. Sato, "Performance of Ultra-Scale Applications on Leading Vector and Scalar HPC Platforms", Journal of the Earth Simulator, January 2005, 3,

Leonid Oliker, Canning, Carter, Shalf, Skinner, Ethier, Biswas, Jahed Djomehri, Rob F. Van der Wijngaart, "Performance evaluation of the SX-6 vector architecture for scientific computations", Concurrency - Practice and Experience, January 2005, 17:69-93, doi: 10.1002/cpe.884

R. Biswas, L. Oliker, H. Shan, "Parallel Computing Strategies for Irregular Algorithms", Annual Review of Scalable Computing, April 2003,

Hongzhang Shan, Jaswinder P. Singh, Leonid Oliker, Rupak Biswas, "Message Passing and Shared Address Space Parallelism on an SMP Cluster", Parallel Computing Journal, Volume 29, Issue 2, February 2003,

L. Oliker. X. Li, P. Husbands, R. Biswas, "Effects of Ordering Strategies and Programming Paradigms on Sparse Matrix Computations", SIAM Review Journal, 2002,

H. Shan, J. P. Singh, L. Oliker, R. Biswas, "A Comparison of Three Programming Models for Adaptive Applications on the Origin2000", Journal of Parallel and Distributed Computing (JPDC), January 1, 2002, doi: doi:10.1006/jpdc.2001.1777

L. Oliker, R. Biswas, S. Das, D. Harvey, "Parallel Dynamic Load Balancing Strategies for Adaptive Irregular Applications", DRAMA special issue of Applied Mathematical Modeling Journal, 2000,

L. Oliker, R. Biswas, "Parallelization of a Dynamic Unstructured Algorithm using Three Leading Programming Paradigms", IEEE Transactions on Parallel and Distributed System (TPDS), 2000,

L. Oliker, R. Biswas and H. Gabow, "Parallel Tetrahedral Mesh Adaptation with Dynamic Load Balancing", Parallel Computing Journal, Special Issue on Graph Partitioning, pp 1583-1608, 2000,

R. Biswas, L. Oliker, "Experiments with Repartitioning and Load Balancing Adaptive Meshes", Grid Generation and Adaptive Algorithms, IMA Volumes in Mathematics and its Applications, Vol. 113, Springer-Verlag, pp.89-112, 1999,

L. Oliker, R. Biswas, "PLUM: Parallel Load Balancing for Adaptive Unstructured Meshes (JPDC version)", Journal of Parallel and Distributed Computing (JPDC), 1998,

R. Strawn, L. Oliker, R. Biswas, "New Computational Methods for the Prediction and Analysis of Helicopter Noise", Journal of Aircraft, 34, pp. 665-672, 1997,

S. Chatterjee, J. Gilbert, L. Oliker, R. Schreiber, and T. Sheffler, "Algorithms for Automatic Alignment of Arrays", Journal of Parallel and Distributed Computing (JPDC), July 1996,

Conference Papers

William Tang, Bei Wang, Stephane Ethier, Grzegorz Kwasniewski, Torsten Hoefler, Khaled Z. Ibrahim4, Kamesh Madduri, Samuel Williams, Leonid Oliker, Carlos Rosales-Fernandez, Tim Williams, "Extreme Scale Plasma Turbulence Simulations on Top Supercomputers Worldwide", Supercomputing, November 2016,

Taylor Barnes, Brandon Cook, Jack Deslippe, Douglas Doerfler, Brian Friesen, Yun (Helen) He, Thorsten Kurth, Tuomas Koskela, Mathieu Lobet, Tareq Malas, Leonid Oliker, Andrey Ovsyannikov, Abhinav Sarje, Jean-Luc Vay, Henri Vincenti, Samuel Williams, Pierre Carrier, Nathan Wichmann, Marcus Wagner, Paul Kent, Christopher Kerr, John Dennis, "Evaluating and Optimizing the NERSC Workload on Knights Landing", Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS), November 2016,

Douglas Doerfer, Jack Deslippe, Samuel Williams, Leonid Oliker, Brandon Cook, Thorsten Kurth, Mathieu Lobet, Tareq Malas, Jean-Luc Vay, and Henri Vincenti, "Applying the Roofline Performance Model to the Intel Xeon Phi Knights Landing Processor", Intel Xeon Phi User Group Workshop (IXPUG), June 2016,

Penporn Koanantakool, Ariful Azad, Aydın Buluç, Dmitriy Morozov, Sang-Yun Oh, Leonid Oliker, Katherine Yelick, "Communication-Avoiding Parallel Sparse-Dense Matrix-Matrix Multiplication", IEEE International Parallel & Distributed Processing Symposium (IPDPS), May 2016,

Abhinav Sarje, Douglas W. Jacobsen, Samuel W. Williams, Todd Ringler, Leonid Oliker, "Exploiting Thread Parallelism for Ocean Modeling on Cray XC Supercomputers", Cray User Group (CUG), London, UK, May 2016,

Evangelos Georganas, Aydın Buluç, Jarrod Chapman, Steven Hofmeyr,
Chaitanya Aluru, Rob Egan, Leonid Oliker, Daniel Rokhsar, Katherine Yelick,
"HipMer: An Extreme-Scale De Novo Genome Assembler", Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC), November 19, 2015,

Veronika Strnadová-Neeley, Aydın Buluç, Jarrod Chapman, John R. Gilbert, Joseph Gonzalez, Leonid Oliker, "Efficient Data Reduction for Large-Scale Genetic Mapping", ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), September 10, 2015,

Abhinav Sarje, Sukhyun Song, Douglas Jacobsen, Kevin Huck, Jeffrey Hollingsworth, Allen Malony, Samuel Williams, and Leonid Oliker, "Parallel Performance Optimizations on Unstructured Mesh-Based Simulations", Procedia Computer Science, 1877-0509, June 2015, 51:2016-2025, doi: 10.1016/j.procs.2015.05.466

This paper addresses two key parallelization challenges the unstructured mesh-based ocean modeling code, MPAS-Ocean, which uses a mesh based on Voronoi tessellations: (1) load imbalance across processes, and (2) unstructured data access patterns, that inhibit intra- and inter-node performance. Our work analyzes the load imbalance due to naive partitioning of the mesh, and develops methods to generate mesh partitioning with better load balance and reduced communication. Furthermore, we present methods that minimize both inter- and intra- node data movement and maximize data reuse. Our techniques include predictive ordering of data elements for higher cache efficiency, as well as communication reduction approaches. We present detailed performance data when running on thousands of cores using the Cray XC30 supercomputer and show that our optimization strategies can exceed the original performance by over 2×. Additionally, many of these solutions can be broadly applied to a wide variety of unstructured grid-based computations.

Protonu Basu, Samuel Williams, Brian Van Straalen, Mary Hall, Leonid Oliker, Phillip Colella, "Compiler-Directed Transformation for Higher-Order Stencils", International Parallel and Distributed Processing Symposium (IPDPS), May 2015,

Evangelos Georganas, Aydın Buluç, Jarrod Chapman, Leonid Oliker, Daniel Rokhsar, Katherine Yelick, "merAligner: A Fully Parallel Sequence Aligner", IEEE International Parallel & Distributed Processing Symposium (IPDPS), 2015,

Hongzhang Shan, Samuel Williams, Wibe de Jong, Leonid Oliker, "Thread-Level Parallelization and Optimization of NWChem for the Intel MIC Architecture", Programming Models and Applications for Multicores and Manycores (PMAM), February 2015,

Evangelos Georganas, Aydin Buluç, Jarrod Chapman, Leonid Oliker, Daniel Rokhsar, Katherine Yelick, "Parallel de bruijn graph construction and traversal for de novo genome assembly", Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC'14), November 2014,

Yu Jung Lo, Samuel Williams, Brian Van Straalen, Terry J. Ligocki, Matthew J. Cordery, Leonid Oliker, Mary W. Hall, "Roofline Model Toolkit: A Practical Tool for Architectural and Program Analysis", Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS), November 2014, doi: 10.1007/978-3-319-17248-4_7

Veronika Strnadova, Aydın Buluç, Joseph Gonzalez, Stefanie Jegelka, Jarrod Chapman, John Gilbert, Daniel Rokhsar, Leonid Oliker, "Efficient and accurate clustering for large-scale genetic mapping", IEEE International Conference on Bioinformatics and Biomedicine (BIBM'14), November 1, 2014,

Protonu Basu, Samuel Williams, Brian Van Straalen, Leonid Oliker, Mary Hall, "Converting Stencils to Accumulations for Communication-Avoiding Optimization in Geometric Multigrid", Workshop on Stencil Computations (WOSC), October 2014,

W.A. de Jong, L. Lin, H. Shan, C. Yang and L. Oliker, "Towards modelling complex mesoscale molecular environments", International Conference on Computational and Mathematical Methods in Science and Engineering (CMMSE), 2014,

Protonu Basu, Anand Venkat, Mary Hall, Samuel Williams, Brian Van Straalen, Leonid Oliker, "Compiler generation and autotuning of communication-avoiding operators for geometric multigrid", 20th International Conference on High Performance Computing (HiPC), December 2013, 452--461,

Bei Wang, Stephane Ethier, William Tang, Timothy Williams, Khaled Z. Ibrahim, Kamesh Madduri, Samuel Williams, Leonid Oliker, "Kinetic Turbulence Simulations at Extreme Scale on Leadership-Class Systems", Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC), November 2013, doi: 10.1145/2503210.2503258

P. Basu, A. Venkat, M. Hall, S. Williams, B. Van Straalen, L. Oliker, "Compiler Generation and Autotuning of Communication-Avoiding Operators for Geometric Multigrid", Workshop on Stencil Computations (WOSC), 2013,

Aydın Buluç, Erika Duriakova, Armando Fox, John Gilbert, Shoaib Kamil, Adam Lugowski, Leonid Oliker, Samuel Williams, "High-Productivity and High-Performance Analysis of Filtered Semantic Graphs", International Parallel and Distributed Processing Symposium (IPDPS), 2013, doi: 10.1145/2370816.2370897

S. Williams, D. Kalamkar, A. Singh, A. Deshpande, B. Van Straalen, M. Smelyanskiy, A. Almgren, P. Dubey, J. Shalf, L. Oliker, "Optimization of Geometric Multigrid for Emerging Multi- and Manycore Processors", Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC), November 2012, doi: 10.1109/SC.2012.85

K. Kandalla, A. Buluç, H. Subramoni, K. Tomko, J. Vienne, L. Oliker, D. K. Panda, "Can network-offload based non-blocking neighborhood MPI collectives improve communication overheads of irregular graph algorithms?", International Workshop on Parallel Algorithms and Parallel Software (IWPAPS 2012), 2012,

A. Buluç, S. Williams, L. Oliker, J. Demmel, "Reduced-Bandwidth Multithreaded Algorithms for Sparse Matrix-Vector Multiplication", International Parallel Distributed Processing Symposium (IPDPS), May 2011, doi: 10.1109/IPDPS.2011.73

P. Narayanan, A. Koniges, L. Oliker, R. Preissl, S. Williams, N. Wright, M. Umansky, X. Xu, S. Ethier, W. Wang, J. Candy, J. Cary, "Performance Characterization for Fusion Co-design Applications", Cray Users Group (CUG), May 2011,

Kamesh Madduri, Khaled Ibrahim, Samuel Williams, Eun-Jin Im, Stephane Ethier, John Shalf, Leonid Oliker, "Gyrokinetic toroidal simulations on leading multi- and manycore HPC systems", Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC), January 2011, 23, doi: 10.1145/2063384.2063415

Samuel Williams, Oliker, Carter, John Shalf, "Extracting ultra-scale Lattice Boltzmann performance via hierarchical and distributed auto-tuning", Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC), New York, NY, USA, ACM, January 2011, 55, doi: 10.1145/2063384.2063458

Jens Krueger, David Donofrio, John Shalf, Marghoob Mohiyuddin, Samuel Williams, Leonid Oliker, Franz-Josef Pfreund, "Hardware/software co-design for energy-efficient seismic modeling", Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC), January 2011, 73, doi: 10.1145/2063384.2063482

R. Sudarsan, J. Borrill, C. Cantalupo, T. Kisner, K. Madduri, L. Oliker, Y. Zheng, H. Simon, "Cosmic microwave background map-making at the petascale and beyond", Proceedings of the International Conference on Supercomputing, 2011, 305-316, doi: 10.1145/1995896.1995944

G. Hendry, J, Chan, S, Kamil, L. Oliker , J. Shalf, L. Carloni , K. Bergman, "Silicon Nanophotonic Network-On-Chip using TDM Arbitration", Hot Interconnects, August 2010,

Testing

S. Ethier, M. Adams, J. Carter, L. Oliker, "Petascale Parallelization of the Gyrokinetic Toroidal Code", VECPAR: High Performance Computing for Computational Science, June 2010,

Shoaib Kamil, Cy Chan, Leonid Oliker, John Shalf, Samuel Williams, "An auto-tuning framework for parallel multicore stencil computations", International Parallel & Distributed Processing Symposium (IPDPS), January 1, 2010, 1-12, doi: 10.1109/IPDPS.2010.5470421

A. Chandramowlishwaran, S. Williams, L. Oliker, I. Lashuk, G. Biros, R. Vuduc, "Optimizing and Tuning the Fast Multipole Method for State-of-the-Art Multicore Architectures", International Parallel & Distributed Processing Symposium (IPDPS), 2010, doi: 10.1109/IPDPS.2010.5470415

Andrew Uselton, Howison, J. Wright, Skinner, Keen, Shalf, L. Karavanic, Leonid Oliker, "Parallel I/O performance: From events to ensembles", International Parallel & Distributed Processing Symposium (IPDPS), 2010, 1-11,

Kamesh Madduri, Samuel Williams, Stephane Ethier, Leonid Oliker, John Shalf, Erich Strohmaier, Katherine Yelick, "Memory-Efficient Optimization of Gyrokinetic Particle-to-Grid Interpolation for Multicore Processors", Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC), November 2009, doi: 10.1145/1654059.1654108

J. Shalf, M. Wehner, L. Oliker, "The Challenge of Energy-Efficient HPC", SCIDAC Review, Fall, 2009,

Shoaib Kamil, Cy Chan, Samuel Williams, Leonid Oliker, John Shalf, Mark Howison, E. Wes Bethel, Prabhat, "A Generalized Framework for Auto-tuning Stencil Computations", Cray User Group Conference (CUG) - BEST PAPER AWARD, Atlanta, GA, May 4, 2009, LBNL 2078E,

S. Williams, J. Carter, L. Oliker, J. Shalf, K. Yelick, "Resource-Efficient, Hierarchical Auto-Tuning of a Hybrid Lattice Boltzmann Computation on the Cray XT4", Proceedings of the Cray User Group (CUG), Atlanta, GA, 2009,

K. Datta, S. Williams, V. Volkov, J. Carter, L. Oliker, J. Shalf, K. Yelick, "Auto-Tuning the 27-point Stencil for Multicore", Proceedings of Fourth International Workshop on Automatic Performance Tuning (iWAPT2009), January 2009,

Joseph Gebis, Oliker, Shalf, Williams, Katherine A. Yelick, "Improving Memory Subsystem Performance Using ViVA: Virtual Vector Architecture", International Conference on Architecture of Computing Systems (ARCS), Delft, Netherlands, 2009, 146-158,

G. Hendry, S.A. Kamil, A. Biberman, J. Chan, B.G. Lee, M Mohiyuddin, A. Jain, K. Bergman, L.P. Carloni, J. Kubiatocics, L. Oliker, J. Shalf, "Analysis of Photonic Networks for Chip Multiprocessor Using Scientific Applications", International Symposium on Networks-on-Chip (NOCS), 2009,

Marghoob Mohiyuddin, Murphy, Oliker, Shalf, Wawrzynek, Samuel Williams, "A design methodology for domain-optimized power-efficient supercomputing", Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC), 2009, doi: 10.1145/1654059.1654072

K. Datta, M. Murphy, V. Volkov, S. Williams, J. Carter, L. Oliker, D. Patterson, J. Shalf, K. Yelick, "Stencil Computation Optimization and Auto-Tuning on State-of-the-Art Multicore Architectures", Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC), November 2008, doi: 10.1109/SC.2008.5222004

S. Williams, J. Carter, L. Oliker, J. Shalf, K. Yelick, "Lattice Boltzmann Simulation Optimization on Leading Multicore Platforms", IEEE International Symposium on Parallel and Distributed Processing. BEST PAPER AWARD - Applications Track, 2008, doi: 10.1109/IPDPS.2008.4536295

William T.C. Kramer, John M. Shalf, E. Wes Bethel, D. Agarwal, Michael Banda, John Hules, Juan C. Meza, Leonid Oliker, Horst Simon, David Skinner, Francesca Verdier, Howard Walter, Michael Wehner, and Katherine Yelick, "HPC in 2016: A View Point from NERSC", Proceedings of the Cray User Group Conference, Helsinki, Finland, 2008,

S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, J. Demmel, "Optimization of Sparse Matrix-Vector Multiplication on Emerging Multicore Platforms", Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC), November 2007, doi: 10.1145/1362622.1362674

J. Borrill, L. Oliker. J. Shalf, H. Shan, "Investigation Of Leading HPC I/O Performance Using A Scientific-Application Derived Benchmark", Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC), 2007,

Shoaib Kamil, Pinar, Gunter, Lijewski, Oliker, John Shalf, "Reconfigurable hybrid interconnection for static and dynamic scientific applications", Conf. Computing Frontiers, 2007, 183-194, LBNL 60060,

Leonid Oliker, Canning, Carter, Iancu, Lijewski, Kamil, Shalf, Shan, Strohmaier, Ethier, Tom Goodale, "Scientific Application Performance on Candidate PetaScale Platforms", IEEE International Symposium on Parallel & Distributed Processing (IPDPS). BEST PAPER AWARD - application track., 2007, 1-12, doi: 10.1109/IPDPS.2007.370259

J. Carter, L. Oliker, J. Shalf, "Performance Evaluation of Scientific Applications on Modern Parallel Vector Systems", Extended Version: Lecture Notes in Computer Science, 2007,

S. Williams, J. Shalf, L. Oliker, P. Husbands, S. Kamil, K. Yelick, "The Potential of the Cell Processor for Scientific Computing", ACM International Conference on Computing Frontiers, 2006, doi: 10.1145/1128022.1128027

Shoaib Kamil, Datta, Williams, Oliker, Shalf, Katherine A. Yelick, "Implicit and explicit optimizations for stencil computations", Memory System Performance and Correctness, 2006, 51-60, doi: 10.1145/1178597.1178605

J. Carter, L. Oliker, J. Shalf, "Performance Evaluation of Scientific Applications on Modern Parallel Vector Systems", VECPAR, 2006,

Michael Welcome, Charles Rendleman, Leonid Okiker, Rupak Biswas, "Performance Characteristics of an Adaptive Mesh Refinement Calculation on Scalar and Vector Platforms", accepted, AMC International Conference on Computing Frontiers, May 2-5, Italy, 2006, LBNL 59238,

J. Carter, L. Oliker, "Performance Evaluation of Lattice-Boltzmann Magnetohyrodynamics Simulations on Modern Parallel Vector Systems", Proceedings of the 2nd Teraflop Workshop. Lecture Notes in Computer Science (LNCS), Stuttgard, Germany, January 1, 2006,

Jonathan Carter, Oliker, John Shalf, "Performance Evaluation of Scientific Applications on Modern Parallel Vector Systems", VECPAR, Springer Berlin/Heidelberg, 2006, 4395:490-503,

J. Carter, L. Oliker, J. Shalf, "Performance Evaluation of Scientific Applications on Modern Parallel Vector Systems", High Performance Computing for Computational Science., 2006,

Highest Ranked Conference Paper

Leonid Oliker, Jonathan Carter, Michael Wehner, Andrew Canning, Stephane Ethier, Art Mirin, David Parks, Patrick Worley, Shigemune Kitawaki, Yoshinori Tsuda, "Leading Computational Methods on Scalar and Vector HEC Platforms", SC 05, Washington, DC, USA, IEEE Computer Society, 2005, 62, doi: 10.1109/SC.2005.41

John Shalf, Kamil, Oliker, David Skinner, "Analyzing Ultra-Scale Application Communication Requirements for a Reconfigurable Hybrid Interconnect", Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC), 2005, 17,

J. Carter, M. Soe, L. Oliker, Y. Tsuda, G. Vahala, L. Vahala, A. Macnab, "Magnetohydrodynamic Turbulence Simulations on the Earth Simulator Using the Lattice Boltzmann Method", International Conference for High Performance Computing, Networking, Storage and Analysis (SC) - Gordon Bell Finalist, Washington, DC, USA, IEEE Computer Society, 2005,

S. Kamil, J. Shalf, L. Oliker, D. Skinner,, "Understanding Ultra-Scale Application Communication Requirements", IEEE International Symposium on Workload Characterization (IISWC), 2005,

Shoaib Kamil, Husbands, Oliker, Shalf, Katherine A. Yelick, "Impact of modern memory subsystems on cache optimizations for stencil computations", Memory System Performance, 2005, 36-43,

J. Borrill, J. Carter, L. Oliker, D. Skinner, R. Biswas, "Integrated performance monitoring of a cosmology application on leading HEC platforms", Proceedings of the International Conference on Parallel Processing, 2005, 2005:119-128, doi: 10.1109/ICPP.2005.47

L. Oliker, R. Biswas, J. Borrill, A. Canning, J. Carter, M.J. Djomehri, H. Shan, D. Skinner, "A performance evaluation of the cray X1 for scientific applications", Lecture Notes in Computer Science, Springer Berlin/Heidelberg, 2005, 3402:51-65,

Horst Simon, William Kramer, William Saphir, John Shalf, David Bailey, Leonid Oliker, Michael Banda, C. William McCurdy, John Hules, Andrew Canning, Marc Day, Philip Colella, David Serafini, Michael Wehner, Peter Nugent, "Science-Driven System Architecture: A New Process for Leadership Class Computing", Journal of the Earth Simulator, Volume 2., 2005, LBNL 56545,

J. Carter, J. Borrill, L. Oliker, "Performance characteristics of a cosmology package on leading HPC architectures", Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Berlin/Heidelberg, 2004, 3296:176-188,

H. Shan, L. Oliker, R. Biswas, W. Smith, "Scheduling in Heterogeneous Grid Environments: The Effects of Data Migration", International Conference on Advanced Computing and Communication: ADCOM, 2004,

Leonid Oliker, Canning, Carter, Shalf, St\ ephane Ethier, "Scientific Computations on Modern Parallel Vector Systems", International Conference for High Performance Computing, Networking, Storage and Analysis (SC). Nominated Best Paper Award, Washington, DC, USA, IEEE Computer Society, 2004, 10, doi: 10.1109/SC.2004.54

L. Oliker, J. Borril, A. Canning, J. Carter, H. Shan, D. Skinner, R. Biswas, J. Djomheri, "A Performance Evaluation of the Cray X1 for Scientific Applications", VECPAR'04: 6th International Meeting on High Performance Computing for Computational Science, 2004,

G. Griem, L. Oliker, J. Shalf, K. Yelick, "Identifying Performance Bottlenecks on Modern Microarchitectures Using an Adaptable Probe", IEEE International Symposium on Parallel & Distributed Processing (IPDPS), 2004,

H. Shan, E. Strohmaier, L. Oliker, "Optimizing Performance of Superscalar Codes for a Single Cray X1 MSP", Proceedings of the 46th Cray User Group Conference:CUG, 2004,

P. A. Agarwal,R. A. Alexander , E. Apra, S. Balay, A. S. Bland, J. Colgan, E. F.D’Azevedo , J. J. Dongarra , T. H. Dunigan, Jr. , M. R. Fahey, R. A. Fahey, A. Geist, M. Gordon, R. J. Harrison , D. Kaushik, M. Krishnakumar , P. Luszczek , A. Mezzacappa, J. A. Nichols , J. Nieplocha, L. Oliker, T. Packwood , M.S. Pindzola, T. C. Schulthess, J. S. Vetter, J. B. White, III , T. L. Windus , P. H. Worley, T. Zacharia, "Cray X1 Evaluation Status Report", Proceedings of the 46th Cray User Group Conference:CUG, 2004,

L. Oliker, G. Griem, "Transitive Closure on the Imagine Stream Processor", Fifth Workshop on Media and Stream Processors (MSP5), 2003,

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, David Skinner, Stephane Ethier, Rupak Biswas, Jahed Djomehri, Rob F. Van der Wijngaart, "Evaluation of Cache-based Superscalar and Cacheless Vector Architectures for Scientific Computations", International Conference for High Performance Computing, Networking, Storage and Analysis (SC), New York, NY, USA, ACM, 2003, 38, doi: 10.1145/1048935.1050213

H. Shan, L. Oliker, R.Biswas, "Job Superscheduler Architecture and Performance in Computational Grid Environments", International Conference for High Performance Computing, Networking, Storage and Analysis (SC), 2003,

S. Chatterji, J. Duell, M. Narayanan, L. Oliker, "Performance Evaluation of Two Emerging Media Processors: VIRAM and Imagine", Workshop on Parallel and Distributed Image Processing, Video Processing, and Multimedia (PDIVM), 2003,

B. Gaeke, P. Husbands, X. Li, L. Oliker, K. Yelick, and R. Biswas, "Memory-Intensive Benchmarks: IRAM vs. Cache-Based Machines", International Parallel & Distributed Processing Symposium (IPDPS), 2002,

H. Shan, J. Singh, L. Oliker, R. Biswas, "Message Passing vs. Shared Address Space on a Cluster of SMPs", International Parallel & Distributed Processing Symposium (IPDPS), 2001,

L. Oliker, X. Li, P. Husbands, R. Biswas, "Ordering Schemes for Sparse Matrices using Modern Programming Paradigms", The IASTED International Conference on Applied Informatics (AI), 2001,

H. Shan, J. Singh, L. Oliker, R. Biswas, "A Comparison of Three Programming Models for Adaptive Applications on the Origin2000", International Conference for High Performance Computing, Networking, Storage and Analysis (SC) - BEST STUDENT PAPER AWARD, 2000,

L. Oliker, A. Wong, W. Kramer, T. Kaltz, D. Bailey, "ESP: A System Utilization Benchmark", International Conference for High Performance Computing, Networking, Storage and Analysis (SC), 2000,

L. Oliker, X. Li. G. Heber, R. Biswas, "Parallel Conjugate Gradient: Effects of Ordering Strategies, Programming Paradigms, and Architectural Platforms", 13th Interational Conference on Parallel and Distributed Computing Systems, 2000,

L. Oliker, A. Wong, W. Kramer, T. Kaltz, D. Bailey, "System Utilization Benchmark on the Cray T3E and IBM SP", Fifth Workshop on Job Scheduling, 2000,

L. Oliker, X. Li, G. Heber, R. Biswas, "Ordering Unstructured Meshes for Sparse Matrix Computations on Leading Parallel Systems", Seventh International Workshop on solving Irregularly Structured Problems in Parallel, 2000,

L. Oliker, R. Biswas, "Multithreaded Implementation of a Dynamic Irregular Application", 5th NASA Computational Aerosciences Workshop, 2000,

L. Oliker, R. Biswas, "Parallelization of a Dynamic Unstructured Application using Three Leading Paradigms", International Conference for High Performance Computing, Networking, Storage and Analysis (SC) - BEST PAPER AWARD, 1999,

R. Biswas, S.K. Das, and D.J. Harvey, L. Oliker, "Portable Parallel Programming for the Dynamic Load Balancing of Unstructured Grid Applications", 13th International Parallel Processing Symposium, 1999,

K. Schloegel, G. Karypis, V. Kumar, R. Biswas, L. Oliker, "A Performance Study of Diffusive vs. Remapped Load-Balancing Schemes", 11th International Conference on Parallel and Distributed Computer Systems, pp. 59-66, 1998,

L. Oliker, R. Biswas, H.N. Gabow, "Performance Analysis and Portability of the PLUM Load Balancing System", Euro-Par'98 Parallel Processing, Lecture Notes in Computer Science, Vol. 1470, Springer-Verlag, pp. 307-317, 1998,

L. Oliker, R. Biswas, "Dynamic Domain Decomposition for Large-Scale Adaptive Calculations", 10th International Conference on Domain Decomposition Methods, 1997,

L. Oliker, R. Biswas, "Load Balancing Unstructured Adaptive Grid Computations", 4th U.S. National Congress on Computaional Mechanics, 1997,

R. Biswas, L. Oliker, "Load Balancing Sequences of Unstructured Adaptive Grids", 4th International Conference on High Performance Computing (HiPC), 1997,

L.Oliker, R. Biswas, "Efficient Load Balancing and Data Remapping for Adaptive Grid Calculations", 9th ACM Symposium on Parallel Algorithms and Architectures (SPAA), 1997,

R. Biswas, L. Oliker, A. Sohn, "Global Load Balancing with Parallel Mesh Adaption on Distributed-Memory Systems", International Conference for High Performance Computing, Networking, Storage and Analysis (SC), 1996,

L. Oliker, R. Biswas, S. Strawn, "Parallel Implementation of an Adaptive Scheme for 3D Unstructured Grids on the SP2", Parallel Algorithms for Irregularly Structured Problems, Lecture notes in Computer Science, Vol. 1117, Springer-Verlag, pp. 35-47, 1996,

L. Oliker, R. Biswas, S. Strawn, "Parallel Mesh Adaption with Global Load Balancing on the SP2", NASA Computational Aerosciences Workshop, 1996,

A.M. Wissink, A.S. Lyrintzis, R.C. Strawn, L. Oliker, R. Biswas, "Efficient Helicopter Aerodynamic and Aeroacoustic Predictions on Parallel Computers", 34th AIAA Aerospace Sciences Meeting, Paper 96-0153, 1996,

Book Chapters

S. Williams, N. Bell, J. W. Choi, M. Garland, L. Oliker, R. Vuduc, "Sparse Matrix-Vector Multiplication on Multicore and Accelerators", chapter in Scientific Computing with Multicore and Accelerators, edited by Jack Dongarra, David A. Bader, Jakub Kurzak, ( 2010)

K. Datta, S. Williams, V. Volkov, J. Carter, L. Oliker, J. Shalf, K. Yelick, "Auto-tuning Stencil Computations on Multicore and Accelerators", Scientific Computing with Multicore and Accelerators, edited by Jack Dongarra, David A. Bader, ( 2010)

L. Oliker, J. Carter, V. Beckner, J. Bell, H. Wasserman, M. Adams, S. Ethier, E. Schnetter, "Large-Scale Numerical Simulations on High-End Computational Platforms", Chapman & Hall/CRC Computational Science, edited by D. H. Bailey, R. F. Lucas, S. W. Williams, (CRC Press: 2010) Pages: 123

Samuel Williams, Kaushik Datta, Leonid Oliker, Jonathan Carter, John Shalf, Katherine Yelick, "Auto-Tuning Memory-Intensive Kernels for Multicore", Performance Tuning of Scientific Applications, edited by D. H. Bailey, R. F. Lucas, S. W. Williams, (CRC Press: 2010) Pages: 219

John Shalf, Donofrio, Rowen, Oliker, Michael F. Wehner, "Green Flash: Climate Machine (LBNL)", Encyclopedia of Parallel Computing, (Springer: 2010) Pages: 809-819

Green Flash is a research project focused on an application-driven manycore chip design that leverages commodity-embedded circuit designs and hardware/software codesign processes to create a highly programmable and energy-efficient HPC design. The project demonstrates how a multidisciplinary hardware/software codesign process that facilitates close interactions between applications scientists, computer scientists, and hardware engineers can be used to develop a system tailored for the requirements of scientific computing.

L. Oliker, A. Canning, J. Carter, C. Iancu, M. Lijewski, S. Kamil, J. Shalf, H. Shan, E. Strohmaier, S. Ethier, T. Goodale, "Performance Characteristics of Potential Petascale Scientific Applications", Petascale Computing: Algorithms and Applications. Chapman & Hall/CRC Computational Science Series (Hardcover), edited by David A. Bader, ( 2007)

Chapter

L. Oliker, R. Biswas, R. Van der Wijngaart, D. Baily, A. Snavely, "Performance Evaluation and Modeling of Ultra-Scale Systems", Parallel Processing for Scientific Computing, edited by Michael A. Heroux, Padma Raghavan, and Horst D. Simon, (SIAM: 2007) doi: 0.1137/1.9780898718133.ch5

J. Shalf, L. Oliker, M. Lijewski, S. Kamil, J. Carter, A. Canning, S. Ethier, "Performance Characteristics of Potential Petascale Scientific Applications", Chapman & Hall/CRC Computational Science, (CRC Press: 2007) Pages: 1

Book Chapter

Presentation/Talks

Kamesh Madduri, Williams, Ethier, Oliker, Shalf, Strohmaier, Katherine A. Yelick, Memory-efficient optimization of Gyrokinetic particle-to-grid interpolation for multicore processors, Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC), 2009,

S. Williams, et al., The Roofline Model: A Pedagogical Tool for Auto-tuning Kernels on Multicore Architectures, Hot Chips 20, August 10, 2008,

M. Wehner, L. Oliker, J. Shalf, Ultra-Efficient Exascale Scientific Computing, 2008,

L. Oliker, J. Shalf, M. Wehner, Climate Modeling at the Petaflop Scale using Semi-Custom Computing, SIAM Conference on Computational Science and Engineering, 2007,

John Shalf, Shoaib Kamil, David Skinner, Leonid Oliker, Interconnect Requirements for HPC Applications, 2007,

Leonid Oliker, Julian Borrill, Hongzhang Shan, John Shalf, Investigation Of Leading HPC I/O Performance Using A Scientific-Application Derived Benchmark., 2007,

L. Oliker, J. Carter, Leading Computational Methods on the Earth Simulator, SIAM Conference on Parallel Processing for Scientific Computing, 2006,

L. Oliker, J. Carter, Evaluation of Vector Architectures for Scientific Codes, SIAM Conference on Parallel Processing for Scientific Computing, 2004,

L. Oliker, M. Wehner, D. Parks, W.S. Wang, High Resolution Atmospheric General Circulation Model Simulations on Vector and Cache-based Architectures, SIAM Conference on Parallel Processing for Scientific Computing, 2004,

H. Shan, J. Singh, L. Oliker, R. Biswas, Design Strategies for Irregularly Adapting Parallel Applications, SIAM Conference on Parallel Processing, 2001,

L. Oliker, R. Biswas, P. Husbands, X. Li, Ordering Sparse Matrices for Cache-Based Systems, SIAM Conference on Parallel Processing, 2001,

L. Oliker, R. Biswas, Multithreading for Dynamic Irregular Applications, First SIAM Conference on Computational Science and Engineering, 2000,

R. Biswas, L. Oliker, Load Balancing Unstructured Adaptive Grids for CFD Problems, 8th SIAM Conference on Parallel Processing for Scientific Computing, 1997,

Reports

Hongzhang Shan, Samuel Williams, Wibe de Jong, Leonid Oliker, "Thread-Level Parallelization and Optimization of NWChem for the Intel MIC Architecture", LBNL Technical Report, October 2014, LBNL 6806E,

Samuel Williams, Dhiraj D. Kalamkar, Amik Singh, Anand M. Deshpande, Brian Van Straalen, Mikhail Smelyanskiy,
Ann Almgren, Pradeep Dubey, John Shalf, Leonid Oliker,
"Implementation and Optimization of miniGMG - a Compact Geometric Multigrid Benchmark", December 2012, LBNL 6676E,

M. Christen, N. Keen, T. Ligocki, L. Oliker, J. Shalf, B. van Straalen, S. Williams, "Automatic Thread-Level Parallelization in the Chombo AMR Library", LBNL Technical Report, 2011, LBNL 5109E,

W. Kramer, J. Carter, D. Skinner, L. Oliker, P. Husbands, P. Hargrove, J. Shalf, O. Marques, E. Ng, A. Drummond, K. Yelick, "Software Roadmap to Plug and Play Petaflop/s", 2006,

S. Williams, J. Shalf, L. Oliker, P. Husbands, K. Yelick, "Dense and Sparse Matrix Operations on the Cell Processor", LBNL Technical Report, 2005,

Simon, H., Kramer, W., Saphir, W., Shalf, J., Bailey, D., Oliker, L., Banda, M., McCurdy, C.W., Hules, J., Canning, A., Day, M., Colella, P., Serafini, D., Wehner, M., Nugent, P., "National Facility for Advanced Computational ScienceL A Sustainable Path to Scientific Discovery", April 2004, LBNL 5500,

Thesis/Dissertations

PLUM: Parallel Load Balancing for Adaptive Unstructured Meshes, L. Oliker, 1998,

Posters

A. Buluç, A. Fox, J. R. Gilbert, S. Kamil, A. Lugowski, L. Oliker, S. Williams, "High-performance analysis of filtered semantic graphs", PACT '12 Proceedings of the 21st international conference on Parallel architectures and compilation techniques (extended abstract), 2012, doi: 10.1145/2370816.2370897

S. Williams, J. Carter, J. Demmel, L. Oliker, D. Patterson, J. Shalf, K. Yelick, R. Vuduc, "Autotuning Scientific Kernels on Multicore Systems", ASCR PI Meeting, 2008,