Jarek Nieplocha's Home Page

phone: 509-372-4469
fax: 509-372-4720
jarek dot nieplocha at pnl dot gov

Dr. Jarek Nieplocha is a Laboratory Fellow and Deputy Director in the Computational Sciences and Mathematics Division of the Fundamental and Computational Science Directorate at Pacific Northwest National Laboratory (PNNL). He is also the Chief Scientist for High Performance Computing in Computational Sciences and Mathematics Division. He leads Advanced Computing Technology Laboratory at PNNL.

His area of research has been in collective and one-sided communication on modern networks, runtime systems, parallel I/O, scalable programming models, multithreading, and component technology for scientific computing. He has led development of Global Arrays, a portable shared memory programming toolkit widely used in scalable computational chemistry applications and other areas, and the ARMCI runtime system that most recently has been used for implementation of the Co-Array Fortran compiler at RiceUniversity, and GPSHMEM, a portable implementation of SHMEM, the popular one-sided communication library developed by Cray, Inc. He has been working with domain scientists on applying high performance computing to several scientific disciplines including chemistry, biology, and power system analysis. He received four best paper awards at leading conferences in high performance computing: IPDPS’03, Supercomputing’98, IEEE High Performance Distributed Computing HPDC-5, and IEEE Cluster’03 conference, and an R&D-100 award for Molecular Sciences Software Suite (MS3). He is sharing with the IBM LAPI development team a patent on event signaling in computer networks that forms a foundation for the LAPI communication library on the IBM SP supercomputer. He authored and coauthored over 100 peer reviewed papers. As an adjunct faculty in Computer Science, Dr. Nieplocha has taught at Washington State University. Dr. Nieplocha participated in MPI Forum in defining the MPI-2 standard. He is Vice-President of HP-CAST, the Hewlett Packard Consortium for Advanced Scientific and Technical Computing. He is also a member of editorial board of International Journal of Computational Science and Engineering.

Professional Activities

Technical Committee Member

CCGrid'2008
ACM Computing Frontiers'07
SC'06, SC'07, SC'08
ICPP'2008
7th, 8th, 9th LCI International Conference on Clusters: The HPC Revolution . 2006,2007, 2008.
2nd Workshop on High Performance Computing. Reliability Issues (HPCRI) of the the 12th International Symposium on High Performance Computer Architecture.
2nd and 3rd Workshop on Performance Optimization for High-Level Languages and Libraries of the 20th IEEE International Parallel & Distributed Processing Symposium (IPDPS 2006/7)
Workshop on Communication Architecture for Clusters of the 20th IEEE International Parallel & Distributed Processing Symposium (2004,2005,2006,2007, 2008)

Organizer

MTAAP'07, MTAAP'08: Workshop on Multithreaded Architectures and Applications (in conjunction with IPDPS)

Peer Reviewer

Journals: The Journal on Parallel and Distributed Processing, IEEE Transactions on Parallel and Distributed Systems, Cluster Journal, International Parallel and Distributing Systems, International Journal High Performance Computing Applications
Conferences: ICPP, HPDC, IPDPS, SC'X

Peer Reviewed Publications

James Dinan, Sriram Krishnamoorthy, D. Brian Larkins, Jarek Nieplocha and P. Sadayappan, Scioto: A Framework for Global-View Task Parallelism, to appear in Proc. ICPP'2008. 2008.

Daniel Chavarria, Andres Marquez, Jarek Nieplocha, Kristyn Maschhoff, Early Experience with Out-of-Core Applications on the Cray XMT, Proceedings MTAAP/IPDPS'08 Workshop. 2008.

A. G. Shet, P. Sadayappan, D. E. Bernholdt, J. Nieplocha, and V. Tipparaju. A Framework for Characterizing Overlap of Communication and Computation in Parallel Applications. In Cluster Computing Journal, 11(1): 75-90, March, 2008.

Juan Piernas, Jarek Nieplocha, Evan J. Felix. "Evaluation of Active Storage Strategies for the Lustre Parallel File System". Proceedings of SC'07. 2007.

Steven Benson, Manojkumar Krishnan, Lois C. McInnes, Jarek Nieplocha, Jason Sarich: Using the GA and TAO toolkits for solving large-scale optimization problems on parallel computers. ACM Trans. Math. Softw. 33(2): 11 (2007).

Daniele Scarpazza, Patrick Mullaney, Oreste Villa, Fabrizio Petrini, Vinod Tipparaju, D.M.L. Brown Jr, Jarek Nieplocha, Transparent System-level Migration of PGAs Applications using Xen on Infiniband, Proceedings IEEE Cluster'07. 2007

Krishnan M, SJ Bohn, WE Cowley, VL Crow, and J Nieplocha, "Scalable Visual Analytics of Massive Textual Datasets", Proc. IEEE International Parallel and Distributed Processing Symposium, 2007.

A. Shet, P. Sadayappan, DE Bernholdt, J. Nieplocha, V. Tipparaju, A framework for characterizing overlap of communication and computation in parallel applications, to appear in Cluster Computing Journal. 2007.

Vinod Tipparaju, Andriy Kot, Jarek Nieplocha, Monika ten Bruggencate, and Nikos Chrisochoides, Evaluation of remote memory access communication on the Cray XT3, Proc. IPDPS/CAC'07. 2007.

Chad Scherrer, Nathaniel Beagley, Jarek Nieplocha, Andres Marquez, John Feo, and Daniel Chavarria, Probability Convergence in a Multithreaded Counting Application, Proc. IPDPS/MTAAP'07 Workshop. 2007.

Huang Z, RT Guttromson, J Nieplocha, and RG Pratt. "Transforming Power Grid Operations via High-Performance Computing.", Scientific Computing, Vol. 24. No. 5, April 2007.

Palmer BJ, SM Kathmann, M Krishnan, V Tipparaju, and J Nieplocha. "The Use of Processor Groups in Molecular Dynamics Simulations to Sample Free Energy States." Journal of Chemical Theory and Computation 3(2):P583-592. 2007.

Fanourgakis GS, V Tipparaju, J Nieplocha, and SS Xantheas. "An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: Application to water." Theoretical Chemistry Accounts (Theoretica Chimica Acta). Volume 117, Number 1 / January, 2007.

C. Oehmen and J. Nieplocha. ScalaBLAST: "A scalable implementation of BLAST for high performance data-intensive bioinformatics analysis." IEEE Trans. Parallel Distributed Systems. Special issue on high-performance computational biology, Vol. 17, No. 8, 2006.

J. Nieplocha, B. Palmer, V. Tipparaju, M. Krishnan, H. Trease, and E. Apra. "Advances, Applications and Performance of the Global Arrays Shared Memory Programming Toolkit." International Journal of High Performance Computing and Applications, 20(2), 2006.

S. Krishnamoorthy, U. Çatalyürek, J. Nieplocha, A. Rountev, P. Sadayappan: Data management and query - Hypergraph partitioning for automatic memory hierarchy management. Proc. SC'2006. 2006.

M. Krishnan and J. Nieplocha. Memory Efficient Parallel Matrix Multiplication Operation for Irregular Problems. In Proceedings of the ACM International Conference on Computing Frontiers, Ischia, Italy, May 2006.

Sriram Krishnamoorthy, Gerald Baumgartner, Chi-Chung Lam, Jarek Nieplocha , P. Sadayappan, Layout transformation support for the Disk Resident Arrays framework, The Journal of Supercomputing, Vol 36, No. 2, pp. 153-170, 2006.

J. Nieplocha, Towards Efficient Power System State Estimators on Shared Memory Computers, Proc. IEEE Power Eng. Society Annual Meeting, Montreal, CA. 2006.

Zhou N, Z Huang, J Nieplocha, and TB Nguyen. "Wide-area Situational Awareness of power grids with limited phasor measurements", Proc. 3rd Conference on Critical Infrastructure (CRIS 2006), International Institute for Critical Infrastructures. 2006.

J. Nieplocha, V. Tipparaju, M. Krishnan, and D. Panda. High Performance Remote Memory Access Comunications: The ARMCI Approach. International Journal of High Performance Computing and Applications, 20(2), 2006.

D. Chavarr´ıa-Miranda, J. Nieplocha, and V. Tipparaju. Topology-aware Tile Mapping for Clusters of SMPs. In Proceedings of the ACM International Conference on Computing Frontiers, Ischia, Italy, May 2006.

Krishnamoorthy S, U Catalyurek, J Nieplocha, and P Sadayappan. 2006. "An Approach to Locality-Conscious Load Balancing and Transparent Memory Hierarchy Management with a Global-Address-Space Parallel Programming Model." In Proc. Workshop on Performance Optimization for High-Level Languages and Libraries of International Parallel and Distributed Symposium (IPDPS'06).

McInnes LC, BA Allan, R Armstrong, SJ Benson, DE Bernholdt, TL Dahlgren, L Diachin, M Krishnan, JA Kohl, J Larson, S Lefantzi, J Nieplocha, B Norris, SG Parker, J Ray, and S Zhou. "Parallel PDE-Based Simulations Using the Common Component Architecture." in Numerical Solution of PDEs on Parallel Computers, Edited by Are Magnus Bruaset, Petter Bjørstad and Aslak Tveito, Volume 51 of Lecture Notes in Computational Science and Engineering (LNCSE), pages 327–-384, Springer-Verlag, 2006.

J. Nieplocha, V. Tipparaju, and Krishnan. Optimizing strided remote memory access operations on the Quadrics QsNet-II network interconnect. In HPC-Asia 2005, Beijing, China, 2005.

Nieplocha J, DJ Baxter, V Tipparaju, C Rasmussen, and RW Numrich. "Symmetric Data Objects and Remote Memory Access Communication for Fortran 95 Applications." In Proceedings of Euro-Par 2005. 2005.

Krishnan M, Y Alexeev, TL Windus, and J Nieplocha. 2005. "Multilevel Parallelism in Computational Chemistry using Common Component Archituecture and Global Arrays." In Proc. SuperComputing (SC’05), The International Conference for High Performance Computing and Communications. 2005.

V. Tipparaju, and J Nieplocha. 2005. "Optimizing All-to-All Collective Communication by Exploiting Concurrency in Modern Networks." In Proc. SuperComputing (SC’05), The International Conference for High Performance Computing and Communications. 2005.

Allan BA, R Armstrong, Bernholdt DE, F Bertrand, K Chiu, TL Dahlgren, K Damevski, WR Elwasif, M Govindaraju, DS Katz, JA Kohl, M Krishnan, GK Kumfert, J Larson, S Lefantzi, MJ Lewis, AD Malony, LC McInnes, J Nieplocha, B Norris, SG Parker, J Ray, S Shende, TL Windus, and S Zhou. "A Component Architecture for High-Performance Scientiﬁc Computing." International Journal of High Performance Computing Applications. 20(2), 2006.

S. Krishnamurthy, P. Saddayappan, Nieplocha J, and M Krishnan. 2005. "Locality-aware Load Balancing for Dynamic and Irregular Computations." In Proc. 1st Workshop on Patterns in High Performance Computing. Urbana-Champaign, 2005.

J. Beecroft, D. Addison, D. Hewson, M. McLaren, D. Roweth, F. Petrini, and J. Nieplocha. Qsnet-II: Defining high-performance network design. IEEE Micro, 25(4), 2005.

Yuri Alexeev, Benjamin A. Allan, Robert C. Armstrong, David E. Bernholdt, Tamara L. Dahlgren, Dennis Gannon, Curtis L. Janssen, Joseph P. Kenny, Manojkumar Krishnan, James A. Kohl, Gary Kumfert, Lois Curfman McInnes, Jarek Nieplocha, Steven G. Parker, Craig Rasmussen, and Theresa L. Windus. Component-Based Software for High-Performance Scientific Computing. In Anthony Mezzacappa, editor, SciDAC 2005, Scientific Discovery through Advanced Computing, 26--30 June 2005, San Francisco, CA, USA, volume 16 of Journal of Physics: Conference Series, pages 536--540, 2005.

Nieplocha J, M Krishnan, BJ Palmer, V Tipparaju, and Y Zhang. 2005. "Exploiting Processor Groups to Extend Scalability of the GA Shared Memory Programming Model." In Proceedings of the ACM SIGMicro Computing Frontiers’2005. 2005.

Nieplocha J, V Tipparaju, and E Apra. 2005. "A Comparison of Two Implementation Strategies for Optimizing One-Sided Atomic Reduction." In Proceedings Communication Architecture for Clusters Workshop of the 19th International Parallel & Distributed Processing Symposium. 2005.

Zhang Y, V Tipparaju, J Nieplocha, and S Hariri. "Parallelization of the NAS Conjugate Gradient Benchmark Using the Global Arrays Shared Memory Programming Model." In Proc. HIPS’05 Workshop of the 19th International Parallel & Distributed Processing Symposium. 2005.

Felix EJ., K. Schmidt, K. Regimbal, J. Nieplocha, Active Storage Processing in a Parallel File System. Proc. 6th LCI International Conference on Linux Clusters: The HPC Revolution 2005 , Chapel Hill, NC on April 26, 2005.

Krishnan M, and J Nieplocha. Optimizing Performance on Linux Clusters Using Advanced Communication Protocols: Achieving Over 10 Teraflops on a 8.6 Teraflops Linpack-Rated Linux Cluster." In Proceedings 6th International Conference on Linux Clusters, The HPC Revolution 2005.

J. Nieplocha, V. Tipparaju, M. Krishnan, G. Santhanaraman, and D. Panda. Optimization and performance evaluation of mechanisms for latency tolerance in remote memory access communication on clusters. Int. J. High Performance Computing and Networking, 2(2/3/4):198–209, 2004.

Sriram Krishnamoorthy, Jarek Nieplocha, Gerald Baumgartner, Chi-Chung Lam and P Sadayappan, Eficient Layout Transformation for Disk-based Multidimensional Arrays, Proc. International Conference on High Performance Computng, HiPC'2004. 2004.

Kenny JP, Benson SJ, Alexeev Y, Sarich JJ, Janssen C, McInnes L, Krishnan M, Nieplocha J, Jurrus ER, Fahlstrom CA and Windus TL. "Components in Computational Chemistry". Journal of Computational Chemistry. 25(14):1717-1725. 2004.

M. Krishnan, V. Tipparaju, B. Palmer, J. Nieplocha, Processor-Group Aware Runtime Support for Shared- and Global-Address Space Models, Proceedings of the 3rd Workshop on Compile and Runtime Techniques for Parallel Computing, International Conference on Parallel Processing, Montreal, Canada. Aug 15, 2004.

Sriram Krishnamoorthy, Gerald Baumgartner, Chi-Chung Lam, Jarek Nieplocha, P Sadayappan, Layout Transformation Support for the Disk Resident Arrays Framework, Proceedings LACSI Symposium. October 12-14, 2004.

C. Rasmussen, M. Sottile, J. Nieplocha, R. Numrich, E. Jones Co-Array Python: A Parallel Extension to the Python Language, Proc. EuroPar-2004. 2004.

R. Mooney, K. Fox., S. Studham, J. Nieplocha, NWPerf: A System Wide Performance Monitoring Tool for Large Linux Clusters, Proceedings of IEEE CLUSTER’04. 2004.

M. Krishnan, J. Nieplocha, Optimizing Parallel Multiplication Operation for Rectangular and Transposed Matrices, 10th IEEE International Conference on Parallel and Distributed Systems (ICPADS’04). 2004.

J. Nieplocha, V. Tipparaju, M. Krishnakumar, G. Santhmaraman, DK Panda, Optimization and Performance Evaluation of Mechanisms for Latency Tolerance in Remote Memory Access Communication on Clusters, accepted for the International Journal of High Performance Computing and Networking, 2004.

V. Tipparaju, G. Santhmaraman, J. Nieplocha, D.K. Panda, Host-assisted zero-copy remote memory access communication on Infiniband, Proceedings International Parallel and Distributed Computing Symposium, IPDPS’04. Santa Fe, NM. 2004.

M. Krishnan, J. Nieplocha, A Matrix Multiplication Algorithm Suitable for Clusters and Scalable Shared Memory Systems, Proceedings International Parallel and Distributed Computing Symposium IPDPS’04. Santa Fe, NM. 2004.

D. Bernholdt, J. Nieplocha, P. Saddayappan, Raising the Level of Programming Abstraction in Scalable Programming Models, Procedings HPCA’04 Workshop on Productivity and Performance in High-End Computing (P-PHEC 2004), Madrid, Spain, 2004.

M. Rosing, J. Nieplocha, S. Yabusaki, Toward Efficient Compilation of User-Defined Extensible Fortran Directives, Proc. High-Level Parallel Programming Models and Supportive Environments, IPDPS-HIPS’2004 Workshop, 2004.

J. Nieplocha, V. Tipparaju, M. Krishnakumar, G. Santhmaraman, DK Panda, Optimizing Mechanisms for Latency Tolerance in Remote Memory Access Operations on Clusters, Proc. IEEE Cluster’03. HK 2003.

B. Palmer, J. Nieplocha, E. Apra, Shared memory mirroring for reducing communication overhead on clusters, Proc. IEEE Cluster’03. HK. 2003.

V. Tipparaju, M. Krishnan, J. Nieplocha, G. Santhanaraman, D. Panda, Exploiting Non-blocking Remote Memory Access Communication in Scientific Benchmarks, Proc. International Conference on High Performance Computng, HiPC'2003.

Rinku Gupta, Pavan Balaji, Dhabaleswar Panda, Jarek Nieplocha, "Efficient Collective Operations using Remote Memory Operations on VIA-Based Clusters," Proc. International Parallel and Distributed Computing Symposium IPDPS’03. 2003.

V. Tipparaju, J. Nieplocha, D. Panda, “Fast Collective Operations Using Shared and Remote Memory Access Protocols on Clusters”, Proc. International Parallel and Distributed Computing Symposium IPDPS’03, Nice, France, April 22-26, 2003.

Darius Buntinas, Amina Saify, Dhabaleswar K. Panda, Jarek Nieplocha, "Optimizing Synchronization Operations for Remote Memory Communication Systems," Proc. IPDPS/CAC’03.

J. Nieplocha, V. Tipparaju, J. Ju, E. Apra, One-sided communication on Myrinet, Cluster Computing, 6, 115-124, 2003.

R. Gupta, V. Tipparaju, J. Nieplocha, and D. K. Panda, "Efficient Barrier using Remote Memory Operations on VIA-Based Clusters," Proc. IEEE Cluster ‘02, Sept. 2002.

J. Nieplocha, R. Harrison, M. Krishnan, B. Palmer, V. Tipparaju, “Combining shared and distributed memory models: Evolution and recent advancements of the Global Array Toolkit”, Proc. POHLL’2002 workshop of ICS-2002, NYC, 2002.

B. Palmer J. Nieplocha, "Efficient algorithms for ghost cell updates on two classes of MPP architectures," Proc. Parallel and Distributed Computing and Systems, PDCS’02. 2002.

J. Nieplocha, V. Tipparaju, A. Saify, D. Panda, Protocols and Strategies for Optimizing Remote Memory Operations on Clusters, Proc. CAC’02 Workshop of IPDPS’02. 2002.

J. Nieplocha, I. Foster, Disk Resident Arrays: An array-oriented I/O library for out-of-core computations, in Rajkumar Buyya, Hai Jin, Toni Cortes (eds) "Disk Arrays and Parallel I/O: Theory and Practice", IEEE CS Press, 2001.

J. Nieplocha, J. Ju, E. Apra, One-sided communication on Myrinet-based SMP clusters using GM message-passing library, Proc. Communication Architecture for Clusters Workshop of IPDPS'01, 2001.

Jarek Nieplocha, Harold Trease, J. Ju, D. Rector, B. Palmer, Building an Application Domain Specific Programming Framework for Computational Fluid Dynamics Calculations on Parallel Computers. Proceedings SIAM Conference on Parallel Processing for Scientific Computing, Portsmouth, Virginia, USA, March 12-14, 2001. SIAM, 2001.

J. Nieplocha, J. Ju, T.P. Straatsma, A multiprotocol communication support for the global address space programming model on the IBM SP, in A. Bode et al (Eds.). Proc. Euro-Par 2000 Parallel Processing, Springer Verlag LNCS 1900, 2000.

R. H. Nobes, A. P. Rendell, J. Nieplocha, Computational Chemistry on Fujitsu Vector-Parallel Processors: Hardware and Programming Environment, Parallel Computing, vol 26, pp. 869-886, 2000.

K. Parzyszek, J. Nieplocha, R.A. Kendall, A generalized portable SHMEM library for high performance computing, Proc. Parallel and Distributed Computing and Systems PDCS-2000, pp. 401-406, 2000.

Kendall RA, Apra E, Bernholdt DE, Bylaska EJ, Dupuis M, Fann GI, Harrison RJ, Ju J, Nichols JA, Nieplocha J, Straatsma T, Windus TL, and Wong AT. "High Performance Computational Chemistry: An Overview of NWChem a Distributed Parallel Application." Computer Physics Communications 28(1-2):260-283. 2000.

S. Anderson, M. Barrios, G. Bhanot, J. Hague, F. Johnson, S. Kandalai, D. Klepacki, J. Levesque, J. Nieplocha, F O’Connell, F. Parpia, C. Pospiech, R. Treumann, J. Tuccillo, B. Walkup, Scientific Applications in RS/6000 SP Environments, IBM Redbook, IBM Corp. SG-245611. 1999.

J. Nieplocha, H. Dachsel, I. Foster, Implementing noncollective parallel I/O in cluster environments using Active Message communication, Cluster Computing, vol 2, 1999.

J. Nieplocha and B. Carpenter, ARMCI: a remote memory copy library for distributed array libraries and compiler run-time systems, volume 1586 of Lecture Notesin Computer Science, pages 533–546. Springer-Verlag, 1999.

J. Nieplocha, I. Foster, H. Dachsel, Distant I/O: One-Sided Access to Secondary Storage on RemoteProcessors, Proceedings of the IEEE Symposium High Performance Distributed Computing HPDC-7, 1998.

H. Dachsel, J. Nieplocha, R.J. Harrison, An out-of-core implementation of the COLUMBUS massively-parallel multireference configuration interaction program, Proceedings of High Performance Networking and Computing Conference, SC'98, 1998.

G. Shah, J. Nieplocha, J. Mirza, C. Kim, R. Harrison, R. Govindraju, K. Gildea, P. DiNicola, C. Bender, “Performance and experience with LAPI- a new high-performance communication library for the IBM RS/6000 SP”, Proc. IEEE International Parallel Processing Symposium IPPS’98, pages 260-266, 1998.

J. Nieplocha, I. Foster, R. Kendall, "ChemIO: High-performance parallel I/O for computational chemistry applications", The International Journal of Supercomputer Applications and High Performance Computing, 12:3, pages 260-266, August, 1998.

T. Muller, S. Xanteas, H. Dachsel, R.J. Harrison, J. Nieplocha, G.S. Kendziora, H. Lischka, A systematic Ab initio investigation of the open ring structures of ozone, Chemical Physics Letters, 293:72-80, 1998.

J Nieplocha and R.J. Harrison, “Shared-memory programming in metacomputing environments: The Global Array approach”, The Journal of Supercomputing, 11:119-136, 1997.

J. Nieplocha, I. Foster, R. Kendall, "ChemIO: High-performance parallel I/O for computational chemistry applications", The International Journal of Supercomputer Applications and High Performance Computing, 1997.

Y. Chen, I. Foster, J. Nieplocha, M. Winslett, “Optimizing Collective I/O Performance on Parallel Computers: A Multisystem Study”, Proc. 11th ACM Intl. Conf. on Supercomputing, 1997.

J. Nieplocha, R.J. Harrison, and I. Foster, “Explicit Management of Memory Hierarchy”, in “Advances in High Performance Computing”, Eds. J. Kowalik, L. Grandinetti, and M. Vajtersic, pages 185-200, Kluwer Academic, 1997.

H. Dachsel, H. Lischka, R.L. Shepard, J. Nieplocha, R.J. Harrison, “A massively parallel multireference configuration interaction program - the parallel COLUMBUS program”, Journal of Chemical Physics, 18:430, 1997.

J. Nieplocha, R.J. Harrison and I. Foster, Explicit Management of Memory Hierarchy, in Advances in High Performance Computing, Editors: L. Grandinetti, J. Kowalik, M. Vajtersic, Kluwer Academic: NATO ASI 3/30: 185-198, 1996

J. Nieplocha, R.J. Harrison, “Shared-memory NUMA programming on I-WAY”, Proc. of IEEE HPDC-5, IEEE Computer Society Press, pp. 432-441, 1996.

J. Nieplocha, R.J. Harrison, R.J. Littlefield, “Global Arrays: A Nonuniform Memory Access Programming Model for High-Performance computers”, The Journal of Supercomputing, vol 10, pp. 197-220, 1996.

J. Nieplocha, I. Foster, “Disk Resident Arrays: An array-oriented I/O library for out-of-core computations”, Proceedings of Frontiers of Massively Parallel Computation, IEEE Computer Society Press, pp. 196-204, 1996.

M.F. Guest, E. Apra, D. E. Bernholdt, H. Fruechtl, R.J. Harrison, R. A. Kendall, R. A. Kutteh, X. Long, J. B. Nicholas, J. A. Nichols, T. Wong, R. J. Littlefield and J. Nieplocha, “High performance computing in chemistry; NWChem”, Future Generation Computer Systems, vol. 12, pp. 273-289, 1996.

M. F. Guest, E. Aprà, D. E. Bernholdt, H. A. Früchtl, R. J. Harrison, R. A. Kendall, R. A. Kutteh, X. Long, J. B. Nicholas, J. A. Nichols, H. L. Taylor, A. T. Wong, G. I. Fann, R. J. Littlefield, and J. Nieplocha, Advances in Parallel Distributed Data Software; Computational Chemistry and NWChem, in Applied Parallel Computing. Computations in Physics, Chemistry and Engineering Science, volume 1041 of Lecture Notes in Computer Science, Springer, Heidelberg, 1996.

R. J. Harrison, M. F. Guest, R. A. Kendall, D. E. Bernholdt, A. T.Wong, M. Stave, J. L. Anchell, A. C. Hess, R.J. Littlefield, G. I. Fann, J. Nieplocha, G. S. Thomas, D. Elwood, J. Tilson, R. L. Shepard, A. F. Wagner, I. T. Foster, E. Lusk and R. Stevens, High Performance Computational Chemistry:(II) A Scalable SCF Program, Journal of Computational Chemistry, 17, 124-132, 1996.

J. Nieplocha, W.C. Schreiber, “The Use of Conjugated Gradient Methods with a Segregated Finite Volume Procedure for Solving Transient Incompressible Navier-Stokes Equations”, Communications in Numerical Methods in Engineering, vol 11, pp. 849-56, 1995.

J. Nieplocha, R.J. Harrison, and R.J. Littlefield. “The Global Array programming model for high performance scientific computing”, SIAM News, August/September, 1995.

J. Nieplocha, R.J. Littlefield, and M. Rosing, “Beyond Message Passing: A case for one-sided communication in MPI”, Proc. 1st MPI Developers Conference, 1995.

D. E. Bernholdt, E. Apra, H. Fruechtl, M.F. Guest, R. J. Harrison, R. A. Kendall, R. A. Kutteh, X. Long, J. B. Nicholas, J. A. Nichols, H. L. Taylor, A. T. Wong, G. I. Fann, R. J. Littlefield and J. Nieplocha, "Parallel Computational Chemistry Made Easier: The Development of NWChem", Int. J. Quantum Chem. Symp., 29, 475-483, 1995.

J. Nieplocha and T.Z. Mai, “Performance improvement of asynchronous iterations by non-uniform load distribution”, Proc. of VII-th SIAM Conf. Parallel Processing for Scientific Applications, 1995.

J. Nieplocha, R.J. Harrison and R.J. Littlefield, “Global Arrays: A Portable Shared Memory Programming Model For Distributed Memory Computers”, Proc. Supercomputing’94, IEEE CS Press, pp. 340-349, 1994.

M.F. Guest, E. Apra, D. E. Bernholdt, H. Fruechtl, R.J. Harrison, R. A. Kendall, R. A. Kutteh, X. Long, J. B. Nicholas, J. A. Nichols, T. Wong, R. J. Littlefield and J. Nieplocha, “High performance Computational Chemistry; Towards Fully Distributed Parallel Algorithms”, in Grand Challenges in Computer Simulation, High Performance Computing 1994, Ed. A.M. Tentner, Society for Computer Simulation, 1994.

J. Nieplocha, C.C. Carroll, “Communication Structures for Asynchronous Algorithms on Distributed MIMD Computers”, Proc. EuroMicro Workshop on Parallel and Distributed Processing, IEEE Computer Soc. Press, 1993.

J. Nieplocha, C.C. Carroll, “Iterative methods for the WLS state estimation on RISC, vector and parallel computers”, Proc. North American Power Symposium’1993, IEEE CS Press, 1993.

A.A. El-Keib, J. Nieplocha, H. Singh, D.J. Maratukulam, “A Decomposed State Estimation Technique Suitable for Parallel Processor Implementation”, IEEE Transactions on Power Systems, Vol. 7, No. 3, August 1992.

J. Nieplocha, C.C. Carroll, T. Mai, “Asynchronous Algorithms for Solving Large Systems of Linear Equations on Parallel Computers,” in Parallel Computing: From Theory to Sound Practice, W. Joosen and E. Milgrom, Eds., IOS Press, 1992.

J. Nieplocha, W. Schreiber, “Lanczos-ORTHOMIN Method Applied to Control Volume for Solving Transient, Incompressible Fluid Flow on Supercomputers”, in Modern Developments in Numerical Simulation of Flow and Heat Transfer, J.L.S. Chen and K. Vafai, Eds., ASME HTD-Vol. 194, 1992.

J. Nieplocha, C.C. Carroll, “Optimal Network Tearing and Mapping to Parallel Computer Architecture”, Proc. IASTED Int. Symposium `Circuits and Systems’, Zurich, Switzerland, 1991.

W. Swiniarski, J. Nieplocha, “Neural Estimation for a Class of Nonlinear Systems”, Proc. Int. AMSE Conf. `Neural Networks in Systems, Control, Vision and Genetics’, San Diego, vol. 2, 1991.

J. Nieplocha, “Discrete-time quadratic optimal control of gas network systems,” Foundations of Control Engineering, vol.13, no. 4, 1988.

B. Szteke, R. Jedrzejczak, J. Nieplocha, B. Tych, “The effect of environmental conditions on heavy metal contents in strawberries”, Fruit Science Reports, vol. 16, no.1, 1989.

J. Nieplocha, “A new algorithm for quadratic optimal control of gas networks”, Gaz, Woda i Technika Sanitarna (in Polish), vol. 62, no. 9, 1988.

J. Nieplocha, “Mean-square approximation of the natural gas compressibility coefficient”, Gaz, Woda i Technika Sanitarna (in Polish), vol. 62, no. 3, 1988.

J. Nieplocha, “Frequency Methods for Gas Network Studies”, Gaz, Woda i Technika Sanitarna, (in Polish) vol. 61, no. 11-12, 1987.

W. Swiniarski, J. Nieplocha, “Modeling, computer simulation, estimation and optimal control of nonlinear continuous culture biotechnological process”, Proc. Int. AMSE Conf. `Modeling and Simulation’, vol 4B, Cairo, Egypt, 1987.

Other Publications

Huang Z, RT Guttromson, J Nieplocha, and RG Pratt. 2007. "Transforming Power Grid Operations via High-Performance Computing.", Scientific Computing, April, 2007.
Jarek Nieplocha, Manojkumar Krishnan and Vinod Tipparaju, “Exploiting Architectural Support for Shared Memory Communication on the Cray X1 to Optimize Bandwidth Intensive Computations”, in Proc. International Cray User Group Conference (CUG), Knoxville, 2004.
Vinod Tipparaju, Manojkumar Krishnan, Bruce Palmer, and Jarek Nieplocha, “Porting and Optimizing Performance of the Global Arrays Toolkit on the Cray X1”, in Proc. International Cray User Group Conference (CUG), Knoxville, 2004.
D.K. Panda, J. Nieplocha, Advanced network interfaces and communication software to deliver petaflop performance on next generation HEC Systems, Whitepaper for High End Computing Revitalization Task Force Workshop, Washington D.C., June 16-18, 2003.
R. Schreiber, S. Studham, Jarek Nieplocha, R. Kaufmann, Revitalizing high-end computing by exploiting assets of the U.S. computer industry and partnership with national laboratories, Whitepaper for High End Computing Revitalization Task Force Workshop, Washington D.C., June 16-18, 2003.
R. Armstrong, D. Bernholdt, T. Dahlgren, W. Elwasif, G. Kumfert L. Curfman McInnes, J. Nieplocha, B. Norris, High Performance Component Technology, Whitepaper for High End Computing Revitalization Task Force Workshop, Washington D.C., June 16-18, 2003.
Jarek Nieplocha, Jialin Ju, Manoj Kumar Krishnan, Bruce Palmer, Vinod Tipparaju, The Global Arrays User's Manual, Technical Report PNNL-13130, Pacific Northwest National Laboratory, 2002.
Harrison RJ, DE Bernholdt, BE Bursten, WA De Jong, DA Dixon, KG Dyall, WC Ermler, GI Fann, PJ Hay, N Ismail Buchner, RA Kendall, J Li, MM Marino, CJ Marsden, RL Martin, Minkoff M, JA Nichols, J Nieplocha, RM Pitzer, LR Pratt, H Schreckenbach, MC Seth, R Shepard, RL Stevens, JL Tilson, AF Wagner, Q Wang, TL Windus, A Wong, and Z Zhang. Computational Chemistry for Nuclear Waste Characterization and Processing: Relativistic Quantum Chemistry of Actinides. PNNL-14001, Pacific Northwest National Laboratory, Richland, WA. 2002.
MJ Peterson, RA Bair, VR Birkenthal, PJ Cowley, JD Myers, J. Nieplocha, JM Price, Annual report: Computing & Information Sciences, PNNL Technical report PNNL-13519, 2000.