Center for Computing Research (CCR)

Center for Computing Research

Jonathan W. Berry (Jon)

Jonathan W. Berry (Jon)
Discrete Math & Optimization
Email: jberry@sandia.gov
Phone: 505/284-4021
Fax: 505/844-4728

Mailing address:
Sandia National Laboratories
P.O. Box 5800, MS 1327
Albuquerque, NM
87185-1320

Jonathan Berry is a Principal Member of the Technical Staff at Sandia National Laboratories.  He holds a Ph.D. in computer science from Rensselaer Polytechnic Institute and spent almost a decade in liberal arts academia before joining Sandia in 2004. He has led a variety of graph-related projects at Sandia, has served on technical program committees of international conferences/workshops more than ten times, including Supercomputing, ACM/SPAA, IEEE/IPDPS and SIAM Data Mining.  Among his roughly 40 refereed publications are several distinguished papers, including the Best Paper in the Algorithms track of IPDPS 2015.  His software and benchmarking interests include the MultiThreaded Graph Library (MTGL), the Mantevo/miniTri mini-app, and variations on the Firehose benchmark, and his current research includes both static and streaming algorithms for the computational kernels underlying graph algorithms and machine learning.

Education/Background

  • Ph.D. in Computer Science, Rensselaer Polytechnic Institute, 1995
  • M.S. in Computer Science, Rensselaer Polytechnic Institute, 1989
  • B.S. in Computer Science and Economics, The American University, 1987

 

Software

Selected Publications & Presentations

2018
  • Berry, Jonathan W., Cynthia A. Phillips, Sivasankaran Rajamanickam, George M Slota, "Scalable Community Detection Benchmark Generation," Abstract, SIAM Workshop on Combinatorial Scientific Computing, June 2018.
  • Wolf, Michael, Daniel Dunlavy, Richard B. Lehoucq, Jonathan W. Berry, "TriData: High Performance Linear Algebra-Based Data Analytic," Presentation, SIAM Parallel Processing, March 2018.
2017
  • Bender, Michael A., Jonathan W. Berry, Simon David Hammond, Karl Scott Hemmert, Samuel McCauley, Branden J. Moore, Benjamin Moseley, Cynthia A. Phillips, David Richard Resnick, Arun F. Rodrigues, "Two-level main memory co-design: Multi-threaded algorithmic primitives, analysis, and simulation," Journal Article, Journal of Parallel and Distributed Computing, Vol. 102, pp. 213–228, Accepted/Published January 2017.
  • Berry, Jonathan W., Michael Collins, Aaron Kearns, Cynthia A. Phillips, Jared Saia, Randy David Smith, "Cooperative Computing for Autonomous Data Centers," Presentation, SIAM (Society for Industrial and Applied Mathematics) Annual Meeting, part of an invited minisymposium in the special discrete-math track , July 2017.
  • Wolf, Michael, Mehmet Deveci, Jonathan W. Berry, Simon David Hammond, Sivasankaran Rajamanickam, "Fast Linear Algebra-Based Triangle Counting with KokkosKernels," Conference Paper, IEEE HPEC 2017 (Graph Challenge), September 2017.
2016
  • Bender, Michael A, Jonathan W. Berry, Robert Timothy Johnson, Thomas M Kroeger, Cynthia A. Phillips, David Zage, Shiksa Singh, Simon Bertrand, "Anti-Persistence on Persistent Storage: History-Independent Sparse Tables and Dictionaries," Conference Paper, 35th ACM Symposium on Principles of Database Systems, April 2016.
  • Bender, Michael A., Jonathan W. Berry, Robert Johnson, Thomas M. Kroeger, Samuel McCauley, Cynthia A. Phillips, Shikha Singh, " Anti-persistence on persistent storage: history-independent sparse tables and dictionaries," Conference Paper, 2016 ACM SIGMOD/PODS, June 2016.
  • Berry, Jonathan W., Michael Collins, Aaron Kearns, Cynthia A. Phillips, Jared Saia, Randy David Smith, "Cooperative computing for autonomous data centers," Presentation, New York Area Theory Day (invited), April 2016.
  • Edwards, Harold C., Stephen Lecler Olivier, Jonathan W. Berry, Greg Edward Mackey, Sivasankaran Rajamanickam, Kyungjoo Kim, George Widgery Stelle, Michael Wolf, "Kokkos Hierarchical Task-­-Data Parallelism for C++ HPC Applica9ons," Presentation, GPU Technology Conference, April 2016.
2015
  • Bender, Michael, Jonathan Berry, Simon David Hammond, Karl Scott Hemmert, Samuel McCauley, Branden J. Moore, Benjamin Moseley, Cynthia Phillips, David Resnick, Arun Rodrigues, "Two-Level Main Memory Co-Design: Multi-Threaded Algorithmic Primitives, Analysis, and Simulation," Conference Paper, IEEE International Parallel and Distributed Computing Symposium, May 2015.
  • Berry, Jonathan, Michael Collins, Aaron Kearns, Cynthia Phillips, Jared Saia, Randy Smith, "Cooperative Computing for Autonomous Data Centers," Conference Paper, IEEE International Parallel and Distributed Computing Symposium, May 2015.
  • Berry, Jonathan W., Aaron Kearns, Cynthia A. Phillips, Jared Saia, "Finding non-human nodes in social networks using only topology," Presentation, Santa Fe Institute Workshop (invited): Inference on Networks: Algorithms, Phase Transitions, New Models and New Data, December 2015.
  • Berry, Jonathan W., Luke Fostvedt, Daniel Nordman, Cynthia A. Phillips, C. Seshadhri, Alyson Wilson, "Why do simple algorithms for triangle enumeration work in the real world?," Journal Article, Internet Mathematics, Vol. 11, No. 6, pp. 555–571, Accepted/Published May 2015.
  • Wolf, Michael, Jonathan W. Berry, Dylan Stark, "A task-based linear algebra building blocks approach for scalable graph analytics," Conference Paper, 2015 IEEE High Performance Extreme Computing Conference, September 2015.
2014
  • Berry, Jonathan, Aaron Kearns, Cynthia A. Phillips, Jared Saia, "Finding a planted clique in a distributed social network," Workshop Paper, SIAM Workshop on Network Science, July 2014.
  • Berry, Jonathan W, Vitus J Leung, Cynthia A Phillips, Ali Pinar, David G Robinson, Tanya Berger-Wolf, Sanjukta Bhowmick, Emily Casleton, Mark Kaiser, Daniel J Nordman, Alyson G Wilson, "Statistically Significant Relational Data Mining: LDRD Report," SAND Report, February 2014.
  • Berry, Jonathan W, Luke K. Fostvedt, Daniel J Nordman, Cynthia A Phillips, C Seshadhri, Alyson G Wilson, "Why do simple algorithms for triangle enumeration work in the real world?," Conference Paper, 5th Innovations in Theoretical Computer Science Conference, January 2014.
  • Berry, Jonathan W., Luke Fostvedt, Daniel Nordman, Cynthia A. Phillips, Seshadhri Comandur, Alyson Wilson, "Why do Simple Algorithms for Triangle Enumeration work in the Real World?," Conference Paper, Innovations in Theoretical Computer Science, January 2014.
2013
  • Berry, Jonathan W, Matthew Oster, Cynthia A Phillips, Steven J Plimpton, Timothy M Shead, "Maintaining connected components for infinite graph streams," Conference Paper, 2nd International Workshop on Big Data, Streams and Heterogeneous Source Mining, August 2013.
2012
  • Berry, Jonathan, Daniel Dunlavy, Jiqiang Guo, Daniel Nordman, David Robinson, Cynthia Phillips, Alyson Wilson, "Parallel Bayesian Methods for Community Detection," Presentation, SIAM Conference on Parallel Processing for Scientific Computing, February 2012.
  • Berry, Jonathan, Daniel Dunlavy, Jiqiang Guo, Daniel Nordman, Cynthia Phillips, David Robinson, Alyson Wilson, "Scalable Bayesian Nonparametric Methods for Community Detection," Poster, Conference on Data Analysis, February 2012.
2011
  • Berry, Jonathan, Matthew Oster, Cynthia A Phillips, Steven Plimpton, "Challenges in Streaming Graph Analysis," Conference Paper, MILCOM 2011, November 2011.
  • Berry, Jonathan W., Bruce Hendrickson, Randall L. LaViolette, Cynthia A. Phillips, "Tolerating the Community Detection Resolution Limit with Edge Weighting," Journal Article, Physical Review E., Accepted/Published February 2011.
2010
  • Berry, Jonathan W, "Graph Analysis with High-Performance Computing (Plenary Presentation)," Presentation, SIAM Parallel Processing 2010, February 2010.
2009
  • Barrett, Brian W, Jonathan W Berry, Richard C Murphy, Kyle B Wheeler, "Implementing a Portable Multi-Threaded Graph Library: the MTGL on Qthreads," Workshop Paper, 2009 IEEE International Symposium on Parallel and Distributed Processing (MTAAP Workshop), May 2009.
  • Berry, Jonathan W., Robert D. Carr, William E. Hart, Vitus J. Leung, Cynthia A. Phillips, Jean-Paul Watson, "Designing Contamination Warning System for Municipal Water Networks Using Imperfect Sensors ," Journal Article, Journal of Water Resources Planning and Management , Vol. 135, No. 4, pp. 253–263, Accepted/Published July 2009.
  • Murray, Regan, Terranna Haxton, Robert Janke, William E. Hart, Cynthia A. Phillips, Jonathan Berry, "Sensor Network Design for Drinking Water Contamination Warning Systems: A Compendium of Research Results and Case Studies using the TEVA-SPOT software INSTITUTION U.S. Environmental Protection Agency," SAND Report, November 2009.
  • Murray, Regan, William E. Hart, Cynthia A. Phillips, Jonathan Berry, Erik Boman, Lee Ann Riesen, Jean-Paul Watson, Terranna Haxton, George Gray, Jonathan Herrmann, Robert Janke, Thomas Taxon, James Uber, Kevin Morley, "U.S. Environmental Protection Agency uses Operations Research to Reduce Drinking Water Contamination Risks," Journal Article, JOURNALINFORMS Interfaces, Accepted/Published January 2009.
2008
  • Berry, Jonathan W, Erik G Boman, Lee Ann Riesen, Cynthia A Phillips, "Low-memory Lagrangian Relaxation Methods for Sensor Placement in Municipal Water Networks ," Conference Paper, Environmental Water Resources Institute, May 2008.
  • Berry, Jonathan W, Erik Boman, Lee Ann Riesen, William E Hart, Cynthia A Phillips, Jean-Paul Watson, "User's Manual: TEVA-SPOT Toolkit 2.0," SAND Report, April 2008.
  • Devine, Karen D, Steven J Plimpton, Jonathan W Berry, "The PageRank Derby," Presentation, Sandia CSRI Student Seminar, July 2008.
  • Devine, Karen D, Steven J Plimpton, Jonathan W Berry, "The PageRank Derby," Conference Paper, Workshop on Data Mining and Data Analysis, July 2008.
  • Hendrickson, Bruce, Jonathan W Berry, "Graph Analysis with High Performance Computing," Journal Article, Computing in Science and Engineering, Vol. 10, No. 2, pp. 14–19, Accepted/Published March 2008.
  • Murray, Regan, William E Hart, Jonathan W Berry, Robert Janke, Tom Taxon, James Uber, "A Decision Framework for Selecting a Sensor Network Design for Contamination Warning Systems," Journal Article, AWWA Journal, Accepted/Published December 2008.
  • Phillips, Cynthia A, Jonathan W Berry, Erik G Boman, Lee Ann Riesen, "Low-memory Lagrangian relaxation methods for sensor placement in municipal water networks," Conference Paper, World Environmental and Water Resources Congress, 2008, May 2008.
  • Watson, Jean-Paul, Jonathan W Berry, William E Hart, Cynthia A Phillips, Avi Ostfeld, James G Uber, "The Battle of the Water Sensor Networks (BWSN): A Design Challenge for Engineers and Algorithms," Journal Article, Journal of Water Resources Planning and Management, Vol. To Appear, Accepted/Published December 2008.
2007
  • Berry, Jonathan W, Carl Laird, William E Hart, James G. Uber, "A Morphing Technique to Disguise Water Networks," Conference Paper, EWRI 2007: Environmental Water Resources Institute, May 2007.
  • Berry, Jonathan W, Bruce Hendrickson, Simon Kahan, Petr Konecny, "Software and Algorithms for Graph Queries on Multithreaded Architectures," Workshop Paper, MTAAP: MulitThreaded Architectures and Applications, March 2007.
  • Berry, Jonathan W., Bruce A. Hendrickson, Randall A. Laviolette, Vitus J. Leung, Cynthia A. Phillips, "Community Detection vis Facility Location," Journal Article, Physical Review E, Submitted December 2007.
  • Hart, William E, Jonathan W Berry, Robert Heaphy, Cynthia A Phillips, "EXACT: The Experimental Algorithmics Computational Toolkit," Conference Paper, Workshop on Experimental Computer Science, June 2007.
  • Hart, William E, Cynthia A Phillips, Erik G Boman, Jonathan W Berry, Lee Ann Riesen, Jean-Paul Watson, "Limited Memory Techniques for Sensor Placement in Water Distribution Networks," Conference Paper, Learning and Intelligent Optimization (LION-2) Workshop, November 2007.
  • Hart, William E, Erik G Boman, Jean-Paul Watson, Lee Ann Riesen, Jonathan W Berry, Cynthia A. Phillips, "Limited-Memory Techniques for Sensor Placement in Water Distribution Networks ," Conference Paper, Learning and Intelligent Optimization (LION) II, December 2007.
  • Hart, William E, Cynthia A Phillips, Jonathan W Berry, Erik G Boman, Lee Ann Riesen, Jean-Paul Watson, R Murray, "The TEVA-SPOT Toolkit for Drinking Water Contaminant Warning System Design," Conference Paper, World Environmental and Water Resources Congress 2008, May 2007.
  • Lumsdaine, Andrew, Doug Gregor, Bruce Hendrickson, Jonathan Berry, "Challenges in Parallel Graph Processing," Journal Article, Parallel Processing Letters, Submitted March 2007.
  • Madduri, Kamesh, David A Bader, Joseph Crobak, Jonathan W Berry, Bruce Hendrickson, "Multithreaded Algorithms for Processing Massive Graphs," Book, Petascale Computing: Algorithms and Applications, December 2007.
  • Madduri, Kamesh, David Bader, Jonathan Berry, Joseph Crobak, Bruce Hendrickson, "Multithreaded Algorithms for Processing Massive Graphs," Journal Article, Chapter in, Submitted October 2007.
  • Phillips, Cynthia A, Jonathan W Berry, Robert D Carr, William E Hart, "Scalable Water Network Sensor Placement via Aggregation," Conference Paper, 2007 World Water and Environmental Resources Congress, May 2007.
2006
  • Berry, Jonathan W, Kamesh Madduri, David Bader, Joseph Crobak, "An Experimental Study of a Parallel Shortest Path Algorithm for Solving Large-Scale Graph Instances," Workshop Paper, ALENEX: Workshop on Algorithm Engineering and Experiments, January 2006.
  • Berry, Jonathan W, Robert D Carr, William E Hart, Vitus J Leung, Cynthia A Phillips, Jean-Paul Watson, "On the Placement of Imperfect Sensors in Municipal Water Networks," Conference Paper, 8th Annual Water Distribution System Analysis Symposium, August 2006.
  • Berry, Jonathan W, William E Hart, Cynthia A Phillips, James G Uber, Jean-Paul Watson, "Sensor Placement in Municipal Water Networks with Temporal Integer Programming Models," Journal Article, Journal of Water Distribution Resources Planning and Management, Accepted/Published January 2006.
  • Berry, Jonathan W., Bruce A. Hendrickson, Simon Kahan, Petr Konecny, "Graph Software Development and Performance on the MTA-2 and Eldorado," Conference Paper, Cray Users Group Meeting, Switzerland, May 2006.
  • Berry, Jonathan W., Robert D. Carr, William E. Hart, Vitus J. Leung, Cynthia A. Phillips, Jean-Paul Watson, "On the placement of imperfect sensors in municipal water networks," Presentation, WDSA 2006, August 2006.
  • Berry, Jonathan W., Erik Lauer, Henry C Lin, Cynthia A Phillips, "Scheduling Manual Sampling for Contamination Detection in Municipal Water Networks," Conference Paper, 8th Annual International Symposium on Water Distribution Systems Analysis, August 2006.
  • Cieslewicz, John, Jonathan Berry, Bruce Hendrickson, Kenneth Ross, "Realizing Parallelism in Database Operations: Insights from a Massively Multithreaded Architecture," Conference Paper, 2nd International Workshop on Data Management on New Hardware, June 2006.
  • Madduri, K, D Bader, Jonathan W. Berry, "An Experimental Study of a Parallel Shortest Path Algorithm for Solving Large-Scale Graph Instances," Conference Paper, ALENEX07: Workshop on Algorithm Engineering and Experiments, January 2006.
  • Madduri, K, D. Bader, Jonathan W. Berry, Joseph Crobak, "Parallel Shortest Path Algorithms for Solving Large-Scale Instances," Presentation, 9th DIMACS Implementation Challenge, January 2006.
  • Madduri, Kamesh, David A Bader, Jonathan W Berry, Joseph Crobak, "Parallel Shortest Path Algorithms for Solving Large-Scale Instances," Workshop Paper, 9th DIMACS Implementation Challenge, November 2006.
  • Murphy, Richard C., Jonathan W. Berry, William C. McLendon, III, Bruce A. Hendrickson, Douglas P. Gregor, Andrew Lumsdaine, "DFS: A Simple to Write Yet Difficult to Execute Benchmark," Symposium Paper, IEEE Int'l Symposium on Workload Characterization, October 2006.
  • Underwood, Keith, Megan Vance, Jonathan Berry, Bruce Hendrickson, "Scalability of Graph Algorithms on Eldorado," Conference Paper, Cray Users Group Meeting, May 2006.
  • Watson, Jean-Paul, Jonathan W Berry, William E Hart, Cynthia A Phillips, "A Facility Location Approach to Sensor Placement Optimization," Workshop Paper, 8th Annual Symposium on Water Distribution Systems Analysis, August 2006.
2005
  • Berry, Jonathan W., William E. Hart, Cynthia A. Phillips, "Scalability of Integer Programming Computations for Sensor Placement in Municipal Water Networks," Conference Paper, 2005 World Water & Environmental Resources Congress, May 2005.
  • Berry, Jonathan W., William E. Hart, Cynthia A. Phillips, James G. Uber, Jean-Paul Watson, "Validation and Assessment of Integer Programming Sensor Placement Models," Conference Paper, 2005 World Water & Environmental Resources Congress, May 2005.
  • Berry, Jonathan W., William E. Hart, Cynthia A. Phillips, James G. Uber, Jean-Paul Watson, "Validation and Assessment of Integer Programming Sensor Placement Models," Conference Paper, 2005 World Water & Environmental Resources Congress, May 2005.
  • Berry, Jonathan W., William E. Hart, Cynthia A. Phillips, James G. Uber, Thomas M. Walski, "Water Quality Sensor Placement in Water Networks with Budget Constraints," Conference Paper, 2005 World Water & Environmental Resources Congress, May 2005.
  • Watson, Jean-Paul, William E. Hart, Jonathan W. Berry, "Scalable High-Performance Heuristics for Sensor Placement in Water Distribution Networks," Conference Paper, 2005 World Water and Environmental Resources Congress, May 2005.
2004
  • Hart, William E., Jonathan W. Berry, Lisa Fleischer, Cynthia A. Phillips, Jean-Paul Watson, "Copy of Sensor Placement in Municipal Water Networks," Journal Article, Journal of Water Resources Planning and Management, Submitted September 2004.
  • Hrozencik, Daniel, Shrisha Rao, Shen Zhizhang, Jonathan Berry, "Finding Central Sets of Tree Structures in synchronous Distributed Systems," Conference Paper, 17th International Conference on Parallel and Distributed Computing Systems PDC, September 2004.

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