Publications and presentations

Generated: 2018-03-21

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Books and Book Chapters

  1. M. Sottile (2010) “Cellular Automata.”, In Encyclopedia of Parallel Computing, Edited by David Padua, Springer, ISBN 978-0-387-09765-7, https://books.google.com/books?vid=ISBN9780387097657

  2. M. Sottile, T. Mattson, C. Rasmussen (2009) “Introduction to Concurrency in Programming Languages.”, Chapman-Hall/CRC Press, ISBN 978-1420072136, http://books.google.com/books?vid=ISBN9781420072136

  3. R. Bramley, R. Armstrong, L. McInnes, M. Sottile (2006) “High-Performance Component Software Systems.”, In Parallel Processing for Scientific Computing, Edited by Michael A. Heroux, Padma Raghavan, and Horst D. Simon, SIAM Press, ISBN 0-89871-619-5, https://books.google.com/books?vid=ISBN0898716195

Journal Publications

  1. M. J. Sottile, J. Dagit, D. Zhang, G. Hendry, D. Dechev (2015) “Static Analysis Techniques for Semi-Automatic Synthesis of Message Passing Software Skeletons.” ACM Transactions on Modeling and Computer Simulation, 2015, https://doi.org/10.1145/2778888

  2. M. J. Sottile, C. E Rasmussen, W. N. Weseloh, R. W. Robey, D. Quinlan, J. Overbey (2013) “ForOpenCL: Transformations Exploiting Array Syntax in Fortran for Accelerator Programming.” International Journal of Computational Science and Engineering (IJCSE), Volume 8, Number 1, 2013, https://doi.org/10.1504/IJCSE.2013.052113

  3. M. A. Abramson, T. J. Asaki, J. E. Dennis, R. Magallanez, M. J. Sottile (2012) “An efficient class of direct search surrogate methods for solving expensive optimization problems with CPU-time-related functions.” Structural and Multidisciplinary Optimization, Volume 45, Number 1, Pages 53-64, January, 2012, https://doi.org/10.1007/s00158-011-0658-3

  4. Kathryn E. McCormick, Bryn E. Gaertner, Matthew Sottile, Patrick C. Phillips, Shawn R. Lockery (2011) “Microfluidic Devices for Analysis of Spatial Orientation Behaviors in Semi-Restrained Caenorhabditis elegans.” PLoS ONE, October 12, 2011, https://doi.org/10.1371/journal.pone.0025710

  5. Serge Faumont, Gary Rondeau, Tod R Thiele, Kristy J Lawton, Kathryn E McCormick, Matthew Sottile, Oliver Griesbeck, Ellie S Heckscher, William M Roberts, Chris Q Doe, Shawn R Lockery (2011) “An image-free opto-mechanical system for creating virtual environments and imaging neuronal activity in freely moving Caenorhabditis elegans.” PLoS ONE, September 28, 2011, https://doi.org/10.1371/journal.pone.0024666

  6. T. J. Asaki, M. Sottile, K. R. Vixie, P. Cherepanov (2010) “Image Denoising by Regularization on Characteristic Graphs.” Applied Mathematical Sciences, 2010

  7. C. D. Rickett, S-E. Choi, C. E Rasmussen, M. J. Sottile (2006) “Rapid Prototyping Frameworks for Developing Scientific Applications: A Case Study.” Journal of Supercomputing, Volume 36, Number 2, Pages 123-134, 2006, https://doi.org/10.1007/s11227-006-7953-6

  8. R. Minnich, M. Sottile, S. Choi, E. Hendriks, J. McKie (2006) “Right-Weight Kernels: an off-the-shelf alternative to custom Light-Weight Kernels.” ACM SIGOPS Operating Systems Review, Volume 40, Number 2, Pages 22-28, 2006, https://doi.org/10.1145/1131322.1131331

  9. R. Armstrong, G. Kumfert, L. Curfman McInnes, S. Parker, B. Allan, M. Sottile, T. Epperly, T. Dahlgren (2006) “The CCA Component Model for High-Performance Scientific Computing.” Concurrency and Computation: Practice and Experience, Volume 18, Number 2, Pages 215-229, 2006, https://doi.org/10.1002/cpe.911

  10. C. E. Rasmussen, M. J. Sottile, S. S. Shende, A. D. Malony (2006) “Bridging the language gap in scientific computing: the Chasm approach.” Concurrency and Computation: Practice and Experience, Volume 18, Number 2, Pages 151-162, 2006, https://doi.org/10.1002/cpe.909

  11. A. Malony, S. Shende, N. Trebon, J. Ray, R. Armstrong, C. Rasmussen, M. Sottile (2005) “Performance Technology for Parallel and Distributed Component Software.” Concurrency and Computation: Practice and Experience, Volume 17, Number 2-4, Pages 117-141, 2005, https://doi.org/10.1002/cpe.931

  12. M. J. Sottile, R. G Minnich (2002) “Scale up your monitoring with Supermon.” IEEE Task Force for Cluster Computing Newsletter, Volume 4, Number 1, 2002

  13. A. D. Malony, J. E. Cuny, J. L. Skidmore, M. J. Sottile (2000) “Computational experiments using distributed tools in a Web-based electronic notebook environment.” Future Generation Computer Systems, Volume 16, Number 5, March, 2000, https://doi.org/10.1016/S0167-739X(99)00135-1

Conference Publications

  1. Craig Rasmussen, Matthew Sottile, Soren Rasmussen, Dan Nagle, William Dumas (2016) “CAFe: Coarray Fortran Extensions for Heterogeneous Computing.” In Proceedings of 21st International Workshop On High-Level Parallel Programming Models And Supportive Environments, at the 30th IEEE IPDPS conference, May, 2016, Chicago, IL

  2. Mark Tullsen, Matthew Sottile (2016) “Array Types for a Graph Processing Language.” In Proceedings of 2016 Graph Algorithms Building Blocks Workshop ,at the 30th IEEE IPDPS conference, May, 2016, Chicago, IL

  3. Jason Dagit, Matthew Sottile (2013) “Identifying change patterns in software history.” In Proceedings of 1st Annual Workshop on (Document) Changes: modeling, detection, storage and visualization (DChanges 2013), at the ACM DocEng 2013 conference, September, 2013

  4. M. J. Sottile, A. Dakshinamurthy, G. Hendry, D. Dechev (2013) “Semi-Automatic Extraction of Software Skeletons for Benchmarking Large-Scale Parallel Applications.” In Proceedings of ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS), May, 2013

  5. G. Hulette, M. J. Sottile, A. D. Malony (2012) “Composing Typemaps in Twig.” In Proceedings of 11th International Conference on Generative Programming and Component Engineering (GPCE’12), 2012, Dresden, Germany

  6. G. Hulette, M. J. Sottile, A. D. Malony (2012) “A Type-based Approach to Separating Protocol from Application Logic: A Case Study in Hybrid Computer Programming.” In Proceedings of EuroPar, 2012, Rhodes, Greece

  7. M. J. Sottile, C. E Rasmussen, W. N. Weseloh, R. W. Robey, D. Quinlan, J. Overbey (2011) “ForOpenCL: Transformations Exploiting Array Syntax in Fortran for Accelerator Programming.” In Proceedings of 2nd International Workshop on GPUs and Scientific Applications (GPUScA 2011), 2011, Galveston, Texas

  8. C. Rasmussen, M. Sottile, G. Kenyon (2010) “Visual Language Recognition with a Feed-Forward Network of Spiking Neurons.” In Proceedings of IADIS International Intelligent Systems and Agents 2010 (ISA 2010) Conference, Pages 26-31, July, 2010, Freiburg, Germany

  9. K. A. Thomas, M. J. Sottile, C. M. Salafia (2010) “Unsupervised segmentation for inflammation detection in histopathology images.” In Proceedings of International Conference on Image and Signal Processing (ICISP), June, 2010, Quebec, Canada

  10. G. Hulette, M. J. Sottile, B. Allan, R. Armstrong (2009) “OnRamp to CCA: Annotation-driven static analysis and code generation.” In Proceedings of Workshop on Component-Based High Performance Computing (CBHPC 2009), held in conjunction with Supercomputing 2009, 2009, Portland, Oregon

  11. M. J. Sottile, G. Hulette, A. D. Malony (2009) “Workflow representation and runtime based on lazy functional streams.” In Proceedings of Workshop on Workflows in Support of Large-Scale Science (WORKS), held in conjunction with Supercomputing 2009, 2009, Portland, Oregon

  12. S. M. Mayanglambam, A. D. Malony, M. J. Sottile (2009) “Performance Measurement of Applications with GPU Acceleration using CUDA.” In Proceedings of International Conference on Parallel Computing, 2009, Lyon, France

  13. A. Salman, A. D. Malony, M. J. Sottile (2009) “An Open Domain-extensible Environment for Simulation-based Scientific Investigation (ODESSI).” In Proceedings of International Conference on Computational Science, 2009

  14. G. Hulette, M. Sottile, A. Malony (2008) “WOOL: A Workflow Programming Language.” In Proceedings of eScience Conference, 2008

  15. A. Nataraj, A. Morris, A. D. Malony, M. Sottile, P. Beckman (2007) “The Ghost in the Machine: Observing the Effects of Kernel Operation on Parallel Application Performance.” In Proceedings of Supercomputing, 2007, Reno, Nevada

  16. A. Nataraj, M. Sottile, A. Morris, A. Malony, S. Shende (2007) “TAUoverSupermon: Low-Overhead Online Parallel Performance Monitoring.” In Proceedings of EuroPar, 2007, Rennes, France

  17. M. Sottile, C. Rasmussen, R. Graham (2006) “Co-Array Collectives: Refined Semantics for Co-Array Fortran.” In Proceedings of International Conference on Computational Science (ICCS 2006), 2006, Edited by V. Alexandrov, D. van Albada, P. Sloot, and J. Dongarra

  18. M. Sottile, V. Chandu, D. Bader (2006) “Performance analysis of parallel programs via message-passing graph traversal.” In Proceedings of IPDPS, 2006, Rhodes, Greece

  19. J. A. Green, et. al. (2006) “Optimizing the tracking efficiency for cosmic ray muon tomography.” In Proceedings of IEEE Nuclear Science Symposium Conference Record, 2006

  20. K. Borozdin, et. al. (2005) “Cosmic-ray muon tomography and its application to the detection of high-Z materials.” In Proceedings of 46th Annual Meeting for the Institute of Nuclear Materials Management, 2005

  21. C. Rasmussen, M. Sottile, C. Rickett (2005) “A Gentle Migration Path to Component-Based Programming.” In Proceedings of International Conference on Parallel Computational Fluid Dynamics (PCFD), 2005, Washington, DC

  22. K. Borozdin, et. al. (2004) “Information extraction from muon radiography data.” In Proceedings of ISAS/CITSA 2004: International Conference on Cybernetics and Information Technologies, Systems and Applications and 10th International Conference on Information Systems Analysis and Synthesis, Volume 2, Pages 27-30, 2004

  23. M. J. Sottile, R. G Minnich (2004) “Analysis of microbenchmarks for performance tuning of clusters.” In Proceedings of Cluster, 2004, San Diego, CA

  24. C. Rasmussen, M. Sottile, J. Nieplocha, R. Numrich, E. Jones (2004) “Co-Array Python: A Parallel Extension to the Python Language.” In Proceedings of EuroPar, 2004, Pisa, Italy

  25. S. Choi, E. Hendriks, R. Minnich, M. Sottile, G. Watson (2004) “Pink: A 1024-node Single-System Image Linux Cluster.” In Proceedings of HPC Asia, Myrinet Users Group Workshop, 2004, Tokyo, Japan

  26. S. Shende, A. D. Malony, C. Rasmussen, M. Sottile (2003) “A Performance Interface for Component-Based Applications.” In Proceedings of International Workshop on Performance Modeling, Evaluation, and Optimization of Parallel and Distributed Systems, IPDPS’03, 2003, Nice, France

  27. M. J. Sottile, R. G Minnich (2002) “Supermon: A high-speed cluster monitoring system.” In Proceedings of Cluster, 2002, Chicago, Illinois

  28. S. Choi, E. Hendriks, R. Minnich, M. Sottile, A. Marks (2002) “Life with Ed: A Case Study of a LinuxBIOS/BProc Cluster.” In Proceedings of 16th Annual International Symposium on High Performance Computing Systems and Applications, 2002, Moncton, New Brunswick, Canada

  29. M. Sottile, A. Malony (1999) “INTERLACE: An Interoperation and Linking Architecture for Computational Engines.” In Proceedings of EuroPar, Pages 135-138, 1999, Toulousse, France

  30. A. Malony, J. Skidmore, M. Sottile (1999) “Computational Experiments using Distributed Tools in a Web-based Electronic Notebook Environment.” In Proceedings of HPCN Europe ’99, 1999, Amsterdam, The Netherlands

  31. J. L. Skidmore, M. J. Sottile, J. E. Cuny, A. D. Malony (1998) “A Prototype Notebook-Based Environment for Computational Tools.” In Proceedings of Supercomputing, 1998, Orlando, Florida

Preprints/arXiv papers

  1. Hossein Noorazar, Matthew Sottile, Kevin Vixie (2017) “Loss of community identity in opinion dynamics models as a function of inter-group interaction strength.”, https://arxiv.org/abs/1708.03317

  2. Hossein Noorazar, Matthew Sottile, Kevin Vixie (2016) “A energy-based interaction model for population opinion dynamics with topic coupling.”, https://arxiv.org/abs/1607.06806

  3. Matthew Sottile (2015) “Blob indentation identification via curvature measurement.”, https://arxiv.org/abs/1501.07692

  4. Matthew Sottile, Geoffrey C. Hulette (2013) “Deriving program transformations by demonstration.”, https://arxiv.org/abs/1301.4334

Published Abstracts

  1. Sean Keeler, Daniel Kiefer, Orion Rust, Nadav Schwartz, Matthew Sottile, Jeffery Dalton, Carolyn Salafia (2008) “141: Collagen integrity of the uterine cervix reflects amniotic fluid cytokine profile.” American Journal of Obstetrics and Gynecology, Volume 199, Number 6, Pages Supplement A, S52, https://doi.org/10.1016/j.ajog.2008.09.168

  2. Nadav Schwartz, Matthew Sottile, Danielle Mandel, Jaclyn Coletta, Ilan E. Timor-Tritsch, Carolyn Salafia (2008) “649: A novel measure of placental vascularity helps predict birthweight variance.” American Journal of Obstetrics and Gynecology, Volume 199, Number 6, Pages Supplement A, S186, https://doi.org/10.1016/j.ajog.2008.09.679

  3. Sean Keeler, Daniel Kiefer, Orion Rust, Eran Bornstein, Matthew Sottile, Jeffrey Dalton, Carolyn Salafia (2008) “804: A novel method of assessing cervical collagen integrity utilizing image segmentation analysis.” American Journal of Obstetrics and Gynecology, Volume 199, Number 6, Pages Supplement A, S227, https://doi.org/10.1016/j.ajog.2008.09.835

  4. Nadav Schwartz, Jaclyn Coletta, Danielle Mandel, Matthew Sottile, Ilan E. Timor-Tritsch, Carolyn Salafia (2008) “650: Placenta vascularization potential is already partly determined by 11-14 weeks.” American Journal of Obstetrics and Gynecology, Volume 199, Number 6, Pages Supplement A, S186, https://doi.org/10.1016/j.ajog.2008.09.680

Posters

  1. G. Hulette, M. Sottile, R. Armstrong, B. Allan (2008) “Using CCA and Onramp to Generate an Application-specific Framework from a Monolithic Application.” In Proceedings of Supercomputing, 2008, Austin, Texas

  2. S. Faumont, G. Rondeau, T. Thiele, M. Sottile, J. Zemek, S. R. Lockery (2008) “Simultaneous recording of neuronal activity and behavior in freely crawling worms.” In Proceedings of Neuronal Development, Synaptic Function and Behavior, C. elegans Topic Meeting No. 2, June, 2008, University of Wisconsin-Madison

  3. C. Rasmussen, M. Sottile, D. Quinlan, W. Weseloh. (2008) “Fortran+- (extensions and restrictions): Is it time for a new parallel language? Not entirely.” In Proceedings of DOE ASCR PI meeting, March, 2008, Denver, CO

  4. T. Asaki, M. Sottile (2005) “DEEPBLUE: A component-based software toolkit for image and shape metrics.” In Proceedings of LANL CCS Division Review, June, 2005

Invited Talks

  1. M. Sottile, D. L. Errington (2018) “Pyx - A Software Synthesis Tool for Python.” Lawrence Livermore National Laboratory, CASC Seminar, January, 2018, Livermore, California

  2. M. Sottile (2017) “Opinion dynamics models based on interaction potentials with topic coupling.” WSU Vancouver Mathematics and Statistics Seminar, January, 2017, Vancouver, Washington

  3. M. Sottile (2016) “Opinion dynamics models based on interaction potentials with topic coupling.” OSU Applied Mathematics Seminar, November, 2016, Corvallis, Oregon

  4. M. Sottile, J. Schoonmaker (2015) “There’s More to See Than Ever Before, The Growing Need for Visual Data Analytics.” AUVSI Cascade Chapter 2015 Dual Track: Unmanned Systems for Emergency Management and Marine Sciences, October, 2015, Newport, Oregon

  5. H. Sorenson, M. Sottile (2015) “Coming Soon - a `Webby’ Store Near You!.” American Marketing Association Analytics with Purpose Conference, March, 2015, San Diego, California

  6. M. Sottile (2015) “Basic Domain Specific Language Concepts in FSharp.” Portland FSharp Meetup Group, January, 2015, Portland, Oregon

  7. M. Sottile (2011) “How many ways can you describe a glass of water (mathematically)?.” Nuts and Bold Ideas Seminar, Portland State University, 2011, Portland, Oregon

  8. M. Sottile (2010) “Lazy functional streams for workflow representation and runtime.” Workshop in Kyoto. Also presented at Tokyo University and Kyoto University, February, 2010

  9. M. Sottile (2008) “CCA On-Ramp.” Quarterly CCA Meeting, July, 2008, Bethesda, Maryland

  10. C. Rasmussen, M. Sottile, D. Quinlan, W. Weseloh. (2008) “SAFe Parallel Programming: Single Assignment Fortran.” Microsoft Research, April 18, 2008, Redmond, Washington

  11. M. Sottile (2007) “Image metrics project (U).” Classified presentation, Los Alamos National Laboratory ASC Simulation Verification and Validation program, 2007

  12. M. Sottile (2006) “Image metrics project (U).” Classified presentation, Los Alamos National Laboratory ASC Simulation Verification and Validation program, 2006

  13. M. Gokhale, M. Sottile (2006) “Program Analysis Tools for Application Specific Architectures.” LACSI 2006 / PACT 2006 / HPEC 2006, 2006

  14. M. Sottile. (2006) “Comparing Simulated and Experimental Images via Shape Metrics.” Algorithms for Image Analysis in Scientific Data Mini-Symposium, SIAM Imaging Science Conference, 2006, Minneapolis, Minnesota

  15. M. Sottile. (2006) “Exploring performance sensitivity of distributed memory parallel programs to system interference.” SIAM Parallel Processing Conference, February, 2006

  16. M. Sottile. (2005) “Right weight kernel: Introduction, concepts, and current work.” DOE FastOS PI Meeting, June 9, 2005, Rockville, Maryland

  17. M. Sottile. (2005) “CCAIN: Essential CCA.” CCA Quarterly Meeting, April 28, 2005, Lincoln City, Oregon

  18. M. Sottile. (2005) “Analysis of microbenchmarks for performance tuning of clusters.” Colloquium, University of New Mexico, Electrical and Computer Engineering Department, March 25, 2005

  19. C. Rasmussen, Matthew Sottile (2004) “Python for High Productivity Scientific Programming.” Los Alamos National Laboratory, November, 2004

  20. S. Choi, E. Hendriks, R. Minnich, M. Sottile, G. Watson (2004) “Clustermatic software suite tutorial.” Supercomputing, 2004, Pittsburgh, Pennsylvania

  21. C. Rasmussen, Matthew Sottile (2004) “Python for High Productivity Scientific Programming.” LACSI, 2004, Santa Fe, New Mexico

  22. S. Choi, E. Hendriks, R. Minnich, M. Sottile, G. Watson (2004) “Clustermatic software suite tutorial.” LACSI, 2004, Santa Fe, New Mexico

  23. S. Choi, E. Hendriks, R. Minnich, M. Sottile, G. Watson (2004) “Clustermatic software suite tutorial.” LCI, 2004, Austin, Texas

  24. M. Sottile. (2004) “Formal methods for component design.” Quarterly CCA Meeting, 2004, Boulder, Colorado

  25. M. Sottile. (2004) “Developing a Formal Representation for Component Design Patterns.” SIAM Parallel Processing Conference, February, 2004, San Francisco, California

  26. S. Choi, E. Hendriks, R. Minnich, M. Sottile, G. Watson (2003) “Clustermatic software suite tutorial.” LACSI, 2003, Santa Fe, New Mexico

  27. M. Sottile. (2003) “PAWS: The parallel application workspace.” ACTS Workshop, Lawrence Berkeley National Laboratory, 2003

  28. M. Sottile. (2002) “Supermon: Scalable cluster monitoring.” University of New Mexico, Computer Science Department Colloquium, November 5, 2002

  29. M. Sottile. (2002) “PAWS: The parallel application workspace.” ACTS Workshop, Lawrence Berkeley National Laboratory, 2002

  30. M. Sottile. (2002) “Supermon: A high-speed cluster monitoring system.” Los Alamos National Laboratory, Advanced Computing Laboratory Colloquium, January, 2002

  31. M. Sottile. (2001) “PAWS: The parallel application workspace.” ACTS Workshop, Lawrence Berkeley National Laboratory, 2001

  32. M. Sottile. (2001) “Automated, compiler based methods for coupling parallel simulations.” Los Alamos National Laboratory, Advanced Computing Laboratory Colloquium, March, 2001

  33. M. Sottile. (1999) “Science and Supercomputing.” Student colloquium, Los Alamos National Laboratory, July, 1999

Technical Reports

  1. David E. Bernholdt, Benjamin A. Allan, Robert C. Armstrong, Daniel Chavarria-Miranda, Tamara L. Dahlgren, Wael R. Elwasif, Tom Epperly, Samantha S. Foley, Geoffrey C. Hulette, Sriram Krishnamoorthy, Adrian Prantl, Ajay Panyala, Matthew Sottile (2012) “COMPOSE-HPC: A Transformational Approach to Exascale.”, Oak Ridge National Laboratory Technical Report, Number ORNL/TM-2012/85

  2. S. DeSalvo, S. Ibrahim, J. Treanor, M. Sottile (2007) “Image Processing for C. elegans Movement Video Streams.”, Los Alamos National Laboratory Technical Report, Number LA-UR-07-5069