Publications

IMPORTANT! This list reflects my publications as of early 2012 – a number of more recent publications are missing.  At some point, I hope to have this page automatically updated when I update my CV bibtex.  In the meantime, check out my Google Scholar page – that tends to be mostly up to date.

Please contact me if you want to obtain copies of any paper listed here, or Google for the title since many are available from various sources online in PDF form. A few of the papers here were initially workshop papers that were expanded, revised, and turned into journal papers. I only list the most recent instance (e.g., the journal version) to prevent anyone from citing the older, less complete work.

Forgive the incomplete bibliography entries – this is automatically generated by a not-quite-done-yet Haskell program that converts BiBTeX to web pages for me. Some metadata, like journal volume, number, and some other bibliography details are omitted in this renderer. Mail me if you want the full citation for any publication listed here.

Books and Book Chapters

  1. Matthew J. Sottile, Timothy G. Mattson, Craig E Rasmussen. 2009. Introduction to Concurrency in Programming Languages. CRC Press, ISBN 978-1420072136.
  2. Matthew J. Sottile. 2010. Cellular Automata. Chapter in Encyclopedia of Parallel Computing, Springer, edited by David Padua.
  3. Randall Bramley, Robert Armstrong, Lois Curfman McInnes, Matthew Sottile. 2006. High-Performance Component Software Systems. Chapter in Parallel Processing for Scientific Computing, SIAM, edited by Michael A. Heroux, Padma Raghavan and Horst D. Simon.

Journal Articles

  1. M. J. Sottile, C. E Rasmussen, W. N. Weseloh, R. W. Robey, D. Quinlan, J. Overbey. 2012. ForOpenCL: Transformations Exploiting Array Syntax in Fortran for Accelerator Programming. International Journal of Computational Science and Engineering.
  2. 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.
  3. 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.
  4. M. A. Abramson, T. J. Asaki, J. E. Dennis, R. Magallanez, M. J. Sottile. 2011. Solving Computationally Expensive Optimization Problems with CPU Time-Correlated Functions. Structural and Multidisciplinary Optimization.
  5. T. J. Asaki, M. Sottile, K. R. Vixie, P. Cherepanov. 2010. Image Denoising by Regularization on Characteristic Graphs. Applied Mathematical Sciences.
  6. Ronald Minnich, Matthew Sottile, Sung-Eun Choi, Eric Hendriks, James McKie. 2006. Right-Weight Kernels: an off-the-shelf alternative to custom Light-Weight Kernels. Special Issue of the ACM Operating Systems Review Journal.
  7. Allen Malony, Sameer Shende, Nick Trebon, Jaideep Ray, Robert Armstrong, Craig Rasmussen, Matthew Sottile. 2005. Performance Technology for Parallel and Distributed Component Software. Concurrency and Computation: Practice and Experience, pp. 117–141.
  8. Robert Armstrong, Gary Kumfert, Lois Curfman McInnes, Steven Parker, Ben Allan, Matthew Sottile, Thomas Epperly, Tamara Dahlgren. 2005. The CCA Component Model for High-Performance Scientific Computing. Concurrency and Computation: Practice and Experience.
  9. Craig E Rasmussen, Matthew Sottile, Sameer Shende, Allen Malony. 2005. Bridging the language gap in scientific computing: the Chasm approach. Concurrency and Computation: Practice and Experience.
  10. Matthew Sottile, Ronald Minnich. 2002. Scale up your monitoring with Supermon. IEEE Task Force for Cluster Computing Newsletter.
  11. Allen Malony, Janice Cuny, Jenifer Skidmore, Matthew Sottile. 2000. Computational experiments using distributed tools in a Web-based electronic notebook environment. Future Generation Computer Systems.

Conference Articles

  1. 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. Proceedings of EuroPar 2012.
  2. Craig E Rasmussen, Matthew J. Sottile, Garrett Kenyon. 2010. Visual Language Recognition with a Feed-Forward Network of Spiking Neurons. IADIS International Intelligent Systems and Agents 2010 (ISA 2010) Conference.
  3. Kristine A. Thomas, Matthew J. Sottile, Carolyn M. Salafia. 2010. Unsupervised segmentation for inflammation detection in histopathology images. Proceedings of the 2010 International Conference on Image and Signal Processing (ICISP).
  4. Adnan Salman, Allen D. Malony, Matthew J. Sottile. 2009. An Open Domain-extensible Environment for Simulation-based Scientific Investigation (ODESSI). Proceedings of the International Conference on Computational Science 2009.
  5. Shangkar Mayanglambam, Allen D. Malony, Matthew J. Sottile. 2009. Performance Measurement of Applications with GPU Acceleration using CUDA. Proceedings of the International Conference on Parallel Computing 2009.
  6. Matthew J. Sottile, Geoffrey Hulette, Allen D. Malony. 2009. Workflow representation and runtime based on lazy functional streams. Proceedings of the 2009 Workshop on Workflows in Support of Large-Scale Science (WORKS).
  7. Geoffrey Hulette, Matthew J. Sottile, Benjamin Allan, Robert Armstrong. 2009. OnRamp to CCA: Annotation-driven static analysis and code generation. Proceedings of the 2009 Workshop on Component-Based High Performance Computing (CBHPC 2009).
  8. Geoffrey Hulette, Matthew J. Sottile, Allen D. Malony. 2008. WOOL: A Workflow Programming Language. Proceedings of eScience 2008.
  9. Aroon Nataraj, Matthew Sottile, Allen D. Malony, Alan Morris, Sameer Shende. 2007. TauOverSupermon: Low-Overhead Online Parallel Performance Monitoring. Proceedings of EuroPar 2007.
  10. Aroon Nataraj, Alan Morris, Allen D. Malony, Matthew Sottile, Pete Beckman. 2007. The Ghost in the Machine: Observing the Effects of Kernel Operation on Parallel Application Performance. Proceedings of Supercomputing 2007.
  11. Matthew Sottile, Craig Rasmussen, Richard Graham. 2006. Co-Array Collectives: Refined Semantics for Co-Array Fortran. International Conference on Computational Science (ICCS 2006).
  12. Matthew Sottile, Vaddadi Chandu, David A. Bader. 2006. Performance analysis of parallel programs via message-passing graph traversal. Proceedings of IPDPS 2006.
  13. J. A. Green, C. Alexander, T. Asaki, J. Bacon, G. Blanpied, K. Borozdin, A. Canabal-Rey, M. Cannon, R. Chartrand, D. Clark, C. Espinoza, E. Figueroa, A. Fraser, M. Galassi, J. Gomez, J. Gonzales, A. Green, N. Hengartner, G. Hogan, A. Klimenko, P. McGaughey, G. McGregor, J. Medina, C. Morris, K. Mosher, C. Orum, F. Pazuchanics, W. Priedhorsky, A. Sanchez, A. Saunders, R. Schirato, L. Schultz, M. Sossong, M. Sottile, J. Tenbrink, R. Van de Water, K. Vixie, B. Wohlberg. 2006. Optimizing the tracking efficiency for cosmic ray muon tomography. Proceedings of the 2006 IEEE Nuclear Science Symposium Conference.
  14. Konstantin Borozdin, Thomas Asaki, Rick Chartrand, Mark Galassi, Andrew Greene, Nicolas Hengartner, Gary Hogan, Alexei Klimenko, Christopher Morris, William Priedhorsky, Alexander Saunders, Richard Schirato, Larry Schultz, Matthew Sottile. 2005. Cosmic-ray muon tomography and its application to the detection of high-Z materials. Proceedings of the 46th Annual Meeting for the Institute of Nuclear Materials Management.
  15. Craig Rasmussen, Matthew Sottile, Christopher Rickett. 2005. A Gentle Migration Path to Component-Based Programming. Proceedings of the International Conference on Parallel Computational Fluid Dynamics (PCFD).
  16. Matthew Sottile, Ronald Minnich. 2004. Analysis of microbenchmarks for performance tuning of clusters. Proceedings of Cluster 2004.
  17. Craig E Rasmussen, Matthew Sottile, Jarek Nieplocha, Robert Numrich, Erik Jones. 2004. Co-Array Python: A Parallel Extension to the Python Language. Proceedings of EuroPar 2004.
  18. Christopher Rickett, Sung-Eun Choi, Craig Rasmussen, Matthew Sottile. 2004. Rapid Prototyping Frameworks for Developing Scientific Applications: A Case Study. Proceedings of the Los Alamos Computer Science Institute (LACSI) Symposium.
  19. Greg Watson, Matthew Sottile, Ronald Minnich, Sung-Eun Choi, Eric Hendriks. 2004. Pink: A 1024-node Single-System Image Linux Cluster. Proceedings of HPC Asia, Myrinet Users Group Workshop.
  20. Matthew Sottile, Robert Armstrong. 2004. Developing a Formal Representation for Component Design Patterns. Proceedings of the SIAM Parallel Programming Conference.
  21. K. Borozdin, T. Asaki, R. Chartrand, N. Hengartner, G. Hogan, C. Morris, W. Priedhorsky, R. Schirato, L. Schultz, M. Sottile, K. Vixie, B. Wohlberg, G. Blanpied. 2004. Information extraction from muon radiography data. ISAS/CITSA 2004: International Conference on Cybernetics and Information Technologies, Systems and Applications and 10th International Conference on Information Systems Analysis and Synthesis, Vol 2, Proceedings: Communications, Information and Control Systems, Technologies and Applications, pp. 27–30.
  22. Sameer Shende, Allen Malony, Craig Rasmussen, Matthew Sottile. 2003. A Performance Interface for Component-Based Applications. Proceedings of IPDPS, Workshop on Performance Modeling, Evaluation, and Optimization of Parallel and Distributed Systems.
  23. Matthew Sottile, Ronald Minnich. 2002. Supermon: A high-speed cluster monitoring system. Proceedings of Cluster 2002.
  24. Sung-Eun Choi, Eric Hendriks, Ronald Minnich, Matthew Sottile, Aaron Marks. 2002. Life with Ed: A Case Study of a LinuxBIOS/BProc Cluster. Proceedings of the 16th Annual International Symposium on High Performance Computing Systems and Applications.
  25. Matthew Sottile, Allen Malony. 1999. INTERLACE: An Interoperation and Linking Architecture for Computational Engines. Proceedings of EuroPar 99, pp. 135–138.
  26. Allen Malony, Jenifer Skidmore, Matthew Sottile. 1999. Computational Experiments using Distributed Tools in a Web-based Electronic Notebook Environment. Proceedings of HPCN Europe.
  27. Jenifer Skidmore, Matthew Sottile, Janice Cuny, Allen Malony. 1998. A Prototype Notebook-Based Environment for Computational Tools. Proceedings of Supercomputing 1998.

Institutional Technical Reports

  1. Matthew Sottile, Stephen DeSalvo, Sharif Ibrahim, Jennifer Treanor. 2007. Image Processing for C. Elegans Movement Video Streams. Los Alamos National Laboratory technical report LA-UR-07-5069.

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