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Daniel

Daniel Chavarria

High Performance Computing
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-30
Richland, WA 99352

Biography

Dr. Daniel Chavarría-Miranda is a Senior Research Scientist and the Team Leader of High Performance Computing at PNNL. Chavarría is currently participating in the Department of Energy Office of Science Center for Technology for Advanced Scientific Component Software (TASCS). He also is involved in the DOE ASCR Center for Scalable Parallel Programming Models (PModels2).

Chavarría-Miranda also serves as co-PI for a DoD-funded Center for Adaptive Supercomputing Software-Multithreaded Architectures (CASS-MT), with a focus on scalable highly irregular applications and systems software. He has also served as the Principal Investigator for several PNNL-funded Laboratory Directed Research & Development projects in the application of reconfigurable and hybrid systems to scientific codes. He also has been a collaborator in PNNL-funded LDRD projects in the application of multithreaded systems to non-traditional scientific applications.

Chavarría-Miranda received his M.S./Ph.D. in Computer Science from Rice University in 2004. As part of his doctoral training, Chavarría-Miranda participated in designing and developing key portions of Rice University's dHPF research compiler.

Research Interests

  • Parallel and distributed systems
  • Compilers for high-performance and parallel computing
  • Reconfigurable computing
  • Programming languages
  • Interactions of Architectural features with software systems

Education and Credentials

  • M.S./Ph.D., Computer Science, Rice University, 2004.
  • M.S., Computer Science, Instituto Tecnol├-gico y de Estudios Superiores de Monterrey, 1998.
  • B.S., Computer Science, Unversidad de Costa Rica, 1994.

Affiliations and Professional Service

  • Team Leader, High Performance Computing, Pacific Northwest National Laboratory, Oct. 2007-Current
  • Senior Research Scientist, Pacific Northwest National Laboratory, Jan. 2005-Current
  • Postdoctoral Research Associate, Rice University, Jan. 2004-Jan. 2005

Awards and Recognitions

  • Best paper award: 2002 International Parallel and Distributed Processing Symposium (IPDPS'02)
  • Best student paper award: 11th International Conference on Parallel Architectures and Compilation Techniques (PACT'02)

PNNL Publications

2013

  • Chavarría-Miranda D, K Agarwal, and TP Straatsma. 2013. "Scalable PGAS Metadata Management on Extreme Scale Systems." In 13th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid'13), May 13-16, 2013, Delft, Netherlands, ed. P Balaji, D Epema and T Fahringer, pp. 103-111.  IEEE Computer Society, Los Alamitos, CA.  doi:10.1109/CCGrid.2013.83
  • Straatsma TP, and D Chavarría-Miranda. 2013. "On Eliminating Synchronous Communication in Molecular Simulations to Improve Scalability ." Computer Physics Communications 184(12):2634-2640.  doi:10.1016/j.cpc.2013.01.009

2012

  • Chavarría-Miranda D, S Krishnamoorthy, and A Vishnu. 2012. "Global Futures: a multithreaded execution model for Global Arrays-based applications." In Proceedings of the 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2012), May 13-16, 2012, Ottawa, Canada, pp. 393-401.  Institute of Electrical and Electronics Engineers , Piscataway, NJ.  doi:10.1109/CCGrid.2012.105
  • Panyala AR, D Chavarría-Miranda, and S Krishnamoorthy. 2012. "On the use of term rewriting for performance optimization of legacy HPC applications." In The 41st International Conference on Parallel Processing (ICPP), September 10-13, 2012, Pittsburgh, Pennsylvania, pp. 399-409.  IEEE Computer Society, Los Alamitos, CA.  doi:10.1109/ICPP.2012.44
  • Tumeo A, O Villa, and D Chavarría-Miranda. 2012. "Aho-Corasick String Matching on Shared and Distributed Memory Parallel Architectures." IEEE Transactions on Parallel and Distributed Systems 23(3):436-443.  doi:10.1109/TPDS.2011.181
  • Tumeo A, O Villa, and D Chavarría-Miranda. 2012. "Hardware Architectures for Data-Intensive Computing Problems: A Case Study for String Matching." Chapter 3 in Data-Intensive Computing: Advances, Applications & Architectures, ed. I Gorton and DK Gracio, pp. 24-47.  Cambridge University Press, New York, NY. 

2011

  • Hui PSY, S Chikkagoudar, D Chavarría-Miranda, and MR Johnston. 2011. "Towards a Real-Time Cluster Computing Infrastructure." In Real-Time Systems Symposium (RTSS 2011): The 32nd IEEE Real-Time Systems Symposium, November 29- December 2, 2011, Vienna, Austria, pp. 17-20.  IEEE, Piscataway, NJ. 
  • Yin J, K Agarwal, MK Krishnan, D Chavarría-Miranda, I Gorton, and TG Epperly. 2011. "Implementing High Performance Remote Method Invocation in CCA." In IEEE International Conference on Cluster Computing (CLUSTER 2011), September 26-30, 2011, Austin, Texas, pp. 547-551.  IEEE Computer Society, Los Alamitos, CA.  doi:10.1109/CLUSTER.2011.78

2010

  • Chen Y, Z Huang, and D Chavarría-Miranda. 2010. "Performance Evaluation of Counter-Based Dynamic Load Balancing Schemes for Massive Contingency Analysis with Different Computing Environments ." In Proceedings of the 2010 IEEE Power and Energy Society General Meeting.  Institute of Electrical and Electronics Engineers, Piscataway, NJ.  doi:10.1109/PES.2010.5589536
  • Goodman EL, DJ Haglin, C Scherrer, D Chavarría-Miranda, JA Mogill, and JT Feo. 2010. "Hashing Strategies for the Cray XMT." In IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW 2010), pp. 1-8.  Institute of Electrical and Electronics Engineers, Piscataway, NJ.  doi:10.1109/IPDPSW.2010.5470688
  • Jin S, Z Huang, Y Chen, D Chavarría-Miranda, JT Feo, and PC Wong. 2010. "A Novel Application of Parallel Betweenness Centrality to Power Grid Contingency Analysis." In IEEE International Symposium on Parallel & Distributed Processing (IPDPS 2010), pp. 1-7.  Institute of Electrical and Electronics Engineers, Piscataway, NJ.  doi:10.1109/IPDPS.2010.5470400
  • Shah AR, JN Adkins, DJ Baxter, WR Cannon, D Chavarría-Miranda, S Choudhury, I Gorton, DK Gracio, TD Halter, N Jaitly, JR Johnson, RT Kouzes, MC Macduff, A Marquez, ME Monroe, CS Oehmen, WA Pike, C Scherrer, O Villa, BJM Webb-Robertson, PD Whitney, and N Zuljevic. 2010. "Applications in Data-Intensive Computing." In Advances in Computers, vol. 79, ed. M Zelkowitz, pp. 1-70.  Academic Press Inc., San Diego, CA. 

2009

  • Chen Y, S Jin, D Chavarría-Miranda, and Z Huang. 2009. "Application of Cray XMT for Power Grid Contingency Selection." In Proceedings of the Cray User Group Meeting: Compute the Future.  Cray User Group, Inc., Corvallis, OR. 
  • Gorton I, D Chavarría-Miranda, and J Nieplocha. 2009. "Design and Implementation of a High-Performance CCA Event Service." Concurrency and Computation. Practice & Experience 21(9):1159-1179. 
  • Gorton I, Z Huang, Y Chen, BK Kalahar, S Jin, D Chavarría-Miranda, DJ Baxter, and JT Feo. 2009. "A High-Performance Hybrid Computing Approach to Massive Contingency Analysis in the Power Grid." In 5th IEEE International Conference on e-Science (e-Science 2009), December 9-11, 2009, Oxford, United Kingdom, pp. 277-283.  IEEE Computer Society, Los Alamitos, CA.  doi:10.1109/e-Science.2009.46
  • Gurumoorthi V, MK Krishnan, Y Fang, BJ Palmer, and D Chavarría-Miranda. 2009. "Multiple Component Multiple Data Programming in Subsurface Simulations: The CCA Approach." In Proceedings of the Workshop on Component-Based High Performance Computing (CBHPC 2009).  ACM Press, New York, NY. 
  • Madduri K, D Ediger, K Jiang, DA Bader, and D Chavarría-Miranda. 2009. "A Faster Parallel Algorithm and Efficient Multithreaded Implementations for Evaluating Betweenness Centrality on Massive Datasets." In Proceedings of the IEEE International Symposium on Parallel & Distributed Processing (IPDPS 2009), May 23-29, 2009, Rome, Italy.  IEEE Computer Society, Los Alamitos, CA. 
  • Villa O, D Chavarría-Miranda, and KJ Maschhoff. 2009. "Input-independent, Scalable and Fast String Matching on the Cray XMT." In IEEE International Symposium on Parallel & Distributed Processing.  IEEE International Parallel & Distributed Processing Symposium, Rome, Italy.  doi:10.1109/IPDPS.2009.5161043
  • Villa O, D Chavarría-Miranda, V Gurumoorthi, A Marquez, and S Krishnamoorthy. 2009. "Effects of floating-point non-associativity on numerical computations on massively multithreaded systems." In Cray User Group Meeting (CUG 2009), May 4-7, 2009, Atlanta, Georgia.  Cray User Group, Inc., Corvallis, OR. 

2008

  • Chavarría-Miranda D, A Marquez, J Nieplocha, KJ Maschhoff, and C Scherrer. 2008. "Early Experience with Out-of-Core Applications on the Cray XMT." In IEEE International Symposium on Parallel and Distributed Processing, IPDPS 2008. , pp. 2379-2386.  IEEE , Piscataway, NJ.  doi:10.1109/IPDPS.2008.4536360
  • Chavarría-Miranda D, DK Gracio, A Marquez, J Nieplocha, C Scherrer, and HJ Sofia. 2008. "Cray XMT Brings New Energy to High-Performance Computing." SciDAC Review Fall 2008(9):36-41. 
  • Chavarría-Miranda D, J Nieplocha, and I Gorton. 2008. "Hardware-accelerated Components for Hybrid Computing Systems." In Proceedings of the 2008 compFrame/HPC-GECO workshop on Component based high performance (CBHPC), p. Art. No. 7.  Association for Computing Machinery, New York, NY. 
  • Chin G, Jr, D Chavarría-Miranda, GC Nakamura, and HJ Sofia. 2008. "BioGraphE: High-performance bionetwork analysis using the Biological Graph Environment." BMC Bioinformatics 9(s6):, doi:10.1186/1471-2105-9-S6-S6
  • Nieplocha J, D Chavarría-Miranda, V Tipparaju, Z Huang, and A Marquez. 2008. "A parallel WLS state estimator on shared memory computers." In Proceedings of The 8th International Power Engineering Conference, IPEC 2007, pp. 395-400.  IEEE , Piscataway, NJ. 

2007

  • Chavarría-Miranda D, and A Marquez. 2007. "Assessing the Potential of Hybrid HPC Systems for Scientific Applications: a case study." In Proceedings of the 4th ACM International Conference on Computing Frontiers, May 7-9, 2007, Ischia, Italy, pp. 173-182.  ACM Press, New York, NY.  doi:10.1145/1242531.1242558
  • Chavarría-Miranda D, BH Clowers, GA Anderson, and ME Belov. 2007. "Simulating data processing for an Advanced Ion Mobility Mass Spectrometer." In Proceedings of the 1st international workshop on High-performance reconfigurable computing technology and applications (HPRCTA'07): held in conjunction with SC07, NOV 10-16, 2007, Reno Nevada, pp. 21-29.  Association for Computing Machinery, New York, NY. 
  • Chin G, Jr, D Chavarría-Miranda, GC Nakamura, and HJ Sofia. 2007. "A high-performance computational framework for bionetwork analysis." In IMSCCS 2007. Second International Multi-Symposiums on Computer and Computational Sciences, pp. 100 - 107.  IEEE Computer Society, Los Alamitos, CA.  doi:10.1109/IMSCCS.2007.8
  • Chin G, Jr, GC Nakamura, D Chavarría-Miranda, and HJ Sofia. 2007. "Graph mining of networks from genome biology." In IEEE Bioinformatics & Bioengineering, pp. 1265-1269.  Institute of Electrical and Electronics Engineers, Boston , ME.  doi:10.1109/BIBE.2007.4375728
  • Gorton I, D Chavarría-Miranda, MK Krishnan, and J Nieplocha. 2007. "A High-Performance Event Service for HPC Applications." In Proceedings of the 3rd International Workshop on Software Engineering for High Performance Computing Applications, p. 5 pages.  Institute of Electrical and Electronics Engineers, Piscataway, NJ.  doi:10.1109/SE-HPC.2007.1
  • Nieplocha J, A Marquez, F Petrini, and D Chavarría-Miranda. 2007. "Unconventional Architectures for High-Throughput Sciences." SciDAC Review (5, Fall 2007):46-50. 
  • Nieplocha J, A Marquez, J Feo, D Chavarría-Miranda, G Chin, Jr, C Scherrer, and N Beagley. 2007. "Evaluating the potential of multithreaded platforms for irregular scientific computations." In Proceedings of 4th ACM International Conference on Computing Frontiers, May 7-9, 2007, Ischia, Italy, pp. 47 - 58.  ACM Press, New York, NY.  doi:10.1145/1242531.1242541
  • Nieplocha J, A Marquez, J Feo, D Chavarría-Miranda, G Chin, Jr, C Scherrer, and N Beagley. 2007. "Evaluating the Potential of Multithreaded Platforms for Irregular Scientific Computations." In Proceedings of the 4th International Conference on Computing Frontiers, Ischia, Italy, May 07 - 09, 2007, pp. 47-58.  ACM Press, New York, NY. 
  • Scherrer C, N Beagley, J Nieplocha, A Marquez, J Feo, and D Chavarría-Miranda. 2007. "Probability Convergence in a Multithreaded Counting Application." In Parallel and Distributed Processing Symposium (IPDPS 2007), pp. 1-5.  IEEE , Piscataway, NY.  doi:10.1109/IPDPS.2007.370688

2006

  • Chavarría-Miranda D, J Nieplocha, and V Tipparaju. 2006. "Topology-aware Tile Mapping for Clusters of SMPs." In Proceedings of the 2006 ACM International Conference on Computing Frontiers.  A C M, Ischia, Italy. 
  • Chassin DP, PR Armstrong, D Chavarría-Miranda, and RT Guttromson. 2006. "Gauss-Seidel Accelerated: Implementing Flow Solvers on Field Programmable Gate Arrays." In 2006 IEEE Power Engineering Society General Meeting, 18-22 June 2006, p. 5 pages.  Institute of Electrical and Electronics Engineers, Piscataway, NJ. 
  • Nieplocha J, A Marquez, V Tipparaju, D Chavarría-Miranda, RT Guttromson, and Z Huang. 2006. "Towards Efficient Parallel State Estimation Solvers on Shared Memory Computers." In Highspeed Computation Panel of the Proceedings of the 2006 IEEE Power Engineering Society General Meeting, 18-22 June 2006 , pp. 1-5.  IEEE , Piscataway, NJ. 

2005

  • Chavarría-Miranda D, and JM Mellor-Crummey. 2005. "Effective communication coalescing for data-parallel applications." In Proceedings of the tenth ACM SIGPLAN symposium on Principles and practice of parallel programming, June 15-17, 2005, Chicago, Illinois, pp. 14-25.  ACM Press, New York, NY. 
  • Coarfa C, Y Dotsenko, JM Mellor-Crummey, F Cantonnet, T El-Ghazawi, A Mohanti, Y Yao, and D Chavarría-Miranda. 2005. "An Evaluation of Global Address Space Languages: Co-Array Fortran and Unified Parallel C." In Proceedings of the tenth ACM SIGPLAN symposium on principles and practice of parallel programming, PPoPP'05, June 15-17, 2005, Chicago, Illinois, pp. 36-47.  ACM Press, New York, NY. 

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