Heshan Lin

Research Scientist, Department of Computer Science, Virginia Tech

 
 
  1. 2217 Knowledgeworks II

  2. Dept. of Computer Science

  3. Virginia Tech

Address

  1. 2202 Kraft Drive,

  2. Blacksburg, VA 24060

Email

  1. hlin2 AT cs.vt.edu

 
Research Overview

  1. My research interests lie broadly at data-intensive parallel and distributed computing. Specifically, my recent research focuses on leveraging cloud computing and GPU computing to accelerate big data analysis in life sciences. I am currently a member of Synergy Lab at Virginia Tech. Here is my Google Scholar Profile.

Education

  1. Ph.D., Computer Science, North Carolina State University, 2009

  2. M.S., Computer Science, Temple University, 2004

  3. B.S., Applied Math, South China University of Technology, 1998

Awards and Honors

  1. Best Papers in the 20-year history of the International ACM Symposium on High-Performance Parallel and Distributed Computing (HPDC), 2012.

  2. NVIDIA Compute the Cure Award Finalist, 2011.

  3. Distinguished Paper Award, International Supercomputing Conference (ISC), 2008.

  4. HPC Storage Challenge Award, IEEE/ACM International Conference for High-Performance Computing, Networking, Storage and Analysis (SC), 2007.

  5. Best Paper Award Finalist, IEEE/ACM International Conference for High-Performance Computing, Networking, Storage and Analysis (SC), 2006.

Publications

  1. Book Chapters

  2. 1. H. Lin, G. Fedak and W. Feng. Chapter “Data-Intensive Computing on Desktop Grids” in Desktop Grid Computing. Chapman and Hall/CRC, 2012

  3. 2. W. Feng and H. Lin. Chapter “From Homology to Sequence Alignment” in Encyclopedia of Parallel Computing. Springer Reference, 2011.

  4. Journal Papers

  5. 3. H. Lin, X. Ma, W. Feng. Reliable MapReduce Computing on Opportunistic Resources. Cluster Computing, 2011.

  6. 4. T. Scogland, H. Lin and W. Feng. A First Look at Integrated GPUs for Green High-Performance Computing. Computer Science - Research and Development, Springer Berlin / Heidelberg, 2010.

  7. 5. H. Lin, X. Ma, W. Feng and N. Samatova. Coordinating Computation and I/O in Massively Parallel Sequence Search. IEEE Transactions on Parallel and Distributed Systems, 2010.

  8. 6. P. Balaji, W. Feng, H. Lin, J. Archuleta, S. Matsuoka, A. Warren, J. Setubal, E. Lusk, R. Thakur, I. Foster, D.S. Katz, S. Jha, K. Shinpaugh, S. Coghlan, and D. Reed. Global-scale Distributed I/O with ParaMEDIC. International Journal of Concurrency and Computation: Practice and Experience (CCPE), 2010.

  9. Refereed Conference Papers

  10. 7. J. Zhang, H. Lin, P. Balaji, and W. Feng.  Optimizing Burrows-Wheeler Transform-Based Sequence Alignment on Multicore Architectures. 13th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid), Delft, the Netherlands, 2013.

  11. 8. N. Mohamed, H. Lin, and W. Feng. Accelerating Data-Intensive Genome Analysis in the Cloud. 5th International Conference on Bioinformatics and Computational Biology (BiCOB), Honolulu, Hawaii, 2013.

  12. 9. K. Lee, H. Lin, W. Feng. Performance Characterization of Data-Intensive Kernels on AMD Fusion Architectures. International Supercomputing Conference, Hamburg, Germany, 2012.

  13. 10. W. Feng, H. Lin, T. Scogland, and J. Zhang. OpenCL and the 13 Dwarfs: A Work in Progress. 3rd ACM/SPEC International Conference on Performance Engineering, Boston, MA, 2012.

  14. 11. S. Xiao, P. Balaji, Q. Zhu, R. Thakur, S. Coghlan, H. Lin, G. Wen, J. Hong, and W. Feng. VOCL: An Optimized Environment for Transparent Virtualization of Graphics Processing Units. In Proc. of the 1st Innovative Parallel Computing (InPar), San Jose, CA, 2012.

  15. 12. S. Xiao, P. Balaji, J. Dinan, Q. Zhu, R. Thakur, S. Coghlan, H. Lin, G. Wen, J. Hong and W. Feng. Transparent Accelerator Migration in a Virtualized GPU Environment. IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid), Ottawa, Canada, 2012.

  16. 13. M. Elteir, H. Lin and W. Feng. StreamMR: An Optimized MapReduce Framework for AMD GPUs. 17th IEEE International Conference on Parallel and Distributed Systems, Taiwan, 2011.

  17. 14. C. Wu, J. K, H. Lin and W. Feng. Optimizing Dynamic Programming on Graphics Processing Units via Adaptive Thread-Level Parallelism. 17th IEEE International Conference on Parallel and Distributed Systems, Taiwan, 2011.

  18. 15. M. Elteir, H. Lin and W. Feng. Performance Characterization and Optimization of Atomic Operations on AMD GPUs. IEEE Cluster, Austin, TX, 2011.

  19. 16. K. Pereira, P. Athanas, H. Lin and W. Feng. Spectral Method Characterization on FPGA and GPU Accelerators. (short paper), International Conference on ReConFigurable Computixng and FPGAs (ReConFig'11), 2011.

  20. 17. F. Ge, A. M. Eltawil, H. Lin, W. Feng, J. Chiang and R. Chadha. Augment Mobile Cloud Computing with Cognitive Radio. IEEE COMSOC MMTC E-Letter, 2011.

  21. 18. T. Ahn, D. Dechev, H. Lin, H. Adalsteinsson and C. Janssen. A Simulation Framework for Evaluation and Optimization of Large-Scale mpiBLAST Applications. International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH), Noordwijkerhout, The Netherlands, 2011.

  22. 19. S. Xiao, H. Lin and W. Feng. Accelerating Protein Sequence Search in a Heterogeneous Computing System. 25th IEEE International Parallel & Distributed Processing Symposium, Alaska, USA, 2011.

  23. 20. Y. Jiao, H. Lin, P. Balaji and W. Feng. Power and Performance Characterization of Computational Kernels on the GPU. IEEE/ACM International Conference on Green Computing and Communications (GreenCom2010), Hangzhou, China, 2010.

  24. 21. M. Elteir, H. Lin and W. Feng. Enhancing MapReduce via Asynchronous Data Processing. 16th IEEE International Conference on Parallel and Distributed Systems, Shanghai, China, 2010.

  25. 22. F. Ge, H. Lin, A. Khajeh, J. Chiang, A. Eltawil, C. Bostian, W. Feng, R. Chadha. Cognitive Radio Rides on the Cloud,” Military Communications Conference (MILCOM). San Jose, CA, 2010.

  26. 23. H. Lin, X. Ma, J. Archuleta, W. Feng, M. Gardner and Z. Zhang. MOON: MapReduce On Opportunistic eNvironments. ACM International Symposium on High Performance Distributed Computing (HPDC), Chicago, IL, (selected among the best papers in the 20-year history of HPDC) 2010.

  27. 24. M. Gardner, A. Herr, D. Mazary, H. Lin, T. Scogland and W. Feng. A Flexible and Extensible Framework for Delivering Designer Images for K-12 Pedagogy. International Conference on the Virtual Computing Initiative (ICVCI), Raleigh, NC, 2009

  28. 25. H. Lin, P. Balaji, R. Poole, C. Sosa, X. Ma and W. Feng. Massively Parallel Genomic Sequence Search on the Blue Gene/P Architecture. IEEE/ACM International Conference for High-Performance Computing, Networking, Storage and Analysis (SC), Austin, TX, 2008.

  29. 26. P. Balaji, W. Feng and H. Lin. Semantics-based Distributed I/O with the ParaMEDIC Framework. ACM International Symposium on High Performance Distributed Computing (HPDC), Boston, MA, 2008.

  30. 27. P. Balaji, W. Feng, H. Lin, J. Archuleta, S. Matsuoka, A. Warren, J. Setubal, E. Lusk, R. Thakur, I. Foster, D. S. Katz, S. Jha, K. Shinpaugh, S. Coghlan and D. Reed. Distributed I/O with ParaMEDIC: Experiences with a Worldwide Supercomputer. International Supercomputing Conference (ISC), Distinguished Paper Award, Dresden, Germany, 2008.

  31. 28. H. Lin, X. Ma, J. Li, T. Yu and N. Samatova. Adaptive Request Scheduling for Parallel Scientific Web Services. International Conference on Scientific and Statistical Database Management (SSDBM), Hong Kong, China, 2008.

  32. 29. P. Balaji, W. Feng, J. Archuleta, H. Lin, R. Kettimuttu, R. Thakur and X. Ma. Semantics-based Distributed I/O for mpiBLAST (short paper). ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP), Salt Lake City, UT, 2008.

  33. 30. O. Thorsen, K. Jiang, A. Peters, B. Smith, H. Lin, W. Feng and C. Sosa. Parallel Genomic Sequence-Search on a Massively Parallel System. ACM International Conference on Computing Frontiers, Ischia, Italy, 2007.

  34. 31. M. Gardner, W. Feng, J. Archuleta, H. Lin and X. Ma. Parallel Genomic Sequence-Searching on an Ad-Hoc Grid: Experiences, Lessons Learned, and Implications. IEEE/ACM International Conference for High-Performance Computing, Networking, Storage and Analysis (SC), Best Paper Finalist, Miami, FL, 2006.

  35. 32. A. Ching, W. Feng, H. Lin, X. Ma and A. Choudhary. Exploring I/O Strategies for Parallel Sequence Database Search Tools with S3aSim. ACM International Symposium on High Performance Distributed Computing (HPDC), Paris, France, 2006.

  36. 33. H. Lin, X. Ma, P. Chandramohan, A. Geist and N. Samatova. Efficient Data Access for Parallel BLAST. IEEE International Parallel and Distributed Processing Symposium (IPDPS), Denver, CO, 2005.

  37. Refereed Workshop Papers

  38. 34. W. Feng and H. Lin. The Green500 List: Year Two. 5th IEEE Workshop on High-Performance, Power-Aware Computing (in conjunction with the 23rd International Parallel & Distributed Processing Symposium), 2010.

  39. Posters

  40. 35. K. Lee, H. Lin and W. Feng. Characterizing the Impact of Memory-Access Techniques on AMD Fusion. IEEE/ACM International Conference for High-Performance Computing, Networking, Storage and Analysis (SC), 2011.

  41. 36. H. Lin, J. Archuleta, X. Ma and W. Feng. MOON: MapReduce on Opportunistic Environments. IEEE/ACM International Conference for High-Performance Computing, Networking, Storage and Analysis (SC), 2009.

  42. 37. H.Lin and X. Ma. High Performance Parallel and Distributed Sequence Search. PhD Forum, IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2008.

Professional Service

  1. Chairs

  2. Workshop Co-Chair, IEEE International Conference on Cloud Computing Technology and Science (CloudCom), 2013

  3. Track Chair (MapReduce), IEEE International Conference on Cloud Computing Technology and Science (CloudCom), 2012

  4. Workshop Co-Chair, 41st International Conference on Parallel Processing (ICPP), 2011

  5. Editorship

  6. Guest Editor, International Journal of Computational Science and Engineering (IJCSE), Special Issue on: "Cloud Computing and Web Services," 2012

  7. Technical Program Committees

  8. IEEE/ACM International Conference for High Performance Computing, Networking, Storage and Analysis (SC), 2013

  9. IEEE International Parallel and Distributed Processing Symposium (IPDPS), PhD Forum, 2011

  10. IEEE International Conference on Parallel and Distributed Systems (ICPADS), 2012

  11. IEEE International Conference on Cloud Computing Technology and Science (CloudCom), 2013

  12. IEEE International Conference on High Performance Computing and Communications (HPCC), 2011

  13. IEEE International Conference on Computational Science and Engineering, 2010, 2011

  14. IEEE International Conference on Computer and Information Technology, 2011

  15. IEEE International Conference on Computer and Information Technology, Bradford, UK, 2010

  16. International Workshop on Parallel Programming Models and Systems Software for High-End Computing (P2S2), San Diego, CA, 2010, 2011, 2012

  17. International Workshop on Accelerators and Hybrid Exascale Systems (AsHES), 2011, 2013

  18. International Workshop on MapReduce and its Application (MapReduce), 2011, 2012

  19. International Workshop on Data-Intensive Scalable Computing Systems (DISCS), 2012

  20. International Workshop on High Performance Computational Biology, 2011, 2012

  21. Workshop on Parallel Computational Biology, Torun, Poland, 2011

  22. Invited Reviews

  23. IEEE Transactions on Parallel and Distributed Systems

  24. BMC Bioinformatics

  25. Springer Journal of Computer Science and Technology

  26. Journal of Grid Computing

  27. International Journal of High Performance Computing

  28. IEEE Computer (The Flagship Publication of IEEE Computer Society)

  29. International Journal of Grid and High Performance Computing (IJGHPC)

  30. Session Chairs

  31. 17th IEEE International Conference on Parallel and Distributed Systems, 2011

  32. IEEE/ACM International Conference on Green Computing and Communications (GreenCom), 2010

  33. 16th IEEE International Conference on Parallel and Distributed Systems, 2010

  34. 1st International Workshop on MapReduce and its Applications (MAPREDUCE'10), in conjunction with 19th ACM International Symposium on High Performance Distributed Computing, 2010

  35. Community Service

  36. Served as the lead researcher and developer of mpiBLAST, an open-source parallel pattern-matching application for bioinformatics (http://www.mpiblast.org).

  37. Served in the development team of the Green500 List, a ranking of the most energy-efficient supercomputers in the world (http://www.green500.org).

Research Grants

  1. Co-PI, CiC (RDDC): Commoditizing Data-Intensive Biocomputing in the Cloud, National Science Foundation Computing in the Cloud, $370,000. Period: 04/15/2011 to 03/31/2013.

  2. Senior Personnel: MRI-R2: Acquisition of a Heterogeneous Supercomputing Instrument for Transformative Interdisciplinary Research, National Science Foundation (NSF) Major Research Instrumentation. Equipment acquisition grant for $2,000,000. Period: 09/01/2010 to 08/31/2015.

  3. Senior Personnel:  Transforming Interdisciplinary Research and Education with Video Cards, Virginia Tech SCHEV ETF COE Competition. Equipment acquisition grant for $75,000. Period: 01/01/2010 to 06/01/2010.

Student Committees

  1. Henry Monti, PhD, Virginia Tech

  2. Marwa Elteir, PhD, Virginia Tech

  3. Kenneth Lee, MS, Virginia Tech

  4. Nabeel Mohamed, MS. Virginia Tech