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IBM Journal of Research and Development

Applications of Massively Parallel Systems   Volume 52, Number 1/2, 2008
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Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system - Author Bios

by S. Kumar,
C. Huang,
G. Zheng,
E. Bohm,
A. Bhatele,
J. C. Phillips,
H. Yu,
and L. V. Kalé
Biographical sketches of authors

Sameer Kumar IBM Research Division, Thomas J. Watson Research Center, P.O. Box 218, Yorktown Heights, New York 10598 (sameerk@us.ibm.com). Dr. Kumar received a B.Tech. (1999) degree in computer science from Indian Institute of Technology, Madras, India, and an M.S. and Ph.D. degrees in computer science from the University of Illinois at Urbana-Champaign. His Ph.D. thesis focused on optimizing communication for massively parallel processing. He is currently a Research Staff Member at the T. J. Watson Research Center and is working on the Blue Gene* Project. His research interests include scaling parallel applications to massively parallel machines and next-generation interconnection network design. He coauthored a paper on scaling the molecular dynamics program NAMD, and it was one of the winners of the Gordon Bell Prize at the 2002 Supercomputing Conference.

Chao Huang Department of Computer Science, Thomas M. Siebel Center, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (chuang10@uiuc.edu). Mr. Huang received a B.E. degree in computer science from Tsinghua University, Beijing, in 2001 and an M.S. degree in computer science from the University of Illinois at Urbana-Champaign in 2004. Mr. Huang is a Ph.D. candidate at the Parallel Programming Laboratory at the University of Illinois. His research focuses on higher-level language that allows expression of overall flow of control in complicated parallel programs.

Gengbin Zheng Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (gzheng@uiuc.edu). Dr. Zheng received B.S. (1995) and M.S. (1998) degrees in computer science from the Beijing University, Beijing, China. His master's thesis concerned a high-performance Fortran compiler. He received a Ph.D. degree in computer science from the University of Illinois at Urbana-Champaign in 2005. He is a postdoctoral research associate in computer science and engineering, working with both the Center for Simulation of Advanced Rockets and Professor Laxmikant V. Kalé. His research interests span various aspects of parallel computing, including dynamic automatic load balancing to scale highly adaptive parallel applications to a large number of processors, simulation-based method to predict performance of applications for large parallel machines, and fault tolerance. He coauthored a paper on scaling the molecular dynamics program NAMD, and it was one of the winners of the Gordon Bell Prize at the 2002 Supercomputing Conference.

Eric Bohm Department of Computer Science, Thomas M. Siebel Center, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (ebohm@uiuc.edu). Mr. Bohm received a B.S. degree in computer science from the State University of New York at Buffalo in 1992. He worked as Director of Software Development for Latpon Corporation from 1992 to 1995, and next as Director of National Software Development from 1995 to 1996. He worked as Enterprise Application Architect at MEDE America from 1996 to 1999 and as an Application Architect at WebMD from 1999 to 2001. Following a career shift toward academia, he joined the Parallel Programming Lab at University of Illinois at Urbana-Champaign in 2003. His current focus as a Research Programmer is on optimizing molecular dynamics codes for tens of thousands of processors.

Abhinav Bhatele Department of Computer Science, Thomas M. Siebel Center, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (bhatele2@uiuc.edu). Mr. Bhatele received a B.Tech. degree in computer science and engineering from Indian Institute of Technology, Kanpur, India, in 2005. He is a Ph.D. student at the Parallel Programming Lab at the University of Illinois. His research is centered on topology-aware mapping and load balancing for parallel applications. He is a co-developer of the molecular dynamics applications NAMD and LeanCP, developed at the Parallel Programming Lab.

James C. Phillips Theoretical and Computational Bio-Physics Group, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801. Dr. Phillips received his B.S. degree in physics and mathematics from Marquette University, Milwaukee, Wisconsin, in 1993, and his M.S. and Ph.D. degrees in physics from the University of Illinois at Urbana-Champaign in 1994 and 2002, respectively. He was supported by a Fannie and John Hertz Graduate Fellowship and a Department of Energy Computational Science Graduate Fellowship. He is currently a Senior Research Programmer in the Theoretical and Computational Biophysics Group at the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign. Dr. Phillips is the lead developer of the scalable molecular dynamics program NAMD, which received a 2002 Gordon Bell Prize, and the NAMD application has been cited in more than 500 published technical papers. His research interests span the field of biomolecular simulation, from potential functions and simulation protocols to numerical methods and parallel computing.

Hao Yu IBM Research Division, Thomas J. Watson Research Center, P.O. Box 218, Yorktown Heights, New York 10598 (yuh@us.ibm.com). Dr. Yu received B.S. and M.S. degrees in computer science from Tsinghua University, Beijing, China, in 1994 and 1997. He received his Ph.D. degree in computer science from Texas A&M University, College Station, Texas, in 2004. He is currently a postdoctoral researcher at the IBM T. J. Watson Research Center. His research interests include compiler optimization for high-performance computing, system software for scalable systems, and parallel I/O.

Laxmikant V. Kalé Department of Computer Science, Thomas M. Siebel Center, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (kale@uiuc.edu). Professor Kalé has been working on various aspects of parallel computing, with a focus on enhancing performance and productivity via adaptive runtime systems. His collaborations involve the widely used biomolecular simulation program NAMD, which won the Gordon Bell Prize at the Supercomputing Conference in 2002. Other collaborative work focuses on computational cosmology, quantum chemistry, rocket simulation, space-time meshes, and other unstructured mesh applications. His group successfully distributes and supports software embodying his research ideas involving Charm++, adaptive MPI, and the ParFUM framework. Professor Kalé received the B.Tech. degree in electronics engineering from Benares Hindu University, Varanasi, India, in 1977, and an M.E. degree in computer science from Indian Institute of Science in Bangalore, India, in 1979. He received a Ph.D. degree in computer science from the State University of New York, Stony Brook, in 1985. He worked as a scientist at the Tata Institute of Fundamental Research from 1979 to 1981. He joined the faculty of the University of Illinois at Urbana-Champaign as an Assistant Professor in 1985, where he is currently employed as a professor.

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