Philip M. Papadopoulos



Program Director, UC Computing Systems
San Diego Supercomputer Center, UCSD

Associate Research Professor (Adjunct)
Computer Science UCSD


Ph.D.: University of California, Santa Barbara , '93. Electrical and Computer Engineering
Advisor: Alan J. Laub
Dissertation: Numerical Algorithms for Large-Scale and Ill-Conditioned Matrix-Valued Equations in Control
M.S.: University of California, Berkeley '87, Mechanical Engineering
B.A.: University of California, San Diego '85, Applied Mathematics


o Rocks - Clustering Toolkit
Rocks Cluster Toolkit is an open-source toolkit that is extensible and scalable. Many groups are using this toolkit to run their clusters. Current version is 5.0. 5.1 Beta was Released September 24, 2008. Rocks is funded the National Science Foundation under Award # OCI-0721623.
o BIRN - Biomedical Informatics Research Network
Co-PI w/ Mark Ellisman (UCSD School of Medicine). Biomedical Informatics Research Network. Building a data grid for researchers at 5 different institutions. 3 years (10/2004 - 10/2009), $12.5M. NIH Award.
o PRAGMA - Pacific Rim Applications and Grid Middleware Assembly
Co-PI w/ Peter Arzberger. Pacific Rim and Grid Middleware Assembly. International Collaborative Framework among Pacific Rim institutions that are building grid applications. 5yrs (10/2006 - 9/2011). $3.2M. NSF Award# OCI-0627026.
o Quartzite
PI (Larry Smarr , Joseph Ford, Shaya Fainman, Co-PI) Quartzite - Development of a Campus-wide, Terabit-Class, Field-Programmable, Hybrid Switching Instrument for Comparative Studies of Optical Circuits, Packet Switching, and Network Topologies as Enablers for e-Science Applications (09/2004 - 09/2008). $1.3M, National Science Foundation Award# CNS 0421555.
o CAMERA Metagenomics
Co-PI With Larry Smarr, Peter Arzberger, Tom Defanti (UCSD) and J. Craig Venter, Marvin Frazier, Saul Kravitz (J. Craig Venter Institute), Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis. $24.5M (01/2006 - 01/2013). Gordon and Betty Moore Foundation
o NBCR - National Biomedical Computation Resource
Co-PI (Peter Arzberger, PI) NBCR National Biomedical Computation Resource. National Institutes of Health, $10.2M (10/2004-9/2009)

Past Projects

o PVM - Parallel Virtual Machine
I used to be an active member of the PVM development team.
CUMULVS is a middle-ware that allows parallel programs to easy incorporate real-time visualization and steering. Jim Kohl and I designed and implemented the software. Jim is in charge of development for CUMULVS now and has taken it to new places.


Conference and Technical Reports

Refereed Articles

Thomas A. DeFanti, Jason Leigh, Luc Renambot, Byungil Jeong, Alan Verlo, Lance Long, Maxine Brown, Daniel J. Sandin, Venkatram Vishwanath, Qian Liu, Mason J. Katz, Philip Papadopoulos, Joseph P. Keefe, Gregory R. Hidley, Gregory L. Dawe, Ian Kaufman, Bryan Glogowski, Kai-Uwe Doerr, Rajvikram Singh, Javier Girado, Jurgen P. Schulze, Falko Kuester, Larry Smarr, "The OptIPortal, a Scalable Visualization, Storage, and Computing Interface Device for the OptiPuter" Future Generation Computer Systems, 25 (2009), pp. 114-123.

Keator, D.; Grethe, J.S.; Marcus, D.; Ozyurt, B.; Gadde, S.; Murphy, S.; Pieper, S.; Greve, D.; Notestine, R.; Bockholt, H.J; Papadopoulos, P.; Function BIRN; Morphometry BIRN; BIRN Coordinating Center. A National Human Neuroimaging Collaboratory Enabled By The Biomedical Informatics Research Network (BIRN). IEEE Trans Inf Technol Biomed. 2008 Mar;12(2):162-72.

Zheng, C., Abramson, D., Arzberger, P., Ayyub, S., Enticott, C., Garic, S., Goscinski, W., Katz, M.J., Lee, B.S., Papadopoulos, P.M., Phatanapherom, S., Sriprayoonsakul, S.,Tanaka, Y., Tanimura, Y., Tatebe, O. and Uthayopas, P. "Lessons learned through driving science applications in the PRAGMA grid", Int. J. Web and Grid Services, Vol.3 No. 3 pp.287-312, 2007

Zheng C, Abramson D, Arzberger P, Ayuub S, Enticott C, Garic S, Katz M, Kwak J, Papadopoulos P, Phatanapherom S, Sriprayoonsakul S, Tanaka Y, Tanimura Y, Tatebe O, Uthayopas P. The PRAGMA Testbed: Building a Multi-Application International Grid 2005 , CCGrid 2006

Nut Taesombut, Frank Uyeda, Larry Smarr, Thomas A. DeFanti, Phil Papadopoulos, Jason Leigh, Mark Ellisman, John Orcutt and Andrew A. Chien. "The OptIPuter: High-Performance, QoS-Guaranteed Network Service for Emerging E-Science Applications," IEEE Communications, Volume 44, Issue 5, May 2006 Page(s): 38 - 45

Federico D. Sacerdoti, Mason J. Katz, and Philip M. Papadopoulos, "411 on Scalable Password Service", IEEE HPC, North Carolina, July 2005.

Jeffrey S. Grethe, Chaitan Baru, Amarnath Gupta, Mark James, Bertram Ludaescher, Maryann E. Martone, Philip M. Papadopoulos, Steven T. Peltier, Arcot Rajasekar, Simone Santini,, Ilya N. Zaslavsky, Mark H. Ellisman, Biomedical Informatics Research Network: Building a National Collaboratory to Hasten the Derivation of New Understanding and Treatment of Disease. From Grid to Healthgrid: Proceedings of Healthgrid 2005.

Jerry P. Greenberg, Mason J. Katz, Greg Bruno, Federico D. Sacerdoti, Philip M. Papadopoulos, and Kim K. Baldridge , "Incorporation of Middleware and Grid Technologies to Enhance Usability in Computational Chemistry Applications," Future Generation Computer Systems, vol 21, 2005.

Federico D. Sacerdoti, Mason J. Katz, and Philip M. Papadopoulos, "411 on Scalable Password Service", IEEE HPC, North Carolina, July 2005.

Greg Bruno, Mason J. Katz, Federico D. Sacerdoti, and Philip M. Papadopoulos, "Rolls: Modifying a Standard System Installer to Support User-Customizable Cluster Frontend Appliances", IEEE Cluster 2004, San Diego, September 2004

Federico D. Sacerdoti, Mason J. Katz, Matthew L. Massie, and David E. Culler, '"Wide Area Cluster Monitoring with Ganglia," IEEE Cluster 2003, Hong Kong, December 2003

Kim Baldridge , Jerry Greenberg, Stephen Elbert, Stephen Mock, Philip Papadopoulos, "QMView and GAMESS: Integration into the World Wide Computational Grid," SC2002, Baltimore, MD, November 16-21, 2002

P.M. Papadopoulos, M.J. Katz, G.D. Bruno, "Leveraging Standard Core Technologies to Programmatically Build Linux Cluster Appliances," IEEE Cluster 2002, Chicago, IL. September, 2002.

P.M. Papadopoulos, M.J. Katz, G.D. Bruno, "NPACI Rocks: Tools and Techniques for Easily Deploying Manageable Linux Clusters", IEEE Cluster 2001, Newport Beach, CA, Oct 2001

G.B. Bruno, A.A. Chien, M.J. Katz, P.M. Papadopoulos, "Performance Enhancements for HPVM with Heterogeneous Messaging Substrates and Commodity Hardware," Proc. PDC Conference, Sweden, 1999.

J.A. Kohl and P.M. Papadopoulos, ``Efficient and Flexible Fault Tolerance and Migration of Scientific Simulations Using CUMULVS,'' 2nd SIGMETRICS Symposium on Parallel and Distributed Tools, Welches, OR, August 1998, to appear. ( postscript version )

T. Sheehan, W. Shelton, T. Pratt, P. Papadopoulos, P. LoCascio, T. Dunigan: ``The Locally Self Consistent Multiple Scattering method in a Geographically Distributed Linked MPP Environment,'' Parallel Computing , to appear.

P.M. Papadopoulos, J.A. Kohl, B.D. Semeraro, `` CUMULVS: Extending a Generic Steering and Visualization Middleware for Application Fault-Tolerance of Parallel Applications'', Proc. Hawaii International Conference on Systems Sciences , pp. 127--136, Vol 8, Kona, HI, January 6-9, 1998. ( postscript version ).

Geist, G.A., J.A. Kohl, P.M. Papadopoulos `` CUMULVS: Providing Fault Tolerance, Visualization and Steering of Parallel Applications'', Intl. J. Supercomputer Applications , 11(3), pp. 224--235, Fall 1997. postscript version )

Geist, G.A, J.A. Kohl, P.M. Papadopoulos, `` PVM and MPI: A Comparison of Features '', Calculateurs Paralleles , 8(2), pp. 137--150, June, 1996. ( postscript version )

Geist, G.A, J.A. Kohl, P.M. Papadopoulos, B.D. Semeraro, W.A. Shelton `` Early Experiences with Distributed Supercomputing on I-WAY: First-Principles Materials Science and Parallel Acoustic Wave Propagation '', Intl. J. of Supercomputer Applications 10(2/3), pp. 157--169, Spring/Summer 1996. ( postscript version )

Kohl, J.A., Papadopoulos, P.M., `` A Library for Visualization and Steering of Distributed Simulations Using PVM and AVS'', Proc. High Performance Computing Symposium '95 , Montreal, Quebec, Canada, July 10--12, 1995. ( postscript version )

Papadopoulos, P.M., C.S. Kenney, and A.J. Laub, ``Least-Squares Solution of Ill-Conditioned Continuous-Time Lyapunov Equations,'' 1993 American Control Conference , San Francisco, CA, June 2-4, 1993.

Kenney, C.S., A.J. Laub, and P.M. Papadopoulos, ``A Newton-Squaring Algorithm for Computing the Negative Invariant Subspace of a Matrix,'' IEEE Trans. on Automatic Control, Vol. 38, No. 6, pp. 1284-1289.

Kenney, C.S., A.J. Laub, and P.M. Papadopoulos, ``Matrix Sign Algorithms for Riccati Equations,'' invited paper for IMA International Conference on Control: Modelling, Computation, Information , Manchester, England, September 1992. Also, IMA Journal of Mathematical Control and Information , Vol. 9, pp. 331-344, Oxford, UK, 1992.

Cheng, J., G. Ianculescu, C.S. Kenney, A.J. Laub, J.Ly, and P.M. Papadopoulos, ``Control-Structure Interaction Study for Space Station Solar Dynamic Power Module,'' IEEE Control Systems Magazine 12(5), Oct. 1992, pp. 4-13.

Papadopoulos, P.M. , A.J. Laub, C.S. Kenney, P.Pandey, G. Ianculescu, and J. Ly, ``Optimal Control Study for the Space Station Solar Dynamic Power Module,'' Proc. IEEE Conf. on Decision and Control , Brighton, England, Dec. 1991, pp. 2224-2229.

Bayo, E., P.M. Papadopoulos, M.A. Serna, and J.R. Stubbe, ``Inverse Dynamics and Kinematics of Multi-Link Elastic Robots. An Iterative Frequency Domain Approach,'' Int. J. of Robotics Research , 8(6), Dec. 1989, pp. 49-62.



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University of California San Diego
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Last modified Tue Sep 30, 2008