CSE Scientific Computation Group Publications

Publication Notice: Copyrights to the following papers are held by the publishers. The following documents are preprints. Please, treat this material in a way consistent with the "fair use" provisions of appropriate copyright law. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.


Papers earlier than 1991

H.P. Baden, S.I. Roth, L.A. Goldsmith, S.B. Baden, L.D. Lee, "Keratohyalin Protein in Disorders of Keratinization, Journal of Investigative Dermatology, 62(4), 1974 (pp. 411-414).

S. B. Baden and D. R. Patel, "Berkeley FP - Experiences with a Functional Programming Language," Conf. Rec. COMPCON '83, San Francisco, California, March 1983 (pp. 274-277).

S. B. Baden, "Low-Overhead Storage Reclamation in the Smalltalk-80 Virtual Machine," in Smalltalk-80: Bits of History, Words of Advice, G. Krasner (editor), Addison Wesley, Reading, Massachusetts, 1983 (pp. 331-342).

S. B. Baden, "Very Large Vortex Calculations in Two Dimensions," in Lecture Notes in Mathematics, vol. 1360, C. Anderson and C. Greengard (editors), Springer-Verlag, New York, 1988 (pp. 96-120).

S. B. Baden and E. G. Puckett, "A Fast Vortex Code for Computing 2-D Flow in a Box," Proc. First National Fluid Dynamics Congress, Cincinnati, Ohio July 25-28, 1988 (pp. 185-192).

S. B. Baden, "Programming Abstractions for Run-Time Partitioning of Scientific Continuum Calculations Running on Multiprocessors," Parallel Processing for Scientific Computing, G. Rodrigue (editor), SIAM, Philadelphia, Pennsylvania, 1989 (pp. 223-230).

S. B. Baden and E. G. Puckett, "A Fast Vortex Code for Computing 2D Viscous Flow," J. Computational Physics 91, 2, December 1990 (pp. 278-297).


Papers for 1991

S. B. Baden, "Programming Abstractions for Dynamically Partitioning and Coordinating Localized Scientific Calculations Running on Multiprocessors," SIAM J. on Scientific and Statistical Computing, 12(145), January 1991 (pp. 145-157).    PDF

Scott B. Baden and Scott R. Kohn, "A Comparison of Load Balancing Strategies for Particle Methods Running on MIMD Multiprocessors," Proc. 5th SIAM conference on Parallel Processing for Scientific Computing, March 25-27, 1991, Houston, TX. (Also CSE Tech. Rept. CS91-199.) Not available on line, contact baden@ucsd.edu


Papers for 1992

The Reference Guide to GenMP -- The Generic Multiprocessor, Scott B. Baden and Scott R. Kohn, June 1992, CSE Tech. Rept. CS92-243.

Blobs: Visualization of Particle Methods on Multiprocessors, Scott R. Kohn and Scott B. Baden, May 1992, CSE Tech. Rept. CS92-241.


Papers for 1993

Lattice Parallelism: A Parallel Programming Model for Non-Uniform, Structured Scientific Computations, Scott B. Baden and Scott R. Kohn, September 1992, CSE Tech. Rept. CS92-261. (Superceded by CS93-330.)

Scott B. Baden and Scott R. Kohn., "Lattice parallelism: a parallel programming model for manipulating non-uniform structured scientific data structures," SIGPLAN Not. 28(1):24-27 (Jan. 1993). DOI

An Implementation of the LPAR Parallel Programming Model for Scientific Computations, Scott R. Kohn and Scott B. Baden, Proc. 6th SIAM conference on Parallel Processing for Scientific Computing, March 1993, Norfolk, VA. (Also CSE Tech. Rept. CS93-280, 2/93.)


Papers for 1994

Programming with LPARX, Scott B. Baden, Scott R. Kohn, Stephen J. Fink, Proc. Intel Supercomputer User's Group Meeting, June 1994, San Diego, CA. (Also CSE Tech. Rept. CS94-377.)

A Robust Parallel Programming Model for Dynamic Non-Uniform Scientific Computations, Scott R. Kohn and Scott B. Baden, March 1994, Proc. 1994 Scalable High Performance Computing Conference, May 23-35, 1994, Knoxville, Tennessee. (Also CSE Tech. Rept. CS94-354.)

Cluster Identification on a Distributed Memory Multiprocessor, Stephen J. Fink, Scott B. Baden, Karl Jansen, March 1994, Proc. 1994 Scalable High Performance Computing Conference, May 23-35, 1994, Knoxville, Tennessee. (Also CSE Tech. Rept. CS94-355.)

Cluster Identification on a Distributed Memory Multiprocessor, Stephen J. Fink, Scott B. Baden, Karl Jansen, March 1994, Proc. 1994 Scalable High Performance Computing Conference, May 23-35, 1994, Knoxville, Tennessee. (Also CSE Tech. Rept. CS94-355.)

Partitioning with Space filling Curves, John R. Pilkington and Scott B. Baden, March 1994, CSE Tech. Rept. CS94-349.


Papers for 1995

A Parallel Software Infrastructure for Structured Adaptive Mesh Methods , (Also available in HTML form. ) Scott R. Kohn and Scott B. Baden, Proc. Supercomputing '95, San Diego, CA, December 1995.

"A Parallel Software Infrastructure for Dynamic Block-Irregular Scientific Calculations," Scott R. Kohn, UCSD CSE Dept. Tech. Rep. CS95-429, Jun. 1995. (PhD Dissertation, send email to kohn1@llnl.gov for hardcopy.)     PDF      ps.gz

Scalable Parallel Numerical Methods and Software Tools for Material Design. E. Bylaska, S. Kohn, S. Baden, M.E.G. Ong, J. Weare, A. Edelman, R. Kawai. PHYSICS COMPUTING '95 (Annual Meeting of the APS Division of Computational Physics), June 5-8 1995, Pittsburgh, PA.

Portable Parallel Programming of Numerical Problems Under the LPAR System, Scott B. Baden and Scott R. Kohn, Journal of Parallel and Distributed Computing, May 1995, vol. 27, pp 38-55. (Also CSE Tech. Rept. CS93-330.)

VIPP: Visual Interactive Parallel Performance Tool, Edmund Johnson, Scott R. Kohn, and Scott B. Baden April 1995.

Performance Analysis of Parallel Strategies for Localized N-body Solvers, Silvia M. Figueira and Scott B. Baden, Proc. 7th SIAM Conf. on Parallel Proc. for Scientific Computing, February 1995, San Francisco, CA. (Also CSE Tech. Rept. CS94-385, 9/94.)

Run-time Data Distribution for Block-Structured Applications on Distributed Memory Computers, Stephen J. Fink and Scott B. Baden, Proc. 7th SIAM Conf. on Parallel Proc. for Scientific Computing, February 1995, San Francisco, CA. (Also CSE Tech. Rept. CS94-386, 9/94.)

The Parallelization of an Adaptive Multigrid Eigenvalue Solver with LPARX, Scott R. Kohn and Scott B. Baden, Proc. 7th SIAM Conf. on Parallel Proc. for Scientific Computing, February 1995, San Francisco, CA. (Also CSE Tech. Rept. CS94-387, 9/94.)

Scalable Parallel Numerical Methods and Software Tools for Material Design, Eric J. Bylaska, Scott R. Kohn, Scott B. Baden, Alan Edelman, Ryiochi Kawai, Maria E. G. Ong, and John H. Weare, Proc. 7th SIAM Conf. on Parallel Proc. for Scientific Computing, February 1995, San Francisco, CA. (Also CSE Tech. Rept. CS94-388, 9/94.)


Papers for 1996

Irregular Coarse-Grain Data Parallelism Under LPARX, Scott R. Kohn and Scott B. Baden, 1996. J. Scientific Programming.

Non-Uniform Partitioning of Finite Difference Methods Running on SMP Clusters. S. J. Fink and S. B. Baden. December 1996.

Flexible Communication Mechanisms for Dynamic Structured Applications, S. J. Fink, S. R. Kohn, and S. B. Baden. Third International Workshop on Parallel Algorithms for Irregularly Structured Problems (IRREGULAR '96), Santa Barbara, CA, August 1996, pp 203-215. Also CSD CSE Dept. Tech. Rep. CS96-490, Aug. 1996.

Analysis of the Numerical Effects of Parallelism on a Parallel Genetic Algorithm," W. E. Hart, S. B. Baden, R. K. Belew, and S. R. Kohn. April 1996. IPPS '96, Honolulu, HI.

Baden, S. B. 1996. Software infrastructure for non-uniform scientific computations on parallel processors. SIGAPP Appl. Comput. Rev. 4, 1 (Apr. 1996), 7-10. DOI

Software Infrastructure for Non-Uniform Scientific Computations on Parallel Processors. S. B. Baden. Applied Computing Review, ACM 4(1), Spring 1996, pp. 7-10.

Dynamic Partitioning of Non-Uniform Structured Workloads with Space filling Curves, J. R. Pilkington and S. B. Baden. IEEE Trans. on Parallel and Distributed Systems , 7(3), March 1996, pp. 288--300.


Papers for 1997

S. J. Fink and S. B. Baden, Runtime Support for Multi-Tier Programming of Block-Structured Applications on SMP Clusters, , Lecture Notes in Computer Science, Volume 1343, edited by Y. Ishikawa et al., Springer Verlag, 1997, pp. 1-8. Proc. 1997 International Scientific Computing in Object-Oriented Parallel Environments Conference (ISCOPE '97), Marina del Ray, California, December 1997.

"Parallel Cluster Identification for Multidimensional Lattices," S. J. Fink, C. Huston, S. B. Baden, and K. Jansen. IEEE Transactions on Parallel and Distributed Systems, 8(11), November 1997, pp. 1089-1097.     DOI     ps

A Preliminary Evaluation of HPF, S. B. Baden, R. Schreiber, K. S Gatlin, S. J. Fink. Proc. 8th SIAM Conf. on Parallel Proc. for Scientific Computing, March 1997, Minneapolis, MN. Also UCSD CSE Dept. Tech. Report CS97-516.


Papers for 1998

J. Saltz, A. Sussman, S. Graham, J. Demmel, S. Baden, and J. Dongarra, "Programming Tools and Environments," Comm. ACM, 41:64-73, Nov. 1998.

Scott B. Baden and Stephen J. Fink, Communication overlap in multi-tier parallel algorithms, Conf. Proc. SC '98, Orlando FL, November 1998.

J. H. Merlin, S. B. Baden. Using KeLP-HPF for Dynamic Block-Structured Applications. 2nd Annual HPF User Group meeting (HUG'98), Porto, Portugal, June 1998.

Stephen J. Fink A Programming Model for Block-Structured Scientific Calculations on SMP Clusters , Ph. D. Dissertation, Department of Computer Science and Engineering, University of California, San Diego, June 1998.

Fink, S.J, Baden, S.B, and Kohn, S.R. Efficient Run-time Support for Irregular Block-Structured Applications, J. Parallel and Distributed Computing, 50(1-2), April-May 1998, pp. 61-82.

J. H. Merlin, S. B. Baden, S. J. Fink and B. M. Chapman. Multiple data parallelism with HPF and KeLP. HPCN '98, Amsterdam, April 1998.

Jeffrey Howe, Scott B. Baden, Tamara Grimmett, and Keiko Nomura. Modernization of Legacy Application Software. B. Kågström, J. Dongarra, E. Elmroth and J. Wasniewski (editors). Applied Parallel Computing, 4th International Workshop, PARA'98, Lecture Notes in Computer Science,No. 1541, Springer-Verlag, Berlin, 1998, pp. 255-262.


Papers for 1999

J. Merlin, S. Baden, S. Fink and B. Chapman, Multiple Data Parallelism with HPF and KeLP, J. Future Generation Computer Systems, 15(3):393--405, May 1999.

Scott Kohn, John Weare, M. Elizabeth Ong, and Scott B. Baden, Software Abstractions and Computational Issues in Parallel Structured Adaptive Mesh Methods for Electronic Structure Calculations IMA Volumes in Mathematics and its Applications, Volume 117, Structured Adaptive Mesh Refinement (SAMR) Grid Methods,   S. B. Baden, N. Chrisochoides, M. Norman, and D. Gannon, Eds., Springer­Verlag, 1999, pp. 75-95. (Proc. Workshop on Structured Adaptive Mesh Refinement Grid Methods, Institute for Mathematics and its Applications, University of Minnesota, Minneapolis, Minnesota, March 12-13, 1997.).

S. B. Baden and S. J. Fink The Data Mover: "A Machine-Independent Abstraction for Managing Customized Data Motion", Proc. LCPC '99, La Jolla, CA, 1999.     PDF and PS


Papers for 2000

S. B. Baden and S. J. Fink A Programming Methodology for Dual-tier Multicomputers . IEEE Transactions on Software Engineering, 26(3): 212-26, March 2000.

P.H.J. Kelly, S. Gorlatch, S.B. Baden and V. Getov, "Topic 10: Programming Languages, Models, and Methods." In A. Bode, T. Ludwig, W. Karl, and R. Wismuller (Eds.): Proc. Euro-Par 2000: Parallel Processing, 6th International Euro-Par Conf, Munich, Germany, August 29 - September 1, 2000, Lecture Notes in Computer Science Vol. 1900, Springer, 2001, (pp 617-770).


Papers for 2001

S. B. Baden and D. Shalit, "Performance tradeoffs in multi-tier formulation of a finite difference method," in Proc. 2001 International Conference on Computational Science, San Francisco, CA, May 2001.

Paul H J Kelly, Olav Beckmann, Tony Field and Scott Baden, Themis: Component dependence metadata in adaptive parallel applications, Parallel Processing Letters, Vol. 11, No. 4 (July 2001), pp. 455-470. (Presented at the International Workshop on High-Level Parallel Programming (HLPP2001), Orleans, France (March 2001).)

S.B. Baden, P. Colella , D. Shalit, B. Van Straalen, "Abstract KeLP", 10th SIAM Conference on Parallel Processing for Scientific Computing, Portsmouth, Virginia, March 2001.

S. P. Peisert and S. B. Baden, A Programming Model for Automated Decomposition on Heterogeneous Clusters of Multiprocessors, Feb. 2001

Scott R. Kohn and Scott B. Baden, Parallel Software Abstractions for Structured Adaptive Mesh Methods, Journal of Parallel and Distributed Computing, 61(6), June 2001, (pp. 713-736)

S. B. Baden, P. H. J. Kelly, S. Gorlatch, and C. Lin, "Topic 10: Parallel Programming: Models, Methods and Programming Languages." In R. Sakellariou, J. Keane, J. R. Gurd, L. Freeman (Eds.): Proc. Euro-Par 2001: Parallel Processing, 7th International Euro-Par Conf, Manchester, UK August 28-31, 2001, Lecture Notes in Computer Science Vol. 2150, Springer, 2001, (pp 491-565).

T. Kaiser and S. B. Baden, "Overlapping Communication and Computation with OpenMP and MPI," J. Scientific Programming, vol 9(2,3) 2001. (pp. 73-81)


Papers for 2002

Peter Diamessis, William Kerney, Scott B. Baden, and Keiko K. Nomura, Automated Tracking of 3-D Overturn Patches in Direct Numerical Simulation of Stratified Homogeneous Turbulence, Juha Fagerholm, Juha Haataja, Jari Järvinen, Mikko Lyly, and Peter Råback.(editors). Applied Parallel Computing, 6th International Conference, PARA'02, Helsinki, Finland, June 2002, Lecture Notes in Computer Science, No. 2367 Springer, Berlin, 2002 (pp. 557-566).

Frederico D. Sacerdoti, A Cache-Friendly Liquid Load Balancer, M.S. Dissertation, Department of Computer Science and Engineering, University of California, San Diego, June 2002

William R. Kerney,  MOLD: A System for Breaking Down Large Visualization and Post-Processing Problems, M.S. Dissertation, Department of Computer Science and Engineering, University of California, San Diego, March 2002


Papers for 2003

Gregory T. Balls, Scott B. Baden, and Phillip Colella, SCALLOP: A Highly Scalable Parallel Poisson Solver in Three Dimensions, Conf. Proc., SC '03, Phoenix AZ, November 2003.

Gregory T. Balls, Scott B. Baden, Thomas M. Bartol, and Terrence J. Sejnowski, Simulation-driven dynamic clamping of neurons, Submitted to Kluwer, December 15, 2003.

Stephen Lau, Using a Proxy to Enable Communication Overlap with Computation (ps.gz), M.S. Dissertation, Department of Computer Science and Engineering, University of California, San Diego, 2003


Papers for 2004

Gregory T. Balls, Scott B. Baden, Tilman Kispersky, Thomas M. Bartol, and Terrence J. Sejnowski, A large scale Monte Carlo simulator for cellular microphysiology, IPDPS-2004, April 2004.

Urvashi R.V. A Performance Model and Load Balancer for a Parallel Monte-Carlo Cellular Microphysiology Simulator, M.S. Dissertation, Department of Computer Science and Engineering, University of California, San Diego, June 2004


Papers for 2005

Sara Miner More, Tim Pevzner, Alin Deutsch, Scott Baden, Paul Kube, Building an XQuery interpreter in a compiler construction course, SIGCSE Bull., 37(11):2-6 (2005). ACM Press.

P. McCorquodale, P. Colella, G. T. Balls, and S. B. Baden, A Scalable Parallel Poisson Solver in Three Dimensions with Infinite-Domain Boundary Conditions, 7th Workshop on High Performance Scientific and Engineering Computing, Oslo, Norway, June 2005, pp 163-172.


Papers for 2006

Jacob Sorensen and Scott B. Baden, A Data Driven Model for Tolerating Communication Delays (Abstract), 12th SIAM Conference on Parallel Processing for Scientific Computing, San Francisco, California, February 2006.

Pietro Cicotti and Scott Baden, Asynchronous Cellular Microphysiology Simulation (Abstract), 12th SIAM Conference on Parallel Processing for Scientific Computing, San Francisco, California, February 2006.

Scott B. Baden, Gregory T. Balls, Terrence Sejnowski, Thomas M. Bartol, MCell-K: A Highly Scalable Cell Microphysiology Simulator on Blue Gene L (Abstract), 12th SIAM Conference on Parallel Processing for Scientific Computing, San Francisco, California, February 2006.

Scott B. Baden, Phillip Colella, Gregory T. Balls, Peter McCorquodale, New Scalability and Accuracy Results for a Latency-Tolerant Elliptic Solver (Abstract), 12th SIAM Conference on Parallel Processing for Scientific Computing, San Francisco, California, February 2006.

Tallat Mahmood Shaffat, Context Dependent Compression using Adaptive Subsampling of Scientific Datasets, MS Thesis, Royal Institute of Technology (KTH) School of Information and Communication, Stockholm, Sweden, 2006. ICT/ECS-2006-12

Faisal Ghias Mir, Data Management of Scientific Datasets on High Performance Interactive Clusters, MS Thesis, Royal Institute of Technology (KTH) School of Information and Communication, Stockholm, Sweden, 2006. ICT/ECS-2006-13

Pietro Cicotti and Scott B. Baden, Asynchronous programming with Tarragon , 15th IEEE International Symposium on High Performance Distributed Computing, pp 375-376, June 19-23 2006.

Tallat M. Shafaat and Scott B. Baden, A Method of Adaptive Coarsening for Compressing Scientific Datasets, In Bo Kågström, Erik Elmroth, Jack Dongarra and Jerzy Wasniewski (Eds.), 8th International Conference on Applied Parallel Computing (PARA '06), Umeå, Sweden, June 2006, Lecture Notes in Computer Science, Springer, 2007.


Papers for 2007

Scott Baden, Terrence Sejnowski, Thomas Bartol, and Joel Stiles Toward Petascale Simulation of Cellular Microphysiology, IEEE 7th International Symposium on Bioinformatics and Bioengineering, Workshop on Progress Toward Petascale Applications in Bioinformatics and Computational Biology, October 14-17, 2007, Boston, MA. (8 pp).

McCorquodale, P.,Colella, P., Balls, G.T., and Baden, S.B. A Local Corrections Algorithm for Solving Poisson's Equation in Three Dimensions Communications in Applied Mathematics and Computational Science Vol.2, No.1 (2007), pp 57-81.

Joey Hammer, CAFE: A Framework for Cell Application Development, M.S. Dissertation, Department of Computer Science and Engineering, University of California, San Diego, December 2007.


Papers for 2008

Pietro Cicotti, Xiaoye Sherry Li, Scott B. Baden, "LUsim: A Framework for Simulation-Based Performance Modeling and Prediction of Parallel Sparse LU Factorization," Lawrence Berkeley National Laboratory, Paper LBNL-196E, May 8, 2008.

Rex A. Kerr, Thomas M. Bartol, Boris Kaminsky, Markus Dittrich, Jen-Chien Jack Chang, Scott B. Baden, Terrence J. Sejnowski, and Joel R. Stiles, Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces," SIAM J. Sci. Comput. 30, 3126-3149, (2008), DOI:10.1137/070692017

Y. Zhu, M. Taylor, S. Baden, and C.K. Cheng, Advancing Supercomputer Performance Through Interconnect Topology Synthesis, ACM/IEEE Int. Conf. on Computer-Aided Design, pp. 555-558, 2008.     (From IEEE Web site)


Papers for 2009

Didem Unat, Theodore Hromadka III, Scott B. Baden, An Adaptive Sub-Sampling Method for in-memory Compression of Scientific Data, Data Compression Conf., Snowbird, UT, March 2009, pp 262-71.    DOI

Jacob Sorensen and Scott B. Baden, Hiding Communication Latency with non-SPMD, Graph-Based Execution International Conference on Computational Science 2009 (ICCS 2009), Baton Rouge, LA, May 2009, pp. 262-271.    DOI

Pietro Cicotti, Xiaoye S. Li and Scott B. Baden, "Performance Modeling Tools for Parallel Sparse Linear Algebra Computations," Proc. International Conf on Parallel Computing (ParCo), September 2009, Lyon, France, 8 pp.     PDF


Papers for 2010

Daniel Hefenbrock, Jason Oberg, Nhat Tan Nguyen Thanh, Ryan Kastner and Scott B. Baden, "Accelerating Viola-Jones Face Detection to FPGA-Level using GPUs," 18th Ann. Intl. IEEE Symp. on Field-Programmable Custom Comput. Machines, Charlotte, NC, May 2-4, 2010, 8 pp. To appear     PDF

Fred Lionetti, "GPU Accelerated Cardiac Electrophysiology," M.S. Dissertation, Department of Computer Science and Engineering, University of California, San Diego (2010)     PDF


Maintained by Scott B. Baden.
Last Modified Sun Apr 18 03:38:37 PDT 2010