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The Virtual Instrument: Support for Grid-Enabled Mcell Simulations

Francine Berman

SAN DIEGO SUPERCOMPUTER CENTER AND DEPT. OF COMPUTER SCIENCE AND ENGINEERING, UNIVERSITY OF CALIFORNIA, SAN DIEGO

Thomas Bartol

Erhan Gokcay

Terry Sejnowski

COMPUTATIONAL NEUROBIOLOGY LABORATORY, SALK INSTITUTE

Adam Birnbaum

SAN DIEGO SUPERCOMPUTER CENTER

Jack Dongarra

Michelle Miller

DEPT. OF COMPUTER SCIENCE, UNIVERSITY OF TENNESSEE, KNOXVILLE

Mark Ellisman

NATIONAL CENTER FOR MICROSCOPY AND IMAGING RESEARCH, UNIVERSITY OF CALIFORNIA, SAN DIEGO

Marcio Faerman

DEPT. OF COMPUTER SCIENCE AND ENGINEERING, UNIVERSITY OF CALIFORNIA, SAN DIEGO

Graziano Obertelli

Rich Wolski

DEPT. OF COMPUTER SCIENCE, UNIVERSITY OF CALIFORNIA, SANTA BARBARA

Stuart Pomerantz

Joel Stiles

PITTSBURGH SUPERCOMPUTER CENTER

Ensembles of widely distributed, heterogeneous resources, or Grids, have emerged as popular platforms for largescale scientific applications. In this paper we present the Virtual Instrument project, which provides an integrated application execution environment that enables end-users to run and interact with running scientific simulations on Grids. This work is performed in the specific context of MCell, a computational biology application. While MCell provides the basis for running simulations, its capabilities are currently limited in terms of scale, ease-of-use, and interactivity. These limitations preclude usage scenarios that are critical for scientific advances. Our goal is to create a scientific "Virtual Instrument" from MCell by allowing its users to transparently access Grid resources while being able to steer running simulations. In this paper, we motivate the Virtual Instrument project and discuss a number of relevant issues and accomplishments in the area of Grid software development and application scheduling. We then describe our software design and report on the current implementation. We verify and evaluate our design via experiments with MCell on a real-world Grid testbed.

Key Words: grid computing • computational neuroscience

References

• Abramson, J., Giddy, D., and Kotler, L. May 2000. High performance parametric modeling with Nimrod/G: Killer application for the global Grid? In Proceedings of the International Parallel and Distributed Processing Symposium (IPDPS), Cancun, Mexico, pp. 520–528 .
• Allen, G., Shalf, J., Benger, W., Dramlitsch, T., Goodale, T., Hege, H.-C., Lanfermann, G., Merzky, A., Radke, T., and Seidel, E. 2001. Cactus tools for Grid applications . Cluster Computing 4(3): 179–188 .[CrossRef]
• Anglister, L., Stiles, J. R., and Salpeter, M. M. 1994. Acetylcholinesterase density and turnover number at frog neuromuscular junctions, with modeling of their role in synaptic function . Neuron 12: 783–794 .[CrossRef][Web of Science][Medline] [Order article via Infotrieve]
• Bartol, T. M., Land, B. R., Salpeter, E. E., and Salpeter, M. M. 1991. Monte Carlo simulation of miniature endplate current generation in the vertebrate neuromuscular junction . Biophysical Journal 59(6): 1290–1307 .[Web of Science][Medline] [Order article via Infotrieve]
• Basney, J. and Livny, M. 1999. Deploying a high throughput computing cluster. In High Performance Cluster Computing, Vol. 1, Chap. 5, Prentice Hall, Englewood Cliffs, NJ .
• Berman, F. 1998. The Grid, Blueprint for a New computing Infrastructure, I. Foster and C. Kesselman, editors, Chap. 12. Morgan Kaufmann Publishers, San Mateo, CA .
• Berman, F., Wolski, R., Figueira, S., Schopf, J., and Shao, G. 1996. Application-level scheduling on distributed heterogeneous networks . In Proceedings of 95’96 , Pittsburgh, PA.
• Berman, F., Chien, A., Cooper, K., Dongarra, J., Foster, I., Dennis Gannon, L. J., Kennedy, K., Kesselman, C., Reed, D., Torczon, L., and Wolski, R. 2001. The GrADS project: Software support for high-level grid application development . International Journal of High Performance Computing Applications 15(4): 327–344 .[Abstract]
• Beynon, M., Kurc, T., Catalyurek, U., Chang, C., Sussman, A., and Saltz, J. 2001. Distributed processing of very large datasets with datacutter . Parallel Computing 27(11): 1457–1478 .[CrossRef]
• Braun, R., Siegel, H., Beck, N., Boloni, L., Maheswaran, M., Reuther, A., Robertson, J., Theys, M., Yao, B., Hensgen, D., and Freund, R. April 1999. A comparison study of static mapping heuristics for a class of meta-tasks on heterogeneous computing systems . In Proceedings of the 8th Heterogeneous Computing Workshop (HCW’99), San Juan, Porto Rico, pp. 15–29 .
• Casanova, H. May 2001. Simgrid: a toolkit for the simulation of application scheduling . In Proceedings of the IEEE International Symposium on Cluster Computing and the Grid (CCGrid’01), Brisbane, Australia, pp. 430–437 .
• Casanova, H. and Berman, F. 2003. Parameter sweeps on the Grid with APST. In Grid Computing: Making the Global Infrastructure a Reality, Chap. 33, Wiley, New York .
• Casanova, H. and Dongarra, J. 1997. NetSolve: a network server for solving computational science problems . International Journal of Supercomputer Applications and High Performance Computing 11(3): 212–223 .[CrossRef][Web of Science]
• Casanova, H., Legrand, A., Zagorodnov, D., and Berman, F. May 2000a. Heuristics for scheduling parameter sweep applications in grid environments . In Proceedings of the 9th Heterogeneous Computing Workshop (HCW’00), Cancun, Mexico, pp. 349–363 .
• Casanova, H., Obertelli, G., Berman, H., and Wolski, R. November 2000b. The AppLeS parameter sweep template: user-level middleware for the Grid . In Proceedings of SC’00, Dallas, TX.
• Casanova, H., Bartol, T., Stiles, J., and Berman, F. 2001. Distributing MCell simulations on the Grid . International Journal of High Performance Computing Applications 14(3): 243–257 .
• Chervenak, A., Foster, I., Kesselman, C., Salisbury, C., and Tuecke, S. 2000. The data Grid: towards an architecture for the distributed management and analysis of large scientific datasets . Journal of Network and Computer Applications 23(3): 187–200 .[CrossRef]
• Czajkowski, K., Foster, I., Karonis, N., Kesselman, C., Martin, S., Smith, W., and Tuecke, S. 1998. A resource management architecture for metacomputing systems . In Proceedings of IPPS/SPDP’98 Workshop on Job Scheduling Strategies for Parallel Processing, Orlando, FL.
• Czajkowski, C., Fitzgerald, S., Foster, I., and Kesselman, C. August 2001. Grid information services for distributed resource sharing . In Proceedings of the 10th IEEE Symposium on High-Performance Distributed Computing, San Francisco, CA.
• Egelman, D. and Montague, P. 1998. Computational properties of peri-dendritic calcium fluctuations . Journal of Neuroscience 18(21): 8580–8589 .[Abstract/Free Full Text]
• Egelman, D., King, R., and Montague, P. 1998. Interaction of nitric oxide and external calcium fluctuations: a possible mechanism for rapid information retrieval . Progress in Brain Research 118: 199–211 .[Web of Science][Medline] [Order article via Infotrieve]
• Faerman, M., Birnbaum, A., Casanova, H., and Berman, F. November 2002. Resource allocation for steerable parallel parameter searches . In Proceedings of the Grid Computing Workshop, Baltimore, MD, pp. 157–169 .
• Foster, I. and Kesselman, C., editors. 1998. The Grid: Blueprint for a New Computing Infrastructure, Morgan Kaufmann Publishers, San Francisco, CA .
• Foster, I. and Kesselman, C. 1999. Globus: A toolkit-based Grid architecture. In The Grid: Blueprint for a New Computing Infrastructure, Morgan Kaufmann Publishers, San Francisco, CA , pp. 259–278.
• Foster, I., Kesselman, C., Tsudik, G., and Tuecke, S. 1998. A security architecture for computational grids . In Proceedings of the 5th ACM Conference on Computer and Communications Security, San Francisco, CA, pp. 83–92 .
• Foster, I., Kesselman, C., and Tuecke, S. 2001. The anatomy of the Grid: enabling scalable virtual organizations . International Journal of High Performance Computing Applications 15(3): 200–222 .[Abstract]
• Foster, I., Kesselman, J., Nick, J., and Tuecke, S. June 2002. The physiology of the Grid: an open grid services architecture for distributed systems integration. Open Grid Service Infrastructure WG, Global Grid Forum .
• Geist, G., Kohl, J., and Papadopoulos, P. 1997. CUMULVS: providing fault tolerance, visualization, and steering of parallel applications . International Journal of Supercomputer Applications and High Performance Computing 11(3): 224–235 .
• Gieger, J., Roth, A., Taskin, B., and Jonas, P. 1999. Glutamatemediated synaptic excitation of cortical interneruons. In Handbook of Experimental Pharmacology, Retinoids, Ionotropic glutamate receptors in the CNS, Vol. 141, P. Jonas and H. Moyner, editors, Springer-Verlag, Berlin , pp. 363–398.
• Hagerup, T. 1997. Allocating independent tasks to parallel processors: an experimental study . Journal of Parallel and Distributed Computing 47: 185–197 .
• Hummel, S. F., Schmidt, J., Uma, R. N., and Wein, J. June 1996. Load-sharing in heterogeneous systems via weighted factoring . In Proceedings of the 8th Annual ACM Symposium on Parallel Algorithms and Architectures, Padua, Italy, pp. 318–328 .
• IBM Corporation. 1993. IBM LoadLeveler User’s Guide.
• Jablonowski, D., Bruner, J., Bliss, B., and Haber, R. 1993. VASE: the visualization and application steering environment . In Proceedings of Supercomputing 1993, Portland, OR, pp. 560–569 .
• Karonis, N., Toonen, B., and Foster, I. 2003. MPICH-G2: a grid-enabled implementation of the message passing interface . Journal of Parallel and Distributed Computing 63(5): 551–563 .[CrossRef]
• Legrand, A., Marchal, L., and Casanova, H. May 2003. Scheduling distributed applications: the SimGrid simulation framework . In Proceedings of the 3rd IEEE International Symposium on Cluster Computing and the Grid (CCGrid’03), Tokyo, Japan.
• Nakada, H., Matsuoka, S., Seymour, K., Dongarra, J., Lee, C., and Casanova, H. November 2002. An overview of Grid-RPC: a remote procedure call API for Grid computing . In Proceedings of the Grid Computing Workshop, Baltimore, MD, pp. 274–279 .
• Novotny, J. 2002. The Grid portal development kit . Concurrency and Computation: Practice and Experience 14(13–15): 1129–1144 .[CrossRef]
• Parker, S., Miller, M., Hansen, C., and Johnson, C. January 1998. An integrated problem solving environment: the SCIRun computational steering system . In Proceedings of the 31st Hawaii International Conference on System Sciences (HICSS-31), Kohala Coast, Hawaii, Vol. VII, pp. 147–156 .
• Rao-Mirotznik, R., Buchsbaum, G., and Sterling, P. 1998. Transmitter concentration at a three-dimensional synapse . Journal of Neurophysiology 80(6): 3163–3172 .[Abstract/Free Full Text]
• Salpeter, M. M., editor. 1987. The Vertebrate Neuromuscular Junction, Alan R. Liss, New York , pages 1–54.
• Stiles, J. R. and Bartol, T. M. 2001. Monte Carlo methods for simulating realistic synaptic microphysiology using MCell. In Computational Neuroscience: Realistic Modeling for Experimentalists, E. DeSchutter, editor, CRC Press, Boca Raton, FL .
• Stiles, J. R., Van Helden, D., Bartol, T. M., Salpeter, E. E., and Salpeter, M. M. 1996. Miniature endplate current rise times < 100 µ s from improved dual recordings can be modeled with passive acetylcholine diffusion from a synaptic vesicle . In Proceedings of the National Academy of Sciences USA 93: 5747–5752 .
• Stiles, J. R., Bartol, T. M., Salpeter, E. E., and Salpeter, M. M. 1998. Monte Carlo simulation of neurotransmitter release using MCell, a general simulator of cellular physiological processes. In Computational Neuroscience, J. M. Bower, editor, Plenum Press, New York , pp. 279–284.
• Stiles, J. R., Kovyazina, I. V., Salpeter, E. E., and Salpeter, M. M. 1999. The temperature sensitivity of miniature endplatecurrents is mostly governed by channel gating: evidence from optimized recordings and Monte Carlo simulations . Biophysical Journal 77: 1177–1187 .[Web of Science][Medline] [Order article via Infotrieve]
• Stiles, J. R., Bartol, T. M., Salpeter, M. M., Salpeter, E. E., and Sejnowski, T. J. 2001. Synaptic variability: new insights from reconstructions and Monte Carlo simulations with MCell. In Synapses, W. M.Cowan, T. C.Südhof, and C. F. Stevens, editors, Johns Hopkins University Press, Baltimore, MD , pp. 681–731.
• Suzumura, T., Nakada, H., Saito, M., Matsuoka, S., Tanaka, Y., and Sekiguchi, S. November 2002. The Ninf portal: an automatic generation tool for the grid portals . In Proceedings of Java Grande, Seattle, WA, pp. 1–7 .
• Thomas, M., Mock, S., Boisseau, J., Dahan, M., Mueller, K., and Sutton, S. August 2001. The GridPort toolkit architecture for building grid portals . In Proceedings of the 10th IEEE International Symposium on High Performance Distributed Computing (HPDC-10), San Francisco, CA.
• Ullman, J. 1975. NP-complete scheduling problems . Journal of Computer and System Sciences 10: 434–439 .
• van Nieuwpoort, R., Kielmann, T., and Bal, H. June 2001. Efficient load balancing for wide-area divide-and-conquer applications . In Proceedings of the 8th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP’01), Snowbird, UT, pp. 34–43 .
• Vetter, J. and Schwan, K. 1995. PROGRESS: a toolkit for interactive program steering . In Proceedings of the 1995 International Conference on Parallel Processing, Urbana-Champaign, IL, pp. 139–149 .
• Vetter, J. and Schwan, K. 1997. High performance computational steering of physical simulations . In Proceedings of IPPS’97, Geneva, Switzerland, pp. 128–132 .
• Wolski, R. August 1997. Dynamically forecasting network performance using the network weather service . In 6th High Performance Distributed Computing Conference, Portland, OR, pp. 316–325 .
• Yarrow, M., McCann, K., Biswas, R., and Van der Wijngaart, R. December 2000. An advanced user interface approach for complex parameter study process specification on the information power Grid. In GRID 2000, Bangalore, India .

International Journal of High Performance Computing Applications, Vol. 18, No. 1, 3-17 (2004)
DOI: 10.1177/1094342004041290


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This Article Abstract Free Full Text (Free PDF) Free Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Alert me to new issues of the journal Add to Saved Citations Download to citation manager Request Permissions Request Reprints Add to My Marked Citations Citing Articles Citing Articles via Google Scholar Citing Articles via Scopus Google Scholar Articles by Casanova, H. Articles by Stiles, J. Search for Related Content Social Bookmarking                         What's this?