This Article Free Full Text (Free PDF) Free References 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?

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

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


CiteULike    Complore    Connotea    Del.icio.us    Digg    Reddit    Technorati    Twitter    What's this?