Deploying Scientific Applications to the PRAGMA Grid Testbed: Strategies and Lessons

Recent advances in grid infrastructure and middleware development have enabled various types of applications in science and engineering to be deployed on the grid. The characteristics of these applications and the diverse infrastructure and middleware solutions developed, utilized or adapted by PRAGMA member institutes are summarized. The applications include those for climate modeling, computational chemistry, bioinformatics and computational genomics, remote control of instruments, and distributed databases. Many of the applications are deployed to the PRAGMA grid testbed in routine basis experiments. Strategies for deploying applications without modifications, and those taking advantage of new programming models on the grid are explored and valuable lessons learned are reported. Comprehensive end to end solutions from PRAGMA member institutes that provide important grid middleware components and generalized models of integrating applications and instruments on the grid are also described.

[1]  Nathan A. Baker,et al.  Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[2]  David Abramson,et al.  High performance parametric modeling with Nimrod/G: killer application for the global grid? , 2000, Proceedings 14th International Parallel and Distributed Processing Symposium. IPDPS 2000.

[3]  Domenico Talia,et al.  A Grid Programming Primer , 2001 .

[4]  R. V. van Nieuwpoort,et al.  The Grid 2: Blueprint for a New Computing Infrastructure , 2003 .

[5]  Henri Casanova,et al.  Parameter Sweeps on the Grid with APST , 2003 .

[6]  Henri Casanova,et al.  Overview of GridRPC: A Remote Procedure Call API for Grid Computing , 2002, GRID.

[7]  Satoshi Matsuoka,et al.  Ninf-G: A Reference Implementation of RPC-based Programming Middleware for Grid Computing , 2003, Journal of Grid Computing.

[8]  David M. J. S. Bowman,et al.  The Australian Summer Monsoon: a Biogeographic Perspective , 2002 .

[9]  David Abramson,et al.  Nimrod: a tool for performing parametrised simulations using distributed workstations , 1995, Proceedings of the Fourth IEEE International Symposium on High Performance Distributed Computing.

[10]  Larry Smarr.  Grids in Context , 2004, The Grid 2, 2nd Edition.

[11]  Greg B. Quinn,et al.  A comparative proteomics resource: proteins of Arabidopsis thaliana , 2003, Genome Biology.

[12]  Wu-chun Feng,et al.  The design, implementation, and evaluation of mpiBLAST , 2003 .

[13]  David Abramson,et al.  The PRAGMA Testbed - Building a Multi-Application International Grid , 2006, Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGRID'06).

[14]  Bin Shen,et al.  Analysis of the bioinformatics grid technique applications in China , 2006, Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGRID'06).

[15]  Liang Hu,et al.  Integrating Local Job Scheduler - LSFTM with GfarmTM , 2005, ISPA.

[16]  Bertsch,et al.  Time-dependent local-density approximation in real time. , 1996, Physical review. B, Condensed matter.

[17]  Osamu Tatebe,et al.  Gfarm v2: A Grid file system that supports high-performance distributed and parallel data computing , 2005 .

[18]  Xuebin Chi,et al.  Analysis of the bioinformatics grid technique applications in China , 2006 .

[19]  David Abramson,et al.  The PRAGMA Testbed - Building a Multi-Application International Grid , 2006 .

[20]  Y. Fukunishi,et al.  The Filling Potential Method: A Method for Estimating the Free Energy Surface for Protein−Ligand Docking , 2003 .

[21]  Anthony Skjellum,et al.  A High-Performance, Portable Implementation of the MPI Message Passing Interface Standard , 1996, Parallel Comput..

[22]  George Yang,et al.  A generalized service-oriented architecture for remote control of scientific imaging instruments , 2005, First International Conference on e-Science and Grid Computing (e-Science'05).

[23]  Rajiv K. Kalia,et al.  Hybrid quantum mechanical/molecular dynamics simulation on parallel computers: density functional theory on real-space multigrids , 2002 .

[24]  Haruki Nakamura,et al.  Ab initio MO study of the chlorophyll dimer in the photosynthetic reaction center. I. A theoretical treatment of the electrostatic field created by the surrounding proteins , 1997 .

[25]  A. Kidera,et al.  Free energy landscapes of peptides by enhanced conformational sampling. , 2000, Journal of molecular biology.