Implementation and performance evaluation of CONFLEX-G: grid-enabled molecular conformational space search program with OmniRPC

  • Authors:

  • Yoshihiro Nakajima;Mitsuhisa Sato;Hitoshi Goto;Taisuke Boku;Daisuke Takahashi

  • Affiliations:

  • University of Tsukuba, Tsukuba, Japan;University of Tsukuba, Tsukuba, Japan;Toyohashi University of Technology, Toyohashi, Japan;Toyohashi University of Technology, Toyohashi, Japan;Toyohashi University of Technology, Toyohashi, Japan

  • Venue:
  • Proceedings of the 18th annual international conference on Supercomputing
  • Year:
  • 2004

Quantified Score

Hi-index 0.00

Visualization

Abstract

CONFLEX-G is the grid-enabled version of a molecular conformational space search program called CONFLEX. We have implemented CONFLEX-G using a grid RPC system called OmniRPC. In this paper, we report the performance of CONFLEX-G in a grid testbed of several geographically distributed PC clusters. In order to explore many conformation of large bio-molecules, CONFLEX-G generates trial structures of the molecules and allocates jobs to optimize a trial structure with a reliable molecular mechanics method in the grid. OmniRPC provides a restricted persistence model to support the parametric search applications. In this model, when the initialization procedure is defined in the RPC module, the module is automatically initialized at the time of invocation by calling the initialization procedure. This can eliminate unnecessary communication and initialization at each call in CONFLEX-G. CONFLEX-G can achieve performance comparable to CONFLEX MPI and can exploit more computing resources by allowing the use of a cluster of multiple clusters in the grid. The experimental result shows that CONFLEX-G achieved a speedup of 56.5 times in the case of the 1BL1 molecule, where the molecule consists of a large number of atoms, and each trial structure optimization requires significant time. The load imbalance of the optimization time of the trial structure may also cause performance degradation.