Lightweight Computational Steering of Very Large Scale Molecular Dynamics Simulations

We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations over standard Internet connections. We demonstrate how we have been able to explore data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show how this approach can be used to integrate common scripting languages (including Python, Tcl/Tk, and Perl), simulation code, user extensions, and commercial data analysis packages.

[1]  Charles D. Hansen,et al.  Massively Parallel Visualization: Parallel Rendering , 1995, PPSC.

[2]  M. Almond,et al.  Computers in Physics , 1971 .

[3]  Doug Brown,et al.  Lex and Yacc , 1990 .

[4]  John K. Ousterhout,et al.  Tcl and the Tk Toolkit , 1994 .

[5]  A. Voter,et al.  Interatomic Potentials for Atomistic Simulations , 1996 .

[6]  Karsten Schwan,et al.  Opportunities and Tools for Highly Interactive Distributed and Parallel Computing , 1994 .

[7]  Karsten Schwan,et al.  Falcon-toward interactive parallel programs: the on-line steering of a molecular dynamics application , 1994, Proceedings of 3rd IEEE International Symposium on High Performance Distributed Computing.

[8]  P. Papadopoulos,et al.  A Library for Visualization and Steering of DistributedSimulations using PVM and AVSJames , 1995 .

[9]  D. M. Beazley,et al.  50 GFlops molecular dynamics on the Connection Machine 5 , 1993, Supercomputing '93.

[10]  David M. Beazley,et al.  SWIG: An Easy to Use Tool for Integrating Scripting Languages with C and C++ , 1996, Tcl/Tk Workshop.

[11]  J. Leigh,et al.  Scientists in wonderland: A report on visualization applications in the CAVE virtual reality environment , 1993, Proceedings of 1993 IEEE Research Properties in Virtual Reality Symposium.

[12]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[13]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[14]  C.R. Johnson,et al.  SCIRun: A Scientific Programming Environment for Computational Steering , 1995, Proceedings of the IEEE/ACM SC95 Conference.

[15]  David M. Beazley,et al.  Message-Passing Multi-Cell Molecular Dynamics on the Connection Machine 5 , 1994, Parallel Comput..

[16]  Steve Bryson.  Exploratory visualization I: real-time interaction , 1995 .

[17]  Y.-F. Deng,et al.  Molecular dynamics on distributed-memory MIMD computers with load balancing , 1994 .

[18]  Steve Bryson.  The Data Glut Revisited , 1995 .