Paper Info
Title
Petascale Tcl with NAMD, VMD, and Swift/T
Abstract
Tcl is the original embeddable dynamic language. Introduced in 1990, Tcl has been the foundation of the scripting interface of the popular biomolecular visualization and analysis program VMD since 1995 and was extended to the parallel molecular dynamics program NAMD in 1999. The two programs together have over 200,000 users who have enjoyed for nearly two decades the stability and flexibility provided by Tcl. VMD users can implement or extend parallel trajectory analysis and movie rendering on thousands of nodes of Blue Waters. NAMD users can implement or extend simulation protocols and multiple-copy algorithms that execute unmodified on any supercomputer without the need to recompile NAMD. We now demonstrate the integration of the Swift/T high-performance parallel scripting language to enable high-level data flow programming in NAMD and VMD. This integration is achieved without modifying or recompiling either program since the Turbine execution engine is itself based on Tcl and is dynamically loaded by the interpreter, as is the platform-specific MPI library on which it depends.
Year
DOI
Venue
2014
10.1109/HPTCDL.2014.7
HPTCDL@SC
Keywords
Field
DocType
algorithms,design,gpu,concurrent programming,molecular visualization,many-core,three-dimensional graphics and realism,molecular simulation,parallel rendering,scripting,performance,parallel,programming,mathematical model,computational modeling,trajectory
Parallel rendering,Supercomputer,Computer science,Visualization,Parallel computing,Interpreter,Rendering (computer graphics),Petascale computing,Operating system,Blue Waters,Scripting language,Distributed computing
Conference
Citations 
PageRank 
References 
4
0.45
25
Authors
7
Name
Order
Citations
PageRank
James C. Phillips11376147.18
John E. Stone2100989.56
Kirby L. Vandivort3546.20
Timothy G. Armstrong437321.73
Justin M. Wozniak546435.32
Michael Wilde640.79
Klaus Schulten72161467.19