Petascale Tcl with NAMD, VMD, and Swift/T

Authors: 
James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, Klaus Schulten

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.

Publication Date: 
September, 2014
Name of Publication Source: 
Proceeding HPTCDL '14 Proceedings of the 1st First Workshop for High Performance Technical Computing in Dynamic Languages
Publisher: 
IEEE Explore
Page Numbers: 
6-17
Conference Location: 
New Orleans, Louisana
DOI: 
10.1109/HPTCDL.2014.7