TCB Publications - Abstract

James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, and Klaus Schulten. Petascale Tcl with NAMD, VMD, and Swift/T. In SC'14 workshop on High Performance Technical Computing in Dynamic Languages, SC '14, pp. 6-17. IEEE Press, 2014.

PHIL2014 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 have between them 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 modification or recompilation of either program as 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.

Download Full Text

The manuscripts available on our site are provided for your personal use only and may not be retransmitted or redistributed without written permissions from the paper's publisher and author. You may not upload any of this site's material to any public server, on-line service, network, or bulletin board without prior written permission from the publisher and author. You may not make copies for any commercial purpose. Reproduction or storage of materials retrieved from this web site is subject to the U.S. Copyright Act of 1976, Title 17 U.S.C.

Download full text: Request a Copy, Journal