Petascale Tcl with NAMD, VMD, and Swift/T

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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.

Original languageEnglish (US)
Title of host publicationProceedings of HPTCDL 2014
Subtitle of host publication1st Workshop for High Performance Technical Computing in Dynamic Languages - Held in Conjunction with SC 2014: The International Conference for High Performance Computing, Networking, Storage and Analysis
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages6-17
Number of pages12
ISBN (Electronic)9781479970209
DOIs
StatePublished - Mar 26 2014
Event1st Workshop for High Performance Technical Computing in Dynamic Languages, HPTCDL 2014 - Held in Conjunction with the International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2014 - New Orleans, United States
Duration: Nov 17 2014 → …

Publication series

NameProceedings of HPTCDL 2014: 1st Workshop for High Performance Technical Computing in Dynamic Languages - Held in Conjunction with SC 2014: The International Conference for High Performance Computing, Networking, Storage and Analysis

Other

Other1st Workshop for High Performance Technical Computing in Dynamic Languages, HPTCDL 2014 - Held in Conjunction with the International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2014
Country/TerritoryUnited States
CityNew Orleans
Period11/17/14 → …

Keywords

  • Algorithms
  • Design
  • Performance

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Software
  • Modeling and Simulation
  • Computational Mathematics

Fingerprint

Dive into the research topics of 'Petascale Tcl with NAMD, VMD, and Swift/T'. Together they form a unique fingerprint.

Cite this