research-article

Petascale Tcl with NAMD, VMD, and Swift/T

Authors:

James C. Phillips,

Kirby L. Vandivort,

Timothy G. Armstrong,

Justin M. Wozniak,

Klaus SchultenAuthors Info & Claims

HPTCDL '14: Proceedings of the 1st First Workshop for High Performance Technical Computing in Dynamic Languages

Pages 6 - 17

https://doi.org/10.1109/HPTCDL.2014.7

Published: 16 November 2014 Publication History

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.

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Cited By

Phillips JSanielevici S(2018)What You Should Know About NAMD and Charm++ But Were Hoping to IgnoreProceedings of the Practice and Experience on Advanced Research Computing: Seamless Creativity10.1145/3219104.3219134(1-6)Online publication date: 22-Jul-2018
https://dl.acm.org/doi/10.1145/3219104.3219134
Hanif MHafeez ASuleman YMustafa Rafique MButt AIqbal S(2016)An accelerated framework for the classification of biological targets from solid-state micropore dataComputer Methods and Programs in Biomedicine10.1016/j.cmpb.2016.06.001134:C(53-67)Online publication date: 1-Oct-2016
https://dl.acm.org/doi/10.1016/j.cmpb.2016.06.001
Wozniak JArmstrong TMaheshwari KKatz DWilde MFoster IMontagnat JTaylor I(2015)Interlanguage parallel scripting for distributed-memory scientific computingProceedings of the 10th Workshop on Workflows in Support of Large-Scale Science10.1145/2822332.2822338(1-11)Online publication date: 15-Nov-2015
https://dl.acm.org/doi/10.1145/2822332.2822338

Index Terms

Petascale Tcl with NAMD, VMD, and Swift/T
1. Computing methodologies
2. Software and its engineering
  1. Software notations and tools
    1. General programming languages
      1. Language types
        Concurrent programming languages

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Published In

cover image ACM Conferences

HPTCDL '14: Proceedings of the 1st First Workshop for High Performance Technical Computing in Dynamic Languages

November 2014

67 pages

ISBN:9781479970209

Conference Chairs:
Jiahao Chen
MIT
,
Alan Edelman
MIT
,
Wade Shen
MIT Lincoln Labs
,
Andy Terrel
Continuum Analytics

Sponsors

SIGHPC: ACM Special Interest Group on High Performance Computing, Special Interest Group on High Performance Computing
IEEE: IEEE Computer Society Technical Committee on Design Automation
ACM: Association for Computing Machinery
SIGARCH: ACM Special Interest Group on Computer Architecture

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IEEE Press

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Published: 16 November 2014

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SC '14

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SC '14: International Conference for High Performance Computing, Networking, Storage and Analysis

November 16 - 21, 2014

Louisiana, New Orleans

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Cited By

Phillips JSanielevici S(2018)What You Should Know About NAMD and Charm++ But Were Hoping to IgnoreProceedings of the Practice and Experience on Advanced Research Computing: Seamless Creativity10.1145/3219104.3219134(1-6)Online publication date: 22-Jul-2018
https://dl.acm.org/doi/10.1145/3219104.3219134
Hanif MHafeez ASuleman YMustafa Rafique MButt AIqbal S(2016)An accelerated framework for the classification of biological targets from solid-state micropore dataComputer Methods and Programs in Biomedicine10.1016/j.cmpb.2016.06.001134:C(53-67)Online publication date: 1-Oct-2016
https://dl.acm.org/doi/10.1016/j.cmpb.2016.06.001
Wozniak JArmstrong TMaheshwari KKatz DWilde MFoster IMontagnat JTaylor I(2015)Interlanguage parallel scripting for distributed-memory scientific computingProceedings of the 10th Workshop on Workflows in Support of Large-Scale Science10.1145/2822332.2822338(1-11)Online publication date: 15-Nov-2015
https://dl.acm.org/doi/10.1145/2822332.2822338

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