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.
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