Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code

Phillips, J. C.; Brunner, Richard; Shinozaki, Aritomo; Bhandarkar, Milind; Krawetz, N.; Gürsoy, Attila; Kalé, Laxmikant V.; Skeel, Robert D.; Schulten, Klaus

doi:10.1007/978-3-642-58360-5_28

Cited by 5 publications

(2 citation statements)

References 7 publications

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“…While the integration algorithm is the clearly visible "outer loop" in a serial program, NAMD's message-driven design could have resulted in much obfuscation (as was experienced even in the simpler NAMD 1.X [4]). This was averted by using Charm++ threads to write a top-level function that is called once for each patch at program start and does not complete until the end of the simulation [101]. This design has allowed pressure and temperature control methods and even a conjugate gradient minimizer to be implemented in NAMD without writing any new code for parallel communication.…”

Section: Goals Design and Implementationmentioning

confidence: 99%

Scalable molecular dynamics with NAMD

et al. 2005

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NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This paper, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Next, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, e.g., the Tcl scripting language. Finally, the paper provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

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Section: Goals Design and Implementationmentioning

confidence: 99%

Scalable molecular dynamics with NAMD

et al. 2005

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“…Also, a reactive and event-driven style of programming obscures the description of the life-cycle of an object. For example, a program would specify that when this message A arrives, execute method F; when B arrives, execute G, but can not specify that the object is going to repeatedly process A and B messages in alternating sequence k times [23]. Structured Dagger (SDAG) [15] is an effort to remedy this problem.…”

Section: Event-driven Objectsmentioning

confidence: 99%

Multiple Flows of Control in Migratable Parallel Programs

Zheng

Kalé

Lawlor

2006 International Conference on Parallel Processing Workshops (ICPPW'06)

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Many important parallel applications require multiple flows of control to run on a single processor. In this paper, we present a study of four flow-of-control mechanisms: processes, kernel threads, user-level threads and event-driven objects. Through experiments, we demonstrate the practical performance and limitations of these techniques on a variety of platforms. We also examine migration of these flows-of-control with focus on thread migration, which is critical for application-independent dynamic load balancing in parallel computing applications. Thread migration, however, is challenging due to the complexity of both user and system state involved. In this paper, we present several techniques to support migratable threads and compare the performance of these techniques.

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