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Abstract: This paper is concerned with the implementation of the molecular dynamics code, CHARMM, on massively parallel distributed-memory computer architectures using a data-parallel approach. The implementation is carried out by creating a set of software tools, which provide an interface between the parallelization issues and the sequential code. Large practical MD problems is solved on the Intel iPSC/860 hypercube. The overall solution efficiency is compared with that obtained when implementation is ... (Update)
Context of citations to this paper: More
...kernel from the explicit Euler solver [14] 5] and Section 2. 2 briefly describes the kernel from the molecular dynamics code CHARMM [3] [7]. 2.1 Unstructured Euler Kernel Unstructured meshes provide a great deal of flexibility in discretizing complex domains and offer the...
.... efficient parallel version of CHARMM using the replicated data approach [4] The parallelization effort of CHARMM done by Das and Saltz [10] was based on the distributed data approach. All data arrays associated with atoms were partitioned over processors in BLOCK...
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Parallelizing Molecular Dynamics Programs for.. - Hwang, Das, Saltz.. (1994) (Correct)
Index Array Flattening Through Program Transformation - Das, Havlak, Saltz, Kennedy (1994) (Correct)
A Parallel Software Infrastructure for Dynamic Block-Irregular.. - Kohn (1995) (Correct)
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0.1: A Manual for the CHAOS Runtime Library - Saltz, Ponnusamy, Sharma, Moon.. (1995) (Correct)
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6: The design and implementation of a parallel unstructured Euler solver using soft.. - Das, Mavriplis et al. - 1992
6: Charmm: A program for macromolecular energy (context) - Brooks, Bruccoleri et al. - 1983
5: Compiler analysis for irregular problems in Fortran D - Hanxleden, Kennedy et al. - 1992
BibTeX entry: (Update)
R. Das and J. Saltz. Parallelizing molecular dynamics codes using the Parti software primitives. In Proceedings of the Sixth SIAM Conference on Parallel Processing for Scientific Computing, pages 187--192. SIAM, March 1993. http://citeseer.ist.psu.edu/das93parallelizing.html More
@inproceedings{ das93parallelizing,
author = "Das, R. and Saltz, J.",
title = "{P}arallelizing {M}olecular {D}ynamics {C}odes using the {P}arti {S}oftware {P}rimitives",
booktitle = "Proceedings of the Sixth {SIAM} Conference on Parallel Processing for Scientific Computing",
pages = "187-192",
year = "1993",
url = "citeseer.ist.psu.edu/das93parallelizing.html" }
Citations (may not include all citations):120 Charmm: A program for macromolecular energy (context) - Brooks, Bruccoleri et al. - 1983
79 Principles of runtime support for parallel processors (context) - Mirchandaney, Saltz et al. - 1988
49 Execution time support for adaptive scientific algorithms on.. (context) - Berryman, Saltz et al. - 1991
44 Distributed memory compiler methods for irregular problems -.. (context) - Das, Ponnusamy et al. - 1992
33 Gromos: Groningen molecular simulation software (context) - van Gunsteren, Berendsen - 1988
31 Parallelization of charmm for mimd machines (context) - Brooks, Hodoscek - 1992
23 Parallel molecular dynamics (context) - Terry, Clark et al. - 1991
14 Amberassisted model building with energy refinement (context) - Kollman, model et al. - 1981
11 Parallel approaches to short range molecular dynamics simula.. (context) - Tamayo, Boghosian - 1991
3 Scalable parallel molecular dynamics on mimd supercomputers (context) - Plimpton, Heffelfinger - 1992
2 Molecular dynamics simulation of liquids on the connection m.. (context) - Mel'cuk, Gould - 1991
The graph only includes citing articles where the year of publication is known.
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Compiler and Runtime Support for Programming in.. - Edjlali, Agrawal, .. (1995) (Correct)
Runtime Compilation Techniques for Data Partitioning.. - Ponnusamy, Saltz.. (1993) (Correct)
Interleaved Parallel Hybrid Arnoldi Method for a Parallel.. - Edjlali, Petiton (1996) (Correct)
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