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Multiparadigm, multilingual interoperability: Experience with converse [chapter]

L. V. Kalé, Milind Bhandarkar, Robert Brunner, Joshua Yelon
1998 Lecture Notes in Computer Science  
A major multilingual multi-paradigm parallel application developed within the Converse framework is described.  ...  b e t ween multi-paradigm modules in a single application.  ...  The case for multilingual programming is vividly made by our new design for the integration logic that is the core of NAMD 2.  ... 
doi:10.1007/3-540-64359-1_682 fatcat:abvvt5pvqnfw7i4kgggroxxmru

Application performance of a linux cluster using converse [chapter]

Laxmikant Kałé, Robert Brunner, James Phillips, Krishnan Varadarajan
1999 Lecture Notes in Computer Science  
By connecting many PCs together in a cluster, one can build a "parallel machine" for a fraction of the cost of dedicated parallel machines such as the Cray T3E, SGI Origin 2000, or the ASCI Red (a one  ...  We consider the question of the performance impact of using inexpensive communication hardware on real applications, using a large production-quality molecular dynamics program, NAMD, that runs on this  ...  We attempt to answer these questions in this paper. As a part of a large collaborative research project, we are developing a parallel molecular dynamics program, called NAMD [6, 9] .  ... 
doi:10.1007/bfb0097933 fatcat:3uozq5xfzfhy5i7ioucvzog5by

NAMD2: Greater Scalability for Parallel Molecular Dynamics

Laxmikant Kalé, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, Klaus Schulten
1999 Journal of Computational Physics  
As a result, different components of applications can be written in the most appropriate parallel paradigms.  ...  Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scalable program.  ...  The program described in this paper, NAMD2, is one of the new parallel programs aimed at utilizing large parallel machines in a scalable manner.  ... 
doi:10.1006/jcph.1999.6201 fatcat:hflr7nuuu5eitidivqkqn7cnni

A Science Gateway for Molecular Simulations

Sandra Gesing, Peter Kacsuk, Miklos Kozlovsky, Georg Birkenheuer, Dirk Blunk, Sebastian Breuers, Andre Brinkmann, Gregor Fels, Richard Grunzke, Sonja Herres-Pawlis, Jens Krüger, Lars Packschies (+6 others)
2011
Molecular dynamics simulations were performed using NAMD v 2.7, a parallel molecular dynamics code, to study the trans-membrane lipid translocation processes.  ...  In recent years EGEE/EGI has proven to be a robust and scalable infrastructure for sequential scientific computation, but hardly usable for parallel programming.  ... 
doi:10.18154/rwth-2015-04977 fatcat:4xsrx6padrdpfflja23ztvudnm