Principles of runtime support for parallel processors
ICS '88 Proceedings of the 2nd international conference on Supercomputing
A manual for the CHAOS runtime library
A manual for the CHAOS runtime library
Supporting Irregular Distributions Using Data-Parallel Languages
IEEE Parallel & Distributed Technology: Systems & Technology
Proceedings of the Third SIAM Conference on Parallel Processing for Scientific Computing
Scalable molecular dynamics for large biomolecular systems
Proceedings of the 2000 ACM/IEEE conference on Supercomputing
Time Stamp Algorithms for Runtime Parallelization of DOACROSS Loops with Dynamic Dependences
IEEE Transactions on Parallel and Distributed Systems
Parallelization of Irregular Problems Based on Hierarchical Domain Representation
HPCN Europe 2000 Proceedings of the 8th International Conference on High-Performance Computing and Networking
Impact of Data Distribution on Performance of Irregular Reductions on Multithreaded Architectures
HPCN Europe 2001 Proceedings of the 9th International Conference on High-Performance Computing and Networking
Optimizing COOP Languages: Study of a Protein Dynamics Program
IPPS '96 Proceedings of the 10th International Parallel Processing Symposium
Compiler and Runtime Support for Irregular Reductions on a Multithreaded Architecture
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
Supporting High Level Programming with High Performance: The Illinois Concert System
HIPS '97 Proceedings of the 1997 Workshop on High-Level Programming Models and Supportive Environments (HIPS '97)
Exchanging messages of different sizes
Journal of Parallel and Distributed Computing
Scalable molecular dynamics for large biomolecular systems
Scientific Programming
Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system
IBM Journal of Research and Development
A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories
Proceedings of the 2008 ACM/IEEE conference on Supercomputing
Proceedings of the international conference on Supercomputing
MSA: multiphase specifically shared arrays
LCPC'04 Proceedings of the 17th international conference on Languages and Compilers for High Performance Computing
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Charmm (Chemistry at Harvard Macromolecular Mechanics) is a program that is widely used to model and simulate macromolecular systems. Charmm has been parallelized by using the Chaos runtime support library on distributed-memory architectures. This implementation distributes both data and computations over processors. This data parallel strategy should make it possible to simulate very large molecules on large numbers of processors. In order to minimize communication among processors and to balance computational load, a variety of partitioning approaches are employed to distribute the atoms and computations over processors. In this implementation, atoms are partitioned based on geometrical positions and computational load by using unweighted or weighted recursive coordinate bisection. The experimental results reveal that taking computational load into account is essential. The performance of two iteration partitioning algorithms, atom decomposition and force decomposition, is also compared. A new irregular force decomposition algorithm is introduced and implemented. The Chaos library is designed to facilitate parallelization of irregular applications. This library couples partitioners to the application programs, remaps data and partitions work among processors, and optimizes interprocessor communications. This paper presents an application of Chaos that can be used to support efficient execution of irregular problems on distributed-memory machines. Readers may contact Hwang at the Dept. of Computer Science, University of Maryland, College Park, MD 20742, e-mail: shin@cs.umd.edu.