A new scalable parallel method for molecular dynamics based on cell-block data structure

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 3358, Issue , 2004, Pages 757-764

  Cao, Xiaolin ^a   Mo, Zeyao ^a  

^a INSTITUTE OF APPLIED PHYSICS AND COMPUTATIONAL MATHEMATICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DATA STRUCTURES; DOMAIN DECOMPOSITION METHODS; INVERSE PROBLEMS; PARALLEL PROCESSING SYSTEMS; MOLECULAR DYNAMICS;

CELL BLOCK; HILBERT SPACE FILLING CURVES; INVERSE SPACE; LARGE-SCALES; MULTILEVELS; NON-UNIFORM; PARALLEL METHOD; SPACE FILLING; THREE DIMENSIONAL SIMULATIONS; UNIFORM PARTICLE DISTRIBUTION; HIGH TEMPERATURE AND HIGH PRESSURE; LOAD BALANCING PROBLEM; LOAD DISTRIBUTIONS; NUMERICAL EXPERIMENTAL; PARTICLES DISTRIBUTION; THREE-DIMENSIONAL DOMAIN;

MOLECULAR DYNAMICS; PARALLEL PROCESSING SYSTEMS;

EID: 33646867096     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-30566-8_88     Document Type: Article

References (10)

1. Mo Zeyao, Zhang Jinglin : Dynamic Load Balancing for Short-Range Parallel Molecular Dynamics Simulations. Intern. J. Computer Math. 79 (2002) 165-172.
2. Hayashi R., Horiguchi S.: Efficiency of Dynamic Load Balancing Based on Permanent Cells for Parallel Molecular Dynamics Simulation. Proc. Of IPDPS, Cancun, Mexio(2000) 85-92.
3. Pilkington R., Baden B.: Dynamic Partitioning of Non-Uniform Structured Workloads with Spacefilling Curves. IEEE Trans. on Parallel and Distributed Systems. 7 (1996) 288-299.
4. Kale, L., Skeel, R., Bhandarkar M.: NAMD2: Greater Scalability for Parallel Molecular Dynamics. J. Computational Physics, 151(1999) 283-312.
5. Sagan, H.: Space-Filling Curves. Springer, New York (1994).
6. http://www.cs.sandia.gov/Zoltan/ug_html/ug_alg_hsfc.html.
7. Mo Zeyao, Zhang Baolin: Multilayer Averaged Weight Method for Dynamic Load Imbalance Problems. Intern. J. Computer Math. 76 (2001) 463-477.
8. Plimpton S.: Fast Parallel Algorithms for Short-range Molecular Dynamics. J. of Computational Physics, 117 (1995) 1-19.
9. Stadler J., Mikulla R., Trebin H. R.: IMD: A Software Package for Molecular Dynamics Studies on Parallel Computes. Intern. J. Modern Physics. 8 (1997) 1131-1140.
10. Roth J., Gahler F., Trebin H.: A Molecular Dynamics Run with 5,180,116,000 Particles. Int. J. Modem Physics C. 11 (2000) 317-322.