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Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system
Sameer Kumar
, Chao Huang
, Gengbin Zheng
, Eric Bohm
, Abhinav Bhatele
,
James C. Phillips
, Hao Yu
,
Laxmikant V. Kalé
National Center for Supercomputing Applications (NCSA)
Siebel School of Computing and Data Science
Research output
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Computer Science
Compiler Optimization
100%
Computer Architecture
100%
Load Balancing
100%
Optimization Technique
100%
Parallel Computer
100%
Processor Core
100%
Single Instruction Multiple Data
100%
Keyphrases
Biological Phenomena
12%
Biomolecular Simulation
25%
Blue Gene
100%
Cell Membrane
12%
Cellular Water
12%
Compiler Optimization
12%
Dynamic Applications
37%
L-system
100%
Load Balancing
12%
Membrane Molecules
12%
Messaging Protocol
12%
Molecular Dynamics
100%
Molecular Systems
12%
Number of Iterations
12%
Parallel Computer Architecture
12%
Performance Results
12%
PowerPC
12%
Problem Size
12%
Processor Core
12%
Sequential Performance
12%
Single Instruction multiple Data
12%
Topology-aware
12%
Torus Topology
12%
Water Molecule
12%