Nearest-neighbor mapping of finite element graphs onto processor meshes
IEEE Transactions on Computers
CHARM++: a portable concurrent object oriented system based on C++
OOPSLA '93 Proceedings of the eighth annual conference on Object-oriented programming systems, languages, and applications
NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Load Balancing in Parallel Molecular Dynamics
IRREGULAR '98 Proceedings of the 5th International Symposium on Solving Irregularly Structured Problems in Parallel
NAMD: biomolecular simulation on thousands of processors
Proceedings of the 2002 ACM/IEEE conference on Supercomputing
Load balancing of molecular dynamics simulation with NWChem
IBM Systems Journal - Deep computing for the life sciences
Achieving high performance on extremely large parallel machines: performance prediction and load balancing
Large-scale electronic structure calculations of high-Z metals on the BlueGene/L platform
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Scalable algorithms for molecular dynamics simulations on commodity clusters
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Blue matter: approaching the limits of concurrency for classical molecular dynamics
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
IEEE Transactions on Computers
Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system
IBM Journal of Research and Development
A Case Study of Communication Optimizations on 3D Mesh Interconnects
Euro-Par '09 Proceedings of the 15th International Euro-Par Conference on Parallel Processing
Uintah: a scalable framework for hazard analysis
Proceedings of the 2010 TeraGrid Conference
Generic topology mapping strategies for large-scale parallel architectures
Proceedings of the international conference on Supercomputing
Proceedings of the 8th ACM International Conference on Computing Frontiers
Empirical Study on Entity Interaction Graph of Large-Scale Parallel Simulations
PADS '11 Proceedings of the 2011 IEEE Workshop on Principles of Advanced and Distributed Simulation
Periodic hierarchical load balancing for large supercomputers
International Journal of High Performance Computing Applications
Quantifying the effectiveness of load balance algorithms
Proceedings of the 26th ACM international conference on Supercomputing
Productive Parallel Linear Algebra Programming with Unstructured Topology Adaption
CCGRID '12 Proceedings of the 2012 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (ccgrid 2012)
Optimized process placement for collective I/O operations
Proceedings of the 20th European MPI Users' Group Meeting
SC '13 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
Predicting application performance using supervised learning on communication features
SC '13 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
Scalability study of molecular dynamics simulation on Godson-T many-core architecture
Journal of Parallel and Distributed Computing
A topology-aware load balancing algorithm for clustered hierarchical multi-core machines
Future Generation Computer Systems
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Molecular Dynamics applications enhance our understanding of biological phenomena through bio-molecular simulations. Large-scale parallelization of MD simulations is challenging because of the small number of atoms and small time scales involved. Load balancing in parallel MD programs is crucial for good performance on large parallel machines. This paper discusses load balancing algorithms deployed in a MD code called NAMD. It focuses on new schemes deployed in the load balancers and provides an analysis of the performance benefits achieved. Specifically, the paper presents the technique of topology-aware mapping on 3D mesh and torus architectures, used to improve scalability and performance. These techniques have a wide applicability for latency intolerant applications.