A Partitioning Strategy for Nonuniform Problems on Multiprocessors
IEEE Transactions on Computers
NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
A system for interactive molecular dynamics simulation
I3D '01 Proceedings of the 2001 symposium on Interactive 3D graphics
Scalable molecular dynamics for large biomolecular systems
Proceedings of the 2000 ACM/IEEE conference on Supercomputing
Run-Time Support for Adaptive Load Balancing
IPDPS '00 Proceedings of the 15 IPDPS 2000 Workshops on Parallel and Distributed Processing
Adapting to Load on Workstation Clusters
FRONTIERS '99 Proceedings of the The 7th Symposium on the Frontiers of Massively Parallel Computation
Blue Matter, an application framework for molecular simulation on blue gene
Journal of Parallel and Distributed Computing - High-performance computational biology
Performance and modularity benefits of message-driven execution
Journal of Parallel and Distributed Computing
A prototype of distributed molecular visualization on computational grids
Future Generation Computer Systems - Special issue: Computational chemistry and molecular dynamics
A New Parallel Kernel-Independent Fast Multipole Method
Proceedings of the 2003 ACM/IEEE conference on Supercomputing
Proceedings of the 2003 ACM/IEEE conference on Supercomputing
Performance Models on QCDOC for Molecular Dynamics with Coulomb Potentials
International Journal of High Performance Computing Applications
System noise, OS clock ticks, and fine-grained parallel applications
Proceedings of the 19th annual international conference on Supercomputing
Massively parallel implementation of a fast multipole method for distributed memory machines
Journal of Parallel and Distributed Computing
Performance characterization of molecular dynamics techniques for biomolecular simulations
Proceedings of the eleventh ACM SIGPLAN symposium on Principles and practice of parallel programming
HPC-Colony: services and interfaces for very large systems
ACM SIGOPS Operating Systems Review
Scaling applications to massively parallel machines using Projections performance analysis tool
Future Generation Computer Systems
Systems research challenges: a scale-out perspective
IBM Journal of Research and Development
Simulation-based performance prediction for large parallel machines
International Journal of Parallel Programming - Special issue: The next generation software program
Scaling an optimistic parallel simulation of large-scale interconnection networks
WSC '05 Proceedings of the 37th conference on Winter simulation
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
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Implicit parallelism with ordered transactions
Proceedings of the 12th ACM SIGPLAN symposium on Principles and practice of parallel programming
Charisma: orchestrating migratable parallel objects
Proceedings of the 16th international symposium on High performance distributed computing
The context-switch overhead inflicted by hardware interrupts (and the enigma of do-nothing loops)
Proceedings of the 2007 workshop on Experimental computer science
The context-switch overhead inflicted by hardware interrupts (and the enigma of do-nothing loops)
ecs'07 Experimental computer science on Experimental computer science
Noncontiguous locking techniques for parallel file systems
Proceedings of the 2007 ACM/IEEE conference on Supercomputing
Proceedings of the 22nd annual international conference on Supercomputing
Blue matter: scaling of N-body simulations to one atom per node
IBM Journal of Research and Development
IBM Journal of Research and Development
Adapting a message-driven parallel application to GPU-accelerated clusters
Proceedings of the 2008 ACM/IEEE conference on Supercomputing
Early evaluation of IBM BlueGene/P
Proceedings of the 2008 ACM/IEEE conference on Supercomputing
Dynamic topology aware load balancing algorithms for molecular dynamics applications
Proceedings of the 23rd international conference on Supercomputing
Hiding Communication Latency with Non-SPMD, Graph-Based Execution
ICCS '09 Proceedings of the 9th International Conference on Computational Science: Part I
PDCS '07 Proceedings of the 19th IASTED International Conference on Parallel and Distributed Computing and Systems
CLOMP: accurately characterizing OpenMP application overheads
International Journal of Parallel Programming
Scaling applications to massively parallel machines using Projections performance analysis tool
Future Generation Computer Systems
Scaling molecular dynamics to 3000 processors with projections: a performance analysis case study
ICCS'03 Proceedings of the 2003 international conference on Computational science
Scalable cosmological simulations on parallel machines
VECPAR'06 Proceedings of the 7th international conference on High performance computing for computational science
Jade: a parallel message-driven java
ICCS'03 Proceedings of the 2003 international conference on Computational science: PartIII
CLOMP: accurately characterizing OpenMP application overheads
IWOMP'08 Proceedings of the 4th international conference on OpenMP in a new era of parallelism
Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
Robust non-intrusive record-replay with processor extraction
Proceedings of the 8th Workshop on Parallel and Distributed Systems: Testing, Analysis, and Debugging
Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
Support for adaptivity in ARMCI using migratable objects
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Achieving strong scaling with NAMD on blue Gene/L
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Debugging large scale applications in a virtualized environment
LCPC'10 Proceedings of the 23rd international conference on Languages and compilers for parallel computing
Exploiting hierarchical parallelisms for molecular dynamics simulation on multicore clusters
The Journal of 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
A 'cool' load balancer for parallel applications
Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis
Periodic hierarchical load balancing for large supercomputers
International Journal of High Performance Computing Applications
Impact of the columbia supercomputer on NASA science and engineering applications
IWDC'05 Proceedings of the 7th international conference on Distributed Computing
HiPC'05 Proceedings of the 12th international conference on High Performance Computing
Early experience with scientific applications on the blue gene/l supercomputer
Euro-Par'05 Proceedings of the 11th international Euro-Par conference on Parallel Processing
Accelerating dock6's amber scoring with graphic processing unit
ICA3PP'10 Proceedings of the 10th international conference on Algorithms and Architectures for Parallel Processing - Volume Part I
OpenTS: an outline of dynamic parallelization approach
PaCT'05 Proceedings of the 8th international conference on Parallel Computing Technologies
Blue matter: strong scaling of molecular dynamics on blue gene/l
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
Congestion avoidance on manycore high performance computing systems
Proceedings of the 26th ACM international conference on Supercomputing
Fine-grain parallelism using multi-core, Cell/BE, and GPU Systems
Parallel Computing
Optimizing fine-grained communication in a biomolecular simulation application on Cray XK6
SC '12 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
Memory-access optimization of parallel molecular dynamics simulation via dynamic data reordering
Euro-Par'12 Proceedings of the 18th international conference on Parallel Processing
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
The Journal of Supercomputing
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NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC2000, presented scaling results for simulations with cutoffelectrostatics on up to 2048 processors of the ASCI Red machine, achieved with an object-based hybrid force and spatial decomposition scheme and an aggressive measurement-based predictive load balancing framework. We extend this work by demonstrating similar scaling on the much faster processors of the PSC Lemieux Alpha cluster, and for simulations employing efficient (order N log N) particle mesh Ewald full electrostatics. This unprecedented scalability in a biomolecular simulation code has been attained through latency tolerance, adaptation to multiprocessor nodes, and the direct use of the Quadrics Elan library in place of MPI by the Charm++/Converse parallel runtime system.