Communicating sequential processes
Communicating sequential processes
Parallel many-body simulations without all-to-all communication
Journal of Parallel and Distributed Computing
Parallel molecular dynamics: implications for massively parallel machines
Journal of Parallel and Distributed Computing
Understanding Molecular Simulation
Understanding Molecular Simulation
NAMD: biomolecular simulation on thousands of processors
Proceedings of the 2002 ACM/IEEE conference on Supercomputing
Blue Matter, an application framework for molecular simulation on blue gene
Journal of Parallel and Distributed Computing - High-performance computational biology
Blue Gene: a vision for protein science using a petaflop supercomputer
IBM Systems Journal - Deep computing for the life sciences
Blue matter on blue gene/L: massively parallel computation for biomolecular simulation
CODES+ISSS '05 Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis
Overview of the Blue Gene/L system architecture
IBM Journal of Research and Development
Blue Gene/L advanced diagnostics environment
IBM Journal of Research and Development
Early performance data on the blue matter molecular simulation framework
IBM Journal of Research and Development
Achieving strong scaling with NAMD on blue Gene/L
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Performance measurements of the 3D FFT on the blue gene/l supercomputer
Euro-Par'05 Proceedings of the 11th international Euro-Par conference on Parallel Processing
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
Anton, a special-purpose machine for molecular dynamics simulation
Proceedings of the 34th annual international symposium on Computer architecture
The blue gene/L supercomputer: a hardware and software story
International Journal of Parallel Programming
Noncontiguous locking techniques for parallel file systems
Proceedings of the 2007 ACM/IEEE conference on Supercomputing
A study of the effects of machine geometry and mapping on distributed transpose performance
Proceedings of the 5th conference on Computing frontiers
Blue matter: scaling of N-body simulations to one atom per node
IBM Journal of Research and Development
Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system
IBM Journal of Research and Development
Overview of the IBM Blue Gene/P project
IBM Journal of Research and Development
Dynamic topology aware load balancing algorithms for molecular dynamics applications
Proceedings of the 23rd international conference on Supercomputing
Millisecond-scale molecular dynamics simulations on Anton
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
Millisecond-scale molecular dynamics simulations on Anton
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
Progress in scaling biomolecular simulations to petaflop scale platforms
Euro-Par'06 Proceedings of the CoreGRID 2006, UNICORE Summit 2006, Petascale Computational Biology and Bioinformatics conference on Parallel processing
Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
Exploiting 162-Nanosecond End-to-End Communication Latency on Anton
Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis
Avoiding hot-spots on two-level direct networks
Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis
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
Topology configuration in hybrid EPS/OCS interconnects
Euro-Par'12 Proceedings of the 18th international conference on Parallel Processing
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This paper describes a novel spatial-force decomposition for N-body simulations for which we observe O(sqrt(p)) communication scaling. This has enabled Blue Matter to approach the effective limits of concurrency for molecular dynamics using particle-mesh (FFT-based) methods for handling electrostatic interactions. Using this decomposition, Blue Matter running on Blue Gene/L has achieved simulation rates in excess of 1000 time steps per second and demonstrated significant speed-ups to O(1) atom per node. Blue Matter employs a Communicating Sequential Process (CSP) style model with application communication state machines compiled to hardware interfaces. The scalability achieved has enabled methodologically rigorous biomolecular simulations on biologically interesting systems, such as membrane-bound proteins, whose time scales dwarf previous work on those systems, Major scaling improvements will require exploration of alternative algorithms for treating the long range electrostatics.