Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
MPI versus MPI+OpenMP on IBM SP for the NAS benchmarks
Proceedings of the 2000 ACM/IEEE conference on Supercomputing
Infiniband
An 8.61 Tflop/s molecular dynamics simulation for NaCl with a special-purpose computer: MDM
Proceedings of the 2001 ACM/IEEE conference on Supercomputing
NAMD: biomolecular simulation on thousands of processors
Proceedings of the 2002 ACM/IEEE conference on Supercomputing
High performance RDMA-based MPI implementation over InfiniBand
ICS '03 Proceedings of the 17th annual international conference on Supercomputing
Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations
Proceedings of the 2003 ACM/IEEE conference on Supercomputing
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
Zonal methods for the parallel execution of range-limited N-body simulations
Journal of Computational Physics
Design and implementation of message-passing services for the Blue Gene/L supercomputer
IBM Journal of Research and Development
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
Anton, a special-purpose machine for molecular dynamics simulation
Proceedings of the 34th annual international symposium on Computer architecture
Noncontiguous locking techniques for parallel file systems
Proceedings of the 2007 ACM/IEEE conference on Supercomputing
Anton, a special-purpose machine for molecular dynamics simulation
Communications of the ACM - Web science
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
A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories
Proceedings of the 2008 ACM/IEEE conference on Supercomputing
0.374 Pflop/s trillion-particle kinetic modeling of laser plasma interaction on Roadrunner
Proceedings of the 2008 ACM/IEEE conference on Supercomputing
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
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
A 32x32x32, spatially distributed 3D FFT in four microseconds 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
Millisecond-scale molecular dynamics simulations on Anton
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
Using piecewise polynomials for faster potential function evaluation
Journal of Computational Physics
Improved twiddle access for fast fourier transforms
IEEE Transactions on Signal Processing
SAQA: A Self-Adaptive QoS-Aware Scheduling Algorithm for Real-Time Tasks on Heterogeneous Clusters
CCGRID '10 Proceedings of the 2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing
Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
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
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
Exploiting hierarchy parallelism for molecular dynamics on a petascale heterogeneous system
Journal of Parallel and Distributed Computing
Journal of Computational Physics
Journal of Parallel and Distributed Computing
Hi-index | 0.01 |
Although molecular dynamics (MD) simulations of biomolecular systems often run for days to months, many events of great scientific interest and pharmaceutical relevance occur on long time scales that remain beyond reach. We present several new algorithms and implementation techniques that significantly accelerate parallel MD simulations compared with current state-of-the-art codes. These include a novel parallel decomposition method and message-passing techniques that reduce communication requirements, as well as novel communication primitives that further reduce communication time. We have also developed numerical techniques that maintain high accuracy while using single precision computation in order to exploit processor-level vector instructions. These methods are embodied in a newly developed MD code called Desmond that achieves unprecedented simulation throughput and parallel scalability on commodity clusters. Our results suggest that Desmond's parallel performance substantially surpasses that of any previously described code. For example, on a standard benchmark, Desmond's performance on a conventional Opteron cluster with 2K processors slightly exceeded the reported performance of IBM's Blue Gene/L machine with 32K processors running its Blue Matter MD code.