Computer simulation using particles
Computer simulation using particles
NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Proceedings of the 14th international conference on Supercomputing
Optimizing compilers for modern architectures: a dependence-based approach
Optimizing compilers for modern architectures: a dependence-based approach
Photon mapping on programmable graphics hardware
Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware
Brook for GPUs: stream computing on graphics hardware
ACM SIGGRAPH 2004 Papers
Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations
Proceedings of the 2003 ACM/IEEE conference on Supercomputing
High-Precision Floating-Point Arithmetic in Scientific Computation
Computing in Science and Engineering
Real-Time Collision Detection (The Morgan Kaufmann Series in Interactive 3-D Technology) (The Morgan Kaufmann Series in Interactive 3D Technology)
Accelerator: using data parallelism to program GPUs for general-purpose uses
Proceedings of the 12th international conference on Architectural support for programming languages and operating systems
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Anton, a special-purpose machine for molecular dynamics simulation
Proceedings of the 34th annual international symposium on Computer architecture
Optimization principles and application performance evaluation of a multithreaded GPU using CUDA
Proceedings of the 13th ACM SIGPLAN Symposium on Principles and practice of parallel programming
Program optimization space pruning for a multithreaded gpu
Proceedings of the 6th annual IEEE/ACM international symposium on Code generation and optimization
A performance study of general-purpose applications on graphics processors using CUDA
Journal of Parallel and Distributed Computing
Adapting a message-driven parallel application to GPU-accelerated clusters
Proceedings of the 2008 ACM/IEEE conference on Supercomputing
Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units
Solving Sparse Linear Systems on NVIDIA Tesla GPUs
ICCS '09 Proceedings of the 9th International Conference on Computational Science: Part I
Probing biomolecular machines with graphics processors
Communications of the ACM - A View of Parallel Computing
Probing Biomolecular Machines with Graphics Processors
Queue - Bioscience
Accelerating MR image reconstruction on GPUs
ISBI'09 Proceedings of the Sixth IEEE international conference on Symposium on Biomedical Imaging: From Nano to Macro
Proceedings of the International Conference and Workshop on Emerging Trends in Technology
An effective GPU implementation of breadth-first search
Proceedings of the 47th Design Automation Conference
A Memory Centric Kernel Framework for Accelerating Short-Range, Interactive Particle Simulation
CCGRID '10 Proceedings of the 2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing
Energy-aware high performance computing with graphic processing units
HotPower'08 Proceedings of the 2008 conference on Power aware computing and systems
Fast bio-inspired computation using a GPU-based systemic computer
Parallel Computing
Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
Accelerating S3D: a GPGPU case study
Euro-Par'09 Proceedings of the 2009 international conference on Parallel processing
Maestro: data orchestration and tuning for OpenCL devices
Euro-Par'10 Proceedings of the 16th international Euro-Par conference on Parallel processing: Part II
Systemic computation using graphics processors
ICES'10 Proceedings of the 9th international conference on Evolvable systems: from biology to hardware
Journal of Computational Physics
Efficient probabilistic and geometric anatomical mapping using particle mesh approximation on GPUs
Journal of Biomedical Imaging - Special issue on Parallel Computation in Medical Imaging Applications
New basic linear algebra methods for simulation on GPUs
Proceedings of the 2011 Grand Challenges on Modeling and Simulation Conference
MIC acceleration of short-range molecular dynamics simulations
Proceedings of the First International Workshop on Code OptimiSation for MultI and many Cores
On-Board Multi-GPU molecular dynamics
Euro-Par'13 Proceedings of the 19th international conference on Parallel Processing
Exploiting hierarchy parallelism for molecular dynamics on a petascale heterogeneous system
Journal of Parallel and Distributed Computing
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The advent of systems biology requires the simulation of ever-larger biomolecular systems, demanding a commensurate growth in computational power. This paper examines the use of the NVIDIA Tesla C870 graphics card programmed through the CUDA toolkit to accelerate the calculation of cutoff pair potentials, one of the most prevalent computations required by many different molecular modeling applications. We present algorithms to calculate electrostatic potential maps for cutoff pair potentials. Whereas a straightforward approach for decomposing atom data leads to low compute efficiency, a newer strategy enables fine-grained spatial decomposition of atom data that maps efficiently to the C870's memory system while increasing work-efficiency of atom data traversal by a factor of 5. The memory addressing flexibility exposed through CUDA's SPMD programming model is crucial in enabling this new strategy. An implementation of the new algorithm provides a greater than threefold performance improvement over our previously published implementation and runs 12 to 20 times faster than optimized CPU-only code. The lessons learned are generally applicable to algorithms accelerated by uniform grid spatial decomposition.