Computer simulation of liquids
Computer simulation of liquids
Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
Simultaneous multithreading: maximizing on-chip parallelism
ISCA '95 Proceedings of the 22nd annual international symposium on Computer architecture
Parallel molecular dynamics: implications for massively parallel machines
Journal of Parallel and Distributed Computing
Active pages: a computation model for intelligent memory
Proceedings of the 25th annual international symposium on Computer architecture
A bandwidth-efficient architecture for media processing
MICRO 31 Proceedings of the 31st annual ACM/IEEE international symposium on Microarchitecture
A design analysis of a hybrid technology multithreaded architecture for petaflops scale computation3
ICS '99 Proceedings of the 13th international conference on Supercomputing
Mapping irregular applications to DIVA, a PIM-based data-intensive architecture
SC '99 Proceedings of the 1999 ACM/IEEE conference on Supercomputing
Piranha: a scalable architecture based on single-chip multiprocessing
Proceedings of the 27th annual international symposium on Computer architecture
Multi-processor performance on the Tera MTA
SC '98 Proceedings of the 1998 ACM/IEEE conference on Supercomputing
Pursuing a Petaflop: Point Designs for 100 TF Computers Using PIM Technologies
FRONTIERS '96 Proceedings of the 6th Symposium on the Frontiers of Massively Parallel Computation
FlexRAM: Toward an Advanced Intelligent Memory System
ICCD '99 Proceedings of the 1999 IEEE International Conference on Computer Design
Blue Gene: a vision for protein science using a petaflop supercomputer
IBM Systems Journal - Deep computing for the life sciences
TiNy Threads: A Thread Virtual Machine for the Cyclops64 Cellular Architecture
IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 14 - Volume 15
Performance characterization of molecular dynamics techniques for biomolecular simulations
Proceedings of the eleventh ACM SIGPLAN symposium on Principles and practice of parallel programming
Landing openMP on cyclops-64: an efficient mapping of openMP to a many-core system-on-a-chip
Proceedings of the 3rd conference on Computing frontiers
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The IBM Blue Gene/C parallel computer aims to demonstrate the feasibility of a cellular architecture computer with millions of concurrent threads of execution. One of the major challenges in this project is showing that applications can successfully scale to this massive amount of parallelism. In this paper we demonstrate that the simulation of protein folding using classical molecular dynamics falls in this category. Starting from the sequential version of a well known molecular dynamics code, we developed a new parallel implementation that exploited the multiple levels of parallelism present in the Blue Gene/C cellular architecture. We performed both analytical and simulation studies of the behavior of this application when executed on a very large number of threads. As a result, we demonstrate that this class of applications can execute efficiently on a large cellular machine.