Computer simulation of liquids
Computer simulation of liquids
Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
Parallel molecular dynamics: implications for massively parallel machines
Journal of Parallel and Distributed Computing
Dynamic statistical profiling of communication activity in distributed applications
SIGMETRICS '02 Proceedings of the 2002 ACM SIGMETRICS international conference on Measurement and modeling of computer systems
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
A New Approach to Fault-Tolerant Wormhole Routing for Mesh-Connected Parallel Computers
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
Dissecting Cyclops: a detailed analysis of a multithreaded architecture
ACM SIGARCH Computer Architecture News
Journal of Parallel and Distributed Computing - Special section best papers from the 2002 international parallel and distributed processing symposium
A New Approach to Fault-Tolerant Wormhole Routing for Mesh-Connected Parallel Computers
IEEE Transactions on Computers
Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system
IBM Journal of Research and Development
Enhanced loop coalescing: a compiler technique for transforming non-uniform iteration spaces
ISHPC'05/ALPS'06 Proceedings of the 6th international symposium on high-performance computing and 1st international conference on Advanced low power systems
A framework to develop symbolic performance models of parallel applications
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
An idiom-finding tool for increasing productivity of accelerators
Proceedings of the international conference on Supercomputing
Exploiting hierarchical parallelisms for molecular dynamics simulation on multicore clusters
The Journal of Supercomputing
Proceedings of the 8th ACM International Conference on Computing Frontiers
Performance modelling and optimization of memory access on cellular computer architecture cyclops64
NPC'05 Proceedings of the 2005 IFIP international conference on Network and Parallel Computing
Hierarchical model validation of symbolic performance models of scientific kernels
Euro-Par'06 Proceedings of the 12th international conference on Parallel Processing
Scalability study of molecular dynamics simulation on Godson-T many-core architecture
Journal of Parallel and Distributed Computing
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The IBM Blue Gene project has endeavored into the development of a cellular architecture computer with millions of concurrent threads of execution. One of the major challenges of this project is demonstrating that applications can successfully exploit this massive amount of parallelism. Starting from the sequential version of a well known molecular dynamics code, we developed a new application that exploits the multiple levels of parallelism in the Blue Gene cellular architecture. We perform 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.