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Blue Gene / NAMD / Charm++ / OpenMP / Jaguar / OpenAtom / Thread / Scalability / Computer cluster / Computing / Parallel computing / Multi-core processor


Enabling and Scaling Biomolecular Simulations of 100 Million Atoms on Petascale Machines with a Multicore-optimized Message-driven Runtime Chao Mei, Yanhua Sun, Gengbin Zheng, Eric J. Bohm, Laxmikant V. Kale
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Document Date: 2011-08-16 16:34:58


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File Size: 4,32 MB

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MPI library / University of Illinois / Computer Science University of Illinois / Chris Harrison Beckman Institute University of Illinois / /

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load balancing / performance analysis tool / appropriate tools / performance computing / cellular systems / input processors / million-atom satellite tobacco mosaic virus / multi-core processors / loaded processors / load balancing algorithms / input processor / larger processor / communication runtime software / molecular systems / chemical role / petascale applications / large systems / parallel applications / atom systems / possible solution / output processors / output processor / load balancing algorithm / biomolecular systems / multimillion-atom systems / neighbor input processors / application specific algorithms / /

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POSIX / /

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National Institute of Health / National Science Foundation / University of Illinois / Institute for Advanced Computing Applications and Technologies / /

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James C.Phillips / Eric J. Bohm / Osman Sarood / Chao Mei / Chris Harrison / /

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Jaguar XT5 Speedup / Impact / /

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C / /

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Illinois / /

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600 input processors / Opteron processors / av / X-ray / load balancing algorithm / output processors / application specific algorithms / same processor / operating system / 1680 processors / shared memory / input processors / input processor / neighbor input processors / load balancing algorithms / one processor / load balancing / symplectic Verlet algorithm / heavily loaded processors / one output processor / simulation / virtual memory / at least one processor / /

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