22 Namd2 PPTs View free & download

NAMD2: Greater Scalability for Parallel Molecular Dynamics PowerPoint PPT Presentation

NAMD2: Greater Scalability for Parallel Molecular Dynamics - Computed by proxies on min(x, y, z) patch. Minimizes communication: 7 down, 7x up. Can use same proxies for non-bonded. Uses lists of atoms in 'tuples' Bonded ...

Computed by proxies on min(x, y, z) patch. Minimizes communication: 7 down, 7x up. Can use same proxies for non-bonded. Uses lists of atoms in 'tuples' Bonded ...

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Parallel Molecular Dynamics PowerPoint PPT Presentation

Parallel Molecular Dynamics - Robert Brunner, Andrew Dalke, Attila Gursoy, Bill Humphrey, Mark Nelson. NAMD2: ... C : fashionable vs. conservative. Aggressive methods where they matter ...

Robert Brunner, Andrew Dalke, Attila Gursoy, Bill Humphrey, Mark Nelson. NAMD2: ... C : fashionable vs. conservative. Aggressive methods where they matter ...

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Same chromophore PowerPoint PPT Presentation

Same chromophore - Isomerization triggers the biological response Isomerization triggers different cellular responses Isomerization triggers the biological response Isomerization ...

Isomerization triggers the biological response Isomerization triggers different cellular responses Isomerization triggers the biological response Isomerization ...

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The performance of NAMD on a large Power4 system PowerPoint PPT Presentation

The performance of NAMD on a large Power4 system - The performance of NAMD on a large Power4 system Joachim Hein EPCC, The University of Edinburgh Measurement based load balancing NAMD measures its performance for the ...

The performance of NAMD on a large Power4 system Joachim Hein EPCC, The University of Edinburgh Measurement based load balancing NAMD measures its performance for the ...

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The%20performance%20of%20NAMD%20on%20a%20large%20Power4%20system PowerPoint PPT Presentation

The%20performance%20of%20NAMD%20on%20a%20large%20Power4%20system - The performance of NAMD on a large Power4 system

The performance of NAMD on a large Power4 system

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Kickstart%20Tutorial/Seminar%20on%20using%20the%2064-nodes%20P4-Xeon%20Cluster%20in%20Science%20Faculty PowerPoint PPT Presentation

Kickstart%20Tutorial/Seminar%20on%20using%20the%2064-nodes%20P4-Xeon%20Cluster%20in%20Science%20Faculty - Kickstart Tutorial/Seminar on using the 64-nodes P4-Xeon Cluster in Science Faculty ... a kickstart tutorial to potential cluster users in Science Faculty, HKBU ...

Kickstart Tutorial/Seminar on using the 64-nodes P4-Xeon Cluster in Science Faculty ... a kickstart tutorial to potential cluster users in Science Faculty, HKBU ...

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The Avian Flu Grid Project PowerPoint PPT Presentation

The Avian Flu Grid Project - sialic acid. DANA. zanamivir (Relenza) Oseltamivir (Tamiflu) ... SDSC Datastar Benchmark: 112 processors, 0.21 days/ns need fast interconnect ...

sialic acid. DANA. zanamivir (Relenza) Oseltamivir (Tamiflu) ... SDSC Datastar Benchmark: 112 processors, 0.21 days/ns need fast interconnect ...

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An FPGA Implementation of SPME Reciprocal Sum Compute Engine PowerPoint PPT Presentation

An FPGA Implementation of SPME Reciprocal Sum Compute Engine - What did we find out about precision? What did we find out about speedup? ... Due to limited logic resource limited precision FFT LogiCore. ...

What did we find out about precision? What did we find out about speedup? ... Due to limited logic resource limited precision FFT LogiCore. ...

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Flexibility and Interoperability in a Parallel MD code PowerPoint PPT Presentation

Flexibility and Interoperability in a Parallel MD code - Collection of [charged] atoms, with bonds. Newtonian mechanics. At each ... Charm , threaded MPI, PVM, Java, md-perl, pc , Nexus, Path, Cid, CC , DP, Agents, ...

Collection of [charged] atoms, with bonds. Newtonian mechanics. At each ... Charm , threaded MPI, PVM, Java, md-perl, pc , Nexus, Path, Cid, CC , DP, Agents, ...

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HisH HisF - Imidazole Glycerol Phosphate Synthase: regulates 5th step histidine biosynthesis ... HisF alpha-beta barrel fold, cyclase rxn. Recently suggested hisF uses ...

Imidazole Glycerol Phosphate Synthase: regulates 5th step histidine biosynthesis ... HisF alpha-beta barrel fold, cyclase rxn. Recently suggested hisF uses ...

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Scalable Molecular Dynamics for Large Biomolecular Systems PowerPoint PPT Presentation

Scalable Molecular Dynamics for Large Biomolecular Systems - ... so, cut-off based computations are important: near-atom calculations are part of the above. multiple time-stepping is ... Sequential step time was 57 seconds ...

... so, cut-off based computations are important: near-atom calculations are part of the above. multiple time-stepping is ... Sequential step time was 57 seconds ...

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Flexibility and Interoperability in a Parallel MD code - Laxmikant Kale, Klaus Schulten, Robert Skeel. Development team ... Mature, robust, portable. http://charm.cs.uiuc.edu. Data driven execution. Scheduler ...

Laxmikant Kale, Klaus Schulten, Robert Skeel. Development team ... Mature, robust, portable. http://charm.cs.uiuc.edu. Data driven execution. Scheduler ...

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STG WW Blue Gene PowerPoint PPT Presentation

STG WW Blue Gene - This tutorial provides a brief introduction to the environment for the Blue Gene ... Condor HTC (porting for BG/P) Parallel Debugger ...

This tutorial provides a brief introduction to the environment for the Blue Gene ... Condor HTC (porting for BG/P) Parallel Debugger ...

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Flexibility and Interoperability in a Parallel MD code - Use most appropriate parallel programming paradigm for each module ... Supports multi-paradigm programming. Provides portability ...

Use most appropriate parallel programming paradigm for each module ... Supports multi-paradigm programming. Provides portability ...

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Overview of Cluster Hardware and Software PowerPoint PPT Presentation

Overview of Cluster Hardware and Software - Hardware Configuration. 1 master node 64 compute nodes ... Hardware Configuration. Compute Nodes. Dell PE2650, P4-Xeon 2.8GHz x 2. 2GB RAM, 36GB U160 SCSI HD ...

Hardware Configuration. 1 master node 64 compute nodes ... Hardware Configuration. Compute Nodes. Dell PE2650, P4-Xeon 2.8GHz x 2. 2GB RAM, 36GB U160 SCSI HD ...

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Massivelyparallel molecular dynamics simulations on New York Blue PowerPoint PPT Presentation

Massivelyparallel molecular dynamics simulations on New York Blue - Steve Smith (Stony Brook) Yaoxing Huang (Aaron Diamond AIDS Research Center) Support: ... AMBER has good support for small molecules (GAFF) ...

Steve Smith (Stony Brook) Yaoxing Huang (Aaron Diamond AIDS Research Center) Support: ... AMBER has good support for small molecules (GAFF) ...

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Scalable%20Molecular%20Dynamics%20for%20Large%20Biomolecular%20Systems PowerPoint PPT Presentation

Scalable%20Molecular%20Dynamics%20for%20Large%20Biomolecular%20Systems - Was getting time for performance tuning runs on parallel machines. 50 ... Both include downloadable software. 53. Parallel Programming Laboratory. Funding: ...

Was getting time for performance tuning runs on parallel machines. 50 ... Both include downloadable software. 53. Parallel Programming Laboratory. Funding: ...

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Supercomputing project in CAS and its applications in earth sciences PowerPoint PPT Presentation

Supercomputing project in CAS and its applications in earth sciences - The Jiujiang earthquake with magnitude 5.7(November 26, 2005 ) is not included ... Parallel simulation of local strong earthquake, test-bed and applications ...

The Jiujiang earthquake with magnitude 5.7(November 26, 2005 ) is not included ... Parallel simulation of local strong earthquake, test-bed and applications ...

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Usage Seminar for the 64nodes P4Xeon Cluster in Science Faculty PowerPoint PPT Presentation

Usage Seminar for the 64nodes P4Xeon Cluster in Science Faculty - Usage Seminar for the 64-nodes P4-Xeon Cluster in Science Faculty ... The above example request only 1 node and deliver the job named prime' in default queue. ...

Usage Seminar for the 64-nodes P4-Xeon Cluster in Science Faculty ... The above example request only 1 node and deliver the job named prime' in default queue. ...

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Techniques for Developing Efficient Petascale Applications PowerPoint PPT Presentation

Techniques for Developing Efficient Petascale Applications - ... special-purpose heuristic work fine when applicable. Still, ... Improvements wrought by network topological aware mapping of computational work to processors ...

... special-purpose heuristic work fine when applicable. Still, ... Improvements wrought by network topological aware mapping of computational work to processors ...

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Techniques for Developing Efficient Petascale Applications - Very powerful parallel computers are being built ... Parallel programming is more complex than ... Using an emulation layer that pretends to be (say) 100k cores ...

Very powerful parallel computers are being built ... Parallel programming is more complex than ... Using an emulation layer that pretends to be (say) 100k cores ...

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A Grid infrastructure that permits the coordination of heterogeneous and distributed computing resources provides a natural testbed for demonstrating the effectiveness of computational steering. - ... of amphiphilic fluids into equilibrium liquid-crystalline cubic ... sophisticated and complex tools for the analysis and management of the output of ...

... of amphiphilic fluids into equilibrium liquid-crystalline cubic ... sophisticated and complex tools for the analysis and management of the output of ...

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Namd2 PowerPoint PPT Presentations