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NAMD PowerPoint PPT Presentation
NAMD - NIH Resource for Biomolecular Modeling and Bioinformatics. http://www.ks.uiuc.edu ... for Biomolecular Modeling and Bioinformatics. http://www.ks.uiuc.edu ...
NIH Resource for Biomolecular Modeling and Bioinformatics. http://www.ks.uiuc.edu ... for Biomolecular Modeling and Bioinformatics. http://www.ks.uiuc.edu ...
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NAMD Development Goals PowerPoint PPT Presentation
NAMD Development Goals - Make NAMD a widely used MD program. For large molecular systems, ... 1.02 TeraFLOPs. NIH Resource for Biomolecular Modeling and Bioinformatics. http://www.ks.uiuc.edu ...
Make NAMD a widely used MD program. For large molecular systems, ... 1.02 TeraFLOPs. NIH Resource for Biomolecular Modeling and Bioinformatics. http://www.ks.uiuc.edu ...
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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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NAMD: Biomolecular Simulation on Thousands of Processors PowerPoint PPT Presentation
NAMD: Biomolecular Simulation on Thousands of Processors - NAMD: Biomolecular Simulation on Thousands of Processors James C. Phillips Gengbin Zheng Sameer Kumar Laxmikant Kale http://charm.cs.uiuc.edu Parallel Programming ...
NAMD: Biomolecular Simulation on Thousands of Processors James C. Phillips Gengbin Zheng Sameer Kumar Laxmikant Kale http://charm.cs.uiuc.edu Parallel Programming ...
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NAMD - Scalable Molecular Dynamics PowerPoint PPT Presentation
NAMD - Scalable Molecular Dynamics - ... .00 14805.00 9288.00 19335.00 8232.00 14667.00 13400.00 25859.00 33920.00 24011.00 32068.00 24130.00 22333.00 19347.00 24575.00 31544.00 21887.00 27641.00 ...
... .00 14805.00 9288.00 19335.00 8232.00 14667.00 13400.00 25859.00 33920.00 24011.00 32068.00 24130.00 22333.00 19347.00 24575.00 31544.00 21887.00 27641.00 ...
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Comparative Study of NAMD and GROMACS PowerPoint PPT Presentation
Comparative Study of NAMD and GROMACS - Comparative Study of NAMD and GROMACS. Yanbin Wu, Joonho Lee and Yi Wang. Team Project for Phy466 ... Both are widely used MD packages. ...
Comparative Study of NAMD and GROMACS. Yanbin Wu, Joonho Lee and Yi Wang. Team Project for Phy466 ... Both are widely used MD packages. ...
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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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Faster, Cheaper, Better: Biomolecular Simulation with NAMD, VMD, and CUDA PowerPoint PPT Presentation
Faster, Cheaper, Better: Biomolecular Simulation with NAMD, VMD, and CUDA - Faster, Cheaper, Better: Biomolecular Simulation with NAMD, VMD, and CUDA John Stone Theoretical and Computational Biophysics Group Beckman Institute for Advanced ...
Faster, Cheaper, Better: Biomolecular Simulation with NAMD, VMD, and CUDA John Stone Theoretical and Computational Biophysics Group Beckman Institute for Advanced ...
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Managing Biomolecular Simulations in a Grid Environment with NAMDG PowerPoint PPT Presentation
Managing Biomolecular Simulations in a Grid Environment with NAMDG - Managing Biomolecular Simulations in a Grid Environment with NAMD-G. Michelle Gower*, Jordi Cohen ... James C. Phillips , Rick Kufrin*, Klaus Schulten ...
Managing Biomolecular Simulations in a Grid Environment with NAMD-G. Michelle Gower*, Jordi Cohen ... James C. Phillips , Rick Kufrin*, Klaus Schulten ...
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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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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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Overcoming Scaling Challenges in Bio-molecular Simulations PowerPoint PPT Presentation
Overcoming Scaling Challenges in Bio-molecular Simulations - HYBRID. DECOMPOSITION. 5. 6. What makes NAMD efficient ? Charm ... Hybrid decomposition scheme. Variants of this hybrid scheme used by Blue Matter and Desmond ...
HYBRID. DECOMPOSITION. 5. 6. What makes NAMD efficient ? Charm ... Hybrid decomposition scheme. Variants of this hybrid scheme used by Blue Matter and Desmond ...
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Scaling to New Heights PowerPoint PPT Presentation
Scaling to New Heights - More than 80 researchers from universities, research centers, and ... Identify/fix bottlenecks; choose new methods? Case Study: NAMD Scalable Molecular Dynamics ...
More than 80 researchers from universities, research centers, and ... Identify/fix bottlenecks; choose new methods? Case Study: NAMD Scalable Molecular Dynamics ...
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Simulation of Protein motion with MSCL PowerPoint PPT Presentation
Simulation of Protein motion with MSCL - Removal of Hydrophobic Tethers in transmembrane region ... tether removal. energy cutoff. embed the protein in lipid bilayer using NAMD of Schulten's group ...
Removal of Hydrophobic Tethers in transmembrane region ... tether removal. energy cutoff. embed the protein in lipid bilayer using NAMD of Schulten's group ...
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Using Lewis and Clark PowerPoint PPT Presentation
Using Lewis and Clark - To encourage you to take advantage of resources available through the UMBC. Running your jobs in ... 13573 shemp 25 0 319m 243m 11m R 99.4 6.2 6871:15 namd9 ...
To encourage you to take advantage of resources available through the UMBC. Running your jobs in ... 13573 shemp 25 0 319m 243m 11m R 99.4 6.2 6871:15 namd9 ...
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PPL Mission and Approach PowerPoint PPT Presentation
PPL Mission and Approach - GRANTS. NSF: ITR. Chemistry. Car-Parinello MD, QM/MM. Sr.STAFF. ENABLING PROJECTS. Fault-Tolerance: ... NIH. Biophysics. NAMD. NSF/NCSA. Track-1: Blue Waters ...
GRANTS. NSF: ITR. Chemistry. Car-Parinello MD, QM/MM. Sr.STAFF. ENABLING PROJECTS. Fault-Tolerance: ... NIH. Biophysics. NAMD. NSF/NCSA. Track-1: Blue Waters ...
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Presentaci PowerPoint PPT Presentation
Presentaci - la ecuaci n de movimiento para propagar la din mica: F = ma (Newton) ... el c digo para propagar la din mica. Eficiencia de paralelizaci n; record mundial: NAMD ...
la ecuaci n de movimiento para propagar la din mica: F = ma (Newton) ... el c digo para propagar la din mica. Eficiencia de paralelizaci n; record mundial: NAMD ...
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Practical Free Energy Calculations PowerPoint PPT Presentation
Practical Free Energy Calculations - CSE 60531 Computational Biophysics and Systems Biology Spring 2006. Outline ... from Steered Molecular Dynamics Simulations Using Jarzynski's Equality,' Journal ...
CSE 60531 Computational Biophysics and Systems Biology Spring 2006. Outline ... from Steered Molecular Dynamics Simulations Using Jarzynski's Equality,' Journal ...
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Molecular Dynamics Method 2 PowerPoint PPT Presentation
Molecular Dynamics Method 2 - Example: Gramicidin A Peptide. D-Val and D-Leu residues ... Example: Solvating Gramicidin. Begin with a block of equilibrated water. ...
Example: Gramicidin A Peptide. D-Val and D-Leu residues ... Example: Solvating Gramicidin. Begin with a block of equilibrated water. ...
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Dynamic Topology Aware Load Balancing Algorithms for MD Applications PowerPoint PPT Presentation
Dynamic Topology Aware Load Balancing Algorithms for MD Applications - Use Newtonian Mechanics to find the positions and velocities of atoms ... Short-range: calculated every time step. Long-range: calculated every fourth time-step (PME) ...
Use Newtonian Mechanics to find the positions and velocities of atoms ... Short-range: calculated every time step. Long-range: calculated every fourth time-step (PME) ...
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Calculating the Potential of Mean Force with Replica Exchange Method in Explicitly Solvated Decalani PowerPoint PPT Presentation
Calculating the Potential of Mean Force with Replica Exchange Method in Explicitly Solvated Decalani - How to get our job done? Current results and difficulties. Decalanine System. Moderate Complicity. Folding Activity. Reference for. Larger System. Simulation Method ...
How to get our job done? Current results and difficulties. Decalanine System. Moderate Complicity. Folding Activity. Reference for. Larger System. Simulation Method ...
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PRAGMA BioSciences Portal PowerPoint PPT Presentation
PRAGMA BioSciences Portal - ... a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a ... 456789:CDEFGHIJSTUVWXYZcdefghijstuvwxyz GpSs tFTO ...
... a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a ... 456789:CDEFGHIJSTUVWXYZcdefghijstuvwxyz GpSs tFTO ...
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Dynamic Topology Aware Load Balancing Algorithms for MD Applications PowerPoint PPT Presentation
Dynamic Topology Aware Load Balancing Algorithms for MD Applications - University of Illinois at Urbana-Champaign Sameer Kumar IBM T. J. Watson Research Center * * * * * * Molecular Dynamics A system of [charged] atoms with bonds Use ...
University of Illinois at Urbana-Champaign Sameer Kumar IBM T. J. Watson Research Center * * * * * * Molecular Dynamics A system of [charged] atoms with bonds Use ...
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Vision Based Scalable Workflow Development using Web Services PowerPoint PPT Presentation
Vision Based Scalable Workflow Development using Web Services - Make sure your Keyboard & Mouse settings are configure this way, so that your ... Right click on inFile and then click on Unbind Wiget. ...
Make sure your Keyboard & Mouse settings are configure this way, so that your ... Right click on inFile and then click on Unbind Wiget. ...
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Binding Free Energy Calculation Using Molecular Simulations PowerPoint PPT Presentation
Binding Free Energy Calculation Using Molecular Simulations - Binding Free Energy Calculation Using Molecular Simulations
Binding Free Energy Calculation Using Molecular Simulations
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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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Statistical Mechanics of Proteins PowerPoint PPT Presentation
Statistical Mechanics of Proteins - Statistical Mechanics of Proteins Ioan Kosztin Department of Physics & Astronomy University of Missouri - Columbia Equilibrium and non-equilibrium properties of proteins
Statistical Mechanics of Proteins Ioan Kosztin Department of Physics & Astronomy University of Missouri - Columbia Equilibrium and non-equilibrium properties of proteins
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Computational Chemistry Software at TACC and The GridChem Computational Chemistry Grid PowerPoint PPT Presentation
Computational Chemistry Software at TACC and The GridChem Computational Chemistry Grid - Molecular dynamics (force field includes AMBER, GROMOS, CHARMM) Coupled QM/MM dynamics ... Force field: CHARMM19, CHARMM22, CHARMM27, Amber, OPLS, Gromacs ...
Molecular dynamics (force field includes AMBER, GROMOS, CHARMM) Coupled QM/MM dynamics ... Force field: CHARMM19, CHARMM22, CHARMM27, Amber, OPLS, Gromacs ...
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Automotive Seat Climate Systems Market to Reach $92.93 Billion, by 2023 PowerPoint PPT Presentation
Automotive Seat Climate Systems Market to Reach $92.93 Billion, by 2023 - The global automotive seat climate systems market was valued at $9,207 million in 2016, and is projected to reach at $14,048 million by 2023, growing at a CAGR of 6.3% from 2017 to 2023.
The global automotive seat climate systems market was valued at $9,207 million in 2016, and is projected to reach at $14,048 million by 2023, growing at a CAGR of 6.3% from 2017 to 2023.
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Spatial Decomposition and Pairlist Management for Molecular Dynamics PowerPoint PPT Presentation
Spatial Decomposition and Pairlist Management for Molecular Dynamics - Anton Arkhipov, Peter L. Freddolino, Lingling Miao, Leonardo Trabuco ... Anton Arkhipov, Peter L. Freddolino, Lingling Miao, Leonardo Trabuco ...
Anton Arkhipov, Peter L. Freddolino, Lingling Miao, Leonardo Trabuco ... Anton Arkhipov, Peter L. Freddolino, Lingling Miao, Leonardo Trabuco ...
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NIH Resource for Biomolecular Modeling and Bioinformatics PowerPoint PPT Presentation
NIH Resource for Biomolecular Modeling and Bioinformatics - The Flying Ice Cube. a molecular dynamics horror story ... a molecular dynamics fairy tale ... a molecular dynamics fairy tale. Steering forces are needed to ...
The Flying Ice Cube. a molecular dynamics horror story ... a molecular dynamics fairy tale ... a molecular dynamics fairy tale. Steering forces are needed to ...
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Acceleration of an Asynchronous Message Driven Programming Paradigm on IBM Blue Gene/Q PowerPoint PPT Presentation
Acceleration of an Asynchronous Message Driven Programming Paradigm on IBM Blue Gene/Q - Title: PowerPoint Presentation Last modified by: ADMINIBM Created Date: 1/1/1601 12:00:00 AM Document presentation format: On-screen Show (4:3) Other titles
Title: PowerPoint Presentation Last modified by: ADMINIBM Created Date: 1/1/1601 12:00:00 AM Document presentation format: On-screen Show (4:3) Other titles
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Progress Report for: H5N1 Receptor Specificity PowerPoint PPT Presentation
Progress Report for: H5N1 Receptor Specificity - Have a database with key mutations in 26 strains of H5N1 ... Saffron shark fin soup. bbq eel. Guess what this is. 218 RMB $28.51. Duck brain. Some Pictures: ...
Have a database with key mutations in 26 strains of H5N1 ... Saffron shark fin soup. bbq eel. Guess what this is. 218 RMB $28.51. Duck brain. Some Pictures: ...
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TOP 5 BADMINTON RACKETS - 2021 PowerPoint PPT Presentation
TOP 5 BADMINTON RACKETS - 2021 - Given presentation will be given anybody an idea about badminton rackets that will be trendy in 2021. Give a look at this.
Given presentation will be given anybody an idea about badminton rackets that will be trendy in 2021. Give a look at this.
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Critical Sections and Semaphores PowerPoint PPT Presentation
Critical Sections and Semaphores - Critical Sections and Semaphores. A critical section is code that contains access ... A. Process 2 cannot proceed until process 1 gets A. This defeats the purpose of ...
Critical Sections and Semaphores. A critical section is code that contains access ... A. Process 2 cannot proceed until process 1 gets A. This defeats the purpose of ...
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Integrated Performance Views in Charm : Projections meets TAU PowerPoint PPT Presentation
Integrated Performance Views in Charm : Projections meets TAU - Callback-based performance module and Projections. Brief introduction to TAU performance system ... module at events. Any registered performance module (client) ...
Callback-based performance module and Projections. Brief introduction to TAU performance system ... module at events. Any registered performance module (client) ...
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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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Brownian Dynamics PowerPoint PPT Presentation
Brownian Dynamics - Brownian Dynamics
Brownian Dynamics
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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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John Matrow, System AdministratorTrainer PowerPoint PPT Presentation
John Matrow, System AdministratorTrainer - John Matrow, System Administrator/Trainer. Short History ... Purchased 16p 300Mhz SGI Origin 2000. April 2001: Added 8p 250Mhz. Magnetohydrodynamic Flows ...
John Matrow, System Administrator/Trainer. Short History ... Purchased 16p 300Mhz SGI Origin 2000. April 2001: Added 8p 250Mhz. Magnetohydrodynamic Flows ...
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Ewald Summation PowerPoint PPT Presentation
Ewald Summation - add in some terms to make this happen. Solve and write for efficient summation ... A Numerical Example. The total electrostatic potential is pairwise-additive ...
add in some terms to make this happen. Solve and write for efficient summation ... A Numerical Example. The total electrostatic potential is pairwise-additive ...
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Accelerating Molecular Dynamics on a GPU PowerPoint PPT Presentation
Accelerating Molecular Dynamics on a GPU - fragment hardware. All mainstream GPUs now incorporate fully programmable processors ... GLSL Sphere Fragment Shader. Written in OpenGL Shading Language ...
fragment hardware. All mainstream GPUs now incorporate fully programmable processors ... GLSL Sphere Fragment Shader. Written in OpenGL Shading Language ...
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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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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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Accelerating Molecular Modeling Applications with GPU Computing PowerPoint PPT Presentation
Accelerating Molecular Modeling Applications with GPU Computing - Accelerating Molecular Modeling Applications with GPU Computing John Stone Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and ...
Accelerating Molecular Modeling Applications with GPU Computing John Stone Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and ...
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Scaling Molecular Dynamics to 3000 Processors with Projections: A Performance Analysis Case Study PowerPoint PPT Presentation
Scaling Molecular Dynamics to 3000 Processors with Projections: A Performance Analysis Case Study - Short-distance: every timestep. Long-distance: using PME (3D FFT) ... The red communication is free, if it is a multicast. 31. Load Balancing Steps. Regular Timesteps ...
Short-distance: every timestep. Long-distance: using PME (3D FFT) ... The red communication is free, if it is a multicast. 31. Load Balancing Steps. Regular Timesteps ...
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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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Processor Virtualization for Scalable Parallel Computing PowerPoint PPT Presentation
Processor Virtualization for Scalable Parallel Computing - Department of Computer Science. University of Illinois at Urbana ... Seek optimal division of labor between 'system' and programmer: Specialization. MPI ...
Department of Computer Science. University of Illinois at Urbana ... Seek optimal division of labor between 'system' and programmer: Specialization. MPI ...
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High Performance Computing and Visualisation for Molecular Biology PowerPoint PPT Presentation
High Performance Computing and Visualisation for Molecular Biology - Computational Vaccinology Darren R Flower http://www.jenner.ac.uk/res-bio.htm darren.flower@jenner.ac.uk
Computational Vaccinology Darren R Flower http://www.jenner.ac.uk/res-bio.htm darren.flower@jenner.ac.uk
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AMPI and Charm PowerPoint PPT Presentation
AMPI and Charm - Heap Data. Heap data is any dynamically allocated data. C 'malloc' and 'free' ... 52. Migrate Heap Data. Automatic solution: isomalloc all h ...
Heap Data. Heap data is any dynamically allocated data. C 'malloc' and 'free' ... 52. Migrate Heap Data. Automatic solution: isomalloc all h ...
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Object based load balancing strategies PowerPoint PPT Presentation
Object based load balancing strategies - Multiple data-driven objects per processor. The runtime system: ... Migration strategy for bipartite object graphs built. Applied to Molecular Dynamics program ...
Multiple data-driven objects per processor. The runtime system: ... Migration strategy for bipartite object graphs built. Applied to Molecular Dynamics program ...
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Runtime Optimizations via Processor Virtualization PowerPoint PPT Presentation
Runtime Optimizations via Processor Virtualization - Title: An Object Based Approach to Developing Scalable Applications: Challenges and Techniques Author: l-kale1 Last modified by: kale Created Date
Title: An Object Based Approach to Developing Scalable Applications: Challenges and Techniques Author: l-kale1 Last modified by: kale Created Date
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Molecular Dynamics of the Bird Flu Virus PowerPoint PPT Presentation
Molecular Dynamics of the Bird Flu Virus - Molecular Dynamics of the Bird Flu Virus. Presented By Team Tamiflu: ... Bird Flu enters the cell with greater efficiency than the 1933 peptide due to ...
Molecular Dynamics of the Bird Flu Virus. Presented By Team Tamiflu: ... Bird Flu enters the cell with greater efficiency than the 1933 peptide due to ...
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ATPase Synthase A Molecular Double Motor PowerPoint PPT Presentation
ATPase Synthase A Molecular Double Motor - ATPase Synthase A Molecular Double Motor
ATPase Synthase A Molecular Double Motor
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Runtime Optimizations PowerPoint PPT Presentation
Runtime Optimizations - What are the alternatives, and what kinds of alternatives are they? ... Josh Unger. Terry Wilmarth. Sameer Kumar. Recent Funding: NSF (NGS: Frederica Darema) ...
What are the alternatives, and what kinds of alternatives are they? ... Josh Unger. Terry Wilmarth. Sameer Kumar. Recent Funding: NSF (NGS: Frederica Darema) ...
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