[PDF] Top 20 Parallel Performance of Molecular Dynamics Trajectory Analysis
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Parallel Performance of Molecular Dynamics Trajectory Analysis
... The performance of biomolecular molecular dynamics (MD) simulations has steadily increased on modern high performance computing (HPC) resources but acceleration of the analysis of the ... See full document
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Task parallel Analysis of Molecular Dynamics Trajectories
... HiMach’s runtime is responsible to parallelize and distribute Map and Reduce phases to resources. Data transfers are done through a communication protocol created specifically for HiMach. Pteros-2.0 [41] is a open-source ... See full document
10
Tools for Analysis of Performance Dynamics of Parallel Applications
... – Location and severity of performance bottlenecks is time-dependent – Performance changes manifest themselves at various time scales – Dimensionality of performance measurements makes m[r] ... See full document
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Parallel Fast Multipole Method for Molecular Dynamics
... and analysis tools that can show real performance profiling for parallel programs, including the ability to high- light time spent waiting for communications to ...data analysis and ... See full document
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Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomo-
... a parallel molecular dynamics code designed for high-performance simulation of large biomo- lecular ...high-end parallel platforms, as well as tens of processors on low-cost commodity ... See full document
22
Molecular dynamics in arbitrary geometries : parallel evaluation of pair forces
... in parallel on 12 and 32 processors gives the same results. Performance tests show that there is an optimal number of cells in a mesh for maximum speed of calculating intermolecular forces, and that having ... See full document
29
Generation of initial molecular dynamics configurations in arbitrary geometries and in parallel
... 3 Computational performance A cubic test system of 50 units side length (in MD reduced units) was chosen to evaluate the performance of molConfig. The commercial CFD meshing software GAMBIT R was used to ... See full document
19
MIDAS- Molecular Dynamics Analysis Tutorial
... NSF 1443054: CIF21 DIBBs: Middleware and High Performance Analytics Libraries for Scalable Data Science2. MIDAS- Molecular Dynamics.[r] ... See full document
22
Performance Analysis of Parallel Programming Tools
... the dynamics and it is designed to be static in nature to improve ...for parallel programs. The parallel programmer does not need to manually select every host where tasks are to be executed and then ... See full document
8
Locality properties of 3D data orderings with application to parallel molecular dynamics simulations
... Application performance on graphical processing units (GPUs), in terms of execution speed and memory usage, depends on the efficient use of hierarchical ...in molecular dynamic simulations will lower the ... See full document
17
Parallel Processor Design and Implementation for Molecular Dynamics Simulations on a FPGA-Based Supercomputer
... in parallel to evaluate the non-bonded potentials, forces and virials was implemented on the nodes of a FPGA-based supercomputer named ...special-purpose parallel machine for the hardware acceleration of MD ... See full document
17
In-Transit Molecular Dynamics Analysis with Apache Flink
... on-line parallel analytics framework is proposed to process and store in transit all the data being generated by a Molecular Dynamics (MD) simulation run using staging nodes in the same cluster ... See full document
9
Machine learning for performance enhancement of molecular dynamics simulations
... the performance of the simulation and improve its usability for research and ...parallelized molecular dynamics simulations designed to extract the distribution of ions in ...explicit ... See full document
14
Inverse dynamics and trajectory tracking control of a new six degrees of freedom spatial 3-RPRS parallel manipulator
... task-space trajectory tracking control ...The trajectory planner provides the desired task-space coordinates namely time trajectories of the task-space position, velocity, and acceleration vectors re- ... See full document
14
IUmd. Performance Analysis of a Molecular Dynamics Code. Thomas William. Dresden, 5/27/13
... in multiple ways (nucleon, pure-ion, ion-mixture) • Located in different files PP01, PP02 and PP03.. • The code blocks are selectable using preprocessor.[r] ... See full document
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Locality data properties of 3D data orderings with application to parallel molecular dynamics simulations
... a performance analysis has been carried out to study the ratio of CPU to GPU execution time, the impact of theoretical occupancy and data locality by using the NVidia ...an analysis has been ... See full document
237
ACHIEVING SCALABLE PARALLEL MOLECULAR DYNAMICS USING DYNAMIC SPATIAL DOMAIN DECOMPOSITION TECHNIQUES
... high performance Molecular Dynam- ics simulator to support biochemists in their ...improve performance, some of which will be mentioned ...of Molecular Dynamics simulations that ... See full document
21
Molecular Dynamics Simulation of Gas Pipeline Steel Based on LAMMPS Parallel Computing Platform
... 3.3 Analysis of Results Under the condition of 300K, the stress-strain curves of cementite surfaces of the four different terminations under tensile loading are obtained, as shown in Figure ... See full document
9
Nonadiabatic Molecular Dynamics on Graphics Processing Units: Performance and Application to Rotary Molecular Motors
... in the next section using up to four GPUs. The Coulomb integrals of II and C are not analyzed because their computational time is too short. Figure 4 again shows the suitability of GPUs for large molecular ... See full document
13
Developing performance portable molecular dynamics kernels in Open CL
... in parallel; the positions of atoms are fixed during this operation, and thus the inter- atomic distance (and force) between all pairs of atoms in the system can be computed ... See full document
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