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Hybrid decomposition method in parallel molecular dynamics simulation based on SMP cluster architecture

Bing Wang, Jiwu Shu, Weimin Zheng, Jinzhao Wang, Min Chen
2005 Tsinghua Science and Technology  
A hybrid decomposition method for molecular dynamics simulations was presented, using simultaneously spatial decomposition and force decomposition to fit the architecture of a cluster of symmetric multi-processor  ...  Simulation results for a nucleation process with 4 000 000 particles show that the hybrid method achieves better parallel performance than either spatial or force decomposition alone, especially when applied  ...  A new hybrid decomposition method was developed for the SMP cluster architecture for parallel molecular dynamics simulations.  ... 
doi:10.1016/s1007-0214(05)70052-3 fatcat:otysyljfjnh6pem6yp3adiqn3y

Analysis of scalable data-privatization threading algorithms for hybrid MPI/OpenMP parallelization of molecular dynamics

Manaschai Kunaseth, David F. Richards, James N. Glosli, Rajiv K. Kalia, Aiichiro Nakano, Priya Vashishta
2013 Journal of Supercomputing  
We propose and analyze threading algorithms for hybrid MPI/OpenMP parallelization of a molecular-dynamics simulation, which are scalable on large multicore clusters.  ...  We observe that memory consumption is reduced by Analysis of scalable data-privatization threading algorithms for hybrid 407 75 % for p = 16 and n = 8,192 compared to a naïve data privatization, while  ...  Domain decomposition molecular dynamics Molecular dynamics simulation follows the phase-space trajectories of an N -particle system, where the forces between particles are given by the gradient of a potential  ... 
doi:10.1007/s11227-013-0915-x fatcat:tkdoyebd7vbd7pfaqerurkza6i

Comparative Study: MD Simulation with different Load Balancing Technique on Heterogeneous Environment

Jitesh M., Sudershan Deshmukh
2016 International Journal of Computer Applications  
MD simulation are used for deeper understating of fluid flows, chemical reaction, and other phenomena due to molecular interaction.  ...  However, such heterogeneous resources cause load imbalances between CPUs and GPUs and they were not utilize all available computation resources.  ...  Authors discuss several important issues in porting a large molecular dynamics code for use on parallel hybrid machines.  ... 
doi:10.5120/ijca2016908137 fatcat:3katg4x3znd6tosdsfob2xzecm

VIRTUALIZATION-AWARE APPLICATION FRAMEWORK FOR HIERARCHICAL MULTISCALE SIMULATIONS ON A GRID [chapter]

Aiichiro Nakano, Rajiv K. Kalia, Ashish Sharma, Priya Vashishta, Shuji Ogata, Fuyuki Shimojo
2005 Computational Methods in Large Scale Simulation  
Multiscale simulations are performed on a Grid to seamlessly integrate quantum mechanical calculation based on the density functional theory and atomistic simulation based on the molecular dynamics method  ...  A virtualization-aware application framework is developed, based on datalocality principles, to perform hierarchical multiscale simulations of materials on a Grid of distributed computing and visualization  ...  Parallel simulations were also performed on the 1,512-processor HPC cluster at the Research Computing Facility and 400+ processor Linux clusters at the Collaboratory for Advanced Computing and Simulations  ... 
doi:10.1142/9789812701084_0005 fatcat:inffikzlhfbhblhvjx57p4s7sm

Optimizing molecular dynamics simulations with product lines

Rui C. Silva, João L. Sobral
2011 Proceedings of the 5th Workshop on Variability Modeling of Software-Intensive Systems - VaMoS '11  
This paper presents a case study of using product-lines to address the variability of optimization methods and target platform mappings in high-performance molecular dynamics simulations.  ...  Developed features encapsulate common optimization methods in molecular dynamics simulations and target platform mappings.  ...  MOLECULAR DYNAMICS SIMULATIONS Molecular dynamics is a technique of computer simulation where a set of particles (atoms) interact during a certain period of time.  ... 
doi:10.1145/1944892.1944911 dblp:conf/vamos/SilvaS11 fatcat:iaiakwczxbahpejomeivx4jzae

Inspector-Executor Load Balancing Algorithms for Block-Sparse Tensor Contractions

David Ozog, Jeff R. Hammond, James Dinan, Pavan Balaji, Sameer Shende, Allen Malony
2013 2013 42nd International Conference on Parallel Processing  
load imbalance).  ...  Developing effective yet scalable load-balancing methods for irregular computations is critical to the successful application of simulations in a variety of disciplines at petascale and beyond.  ...  In this paper, we demonstrate that the inspector-executor model (IE) is effective in reducing load imbalance as well as eliminating the overhead from the NXTVAL dynamic load balancer.  ... 
doi:10.1109/icpp.2013.12 dblp:conf/icpp/OzogHDBSM13 fatcat:an2u6ksugzgphdrhu6fcdgpooq

Applying Parallel Design Patterns on Molecular Dynamics Simulation

Nilesh Maltare, Vithal N.
2019 International Journal of Computer Applications  
Molecular dynamics simulates behavior of atoms and molecules. Molecular dynamics Simulation demonstrates and derives macroscopic properties by atomic interactions.  ...  In this experiment we have redesigned Molecular Dynamics (MD) Simulation by applying different parallel design pattern.  ...  Molecular dynamics simulation started at 1960s [1] , at that time they developed to simulate 100 of atoms. MD Simulation is continuously evolved [2] [3] and experimented.  ... 
doi:10.5120/ijca2019918674 fatcat:ykfk7ugacjanbmhisa3p2dsnae

Adaptive Computing Library for Quantum Monte Carlo Simulations

Zeki Bozkus, Ahmad Anbar, Tarek El-Ghazawi
2014 Journal of clean energy technologies  
Index Terms-Hybrid parallel programming, load balancing, QMC simulation. II.  ...  In this work, we presented an adaptive computing approach which learns the system work load dynamically by using our Adaptive Computing Library at run-time and then creates sufficient amount of OpenMP  ...  Jim Freericks at George Town University Physics department for developing the theory of the simulation as well as providing us MPI-only implementation of the simulation.  ... 
doi:10.7763/ijcte.2014.v6.862 fatcat:k2mbtqsn35fdxdl3xdpwiln4h4

Early experiences scaling VMD molecular visualization and analysis jobs on blue waters

John E. Stone, Barry Isralewitz, Klaus Schulten
2013 2013 Extreme Scaling Workshop (xsw 2013)  
Extraction of details about the dynamics of biomolecules from terabytes of simulation output requires powerful user-extensible molecular analysis and visualization tools.  ...  Petascale molecular dynamics simulations provide a powerful tool for probing the dynamics of cellular processes at atomic and nanosecond resolution not achievable by experimental methods alone.  ...  Perilla for providing simulation trajectories.  ... 
doi:10.1109/xsw.2013.10 fatcat:czjno62d5ngb3dnmapwqq5yk6q

Dynamic topology aware load balancing algorithms for molecular dynamics applications

Abhinav Bhatelé, Laxmikant V. Kalé, Sameer Kumar
2009 Proceedings of the 23rd international conference on Conference on Supercomputing - ICS '09  
Molecular Dynamics applications enhance our understanding of biological phenomena through bio-molecular simulations.  ...  Large-scale parallelization of MD simulations is challenging because of the small number of atoms and small time scales involved.  ...  -04 for Molecular Dynamics.  ... 
doi:10.1145/1542275.1542295 dblp:conf/ics/BhateleKK09 fatcat:xp2lotrsqfaafayy7hp5jb7fny

Metascalable molecular dynamics simulation of nano-mechano-chemistry

F Shimojo, R K Kalia, A Nakano, K Nomura, P Vashishta
2008 Journal of Physics: Condensed Matter  
We have also used the framework for automated execution of adaptive hybrid DFT/MD simulation on a grid of six supercomputers in the US and Japan, in which the number of processors changed dynamically on  ...  The EDC-STEP-HCD framework exposes and expresses maximal concurrency and data locality, thereby achieving parallel efficiency as high as 0.99 for 1.59-billion-atom reactive force field molecular dynamics  ...  Simulations were performed at the University of Southern California using the 5384-processor Linux cluster at the Research Computing Facility and the 2048-processor Linux cluster at the Collaboratory for  ... 
doi:10.1088/0953-8984/20/29/294204 fatcat:u7vvl52cgvdoxckgzehtlrgdam

NAMD: Biomolecular Simulation on Thousands of Processors

J.C. Phillips, Gengbin Zheng, S. Kumar, L.V. Kale
2002 ACM/IEEE SC 2002 Conference (SC'02)  
NAMD is a parallel, object-oriented molecular dynamics program designed for high performance simulation of large biomolecular systems.  ...  This paper discusses the techniques which have allowed NAMD to effectively employ over one thousand processors in production simulations of biomedical relevance.  ...  Importance of molecular dynamics simulation software.  ... 
doi:10.1109/sc.2002.10019 dblp:conf/sc/PhillipsZKK02 fatcat:slik5zdeqvbzpm6h4722seroku

Parallel atomistic simulations

Grant S. Heffelfinger
2000 Computer Physics Communications  
Because this approach is essentially a hybridization of Monte Carlo and molecular dynamics simulation methods, the parallel algorithm developed for the method combined spatial decomposition molecular dynamics  ...  Conversely, in a liquid phase, the achievable time step of hybrid Monte Carlo is approximately equal to that of molecular dynamics.  ... 
doi:10.1016/s0010-4655(00)00050-3 fatcat:kj2ce3cjzvgf5khzk4t3qqyz7m

Hybrid MPI-OpenMP Paradigm on SMP Clusters: MPEG-2 Encoder and N-Body Simulation [article]

Truong Vinh Truong Duy, Katsuhiro Yamazaki, Kosai Ikegami, Shigeru Oyanagi
2012 arXiv   pre-print
The hierarchical image data structure of the MPEG bit-stream is eminently suitable for the hybrid model to achieve multiple levels of parallelism: MPI for parallelism at the group of pictures level across  ...  Besides, loop scheduling of OpenMP threads is adopted with appropriate chunk size to provide better load balance of work, leading to enhanced performance.  ...  Hence, it is important to divide space into domains with equal work-loads to avoid load imbalance.  ... 
arXiv:1211.2292v1 fatcat:wqiucpiacneqjeabuwbagvlqjq

An Efficient Approach for Self-scheduling Parallel Loops on Multiprogrammed Parallel Computers [chapter]

Arun Kejariwal, Alexandru Nicolau, Constantine D. Polychronopoulos
2006 Lecture Notes in Computer Science  
In this paper, we present a dynamic scheduling technique for scheduling iterations of a DOALL loop (of a single application) to achieve load balance between a given set of processors.  ...  Although a significant amount of work has been done in scheduling parallel jobs on multiprocessor systems, the problem of scheduling parallel tasks of an individual job on a multiprogrammed parallel system  ...  For our experiments, we extracted kernels (parallel nested loops) from LAMMPS [12] (a classical molecular dynamics code designed to simulate systems at the atomic and molecular level) and DAKOTA [13]  ... 
doi:10.1007/978-3-540-69330-7_31 fatcat:ommmuq5btfc3zjocfwslsfjhy4
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