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Modeling dynamic load balancing in molecular dynamics to achieve scalable parallel execution [chapter]

Lars Nyland, Jan Prins, Ru Huai Yun, Jan Hermans, Hye-Chung Kum, Lei Wang
1998 Lecture Notes in Computer Science  
load balance.  ...  To achieve scalable parallel performance in Molecular Dynamics Simulation, we have modeled and implemented several dynamic spatial domain decomposition algorithms.  ...  Implementation of Dynamic Load Balancing in Molecular Dynamics The results of the previous section are a stepping stone in the pursuit of our overall goal.  ... 
doi:10.1007/bfb0018552 fatcat:evotkoeo4zccdi7ui7nam5kspe

A Novel Force Matrix Transformation with Optimal Load-Balance for 3-Body Potential Based Parallel Molecular Dynamics Using Atom-Decomposition in a Heterogeneous Cluster Environment [chapter]

J. V. Sumanth, David Swanson, Hong Jiang
High Performance Computing – HiPC 2007  
We also derive theoretical bounds for efficiency and load balance for prior work in the literature.  ...  Evaluating the Force Matrix constitutes the most computationally intensive part of a Molecular Dynamics (MD) simulation.  ...  Introduction Molecular Dynamics (MD) is a powerful technique used to obtain static or dynamic properties of liquids and solids.  ... 
doi:10.1007/978-3-540-77220-0_50 dblp:conf/hipc/SumanthSJ07 fatcat:6u35sauvpncxtnoldjtm6gb4r4

Load balancing of molecular dynamics simulation with NWChem

T. P. Straatsma, J. A. McCammon
2001 IBM Systems Journal  
This contribution provides details of the classical molecular dynamics module and focuses on issues related to load balancing on massively parallel computers, in particular the IBM SP TM and the Cray T3E  ...  NWChem is a computational chemistry software suite developed for massively parallel computers in the W. R. Wiley Environmental Molecular Sciences Laboratory at the U.S.  ...  Load-balancing efficiency of NWChem The basic components in a molecular dynamics step as implemented in NWChem are depicted in Figure 3 from the top down and include the following: the load-balancing  ... 
doi:10.1147/sj.402.0328 fatcat:45of457fjvhmzpnsiftdliabia

Performance Tuning of Parallel Fragment Molecular OrbitalProgram (OpenFMO) for Effective Execution on K-computer
京コンピュータでの効率的な動作を目指した並列FMOプログラムOpenFMOの高性能化

Yuichi INADOMI, Jun MAKI, Hiroaki HONDA, Toshiya TAKAMI, Taizo KOBAYASHI, Mutsumi AOYAGI, Kazuo MINAMI
2013 Journal of Computer Chemistry, Japan  
As a result of applying the dynamic load-balancing using our global counter, the load of molecular integral calculation for each process was well-balanced in each small-scale calculation (see Figure 7  ...  (lower) with dynamic load-balancing using global counter.  ... 
doi:10.2477/jccj.2012-0031 fatcat:aaq47sqezfcflix53xl7esgt2i

Molecular dynamics on distributed-memory MIMD computers with load balancing

Y.-F. Deng, R.A. McCoy, R.B. Marr, R.F. Peierls, O. Yasar
1995 Applied Mathematics Letters  
computers with up to 1024 nodes for 400 million particles and (2) a new method for dynamic load balancing.  ...  We report two aspects of a computational molecular dynamics study of large-scale problems on a distributed-memory MIMD parallel computer: (1) efficiency and scalability results on Intel Paragon parallel  ...  For such systems, a dynamic load balancer is essential. We have developed a parallel MD algorithm with dynamic load balancing for large-scale atomistic simulations on MIMD computers.  ... 
doi:10.1016/0893-9659(95)00027-n fatcat:wamsb4lclzdltldqdqkvmgjofe

Parallel Fock Matrix Construction Algorithm for Molecular Orbital Calculation Specific Computer
分子軌道計算専用計算機のためのフォック行列並列計算アルゴリズムの開発

Hiroaki UMEDA, Yuichi INADOMI, Hiroaki HONDA, Umpei NAGASHIMA
2005 Journal of Computer Chemistry, Japan  
PUs can communicate only with their parent and child PU in a tree. Figure 4 . 4 Global counter in DDI library for dynamic load balance.  ...  In order to obtain high parallelization efficiency for Fock matrix construction ( Figure 5 ) on the layered architecture, multi-level dynamic load balance scheme (Figure 6 ) is adopted to get better  ... 
doi:10.2477/jccj.4.179 fatcat:h3vial4zrrbf5og3x3x4itxqty

Scalable Molecular Dynamics for Large Biomolecular Systems

Robert K. Brunner, James C. Phillips, Laxmikant V. Kalé
2000 Scientific Programming  
We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD.  ...  With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than  ...  We are thankful to CSAR for allowing the use of the Turing cluster of Linux PCs, and the ASCI machines to test the load balancing strategies in the context of a challenging application.  ... 
doi:10.1155/2000/750827 fatcat:zazexvmbvnektgmgyx4jkk4v74

Scalable Molecular Dynamics for Large Biomolecular Systems

R.K. Brunner, J.C. Phillips, L.V. Kale
2000 ACM/IEEE SC 2000 Conference (SC'00)  
We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD.  ...  With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than  ...  We are thankful to CSAR for allowing the use of the Turing cluster of Linux PCs, and the ASCI machines to test the load balancing strategies in the context of a challenging application.  ... 
doi:10.1109/sc.2000.10038 dblp:conf/sc/BrunnerPK00 fatcat:hyhy6i3czfhcrksqh4hltj2bqi

Point-centered domain decomposition for parallel molecular dynamics simulation

R Koradi, M Billeter, P Güntert
2000 Computer Physics Communications  
A new algorithm for molecular dynamics simulations of biological macromolecules on parallel computers, point-centered domain decomposition, is introduced.  ...  The point-centered domain decomposition algorithm is implemented in the new program OPALp using a standard message passing library, so that it runs on both shared memory and massively parallel distributed  ...  Most of the parallelization strategy described for molecular dynamics in the previous sections applies also to the implementation of energy minimization in OPALp.  ... 
doi:10.1016/s0010-4655(99)00436-1 fatcat:ul7blsyl3fbbfleczx3kuldlfq

An adaptive curvilinear-coordinate approach to dynamic load balancing of parallel multiresolution molecular dynamics

Aiichiro Nakano, Timothy Campbell
1997 Parallel Computing  
We present a practical experience in adding a dynamic-load-balancing capability to an existing large parallel applicationmultiresolution molecular dynamics (MRMD) -which is based on uniform mesh decomposition  ...  The new load-balancing scheme uses adaptive curvilinear ccordinates to represent partition boundaries.  ...  Discussion A new dynamic load balancing scheme has been developed for parallel multiresolution molecular dynamics simulations, based on adaptive curvilinear coordinates to represent partition boundaries  ... 
doi:10.1016/s0167-8191(97)00060-4 fatcat:gilmi5dggrb7zmg6mibicuj6te

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.  ...  molecular dynamics protocol.  ... 
doi:10.1109/sc.2002.10019 dblp:conf/sc/PhillipsZKK02 fatcat:slik5zdeqvbzpm6h4722seroku

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  
The method also partitions particle pairs within each node using the force decomposition strategy to improve the load balance for each node.  ...  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  ...  problems such as molecular dynamics simulations [1] .  ... 
doi:10.1016/s1007-0214(05)70052-3 fatcat:otysyljfjnh6pem6yp3adiqn3y

Event-driven molecular dynamics in parallel

S. Miller, S. Luding
2004 Journal of Computational Physics  
In this paper we present a parallel event-driven algorithm including dynamic load-balancing, which can be easily implemented on any computer architecture.  ...  The main obstacle seems to be the difficulty of parallelizing event-driven molecular dynamics.  ...  Domain Decomposition and Dynamic Load-Balancing Parallelization is achieved via domain decomposition.  ... 
doi:10.1016/j.jcp.2003.08.009 fatcat:f53bcwpijrfexauvi4fvhi3way

Heterogeneous computing

Alexey Kalinov, Alexey Lastovetsky, Yves Robert
2005 Parallel Computing  
For such applications, dynamic load balancing allows to respond to variations in the system characteristics. Advanced dynamic load balancing algorithms are far from trivial to design and implement.  ...  Pabico and Mahadevan Balasubramaniam considers dynamic load balancing for applications with computationally intensive parallel loops.  ... 
doi:10.1016/j.parco.2005.04.001 fatcat:22ixpqa5ejaxnfrdaryql7p5vu

Decentralized load balancing for highly irregular search problems

Giuseppe Di Fatta, Michael R. Berthold
2007 Microprocessors and microsystems  
The framework is based on a peer-to-peer computing environment and dynamic load balancing.  ...  Dynamic load balancing policies based on global statistics are known to provide optimal load balancing performance, while randomized techniques provide high scalability.  ...  Distributed computing framework The parallel application is mainly a work load distribution process based on dynamic partitioning of the search space, a dynamic load balancing policy and a peer-to-peer  ... 
doi:10.1016/j.micpro.2007.01.004 fatcat:zecgpmydzvafzd4glb6xuntevm
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