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Modeling dynamic load balancing in molecular dynamics to achieve scalable parallel execution
[chapter]
1998
Lecture Notes in Computer Science
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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]
High Performance Computing – HiPC 2007
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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
2001
IBM Systems Journal
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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
2013
Journal of Computer Chemistry, Japan
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
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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
1995
Applied Mathematics Letters
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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
2005
Journal of Computer Chemistry, Japan
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
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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
2000
Scientific Programming
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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
2000
ACM/IEEE SC 2000 Conference (SC'00)
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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
2000
Computer Physics Communications
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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
1997
Parallel Computing
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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
2002
ACM/IEEE SC 2002 Conference (SC'02)
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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
2005
Tsinghua Science and Technology
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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
2004
Journal of Computational Physics
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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
2005
Parallel Computing
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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
2007
Microprocessors and microsystems
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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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