NAMD: Biomolecular Simulation on Thousands of Processors

Phillips, J. C.; Zheng, Gengbin; Kumar, Sameer; Kalé, Laxmikant V.

doi:10.1109/sc.2002.10019

Cited by 176 publications

(169 citation statements)

References 12 publications

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“…Such a pattern is representative of applications that perform many parallel Fast Fourier transform, e.g. pF3D [25], PARATEC, NAMD [26], and VASP [27]. Using the configuration presented in Table I, an MPI process's communicating partners are separated by multiples of 384 , i.e.…”

Section: Many To Many Pattern (M2m)mentioning

confidence: 99%

Maximizing Throughput on a Dragonfly Network

Jain

Bhatelé

et al. 2014

SC14: International Conference for High Performance Computing, Networking, Storage and Analysis

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Abstract-Interconnection networks are a critical resource for large supercomputers. The dragonfly topology, which provides a low network diameter and large bisection bandwidth, is being explored as a promising option for building multi-Petaflop/s and Exaflop/s systems. Unlike the extensively studied torus networks, the best choices of message routing and job placement strategies for the dragonfly topology are not well understood. This paper aims at analyzing the behavior of an interconnect based on the dragonfly topology for various routing strategies, job placement policies, and application communication patterns. Our study is based on a novel model that predicts traffic on individual links for direct, indirect, and adaptive routing strategies. We analyze results for individual communication patterns and some common parallel job workloads. The predictions presented in this paper are for a 100+ Petaflop/s prototype machine with 92,160 highradix routers and 8.8 million cores.

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Section: Many To Many Pattern (M2m)mentioning

confidence: 99%

Maximizing Throughput on a Dragonfly Network

Jain

Bhatelé

et al. 2014

SC14: International Conference for High Performance Computing, Networking, Storage and Analysis

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“…Modern parallel applications running on large clusters often involve simulations of dynamic and complex systems [1,2]. A significant amount of effort is spent on writing these parallel applications in order to fully exploit the processing power of large systems and show scalability.…”

Section: Introductionmentioning

confidence: 99%

Automated Load Balancing Invocation Based on Application Characteristics

Menon

Jain

Zheng

et al. 2012

2012 IEEE International Conference on Cluster Computing

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Abstract-Performance of applications executed on large parallel systems suffer due to load imbalance. Load balancing is required to scale such applications to large systems. However, performing load balancing incurs a cost which may not be known a priori. In addition, application characteristics may change due to its dynamic nature and the parallel system used for execution. As a result, deciding when to balance the load to obtain the best performance is challenging. Existing approaches put this burden on the users, who rely on educated guess and extrapolation techniques to decide on a reasonable load balancing period, which may not be feasible and efficient.In this paper, we propose the Meta-Balancer framework which relieves the application programmers of deciding when to balance load. By continuously monitoring the application characteristics and using a set of guiding principles, MetaBalancer invokes load balancing on its own without any prior application knowledge. We demonstrate that Meta-Balancer improves or matches the best performance that can be obtained by fine tuning periodic load balancing. We also show that in some cases Meta-Balancer improves performance by 18% whereas periodic load balancing gives only a 1.5% benefit.

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“…Loop sizes available for OpenMP parallelization vary widely, from dense large matrix operations to very short loops. LLNL science applications include first principles molecular dynamics codes [8], traditional molecular dynamics codes [7,12,15] and ParaDiS, a dislocation dynamics application [3].…”

Section: Characteristics Of Scientific Applicationsmentioning

confidence: 99%

CLOMP: Accurately Characterizing OpenMP Application Overheads

Bronevetsky

Gyllenhaal

Supinski

2008

OpenMP in a New Era of Parallelism

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Abstract. Despite its ease of use, OpenMP has failed to gain widespread use on large scale systems, largely due to its failure to deliver sufficient performance. Our experience indicates that the cost of initiating OpenMP regions is simply too high for the desired OpenMP usage scenario of many applications. In this paper, we introduce CLOMP, a new benchmark to characterize this aspect of OpenMP implementations accurately. CLOMP complements the existing EPCC benchmark suite to provide simple, easy to understand measurements of OpenMP overheads in the context of application usage scenarios. Our results for several OpenMP implementations demonstrate that CLOMP identifies the amount of work required to compensate for the overheads observed with EPCC. Further, we show that CLOMP also captures limitations for OpenMP parallelization on NUMA systems.

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NAMD: Biomolecular Simulation on Thousands of Processors

Cited by 176 publications

References 12 publications

Maximizing Throughput on a Dragonfly Network

Maximizing Throughput on a Dragonfly Network

Automated Load Balancing Invocation Based on Application Characteristics

CLOMP: Accurately Characterizing OpenMP Application Overheads

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