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检索条件"任意字段=21st International Symposium on Computer Architecture and High Performance Computing"

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Optimized Force Calculation in Molecular Dynamics Simulations for the Intel Xeon Phi

Optimized Force Calculation in Molecular Dynamics Simulation...

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21st international Conference on Parallel and Distributed computing (Euro-Par)

作者： Tchipev, Nikola Wafai, Amer Glass, Colin W. Eckhardt, Wolfgang Heinecke, Alexander Bungartz, Hans-Joachim Neumann, Philipp Tech Univ Munich Dept Informat Boltzmannstr 3 D-85748 Garching Germany High Performance Comp Ctr Stuttgart D-70569 Stuttgart Germany Intel Corp Santa Clara CA USA

ISBN: (纸本)9783319273082;9783319273075

We provide details on the shared-memory parallelization for manycore architectures of the molecular dynamics framework ls1-mardyn, including an optimization of the SIMD vectorization for multi-centered molecules. The novel shared-memory parallelization scheme allows to retain Newton's third law optimization and exhibits very good scaling on many-core devices such as a full Xeon Phi card running 240 threads. The Xeon Phi can thus be exploited and delivers comparable performance as IvyBridge nodes in our experiments.

关键词： Molecular dynamics

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A Holistic Approach to Log Data Analysis in high-performance computing Systems: The Case of IBM Blue Gene/Q

A Holistic Approach to Log Data Analysis in High-Performance...

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21st international Conference on Parallel and Distributed computing (Euro-Par)

作者： Sirbu, Alina Babaoglu, Ozalp Univ Bologna Dept Comp Sci & Engn Mura Anteo Zamboni 7 I-40126 Bologna Italy

ISBN: (纸本)9783319273082;9783319273075

The complexity and cost of managing high-performance computing infrastructures are on the rise. Automating management and repair through predictive models to minimize human interventions is an attempt to increase system availability and contain these costs. Building predictive models that are accurate enough to be useful in automatic management cannot be based on restricted log data from subsystems but requires a holistic approach to data analysis from disparate sources. Here we provide a detailed multi-scale characterization study based on four datasets reporting power consumption, temperature, workload, and hardware/software events for an IBM Blue Gene/Q installation. We show that the system runs a rich parallel workload, with low correlation among its components in terms of temperature and power, but higher correlation in terms of events. As expected, power and temperature correlate strongly, while events display negative correlations with load and power. Power and workload show moderate correlations, and only at the scale of components. The aim of the study is a systematic, integrated characterization of the computing infrastructure and discovery of correlation sources and levels to serve as basis for future predictive modeling efforts.

关键词： Data science Correlation analysis HPC system monitoring Log data integration Predictive modeling

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mTrack: high-Precision Passive Tracking Using Millimeter Wave Radios 15

mTrack: High-Precision Passive Tracking Using Millimeter Wav...

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21st Annual international Conference on Mobile computing and Networking (MobiCom)

作者： Wei, Teng Zhang, Xinyu Univ Wisconsin Dept Elect & Comp Engn Madison WI 53706 USA

ISBN: (纸本)9781450336192

Radio-based passive-object sensing can enable a new form of pervasive user-computer interface. Prior work has employed various wireless signal features to sense objects under a set of predefined, coarse motion patterns. But an operational UI, like a trackpad, often needs to identify fine-grained, arbitrary motion. This paper explores the feasibility of tracking a passive writing object (e.g., pen) at sub-centimeter precision. We approach this goal through a practical design, mTrack, which uses highly-directional 60 GHz millimeter wave radios as key enabling technology. mTrack runs a discrete beam scanning mechanism to pinpoint the object's initial location, and tracks its trajectory using a signal-phase based model. In addition, mTrack incorporates novel mechanisms to suppress interference from background reflections, taking advantage of the short wavelength of 60 GHz signals. We prototype mTrack and evaluate its performance on a 60 GHz reconfigurable radio platform. Experimental results demonstrate that mTrack can locate/track a pen with 90-percentile error below 8 mm, enabling new applications such as wireless transcription and virtual trackpad.

关键词： 60 GHz Millimeter-wave Tracking Phase Shift Background Cancellation

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SCOC: high-radix switches made of bufferless clos networks

SCOC: High-radix switches made of bufferless clos networks

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IEEE symposium on high-performance computer architecture

作者： Nikolaos Chrysos Cyriel Minkenberg Mark Rudquist Claude Basso Brian Vanderpool Foundation For Research and Technology (FORTH) IBM Research Zurich Switzerland IBM Systems & Technology Group Rochester USA

In today's datacenters handling big data and for exascale computers of tomorrow, there is a pressing need for high-radix switches to economically and efficiently unify the computing and storage resources that are dispersed across multiple racks. In this paper, we present SCOC, a switch architecture suitable for economical IC implementation that can efficiently replace crossbars for high-radix switch nodes. SCOC is a multi-stage bufferless network with O(N 2 /m) cost, where m is a design parameter, practically ranging between 4-16. We identify and resolve more than five fairness violations that are pertinent to hierarchical scheduling. Effectively, from a performance perspective, SCOC is indistinguishable from efficient flat crossbars. computer simulations show that it competes well or even outperforms flat crossbars and hierarchical switches. We report data from our ASIC implementation at 32 nm of a SCOC 136×136 switch, with shallow buffers, connecting 25 Gb/s links. In this first incarnation, SCOC is used at the spines of a server-rack, fat-tree network. Internally, it runs at 9.9 Tb/s, thus offering a speedup of 1.45 ×, and provides a fall-through latency of just 61 ns.

关键词： Clocks Ports (computers) Wires Scheduling System-on-chip Topology computer architecture

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Development of a parallel computing enabled optimisation tool for hydrological model calibration 21

Development of a parallel computing enabled optimisation too...

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21st international Congress on Modelling and Simulation (MODSIM) held jointly with the 23rd National Conference of the Australian-Society-for-Operations-Research / DstO led Defence Operations Research symposium (DORS

作者： Yang, Ang Hughes, Justin Dutta, Dushmanta Kim, Shaun Vaze, Jai CSIRO Land & Water Canberra ACT Australia

ISBN: (纸本)9780987214355

A river model is a semi-distributed hydrological model and it includes many processes such as flow routing, irrigation diversion, overbank flow, ground water interaction for simulating flows a river system for water resources planning and management. A number of calibration parameters are introduced in such models to represent various processes using simplified mathematical equations. Traditionally, a river model is calibrated using a reach-by-reach calibration approach starting from the top of the system cascading down to the end of the system. While the reach-by-reach approach is suitable for obtaining optimum model performance at a single river reach with high quality observed data, it does have the limitation of error propagation from upstream to downstream reaches if poor quality data are used in the calibration. A system-wide calibration approach has recently been developed for river system modelling in large river basins. Comparing with traditional reach-by-reach calibration, this new method optimises parameters of all river reaches within a region simultaneously using a weighted global objective function. The results of its application of this new approach in the Murray-Darling basin, Australia have shown its potential to overcome over-fitting and improve fitness of each individual gauge. However, due to the system-wide optimization of multiple reach parameters in a region, the search space and computational time required for system calibration increase exponentially with the increase of number of parameters. This limits the number of parameters that can be optimised and thus, the size of the region. To potentially overcome this limitation, a parallel computing enabled shuffled complex evolution (SCE) optimisation tool has been developed. A series of comparison studies have been conducted to evaluate the performance of this approach over normal SCE. These are: 1) comparison of computation time and performance for the same number of parameters;2) comparison o

关键词： River system model Australian Water Resources Assessment Shuffled complex evolution parallel computing optimisation

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Understanding GPU errors on large-scale HPC systems and the implications for system design and operation

Understanding GPU errors on large-scale HPC systems and the ...

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IEEE symposium on high-performance computer architecture

作者： Devesh Tiwari Saurabh Gupta James Rogers Don Maxwell Paolo Rech Sudharshan Vazhkudai Daniel Oliveira Dave Londo Nathan DeBardeleben Philippe Navaux Luigi Carro Arthur Bland Oak Ridge Leadership Computing Facility Oak Ridge National Laboratory Federal University of Rio Grande do Sul Cray Inc. Los Alamos National Laboratory

Increase in graphics hardware performance and improvements in programmability has enabled GPUs to evolve from a graphics-specific accelerator to a general-purpose computing device. Titan, the world's second fastest supercomputer for open science in 2014, consists of more dum 18,000 GPUs that scientists from various domains such as astrophysics, fusion, climate, and combustion use routinely to run large-scale simulations. Unfortunately, while the performance efficiency of GPUs is well understood, their resilience characteristics in a large-scale computing system have not been fully evaluated. We present a detailed study to provide a thorough understanding of GPU errors on a large-scale GPU-enabled system. Our data was collected from the Titan supercomputer at the Oak Ridge Leadership computing Facility and a GPU cluster at the Los Alamos National Laboratory. We also present results from our extensive neutron-beam tests, conducted at Los Alamos Neutron Science Center (LANSCE) and at ISIS (Rutherford Appleron Laboratories, UK), to measure the resilience of different generations of GPUs. We present several findings from our field data and neutron-beam experiments, and discuss the implications of our results for future GPU architects, current and future HPC computing facilities, and researchers focusing on GPU resilience.

关键词： Graphics processing units Neutrons computer crashes Error correction codes Resilience Laboratories Supercomputers

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Towards Community Detection on Heterogeneous Platforms

Towards Community Detection on Heterogeneous Platforms

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21st international Conference on Parallel and Distributed computing (Euro-Par)

作者： Heldens, stijn Varbanescu, Ana Lucia Prat-Perez, Arnau Larriba-Pey, Josep-Lluis Univ Amsterdam Inst Informat Amsterdam Netherlands Univ Politecn Cataluna DAMA UPC Barcelona Spain

ISBN: (纸本)9783319273082;9783319273075

Over the last decade, community detection has become an increasingly important topic of research due to its many applications in different fields of research, such as biology and sociology. One example of a modern community detection algorithm is Scalable Community Detection (SCD), which has been shown to produce high-quality results, but its performance remains an issue on large graphs. In this work, we demonstrate how SCD can benefit from the heterogeneity offered by hybrid CPU-GPU platforms by presenting Het-SCD: a heterogeneous version of SCD which combines the larger memory capacity of the CPU with the larger computational power of the GPU. To enable this, we have designed an entirely new version of SCD which efficiently uses the fine-grained parallelism of GPUs. We report performance results on six real-world graphs (up to 1.8B edges) and six platforms. We observe excellent performance for only the GPU (e.g., 70x speedup over sequential CPU version on graph of 117M edges) and for combining the CPU and GPU (e.g., 40x speedup for same graph on low-end GPU with insufficient memory to store entire dataset). These results demonstrate that Het-SCD is an excellent solution for large-scale community detection, since it provides high performance while preserving the high quality of the original algorithm.

关键词： Community detection Heterogeneous computing GPU computing SCD algorithm WCC metric

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Large-Scale Agent-Based Modeling with Repast HPC: A Case study in Parallelizing an Agent-Based Model

Large-Scale Agent-Based Modeling with Repast HPC: A Case Stu...

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21st international Conference on Parallel and Distributed computing (Euro-Par)

作者： Collier, Nicholson Ozik, Jonathan Macal, Charles M. Argonne Natl Lab Global Secur Sci 9700 S Cass Ave Argonne IL 60439 USA Univ Chicago Computat Inst Chicago IL 60637 USA

ISBN: (纸本)9783319273082;9783319273075

We present a case study for parallelizing a large-scale epidemiologic ABM developed with Repast HPC, the Chicago Social Interaction Model (chiSIM). The original serial model is a CA-MRSA model which tracks CA-MRSA transmission dynamics and infection in Chicago, and represents the spread of CA-MRSA in the population of Chicago. We utilize both within compute node parallelization using the OpenMP toolkit and distributed parallelization across multiple processes using MPI. The combined approach yields a 1350 % increase in run time performance utilizing 128 compute nodes.

关键词： Agent-based modeling ABMS Repast HPC Parallel simulation Distributed simulation high performance computing

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SWIFT2: high performance software for short-medium term ensemble streamflow forecasting research and operations 21

SWIFT2: High performance software for short-medium term ense...

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作者： Perraud, Jean-Michel Bridgart, Robert Bennett, James C. Robertson, David CSIRO Land & Water Clayton Vic Australia

ISBN: (纸本)9780987214355

The second version of the Short-term Water Information and Forecasting Tools (SWIFT2) is a suite of tools for flood and short-term streamflow forecasting, consisting of a collection of hydrologic model components and utilities. It is currently developed within the Water Information Research and Development Alliance, with a requirement to address both research and operational modelling needs. Catchments are modelled using a traditional approach for semi-distributed models: conceptual subareas and a node-link structure for channel routing. SWIFT2 comprises modules for calibration, model state updating, ensemble runs, output error correction and data assimilation. While applicable to simpler modelling tasks, SWIFT2 is designed from the ground up to tackle computationally intensive problems in probabilistic forecasting research, with sub-daily time steps over decades, and ensemble sizes in the thousands. Typical retrospective ensemble simulation outputs can reach hundreds of gigabytes, and projected runtimes can reach days if not parallelized. SWIFT2 simulations are safe for in-memory copy and parallel executions, can make effective use of multi-core personal computers or high-performance compute clusters to address computationally demanding research or operational requirements. SWIFT2 is written in modern C++ and is platform-agnostic. SWIFT2 is architected to offer several options for user interfaces. Driven by the needs of current users, it is seamlessly accessible from high-level interactive languages including R, Python and MATLAB (Figure 1). To achieve this, the SWIFT API (Application Programming Interface) offers a controlled yet fully fledged access to core modelling features and concepts. The time series handling is performed in a separate library for reuse outside of SWIFT2, using advanced C++ templates, similar to the Boost libraries. Users have access via concise commands in their interactive language of choice to high level modelling concepts, such as simula

关键词： Ensemble streamflow forecasting high-performance computing semi-distributed model

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Addressing the Last Roadblock for Message Logging in HPC: Alleviating the Memory Requirement Using Dedicated Resources

Addressing the Last Roadblock for Message Logging in HPC: Al...

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21st international Conference on Parallel and Distributed computing (Euro-Par)

作者： Martsinkevich, Tatiana Ropars, Thomas Cappello, Franck Univ Paris 11 Inria Orsay France Inria Bordeaux France Argonne Natl Lab Argonne Lemont IL USA

ISBN: (纸本)9783319273082;9783319273075

Currently used global application checkpoint-restart will not be a suitable solution for HPC applications running on large scale as, given the predicted fault rates, it will impose a high load on the I/O subsystem and lead to inefficient resource usage. Combining application checkpointing with message logging is appealing as it allows restarting only the processes that actually failed. One major issue with message logging protocols is the high amount of memory required to store logs. In this work we propose to use additional dedicated resources to save the part of the logs that would not fit in the memory of a compute node. We show that, combined with a cluster-based hierarchical logging technique, only few dedicated nodes would be required to accommodate the memory requirement of message logging protocols. We additionally show that the proposed technique achieves a reasonable performance overhead.

关键词： high-performance computing Fault tolerance Message logging Hierarchical message-logging protocols Dedicated resources

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