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2015 International Conference on High Performance Computing & Simulation (HPCS)最新文献

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On the fly reconfiguration of interactive scientific visualization applications 交互式科学可视化应用程序的动态重构
Pub Date : 2015-07-20 DOI: 10.1109/HPCSim.2015.7237078
Abderrahim Ait Wakrime, Sébastien Limet, S. Robert
An interactive scientific visualization application is constructed from different codes to implement simulation, data treatment, visualization and interaction parts. The application construction requires support for the assembly of the different parts considering their heterogeneity in the one hand and the need to achieve an efficient application to be run in real time on the other hand. Component-based approach is an interesting paradigm to handle such applications. Moreover in a context of visual analytics, some applications need to be dynamically reconfigured since some components as analysis steps are not persistent and need to be restarted or stopped on the fly. This paper describes a reconfiguration process for ComSA applications, a component based approach dedicated to interactive scientific visualization applications that relies on an exogenous coordination model. This process enables the reconfiguration of running applications. It aims to minimize the number of stopped components during the reconfiguration phase while avoiding the application to crash. It uses the properties of the coordination model to circumscribe the part of the application impacted by the reconfiguration. This region is safely paused, then modified and finally restarted.
用不同的代码实现了仿真、数据处理、可视化和交互部分,构建了交互式科学可视化应用程序。应用程序的构建一方面需要考虑到不同部件的异构性,另一方面需要实现应用程序的高效实时运行。基于组件的方法是处理此类应用程序的有趣范例。此外,在可视化分析的上下文中,一些应用程序需要动态地重新配置,因为作为分析步骤的一些组件不是持久的,需要动态地重新启动或停止。本文描述了ComSA应用程序的重构过程,这是一种基于组件的方法,专门用于依赖外生协调模型的交互式科学可视化应用程序。此过程允许重新配置正在运行的应用程序。它的目的是在重新配置阶段尽量减少停止的组件数量,同时避免应用程序崩溃。它使用协调模型的属性来限定受重构影响的应用程序部分。该区域安全暂停,然后修改,最后重新启动。
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引用次数: 2
Wireless Power transfer system modelling based on neural Network with adaptive filtering 基于神经网络自适应滤波的无线电力传输系统建模
Pub Date : 2015-07-20 DOI: 10.1109/HPCSim.2015.7237054
Karim Elsayed, Nesrine Amin Elessawy, A. El-Shenawy
This paper propose a Simulink model for Wireless Power transfer to emulate the effect of air gap and the distance, misalignment, noise and harmonic. This model is based on practical neural Network weight matrix where it read the value of output voltage from the transmitter coil and then calculates the voltage produced in the received coil with taken in consideration the circuit configuration variable as capacitor, inductor, and number of turns. The frequency in the receiver part is controlled by an adaptive filter where the band width of operating frequency is very large and contains a lot of noise otherwise known it is very important for the accuracy of neural network. The system is tested in simulation and the hardware set up and showed acceptable performance illustrated by presented experiments.
本文提出了一种用于无线电力传输的Simulink模型,以模拟气隙、距离、不对准、噪声和谐波对无线电力传输的影响。该模型基于实用的神经网络权重矩阵,从发送线圈读取输出电压值,然后考虑电路配置变量如电容、电感和匝数,计算接收线圈产生的电压。接收部分的频率由自适应滤波器控制,其中工作频率的带宽很大,并且包含大量的噪声,这对神经网络的精度非常重要。系统进行了仿真测试和硬件搭建,实验结果表明系统性能良好。
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引用次数: 2
Current challenges in simulations of HPC systems 当前HPC系统仿真的挑战
Pub Date : 2015-07-20 DOI: 10.1109/HPCSim.2015.7237110
S. Petit
Simulation of many-core HPC systems is nowadays an active and fruitful area of research. Recent and future proposals are driven by the need of a fast, efficient, and comprehensive simulation framework. This simulation framework should be complete in several ways. First, it should model a wide range of components and provide the mechanisms necessary to plug-in more components as needed. Second, it should allow the designer to focus on critical components while avoiding a large part of the simulation complexity. Each of these components should be able to be evaluated with multiple models with distinct detail levels, ranging from simply analytical models to detailed cycle-accurate simulations. Third, a complete simulation framework should provide a wide range of metrics of interest for the designer and the market. Finally, support for heterogeneous architectures combining CPU and GPU, as well as some degree of reconfigurability is surely required. Building such titanic framework is and will be a collaborative process between researchers around the globe and it is expected to be a hot research topic for the next years.
多核高性能计算系统的仿真是当今一个活跃而富有成果的研究领域。最近和未来的建议是由需要一个快速,高效和全面的仿真框架驱动的。这个模拟框架应该以几种方式完成。首先,它应该为广泛的组件建模,并提供必要的机制,以便根据需要插入更多组件。其次,它应该允许设计师专注于关键组件,同时避免大部分模拟复杂性。每个组件都应该能够使用具有不同细节级别的多个模型进行评估,范围从简单的分析模型到详细的周期精确模拟。第三,一个完整的模拟框架应该为设计师和市场提供广泛的兴趣指标。最后,还需要支持CPU和GPU的异构架构,以及一定程度的可重构性。构建这样一个巨大的框架是全球研究人员之间的合作过程,预计将成为未来几年的一个热门研究课题。
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引用次数: 0
Comparison of hexagonal and rectangular processor arrays 六边形和矩形处理器阵列的比较
Pub Date : 2015-07-20 DOI: 10.1109/HPCSim.2015.7237064
E. Kresch
This paper presents a comparison of the performance between a hexagonal network and a rectangular network under similar conditions. It also presents a comparison of performance of data transmission among cores between a proposed technique and a more standard technique. A hexagonal arrangement was used in the hopes that the additional connectivity would provide an increase in performance. An increase in performance was found, but only a modest one. The proposed technique does quite well at low injection rates compared with the standard technique, but not so well at high injection rates.
本文比较了相似条件下六角形网络和矩形网络的性能。还比较了所提出的技术和更标准的技术在核心间的数据传输性能。使用六角形排列是希望额外的连接性能够提高性能。结果发现,性能有所提高,但幅度不大。与标准技术相比,该技术在低注入速率下表现良好,但在高注入速率下表现不佳。
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引用次数: 1
A security framework for population-scale genomics analysis 群体规模基因组学分析的安全框架
Pub Date : 2015-07-20 DOI: 10.1109/HPCSim.2015.7237028
A. Gholami, J. Dowling, E. Laure
Biobanks store genomic material from identifiable individuals. Recently many population-based studies have started sequencing genomic data from biobank samples and cross-linking the genomic data with clinical data, with the goal of discovering new insights into disease and clinical treatments. However, the use of genomic data for research has far-reaching implications for privacy and the relations between individuals and society. In some jurisdictions, primarily in Europe, new laws are being or have been introduced to legislate for the protection of sensitive data relating to individuals, and biobank-specific laws have even been designed to legislate for the handling of genomic data and the clear definition of roles and responsibilities for the owners and processors of genomic data. This paper considers the security questions raised by these developments. We introduce a new threat model that enables the design of cloud-based systems for handling genomic data according to privacy legislation. We also describe the design and implementation of a security framework using our threat model for BiobankCloud, a platform that supports the secure storage and processing of genomic data in cloud computing environments.
生物银行存储来自可识别个体的基因组材料。最近,许多基于人群的研究已经开始对生物库样本的基因组数据进行测序,并将基因组数据与临床数据交联,目的是发现对疾病和临床治疗的新见解。然而,使用基因组数据进行研究对隐私和个人与社会之间的关系有着深远的影响。在一些司法管辖区,主要是在欧洲,正在或已经制定新的法律,以立法保护与个人有关的敏感数据,甚至还制定了针对生物库的法律,以立法处理基因组数据,并明确定义基因组数据所有者和处理者的角色和责任。本文考虑了这些发展所带来的安全问题。我们引入了一种新的威胁模型,使基于云的系统设计能够根据隐私立法处理基因组数据。我们还描述了使用BiobankCloud威胁模型的安全框架的设计和实现,BiobankCloud是一个支持在云计算环境中安全存储和处理基因组数据的平台。
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引用次数: 9
Performance analysis with a memory-bound Monte Carlo simulation on Xeon Phi 在Xeon Phi处理器上使用内存绑定蒙特卡罗模拟进行性能分析
Pub Date : 2015-07-20 DOI: 10.1109/HPCSim.2015.7237074
Pierre Schweitzer, C. Mazel, D. Hill, C. Cârloganu
Physics simulations are known to be great resources exhausters (CPU, memory). Hardware acceleration can help reduce the need for CPU time and increase the available memory bandwidth. In this paper, we present the performance gain when running a memory-bound muon Monte Carlo simulation on an Intel Xeon Phi and an Intel Xeon CPU. We show how to increase performance on the Xeon Phi without modifying the Physics software frameworks we are using for our application. We investigate distributed simulations on multicore and manycore systems and also the impact of hyper-threading on performance. We extend this to a hybrid computing model, balancing the computing burden between both the manycore and multicore processors of a computing node. Finally, we improved memory usage on the Xeon Phi by sharing Kernel Memory pages using KSM, and we show that, using this approach, we can run 16% more simulation instances.
物理模拟被认为是巨大的资源消耗者(CPU,内存)。硬件加速可以帮助减少对CPU时间的需求,并增加可用内存带宽。在本文中,我们展示了在Intel Xeon Phi和Intel Xeon CPU上运行内存绑定μ子蒙特卡罗模拟时的性能增益。我们展示了如何在不修改我们应用程序使用的物理软件框架的情况下提高Xeon Phi的性能。我们研究了多核和多核系统上的分布式模拟,以及超线程对性能的影响。我们将其扩展到混合计算模型,在计算节点的多核和多核处理器之间平衡计算负担。最后,我们通过使用KSM共享内核内存页面来改善Xeon Phi处理器的内存使用情况,并且我们表明,使用这种方法,我们可以多运行16%的模拟实例。
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引用次数: 1
Performance analysis of the COSMO-CLM model cosmos - clm模型的性能分析
Pub Date : 2015-07-20 DOI: 10.1109/HPCSim.2015.7237096
S. Mocavero, A. Nigro, Arianna Resta, C. Rosato, Giacomo Sciolti, I. Epicoco, G. Aloisio
COSMO-CLM is a non-hydrostatic parallel atmospheric model, developed by the CLM-Community starting from the Local Model (LM) of the German Weather Service. Since 2005, it is the reference model used by the german researchers for the climate studies on different temporal scales (from few to hundreds of years) with a spatial resolution from 1 up to 50 kilometers. It is also used and developed from other meteorological research centres belonging to the Consortium for Small-scale Modelling (COSMO). The present work is focused on the analysis of the CCLM model from the computational point of view. The main goal is to verify if the model can be optimised by means of an appropriate tuning of the input parameters, to identify the performance bottlenecks and to suggest possible approaches for a further code optimisation. We started analysing if the strong scalability (which measures the improvement factor due to the parallelism given a fixed domain size) can be improved acting on some parameters such as the subdomain shape, the number of processes dedicated to the I/O operations, the output frequency and the communication strategies. Then we profiled the code to highlight the bottlenecks to the scalability and finally we performed a detailed performance analysis of the main kernels using the roofline model.
cosmos - clm是非流体静力平行大气模式,由CLM-Community从德国气象局的本地模式(LM)发展而来。自2005年以来,它是德国研究人员用于不同时间尺度(从几到几百年)气候研究的参考模型,空间分辨率从1到50公里。它也由属于小尺度模拟联合会(COSMO)的其他气象研究中心使用和发展。本文主要从计算的角度对CCLM模型进行分析。主要目标是验证是否可以通过适当调整输入参数来优化模型,确定性能瓶颈,并为进一步的代码优化提出可能的方法。我们开始分析是否可以根据子域形状、专用于I/O操作的进程数量、输出频率和通信策略等参数来改进强可伸缩性(衡量给定固定域大小的并行性所带来的改进因子)。然后我们对代码进行了分析,以突出可伸缩性的瓶颈,最后我们使用rooline模型对主要内核进行了详细的性能分析。
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引用次数: 0
A fuzzy logic controlled mobility model based on simulated traffics' characteristics in MANET 基于仿真交通特性的模糊逻辑控制机动网络模型
Pub Date : 2015-07-20 DOI: 10.1109/HPCSim.2015.7237051
Chen Chen, Qingqi Pei
In this paper, we investigate the self-similarity characteristic of MANET(Mobile Ad-hoc NETworks) traffics through simulations and then construct a fuzzy logic controlled mobility model according to the traffic feature to optimize the network performance. First, based on the generated traffics using OPNET, the self-similarity of MANET traffics has been verified with a qualitative analysis. Then, by exploring the relation between the self-similarity indicator, i.e., Hurst and some network performance metrics, such as Packets Delivery Ratio(PDR), Average Transmission Delay(ATD) and nodal Average Moving Speed(AMS), a fuzzy logic controller is designed to make the mobility model adaptively work in order to output satisfied performance. By online estimating the self-similarity of incoming traffics using R/S analysis, the Packet Size(PS) and AMS of each vehicle could be intelligently adjusted to maximize the PDR and minimize the experienced ATD. Numerical results indicate that our proposed mobility model, compared to the classic mobility model RWP(Random WayPoint), has a better performance in terms of PDR and ATD.
本文通过仿真研究了MANET(Mobile Ad-hoc network)业务的自相似特性,并根据业务特征构建了模糊逻辑控制的移动性模型,以优化网络性能。首先,基于OPNET生成的流量,通过定性分析验证了MANET流量的自相似性。然后,通过探索自相似指标Hurst与网络性能指标PDR、平均传输延迟(ATD)和节点平均移动速度(AMS)之间的关系,设计模糊逻辑控制器,使迁移模型自适应工作,以输出满意的性能。通过R/S分析在线估计入路流量的自相似度,智能调整每辆车的包大小(PS)和AMS,以最大化PDR和最小化经验ATD。数值结果表明,与经典的RWP(Random WayPoint)移动模型相比,我们提出的移动模型在PDR和ATD方面具有更好的性能。
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引用次数: 2
Acceleration of dRMSD calculation and efficient usage of GPU caches dRMSD计算的加速和GPU缓存的有效使用
Pub Date : 2015-07-20 DOI: 10.1109/HPCSim.2015.7237020
J. Filipovič, Jan Plhak, D. Střelák
In this paper, we introduce the GPU acceleration of dRMSD algorithm, used to compare different structures of a molecule. Comparing to multithreaded CPU implementation, we have reached 13.4× speedup in clustering and 62.7× speedup in I:I dRMSD computation using mid-end GPU. The dRMSD computation exposes strong memory locality and thus is compute-bound. Along with conservative implementation using shared memory, we have decided to implement variants of the algorithm using GPU caches to maintain memory locality. Our implementation using cache reaches 96.5% and 91.6% of shared memory performance on Fermi and Maxwell, respectively. We have identified several performance pitfalls related to cache blocking in compute-bound codes and suggested optimization techniques to improve the performance.
本文介绍了dRMSD算法的GPU加速,用于比较分子的不同结构。与多线程CPU实现相比,使用中端GPU,我们在集群方面的加速达到13.4倍,在I:I dRMSD计算方面的加速达到62.7倍。dRMSD计算暴露了强内存局部性,因此受计算约束。除了使用共享内存的保守实现外,我们还决定使用GPU缓存来实现算法的变体,以维护内存局部性。我们使用缓存的实现在Fermi和Maxwell上分别达到96.5%和91.6%的共享内存性能。我们已经确定了与计算绑定代码中的缓存阻塞相关的几个性能缺陷,并提出了改进性能的优化技术。
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引用次数: 0
A new reality requiers new ecosystems 新的现实需要新的生态系统
Pub Date : 2015-07-20 DOI: 10.1109/HPCSim.2015.7237115
S. Klous
We live in a time where borders between organizations are vanishing. A time where division equals multiplication. Where Open Source is the new alternative for a patent application. And in a time where Big Data offers new ways to add value to business and society. Such a time requires new ways of collaboration and organization of partners in the value chain. What we need is ecosystems that assure responsible application of data analysis and stimulate quality and innovation. In such a way that participants can easily plug in and out.
我们生活在一个组织之间的边界正在消失的时代。除法等于乘法的时间。其中开源是专利申请的新选择。在这个时代,大数据为企业和社会增加价值提供了新的途径。这样的时代需要新的合作方式和价值链中合作伙伴的组织。我们需要的是确保负责任地应用数据分析并刺激质量和创新的生态系统。以这样的方式,参与者可以很容易地插入和退出。
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引用次数: 0
期刊
2015 International Conference on High Performance Computing & Simulation (HPCS)
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