2015 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing最新文献

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Parallel Exploration of the Nuclear Chromosome Conformation with NuChart-II 用NuChart-II平行探索核染色体构象
Fabio Tordini, M. Drocco, Claudia Misale, L. Milanesi, P. Lio’, I. Merelli, Marco Aldinucci
{"title":"Parallel Exploration of the Nuclear Chromosome Conformation with NuChart-II","authors":"Fabio Tordini, M. Drocco, Claudia Misale, L. Milanesi, P. Lio’, I. Merelli, Marco Aldinucci","doi":"10.1109/PDP.2015.104","DOIUrl":"https://doi.org/10.1109/PDP.2015.104","url":null,"abstract":"High-throughput molecular biology techniques are widely used to identify physical interactions between genetic elements located throughout the human genome. Chromosome Conformation Capture (3C) and other related techniques allow to investigate the spatial organisation of chromosomes in the cell's natural state. Recent results have shown that there is a large correlation between co-localization and co-regulation of genes, but these important information are hampered by the lack of biologists-friendly analysis and visualisation software. In this work we introduce NuChart-II, a tool for Hi-C data analysis that provides a gene-centric view of the chromosomal neighbourhood in a graph-based manner. NuChart-II is an efficient and highly optimized C++ re-implementation of a previous prototype package developed in R. Representing Hi-C data using a graph-based approach overcomes the common view relying on genomic coordinates and permits the use of graph analysis techniques to explore the spatial conformation of a gene neighbourhood.","PeriodicalId":285111,"journal":{"name":"2015 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing","volume":"91 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124203643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
Preprocessing of Scenarios for Fast and Efficient Routing Reconfiguration in Fault-Tolerant NoCs 容错网络中快速高效路由重构的场景预处理
J. Silveira, C. Marcon, P. Cortez, G. Barroso, J. M. Ferreira, R. Mota
{"title":"Preprocessing of Scenarios for Fast and Efficient Routing Reconfiguration in Fault-Tolerant NoCs","authors":"J. Silveira, C. Marcon, P. Cortez, G. Barroso, J. M. Ferreira, R. Mota","doi":"10.1109/PDP.2015.22","DOIUrl":"https://doi.org/10.1109/PDP.2015.22","url":null,"abstract":"Newest processes of CMOS manufacturing allow integrating billions of transistors in a single chip. This huge integration enables to perform complex circuits, which require an energy efficient communication architecture with high scalability and parallelism degree, such as a Network-on-Chip (NoC). However, these technologies are very close to physical limitations implying the susceptibility increase of faults on manufacture and at runtime. Therefore, it is essential to provide a method for efficient fault recovery, enabling the NoC operation even in the presence of faults on routers or links, and still ensure deadlock-free routing even for irregular topologies. A preprocessing approach of the most probable fault scenarios enables to anticipate the computation of deadlock-free routings, reducing the time necessary to interrupt the system operation in a fault event. This work describes a preprocessing technique of fault scenarios based on forecasting fault tendency, which employs a fault threshold circuit and a high-level software that identifies the most relevant fault scenarios. We propose methods for dissimilarity analysis of scenarios based on measurements of cross-correlation of link fault matrices. At runtime, the preprocessing technique employs analytic metrics of average distance routing and links load for fast search of sound fault scenarios. Finally, we use RTL simulation with synthetic traffic to prove the quality of our approach.","PeriodicalId":285111,"journal":{"name":"2015 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing","volume":"706 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114769603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Enabling Secure Communication over Existing Peer-to-Peer Frameworks 在现有的对等框架上实现安全通信
Andreas Reiter
{"title":"Enabling Secure Communication over Existing Peer-to-Peer Frameworks","authors":"Andreas Reiter","doi":"10.1109/PDP.2015.10","DOIUrl":"https://doi.org/10.1109/PDP.2015.10","url":null,"abstract":"Peer-to-peer technologies are, due to their distributed nature and the absence of a single point of failure, most promising in the field of providing privacy and security if appropriate mechanisms are in place. Currently security and privacy in peer-to-peer networks is tightly bound to specific frameworks. In this paper a flexible and modular approach for existing peer-to-peer frameworks to enable a secure communication using well-established and proven protocols and algorithms called SP2P is proposed. An interoperability layer is introduced where existing peer-to-peer frameworks, transport security protocols, different types of identities and appropriate identity authentication services can be plugged in seamlessly. The identity authentication service is designed to be compatible with existing quality level assurance frameworks which can be chosen depending on the deployment environment and requirements. Further the different components of end-to-end security protocols and their impact on the overall security and privacy level is analysed. This enables developers to use proven and well established security mechanisms without diving in the very specifics of different peer-to-peer framework specifications.","PeriodicalId":285111,"journal":{"name":"2015 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing","volume":"692 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116967661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Progression of MPI Non-blocking Collective Operations Using Hyper-Threading 使用超线程的MPI非阻塞集体操作的进展
Masahiro Miwa, Kohta Nakashima
{"title":"Progression of MPI Non-blocking Collective Operations Using Hyper-Threading","authors":"Masahiro Miwa, Kohta Nakashima","doi":"10.1109/PDP.2015.68","DOIUrl":"https://doi.org/10.1109/PDP.2015.68","url":null,"abstract":"MPI non-blocking collective operations offer a high level interface to MPI library users, and potentially allow communication to be overlapped with calculation. Progression, which controls communications running in the background of the calculation, is the key factor to achieve an efficient overlap. The most commonly used progression method is manual progression, in which a progression function is called in the main calculation. In manual progression, MPI library users have to estimate the communication timing to maximize the overlap effect and thus to manage the complex communication optimization. An alternative approach for progression is the use of separate communication threads. By using communication threads, communication calculation overlap can be achieved simply. However, context switches between the calculation thread and the communication thread cause lower performance in the frequent case where all cores are used for calculation. In this paper, we propose a novel threaded progression method using Hyper-Threading to maximize the overlap effect of non-blocking collective operations. We apply MONITOR/MWAIT instructions to the communication thread on Hyper-Threading so as not to degrade the calculation thread due to shared core resource conflict. Evaluation on 8-node Infini Band connected IA server clustered systems confirmed that the latency is suppressed to a small level and that our approach has an advantage over manual progression in terms of communication-calculation overlap. Using a real application of CG benchmark, our method achieved 32% reduction in execution time compared to using blocking collective operation, and that is nearly perfect overlap. Although manual progression also achieved perfect overlap, our method has the advantage that no communication timing tuning is required for each application.","PeriodicalId":285111,"journal":{"name":"2015 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing","volume":"77 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117306220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
pioman: A Pthread-Based Multithreaded Communication Engine pioman:一个基于pthread的多线程通信引擎
Alexandre Denis
{"title":"pioman: A Pthread-Based Multithreaded Communication Engine","authors":"Alexandre Denis","doi":"10.1109/PDP.2015.78","DOIUrl":"https://doi.org/10.1109/PDP.2015.78","url":null,"abstract":"Recent cluster architectures include dozens of cores per node, with all cores sharing the network resources. To program such architectures, hybrid models mixing MPI+threads, and in particular MPI+OpenMP are gaining popularity. This imposes new requirements on communication libraries, such as the need for MPI_THREAD_MULTIPLE level of multi-threading support. Moreover, the high number of cores brings new opportunities to parallelize communication libraries, so as to have proper background progression of communication and communication/computation overlap. In this paper, we present pioman, a generic framework to be used by MPI implementations, that brings seamless asynchronous progression of communication by opportunistically using available cores. It uses system threads and thus is composable with any runtime system used for multithreading. Through various benchmarks, we demonstrate that our pioman-based MPI implementation exhibits very good properties regarding overlap, progression, and multithreading, and outperforms state-of-art MPI implementations.","PeriodicalId":285111,"journal":{"name":"2015 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129856735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 17
Iterative Selection of Cost-Effective Countermeasures for Intelligent Threat Agents 智能威胁代理经济有效对策的迭代选择
F. Baiardi, F. Tonelli, A. Bertolini, R. Bertolotti
{"title":"Iterative Selection of Cost-Effective Countermeasures for Intelligent Threat Agents","authors":"F. Baiardi, F. Tonelli, A. Bertolini, R. Bertolotti","doi":"10.1109/PDP.2015.20","DOIUrl":"https://doi.org/10.1109/PDP.2015.20","url":null,"abstract":"We describe the tools of the Haruspex suite to manage the risk due to intelligent agents. The suite applies a Monte Carlo method and it return a statistical samples on the attacks these agents implement. Some tools of the suite analyzes these samples to select the countermeasures to deploy. The tools work in an iterative way that alternates the selection of countermeasures and the application of the Monte Carlo method. This takes into account that an intelligent agent may select distinct attacks to replace those affected by the countermeasures. Lastly, we apply the tools to three industrial control systems.","PeriodicalId":285111,"journal":{"name":"2015 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127397851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Load Balance Strategies for DEVS Approximated Parallel and Distributed Discrete-Event Simulations DEVS近似并行和分布式离散事件模拟的负载平衡策略
Alonso Inostrosa-Psijas, V. Gil-Costa, Roberto Solar, Mauricio Marín
{"title":"Load Balance Strategies for DEVS Approximated Parallel and Distributed Discrete-Event Simulations","authors":"Alonso Inostrosa-Psijas, V. Gil-Costa, Roberto Solar, Mauricio Marín","doi":"10.1109/PDP.2015.13","DOIUrl":"https://doi.org/10.1109/PDP.2015.13","url":null,"abstract":"DEVS is a formalism for modeling and analysis of discrete event systems. PDEVS is an extension of DEVS for supporting Parallel and Discrete Event Simulation (PDES). PCD++ is a simulation platform that supports parallel simulations of DEVS models, where the model component allocation in processors is not an automatic process. This can be a time consuming task requiring knowledge of communication patterns among model components. In this paper, we propose and evaluate different allocation strategies devised to improve load balance of parallel DEVS simulations. The experimentation is made on a Web search engine application whose workload is featured by dynamic and unpredictable user query bursts, and high message traffic among processors.","PeriodicalId":285111,"journal":{"name":"2015 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing","volume":"136 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127410976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
A Monitoring System for Runtime Adaptations of Streaming Applications 流应用运行时适应的监控系统
Manuel Selva, L. Morel, K. Marquet, S. Frénot
{"title":"A Monitoring System for Runtime Adaptations of Streaming Applications","authors":"Manuel Selva, L. Morel, K. Marquet, S. Frénot","doi":"10.1109/PDP.2015.53","DOIUrl":"https://doi.org/10.1109/PDP.2015.53","url":null,"abstract":"Streaming languages are adequate for expressing many applications quite naturally and have been proven to be a good approach for taking advantage of the intrinsic parallelism of modern CPU architectures. While numerous works focus on improving the throughput of streaming programs, we rather focus on satisfying quality-of-service requirements of streaming applications executed along-side non-streaming processes. We monitor synchronous dataflow (SDF) programs at runtime both at the application and system levels in order to identify violations of quality-of-service requirements. Our monitoring requires the programmer to provide the expected throughput of its application (e.g. 25 frames per second for a video decoder), then takes full benefit from the compilation of the SDF graph to detect bottlenecks in this graph and identify causes among processor or memory overloading. It can then be used to perform dynamic adaptations of the applications in order to optimize the use of computing and memory resources.","PeriodicalId":285111,"journal":{"name":"2015 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130010590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
I/O Optimization in the Checkpointing of OpenMP Parallel Applications OpenMP并行应用程序检查点中的I/O优化
Nuria Losada, María J. Martín, Gabriel Rodríguez, P. González
{"title":"I/O Optimization in the Checkpointing of OpenMP Parallel Applications","authors":"Nuria Losada, María J. Martín, Gabriel Rodríguez, P. González","doi":"10.1109/PDP.2015.39","DOIUrl":"https://doi.org/10.1109/PDP.2015.39","url":null,"abstract":"Despite the increasing popularity of shared-memory systems, there is a lack of tools for providing fault tolerance support to shared-memory applications. Check pointing is one of the most popular fault tolerance techniques. However, check pointing cost in terms of computing time, network utilization or storage resources can be a limitation for its practical use. This work proposes different techniques for the optimization of the I/O cost in the check pointing of shared-memory parallel applications. The proposals are extensively evaluated using the OpenMP NAS Parallel Benchmarks. Results show a significant decrease of the check pointing overhead.","PeriodicalId":285111,"journal":{"name":"2015 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125920855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
A Generic and Highly Efficient Parallel Variant of Boruvka's Algorithm Boruvka算法的一种通用且高效的并行变体
Cristiano da Silva Sousa, Artur Mariano, A. Proença
{"title":"A Generic and Highly Efficient Parallel Variant of Boruvka's Algorithm","authors":"Cristiano da Silva Sousa, Artur Mariano, A. Proença","doi":"10.1109/PDP.2015.72","DOIUrl":"https://doi.org/10.1109/PDP.2015.72","url":null,"abstract":"This paper presents (i) a parallel, platform independent variant of Boruvka's algorithm, an efficient Minimum Spanning Tree (MST) solver, and (ii) a comprehensive comparison of MST-solver implementations, both on multi-core CPU-chips and GPUs. The core of our variant is an effective and explicit contraction of the graph. Our multi-core CPU implementation scales linearly up to 8 threads, whereas the GPU implementation performs considerably better than the optimal number of threads running on the CPU. We also show that our implementations outperform all other parallel MST-solver implementations in (ii), for a broad set of publicly available road network graphs.","PeriodicalId":285111,"journal":{"name":"2015 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing","volume":"44 2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131265504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 15
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