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检索条件"任意字段=Proceedings of the first international symposium on Databases in parallel and distributed systems"

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Investigating distributed Approaches to Efficiently Extract Textual Evidences for Biomedical Ontologies

Investigating Distributed Approaches to Efficiently Extract ...

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IEEE symposium on Bioinformatics and Bioengineering (BIBE)

作者： Long Cheng Yue Ma Department of Computer Science Technische Universitat Dresden Germany LRI - CNRS & Univcrsite Paris Sud Orsay France

ISBN: (纸本)9781479975037

Heterogeneous data resources in biomedicine become available both in structured and unstructured formats, such as scientific publications, healthcare guidelines, controlled vocabularies, and formal ontologies. %Increasing researches have been conducted to Bridging the gaps among these heterogeneous data is useful to discovery implicit knowledge. To make this happen, efficient computational approaches are a necessity for applications in such a knowledge- and data-intensive domain. In this paper, we first define a particular task, relation alignment, which is to identify textual evidences for biomedical ontologies. Then, we investigate two parallel approaches for this task over distributed systems and present the details of their implementations. Moreover, we characterize the performance of our methods through extensive experiments, thereby allowing researchers to make a more informed choice in the presence of large-scale biomedical data.

关键词： Ontologies Runtime distributed databases Bioinformatics Semantics Scalability Medical services

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Not seeing the parse trees from the parse forest of a context-free parallel communicating grammar system

Not seeing the parse trees from the parse forest of a contex...

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2013 IEEE 12th international symposium on parallel and distributed Computing, ISPDC 2013

作者： Bruda, Stefan D. Wilkin, Mary Sarah Ruth Department of Computer Science Bishop's University Sherbrooke QC Canada

ISBN: (纸本)9780769550183

parallel communicating grammar systems (PCGS) were introduced awhile ago purportedly to analyze concurrent systems on a language-theoretic level. To our knowledge however no actual relationship between PCGS and practical computing systems was ever investigated. We believe that PGCS with context-free components (CF-PCGS) have high practical potential, especially in the area of formal methods, so we started to bring CF-PCGS to a more practical level by studying a construct that has proven useful elsewhere: the parse tree (and forest). We show first that the original definition we introduced earlier falls short of all the desired properties: While each derivation has a corresponding parse forest, there are parse forests that do not correspond to any derivation, this applies to all the CF-PCGS variants. Because of this limitation we introduce a tighter version of parse trees (and forests) for CF-PCGS. Unfortunately we find that the new version does not bring any advantage over the original definition except for one, very restrictive variant of CF-PCGS. Overall beside providing a convenient tool to be used in conjunction with CF-PCGS, this work strongly suggests the aforementioned PCGS variant as the most promising model for practical applications in general and for grammatical approaches to formal verification of concurrent, recursive systems in particular. © 2013 IEEE.

关键词： Forestry

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A parallel spatial data analysis infrastructure for the cloud 13

A parallel spatial data analysis infrastructure for the clou...

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21st ACM SIGSPATIAL international Conference on Advances in Geographic Information systems, ACM SIGSPATIAL GIS 2013

作者： Ray, Suprio Simion, Bogdan Brown, Angela Demke Johnson, Ryan Department of Computer Science University of Toronto Canada

ISBN: (纸本)9781450325219

Spatial data analysis applications are emerging from a wide range of domains such as building information management, environmental assessments and medical imaging. Time-consuming computational geometry algorithms make these applications slow, even for medium-sized datasets. At the same time, there is a rapid expansion in available processing cores, through multicore machines and Cloud computing. The confluence of these trends demands effective parallelization of spatial query processing. Unfortunately, traditional parallel spatial databases are ill-equipped to deal with the performance heterogeneity that is common in the Cloud. We introduce Niharika, a parallel spatial data analysis infrastructure that exploits all available cores in a heterogeneous cluster. Niharika first uses a declustering technique that creates balanced spatial partitions. Then, Niharika adapts to performance heterogeneity and processing skew in the spatial dataset using dynamic load-balancing. We evaluate Niharika with three load-balancing algorithms and two different spatial datasets (both from TIGER) using Amazon EC2 instances. Niharika adapts to the performance heterogeneity in the EC2 nodes, thereby achieving excellent speedups (e.g., 63.6X using 64 cores on 16 4-core EC2 nodes, in the best case) and outperforming an approach that does not adapt. © 2013 ACM.

关键词： Information management

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HPC system software for regular and irregular parallel applications

HPC system software for regular and irregular parallel appli...

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2013 IEEE 37th Annual Computer Software and Applications Conference, COMPSAC 2013

作者： Morari, Alessandro Valero, Mateo Barcelona Supercomputing Center Barcelona Spain Universitat Politecnica de Catalunya Barcelona Spain

ISBN: (纸本)9780769549798

The upcoming generation of system software for High Performance Computing is expected to provide a richer set of functionalities without compromising application performance. This Ph.D. thesis addresses the problem of designing scalable system software for both regular and irregular applications. The contributions are two-fold. first, we evaluate the drawbacks of current HPC system software for regular applications. We describe a methodology to precisely measure jitter on a general-purpose OS. Considering a lightweight operating system (IBM CNK), we analyze the overhead of adding support for a missing feature such as dynamic memory management. Second, we focus on irregular applications and build a specialized runtime system to enhance this kind of applications on common HPC flop intensive systems. The proposed runtime system provides a global address space abstraction of a distributed memory machine combined with a transparent fork/join execution model and it also includes lightweight multithreading and network message aggregation. © 2013 IEEE.

关键词： Jitter

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Designing Hybrid Architectures for Massive-Scale Graph Analysis

Designing Hybrid Architectures for Massive-Scale Graph Analy...

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IEEE international symposium on parallel and distributed Processing Workshops and Phd Forum (IPDPSW)

作者： David Ediger David A. Bader Georgia Institute of Technology

ISBN: (纸本)9781479913725

Turning large volumes of data into actionable knowledge is a top challenge in high performance computing. Our previous work in this area demonstrated algorithmic techniques for massively parallel graph analysis on multithreaded systems. This work led to the development of GraphCT, the first end-to-end graph analytics platform for the Cray XMT and x86-class systems with OpenMP, and STINGER, a high performance, multithreaded, dynamic graph data structure and algorithms. Both of these packages are freely available as open source software. This dissertation research culminates in experimental and analytical techniques to study the marriage of disk-based systems, such as Hadoop, with shared memory-based systems, such as the Cray XMT, for data-intensive applications. David Ediger is a fifth year PhD candidate in Electrical and Computer Engineering.

关键词： Algorithm design and analysis databases Data models Data warehouses Computational modeling Memory management

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Accelerating all-to-All protein structures comparison with tmalign using a noc many-cores processor architecture

Accelerating all-to-All protein structures comparison with t...

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2013 IEEE 37th Annual Computer Software and Applications Conference, COMPSAC 2013

作者： Sharma, Anuj Papanikolaou, Antonis Manolakos, Elias S. Department of Informatics and Telecommunications University of Athens Athens Greece Institute of Communication and Computer Systems National Technical University Athens Greece

ISBN: (纸本)9780769549798

Computational challenges for the one-to-many and many-to-many protein structure comparison (PSC) problem are a result of several factors: constantly expanding large-size structural proteomics databases, high computational complexity of pair wise protein comparison algorithms, and the multitude of pair wise comparison approaches used in the field. Advances in processor architectures, such as manycore CPUs, have enabled them to support parallelism making them of interest in speeding up PSC techniques. We presentrckAlign, an implementation of the popularly used TM-AlignPSC algorithm, designed for the Single-Chip Cloud Computer(SCC), an experimental processor created by Intel Labs. We developed a skeleton library, rckskel, and implemented amaster-slaves variant of TM-Align to exploit the parallelism offered by the SCC. We evaluated rckAlign on the SCC and compared it with existing TM-Align software running on a dualcore AMD CPU (2.4 GHz) and on a single-core Intel P54CPentium CPU (800 MHz). We observed an 11-fold speedup relatively to the former and a 44-fold speedup relatively to the latter. A key aspect of the performance of rckAlign on the SCC, is the almost linear speedup achieved with the number of SCC cores used as slaves. The method presented can easily be applied to other PSC algorithms and extended to running multiple PSC algorithms within the same SCC chip. © 2013 IEEE.

关键词： parallel algorithms

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Symmetric comparison-based fault diagnosis of multiprocessor and distributed systems using nonlinear support vector machines

Symmetric comparison-based fault diagnosis of multiprocessor...

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2013 IEEE 37th Annual Computer Software and Applications Conference, COMPSAC 2013

作者： Elhadef, Mourad College of Engineering and Computer Science Abu-Dhabi University PO.Box 59911 Abu-Dhabi United Arab Emirates

ISBN: (纸本)9780769549798

In this paper, the problem of identifying the set of permanent faulty nodes using partial syndromes, i.e., when not all the comparison outcomes are available prior to initiating the diagnosis phase, is considered. A new diagnosis approach, using nonlinear support vector machines (SVMs), is described. We consider the symmetric comparison diagnosis model which assumes that nodes are assigned a set of tasks and their outcomes are compared, and that at most t nodes can fail simultaneously. Based on the agreements and disagreements among the nodes' outputs, the diagnosis algorithm must identify all faulty nodes. The new nonlinear SVM-based fault identification algorithm is first trained using various syndromes with known fault sets. Then, it is extensively tested using randomly generated diagnosable systems of different sizes and under various fault scenarios. Simulations showed that the nonlinear SVM-based diagnosis performed efficiently, i.e. the diagnosis algorithm correctly identified almost all the faulty nodes even when at most half of the comparison outcomes are missing. In addition, results from the thorough simulation study demonstrate the effectiveness of the nonlinear SVM-based fault identification algorithm, in terms of diagnosis correctness, latency, and scalability. © 2013 IEEE.

关键词： Fault tolerance

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On partitioning and reordering problems in a hierarchically parallel hybrid linear solver

On partitioning and reordering problems in a hierarchically ...

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2013 IEEE 37th Annual Computer Software and Applications Conference, COMPSAC 2013

作者： Yamazaki, Ichitaro Li, Xiaoye S. Rouet, Francois-Henry Ucar, Bora Electrical Engineering and Computer Science Department University of Tennessee Knoxville United States Computational Research Division Lawrence Berkeley National Laboratory United States ENSEEIHT-IRIT Lawrence Berkeley National Laboratory United States CNRS and LIP UMR CNRS-ENS-INRIA-UCBL Lyon France

ISBN: (纸本)9780769549798

PDSLin is a general-purpose algebraic parallel hybrid (direct/iterative) linear solver based on the Schur complement method. The most challenging step of the solver is the computation of a preconditioner based on the global Schur complement. Efficient parallel computation of the preconditioner gives rise to partitioning problems with sophisticated constraints and objectives. In this paper, we identify two such problems and propose hyper graph partitioning methods to address them. The first problem is to balance the work loads associated with different sub domains to compute the preconditioner. We first formulate an objective function and a set of constraints to model the preconditioner computation time. Then, to address these complex constraints, we propose a recursive hyper graph bisection method. The second problem is to improve the data locality during the parallel solution of a sparse triangular system with multiple sparse right-hand sides. We carefully analyze the objective function and show that it can be well approximated by a standard hyper graph partitioning method. Moreover, an ordering compatible with a post ordering of the sub domain elimination tree is shown to be very effective in preserving locality. To evaluate the two proposed methods in practice, we present experimental results using linear systems arising from some applications of our interest. first, we show that in comparison to a commonly-used nested graph dissection method, the proposed recursive hyper graph partitioning method reduces the preconditioner construction time, especially when the number of sub domains is moderate. This is the desired result since PDSLin is based on a two-level parallelization to keep the number of sub domains small by assigning multiple processors to each sub domain. We also show that our second proposed hyper graph method improves the data locality during the sparse triangular solution and reduces the solution time. Moreover, we show that partitioning time can be

关键词： Linear systems

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Reducing false transactional conflicts with speculative sub-blocking state-An empirical study for ASF transactional memory system

Reducing false transactional conflicts with speculative sub-...

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2013 IEEE 37th Annual Computer Software and Applications Conference, COMPSAC 2013

作者： Nai, Lifeng Lee, Hsien-Hsin S. School of Electrical and Computer Engineering Georgia Institute of Technology United States

ISBN: (纸本)9780769549798

Conflict detection and resolution are among the most fundamental issues in transactional memory systems. Hardware transactional memory (HTM) systems such as AMD's Advanced Synchronization Facility (ASF) employ inherent cache coherence protocol messages to perform conflict detection among transactions. Such an implementation has the advantage of design simplicity, nonetheless, it also generates false transactional conflicts due to false sharing within cache lines, unnecessarily reducing the overall performance. In this work, we first investigated the behavior of false transactional conflicts under the AMD's ASF system. It is found that false conflicts showed rather stable pattern within each cache line that subsequently inspired our false transactional conflict reduction technique using our proposed speculative sub-blocking state. By adding an extra speculative state for each cache line's sub-block, we can maintain conflict detection at the granularity of sub-blocks while keeping the original cache coherence protocol intact. The overall design is simple and highly implementable for achieving a high-efficiency HTM system with minimum impact in hardware. We evaluated our proposed technique using PTLsim-ASF and compared it with a baseline ASF HTM system and an ideal system with no false transactional conflict. Our results showed that the proposed lightweight technique can avoid false conflicts effectively and efficiently. With four sub-blocks in a cache line, our technique can eliminate 56.4% false transactional conflicts and 31.3% of all transactional conflicts on average, which approaches the performance of an ideal system. © 2013 IEEE.

关键词： parallel programming

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Introducing a Data Sliding Mechanism for Cooperative Caching in Manycore Architectures

Introducing a Data Sliding Mechanism for Cooperative Caching...

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IEEE international symposium on parallel and distributed Processing Workshops and Phd Forum (IPDPSW)

作者： Safae Dahmani Loïc Cudennec Guy Gogniat Lab-STICC Laboratory University of Bretagne Sud Lorient France CEA LIST Embedded Real Time Systems Laboratory Gif-sur-Yvette France

ISBN: (纸本)9781479913725

In future micro-architectures, the increase of the number of cores and wire network complexity is leading to several performance degradation. These platforms are intended to process large amount of data. One of the biggest challenges for systems scalability is actually the memory wall: the memory latency is hardly increasing compared to technology expectations. Recent works explore potential software and hardware solutions mainly based on different caching schemes for addressing off-chip access issues. In this paper, we propose a new cooperative caching method improving the cache miss rate for many core micro-architectures. The work is motivated by some limitations of recent adaptive cooperative caching proposals. Elastic Cooperative caching (ECC), is a dynamic memory partitioning mechanism that allows sharing cache across cooperative nodes according to the application behavior. However, it is mainly limited with cache eviction rate in case of highly stressed neighborhood. Another system, the adaptive Set-Granular Cooperative Caching (ASCC), is based on finer set-based mechanisms for a better adaptability. However, heavy localized cache loads are not efficiently managed. In such a context, we propose a cooperative caching strategy that consists in sliding data through closer neighbors. When a cache receives a storing request of a neighbor's private block, it spills the least recently used private data to a close neighbor. Thus, solicited saturated nodes slide local blocks to their respective neighbors to always provide free cache space. We also propose a new Priority-based Data Replacement policy to decide efficiently which blocks should be spilled, and a new mechanism to choose host destination called Best Neighbor selector. The first analytic performance evaluation shows that the proposed cache management policies reduce by half the average global communication rate. As frequent accesses are focused in the neighboring zones, it efficiently improves on-Chip traffic

关键词： Cooperative caching Radiation detectors Protocols System-on-chip Context Large Hadron Collider distributed databases

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