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SNAP, Small-world Network Analysis and Partitioning: an open-source parallel graph framework for the exploration of large-scale networks

SNAP, Small-world Network Analysis and Partitioning: an open...

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10th Workshop on Advances in parallel and distributed Computational Models/22nd ieee International parallel and distributed processing symposium

作者： Bader, David A. Madduri, Kamesh Georgia Inst Technol Coll Comp Atlanta GA 30332 USA

ISBN: (纸本)9781424416936

We present SNAP (Small-world Network Analysis and Partitioning), an open-source graph framework for exploratory study and partitioning of large-scale networks. To illustrate the capability of SNAP, we discuss the design, implementation, and performance of three novel parallel community detection algorithms that optimize modularity, a popular measure for clustering quality in social network analysis. In order to achieve scalable parallel performance, we exploit typical network characteristics of small-world networks, such as the low graph diameter sparse connectivity, and skewed degree distribution. We conduct an extensive experimental study on real-world graph instances and demonstrate that our parallel schemes, coupled with aggressive algorithm engineering for small world networks, give significant running time improvements over existing modularity-based clustering heuristics, with little or no loss in clustering quality. For instance, our divisive clustering approach based on approximate edge betweenness centrality is more than two orders of magnitude faster than a competing greedy approach, for a variety of large graph instances on the Sun Fire T2000 multicore system. SNAP also contains parallel implementations of fundamental graph-theoretic kernels and topological analysis metrics (e.g., breadth-first search, connected components, vertex and edge centrality) that are optimized for small-world networks. the SNAP framework is extensible;the graph kernels are modular, portable across shared memory multicore and symmetric multiprocessor systems, and simplify the design of high-level domain-specific applications.

关键词： Small-world networks

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parallel, scalable, memory-efficient backtracking for combinatorial modeling of large-scale biological systems

Parallel, scalable, memory-efficient backtracking for combin...

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10th Workshop on Advances in parallel and distributed Computational Models/22nd ieee International parallel and distributed processing symposium

作者： Park, Byung-Hoon Schmidt, Matthew thomas, Kevin Karpinets, Tatiana Samatova, Nagiza F. Oak Ridge Natl Lab Comp Sci & Math Div Oak Ridge TN 37831 USA N Carolina State Univ Comp Sci Dept Raleigh NC 27695 USA

ISBN: (纸本)9781424416936

Data-driven modeling of biological systems such as protein-protein interaction networks is data-intensive and combinatorially challenging. Backtracking can constrain a combinatorial search space. Yet, its recursive nature, exacerbated by dida-intensity, limits its applicability for large-scale systems. parallel, scalable, and memory-efficient backtracking is a promising approach parallel backtracking suffers from unbalanced loads. Load rebalancing via synchronization and data movement is prohibitively expensive. Balancing these discrepancies, while minimizing end-to-end execution time and memory requirements, is desirable. this paper introduces such a framework. Its scalability and efficiency, demonstrated on the maximal clique enumeration problem, are attributed to the proposed: (a) representation of search tree decomposition to enable parallelization;(b) depth-first parallel search to minimize memory requirement;(c) least stringent synchronization to minimize data movement;and (d) on-demand work stealing with stack splitting to minimize processors' idle time. the applications of this framework to real biological problems related to bioethanol production are discussed.

关键词： Biological systems

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An optimal checkpoint/restart model for a large scale High Performance Computing system

An optimal checkpoint/restart model for a large scale High P...

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10th Workshop on Advances in parallel and distributed Computational Models/22nd ieee International parallel and distributed processing symposium

作者： Liu, Yudan Nassar, Raja Leangsuksun, Chokchai (Box) Naksinehaboon, Nichanion Paun, Mihaela Scott, Stephen L. Louisiana Tech Univ Coll Engn & Sci Ruston LA 71270 USA Oak Ridge Natl Lab Comp Sci & Math Div Oak Ridge TN 37831 USA

ISBN: (纸本)9781424416936

the increase in the physical size of High Performance Computing (HPC) platform makes system reliability more challenging. In order to minimize the performance loss (rollback and checkpoint overheads) due to unexpected failures or unnecessary overhead of fault tolerant mechanisms, we present a reliability-aware method for an optimal checkpoint/restart strategy. Our scheme aims at addressing fault tolerance challenge, especially in a large-scale HPC system, by providing optimal checkpoint placement techniques that are derived from the actual system reliability. Unlike existing checkpoint models, which can only handle Poisson failure and a constant checkpoint interval, our model can deal with a varying checkpoint interval and with different failure distributions. In addition, the approach considers optimality for both checkpoint overhead and rollback time. Our validation results suggest a significant improvement over existing techniques.

关键词： large-scale distributed system events log analysis reliability fault-tolerance checkpoint/restart model HPC

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parallel biological sequence alignments on the Cell Broadband Engine

Parallel biological sequence alignments on the Cell Broadban...

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10th Workshop on Advances in parallel and distributed Computational Models/22nd ieee International parallel and distributed processing symposium

作者： Sarje, Abhinav Aluru, Srinivas Iowa State Univ Dept Elect & Comp Engn Ames IA 50011 USA

ISBN: (纸本)9781424416936

Sequence alignment and its many variants are a fundamental tool in computational biology. there is considerable recent interest in using the Cell Broadband Engine, a heterogenous multi-core chip that provides high performance, for biological applications. However, work so far has been limited to computing optimal alignment scores using quadratic space under the basic global/local alignment algorithm. In this paper we present a comprehensive study of developing sequence alignment algorithms on the Cell exploiting its thread and data level parallelism features. First, we develop a Cell implementation that computes optimal alignments and adopts Hirschberg's linear space technique. the former is essential as merely computing optimal alignment scores is not useful while the latter is needed to permit alignments of longer sequences. We then present Cell implementations of two advanced alignment techniques - spliced alignments and syntenic alignments. In a spliced alignment, consecutive non-overlapping portions of a sequence align with ordered non-overlapping, but non-consecutive portions of another sequence. Spliced alignments are useful in aligning mRNA sequences with corresponding genomic sequences to uncover gene structure. Syntenic alignments are used to discover conserved exons and other sequences between long genomic sequences from different organisms. We present experimental results for these three types of alignments on the Cell BE and report speedups of about 4 on six SPUs on the Playstation 3, when compared to the respective best serial algorithms on the Cell BE and the Pentium 4 processor.

关键词： Alignment

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Xen-Based HPC: A parallel I/O Perspective 08

Xen-Based HPC: A Parallel I/O Perspective

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8th ieee International symposium on Cluster Computing and the Grid

作者： Yu, Weikuan Vetter, Jeffrey S. Oak Ridge Natl Lab Oak Ridge TN 37831 USA

ISBN: (纸本)9781424442379

Virtualization using Xen-based virtual machine environment has yet to permeate the field of high performance computing (HPC). One major requirement for HPC is the availability of scalable and high performance I/O. Conventional wisdom suggests that virtualization of system services must lead to degraded performance. In this presentation, we take on a parallel I/O perspective to study the viability of Xen-based HPC for data-intensive programs. We have analyzed the overheads and migration costs for parallel I/O programs in a Xen-based virtual machine cluster. Our analysis covers PVFS-based parallel I/O over two different networking protocols: TCP-based Gigabit Ethernet and VMM-bypass InfiniBand. Our experimental results suggest that network processing in Xen-based virtualization can significantly impact the performance of parallel I/O. By carefully tuning the networking layers, we have demonstrated the following for Xen-based HPC I/O: (1) TCP offloading can help achieve low overhead parallel I/O;(2) parallel reads and writes require different network tuning to achieve good I/O bandwidth;and (3) Xen-based HPC environment can support high performance parallel I/O with both negligible overhead and little migration cost.

关键词： File systems Application software Costs Virtual machining Degradation Application virtualization High performance computing Ethernet networks Concurrent computing Grid computing

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A plug-and-play model for evaluating wavefront computations on parallel architectures

A plug-and-play model for evaluating wavefront computations ...

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10th Workshop on Advances in parallel and distributed Computational Models/22nd ieee International parallel and distributed processing symposium

作者： Mudalige, Gihan R. Vernon, Mary K. Jarvis, Stephen A. Univ Warwick Dept Comp Sci Coventry CV4 7AL W Midlands England Univ Wisconsin Dept Comp Sci Madison WI 53706 USA

ISBN: (纸本)9781424416936

this paper develops a plug-and-play reusable LogGP model that can be used to predict the runtime and scaling behavior of different MPI-based pipelined wavefront applications running on modern parallel platforms with multicore nodes. A key new feature of the model is that it requires only a few simple input parameters to project performance for wavefront codes with different structure to the sweeps in each iteration as well as different behavior during each wavefront computation and/or between iterations. We apply the model to three key benchmark applications that are used in high performance computing procurement, illustrating that the model parameters yield insight into the key differences among the codes. We also develop new, simple and highly accurate models of MPI send, receive, and group communication primitives on the dual-core Cray XT system. We validate the reusable model applied to each benchmark on up to 8192 processors on the XT3/XT4. Results show excellent accuracy for all high performance application and platform configurations that we were able to measure. Finally we use the model to assess application and hardware configurations, develop new metrics for procurement and configuration, identify bottlenecks, and assess new application design modifications that, to our knowledge, have not previously been explored.

关键词： Wavefronts

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Fault Tolerance Management for a Hierarchical GridRPC Middleware 08

Fault Tolerance Management for a Hierarchical GridRPC Middle...

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8th ieee International symposium on Cluster Computing and the Grid

作者： Bouteiller, Aurelien Desprez, Frederic UCBL INRIA CNRS ENS Lyon LIP ENS LyonUMR 5668 F-69364 Lyon 07 France

ISBN: (纸本)9781424442379

the GridRPC model is well suited for high performance computing on grids thanks to efficiently solving most of the issues raised by geographically and administratively split resources. Because of large scale, long range networks and heterogeneity, Grids are extremely prone to failures. GridRPC middleware are usually managing failures by using 1) TCP or other link network layer provided failure detector, 2) automatic checkpoints of sequential jobs and 3) a centralized stable agent to perform scheduling. Most recent developments have provided some new mechanisms like the optimal Chandra & Toueg & Aguillera failure detector, most numerical libraries now providing their own optimized checkpoint routine and distributed scheduling GridRPC architectures. In this paper we aim at adapting to these novelties by providing the first implementation and evaluation in a grid system of the optimal fault detector, a novel and simple checkpoint API allowing to manage both service provided checkpoint and automatic checkpoint (even for parallel services) and a scheduling hierarchy recovery algorithm tolerating several simultaneous failures. All those mechanisms are implemented and evaluated on a real grid in the DIET middleware.

关键词： GridRPC Fault tolerant Failure detector Checkpoint distributed algorithm

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Optimized distributed Data Sharing Substrate in Multi-Core Commodity Clusters: A Comprehensive Study with Applications 08

Optimized Distributed Data Sharing Substrate in Multi-Core C...

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8th ieee International symposium on Cluster Computing and the Grid

作者： Vaidyanathan, K. Lai, P. Narravula, S. Panda, D. K. Ohio State Univ Dept Comp Sci & Engn Columbus OH 43210 USA

ISBN: (纸本)9781424442379

distributed applications tend to have a complex design due to issues such as concurrency, synchronization and communication. Researchers in the past have proposed simpler abstractions to hide these complexities. However, many of the proposed techniques use messaging protocols which incur high overhead and are not very scalable. To address these limitations, in our previous work [20], we proposed an efficient distributed Data Sharing Substrate (DDSS) using the features of high-speed networks. In this paper we propose several design optimizations for DDSS in multi-core systems such as the combination of shared memory and message queues for inter-process communication, dedicated thread for communication progress and for onloading DDSS operations such as get and put. Our micro-benchmark results not only show a very low latency in DDSS operations but also demonstrate the scalability of DDSS with increasing number of processes. Application evaluations with R-Tree and B-Tree query processing and distributed STORM shows an improvement of up to 56%, 45% and 44%, respectively, as compared to traditional implementations. Evaluations with application checkpointing using DDSS demonstrate the scalability with increasing number of checkpointing applications. Further in our evaluations, we demonstrate the portability of DDSS across multiple modem interconnects including InfiniBand and iWARP-capable 10-Gigabit Ethernet networks (applicable for both LAN/WAN environments).

关键词： High-Performance Networks Multi-Core Data-Centers distributed Shared State

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An efficient hybrid peer-to-peer system for distributed data sharing

An efficient hybrid peer-to-peer system for distributed data...

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10th Workshop on Advances in parallel and distributed Computational Models/22nd ieee International parallel and distributed processing symposium

作者： Yang, Min Yang, Yaanyuan SUNY Stony Brook Dept Elect & Comp Engn Stony Brook NY 11794 USA

ISBN: (纸本)9781424416936

Peer-to-peer overlay networks are widely used in distributed systems. Based on whether a regular topology is maintained among peers, peer-to-peer networks can be divided into two categories: structured peer-to-peer networks in which peers are connected by a regular topology, and unstructured peer-to-peer networks in which the topology is arbitrary. Structured peer-to-peer networks usually can provide efficient and accurate services but need to spend a lot of efforts in maintaining the regular topology. On the other hand, unstructured peer-to-peer networks are extremely resilient to the frequent peer joining and leaving but this is usually achieved at the expense of efficiency. the objective of this work is to design a hybrid peer-to-peer system for distributed data sharing which combines the advantages of both types of peer-to-peer networks and minimizes their disadvantages. the proposed hybrid peer-to-peer system is composed of two parts: the first part is a structured core network which forms the backbone of the hybrid system;the second part is multiple unstructured peer-to-peer networks each of which is attached to a node in the core network. the core structured network can narrow down the data lookup within a certain unstructured network accurately, while the unstructured networks provide a low cost mechanism for peers to join or leave the system freely. A data lookup operation first checks the local unstructured network and then the structured network. this two-tier hierarchy can decouple the flexibility of the system from the efficiency of the system. Our simulation results demonstrate that the hybrid peer-to-peer system can utilize both the efficiency of structured peer-to-peer network and the flexibility of the unstructured peer-to-peer network and achieve a good balance between the two types of networks.

关键词： peer-to-peer systems P2P structured peer-to-peer unstructured peer-to-peer hybrid overlay networks.

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Synthesizing Byzantine Fault-Tolerant Grid Application Wrapper Services 08

Synthesizing Byzantine Fault-Tolerant Grid Application Wrapp...

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8th ieee International symposium on Cluster Computing and the Grid

作者： Hofer, Juergen Fahringer, thomas Univ Innsbruck Inst Comp Sci Distributed & Parallel Syst Grp A-6020 Innsbruck Austria

ISBN: (纸本)9781424442379

the Grid is inherently unreliable due to its geographical dispersion, heterogeneity and the involvement of multiple administrative domains. the most general case of failures are so-called Byzantine failures where no assumptions about the behavior of faulty components can be made. In this paper a novel system is described that allows to diagnose and tolerate byzantine faults based on service replication. We suggest, briefly describe and compare two fail-stop and two byzantine fault tolerance algorithms. Given that many scientific larger-scale Grid applications have complex outputs the comparison of replica results as needed to implement byzantine fault tolerance becomes a non-trivial task. therefore we include an automation mechanism based on a generic description language and code generation for this particualar problem. Our approach has been implemented as extension to the Otho Toolkit, a system that synthesizes tailor-made wrapper services for a given application, Grid environment and resource. An analysis of performance and overheads for three real-world applications completes our work.

关键词： Byzantine Fault Tolerance

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