40224327
Performance and cost effectiveness of a cluster of workstations and MD-GRAPE 2 for MD simulations
Molecular dynamics (MD) simulations are performed on systems of various sizes up to 32 million atoms. Performance is compared between an MD-GRAPE 2 board, specialized hardware optimized for MD, and a general purpose cluster computer utilizing varied numbers of processors for both short- and long-range potentials. While it is possible to outperform a single MD-GRAPE 2 board with a sufficient number of processors, tests verses a local cluster and comparison of original purchase price show the MD-GRAPE 2 board is often cost-effective. Potential-specific considerations are discussed.
16880603
Adaptive Load Balancing for Long-Range MD Simulations in A Distributed Environment
Molecular dynamics, a computationally intensive application is used by researchers in various fields. The inherent parallelism (Plimpton and Hendrickson, 1994) in the computations involved with this application can be exploited in parallel and distributed environments. However, in distributed environments such as the grid (Foster et al., 2001), the available resources, namely the network and computational power, are continually changing with respect to every available node. To optimally utilize these dynamic resources, a scheduler should be able to continually adapt to the changes and suitably vary the load scheduled to every available node. We propose one such scheduling algorithm. The proposed scheduling algorithm builds and continually updates a model of the distributed system, which it then uses to make decisions about how to optimally redistribute the load in the system at every time step of the MD simulation. The scheduling algorithm can additionally handle dynamic changes in the number of nodes available for computation at runtime. We then demonstrate the efficiency of our scheduling algorithm when applied to MD simulations in a distributed environment
26735928
I/O Response Time in a Fault-Tolerant Parallel Virtual File System
A fault tolerant parallel virtual file system is designed and implemented to provide high I/O performance and high reliability. A queuing model is used to analyze in detail the average response time when multiple clients access the system. The results show that I/O response time is with a function of several operational parameters. It decreases with the increase in I/O buffer hit rate for read requests, write buffer size for write requests and number of server nodes in the parallel file system, while higher I/O requests arrival rate increases I/O response time.
8918525
An efficient, low-cost inconsistency detection framework for data and service sharing in an Internet-scale system
In this paper, we argue that a broad range of Internet-scale distributed applications can benefit from an underlying low-cost consistency detection framework that is an alternative to inconsistency avoidance and can detect inconsistency among nodes sharing data or services in a timely manner. This paper first presents an overview of the inconsistency detection framework. Then, it discusses the detailed design of the two-layer inconsistency detection module, the core component of this framework, which can detect inconsistency among nodes in a timely manner. The proposed two-layer inconsistency detection module is evaluated both analytically and via simulations, which shows that this module can significantly reduce the time to detect inconsistency among nodes without adding much maintenance cost. Finally, this paper outlines the possible mechanisms to discern the application semantics and to resolve the detected inconsistencies
1546029
Design and Analysis of Hierarchical Ring Networks for Shared-Memory Multiprocessors
ÐWe study four augmentations of ring networks which are intended to enhance a ring's efficiency as a communication medium significantly, while increasing its structural complexity only modestly. Chordal rings add ashortcuto edges, which can be viewed as chords, to the ring. Express rings are chordal rings whose chords are routed outside the ring. Multirings append subsidiary rings to edges of a ring and, recursively, to edges of appended subrings. Hierarchical ring networks (HRN's) append subsidiary rings to nodes of a ring and, recursively, to nodes of appended subrings. We show that these four modes of augmentation are very closely related: 1) Planar chordal rings, planar express rings, and multirings are topologically equivalent families of networks with the acutwidtho of an express ring translating into the atree deptho of its isomorphic multiring and vice versa. 2) Every depth-d HRN is a spanning subgraph of a depth-2dÿ 1 multiring. 3) Every depth-d multiring M can be embedded into a d-dimensional mesh with dilation 3 in such a way that some node of M resides at a corner of the mesh. 4) Every depth-d HRN H can be embedded into a d-dimensional mesh with dilation 2 in such a way that some node of H resides at a corner of the mesh. In addition to demonstrating that these four augmented ring networks are grid graphs, our embedding results afford us close bounds on how much decrease in diameter is achievable for a given increase in structural complexity for the networks. Specifically, we derive upper and lower bounds on the optimal diameters of N-node depth-d multirings and HRNs that are asymptotically tight for large N and d. Index TermsÐRing networks, chordal rings, express rings, multirings, hierarchical ring networks, grid graphs, graph embedding, diameter trade-offs.
9864742
JOPI: a Java object-passing interface
Recently there has been an increasing interest in developing parallel programming capabilities in Java to harness the vast resources available in clusters, grids and heterogeneous networked systems. In this paper, we introduce a Java object-passing interface (JOPI) library. JOPI provides Java programmers with the necessary functionality to write object-passing parallel programs in distributed heterogeneous systems. JOPI provides an MPI-like interface that can be used to exchange objects among processes. In addition to the well-known benefits of the object-oriented development model, using objects to exchange information in JOPI is advantageous because it facilitates passing complex structures and enables the programmer to isolate the problem space from the parallelization problem. The run-time environment for JOPI is portable, efficient and provides the necessary functionality to deploy and execute parallel Java programs. Experiments were conducted on a cluster system and a collection of heterogeneous platforms to measure JOPI's performance and compare it with MPI. The results show good performance gains using JOPI.
16906364
Scalable and Robust Aggregation Techniques for Extracting Statistical Information in Sensor Networks
Wireless sensor networks have stringent constraints on system resources and data aggregation techniques are critically important. However, accurate data aggregation is difficult due to the variation of sensor readings and due to the frequent communication failures. To address these difficulties, we propose a scalable and robust data aggregation algorithm. The novelty of our work includes two aspects. First, our algorithm exploits the mixture model and the Expectation Maximization (EM) algorithm for parameter estimation. Hence, it captures the effects of aggregation over different scales while keeping the communication cost low. Second, our algorithm exploits loss-tolerant multi-path routing schemes. Hence, it obtains accurate statistical information even in the presence of high link and node failure rates. We demonstrate that our techniques reduce communication cost while retaining the precious statistical information otherwise neglected by other aggregation techniques. Our evaluation shows the proposed techniques are robust against link and node failures, and perform consistently well.
16310485
Stably Computable Properties of Network Graphs
We consider a scenario in which anonymous, finite-state sensing devices are deployed in an ad-hoc communication network of arbitrary size and unknown topology, and explore what properties of the network graph can be stably computed by the devices. We show that they can detect whether the network has degree bounded by a constant d, and, if so, organize a computation that achieves asymptotically optimal linear memory use. We define a model of stabilizing inputs to such devices and show that a large class of predicates of the multiset of final input values are stably computable in any weakly-connected network. We also show that nondeterminism in the transition function does not increase the class of stably computable predicates.
22543009
Self-stabilizing Population Protocols
Self-stabilization in a model of anonymous, asynchronous interacting agents deployed in a network of unknown size is considered. Dijkstra-style round-robin token circulation can be done deterministically with constant space per node in this model. Constant-space protocols are given for leader election in rings, local-addressing in degree-bounded graphs, and establishing consistent global direction in an undirected ring. A protocol to construct a spanning tree in regular graphs using O(logD) memory is also given, where D is the diameter of the graph. A general method for eliminating nondeterministic transitions from the self-stabilizing implementation of a large family of behaviors is used to simplify the constructions, and general conditions under which protocol composition preserves behavior are used in proving their correctness.
2540895
Large margin hidden Markov models for speech recognition
In this paper, motivated by large margin classifiers in machine learning, we propose a novel method to estimate continuous-density hidden Markov model (CDHMM) for speech recognition according to the principle of maximizing the minimum multiclass separation margin. The approach is named large margin HMM. First, we show this type of large margin HMM estimation problem can be formulated as a constrained minimax optimization problem. Second, we propose to solve this constrained minimax optimization problem by using a penalized gradient descent algorithm, where the original objective function, i.e., minimum margin, is approximated by a differentiable function and the constraints are cast as penalty terms in the objective function. The new training method is evaluated in the speaker-independent isolated E-set recognition and the TIDIGITS connected digit string recognition tasks. Experimental results clearly show that the large margin HMMs consistently outperform the conventional HMM training methods. It has been consistently observed that the large margin training method yields significant recognition error rate reduction even on top of some popular discriminative training methods
17152151
Application of fuzzy measures in multi-criteria evaluation in GIS
Multi-criteria evaluation (MCE) is perhaps the most fundamental of decision support operations in geographical information systems (GIS). This paper reviews two main MCE approaches employed in GIS, namely Boolean and Weighted Linear Combination (WLC), and discusses issues and problems associated with both. To resolve the conceptual differences between the two approaches, this paper proposes the application of fuzzy measures, a concept that is broader but that includes fuzzy set membership, and argues that the standardized factors of MCE belong to a general class of fuzzy measures and the more specific instance of fuzzy set membership. This perspective provides a strong theoretical basis for the standardization of factors and their subsequent aggregation. In this context, a new aggregation operator that accommodates and extends the Boolean and WLC approaches is discussed: the Ordered Weighted Average. A case study of industrial allocation in Nakuru, Kenya is employed to illustrate the different approaches.