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A parallel approximation hitting set algorithm for gene expression analysis

A parallel approximation hitting set algorithm for gene expr...

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International symposium on computer architecture and high performance computing (SBAC-PAD)

作者： D.P. Ruchkys S.W. Song Instituto de Matemaática e Estatiística Departmento de Cieência da Computacaão Universidade de Saão Paulo Sao Paulo Brazil

With the recent DNA-microarray technology, it is possible to measure the expression levels of thousands of genes simultaneously in the same experiment. A genetic network is a model that describes how the expression level of each gene is affected by the expression levels of other genes in the network. Given the results of an experiment with n genes and m measures over time (m << n), we consider the problem of finding a subset of genes (k genes, where k < < n) that explain the expression level of a given target gene under study. We consider the coarse-grained multicomputer (CGM) model, with p processors. In this paper we first present a sequential approximation algorithm of O(m/sup 4/n) time and O(m/sup 2/n) space. the main result is a new parallel approximation algorithm that determines the k genes in O(m/sup 4/n/p) local computing time plus O(k) communication rounds, and with space requirement of O(m/sup 2/n/p). the p factor in the parallel time and space complexities indicates a good parallelization. We also show preliminary promising experimental results on a Beowulf machine. To our knowledge there are no CGM algorithms for the problem considered in this paper.

关键词： Approximation algorithms Gene expression Algorithm design and analysis Genetics User-generated content Time measurement Space technology DNA computing Monitoring computer networks

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Parallel out-of-core matrix inversion

Parallel out-of-core matrix inversion

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International symposium on Parallel and Distributed Processing (IPDPS)

作者： E. Caron G. Utard Laboratoire de lľInformatique du Parallélisme École Normale Supérieure de Lyon INRIA-Project ReMaP Lyon France

this paper presents a parallel out-of-core algorithm to invert huge dense matrices, that is matrices larger than the available physical memory by one or more orders of magnitude. Preliminary performance results are shown for a commodity cluster. An accurate prediction performance model of the algorithm is given. thanks to the prediction model, optimizations that avoid the overhead of the out-of-core algorithm are derived. performance of the optimized algorithm using O(N) memory size are similar to the performance of the best known parallel in-core algorithm using O(N 2 ) memory size (where N is the matrix order). there is no memory restriction for inversion of huge matrices!

关键词： Clustering algorithms Matrix decomposition Predictive models Matrices Concurrent computing Gas insulated transmission lines computer applications Parallel processing Linear systems Electromagnetic scattering

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Design and evaluation of data access prediction strategies in SDSM systems

Design and evaluation of data access prediction strategies i...

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International symposium on computer architecture and high performance computing (SBAC-PAD)

作者： E.J. Pineschi M.C.S. de Castro C.L. de Amorim COPPE System Engineering Federal University of Rio de Janeiro Brazil Rio de Janeiro State University Rio de Janeiro Brazil

Software Distributed Shared Memory (SDSM) systems provide the shared memory abstraction on top of a message passing hardware, simplifying application programming in these architectures. However, some memory references exhibit long latencies due to remotely cached data. In order to hide this latency, many techniques that propagate data speculatively were developed. this requires that the data access behavior of the applications be determined. Traditionally, many of these techniques were directed at specific data sharing patterns such as producer-consumer and migratory. In this paper, we propose and evaluate generic data access prediction techniques for SDSM systems. By generic we mean.: that our strategies don't try to detect specific sharing patterns known a priori. the prediction strategies proposed can be divided into two classes: local information predictors (LIP), that are guided only by local information in each processor and global information predictors (GIP) that use the data access pattern of all processors in order to make predictions. Our experimental result show that techniques within both classes can attain high hit ratios in most of the applications evaluated. Overall, the results allow us to conclude that the prediction strategies for data accesses we propose can contribute to increase the performance of current page-based SDSMs significantly.

关键词： Programming profession Adaptive systems Message passing Application software computer architecture Delay Personal communication networks Costs Access protocols Systems engineering and theory

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Generalized multipartitioning for multi-dimensional arrays

Generalized multipartitioning for multi-dimensional arrays

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International symposium on Parallel and Distributed Processing (IPDPS)

作者： A. Darte D. Chavarria-Miranda R. Fowler J. Mellor-Crummey LIP Lyon France C. S. Dept. MS-132 Rice University Houston TX USA

Multipartitioning is a strategy for parallelizing computations that require solving 1D recurrences along each dimension of a multi-dimensional array. Previous techniques for multipartitioning yielded efficient parallelizations over 3D domains only when the number of processors was a perfect square. this paper considers the general problem of computing multipartitionings for d-dimensional data volumes on an arbitrary number of processors. We describe an algorithm that computes an optimal multipartitioning on to all of the processors for this general case. Finally, we describe how we extended Rice University's dHPF (data-parallel high performance Fortran) compiler to generate code that exploits generalized multipartitioning and show that the compiler's generated code for the NAS (Numerical Aerospace Simulation) SP (Scalar Pentadiagonal) computational fluid dynamics benchmark achieves scalable high performance.

关键词： Concurrent computing Tiles Parallel processing Contracts Pipelines Distributed computing Slabs Computational fluid dynamics Partial differential equations Navier-Stokes equations

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Fine-grain access control for securing shared resources in computational grids

Fine-grain access control for securing shared resources in c...

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International symposium on Parallel and Distributed Processing (IPDPS)

作者： A.R. Butt S. Adabala N.H. Kapadia R. Figueiredo J.A.B. Fortes School of ECE Pirdue University West Lafayette IN USA School of-ECE Purdue University W Lafayette IN Department of ECE Northwestern University Evanston IL USA Dept. of ECE University of Florida Gainesville FL

Computational grids provide computing power by sharing resources across administrative domains. this sharing, coupled with the need to execute untrusted code from arbitrary users, introduces security hazards. this paper addresses the security implications of making a computing resource available to untrusted applications via computational grids. It highlights the problems and limitations of current grid environments and proposes a technique that employs run-time monitoring and a restricted shell. the technique can be used for setting up an execution environment that supports the full legitimate use allowed by the security policy of a shared resource. performance analysis shows up to 2.14 times execution overhead improvement for shell-based applications. the approach proves effective and provides a substrate for hybrid techniques that combine static and dynamic mechanisms to minimize monitoring overheads.

关键词： Access control Grid computing Security Monitoring Runtime environment Hazards computer applications performance analysis Authorization World Wide Web

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Using kernel couplings to predict parallel application performance

Using kernel couplings to predict parallel application perfo...

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International symposium on high performance Distributed computing

作者： V. Taylor Xingfu Wu J. Geisler R. Stevens Department of Electrical and Computer Engineering Northwestern University Evanston IL USA Mathematics and Computer Science Division Argonne National Laboratory Argonne IL USA

performance models provide significant insight into the performance relationships between an application and the system used for execution. the major obstacle to developing performance models is the lack of knowledge about the performance relationships between the different functions that compose an application. this paper addresses the issue by using a coupling parameter, which quantifies the interaction between kernels, to develop performance predictions. the results, using three NAS parallel application benchmarks, indicate that the predictions using the coupling parameter were greatly improved over a traditional technique of summing the execution times of the individual kernels in an application. In one case the coupling predictor had less than 1% relative error in contrast the summation methodology that had over 20% relative error. Further, as the problem size and number of processors scale, the coupling values go through a finite number of major value changes that is dependent on the memory subsystem of the processor architecture.

关键词： Kernel Analytical models Predictive models Application software performance analysis Algebra Mathematics computer science Laboratories Mathematical model

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WDM optical interconnect architectures under two connection models

WDM optical interconnect architectures under two connection ...

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IEEE symposium on high performance Interconnects

作者： Yuanyuan Yang Jianchao Wang Department of Electrical & Computer Engineering State University of New York Stony Brook NY USA Data Treasury Corporation Melville NY USA

ISBN: (纸本)0769516505

Optical communication, in particular, the wavelength-division multiplexing (WDM) technique, has become a promising networking choice to meet ever-increasing demands on bandwidth. We consider cost-effective architecture designs of WDM optical interconnects for current and future generation parallel and distributed computing and communication systems. We first categorize WDM optical interconnects into two different connection models based on their intended applications: the wavelength-based model and the fiber-link-based model. Most existing WDM optical interconnect architectures belong to the first category. However, in this paper we show that for applications that use the fiber-link-based model, network cost can be significantly reduced. We then present such a minimum cost architecture design for WDM optical interconnects under the fiber-link-based model. We also generalize the idea used in this design to WDM optical interconnects under the wavelength-based model, and obtain a new architecture design which can trade-off the cost of wavelength converters with the number of crosspoints in this type of WDM optical interconnect.

关键词： Wavelength division multiplexing Optical interconnections Optical design Optical wavelength conversion Optical fiber communication Costs Bandwidth computer architecture Distributed computing high speed optical techniques

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Grid-based knowledge discovery services for high throughput informatics 02

Grid-based knowledge discovery services for high throughput ...

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International symposium on high performance Distributed computing

作者： M. Ghanem Y. Guo A. Rowe P. Wendel Imperial College of Science Technology and Medicine London UK

ISBN: (纸本)9780769516868

Discovery Net is an application layer for providing grid-based knowledge discovery services. these services allow scientists to create and manage complex knowledge discovery workflows that integrate data and analysis routines provided as remote services. they also allow scientists to store, share and execute these workflows as well as publish them as new services. Discovery Net provides a higher level of abstraction of the Grid for knowledge discovery activities, thus separating the end-users from resource management issues already handled by existing and emerging standards.

关键词： throughput Data analysis Knowledge management Resource management Remote sensing Prototypes Data mining computer architecture Biomedical informatics Educational institutions

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Issues concerning Linux clustering: cluster management and application porting

Issues concerning Linux clustering: cluster management and a...

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International symposium on Parallel and Distributed Processing (IPDPS)

作者： J. Harr G. Denault Linux NetworX

Linux clusters have become the high performance compute (HPC) engine of choice for many industries seeking raw number crunching power with greater flexibility, reliability, scalability and price/performance over traditional supercomputers. Early adopters of the technology viewed the task of setting up an efficient and powerful Linux cluster system as a challenge, and typically have had access to a dedicated administration staff to ensure cluster stability. In today's competitive environment, organizations must focus on their core competencies instead of spending valuable resources integrating, configuring and managing such systems. this being the case, cluster management is a top issue concerning the future adoption of the technology. As cluster systems scale from dozens, to hundreds, and even to thousands of processors, management becomes exponentially complex, and can be a daunting challenge for any organization. Keeping software up to date, monitoring hardware and software status, and even performing routine maintenance requires significant effort. To alleviate these efforts, administrators need to identify cluster management tools to help them gain control of cluster administration. the goal of any organization and administrator is to dedicate resources to computational processing - not system management. that is why Linux NetworX developed a suite of software and hardware tools to help alleviate cluster management issues. Linux NetworX is also developing application porting programs so both commercial general purpose and captive code applications can be used ported to the Linux platform and therefore take advantage of the benefits of Linux clustering.

关键词： Linux Resource management Power system management Software maintenance Software performance Hardware Application software high performance computing Engines computer industry

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performance characterization of a molecular dynamics code on PC clusters: is there any easy parallelism in CHARMM?

Performance characterization of a molecular dynamics code on...

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International symposium on Parallel and Distributed Processing (IPDPS)

作者： M. Taufer E. Perathoner A. Cavalli A. Caflisch T. Stricker Department of Computer Science ETH Zurich Zentrum Zurich Switzerland Dipartimento di Elettronica ed Informatica Università degli Studi di Padova Padova Italy Department of Biochemistry University of Zurich Zurich Switzerland

the molecular dynamics code CHARMM is a popular research tool for computational biology. An increasing number of researchers are currently looking for affordable and adequate platforms to execute CHARMM or similar codes. To address this need, we analyze the resource requirements of a CHARMM molecular dynamics simulation on PC clusters with a particle mesh Ewald (PME) treatment of long range electrostatics, and investigate the scalability of the short-range interactions and PME separately. We look at the workload characterization and the performance gain of CHARMM with different network technologies and different software infrastructures and show that the performance depends more on the software infrastructures than on the hardware components. In the present study, powerful communication systems like Myrinet deliver performance that comes close to the MPP supercomputers of the past decade, but improved scalability can also be achieved with better communication system software like SCore without the additional hardware cost. the experimental method of workload characterization presented can be easily applied to other codes. the detailed performance figures of the breakdown of the calculation into computation, communication and synchronization allow one to derive good estimates about the benefits of moving applications to novel computing platforms such as widely distributed computers (grid).

关键词： Distributed computing Grid computing Scalability Software performance Hardware Computational biology Electrostatic analysis Biological system modeling Computational modeling Analytical models

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