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An Optimized Reconfigurable System for computing the Phylogenetic Likelihood Function on DNA Data

An Optimized Reconfigurable System for Computing the Phyloge...

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

作者： Simon A. Berger Nikolaos Alachiotis Alexandros Stamatakis Exelixis Laboratory Scientific Computing Group Heidelberg Institute for Theoretical Studies Heidelberg Germany

The Phylogenetic Likelihood Function (PLF) is an important statistical function for evaluating phylogenetic trees. To this end, the PLF is the computational kernel of all state-of-the-art likelihood-based phylogenetic inference programs. Typically, it accounts for more than 85% of total execution time in such programs. We present a substantially improved hardware architecture for computing the PLF based on previous experiences with implementing the PLF on reconfigurable logic. Our new design is optimized for computing the PLF on four-state (DNA) input data. It is also adapted to the computational requirements of real-world tree inference programs and completely independent of the specific tree search algorithm at hand. Furthermore, we describe how our architecture can be modified and adapted to handle general n-state data, such as protein (20 states) or RNA secondary structure data (6, 7, or 16 states, depending on the model). Finally, we designed an interface mechanism such that our PLF hardware architecture can interact with the widely-used phylogenetic inference tool RAxML. We deploy FPGA technology to verify the correctness of the architecture and to evaluate performance.

关键词： Vectors Phylogeny Field programmable gate arrays Vegetation Computer architecture DNA Pipelines

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A Fault-Tolerant distributed Solution for the parallel Gaussian Reduction of Huge Arrays

A Fault-Tolerant Distributed Solution for the Parallel Gauss...

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international symposium on Symbolic and Numeric Algorithms for Scientific computing (SYNASC)

作者： Adrian Mocanu Nicolae Tapus Department of Computer Science POLITEHNICA University of Bucharest Romania

Solving a linear system of equations is a common task performed for most of the scientific experiments. Everyday, these applications increase their demands, pushing the computational capacity to the limits. At a certain point, our systems, running common algorithms, become unable to process such massive amounts of information. The paper analyses and modifies the standard Gaussian reduction so that a huge array may be handled by almost any distributed system. Moreover, the paper focuses on providing a decent level of fault tolerance in order to comply with a real, heterogeneous distributed system and on becoming a solution for sensitive applications.

关键词： Peer-to-peer computing Fault tolerance Fault tolerant systems Equations Computer architecture Monitoring Graphics processing units

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Multi-core Spanning Forest Algorithms using the Disjoint-set Data Structure

Multi-core Spanning Forest Algorithms using the Disjoint-set...

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international symposium on parallel and distributed Processing (IPDPS)

作者： Md. Mostofa Ali Patwary Peder Refsnes Fredrik Manne EECS Department Northwestern University Evanston IL USA Department of Informatics University of Bergen Bergen Norway

ISBN: (纸本)9781467309752

We present new multi-core algorithms for computing spanning forests and connected components of large sparse graphs. The algorithms are based on the use of the disjoint-set data structure. When compared with the previous best algorithms for these problems our algorithms are appealing for several reasons: Extensive experiments using up to 40 threads on several different types of graphs show that they scale better. Also, the new algorithms do not make use of any hardware specific routines, and thus are highly portable. Finally, the algorithms are quite simple and easy to implement.

关键词： Vegetation Partitioning algorithms Computers parallel algorithms Heuristic algorithms Instruction sets

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Evaluating the Performance of a parallel Multiobjective Artificial Bee Colony Algorithm for Inferring Phylogenies on Multicore Architectures

Evaluating the Performance of a Parallel Multiobjective Arti...

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international symposium on parallel and distributed Processing with Applications, ISPA

作者： Sergio Santander-Jiménez Miguel A. Vega-Rodríguez Juan A. Gómez-Pulido Juan M. S'nchez-Pérez University of Extremadura Department of Technologies of Computers and Communications ARCO Research Group. Escuela Politecnica Campus Universitario s/n Cáceres SPAIN Universidad de Extremadura Caceres Extremadura ES

A wide variety of optimization problems requires the combination of Bioinspired and parallel computing to address the complexity needed to get optimal solutions in reduced times. The multicore era allows the researcher to exploit modern arqitectures to resolve these NP-Hard problems. Inferring phylogenetic trees which describe a hypothesis of the evolution of species is a well-known example of this kind of problems. As the space of possible tree topologies increases exponentially with the number of species, exhaustive searches cannot be applied. Also, additional difficulties arise when we must consider simultaneously multiple optimality measures to resolve the problem. In this paper, we report a performance study on multicore machines of a parallel multiobjective adaptation of the Artificial Bee Colony algorithm for inferring phylogenies according to the maximum parsimony and maximum likelihood criteria. Experimental results reveal that our proposal can improve other approaches based on advanced High Performance computing techniques on large data sets.

关键词： Phylogeny parallel processing Algorithm design and analysis Optimization Topology Multicore processing Vegetation

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Service Datastores in Cloud Governance

Service Datastores in Cloud Governance

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international symposium on parallel and distributed Processing with Applications, ISPA

作者： Adrian Copie Teodor-Florin Fortis Victor Ion Munteanu Viorel Negru Faculty of Mathematics and Informatics Department of Computer Science West University of Timişoara Timisoara Romania

A direct consequence of adopting Cloud computing is the creation of new marketplaces for small and medium sized enterprises (SMEs). Having a strong support offered by Platform as a Service (PaaS) paradigm in terms of automation and management, combined with cloud governance, SMEs have a real chance to get back in competition with the large enterprises. The implementation of Cloud Governance solutions offers the necessary support for storing and manipulating data which is relevant for various aspects of applications, ranging from business to technical support for deployed services. Our paper focuses on analysing and detailing governance specific data stores and the way they are able to provide system-wide services.

关键词： distributed databases Security Monitoring Contracts Publishing Semantics

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Graph Partitioning for Reconfigurable Topology

Graph Partitioning for Reconfigurable Topology

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international symposium on parallel and distributed Processing (IPDPS)

作者： Deepak Ajwani Shoukat Ali John P. Morrison The Centre for Unified Computing University College Cork Cork Ireland Exascale Systems Group IBM Research and Development Laboratory Dublin Ireland

ISBN: (纸本)9781467309752

Optical circuit switches have recently been proposed as a low-cost, low-power and high-bandwidth alternative to electronic switches for the design of high-performance compute clusters. An added advantage of these switches is that they allow for a reconfiguration of the network topology to suit the requirements of the application. To realize the full potential of a high-performance computing system with a reconfigurable interconnect, there is a need to design algorithms for computing a topology that will allow for a high-throughput load distribution, while simultaneously partitioning the computational task graph of the application for the computed topology. In this paper, we propose a new framework that exploits such reconfigurable interconnects to achieve these interdependent goals, i.e., to iteratively co-optimize the network topology configuration, application partitioning and network flow routing to maximize throughput for a given application. We also present a novel way of computing a high-throughput initial topology based on the structural properties of the application to seed our co-optimizing framework. We show the value of our approach on synthetic graphs that emulate the key characteristics of a class of stream computing applications that require high throughput. Our experiments show that the proposed technique is fast and computes high-quality partitions of such graphs for a broad range of hardware parameters that varies the bottleneck from computation to communication.

关键词： Topology Throughput Network topology Routing Optical switches Integrated circuit interconnections Partitioning algorithms

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All-to-all gradecast using coding with byzantine failures

All-to-all gradecast using coding with byzantine failures

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14th international symposium on Stabilization, Safety, and Security of distributed Systems, SSS 2012

作者： Bridgman III, John F. Garg, Vijay K. Parallel and Distributed Systems Lab. Electrical and Computer Engineering University of Texas at Austin Austin TX United States

ISBN: (纸本)9783642335358

This paper presents a method that uses forward error correction codes to minimize the message bit complexity when acquiring consistent global information in the presence of faulty processes. We show a modification to the gradecast algorithm that implements our method. Gradecast, first proposed by Feldman and Micali, is a broadcast algorithm for distributed systems that can handle Byzantine failures. It can be used as a basic building block to solve many important problems in distributed computing in the presence of Byzantine failures, such as agreement, clock synchronization, and approximate agreement. Many of these problems require a step where all processes need to send information to all other processes. We refer to the version of gradecast where all processes broadcast to all other processes as all-to-all gradecast. In a distributed system with n processes, n instances of the original gradecast algorithm to perform all-to-all gradecast has a message bit complexity of O(mn3), where m is the length of the message. In this paper, we present an all-to-all gradecast algorithm that takes O(mtn2) message bits, where t is the maximum number of faulty processes. This is a significant reduction in message bit complexity in real systems where t n. Our all-to-all gradecast algorithm uses coding theory to mask Byzantine failures and has wide applicability in distributed systems. For example, by replacing the original gradecast in the byzantine agreement algorithm proposed by Ben-Or, Dolev and Hoch with O(mtn3) message bit complexity, we get a new byzantine agreement algorithm with O(mt2 n2) message bit complexity. Also, this algorithm can be used with their approximate agreement algorithm to get O(kn2 t) instead of O(kn3) message bit complexity. © 2012 Springer-Verlag.

关键词： distributed computer systems

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SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model

SlimCodeML: An Optimized Version of CodeML for the Branch-Si...

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

作者： Hannes Schabauer Mario Valle Christoph Pacher Heinz Stockinger Alexandros Stamatakis Marc Robinson-Rechavi Ziheng Yang Nicolas Salamin University of Lausanne Department of Ecology and Evolution and SIB Swiss Institute of Bioinformatics (CH) Swiss National Supercomputing Centre Scientific Computing Group (CH) AIT Austrian Institute of Technology Safety & Security Department (AT) SIB Swiss Institute of Bioinformatics Vital-IT Group (CH) Heidelberg Institute for Theoretical Studies Scientific Computing Group (DE) Department of Biology University College London (UK)

CodeML (part of the PAML package) implements a maximum likelihood-based approach to detect positive selection on a specific branch of a given phylogenetic tree. While CodeML is widely used, it is very compute-intensive. We present SlimCodeML, an optimized version of CodeML for the branch-site model. Our performance analysis shows that SlimCodeML substantially outperforms CodeML (up to 9.38 times faster), especially for large-scale genomic analyses.

关键词： Symmetric matrices Phylogeny Computational modeling Matrices Vectors Bioinformatics Genomics

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Large-scale visual data analysis

Large-scale visual data analysis

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international symposium on parallel and distributed Processing (IPDPS)

作者： Chris Johnson Scientific Computing and Imaging Institute University of Utah USA

Summary form only give, as follows. Modern high performance computers have speeds measured in petaflops and handle data set sizes measured in terabytes and petabytes. Although these machines offer enormous potential for solving very large-scale realistic computational problems, their effectiveness will hinge upon the ability of human experts to interact with their simulation results and extract useful information. One of the greatest scientific challenges of the 21st century is to effectively understand and make use of the vast amount of information being produced. Visual data analysis will be among our most important tools in helping to understand such large-scale information. Our research at the Scientific computing and Imaging (SCI) Institute at the University of Utah has focused on innovative, scalable techniques for large-scale 3D visual data analysis. In this talk, I will present state-of-the-art visualization techniques, including scalable visualization algorithms and software, cluster-based visualization methods and innovative visualization techniques applied to problems in computational science, engineering, and medicine. I will conclude with an outline for future high performance visualization research challenges and opportunities.

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HERCULES: A Pattern Driven Code Transformation System

HERCULES: A Pattern Driven Code Transformation System

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

作者： Christos Kartsaklis Oscar Hernandez Chung-Hsing Hsu Thomas Ilsche Wayne Joubert Richard L. Graham Application Performance Tools Group Computing Science and Mathematics Division Oak Ridge National Laboratory Oak Ridge TN USA Scientific Computing Center for Computational Sciences Oak Ridge National Laboratory Oak Ridge TN USA

New parallel computers are emerging, but developing efficient scientific code for them remains difficult. A scientist must manage not only the science-domain complexity but also the performance-optimization complexity. HERCULES is a code transformation system designed to help the scientist to separate the two concerns, which improves code maintenance, and facilitates performance optimization. The system combines three technologies, code patterns, transformation scripts and compiler plugins, to provide the scientist with an environment to quickly implement code transformations that suit his needs. Unlike existing code optimization tools, HERCULES is unique in its focus on user-level accessibility. In this paper we discuss the design, implementation and an initial evaluation of HERCULES.

关键词： Optimization Pattern matching Prototypes Complexity theory Computers Maintenance engineering Syntactics

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