the increasing number of sequenced organisms has opened new possibilities for the computational discovery of cis-regulatory elements ('motifs') based on phylogenetic footprinting. Word-based, exhaustive approa...
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ISBN:
(数字)9783642551956
ISBN:
(纸本)9783642551956
the increasing number of sequenced organisms has opened new possibilities for the computational discovery of cis-regulatory elements ('motifs') based on phylogenetic footprinting. Word-based, exhaustive approaches are among the best performing algorithms, however, they pose significant computational challenges as the number of candidate motifs to evaluate is very high. In this contribution, we describe a parallel, distributed-memory framework for de novo comparative motif discovery. Within this framework, two approaches for phylogenetic footprinting are implemented: an alignment-based and an alignment-free method. the framework is able to statistically evaluate the conservation of motifs in a search space containing over 160 million candidate motifs using a distributed-memory cluster with 200 CPU cores in a few hours. Software available from http://***/blsspeller/
the paper presents Comcute which is a novel multi-level implementation of the volunteer based computing paradigm. Comcute was designed to let users donate the computing power of their PCs in a simplified manner, requi...
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ISBN:
(纸本)9783642552243
the paper presents Comcute which is a novel multi-level implementation of the volunteer based computing paradigm. Comcute was designed to let users donate the computing power of their PCs in a simplified manner, requiring only pointing their web browser at a specific web address and clicking a mouse. the server side appoints several servers to be in charge of execution of particular tasks. thanks to that the system can survive failures of individual computers and allow definition of redundancy of desired order. On the client side, computations are executed within web browsers using technologies such as Java, JavaScript, Adobe Flash etc. without the need for installation of additional software. this paper presents results of scalability experiments carried on the Comcute system.
Hardware Accelerators are playing increasingly important roles in achieving desired performance from desktop to cluster computing. While General Purpose computing on Graphics Processing Units (GPGPU) technologies have...
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ISBN:
(纸本)9781479941162
Hardware Accelerators are playing increasingly important roles in achieving desired performance from desktop to cluster computing. While General Purpose computing on Graphics Processing Units (GPGPU) technologies have been widely applied to computing intensive applications, there is relatively little work on using GPUs and GPU-accelerated clusters for data intensive computingthat typically involves significant irregular data accesses. In this study, we report our designs and implementations of a popular geospatial operation called Zonal Histogramming on Nvidia GPUs. Given a zonal dataset in the form of a collection of polygons and a geospatial raster that can be considered as a 2D grid, for each polygon, Zonal Histogramming computes a histogram of the values of raster cells that fall within the polygon. Our experiments on 3000+ US counties (polygons) over 20+ billion NASA Shuttle Radar Topography Mission (SRTM) 30 meter resolution Digital Elevation Model (DEM) raster cells have shown that, an impressive 46 seconds end-to-end runtime can be achieved using a single Nvidia GTX Titan GPU device. the runtime is further reduced to similar to 10 seconds using 8 nodes on ORNL's Titan GPU-accelerated cluster. the desired high performance opens many possibilities for large-scale geospatial computingthat is important for environmental and climate research.
Verifiable secret sharing (VSS) is a fundamental tool of threshold cryptography and distributedcomputing. A number of VSS schemes for sharing a secret that is an element of a finite field, either on threshold access ...
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Location-based applications (LBAs) like geo-social networks, points of interest finders, and real-time traffic monitoring applications have entered people's daily life. Advanced LBAs rely on location services (LSs...
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ISBN:
(纸本)9783319115689
Location-based applications (LBAs) like geo-social networks, points of interest finders, and real-time traffic monitoring applications have entered people's daily life. Advanced LBAs rely on location services (LSs) managing movement trajectories of multiple users in a scalable fashion. However, exposing trajectory information raises user privacy concerns, in particular if LSs are non-trusted. For instance, an attacker compromising an LS can use the retrieved user trajectory for stalking, mugging, or to trace user movement. To limit the misuse of trajectory data, we present a new approach for the secure management of trajectories on non-trusted servers. Instead of providing the complete trajectory of a user to a single LS, we split up the trajectory into a set of fragments and distribute the fragments among LSs of different providers. By distributing fragments, we avoid a single point of failure in case of compromised LSs, while different LBAs can still reconstruct the trajectory based on user-defined access rights. In our evaluation, we show the effectiveness of our approach by using real world trajectories and realistic attackers using map knowledge and statistical information to predict and reconstruct the user's movement.
Selection algorithms find the kth smallest element from a set of elements. Although there are optimal parallel selection algorithms available for theoretical machines, these algorithms are not only difficult to implem...
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ISBN:
(纸本)9783642552243
Selection algorithms find the kth smallest element from a set of elements. Although there are optimal parallel selection algorithms available for theoretical machines, these algorithms are not only difficult to implement but also inefficient in practice. Consequently, scalable applications can only use few special cases such as minimum and maximum, where efficient implementations exist. To overcome such limitations, we propose a general parallel selection algorithm that scales even on today's largest supercomputers. Our approach is based on an efficient, unbiased median approximation method, recently introduced as median-of-3 reduction, and Hoare's sequential QuickSelect idea from 1961. the resulting algorithm scales with a time complexity of O(log(2) n) for n distributed elements while needing only O(1) space. Furthermore, we prove it to be a practical solution by explaining implementation details and showing performance results for up to 458, 752 processor cores.
We present FooPar, an extension for highly efficient parallelcomputing in the multi-paradigm programming language Scala. Scala offers concise and clean syntax and integrates functional programming features. Our frame...
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ISBN:
(数字)9783642551956
ISBN:
(纸本)9783642551956
We present FooPar, an extension for highly efficient parallelcomputing in the multi-paradigm programming language Scala. Scala offers concise and clean syntax and integrates functional programming features. Our framework FooPar combines these features withparallelcomputing techniques. FooPar is designed to be modular and supports easy access to different communication backends for distributed memory architectures as well as high performance math libraries. In this article we use it to parallelize matrix-matrix multiplication and show its scalability by a isoefficiency analysis. In addition, results based on a empirical analysis on two supercomputers are given. We achieve close-to-optimal performance wrt. theoretical peak performance. Based on this result we conclude that FooPar allows programmers to fully access Scalas design features without suffering from performance drops when compared to implementations purely based on C and MPI.
this book constitutes the thoroughly refereed post-conference proceedings of the 9thinternationalconference on Large-Scale Scientific Computations, LSSC 2013, held in Sozopol, Bulgaria, in June 2013. the 74 revised ...
ISBN:
(纸本)9783662438817
this book constitutes the thoroughly refereed post-conference proceedings of the 9thinternationalconference on Large-Scale Scientific Computations, LSSC 2013, held in Sozopol, Bulgaria, in June 2013. the 74 revised full papers presented together with 5 plenary and invited papers were carefully reviewed and selected from numerous submissions. the papers are organized in topical sections on numerical modeling of fluids and structures; control and uncertain systems; Monte Carlo methods: theory, applications and distributedcomputing; theoretical and algorithmic advances in transport problems; applications of metaheuristics to large-scale problems; modeling and numerical simulation of processes in highly heterogeneous media; large-scale models: numerical methods, parallel computations and applications; numerical solvers on many-core systems; cloud and grid computing for resource-intensive scientific applications.
the amount of data generated by traditional business activities, has resulted data warehouses with a size up to petabytes. the ability to analyze this torrent of data will become the basis of competition and growth fo...
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ISBN:
(纸本)9781479979783
the amount of data generated by traditional business activities, has resulted data warehouses with a size up to petabytes. the ability to analyze this torrent of data will become the basis of competition and growth for individual firms by ever-narrower segmentation of customers, improvement of decision-making and unearth valuable insights that would otherwise remain hidden. For this purpose, the large size of data to be processed requires the use of high-performance analytical systems running on distributed environments. Because the data is so big it affects the types of algorithms we are willing to consider. then standard analytics algorithms need to be adapted to take advantage of cloud computing models which provide scalability and flexibility. this work illustrates an implementation of a parallel version of the multiple linear regression. It can extract coefficients from large amounts of data, based on MapReduce Framework with large scale. parallel processing of multiple linear regression will be based on the QR decomposition and the ordinary least squares method adapted to Map Reduce. Our platform in deployed on Cloud Amazon EMR. Experimental results demonstrate that the our parallel version of the multiple linear regression can efficiently handle very large datasets on commodity hardware with a good performance on different evaluation criterions, including number, size and structure of machines in the cluster.
the problem of providing quality of service (QoS) guarantees is studied in many areas of information technologies. For network services three attributes are directly related to everyday perception of the QoS by the en...
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ISBN:
(纸本)9783642552243
the problem of providing quality of service (QoS) guarantees is studied in many areas of information technologies. For network services three attributes are directly related to everyday perception of the QoS by the end user: availability, usability, and performance. the paper focuses on performance issues of service delivery with use of virtualization of services and processing resources. there are presented general issues of efficient service delivery, and proposed solutions with different formulation of guaranties for service processing. the best effort and SLA-based approaches are considered. the selected aspects of utilizing processing resources virtualization are also discussed.
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