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IEEE International Conference on Cluster Computing

作者： Jan C. Kässens Jorge González-Domínguez Lars Wienbrandt Bertil Schmidt Department of Computer Science Christian-Albrechts-University of Kiel Johannes Gutenberg Universitat Mainz Mainz Rheinland-Pfalz DE Parallel and Distributed Architecturess Group Johannes Gutenberg University-Mainz

Modern genotyping technologies are able to obtain up to a few million genetic markers (such as SNPs) of an individual within a few minutes of time. Detecting epistasis, such as SNP-SNP interactions, in Genome-Wide Association Studies is an important but time-consuming operation since statistical computations have to be performed for each pair of measured markers. Therefore, a variety of HPC architectures have been used to accelerate these studies. In this work we present a parallel approach for multi-core clusters, which is implemented with UPC++ and takes advantage of the features available in the Partitioned Global Address Space and Object Oriented Programming models. Our solution is based on a well-known regression model (used by the popular BOOST tool) to test SNP-pairs interactions. Experimental results show that UPC++ is suitable for parallelizing data-intensive bioinformatics applications on clusters. For instance, it reduces the time to analyze a real-world dataset with more than 500,000 SNPs and 5,000 individuals from several days when using a single core to less than one minute using 512 nodes (12,288 cores) of a Cray XC30 supercomputer.

关键词： Object oriented modeling Electronics packaging Bioinformatics Genetics Computational modeling Diseases Optimization

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The Role of Inference in the Anonymization of Medical Records

The Role of Inference in the Anonymization of Medical Record...

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Annual IEEE Symposium on computer-Based Medical systems

作者： Athanasios Zigomitros Agusti Solanas Constantinos Patsakis Department of Informatics University of Piraeus Greece Smart Health Research Group Universitat Rovira i Virgili Tarragona Spain Distributed Systems Group School of Computer Science and Statistics Dublin Ireland

The quality of life has been significantly improved and one of the main reasons is the medical advances of the past decades. Nevertheless, to further advance the research and services in the field, practitioners, researchers and health organizations should share more information. While this need is indisputable, the sensitivity of the information demands that it is preprocessed, so that the published data are anonym zed and individuals cannot be identified. The scope of this work is to highlight the difficulties in providing automated anonymization approaches for medical records without consulting experts in the field. One of the major problems that is going to be highlighted is that Quasi-Identifiers (QI) are not independent. It is well known that combinations of QIs can be used to infer other relevant information. Nevertheless, this work tries to exploit the other way of information flow, we show how sensitive attributes can be exploited to derive information about the QIs, leading to many privacy hazards for the patients whose records are shared. To this extent, we illustrate some relevant examples and discuss probable counter-measures.

关键词： Diseases Cancer Heart Stomach Privacy Databases Lattices

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LSB and DCT steganographic detection using compressive sensing

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Journal of Information Hiding and Multimedia Signal Processing 2014年第1期5卷 20-32页

作者： Patsakis, Constantinos Aroukatos, Nikolaos G. Distributed Systems Group School of Computer Science and Statistics Trinity College College Green Dublin 2 Ireland Department of Informatics University of Piraeus 80 Karaoli and Dimitriou str 18534 Piraeus Greece

During the last years, a large number of information in digital form has been exchanged all over the world. Several techniques have been developed in order to protect the users' privacy of digital content. Steganography is one of them. Its use dates back for many centuries, yet it has been used profoundly in the last decades, as the proper mathematical background has been developed along with the need of the music and film industries. One aspect of this development is the use of DRM (Digital Right Management) as the main method of protecting digital assets. This work presents two new detection methods of steganographic content through the use of compressive sensing. The first method is a probabilistic filter that can increase the probability of detecting steganographic content in images, in case where the LSB method is used. The second one helps identifying the original from stego images when DCT steganography is used, after applying a filter with compressive sensing technique. © 2014.

关键词： Steganography

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Balancing CPU-GPU Collaborative High-Order CFD Simulations on the Tianhe-1A Supercomputer

Balancing CPU-GPU Collaborative High-Order CFD Simulations o...

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International Symposium on parallel and distributed Processing (IPDPS)

作者： Chuanfu Xu Lilun Zhang Xiaogang Deng Jianbin Fang Guangxue Wang Wei Cao Yonggang Che Yongxian Wang Wei Liu College of Computer Science National University of Defense Technology Changsha P.R. China parallel and Distributed Systems Group Delft University of Technology Delft The Netherlands State Key Laboratory of Aerodynamics Mianyang P.R. China National University of Defense Technology Changsha Hunan CN

ISBN: (纸本)9781479938018

HOSTA is an in-house high-order CFD software that can simulate complex flows with complex geometries. Large scale high-order CFD simulations using HOSTA require massive HPC resources, thus motivating us to port it onto modern GPU accelerated supercomputers like Tianhe-1A. To achieve a greater speedup and fully tap the potential of Tianhe-1A, we collaborate CPU and GPU for HOSTA instead of using a naive GPU-only approach. We present multiple novel techniques to balance the loads between the store-poor GPU and the store-rich CPU, and overlap the collaborative computation and communication as far as possible. Taking CPU and GPU load balance into account, we improve the maximum simulation problem size per Tianhe-1A node for HOSTA by 2.3X, meanwhile the collaborative approach can improve the performance by around 45% compared to the GPU-only approach. Scalability tests show that HOSTA can achieve a parallel efficiency of above 60% on 1024 Tianhe-1A nodes. With our method, we have successfully simulated China's large civil airplane configuration C919 containing 150M grid cells. To our best knowledge, this is the first paper that reports a CPUGPU collaborative high-order accurate aerodynamic simulation result with such a complex grid geometry.

关键词： Graphics processing units Kernel Collaboration Computational fluid dynamics Computational modeling Memory management Performance evaluation

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Opportunities and pitfalls of multi-core scaling using hardware transaction memory 13

Opportunities and pitfalls of multi-core scaling using hardw...

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4th Asia-Pacific Workshop on systems, APSys 2013

作者： Wang, Zhaoguo Qian, Hao Chen, Haibo Li, Jinyang School of Computer Science Fudan University China Institute of Parallel and Distributed Systems Shanghai Jiao Tong University China Department of Computer Science New York University United States

ISBN: (纸本)9781450323161

Hardware transactional memory, which holds the promise to simplify and scale up multicore synchronization, has recently become available in main stream processors in the form of Intel's restricted transactional memory (RTM). Will RTM be a panacea for multicore scaling? This paper tries to shed some light on this question by studying the performance scalability of a concurrent skip list using competing synchronization techniques, including fine-grained locking, lock-free and RTM (using both Intel's RTM emulator and a real RTM machine). Our experience suggests that RTM indeed simplifies the implementation, however, a lot of care must be taken to get good performance. Specifically, to avoid excessive aborts due to RTM capacity miss or conflicts, programmers should move memory allocation/deallocation out of RTM region, tuning fallback functions, and use compiler optimization. Copyright 2013 ACM.

关键词： Storage allocation (computer)

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Supporting environmental modelling with Taverna workflows, web services and desktop grid technology 7

Supporting environmental modelling with Taverna workflows, w...

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7th International Congress on Environmental Modelling and Software, iEMSs 2014

作者： Horváth, Ferenc Ittzés, Péter Ittzés, Dóra Barcza, Zoltán Dobor, Laura Hidy, Dóra Marosi, Attila Hardisty, Alex Institute of Ecology and Botany Centre for Ecological Research Hungarian Academy of Sciences Alkotmány u. 2-4. Vácrátót2163 Hungary Department of Meteorology Eötvös Loránd University Pázmány sétány 1/A Budapest1117 Hungary Institute of Botany and Ecophysiology Szent Istvan University Páter K. u.1. Gödöllo2100 Hungary Laboratory of Parallel and Distributed Systems Institute for Computer Science and Control Hungarian Academy of Sciences P.O. Box 63 Budapest1518 Hungary School of Computer Science and Informatics Cardiff University Queen's Buildings 5 The Parade Roath CardiffCF24 3AA United Kingdom

Ecosystem functioning, climate change, and multiple interactions among biogeochemical cycles, climate system, site conditions and land use options are leading-edge topics in recent environmental modelling. Terrestrial ecosystem models are widely used to support carbon sequestration and ecosystem studies under various ecological circumstances. Our team uses the Biome-BGC model (Numerical Terradynamic Simulation group, University of Montana), and develops an improved model version of it, called Biome-BGC MuSo. Both the original and the improved model estimate the ecosystem scale storage and fluxes of energy, carbon, nitrogen and water, controlled by various physical and biological processes on a daily time-scale. Web services were also developed and integrated with parallel processing desktop grid technology. Taverna workflow management system was used to build up and carry out elaborated workflows like seamless data flow to model simulation, Monte Carlo experiment, model sensitivity analysis, model-data fusion, estimation of ecosystem service indicators or extensive spatial modelling. Straightforward management of complex data analysis tasks, organized into appropriately documented, shared and reusable scientific workflows enables researchers to carry out detailed and scientifically challenging 'in silico' experiments and applications that could open new directions in ecosystem research and in a broader sense it supports progress in environmental modelling. The workflow approach built upon these web services allows even the most complicated computations to be initiated without the need of programming skills and deep understanding of model structure and initialization. The developments enable a wider array of scientists to perform ecosystem scale simulations, and to perform analyses not previously possible due to high complexity and computational demand.

关键词： Web services

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Real-Time Environmental Monitoring for Cloud-Based Hydrogeological Modeling with HydroGeoSphere

Real-Time Environmental Monitoring for Cloud-Based Hydrogeol...

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IEEE International Conference on High Performance Computing and Communications (HPCC)

作者： Andrei Lapin Eryk Schiller Peter Kropf Oliver Schilling Philip Brunner Almerima Jamakovic Kapic Torsten Braun Sergio Maffioletti Computer Science Department (IIUN) Université de Neuchâtel Neuchâtel Switzerland Centre for Hydrogeology and Geothermics (CHYN) Université de Neuchâtel Neuchâtel Switzerland Universitat Bern Bern BE CH Communication and Distributed Systems Group (CDS) Universität Bern Bern Switzerland Universitat Zurich Zurich ZH CH

This paper describes an architecture for real-time environmental modeling. It consists of a wireless mesh network equipped with sensors and a cloud-based infrastructure to perform real-time environmental simulations using a physics-based model combined with an Ensemble Kalman Filter. The purpose of the system is to optimize groundwater abstraction close to a river. These initial studies demonstrate that the cloud infrastructure can simultaneously compute a large number of simulations, thus allowing for the implementation of Ensemble Kalman Filters in real-time.

关键词： Computational modeling Sensors Real-time systems Data models Predictive models Wireless sensor networks computer architecture

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A search-based approach for architectural design of feedback control concerns in Self-Adaptive systems

A search-based approach for architectural design of feedback...

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2013 IEEE 7th International Conference on Self-Adaptive and Self-Organizing systems, SASO 2013

作者： Andrade, Sandro S. De A. Macedo, Raimundo Jose GSORT Distributed Systems Group Federal Institute of Education Science and Technology of Bahia Salvador-Ba Brazil Department of Computer Science Federal University of Bahia Salvador-Ba Brazil

ISBN: (纸本)9780769551296

A number of approaches for endowing systems with self-Adaptive behavior have been proposed over the past years. Among such efforts, architecture-centric solutions with explicit representation of feedback loops have currently been advocated as a promising research landscape. Although noteworthy results have been achieved on some fronts, the lack of systematic representations of architectural knowledge and effective support for well-informed trade-off decisions still poses significant challenges when designing modern self-Adaptive systems. In this paper, we present a systematic and flexible representation of design dimensions related to feedback control concerns, a set of metrics which estimate quality attributes of resulting automated designs, and a search-based approach to find out a set of Pareto-optimal candidate architectures. The proposed approach has been fully implemented in a supporting tool and a case study with a self-Adaptive cloud computing environment has been undertaken. The results indicate that our approach effectively captures the most prominent degrees of freedom when designing self-Adaptive systems, helps to elicit effective subtle designs, and provides useful support for early analysis of trade-off decisions. © 2013 IEEE.

关键词： Economic and social effects

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Performance analysis of computational approaches to solve Multiple Sequence Alignment

Performance analysis of computational approaches to solve Mu...

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作者： Montañola, Alberto Roig, Concepció Guirado, Fernando Hernández, Porfidio Notredame, Cedric Distributed Computing Group Computer Science and Industrial Engineering Department Universitat de Lleida Lleida Spain Computer Architecture and Operating Systems Department Universitat Autònoma de Barcelona Cerdanyola del Vallès Spain Barcelona Spain

In the biotechnology field, the deployment of the Multiple Sequence Alignment (MSA) problem, which is a high performance computing demanding process, is one of the new challenges to address on the new parallel systems. The aim of this problem is to find similar regions on biological sequences. Furthermore, the goal of MSA applications is to align as much sequences as possible with a level of quality that makes the alignment biologically meaningful. An efficiency study of different MSA implementations, based on T-Coffee (one of the most used MSA aligners), has been performed in order to find new optimizations that may improve the average execution time on multi-core systems. We found that the current parallel implementations have some performance issues, affecting negatively the scalability of the process. Finally, the proposed implementation based on the usage of threads in conjunction with a message-passing library is presented, with the aim to optimize the execution of the MSA problem in multi-core-based clusters. © 2012 Springer science+Business Media, LLC.

关键词： Message passing

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Approximating the geographical area of a wireless ad-hoc network

Approximating the geographical area of a wireless ad-hoc net...

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IEEE International Conference on Wireless and Mobile Computing, Networking And Communications (WiMob)

作者： Joanna Geibig Bratislav Milic Department of Parallel and Distributed Systems Zuse Institute Berlin Germany Department of Computer Science Humboldt University of Berlin Germany

Wireless ad-hoc networks are typically deployed in a decentralized way, without an authority that determines the location of nodes or the time they join the network. Additionally, existing nodes may fail during network lifetime. Consequently, the geographical span (area) of the network is irregular and unknown. However, if known, this information can be used to improve efficiency of many wireless applications; in some existing applications this information is necessary for their operation in the real use cases. For this purpose, we propose a distributed algorithm that determines the geographical network area. It is the first algorithm that simultaneously discovers network border, approximates the network area with a data structure of a constant size, and disseminates this information to all network nodes. Our algorithm uses only the nodes' local information, has a constant computational complexity and is resilient to link unreliability. The algorithm is evaluated by simulation on realistic network topologies of different sizes. The simulations demonstrate that the algorithm has high accuracy in its estimation of the network area, scales well with the number of nodes, and that it creates a low communication overhead.

关键词： Decision support systems Conferences Mobile communication Wireless communication Handheld computers

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