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Massively parallel Sequence Alignment with BLAST through Work Distribution Implemented Using PCJ Library 17th

Massively Parallel Sequence Alignment with BLAST Through Wor...

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17th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Nowicki, Marek Bzhalava, Davit Bala, Piotr Nicolaus Copernicus Univ Fac Math & Comp Sci Chopina 12-18 PL-87100 Torun Poland Karolinska Inst Dept Lab Med F46 S-14186 Stockholm Sweden Univ Warsaw Interdisciplinary Ctr Math & Computat Modelling Pawinskiego 5a PL-02106 Warsaw Poland

ISBN: (纸本)9783319654829;9783319654812

this article presents massively parallel execution of the BLAST algorithm on supercomputers and HPC clusters using thousands of processors. Our work is based on the optimal splitting up the set of queries running with the non-modified NCBI-BLAST package for sequence alignment. the work distribution and search management have been implemented in Java using a PCJ (parallel Computing in Java) library. the PCJ-BLAST package is responsible for reading sequence for comparison, splitting it up and start multiple NCBI-BLAST executables. We also investigated a problem of parallel I/O and thanks to PCJ library we deliver high throughput execution of BLAST. the presented results show that using Java and PCJ library we achieved very good performance and efficiency. In result, we have significantly reduced time required for sequence analysis. We have also proved that PCJ library can be used as an efficient tool for fast development of the scalable applications.

关键词： Sequence alignment NGS Next Generation Sequencing parallel programming Java BLAST NCBI-BLAST PCJ

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On the Use of Binary Trees for DNA Hydroxymethylation Analysis 17th

On the Use of Binary Trees for DNA Hydroxymethylation Analys...

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17th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Gonzalez, Cesar Perez, Mariano Orduna, Juan M. Chaves, Javier Garcia, Ana-Barbara Univ Valencia Dept Informat Avda Univ S-N Valencia 46100 Spain CIBERDEM Carlos III Hlth Inst INCLIVA Hlth Res Inst Avda Menendez Pelayo 4 Accesorio Valencia 46010 Spain

ISBN: (纸本)9783319654829;9783319654812

DNA methylation (mC) and hydroxymethylation (hmC) can have a significant effect on normal human development, health and disease status. Hydroxymethylation studies require specific treatment of DNA, as well as software tools for their analysis. In this paper, we propose a parallel software tool for analyzing the DNA hydroxymethylation data obtained by TAB-seq. the software is based on the use of binary trees for searching the different occurrences of methylation and hydroxymethylation in DNA samples. the binary trees allow to efficiently store and access the information about the methylation of each methylated/hydroxymethylated cytosines in the samples. Evaluation results shows that the performance of the application is only limited by the computer input/output bandwidth, even for the case of very long samples.

关键词： High performance computing DNA hydroxymethylation parallel pipeline

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parallel Multi-objective Optimization for High-Order Epistasis Detection 17th

Parallel Multi-objective Optimization for High-Order Epistas...

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17th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Gallego-Sanchez, Daniel Granado-Criado, Jose M. Santander-Jimenez, Sergio Rubio-Largo, Alvaro Vega-Rodriguez, Miguel A. Univ Extremadura Caceres Spain Univ Lisbon Lisbon Portugal Univ NOVA Lisboa Lisbon Portugal

ISBN: (纸本)9783319654829;9783319654812

Many studies have shown that there is a direct relationship between Single Nucleotide Polymorphisms (SNPs) and the appearance of complex diseases, such as Alzheimer's or Parkinson's. However, recent advances in the Study of the Complete Genome Association indicate that the relationship between SNPs and these diseases goes beyond a simple one-to-one relationship, that is, the appearance of multiple SNPs (epistasis) influences the appearance of these diseases. In this sense, this work proposes the application of the NSGA-II multi-objective algorithm for the detection of epistasis of multiple loci in a database with 31,341 SNPs. Moreover, a parallel study has been performed to reduce the execution time of this problem. Our implementation not only achieves a reasonable good parallel performance and scalability, but also its biological significance overcomes other approaches published in the literature.

关键词： parallelism NSGA-II Epistasis SNP

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the Impact of Panel Factorization on the Gauss-Huard Algorithm for the Solution of Linear Systems on Modern architectures 16th

The Impact of Panel Factorization on the Gauss-Huard Algorit...

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16th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Catalan, Sandra Ezzatti, Pablo Quintana-Orti, Enrique S. Remon, Alfredo Univ Jaime I Dep Ingn & Ciencia Compuatc Castellon de La Plana 12701 Spain Univ Republica Inst Computat Montevideo 11300 Uruguay Max Planck Inst Dynam Complex Tech Syst D-30106 Magdeburg Germany

ISBN: (纸本)9783319495835;9783319495828

the Gauss-Huard algorithm (the GHA) is a specialized version of Gauss-Jordan elimination for the solution of linear systems that, enhanced with column pivoting, exhibits numerical stability and computational cost close to those of the conventional solver based on the LU factorization with row pivoting. Furthermore, the GHA can be formulated as a procedure rich in matrix multiplications, so that high performance can be expected on current architectures with multi-layered memories. Unfortunately, in principle the GHA does not admit the introduction of look-ahead, a technique that has been demonstrated to be rather useful to improve the performance of the LU factorization on multi-threaded platforms with high levels of hardware concurrency. In this paper we analyze the effect of this drawback on the implementation of the GHA on systems accelerated with graphics processing units (GPUs), exposing the roles of the CPU-to-GPU and single precision-to-double precision performance ratios, as well as the contribution from the operations in the algorithm's critical path.

关键词： Linear systems of equations Gauss-Huard algorithm LU factorization Multicore processors Graphics processing units (GPUs) Mixed precision High performance

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parallel Statistical and Machine Learning Methods for Estimation of Physical Load 18th

Parallel Statistical and Machine Learning Methods for Estima...

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18th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Stirenko, Sergii Gang, Peng Zeng, Wei Gordienko, Yuri Alienin, Oleg Rokovyi, Oleksandr Gordienko, Nikita Pavliuchenko, Ivan Rojbi, Anis Natl Tech Univ Ukraine Igor Sikorsky Kyiv Polytech Inst Kiev Ukraine Huizhou Univ Huizhou Peoples R China Univ Paris 08 CHArt Lab Human & Artificial Cognit Paris France

ISBN: (纸本)9783030050511;9783030050504

Several statistical and machine learning methods are proposed to estimate the type and intensity of physical load and accumulated fatigue. they are based on the statistical analysis of accumulated and moving window data subsets with construction of a kurtosis-skewness diagram. this approach was applied to the data gathered by the wearable heart monitor for various types and levels of physical activities, and for people with various physical conditions. the different levels of physical activities, loads, and fitness can be distinguished from the kurtosis-skewness diagram, and their evolution can be monitored. Several metrics for estimation of the instant effect and accumulated effect (physical fatigue) of physical loads were proposed. the data and results presented allow to extend application of these methods for modeling and characterization of complex human activity patterns, for example, to estimate the actual and accumulated physical load and fatigue, model the potential dangerous development, and give cautions and advice in real time.

关键词： Statistical analysis Physiological signals Heart beat Classification Machine learning HCI and human behaviour

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the Co-design of Astrophysical Code for Massively parallel Supercomputers 16th

The Co-design of Astrophysical Code for Massively Parallel S...

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16th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Glinsky, Boris Kulikov, Igor Chernykh, Igor Weins, Dmitry Snytnikov, Alexey Nenashev, Vladislav Andreev, Andrey Egunov, Vitaly Kharkov, Egor Inst Computat Math & Math Geophys SB RAS Lavrentjeva Ave 6 Novosibirsk 630090 Russia Novosibirsk State Tech Univ Novosibirsk 630073 Russia Volgograd State Tech Univ Volgograd 400005 Russia

ISBN: (纸本)9783319499567;9783319499550

the rapid growth of supercomputer technologies became a driver for the development of natural sciences. Most of the discoveries in astronomy, in physics of elementary particles, in the design of new materials in the DNA research are connected with numerical simulation and with supercomputers. Supercomputer simulation became an important tool for the processing of the great volume of the observation and experimental data accumulated by the mankind. Modern scientific challenges put the actuality of the works in computer systems and in the scientific software design to the highest level. the architecture of the future exascale systems is still being discussed. Nevertheless, it is necessary to develop the algorithms and software for such systems right now. It is necessary to develop software that is capable of using tens and hundreds of thousands of processors and of transmitting and storing of large volumes of data. In the present work the technology for the development of such algorithms and software is proposed. As an example of the use of the technology, the process of the software development is considered for some problems of astrophysics.

关键词： Exascale systems Co-design High performance computing Computational astrophysics Physics of plasmas

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TAMM: A New Topology-Aware Mapping Method for parallel Applications on the Tianhe-2A Supercomputer 18th

TAMM: A New Topology-Aware Mapping Method for Parallel Appli...

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18th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Chen, Xinhai Liu, Jie Li, Shengguo Xie, Peizhen Chi, Lihua Wang, Qinglin Natl Univ Def Technol Sci & Technol Parallel & Distributed Proc Lab Changsha 410073 Peoples R China Hunan Inst Traff Engn Inst Adv Sci & Technol Hengyang 421001 Peoples R China

ISBN: (纸本)9783030050511;9783030050504

With the increasing size of high performance computing systems, the expensive communication overhead between processors has become a key factor leading to the performance bottleneck. However, default process-to-processor mapping strategies do not take into account the topology of the interconnection network, and thus the distance spanned by communication messages may be particularly far. In order to enhance the communication locality, we propose a new topology-aware mapping method called TAMM. By generating an accurate description of the communication pattern and network topology, TAMM employs a two-step optimization strategy to obtain an efficient mapping solution for various parallel applications. this strategy first extracts an appropriate subset of all idle computing resources on the underlying system and then constructs an optimized one-to-one mapping with a refined iterative algorithm. Experimental results demonstrate that TAMM can effectively improve the communication performance on the Tianhe-2A supercomputer.

关键词： High performance computing systems Topology-aware mapping Communication pattern Network topology

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vPlacer: A Co-scheduler for Optimizing the Performance of parallel Jobs in Xen 18th

vPlacer: A Co-scheduler for Optimizing the Performance of Pa...

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18th international conference on algorithms and architectures for parallel processing (ica3pp)

作者： Jiang, Peng He, Ligang Ren, Shenyuan Chen, Zhiyan Mao, Rui Univ Warwick Dept Comp Sci Coventry CV4 7ES W Midlands England Shenzhen Univ Coll Comp Sci & Software Engn Shenzhen Peoples R China

ISBN: (纸本)9783030050511;9783030050504

Xen, a popular virtualization platform which enables multiple operating systems sharing one physical host, has been widely used in various fields nowadays. Currently, the existing schedulers of Xen are initially targeting at serial jobs, which achieves a remarkable utilization of computer hardware and impressive overall performance. However, the virtualized systems are expected to accommodate both parallel jobs and serial jobs in practice, and resource contention between virtual machines results in severe performance degradation of the parallel jobs. Moreover, the physical resource is vastly wasted during the communication process due to the ineffective scheduling of parallel jobs. this paper aims to optimize the performance of the parallel jobs in Xen using the co-scheduling mechanism. In this paper, we statistically analyze the process of scheduling parallel jobs in Xen, which points out that the credit scheduler is not capable of properly scheduling a parallel job. Moreover, we propose vPlacer, a conservative co-scheduler to improve the performance of the parallel job in Xen. Our co-scheduler is able to identify the parallel jobs and optimize the scheduling process to satisfy the particularity of the parallel job. the prototype of our vPlacer is implemented, and the experimental results show that the performance of the parallel job is significantly improved and the utilization of the hardware resource is optimized.

关键词： Xen Virtualization parallel job Scheduler

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algorithms and architectures for parallel processing 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： Xian-he Sun Wenyu Qu Ivan Stojmenovic Wanlei Zhou Zhiyang Li Hua Guo Geyong Min Tingting Yang Yulei Wu Lei Liu

ISBN: (数字)9783319111940

ISBN: (纸本)9783319111933

this two volume set LNCS 8630 and 8631 constitutes the proceedings of the 14th international conference on algorithms and architectures for parallel processing, ica3pp 2014, held in Dalian, China, in August 2014. the 70 revised papers presented in the two volumes were selected from 285 submissions. the first volume comprises selected papers of the main conference and papers of the 1st international Workshop on Emerging Topics in Wireless and Mobile Computing, ETWMC 2014, the 5th international Workshop on Intelligent Communication Networks, IntelNet 2014, and the 5th international Workshop on Wireless Networks and Multimedia, WNM 2014. the second volume comprises selected papers of the main conference and papers of the Workshop on Computing, Communication and Control Technologies in Intelligent Transportation System, 3C in ITS 2014, and the Workshop on Security and Privacy in Computer and Network Systems, SPCNS 2014.

关键词： Algorithm Analysis and Problem Complexity Software Engineering Computer Communication Networks Database Management

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algorithms and architectures for parallel processing 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： Xian-he Sun Wenyu Qu Ivan Stojmenovic Wanlei Zhou Zhiyang Li Tingting Yang Hua Guo Geyong Min Yulei Wu Lei Liu

ISBN: (数字)9783319111971

ISBN: (纸本)9783319111964

关键词： Algorithm Analysis and Problem Complexity Software Engineering Computer Communication Networks Database Management

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