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检索条件"任意字段=6th International Conference on Algorithms and Architectures for Parallel Processing, ICA3PP"

共 292 条记录，以下是111-120 订阅

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the Open Community Runtime on the Intel Knights Landing Architecture 17th

The Open Community Runtime on the Intel Knights Landing Arch...

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

作者： Dokulil, Jiri Benkner, Siegfried Yaghob, Jakub Univ Vienna Fac Comp Sci Vienna Austria Charles Univ Prague Dept Software Engn Prague Czech Republic

ISBN: (纸本)9783319654829;9783319654812

the Intel Xeon Phi Knights Landing manycore processor comes with new interesting features: on-chip high-bandwidth memory and several user-selectable NUMA configurations. In this paper, we look into how these affect applications that target the Open Community Runtime (OCR), an asynchronous tasked-based runtime system for future parallel architectures. We have extended our OCR runtime to make it NUMA aware and to allow it to use the high-bandwidth memory. We have conducted a range of experiments, comparing OpenMP, TBB, our OCR implementation, and the reference OCR implementation on different machine configurations using a memory intensive seismic simulation.

关键词： Open Community Runtime Knights Landing Intel Xeon Phi High-bandwidth memory parallel runtime systems NUMA

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Accelerating Exhaustive Pairwise Metagenomic Comparisons 17th

Accelerating Exhaustive Pairwise Metagenomic Comparisons

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

作者： Perez-Wohlfeil, Esteban Torreno, Oscar Trelles, Oswaldo Univ Malaga Dept Comp Architecture Blvd Louis Pasteur 35 Malaga Spain

ISBN: (纸本)9783319654829;9783319654812

In this manuscript, we present an optimized and parallel version of our previous work IMSAME, an exhaustive gapped aligner for the pairwise and accurate comparison of metagenomes. parallelization strategies are applied to take advantage of modern multiprocessor architectures. In addition, sequential optimizations in CPU time and memory consumption are provided. these algorithmic and computational enhancements enable IMSAME to calculate near optimal alignments which are used to directly assess similarity between metagenomes without requiring reference databases. We show that the overall efficiency of the parallel implementation is superior to 80% while retaining scalability as the number of parallel cores used increases. Moreover, we also show that sequential optimizations yield up to 8x speedup for scenarios with larger data.

关键词： High Performance Computing Pairwise comparison parallel computing Next Generation Sequencing Metagenome comparison

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Power-Performance Evaluation of parallel Multi-objective EEG Feature Selection on CPU-GPU Platforms 17th

Power-Performance Evaluation of Parallel Multi-objective EEG...

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

作者： Jose Escobar, Juan Ortega, Julio Francisco Diaz, Antonio Gonzalez, Jesus Damas, Miguel Univ Granada Dept Comp Architecture & Technol CITIC Granada Spain

ISBN: (纸本)9783319654829;9783319654812

Heterogeneous CPU-GPU platforms include resources to benefit from different kinds of parallelism present in many data mining applications based on evolutionary algorithms that evolve solutions with time-demanding fitness evaluation. this paper describes an evolutionary parallel multi-objective feature selection procedure with subpopulations using two scheduling alternatives for evaluation of individuals according to the number of subpopulations. Evolving subpopulations usually provides good diversity properties and avoids premature convergence in evolutionary algorithms. the proposed procedure has been implemented in OpenMP to distribute dynamically either subpopulations or individuals among devices and OpenCL to evaluate the individuals taking into account the devices characteristics, providing two parallelism levels in CPU and up to three levels in GPUs. Different configurations of the proposed procedure have been evaluated and compared with a master-worker approach considering not only the runtime and achieved speedups but also the energy consumption between both scheduling models.

关键词： Heterogeneous subpopulations scheduling Energy-aware computing EEG classification Multi-objective feature selection GPU

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Configuring Concurrent Computation of Phylogenetic Partial Likelihoods: Accelerating Analyses Using the BEAGLE Library 17th

Configuring Concurrent Computation of Phylogenetic Partial L...

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

作者： Ayres, Daniel L. Cummings, Michael P. Univ Maryland Ctr Bioinformat & Computat Biol College Pk MD 20742 USA

ISBN: (纸本)9783319654829;9783319654812

We describe our approach in augmenting the BEAGLE library for high-performance statistical phylogenetic inference to support concurrent computation of independent partial likelihoods arrays. Our solution involves identifying independent likelihood estimates in analyses of partitioned datasets and in proposed tree topologies, and configuring concurrent computation of these likelihoods via CUDA and opencL frameworks. We evaluate the effect of each increase in concurrency on throughput performance for our partial likelihoods kernel for a four-state nucleotide substitution model on a variety of parallel computing hardware, such as NVIDIA and AMD GPU5, and Intel multicore cPus, observing up to 16-fold speedups over our previous implementation. Finally, we evaluate the effect of these gains on an domain application program, MrBayes. For a partitioned nucleotide-model analysis we observe an average speedup for the overall run time of 2.1-fold over our previous parallel implementation, and 10-fold over the native MrBayes with SSE.

关键词： Bayes methods Biology computing Evolution (biology) Phylogeny Maximum likelihood estimation Multicore processing parallel programming High performance computing

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A Hybrid parallel Search Algorithm for Solving Combinatorial Optimization Problems on Multicore Clusters 17th

A Hybrid Parallel Search Algorithm for Solving Combinatorial...

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

作者： Sanz, Victoria De Giusti, Armando Naiouf, Marcelo Natl Univ La Plata III LIDI Sch Comp Sci La Plata Argentina CIC Buenos Aires DF Argentina Consejo Nacl Invest Cient & Tecn Buenos Aires DF Argentina

ISBN: (纸本)9783319654829;9783319654812

Multicore clusters are widely used to solve combinatorial optimization problems, which require high computing power and a large amount of memory. In this sense, Hash Distributed A* (HDA*) parallelizes A*, a combinatorial optimization algorithm, using the MPI library. HDA* scales well on multicore clusters and on multicore machines. Additionally, there exist several versions of HDA* that were adapted for multicore machines, using the Pthreads library. In this paper, we present Hybrid HDA* (HHDA*), a hybrid parallel search algorithm based on HDA* that combines message-passing (MPI) with shared-memory programming (Pthreads) to better exploit the computing power and memory of multicore clusters. We evaluate the performance and memory consumption of HHDA* on a multicore cluster, using the 15-puzzle as a case study. the results reveal that HHDA* achieves a slightly higher average performance and uses considerably less memory than HDA*. these improvements allowed HHDA* to solve one of the hardest 15-Puzzle instances.

关键词： parallel search algorithms Hybrid programming Multicore cluster Combinatorial optimization problems Hash Distributed A

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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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Pipelining Computation and Optimization Strategies for Scaling GROMACS on the Sunway Many-Core Processor 17th

Pipelining Computation and Optimization Strategies for Scali...

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

作者： Yu, Yang An, Hong Chen, Junshi Liang, Weihao Xu, Qingqing Chen, Yong Univ Sci & Technol China Hefei Anhui Peoples R China Texas Tech Univ Dept Comp Sci Lubbock TX 79409 USA

ISBN: (纸本)9783319654829;9783319654812

the increasing gap between plentiful computing elements and limited memory bandwidth makes it increasingly difficult and sometimes even infeasible for HPC community to port more applications onto many-core processor architectures. the Sunway many-core processor SW26010 used to build the Sunway TaihuLight System contains a total of 260 heterogeneous cores. All these cores can be divided into 4 core groups (CGs). Each CG includes a Management processing Element (MPE) core and 64 Computing processing Elements (CPEs) cores. In this paper, we refactor an important molecular dynamics (MD) application GROMACS on the Sunway Taihulight system. By rewriting the compute-intensive kernel of GROMACS, we exploit a suitable parallelism for CPE cluster and implement pipelining computation between MPE and CPE cluster. Optimization strategies including the efficient use of scratchpad, the software-emulated cache and a hybrid parallel algorithm are adopted to solve the challenging memory bandwidth limitation. When comparing the refactored version using MPE and 64 CPEs with the original ported version using only MPE, we achieve a 16x speedup for the compute-intensive kernel. For simulating a molecule with 3 million atoms, we currently have managed to scale to 798,720 cores. Moreover, we analyze the adaptability of our mapping and optimization strategies for solving the memory bandwidth limitation when refactoring a real-world application on the Sunway heterogeneous many-core processor system.

关键词： Sunway TaihuLight system GROMACS parallel model Performance optimization Bandwidth competition Adaptability

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the Impact of international Inter-City Investment on Enterprises Performance: Pluralistic Interpretation of Geographical Death 17th

The Impact of International Inter-City Investment on Enterpr...

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

作者： Zhan, Yanghao Chen, Yan Zhai, Ruirui Beijing Univ Posts & Telecommun Beijing Peoples R China

ISBN: (纸本)9783319654829;9783319654812

this paper aims to test the impact of inter-city investment on enterprises performance. By using a panel dataset of Chinese firms which have invested in 43 countries and regions over the of 2003-2009 and gravity model, we find that institutional distance is favorable to Chinas outward direct investment, which implies that the Chinese multinationals dont seem willing to enter those countries that have similar institutions with their home country, in this sense, Chinese enterprises outward direct investment can be interpreted as being driven by the motivation of institutional escape. Technology distance displays an Inversed-U shape which suggests some technical distance is the premise for ODI and may reflect the fact of simultaneous existence of both the technology utilization ODI and the technology-seeking ODI of China. Geographical distance has no significant impact on Chinas outward direct investment which supports the proposition of death of distance. these findings point to the importance of going beyond firm boundary to consider various distances between home and host countries in making investment decisions, which not only overcome the defects of the existing studies, but also propose new theoretical explanations for the phenomenon that Chinese enterprises are still capable of ODI even when the ownership advantages are missing. According to the results of this paper, Chinese enterprises should choose to invest in the countries with large institutional distance, small economic and medium technical distance from the home country, and, at the same time, they should not bother geographical distance too much.

关键词： ODI Enterprises performance Geographical distance

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