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Exploration of de Bruijn graph filtering for de novo assembly using GraphLab 31

Exploration of de Bruijn graph filtering for <i>de novo</i> ...

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31st IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPS)

作者： Collet, Julien Sassolas, Tanguy Lhuillier, Yves Sirdey, Renaud Carlier, Jacques CEA LIST F-91191 Gif Sur Yvette France Univ Technol Compiegne Heudiasyc F-60203 Compiegne France

ISBN: (纸本)9780769561493

The emergence of next generation DNA sequencers has raised interest in short read de novo assembly of whole genomes. Though numerous frameworks were developed in the field, the presence of errors in reads as well as the increasing size of datasets call for scalable preprocessing methods for noise filtering. In this paper we present a filtering algorithm that targets determination of valid k-mers in a de Bruijn graph built from short reads. Such preprocessing will help increase accuracy and reduce memory footprint in further assembly procedures by removing erroneous k-mers from the datasets at an early stage. The algorithm leverages GraphLab, a scalable graph processing framework not previously used in traditional assembly toolchains. The accuracy of the algorithm was evaluated with synthetic datasets exhibiting various error rates and proven to be able to determine large parts of de Bruijn graphs on datasets with error level greater than real-life datasets. The implementation is executed on a distributed cluster and a study of its scalability and operating performances is conducted and exhibits interesting scaling properties, hence demonstrating the relevance of GraphLab in such a context.

关键词： De novo assembly De Bruijn Graphs libraries and programming environments Parallel and distributed computing Big Data and Data Analytics GraphLab

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Leveraging Distributed GraphLab for Program Trace Analysis 14

Leveraging Distributed GraphLab for Program Trace Analysis

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International Workshop on Parallel Optimization using/for Multi and Many-Core High Performance Computing (POMCO) in conjunction with 14th International Conference on High Performance Computing and Simulation (HPCS)

作者： Collet, Julien Sassolas, Tanguy Lhuillier, Yves Sirdey, Renaud Carlier, Jacques CEA LIST F-91191 Gif Sur Yvette France Univ Technol Compiegne Heudiasyc F-60203 Compiegne France

ISBN: (纸本)9781509020881

Graph-mining is a class of data-mining problems where programs involve the processing of data modeled as graphs. These applications often exhibit irregular and data-dependent communication patterns, hampering parallelization opportunities on distributed architectures. Many tools and frameworks were created for the scalable processing of graphs but their comparison is non-trivial on distributed architectures as there is no efficiency metrics with respect to distributed resource usage. Considering an in-house use-case, program trace analysis for parallelization optimizations, we study the benefits and limits of a graph-processing framework for a tangible application. The algorithm was implemented using GraphLab and executed on a humble 7-node commodity cluster with input instances up to 40 million vertices and 50 million edges. We propose in this paper an in-depth analysis of the GraphLab system to evaluate its performance and scalability in the context of program trace analysis. The analysis is driven both by traditional and domain-specific metrics and contributes to a better understanding of the system behavior.

关键词： libraries and programming environments Software Monitoring and Measurements Big Data and Data Analytics

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A Selective and Incremental Backup Scheme for Task Pools 16

A Selective and Incremental Backup Scheme for Task Pools

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International Conference on High Performance Computing & Simulation (HPCS)

作者： Fohry, Claudia Posner, Jonas Reitz, Lukas Univ Kassel Res Grp Programming Languages Methodol Kassel Germany

ISBN: (纸本)9781538678794

Checkpointing is a common approach to prevent loss of a program's state after permanent node failures. When it is performed on application-level, less data need to be saved. This paper suggests an uncoordinated application-level check-pointing technique for task pools. It selectively and incrementally saves only those tasks that have stayed in the pool during some period of time and that have not been saved before. The checkpoints are held in a resilient in-memory data store. Our technique applies to any task pool variant in which workers operate at the top of local pools, and work stealing operates at the bottom. Furthermore, the tasks must be free of side effects, and the final result must be calculated by reduction from individual task results. We implemented the technique for the lifeline-based global load balancing variant of task pools. This variant couples random victim selection with an overlay graph for termination detection. A fault-tolerant realization already exists in the form of a Java library, called JFT_GLB. It uses the APGAS and Hazelcast libraries underneath. Our implementation modifies JFT_GLB by replacing its nonselective checkpointing scheme with our new one. In experiments, we compared the overhead of the new scheme to that of JFT_GLB, with UTS, BC and two synthetic benchmarks. The new scheme required slightly more running time when local pools were small, and paid off otherwise.

关键词： Algorithms Reliable Parallel, and Distributed, Algorithms, Algorithms Fault Tolerance and Resilience in HPC Systems, Algorithms Load Balancing and Sharing, Software and Middleware in HPC Systems libraries and programming environments

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programming for malleability with hybrid MPI-2 and OpenMP -: Experiences with a simulation program for global water prognosis

Programming for malleability with hybrid MPI-2 and OpenMP -:...

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20th European Conference on Modelling and Simulation

作者： Leopold, Claudia Suess, Michael Breitbart, Jens Univ Kassel Res Grp Programming Languages Methodol Wilhelmshoher Allee 73 D-34121 Kassel Germany

ISBN: (纸本)0955301807

This paper reports on our experiences in parallelizing WatcrGAP, an originally sequential C++ program for global assessment and prognosis of water availability. The parallel program runs on a heterogeneous SMP cluster and combines different parallel programming paradigms: First, at its outer level, it uses master/slave communication implemented with MPI. Second, within the slave processes, multiple threads are spawned by OpenMP directives to exploit data parallelism. Time measurements show that the hybrid scheme pays off. It adapts to the heterogeneity of the cluster by using multiple threads only for the largest tasks and mapping these to multiprocessor nodes. Third, the program is malleable, which has been accomplished with the dynamic process management facilities of MPI-2, based on the MPICH2 implementation. In particular, it is possible to increase the number of processes while the program is running. Malleability is an important feature in both batch systems and grid environments. We discuss the support that MPI-2 provides for malleability.

关键词： paralielization of simulation libraries and programming environments message passing

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Analyzing the Impact of programming Models for Efficient Communication Overlap in High-Speed Networks

Analyzing the Impact of Programming Models for Efficient Com...

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International Conference on High Performance Computing & Simulation (HPCS)

作者： Utrera, Gladys Gil, Marisa Martorell, Xavier Univ Politecn Cataluna BarcelonaTECH Barcelona Spain

ISBN: (纸本)9781479953134

Exascale applications for civil engineering, simulations and other fields related with current research make intensive use of large sparse matrices. A characteristic of these matrices is the difficulty of balancing communication and computation, so that even when these two phases are overlapped the application does not achieve a good overall scalability, but instead suffers from a loss of performance. Some proposals have been presented in order to diminish this drawback, based on the hybrid use of programming models, using MPI as the communication basis and threads for computation -mainly OpenMP, but also Cilk, CUDA or OpenCL, to adapt to new heterogeneous platforms. In this work, we evaluate the impact of providing task-based parallelism instead of fork-join parallelism. As regards communication, the appearance of faster networks with specific optimizations and internal protocol characteristics makes it appealing to analyze and evaluate the influence of these networks on performance execution. We evaluate our results on two different communication networks: 10Gigabit Ethernet and Infiniband. For our evaluations we run the miniFE miniapplication of the Mantevo suite benchmark, in a homogeneous supercomputer platform based on Intel SandyBridge processors. Experimental results show how the network behavior can affect performance and how it can be managed via task-based models: from a hybrid MPI/OpenMP version that overlaps communication and computation, our taskbased proposal MPI/OmpSs obtains up to 60% improvement.

关键词： scalable computing high performance interconnection networks Message passing libraries and programming environments

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Extending OmpSs to Support Data Analytics Workload 15

Extending OmpSs to Support Data Analytics Workload

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15th International Conference on High Performance Computing & Simulation (HPCS)

作者： Maronas, Marcos BSC Barcelona Spain

ISBN: (纸本)9781538632505

In the era of big data, new scientific applications such as those used in astronomy [1] are emerging and challenging High Performance Computing (HPC) systems and software. Traditionally, HPC applications were compute-bounded, with a light use of the I/O capabilites at the start and end of the execution. In contrast, emergent applications present data- intensive behaviors arising several new challenges to be faced by hardware and software.

关键词： Big Data and Data Analytics Data Intensive Supercomputing libraries and programming environments Fault Tolerance and Resiliency in HPC Systems

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