964 research outputs found
Optimizing the MapReduce Framework on Intel Xeon Phi Coprocessor
With the ease-of-programming, flexibility and yet efficiency, MapReduce has
become one of the most popular frameworks for building big-data applications.
MapReduce was originally designed for distributed-computing, and has been
extended to various architectures, e,g, multi-core CPUs, GPUs and FPGAs. In
this work, we focus on optimizing the MapReduce framework on Xeon Phi, which is
the latest product released by Intel based on the Many Integrated Core
Architecture. To the best of our knowledge, this is the first work to optimize
the MapReduce framework on the Xeon Phi.
In our work, we utilize advanced features of the Xeon Phi to achieve high
performance. In order to take advantage of the SIMD vector processing units, we
propose a vectorization friendly technique for the map phase to assist the
auto-vectorization as well as develop SIMD hash computation algorithms.
Furthermore, we utilize MIMD hyper-threading to pipeline the map and reduce to
improve the resource utilization. We also eliminate multiple local arrays but
use low cost atomic operations on the global array for some applications, which
can improve the thread scalability and data locality due to the coherent L2
caches. Finally, for a given application, our framework can either
automatically detect suitable techniques to apply or provide guideline for
users at compilation time. We conduct comprehensive experiments to benchmark
the Xeon Phi and compare our optimized MapReduce framework with a
state-of-the-art multi-core based MapReduce framework (Phoenix++). By
evaluating six real-world applications, the experimental results show that our
optimized framework is 1.2X to 38X faster than Phoenix++ for various
applications on the Xeon Phi
Counting Triangles in Large Graphs on GPU
The clustering coefficient and the transitivity ratio are concepts often used
in network analysis, which creates a need for fast practical algorithms for
counting triangles in large graphs. Previous research in this area focused on
sequential algorithms, MapReduce parallelization, and fast approximations.
In this paper we propose a parallel triangle counting algorithm for CUDA GPU.
We describe the implementation details necessary to achieve high performance
and present the experimental evaluation of our approach. Our algorithm achieves
8 to 15 times speedup over the CPU implementation and is capable of finding 3.8
billion triangles in an 89 million edges graph in less than 10 seconds on the
Nvidia Tesla C2050 GPU.Comment: 2016 IEEE International Parallel and Distributed Processing Symposium
Workshops (IPDPSW
Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges.
The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data. This in turn requires massive computational resources. Therefore, high performance computing (HPC) platforms are highly needed as well as efficient and scalable algorithms that can take advantage of these platforms. In this paper, we survey the state-of-the-art HPC platforms for big biological data analytics. We first list the characteristics of big biological data and popular computing platforms. Then we provide a taxonomy of different biological data analysis applications and a survey of the way they have been mapped onto various computing platforms. After that, we present a case study to compare the efficiency of different computing platforms for handling the classical biological sequence alignment problem. At last we discuss the open issues in big biological data analytics
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