17,435 research outputs found

    The Parallelism Motifs of Genomic Data Analysis

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    Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing

    Distributed-Memory Breadth-First Search on Massive Graphs

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    This chapter studies the problem of traversing large graphs using the breadth-first search order on distributed-memory supercomputers. We consider both the traditional level-synchronous top-down algorithm as well as the recently discovered direction optimizing algorithm. We analyze the performance and scalability trade-offs in using different local data structures such as CSR and DCSC, enabling in-node multithreading, and graph decompositions such as 1D and 2D decomposition.Comment: arXiv admin note: text overlap with arXiv:1104.451

    Recent Advances in Graph Partitioning

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    We survey recent trends in practical algorithms for balanced graph partitioning together with applications and future research directions

    An efficient multi-core implementation of a novel HSS-structured multifrontal solver using randomized sampling

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    We present a sparse linear system solver that is based on a multifrontal variant of Gaussian elimination, and exploits low-rank approximation of the resulting dense frontal matrices. We use hierarchically semiseparable (HSS) matrices, which have low-rank off-diagonal blocks, to approximate the frontal matrices. For HSS matrix construction, a randomized sampling algorithm is used together with interpolative decompositions. The combination of the randomized compression with a fast ULV HSS factorization leads to a solver with lower computational complexity than the standard multifrontal method for many applications, resulting in speedups up to 7 fold for problems in our test suite. The implementation targets many-core systems by using task parallelism with dynamic runtime scheduling. Numerical experiments show performance improvements over state-of-the-art sparse direct solvers. The implementation achieves high performance and good scalability on a range of modern shared memory parallel systems, including the Intel Xeon Phi (MIC). The code is part of a software package called STRUMPACK -- STRUctured Matrices PACKage, which also has a distributed memory component for dense rank-structured matrices

    Some Pattern Recognition Challenges in Data-Intensive Astronomy

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    We review some of the recent developments and challenges posed by the data analysis in modern digital sky surveys, which are representative of the information-rich astronomy in the context of Virtual Observatory. Illustrative examples include the problems of an automated star-galaxy classification in complex and heterogeneous panoramic imaging data sets, and an automated, iterative, dynamical classification of transient events detected in synoptic sky surveys. These problems offer good opportunities for productive collaborations between astronomers and applied computer scientists and statisticians, and are representative of the kind of challenges now present in all data-intensive fields. We discuss briefly some emergent types of scalable scientific data analysis systems with a broad applicability.Comment: 8 pages, compressed pdf file, figures downgraded in quality in order to match the arXiv size limi
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