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Parallel Access of Out-Of-Core Dense Extendible Arrays

机译:平行访问外核密集的伸长型阵列

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Datasets used in scientific and engineering applications are often modeled as dense multi-dimensional arrays. For very large datasets, the corresponding array models are typically stored out-of-core as array files. The array elements are mapped onto linear consecutive locations that correspond to the linear ordering of the multi-dimensional indices. Two conventional mappings used are the row-major order and the column-major order of multi-dimensional arrays. Such conventional mappings of dense array files highly limit the performance of applications and the extendibility of the dataset. Firstly, an array file that is organized in say row-major order causes applications that subsequently access the data in column-major order, to have abysmal performance. Secondly, any subsequent expansion of the array file is limited to only one dimension. Expansions of such out-of-core conventional arrays along arbitrary dimensions, require storage reorganization that can be very expensive. We present a solution for storing out-of-core dense extendible arrays that resolve the two limitations. The method uses a mapping function F{sub}*(), together with information maintained in axial vectors, to compute the linear address of an extendible array element when passed its k-dimensional index. We also give the inverse function, (F{sub}*){sup}(-1)() for deriving the k-dimensional index when given the linear address. We show how the mapping function, in combination with MPI-IO and a parallel file system, allows for the growth of the extendible array without reorganization and no significant performance degradation of applications accessing elements in any desired order. We give methods for reading and writing sub-arrays into and out of parallel applications that run on a cluster of workstations, The axial-vectors are replicated and maintained in each node that accesses sub-array elements.
机译:科学和工程应用中使用的数据集通常是致密的多维阵列。对于非常大的数据集,相应的阵列模型通常作为数组文件存储超核。阵列元素被映射到对应于多维索引的线性排序的线性连续位置。使用的两个传统映射是线主要顺序和多维阵列的列主要顺序。密集阵列文件的这种传统映射高度限制了应用程序的性能和数据集的可扩展性。首先,以沿着行主要顺序组织的数组文件导致随后以列主要顺序访问数据的应用程序,以具有Abysmal性能。其次,数组文件的任何后续扩展都仅限于一个维度。沿任意维度的这种核心传统阵列的扩展需要可以非常昂贵的存储重组。我们提出了一种用于存储核心密集的延伸阵列的解决方案,该延伸阵列解决了两个限制。该方法使用映射函数f {sub} *()与保持在轴向矢量的信息一起,以在通过其K维索引时计算可扩展阵列元素的线性地址。我们还提供逆函数(f {sub} *){sup}( - 1)(),用于在给定线性地址时导出k维索引。我们展示了如何与MPI-IO和并行文件系统组合的映射函数如何允许扩展阵列的增长而无需重组,并且无法以任何所需顺序访问元素的应用程序的显着性能下降。我们提供读取和写入子阵列的方法,进出在工作站集群上运行的并行应用程序,轴向向量被复制和维护在访问子阵列元素的每个节点中。

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