PEXTA: A Parallel Chunked Extendible Dense Array I/O for global array (GA)
Gideon Nimako, Ekow J. Otoo, Daniel Ohene‐Kwofie · 2013
Over the past decade, I/O is has been a limiting factor for extreme scale parallel computing even though there has been substantial growth in the amount of data produced by parallel scientific applications. The datasets usually grow incrementally to massive sizes of the order of terabytes and petabytes. As such, the storage of such datasets, typically modelled as multidimensional arrays, requires efficient dynamic storage schemes where the array is allowed to arbitrary extend the bounds of the dimensions. This paper introduces PEXTA, a new parallel I/O model for the Global Array Toolkit. PEXTA provides the necessary APIs for explicit transfer between the memory resident global array and its secondary storage counterpart but also allows the persistent array to be extended on any dimension without compromising on the access time of an element or sub-array elements. Such a feature currently exists in the Hierarchical Data Format version 5 (HDF5) and parallel HDF5. However, extending the bound of a dimension in the HDF5 array file can be unusually expensive in time. Extensions, in our storage scheme for parallel dense array files, can still be performed while still accessing elements of the array much faster than parallel HDF5. We illustrate the PEXTA APIs with three applications; an out-of-core matrix-matrix multiplication, lattice Boltzmann simulation and Molecular Dynamics of Lennard Jones System.