13,415 research outputs found

    Sparse array representations and some selected array operations on GPUs

    Get PDF
    A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science. Johannesburg, 2014.A multi-dimensional data model provides a good conceptual view of the data in data warehousing and On-Line Analytical Processing (OLAP). A typical representation of such a data model is as a multi-dimensional array which is well suited when the array is dense. If the array is sparse, i.e., has a few number of non-zero elements relative to the product of the cardinalities of the dimensions, using a multi-dimensional array to represent the data set requires extremely large memory space while the actual data elements occupy a relatively small fraction of the space. Existing storage schemes for Multi-Dimensional Sparse Arrays (MDSAs) of higher dimensions k (k > 2), focus on optimizing the storage utilization, and offer little flexibility in data access efficiency. Most efficient storage schemes for sparse arrays are limited to matrices that are arrays in 2 dimensions. In this dissertation, we introduce four storage schemes for MDSAs that handle the sparsity of the array with two primary goals; reducing the storage overhead and maintaining efficient data element access. These schemes, including a well known method referred to as the Bit Encoded Sparse Storage (BESS), were evaluated and compared on four basic array operations, namely construction of a scheme, large scale random element access, sub-array retrieval and multi-dimensional aggregation. The four storage schemes being proposed, together with the evaluation results are: i.) The extended compressed row storage (xCRS) which extends CRS method for sparse matrix storage to sparse arrays of higher dimensions and achieves the best data element access efficiency among the methods compared; ii.) The bit encoded xCRS (BxCRS) which optimizes the storage utilization of xCRS by applying data compression methods with run length encoding, while maintaining its data access efficiency; iii.) A hybrid approach (Hybrid) that provides the best control of the balance between the storage utilization and data manipulation efficiency by combining xCRS and BESS. iv.) The PATRICIA trie compressed storage (PTCS) which uses PATRICIA trie to store the valid non-zero array elements. PTCS supports efficient data access, and has a unique property of supporting update operations conveniently. v.) BESS performs the best for the multi-dimensional aggregation, closely followed by the other schemes. We also addressed the problem of accelerating some selected array operations using General Purpose Computing on Graphics Processing Unit (GPGPU). The experimental results showed different levels of speed up, ranging from 2 to over 20 times, on large scale random element access and sub-array retrieval. In particular, we utilized GPUs on the computation of the cube operator, a special case of multi-dimensional aggregation, using BESS. This resulted in a 5 to 8 times of speed up compared with our CPU only implementation. The main contributions of this dissertation include the developments, implementations and evaluations of four efficient schemes to store multi-dimensional sparse arrays, as well as utilizing massive parallelism of GPUs for some data warehousing operations

    Formal Representation of the SS-DB Benchmark and Experimental Evaluation in EXTASCID

    Full text link
    Evaluating the performance of scientific data processing systems is a difficult task considering the plethora of application-specific solutions available in this landscape and the lack of a generally-accepted benchmark. The dual structure of scientific data coupled with the complex nature of processing complicate the evaluation procedure further. SS-DB is the first attempt to define a general benchmark for complex scientific processing over raw and derived data. It fails to draw sufficient attention though because of the ambiguous plain language specification and the extraordinary SciDB results. In this paper, we remedy the shortcomings of the original SS-DB specification by providing a formal representation in terms of ArrayQL algebra operators and ArrayQL/SciQL constructs. These are the first formal representations of the SS-DB benchmark. Starting from the formal representation, we give a reference implementation and present benchmark results in EXTASCID, a novel system for scientific data processing. EXTASCID is complete in providing native support both for array and relational data and extensible in executing any user code inside the system by the means of a configurable metaoperator. These features result in an order of magnitude improvement over SciDB at data loading, extracting derived data, and operations over derived data.Comment: 32 pages, 3 figure

    A Survey on Array Storage, Query Languages, and Systems

    Full text link
    Since scientific investigation is one of the most important providers of massive amounts of ordered data, there is a renewed interest in array data processing in the context of Big Data. To the best of our knowledge, a unified resource that summarizes and analyzes array processing research over its long existence is currently missing. In this survey, we provide a guide for past, present, and future research in array processing. The survey is organized along three main topics. Array storage discusses all the aspects related to array partitioning into chunks. The identification of a reduced set of array operators to form the foundation for an array query language is analyzed across multiple such proposals. Lastly, we survey real systems for array processing. The result is a thorough survey on array data storage and processing that should be consulted by anyone interested in this research topic, independent of experience level. The survey is not complete though. We greatly appreciate pointers towards any work we might have forgotten to mention.Comment: 44 page

    Data Cube Approximation and Mining using Probabilistic Modeling

    Get PDF
    On-line Analytical Processing (OLAP) techniques commonly used in data warehouses allow the exploration of data cubes according to different analysis axes (dimensions) and under different abstraction levels in a dimension hierarchy. However, such techniques are not aimed at mining multidimensional data. Since data cubes are nothing but multi-way tables, we propose to analyze the potential of two probabilistic modeling techniques, namely non-negative multi-way array factorization and log-linear modeling, with the ultimate objective of compressing and mining aggregate and multidimensional values. With the first technique, we compute the set of components that best fit the initial data set and whose superposition coincides with the original data; with the second technique we identify a parsimonious model (i.e., one with a reduced set of parameters), highlight strong associations among dimensions and discover possible outliers in data cells. A real life example will be used to (i) discuss the potential benefits of the modeling output on cube exploration and mining, (ii) show how OLAP queries can be answered in an approximate way, and (iii) illustrate the strengths and limitations of these modeling approaches

    Communication channel analysis and real time compressed sensing for high density neural recording devices

    Get PDF
    Next generation neural recording and Brain- Machine Interface (BMI) devices call for high density or distributed systems with more than 1000 recording sites. As the recording site density grows, the device generates data on the scale of several hundred megabits per second (Mbps). Transmitting such large amounts of data induces significant power consumption and heat dissipation for the implanted electronics. Facing these constraints, efficient on-chip compression techniques become essential to the reduction of implanted systems power consumption. This paper analyzes the communication channel constraints for high density neural recording devices. This paper then quantifies the improvement on communication channel using efficient on-chip compression methods. Finally, This paper describes a Compressed Sensing (CS) based system that can reduce the data rate by > 10x times while using power on the order of a few hundred nW per recording channel

    A Unified Optimization Approach for Sparse Tensor Operations on GPUs

    Full text link
    Sparse tensors appear in many large-scale applications with multidimensional and sparse data. While multidimensional sparse data often need to be processed on manycore processors, attempts to develop highly-optimized GPU-based implementations of sparse tensor operations are rare. The irregular computation patterns and sparsity structures as well as the large memory footprints of sparse tensor operations make such implementations challenging. We leverage the fact that sparse tensor operations share similar computation patterns to propose a unified tensor representation called F-COO. Combined with GPU-specific optimizations, F-COO provides highly-optimized implementations of sparse tensor computations on GPUs. The performance of the proposed unified approach is demonstrated for tensor-based kernels such as the Sparse Matricized Tensor- Times-Khatri-Rao Product (SpMTTKRP) and the Sparse Tensor- Times-Matrix Multiply (SpTTM) and is used in tensor decomposition algorithms. Compared to state-of-the-art work we improve the performance of SpTTM and SpMTTKRP up to 3.7 and 30.6 times respectively on NVIDIA Titan-X GPUs. We implement a CANDECOMP/PARAFAC (CP) decomposition and achieve up to 14.9 times speedup using the unified method over state-of-the-art libraries on NVIDIA Titan-X GPUs
    corecore