Many analytics tasks and machine learning problems can be naturally expressed by iterative linear algebra programs. In this paper, we study the incremental view maintenance problem for such complex analytical queries. We develop a framework, called LINVIEW, for capturing deltas of linear algebra programs and understanding their computational cost. Linear algebra operations tend to cause an avalanche effect where even very local changes to the input matrices spread out and infect all of the intermediate results and the final view, causing incremental view maintenance to lose its performance benefit over re-evaluation. We develop techniques based on matrix factorizations to contain such epidemics of change. As a consequence, our techniques make incremental view maintenance of linear algebra practical and usually substantially cheaper than re-evaluation. We show, both analytically and experimentally, the usefulness of these techniques when applied to standard analytics tasks. Our evaluation demonstrates the efficiency of LINVIEW in generating parallel incremental programs that outperform re-evaluation techniques by more than an order of magnitude.
Scientific Databases. There are also database systems specialized in array processing. RasDaMan @cite_4 and AML @cite_42 provide support for expressing and optimizing queries over multidimensional arrays, but are not geared towards scientific and numerical computing. ASAP @cite_45 supports scientific computing primitives on a storage manager optimized for storing multidimensional arrays. RIOT @cite_8 also provides an efficient framework for scientific computing. However, none of these systems support incremental view maintenance for their workloads.
@cite_8 @cite_42 @cite_4 @cite_45
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Scientific experiments and large-scale simulations produce massive amounts of data. Many of these scientific datasets are arrays, and are stored in file formats such as HDF5 and NetCDF. Although scientific data management systems, such as SciDB, are designed to manipulate arrays, there are challenges in integrating these systems into existing analysis workflows. Major barriers include the expensive task of preparing and loading data before querying, and converting the final results to a format that is understood by the existing post-processing and visualization tools. As a consequence, integrating a data management system into an existing scientific data analysis workflow is time-consuming and requires extensive user involvement. In this paper, we present the design of a new scientific data analysis system that efficiently processes queries directly over data stored in the HDF5 file format. This design choice eliminates the tedious and error-prone data loading process, and makes the query results readily available to the next processing steps of the analysis workflow. Our design leverages the increasing main memory capacities found in supercomputers through bitmap indexing and in-memory query execution. In addition, query processing over the HDF5 data format can be effortlessly parallelized to utilize the ample concurrency available in large-scale supercomputers and modern parallel file systems. We evaluate the performance of our system on a large supercomputing system and experiment with both a synthetic dataset and a real cosmology observation dataset. Our system frequently outperforms the relational database system that the cosmology team currently uses, and is more than 10X faster than Hive when processing data in parallel. Overall, by eliminating the data loading step, our query processing system is more effective in supporting in situ scientific analysis workflows. RasDaMan is a universal — i.e., domain-independent — array DBMS for multidimensional arrays of arbitrary size and structure. A declarative, SQL-based array query language offers flexible retrieval and manipulation. Efficient server-based query evaluation is enabled by an intelligent optimizer and a streamlined storage architecture based on flexible array tiling and compression. RasDaMan is being used in several international projects for the management of geo and healthcare data of various dimensionality. Science applications are accumulating an ever-increasing amount of multidimensional data. Although some of it can be processed in a relational database, much of it is better suited to array-based engines. As such, it is important to optimize the query processing of these systems. This paper focuses on efficient query processing of join operations within an array database. These engines invariably chunk'' their data into multidimensional tiles that they use to efficiently process spatial queries. As such, traditional relational algorithms need to be substantially modified to take advantage of array tiles. Moreover, most n-dimensional science data is unevenly distributed in array space because its underlying observations rarely follow a uniform pattern. It is crucial that the optimization of array joins be skew-aware. In addition, owing to the scale of science applications, their query processing usually spans multiple nodes. This further complicates the planning of array joins. In this paper, we introduce a join optimization framework that is skew-aware for distributed joins. This optimization consists of two phases. In the first, a logical planner selects the query's algorithm (e.g., merge join), the granularity of the its tiles, and the reorganization operations needed to align the data. The second phase implements this logical plan by assigning tiles to cluster nodes using an analytical cost model. Our experimental results, on both synthetic and real-world data, demonstrate that this optimization framework speeds up array joins by up to 2.5X in comparison to the baseline. Databases can provide scalability by partitioning data across several servers. However, multi-partition, multi-operation transactional access is often expensive, employing coordination-intensive locking, validation, or scheduling mechanisms. Accordingly, many real-world systems avoid mechanisms that provide useful semantics for multi-partition operations. This leads to incorrect behavior for a large class of applications including secondary indexing, foreign key enforcement, and materialized view maintenance. In this work, we identify a new isolation model---Read Atomic (RA) isolation---that matches the requirements of these use cases by ensuring atomic visibility: either all or none of each transaction's updates are observed by other transactions. We present algorithms for Read Atomic Multi-Partition (RAMP) transactions that enforce atomic visibility while offering excellent scalability, guaranteed commit despite partial failures (via synchronization independence), and minimized communication between servers (via partition independence). These RAMP transactions correctly mediate atomic visibility of updates and provide readers with snapshot access to database state by using limited multi-versioning and by allowing clients to independently resolve non-atomic reads. We demonstrate that, in contrast with existing algorithms, RAMP transactions incur limited overhead---even under high contention---and scale linearly to 100 servers.