A Survey on Array Storage, Query Languages, and Systems

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

Executing matrix multiply on a process oriented data flow machine

The Process-Oriented Dataflow System (PODS) is an execution model that combines the von Neumann and dataflow models of computation to gain the benefits of each. Central to PODS is the concept of array distribution and its effects on partitioning and mapping of processes.In PODS arrays are partitioned by simply assigning consecutive elements to each processing element (PE) equally. Since PODS uses single assignment, there will be only one producer of each element. This producing PE owns that element and will perform the necessary computations to assign it. Using this approach the filling loop is distributed across the PEs. This simple partitioning and mapping scheme provides excellent results for executing scientific code on MIMD machines. In this way PODS allows MIMD machines to exploit vector and data parallelism easily while still providing the flexibility of MIMD over SIMD for multi-user systems.In this paper, the classic matrix multiply algorithm, with 1024 data points, is executed on a PODS simulator and the results are presented and discussed. Matrix multiply is a good example because it has several interesting properties: there are multiple code-blocks; a new array must be dynamically allocated and distributed; there is a loop-carried dependency in the innermost loop; the two input arrays have different access patterns; and the sizes of the input arrays are not known at compile time. Matrix multiply also forms the basis for many important scientific algorithms such as: LU decomposition, convolution, and the Fast-Fourier Transform.The results show that PODS is comparable to both Iannucci's Hybrid Architecture and MIT's TTDA in terms of overhead and instruction power. They also show that PODS easily distributes the work load evenly across the PEs. The key result is that PODS can scale matrix multiply in a near linear fashion until there is little or no work to be performed for each PE. Then overhead and message passing become a major component of the execution time. With larger problems (e.g., >/=16k data points) this limit would be reached at around 256 PEs

Distributed memory compiler design for sparse problems

A compiler and runtime support mechanism is described and demonstrated. The methods presented are capable of solving a wide range of sparse and unstructured problems in scientific computing. The compiler takes as input a FORTRAN 77 program enhanced with specifications for distributing data, and the compiler outputs a message passing program that runs on a distributed memory computer. The runtime support for this compiler is a library of primitives designed to efficiently support irregular patterns of distributed array accesses and irregular distributed array partitions. A variety of Intel iPSC/860 performance results obtained through the use of this compiler are presented

Unifying mesh- and tree-based programmable interconnect

We examine the traditional, symmetric, Manhattan mesh design for field-programmable gate-array (FPGA) routing along with tree-of-meshes (ToM) and mesh-of-trees (MoT) based designs. All three networks can provide general routing for limited bisection designs (Rent's rule with p<1) and allow locality exploitation. They differ in their detailed topology and use of hierarchy. We show that all three have the same asymptotic wiring requirements. We bound this tightly by providing constructive mappings between routes in one network and routes in another. For example, we show that a (c,p) MoT design can be mapped to a (2c,p) linear population ToM and introduce a corner turn scheme which will make it possible to perform the reverse mapping from any (c,p) linear population ToM to a (2c,p) MoT augmented with a particular set of corner turn switches. One consequence of this latter mapping is a multilayer layout strategy for N-node, linear population ToM designs that requires only /spl Theta/(N) two-dimensional area for any p when given sufficient wiring layers. We further show upper and lower bounds for global mesh routes based on recursive bisection width and show these are within a constant factor of each other and within a constant factor of MoT and ToM layout area. In the process we identify the parameters and characteristics which make the networks different, making it clear there is a unified design continuum in which these networks are simply particular regions

Recent Advances in Graph Partitioning

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

Revisiting the radio interferometer measurement equation. IV. A generalized tensor formalism

The radio interferometer measurement equation (RIME), especially in its 2x2 form, has provided a comprehensive matrix-based formalism for describing classical radio interferometry and polarimetry, as shown in the previous three papers of this series. However, recent practical and theoretical developments, such as phased array feeds (PAFs), aperture arrays (AAs) and wide-field polarimetry, are exposing limitations of the formalism. This paper aims to develop a more general formalism that can be used to both clearly define the limitations of the matrix RIME, and to describe observational scenarios that lie outside these limitations. Some assumptions underlying the matrix RIME are explicated and analysed in detail. To this purpose, an array correlation matrix (ACM) formalism is explored. This proves of limited use; it is shown that matrix algebra is simply not a sufficiently flexible tool for the job. To overcome these limitations, a more general formalism based on tensors and the Einstein notation is proposed and explored both theoretically, and with a view to practical implementations. The tensor formalism elegantly yields generalized RIMEs describing beamforming, mutual coupling, and wide-field polarimetry in one equation. It is shown that under the explicated assumptions, tensor equations reduce to the 2x2 RIME. From a practical point of view, some methods for implementing tensor equations in an optimal way are proposed and analysed. The tensor RIME is a powerful means of describing observational scenarios not amenable to the matrix RIME. Even in cases where the latter remains applicable, the tensor formalism can be a valuable tool for understanding the limits of such applicability.Comment: 16 pages, no figures, accepted by A&

Run-time scheduling and execution of loops on message passing machines

Sparse system solvers and general purpose codes for solving partial differential equations are examples of the many types of problems whose irregularity can result in poor performance on distributed memory machines. Often, the data structures used in these problems are very flexible. Crucial details concerning loop dependences are encoded in these structures rather than being explicitly represented in the program. Good methods for parallelizing and partitioning these types of problems require assignment of computations in rather arbitrary ways. Naive implementations of programs on distributed memory machines requiring general loop partitions can be extremely inefficient. Instead, the scheduling mechanism needs to capture the data reference patterns of the loops in order to partition the problem. First, the indices assigned to each processor must be locally numbered. Next, it is necessary to precompute what information is needed by each processor at various points in the computation. The precomputed information is then used to generate an execution template designed to carry out the computation, communication, and partitioning of data, in an optimized manner. The design is presented for a general preprocessor and schedule executer, the structures of which do not vary, even though the details of the computation and of the type of information are problem dependent