The Omegahat Environment: New Possibilities for Statistical Computing

Abstract

Statistical environments such as S, R, XLisp-Stat, and others have had a dramatic effect on the way we, statistics practitioners, think about data and statistical methodology. However, the possibilities and challenges introduced by recent technological developments and the general ways we use computing conflict with the computational model of these systems. This article explores some of these challenges and identifies the need to support easy integration of functionality from other domains, and to export statistical methodology to other audiences and applications, both statically and dynamically. Existing systems can be improved in these domains with some already implemented extensions (see Section 5). However, the development of a new environment and computational model that exploits modern tools designed to handle many general aspects of these challenges appears more promising as a long-term approach. We present the architecture for such a new model named Omegahat. It lends itself to entirely new statistical computing paradigms. It is highly extensible at both the user and programmer level, and also encourages the development of new environments for different user groups. The Omegahat interactive language offers a continuity between the different programming tasks and levels via optional type checking and seamless access between the interpreted user language and the implementation language, Java. Parallel and distributed computing, network and database access, interactive graphics, and many other aspects of statistical computing are directly accessible to the user as a consequence of this seamless access. We describe the benefits of using Java as the implementation language for the environment and several innovative features of the user-level language which promise to assist development of software that can be used in many contexts. We also outline how this architecture can be integrated with existing environments such as R and S.

The ideas are drawn from work within the Omega Project for Statistical Computing. The project provides open-source software for researching and developing next generation statistical computing tools.     

Heavy-tailed limits for medium size jobs and comparison scheduling

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Finding regions of similarity between two very long data streams is a computationally intensive problem referred to as sequence alignment. Alignment algorithms must allow for imperfect sequence matching with different starting locations and some gaps and errors between the two data sequences. Perhaps the most well known application of sequence matching is the testing of DNA or protein sequences against genome databases. The Smith–Waterman algorithm is a method for precisely characterizing how well two sequences can be aligned and for determining the optimal alignment of those two sequences. Like many applications in computational science, the Smith–Waterman algorithm is constrained by the memory access speed and can be accelerated significantly by using graphics processors (GPUs) as the compute engine. In this work we show that effective use of the GPU requires a novel reformulation of the Smith–Waterman algorithm. The performance of this new version of the algorithm is demonstrated using the SSCA#1 (Bioinformatics) benchmark running on one GPU and on up to four GPUs executing in parallel. The results indicate that for large problems a single GPU is up to 45 times faster than a CPU for this application, and the parallel implementation shows linear speed up on up to 4 GPUs.     

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