Parallel integer sorting

This paper presents algorithms and experiments for internal (in core) and external (secondary memory) parallel sorting. It concentrates on algorithms appropriate for medium scale MIMD parallel computers, with all experiments being performed on a 128 processor Fujitsu AP1000. Data sizes ranging from a few hundred thousand to a few hundred million elements are considered, with all elements being either 64 bit or 128 bit integers. The internal sorting algorithm is based on earlier work by Andrew Tridgell and Richard Brent[11], while the external sorting algorithm was developed for this paper. The paper also takes a quick look at serial sorting algorithms, as they play an important part as subroutines in the parallel sorting algorithms

Simulating a dual-recycled gravitational wave interferometer with realistically imperfect optics

We simulate the performance of a gravitational wave interferometer in the Dual Recycling (DR) configuration, as will be used for systems like Advanced-LIGO. Our grid-based simulation program models complex interferometric detectors with realistic optical deformations (e.g., fine-scale mirror surface roughness). Broadband and Tuned DR are modeled here; the results are also applied qualitatively to Resonant Sideband Extraction (RSE). Several beneficial properties anticipated for DR detectors are investigated: signal response tuning and narrowbanding, power loss reduction, and the reclamation of lost power as useful light for signal detection. It is shown that these benefits would be limited by large scattering losses in large (multi-kilometer) systems. Furthermore, losses may be resonantly enhanced (particularly for RSE), if the interferometer's modal resonance conditions are not well chosen. We therefore make two principal recommendations for DR/RSE interferometers: the DR/RSE cavity must be modally nondegenerate; and fabricated mirror surfaces and coatings must be as smooth as is practically feasible.Comment: 50 pages, 11 figure

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software. We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms. The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing.https://doi.org/10.1186/1471-2105-12-35

A PADRE in MUFTI (A Multi User Free Text retrieval Intermediary)

The Parallel Document Retrieval Engine (PADRE) has hitherto lacked the ability to support multiple time-sharing searchers, a deficiency which detracted from its cost effectiveness. Extensions, adjuncts and performance improvements are now proposed to permit multiple use and to ensure reasonable response times. This paper describes the proposed multi-user architecture, reports query-processing speed-ups, outlines a number of alternative types of user-interaction client including an interface to network browsers in common use. Implementation progress is reported and potential load handling capacity is discussed. KEYWORDS Text retrieval, information retrieval, parallel computing. 1 Introduction The Parallel Document Retrieval Engine (PADRE) has previously demonstrated that full text scanning methods supported by parallel hardware permit powerful query constructors and rapid response to changing document collections [3, 5, 6]. The addition of paralleldisk -resident inverted file indexes ..

Mesh-Based Content Routing using XML

We have developed a new approach for reliably multicasting timecritical data to heterogeneous clients over mesh-based overlay networks. To facilitate intelligent content pruning, data streams are comprised of a sequence of XML packets and forwarded by application-level XML routers. XML routers perform contentbased routing of individual XML packets to other routers or clients based upon queries that describe the information needs of downstream nodes. Our PC-based XML router prototype can route an 18 Mbit per second XML stream. Our routers us

KANGA(ROO): Handling the microDST of the BABAR experiment with ROOT

A system based on ROOT for handling the micro-DST of the BaBar experiment is described. The purpose of the Kanga system is to have micro-DST data available in a format well suited for data distribution within a world-wide collaboration with many small sites. The design requirements, implementation and experience in practice after three years of data taking by the BaBar experiment are presented.Comment: To be submitted to Computer Physics Communications. 32 pages, 12 figure