882 research outputs found

    On the Behavior of Programs with Remote Procedures

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    FAST: FAST Analysis of Sequences Toolbox.

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    FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought

    System performance advisor user guide

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    Journal ArticleThe usage of the System Performance Advisor (SPA) expert system is described. Documentation of SPA system commands, system variables, diagnostic rules is given. Information on how to run the SPA system is discussed. In addition, an overview of how SPA searches for problems is supplied. The purpose of SPA is to assist a system administrator in system performance management. Generally, system performance management can be described as those activities performed by a system administrator to ensure a computer system is providing as much of its capacity for the use of its users. SPA assists in performing these duties by attempting to locate the source of performance problems and then notifying the system administrator. SPA makes diagnoses about hosts and processes by monitoring current levels of activity and maintaining a history of these activity levels. By comparing historic knowledge of behavior to dynamic (current) knowledge, SPA can detect when a system is experiencing performance problems

    Measurements over distributed high performance computing and storage systems

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    A strawman proposal is given for a framework for presenting a common set of metrics for supercomputers, workstations, file servers, mass storage systems, and the networks that interconnect them. Production control and database systems are also included. Though other applications and third part software systems are not addressed, it is important to measure them as well

    An accurate prefetching policy for object oriented systems

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    PhD ThesisIn the latest high-performance computers, there is a growing requirement for accurate prefetching(AP) methodologies for advanced object management schemes in virtual memory and migration systems. The major issue for achieving this goal is that of finding a simple way of accurately predicting the objects that will be referenced in the near future and to group them so as to allow them to be fetched same time. The basic notion of AP involves building a relationship for logically grouping related objects and prefetching them, rather than using their physical grouping and it relies on demand fetching such as is done in existing restructuring or grouping schemes. By this, AP tries to overcome some of the shortcomings posed by physical grouping methods. Prefetching also makes use of the properties of object oriented languages to build inter and intra object relationships as a means of logical grouping. This thesis describes how this relationship can be established at compile time and how it can be used for accurate object prefetching in virtual memory systems. In addition, AP performs control flow and data dependency analysis to reinforce the relationships and to find the dependencies of a program. The user program is decomposed into prefetching blocks which contain all the information needed for block prefetching such as long branches and function calls at major branch points. The proposed prefetching scheme is implemented by extending a C++ compiler and evaluated on a virtual memory simulator. The results show a significant reduction both in the number of page fault and memory pollution. In particular, AP can suppress many page faults that occur during transition phases which are unmanageable by other ways of fetching. AP can be applied to a local and distributed virtual memory system so as to reduce the fault rate by fetching groups of objects at the same time and consequently lessening operating system overheads.British Counci

    Proceedings of the NSSDC Conference on Mass Storage Systems and Technologies for Space and Earth Science Applications

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    The proceedings of the National Space Science Data Center Conference on Mass Storage Systems and Technologies for Space and Earth Science Applications held July 23 through 25, 1991 at the NASA/Goddard Space Flight Center are presented. The program includes a keynote address, invited technical papers, and selected technical presentations to provide a broad forum for the discussion of a number of important issues in the field of mass storage systems. Topics include magnetic disk and tape technologies, optical disk and tape, software storage and file management systems, and experiences with the use of a large, distributed storage system. The technical presentations describe integrated mass storage systems that are expected to be available commercially. Also included is a series of presentations from Federal Government organizations and research institutions covering their mass storage requirements for the 1990's

    Rethinking Timestamping: Time Stamp Counter Design for Virtualized Environment

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    Almost every processor supports Time Stamp Counter (TSC), which is a hardware register that increments its value every clock cycle. Due to its high resolution and accessibility, TSC is now widely used for a variety tasks that need time measurements such as wall clock, code benchmarking, or metering hardware usage for account billing. However, if not carefully configured and interpreted, TSC-based time measurements can yield inaccurate readings. For instance, modern CPU may dynamically change its frequency or enter into low-power states. Also, time spent on scheduling events, system calls, page faults, etc. should be correctly accounted for. Even more complications arise when TSC measurements are done in virtual environments; virtual machines, on which TSC readings are taken, can be suspended, migrated, and scheduled on a machine with different clock rate and performance. In production virtualization systems, some management tasks are executed inside guests on behalf of the management system, effectively consuming end-user’s CPU time, which we believe should be excluded from end-user billing. We argue that the main problem with current TSC is that its hardware semantic is too vague to serve as a multi-purpose time source. In this thesis, we propose an improved TSC design, called Caviar, to address most of the issues. Caviar extends existing TSC hardware interface by adding a control-register based configuration interface through which a system can set up secondary TSCs whose behavior should be correct when accessed in a localized execution context including virtualized environment. We experimentally confirmed inaccurate readings with current TSC by conducting a series of TSC measurements on various x86 platforms, including virtualized cloud computing servers. We analyzed some of the results and argue that how our proposed solution can fix the problems. In conclusion, we believe that the simple interface of Caviar can solve most of current TSC complications, be implemented with minimal hardware cost, and be adopted easily by system software
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