A co-locating fast file system for UNIX

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1998.Includes bibliographical references (p. 53-54).by Constantine Sapuntzakis.M.Eng

Scalable Global Grid catalogue for LHC Run3 and beyond

The AliEn (ALICE Environment) file catalogue is a global unique namespace providing mapping between a UNIX-like logical name structure and the corresponding physical files distributed over 80 storage elements worldwide. Powerful search tools and hierarchical metadata information are integral parts of the system and are used by the Grid jobs as well as local users to store and access all files on the Grid storage elements. The catalogue has been in production since 2005 and over the past 11 years has grown to more than 2 billion logical file names. The backend is a set of distributed relational databases, ensuring smooth growth and fast access. Due to the anticipated fast future growth, we are looking for ways to enhance the performance and scalability by simplifying the catalogue schema while keeping the functionality intact. We investigated different backend solutions, such as distributed key value stores, as replacement for the relational database. This contribution covers the architectural changes in the system, together with the technology evaluation, benchmark results and conclusions.Comment: Proceedings of the 22nd International Conference on Computing in High Energy and Nuclear Physics, CHEP 2016, 10-14 October 2016, San Francisco. Submitted to Journal of Physics: Conference Series (JPCS

FAST: FAST Analysis of Sequences Toolbox.

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

Process Management in Distributed Operating Systems

As part of designing and building the Amoeba distributed operating system, we have come up with a simple set of mechanisms for process management that allows downloading process migration, checkpointing, remote debugging and emulation of alien operating system interfaces.\ud The basic process management facilities are realized by the Amoeba Kernel and can be augmented by user-space services: Debug Service, Load-Balancing Service, Unix-Emulation Service, Checkpoint Service, etc.\ud The Amoeba Kernel can produce a representation of the state of a process which can be given to another Kernel where it is accepted for continued execution. This state consists of the memory contents in the form of a collection of segments, and a Process Descriptor which contains the additional state, program counters, stack pointers, system call state, etc.\ud Careful separation of mechanism and policy has resulted in a compact set of Kernel operations for process creation and management. A collection of user-space services provides process management policies and a simple interface for application programs.\ud In this paper we shall describe the mechanisms as they are being implemented in the Amoeba Distributed System at the Centre for Mathematics and Computer Science in Amsterdam. We believe that the mechanisms described here can also apply to other distributed systems

Iceberg database system for the graduate advisors of Computer and Information Science Department of New Jersey Institute of Technology

Iceberg system is a departmental database system. It is built for the graduate advisors of the CIS department. It stores the graduate student\u27s information, such as background, bridge requirement and transcript. The graduate advisors can process the student\u27s records using the graphic user interface of Iceberg system. Iceberg system is an example of the powerful Java language. We use the latest Java technologies to build a flexible system, which is easily extended. The system consists of Iceberg client, Iceberg server and Oracle data source. The Iceberg client is a web-based applet, which can be easily accessed using a browser. The Iceberg server runs on a fast UNIX machine, providing service to the Iceberg client through RMI. The most interesting feature of Iceberg system is the component architecture of the Iceberg client. The Iceberg client is consisted of visual components that have no knowledge of each other at compile time. They are assembled together at run time, following the instruction of a script file. Since the container component can hold any components the Iceberg system is readily extendable