A Revised Analysis of the Open Grid Services Infrastructure

This paper began its life as an unpublished technical review citeanalysis of the proposed Open Grid Services Architecture (OGSA) as described in the papers, ``The Physiology of the Grid'' citefoster by Ian Foster, Carl Kesselman, Jeffrey Nick and Steven Tuecke, and ``The Grid Service Specification (Draft 2/15/02) citeogsi'' by Foster, Kesselman, Tuecke and Karl Czajkowski, Jeffrey Frey and Steve Graham. However, much has changed since the publication of the original documents. The architecture has evolved substantially and the vast majority of our initial concerns have been addressed. In this paper we will describe the evolution of the specification from its original form to the current draft of 10/4/02 authored by S. Tuecke, K. Czajkowski, J. Frey, S. Graham, C. Kesselman, and P. Vanderbilt, which is now the central component of the Global Grid Forum Open Grid Service Infrastructure (OGSI) working group which is co-chaired by Steven Tuecke and David Snelling

The Center for Component Technology for Terascale Software Simulation (CCTTSS) at Indiana University

Final report for the Indiana University portion of the CCTTSS project

Directions in parallel programming: HPF, shared virtual memory and object parallelism in pC++

Fortran and C++ are the dominant programming languages used in scientific computation. Consequently, extensions to these languages are the most popular for programming massively parallel computers. We discuss two such approaches to parallel Fortran and one approach to C++. The High Performance Fortran Forum has designed HPF with the intent of supporting data parallelism on Fortran 90 applications. HPF works by asking the user to help the compiler distribute and align the data structures with the distributed memory modules in the system. Fortran-S takes a different approach in which the data distribution is managed by the operating system and the user provides annotations to indicate parallel control regions. In the case of C++, we look at pC++ which is based on a concurrent aggregate parallel model

Extensible Terascale Facility (ETF): Indiana-Purdue Grid (IP-Grid)

NSF Award ID: ACI-0338618 Project Dates: 10/1/03-9/30/0

Peer-to-Peer Grids

We describe Peer-to-Peer Grids built around Integration of technologies from the peer-to-peer and Grid fields. We focus on the role of Web services linked by a powerful event service using uniform XML interfaces and application level routing. We describe how a rich synchronous and asynchronous collaboration environment can support virtual communities built on top of such infrastructure. Universal access mechanisms are discussed

Intercellular Genomics of Subsurface Microbial Colonies

This report summarizes progress in the second year of this project. The objective is to develop methods and software to predict the spatial configuration, properties and temporal evolution of microbial colonies in the subsurface. To accomplish this, we integrate models of intracellular processes, cell-host medium exchange and reaction-transport dynamics on the colony scale. At the conclusion of the project, we aim to have the foundations of a predictive mathematical model and software that captures the three scales of these systems – the intracellular, pore, and colony wide spatial scales. In the second year of the project, we refined our transcriptional regulatory network discovery (TRND) approach that utilizes gene expression data along with phylogenic similarity and gene ontology analyses and applied it successfully to E.coli, human B cells, and Geobacter sulfurreducens. We have developed a new Web interface, GeoGen, which is tailored to the reconstruction of microbial TRNs and solely focuses on Geobacter as one of DOE’s high priority microbes. Our developments are designed such that the frameworks for the TRND and GeoGen can readily be used for other microbes of interest to the DOE. In the context of modeling a single bacterium, we are actively pursuing both steady-state and kinetic approaches. The steady-state approach is based on a flux balance that uses maximizing biomass growth rate as its objective, subjected to various biochemical constraints, for the optimal values of reaction rates and uptake/release of metabolites. For the kinetic approach, we use Karyote, a rigorous cell model developed by us for an earlier DOE grant and the DARPA BioSPICE Project. We are also investigating the interplay between bacterial colonies and environment at both pore and macroscopic scales. The pore scale models use detailed representations for realistic porous media accounting for the distribution of grain size whereas the macroscopic models employ the Darcy-type flow equations and up-scaled advective-diffusive transport equations for chemical species. We are rigorously testing the relationship between these two scales by evaluating macroscopic parameters using the volume averaging methodology applied to pore scale model results

Asynchronous Peer-to-Peer Web Services and Firewalls

In this paper we test the suitability of Java to implement a scalable Web Service that solves a set of problems related to peer-to-peer interactions between Web Services that behind firewalls or not generally accessible. In particular we describe how to enable reliable and long running conversations through firewalls betweenWeb Service peers have no accessible network endpoints. Our solution is to implement in Java aWeb Services Dispatcher (WSD) that is an intermediary service that forwards messages and can facilitate message exchanges by supporting SOAP RPC over HTTP and WS-Addressing for asynchronous messaging. We describe how Web Service clients that have no network endpoints, such as applets, can become Web Service peers by using an additional message store-and-forward service ("mailbox"). Then we conduct a set of experiments to evaluate performance of Java implementation in realistic Web Service scenarios, involving intercontinental tests between France and the US