Simulation of a tree processor /

Thesis (M. S.)--University of Illinois at Urbana-Champaign.

Interprocessor connections : cabilities, exploitation and effectiveness /

Vita.

Further results regarding multiprocessor systems /

"NSF-OCA-MCS76-81686-000030."

Parallelism exploitation and scheduling,

Vita.

Focusing in on structural genomics: The University of Queensland structural biology pipeline

The flood of new genomic sequence information together with technological innovations in protein structure determination have led to worldwide structural genomics (SG) initiatives. The goals of SG initiatives are to accelerate the process of protein structure determination, to fill in protein fold space and to provide information about the function of uncharacterized proteins. In the long-term, these outcomes are likely to impact on medical biotechnology and drug discovery, leading to a better understanding of disease as well as the development of new therapeutics. Here we describe the high throughput pipeline established at the University of Queensland in Australia. In this focused pipeline, the targets for structure determination are proteins that are expressed in mouse macrophage cells and that are inferred to have a role in innate immunity. The aim is to characterize the molecular structure and the biochemical and cellular function of these targets by using a parallel processing pipeline. The pipeline is designed to work with tens to hundreds of target gene products and comprises target selection, cloning, expression, purification, crystallization and structure determination. The structures from this pipeline will provide insights into the function of previously uncharacterized macrophage proteins and could lead to the validation of new drug targets for chronic obstructive pulmonary disease and arthritis. (c) 2006 Elsevier B.V. All rights reserved.

How to Use a Desktop Version of a DBMS for Client-Server Applications

DBMS (Data base management systems) still have a very high price for small and middle enterprises in Bulgaria. Desktop versions are free but they cannot function in multi-user environment. We will try to make an application server which will make a Desktop version of a DBMS open to many users. Thus, this approach will be appropriate for client-server applications. The author of the article gives a concise observation of the problem and a possible way of solution.

A Real-time Decision Support System Prototype for Management of a Power Block

This paper describes the basic tools for a real-time decision support system of a semiotic type on the example of the prototype for management and monitoring of a nuclear power block implemented on the basis of the tool complex G2+GDA using cognitive graphics and parallel processing. This work was supported by RFBR (project 02-07-90042).

Extending Science Gateway Frameworks to Support Big Data Applications in the Cloud

Cloud computing offers massive scalability and elasticity required by many scien-tific and commercial applications. Combining the computational and data handling capabilities of clouds with parallel processing also has the potential to tackle Big Data problems efficiently. Science gateway frameworks and workflow systems enable application developers to implement complex applications and make these available for end-users via simple graphical user interfaces. The integration of such frameworks with Big Data processing tools on the cloud opens new oppor-tunities for application developers. This paper investigates how workflow sys-tems and science gateways can be extended with Big Data processing capabilities. A generic approach based on infrastructure aware workflows is suggested and a proof of concept is implemented based on the WS-PGRADE/gUSE science gateway framework and its integration with the Hadoop parallel data processing solution based on the MapReduce paradigm in the cloud. The provided analysis demonstrates that the methods described to integrate Big Data processing with workflows and science gateways work well in different cloud infrastructures and application scenarios, and can be used to create massively parallel applications for scientific analysis of Big Data.

A solution to the three disjoint path problem on honeycomb tori

In a previous paper we solved an open problem named as the three disjoint path problem on honeycomb meshes. In this paper we extend the technique used to solve the related problem on honeycomb tori. The result gives the minimum possible length of the longest of any three disjoint paths between two given nodes in a torus. The problem has practical benefits in the fault tolerant aspects of interconnection topologies.

A solution to the three disjoint path problem on honeycomb meshes

Recently honeycomb meshes have been considered as alternative candidates for interconnection networks in parallel and distributed computer systems. This paper presents a solution to one of the open problems about honeycomb meshes—the so-called three disjoint path problem. The problem requires minimizing the length of the longest of any three disjoint paths between 3-degree nodes. This solution provides information on the re-routing of traffic along the network in the presence of faults.

Parallelisation of ESAUNA within EUROPORT-1: A structured/unstructured aeronautical CFD flow code

General-purpose parallel processing for solving day-to-day industrial problems has been slow to develop, partly because of the lack of suitable hardware from well-established, mainstream computer manufacturers and suitably parallelized application software. The parallelization of a CFD-(computational fluid dynamics) flow solution code is known as ESAUNA. This code is part of SAUNA, a large CFD suite aimed at computing the flow around very complex aircraft configurations including complete aircraft. A novel feature of the SAUNA suite is that it is designed to use either block-structured hexahedral grids, unstructured tetrahedral grids, or a hybrid combination of both grid types. ESAUNA is designed to solve the Euler equations or the Navier-Stokes equations, the latter in conjunction with various turbulence models. Two fundamental parallelization concepts are used—namely, grid partitioning and encapsulation of communications. Grid partitioning is applied to both block-structured grid modules and unstructured grid modules. ESAUNA can also be coupled with other simulation codes for multidisciplinary computations such as flow simulations around an aircraft coupled with flutter prediction for transient flight simulations.

Multilevel mesh partitioning for aspect ratio

Multilevel algorithms are a successful class of optimisation techniques which address the mesh partitioning problem. They usually combine a graph contraction algorithm together with a local optimisation method which refines the partition at each graph level. To date these algorithms have been used almost exclusively to minimise the cut-edge weight, however it has been shown that for certain classes of solution algorithm, the convergence of the solver is strongly influenced by the subdomain aspect ratio. In this paper therefore, we modify the multilevel algorithms in order to optimise a cost function based on aspect ratio. Several variants of the algorithms are tested and shown to provide excellent results.

Aspect ratio for mesh partitioning

This paper deals with the measure of Aspect Ratio for mesh partitioning and gives hints why, for certain solvers, the Aspect Ratio of partitions plays an important role. We define and rate different kinds of Aspect Ratio, present a new center-based partitioning method which optimizes this measure implicitly and rate several existing partitioning methods and tools under the criterion of Aspect Ratio.

The MUSE Machine -- an Architecture for Structured Data Flow Computation

Computers employing some degree of data flow organisation are now well established as providing a possible vehicle for concurrent computation. Although data-driven computation frees the architecture from the constraints of the single program counter, processor and global memory, inherent in the classic von Neumann computer, there can still be problems with the unconstrained generation of fresh result tokens if a pure data flow approach is adopted. The advantages of allowing serial processing for those parts of a program which are inherently serial, and of permitting a demand-driven, as well as data-driven, mode of operation are identified and described. The MUSE machine described here is a structured architecture supporting both serial and parallel processing which allows the abstract structure of a program to be mapped onto the machine in a logical way.

Development of a Real Time System in Algol 68.

For various reasons, many Algol 68 compilers do not directly implement the parallel processing operations defined in the Revised Algol 68 Report. It is still possible however, to perform parallel processing, multitasking and simulation provided that the implementation permits the creation of a master routine for the coordination and initiation of processes under its control. The package described here is intended for real time applications and runs in conjunction with the Algol 68R system; it extends and develops the original Algol 68RT package, which was designed for use with multiplexers at the Royal Radar Establishment, Malvern. The facilities provided, in addition to the synchronising operations, include an interface to an ICL Communications Processor enabling the abstract processes to be realised as the interaction of several teletypes or visual display units with a real time program providing a useful service.