A Reverse Engineering Methodology for Extracting Parallelism From Design Abstractions.

Migration of code from sequential environments to the parallel processing environments is often done in an ad hoc manner. The purpose of this research is to develop a reverse engineering methodology to facilitate systematic migration of code from sequential to the parallel processing environments. The research results include the development of a three-phase methodology and the design and development of a reverse engineering toolkit (abbreviated as RETK) which serves to establish a working model for the methodology. The methodology consists of three phases: Analysis, Synthesis, and Transformation. The Analysis phase uses concepts from reverse engineering research to recover the sequential design description from programs using a new design recovery technique. The Synthesis phase is comprised of processes that compute the data and control dependences by using the design abstractions produced by the Analysis phase to construct the program dependence graph. The Transformation phase consists of processes that require knowledge-based analysis of the program and dependence information produced by the Analysis and Synthesis phases, respectively. Design recommendations for parallel environments are the key output of the Transformation phase. The main components of RETK are an Information Extractor, a Dependence Analyzer, and a Design Assistant that implement the processes of the Analysis, Synthesis, and Transformation phases, respectively. The object-oriented design and implementation of the Information Extractor and Dependence Analyzer are described. The design and implementation of the Design Assistant using C Language Interface Production System (CLIPS) are described. In addition, experimental results of applying the methodology to test programs by RETK are presented. The results include analysis of a Numerical Aerodynamic Simulation (NAS) benchmark program. By uniquely combining research in reverse engineering, dependence analysis, and knowledge-based analysis, the methodology provides a systematic approach for code migration. The benefits of using the methodology are increased comprehensibility and improved efficiency in migrating sequential systems to parallel environments

Leveraging legacy codes to distributed problem solving environments: A web service approach

This paper describes techniques used to leverage high performance legacy codes as CORBA components to a distributed problem solving environment. It first briefly introduces the software architecture adopted by the environment. Then it presents a CORBA oriented wrapper generator (COWG) which can be used to automatically wrap high performance legacy codes as CORBA components. Two legacy codes have been wrapped with COWG. One is an MPI-based molecular dynamic simulation (MDS) code, the other is a finite element based computational fluid dynamics (CFD) code for simulating incompressible Navier-Stokes flows. Performance comparisons between runs of the MDS CORBA component and the original MDS legacy code on a cluster of workstations and on a parallel computer are also presented. Wrapped as CORBA components, these legacy codes can be reused in a distributed computing environment. The first case shows that high performance can be maintained with the wrapped MDS component. The second case shows that a Web user can submit a task to the wrapped CFD component through a Web page without knowing the exact implementation of the component. In this way, a user’s desktop computing environment can be extended to a high performance computing environment using a cluster of workstations or a parallel computer

Experimental and computational analyses reveal that environmental restrictions shape HIV-1 spread in 3D cultures

Here, using an integrative experimental and computational approach, Imle et al. show how cell motility and density affect HIV cell-associated transmission in a three-dimensional tissue-like culture system of CD4+ T cells and collagen, and how different collagen matrices restrict infection by cell-free virions

A parallel transformations framework for cluster environments.

In recent years program transformation technology has matured into a practical solution for many software reengineering and migration tasks. FermaT, an industrial strength program transformation system, has demonstrated that legacy systems can be successfully transformed into efficient and maintainable structured C or COBOL code. Its core, a transformation engine, is based on mathematically proven program transformations and ensures that transformed programs are semantically equivalent to its original state. Its engine facilitates a Wide Spectrum Language (WSL), with low-level as well as high-level constructs, to capture as much information as possible during transformation steps. FermaT’s methodology and technique lack in provision of concurrent migration and analysis. This provision is crucial if the transformation process is to be further automated. As the constraint based program migration theory has demonstrated, it is inefficient and time consuming, trying to satisfy the enormous computation of the generated transformation sequence search-space and its constraints. With the objective to solve the above problems and to extend the operating range of the FermaT transformation system, this thesis proposes a Parallel Transformations Framework which makes parallel transformations processing within the FermaT environment not only possible but also beneficial for its migration process. During a migration process, many thousands of program transformations have to be applied. For example a 1 million line of assembler to C migration takes over 21 hours to be processed on a single PC. Various approaches of search, prediction techniques and a constraint-based approach to address the presented issues already exist but they solve them unsatisfactorily. To remedy this situation, this dissertation proposes a framework to extend transformation processing systems with parallel processing capabilities. The parallel system can analyse specified parallel transformation tasks and produce appropriate parallel transformations processing outlines. To underpin an automated objective, a formal language is introduced. This language can be utilised to describe and outline parallel transformation tasks whereas parallel processing constraints underpin the parallel objective. This thesis addresses and explains how transformation processing steps can be automatically parallelised within a reengineering domain. It presents search and prediction tactics within this field. The decomposition and parallelisation of transformation sequence search-spaces is outlined. At the end, the presented work is evaluated on practical case studies, to demonstrate different parallel transformations processing techniques and conclusions are drawn