A Study of Speed of the Boundary Element Method as applied to the Realtime Computational Simulation of Biological Organs

In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated. Biological organs are assumed to follow linear elastostatic material behavior, and constant boundary element is the element type used. First, a Graphics Processing Unit (GPU) is used to speed up the BEM computations to achieve the realtime performance. Next, instead of the GPU, a computer cluster is used. Results indicate that BEM is fast enough to provide for realtime graphics if biological organs are assumed to follow linear elastostatic material behavior. Although the present work does not conduct any simulation using nonlinear material models, results from using the linear elastostatic material model imply that it would be difficult to obtain realtime performance if highly nonlinear material models that properly characterize biological organs are used. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature.Comment: preprint, draft, 2 tables, 47 references, 7 files, Codes that can solve three dimensional linear elastostatic problems using constant boundary elements (of triangular shape) while ignoring body forces are provided as supplementary files; codes are distributed under the MIT License in three versions: i) MATLAB version ii) Fortran 90 version (sequential code) iii) Fortran 90 version (parallel code

The role of computational logic as a hinge paradigm among deduction, problem solving, programming, and parallelism

This paper presents some brief considerations on the role of Computational Logic in the construction of Artificial Intelligence systems and in programming in general. It does not address how the many problems in AI can be solved but, rather more modestly, tries to point out some advantages of Computational Logic as a tool for the AI scientist in his quest. It addresses the interaction between declarative and procedural views of programs (deduction and action), the impact of the intrinsic limitations of logic, the relationship with other apparently competing computational paradigms, and finally discusses implementation-related issues, such as the efficiency of current implementations and their capability for efficiently exploiting existing and future sequential and parallel hardware. The purpose of the discussion is in no way to present Computational Logic as the unique overall vehicle for the development of intelligent systems (in the firm belief that such a panacea is yet to be found) but rather to stress its strengths in providing reasonable solutions to several aspects of the task

How do programs become more concurrent? A story of program transformations

For several decades, programmers have relied onMooreâ s Law to improve the performance of their softwareapplications. From now on, programmers need to programthe multi-cores if they want to deliver efficient code. Inthe multi-core era, a major maintenance task will be tomake sequential programs more concurrent. What are themost common transformations to retrofit concurrency intosequential programs?We studied the source code of 5 open-source Javaprojects. We analyzed qualitatively and quantitatively thechange patterns that developers have used in order toretrofit concurrency. We found that these transformationsbelong to four categories: transformations that improve thelatency, the throughput, the scalability, or correctness of theapplications. In addition, we report on our experience ofparallelizing one of our own programs. Our findings caneducate software developers on how to parallelize sequentialprograms, and can provide hints for tool vendors aboutwhat transformations are worth automating

EasyFJP: Providing Hybrid Parallelism as a Concern for Divide and Conquer Java Applications

Because of the increasing availability of multi-core machines, clus- ters, Grids, and combinations of these there is now plenty of computational power,but today's programmers are not fully prepared to exploit parallelism. In particular, Java has helped in handling the heterogeneity of such environments. However, there is a lot of ground to cover regarding facilities to easily and elegantly parallelizing applications. One path to this end seems to be the synthesis of semi- automatic parallelism and Parallelism as a Concern (PaaC). The former allows users to be mostly unaware of parallel exploitation problems and at the same time manually optimize parallelized applications whenever necessary, while the latter allows applications to be separated from parallel-related code. In this paper, we present EasyFJP, an approach that implicitly exploits parallelism in Java applications based on the concept of fork-join synchronization pattern, a simple but effective abstraction for creating and coordinating parallel tasks. In addition, EasyFJP lets users to explicitly optimize applications through policies, or user-provided rules to dynamically regulate task granularity. Finally, EasyFJP relies on PaaC by means of source code generation techniques to wire applications and parallel-specific code together. Experiments with real-world applications on an emulated Grid and a cluster evidence that EasyFJP delivers competitive performance compared to state-of-the-art Java parallel programming tools.Fil: Mateos Diaz, Cristian Maximiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - CONICET - Tandil. Instituto Superior de Ingenieria del Software; Argentina;Fil: Zunino Suarez, Alejandro Octavio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - CONICET - Tandil. Instituto Superior de Ingenieria del Software; Argentina;Fil: Hirsch Jofré, Matías Eberardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - CONICET - Tandil. Instituto Superior de Ingenieria del Software; Argentina

A semi-automatic parallelization tool for Java based on fork-join synchronization patterns

Because of the increasing availability of multi-core machines, clusters, Grids, and combinations of these environments, there is now plenty of computational power available for executing compute intensive applications. However, because of the overwhelming and rapid advances in distributed and parallel hardware and environments, today?s programmers are not fully prepared to exploit distribution and parallelism. In this sense, the Java language has helped in handling the heterogeneity of such environments, but there is a lack of facilities and tools to easily distributing and parallelizing applications. One solution to mitigate this problem and make some progress towards producing general tools seems to be the synthesis of semi-automatic parallelism and Parallelism as a Concern (PaaC), which allows parallelizing applications along with as little modifications on sequential codes as possible. In this paper, we discuss a new approach that aims at overcoming the drawbacks of current Java-based parallel and distributed development tools, which precisely exploit these new conceptsFil: Hirsch, Matias. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - CONICET - Tandil. Instituto Superior de Ingenieria del Software; Argentina;Fil: Zunino, Alejandro. Consejo Nacional de Invest.cientif.y Tecnicas. Ctro Cientifico Tecnologico Conicet - Tandil. Instituto Superior de Ingenieria del Software;Fil: Mateos Diaz, Cristian Maximiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - CONICET - Tandil. Instituto Superior de Ingenieria del Software

Functional requirements document for the Earth Observing System Data and Information System (EOSDIS) Scientific Computing Facilities (SCF) of the NASA/MSFC Earth Science and Applications Division, 1992

Five scientists at MSFC/ESAD have EOS SCF investigator status. Each SCF has unique tasks which require the establishment of a computing facility dedicated to accomplishing those tasks. A SCF Working Group was established at ESAD with the charter of defining the computing requirements of the individual SCFs and recommending options for meeting these requirements. The primary goal of the working group was to determine which computing needs can be satisfied using either shared resources or separate but compatible resources, and which needs require unique individual resources. The requirements investigated included CPU-intensive vector and scalar processing, visualization, data storage, connectivity, and I/O peripherals. A review of computer industry directions and a market survey of computing hardware provided information regarding important industry standards and candidate computing platforms. It was determined that the total SCF computing requirements might be most effectively met using a hierarchy consisting of shared and individual resources. This hierarchy is composed of five major system types: (1) a supercomputer class vector processor; (2) a high-end scalar multiprocessor workstation; (3) a file server; (4) a few medium- to high-end visualization workstations; and (5) several low- to medium-range personal graphics workstations. Specific recommendations for meeting the needs of each of these types are presented

Parallelizing Scale Invariant Feature Transform on a Distributed Memory Cluster

Scale Invariant Feature Transform (SIFT) is a computer vision algorithm that is widely-used to extract features from images. We explored accelerating an existing implementation of this algorithm with message passing in order to analyze large data sets. We successfully tested two approaches to data decomposition in order to parallelize SIFT on a distributed memory cluster