scholarly journals Application of Pfortran and Co-Array Fortran in the Parallelization of the GROMOS96 Molecular Dynamics Module

2001 ◽  
Vol 9 (1) ◽  
pp. 61-68 ◽  
Author(s):  
Piotr Bała ◽  
Terry Clark ◽  
L. Ridgway Scott
Keyword(s):  
Molecular Dynamics ◽  
Algorithm Design ◽  
Parallel Structure ◽  
Tool Development ◽  
Data Movement ◽  
Programming Tool ◽  
Linear Speedup ◽  
Programming Tools ◽  
Level Data ◽  
Tool Set

After at least a decade of parallel tool development, parallelization of scientific applications remains a significant undertaking. Typically parallelization is a specialized activity supported only partially by the programming tool set, with the programmer involved with parallel issues in addition to sequential ones. The details of concern range from algorithm design down to low-level data movement details. The aim of parallel programming tools is to automate the latter without sacrificing performance and portability, allowing the programmer to focus on algorithm specification and development. We present our use of two similar parallelization tools, Pfortran and Cray's Co-Array Fortran, in the parallelization of the GROMOS96 molecular dynamics module. Our parallelization started from the GROMOS96 distribution's shared-memory implementation of the replicated algorithm, but used little of that existing parallel structure. Consequently, our parallelization was close to starting with the sequential version. We found the intuitive extensions to Pfortran and Co-Array Fortran helpful in the rapid parallelization of the project. We present performance figures for both the Pfortran and Co-Array Fortran parallelizations showing linear speedup within the range expected by these parallelization methods.

Design and Realization of Algorithm Visualization Teaching Presentation System on Computer Graphics

2014 ◽  
Vol 687-691 ◽  
pp. 2768-2771
Author(s):  
Zu Wei Wang
Keyword(s):  
Computer Graphics ◽  
Algorithm Design ◽  
Visual Programming ◽  
Straight Line Segment ◽  
Course Content ◽  
Visual Theory ◽  
Programming Tool ◽  
Teaching Content ◽  
Straight Line ◽  
Algorithm Visualization

Based on the study of abroad foundation on visual theory, we conduct depth discussion of the current introduction of visual teaching meaning. For the current computer graphics course content, we determine a visual teaching content and objectives, carry out the study and practice of computer graphics algorithm visualization teaching. This paper uses VB 6.0 visual programming tool to generate the basic primitives, polygon filling, cut a straight line segment, curve generation and visualization of fractal algorithm design and realization. Through analysis, this paper hold that use of visual teaching has a positive effect and influence for professors to change the way teachers help students understand computer graphics algorithm. In the process of teaching, students improve the understanding, exploration, discovery and creativity through observation, conjecture and verify.

scholarly journals Koios: Design, Development, and Evaluation of an Educational Visual Tool for Greek Novice Programmers

2018 ◽  
Vol 57 (5) ◽  
pp. 1227-1259 ◽  
Author(s):  
Ioannis V. Vasilopoulos ◽  
Paul van Schaik
Keyword(s):  
Visual Programming ◽  
The Body ◽  
Design Development ◽  
Visual Tool ◽  
Programming Tool ◽  
Programming Tools ◽  
Novice Programming ◽  
Empirical Demonstration ◽  
Psychology Of Programming ◽  
Better Than

This article discusses the design and implementation of a new programming tool for Greek novices as a means to improve introductory programing instruction in Greece. We implemented Koios, a new highly interactive and visual programming tool for Greek novices, based on the body of research in the field of psychology of programming. The main contribution of this article is the empirical demonstration of the benefit of this tool in novice programming, compared with two other popular programming tools for Greek novices. The results show that users of Koios performed significantly better than users of the other two programming tools.

scholarly journals gmxapi: a Gromacs-native Python interface for molecular dynamics with ensemble and plugin support

2021 ◽  
Author(s):  
M. Eric Irrgang ◽  
Caroline Davis ◽  
Peter Kasson
Keyword(s):  
Molecular Dynamics ◽  
Flow Simulation ◽  
Dynamics Simulation ◽  
Command Line ◽  
Level Data ◽  
Python Scripting ◽  
Multiple Levels ◽  
Dynamics Simulations ◽  
High Level ◽  
Levels Of Integration

Gmxapi provides an integrated, native Python API for both standard and advanced molecular dynamics simulations in GROMACS. The Python interface permits multiple levels of integration with the core GROMACS libraries, and legacy support is provided via an interface that mimics the command-line syntax, so that all GROMACS commands are fully available. Gmxapi has been officially supported since the GROMACS 2019 release and is installed by default in current versions of the software. Beyond simply wrapping GROMACS library operations, the API permits several advanced operations that are not feasible using the prior command-line interface. First, API allows custom user plugin code within the molecular dynamics force calculations, so users can execute custom algorithms without modifying the GROMACS source. Second, the Python interface allows tasks to be dynamically defined, so high-level algorithms for molecular dynamics simulation and analysis can be coordinated with loop and conditional operations. Gmxapi makes GROMACS more accessible to custom Python scripting while also providing support for high-level data-flow simulation algorithms that were previously feasible only in external packages.

CorTag

2010 ◽  
pp. 177-189
Author(s):  
Yves Kodratoff ◽  
Jérôme Azé ◽  
Lise Fontaine
Keyword(s):  
Text Analysis ◽  
Programming Tool ◽  
Analysis Tools ◽  
Programming Tools ◽  
Programming Effort

This chapter argues that in order to extract significant knowledge from masses of technical texts, it is necessary to provide the field specialists with programming tools with which they themselves may use to program their text analysis tools. These programming tools, besides helping the programming effort of the field specialists, must also help them to gather the field knowledge necessary for defining and retrieving what they define as significant knowledge. This necessary field knowledge must be included in a well-structured and easy to use part of the programming tool. In this chapter, we present CorTag, a programming tool which is designed to correct existing tags in a text and to assist the field specialist to retrieve the knowledge and/or information he or she is looking for.

Exploring the Effectiveness and Moderators of Block-Based Visual Programming on Student Learning: A Meta-Analysis

2020 ◽  
Vol 58 (8) ◽  
pp. 1467-1493
Author(s):  
Yue Hu ◽  
Cheng-Huan Chen ◽  
Chien-Yuan Su
Keyword(s):  
Academic Achievement ◽  
Effect Size ◽  
Meta Analysis ◽  
Empirical Studies ◽  
Experimental Treatment ◽  
Fixed Effect Model ◽  
Visual Programming ◽  
Programming Tool ◽  
Programming Tools ◽  
Block Based

Block-based visual programming tools, such as Scratch, Alice, and MIT App Inventor, provide an intuitive and easy-to-use editing interface through which to promote programming learning for novice students of various ages. However, very little attention has been paid to investigating these tools’ overall effects on students’ academic achievement and the study features that may moderate the effects of block-based visual programming from a comprehensive perspective. Thus, the present study carried out a meta-analysis to systemically examine 29 empirical studies (extracting 34 effect sizes) using experimental or quasi-experiments involving the programming learning effects of employing block-based visual programming tools to date (until the end of 2019). The results showed a small to medium significant positive overall mean effect size (fixed-effect model g = 0.37; random-effects model g = 0.47) of the use of these block-based visual programming tools with respect to students’ academic achievement. Furthermore, the overall mean effect size was significantly affected by the educational stage, programming tool used, experimental treatment, and school location. Discussions and implications based on the findings are provided.

Application of Dynamic Programming to Optimize Tool Replacement Schedules for Multi-Tool Operations Involving Distributed Tool Lives

1980 ◽  
Vol 102 (3) ◽  
pp. 446-451 ◽  
Author(s):  
H. Bao
Keyword(s):  
Dynamic Programming ◽  
Machining Process ◽  
Large Set ◽  
Moderate Number ◽  
Programming Tool ◽  
Indefinite Number ◽  
Replacement Model ◽  
Tool Replacement ◽  
Tool Set ◽  
Set Up

There have been a number of models developed to provide the optimum tool replacement schedule for a multi-tool set-up. However, most of these models are quite complex and are geared to yield solutions for a very large set-up involving an indefinite number of parts. In this paper a new tool replacement model aimed at a machining process involving a moderate number of tools (2 to 6) and a discrete number of parts (50 to 100) is developed based on the technique of Dynamic Programming. Tool lives in the set-up are assumed to be distributed.

scholarly journals Locality properties of 3D data orderings with application to parallel molecular dynamics simulations

2019 ◽  
Vol 33 (5) ◽  
pp. 998-1018
Author(s):  
Ibrahim Al-Kharusi ◽  
David W Walker
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Spatial Data ◽  
Data Locality ◽  
Data Reuse ◽  
Dynamic Simulations ◽  
Data Movement ◽  
Execution Speed ◽  
Dynamics Simulations ◽  
The Impact

Application performance on graphical processing units (GPUs), in terms of execution speed and memory usage, depends on the efficient use of hierarchical memory. It is expected that enhancing data locality in molecular dynamic simulations will lower the cost of data movement across the GPU memory hierarchy. The work presented in this article analyses the spatial data locality and data reuse characteristics for row-major, Hilbert and Morton orderings and the impact these have on the performance of molecular dynamics simulations. A simple cache model is presented, and this is found to give results that are consistent with the timing results for the particle force computation obtained on NVidia GeForce GTX960 and Tesla P100 GPUs. Further analysis of the observed memory use, in terms of cache hits and the number of memory transactions, provides a more detailed explanation of execution behaviour for the different orderings. To the best of our knowledge, this is the first study to investigate memory analysis and data locality issues for molecular dynamics simulations of Lennard-Jones fluids on NVidia’s Maxwell and Tesla architectures.

scholarly journals Scientific Programming Tools for Water Management

2021 ◽  
Vol 2021 ◽  
pp. 1-3
Author(s):  
Francisco J. Alcalá ◽  
Jaime Martínez-Valderrama ◽  
Francisco Gomáriz-Castillo ◽  
Carlos G. Hernández ◽  
José M. Cecilia
Keyword(s):  
Algorithm Design ◽  
Water Recovery ◽  
Special Issue ◽  
Programming Tools ◽  
Hardware Architectures ◽  
Groundwater Quality Monitoring ◽  
Software Platforms ◽  
Design Software ◽  
Irrigation Agriculture ◽  
Desertification Risk

This special issue delivers a platform in which researchers expose intersections between algorithm design, software platforms, and hardware architectures to deal with emerging challenges in the scientific field of management of water and water-dependent resources. Since the call for papers was announced in June 2019, this special issue has received 10 manuscripts. After a rigorous review process, 6 papers have been finally accepted for publication. Published papers deal with groundwater quality monitoring, coastal groundwater-dependent irrigation agriculture, desertification risk, water recovery from tailings, future scenarios of water resources, and vulnerability of coastal aquifers.

scholarly journals Analysis of Programming Tools and Techniques in 3D Printing Technology

2019 ◽  
Vol 9 (2S2) ◽  
pp. 788-793
Keyword(s):  
3D Printing ◽  
Material System ◽  
4D Printing ◽  
Complexity Management ◽  
Advantages And Disadvantages ◽  
Programming Tool ◽  
Form Function ◽  
Programming Tools ◽  
Materials Used ◽  
Tools And Techniques

This paper explains and analyses the additive manufacturing process from its varieties, types and usage of different programming tools. Printing process need to be selected mainly based on applications and the materials used for development. More applications of 3D printing, were found to be in electronic industries which is mainly due to complexities in shape and size. Understanding of the prompt programming tool to be selected during complexity management is one of the major requirement. This requirement drives the research community from 3D to 4D-Printing. Mainly, in 4D printing concept, the object or the material system has the ability to change its form/function after it is being printed. The advantages and disadvantages of this technology towards the significant growth of applications were analyzed and presented in this paper

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