A Compiler and Runtime Infrastructure for Automatic Program Distribution

This paper presents the design and the implementation of a compiler and runtime infrastructure for automatic program distribution. We are building a research infrastructure that enables experimentation with various program partitioning and mapping strategies and the study of automatic distribution's effect on resource consumption (e.g., CPU, memory, communication). Since many optimization techniques are faced with conflicting optimization targets (e.g., memory and communication), we believe that it is important to be able to study their interaction. We present a set of techniques that enable flexible resource modeling and program distribution. These are: dependence analysis, weighted graph partitioning, code and communication generation, and profiling. We have developed these ideas in the context of the Java language. We present in detail the design and implementation of each of the techniques as part of our compiler and runtime infrastructure. Then, we evaluate our design and present preliminary experimental data for each component, as well as for the entire system

Using High-Rising Cities to Visualize Performance in Real-Time

For developers concerned with a performance drop or improvement in their software, a profiler allows a developer to quickly search and identify bottlenecks and leaks that consume much execution time. Non real-time profilers analyze the history of already executed stack traces, while a real-time profiler outputs the results concurrently with the execution of software, so users can know the results instantaneously. However, a real-time profiler risks providing overly large and complex outputs, which is difficult for developers to quickly analyze. In this paper, we visualize the performance data from a real-time profiler. We visualize program execution as a three-dimensional (3D) city, representing the structure of the program as artifacts in a city (i.e., classes and packages expressed as buildings and districts) and their program executions expressed as the fluctuating height of artifacts. Through two case studies and using a prototype of our proposed visualization, we demonstrate how our visualization can easily identify performance issues such as a memory leak and compare performance changes between versions of a program. A demonstration of the interactive features of our prototype is available at https://youtu.be/eleVo19Hp4k.Comment: 10 pages, VISSOFT 2017, Artifact: https://github.com/sefield/high-rising-city-artifac

Integrating Existing Software Toolkits into VO System

Virtual Observatory (VO) is a collection of interoperating data archives and software tools. Taking advantages of the latest information technologies, it aims to provide a data-intensively online research environment for astronomers all around the world. A large number of high-qualified astronomical software packages and libraries are powerful and easy of use, and have been widely used by astronomers for many years. Integrating those toolkits into the VO system is a necessary and important task for the VO developers. VO architecture greatly depends on Grid and Web services, consequently the general VO integration route is "Java Ready - Grid Ready - VO Ready". In the paper, we discuss the importance of VO integration for existing toolkits and discuss the possible solutions. We introduce two efforts in the field from China-VO project, "gImageMagick" and " Galactic abundance gradients statistical research under grid environment". We also discuss what additional work should be done to convert Grid service to VO service.Comment: 9 pages, 3 figures, will be published in SPIE 2004 conference proceeding

Teaching programming at a distance: the Internet software visualization laboratory

This paper describes recent developments in our approach to teaching computer programming in the context of a part-time Masters course taught at a distance. Within our course, students are sent a pack which contains integrated text, software and video course material, using a uniform graphical representation to tell a consistent story of how the programming language works. The students communicate with their tutors over the phone and through surface mail. Through our empirical studies and experience teaching the course we have identified four current problems: (i) students' difficulty mapping between the graphical representations used in the course and the programs to which they relate, (ii) the lack of a conversational context for tutor help provided over the telephone, (iii) helping students who due to their other commitments tend to study at 'unsociable' hours, and (iv) providing software for the constantly changing and expanding range of platforms and operating systems used by students. We hope to alleviate these problems through our Internet Software Visualization Laboratory (ISVL), which supports individual exploration, and both synchronous and asynchronous communication. As a single user, students are aided by the extra mappings provided between the graphical representations used in the course and their computer programs, overcoming the problems of the original notation. ISVL can also be used as a synchronous communication medium whereby one of the users (generally the tutor) can provide an annotated demonstration of a program and its execution, a far richer alternative to technical discussions over the telephone. Finally, ISVL can be used to support asynchronous communication, helping students who work at unsociable hours by allowing the tutor to prepare short educational movies for them to view when convenient. The ISVL environment runs on a conventional web browser and is therefore platform independent, has modest hardware and bandwidth requirements, and is easy to distribute and maintain. Our planned experiments with ISVL will allow us to investigate ways in which new technology can be most appropriately applied in the service of distance education

Updates in metabolomics tools and resources: 2014-2015

Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platforms (MS or NMR spectroscopy based) used for data acquisition. Improved machinery in metabolomics generates increasingly complex datasets that create the need for more and better processing and analysis software and in silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources—in the form of tools, software, and databases—is currently lacking. Thus, here we provide an overview of freely-available, and open-source, tools, algorithms, and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR-based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table

A visual workspace for constructing hybrid MDS algorithms and coordinating multiple views

Data can be distinguished according to volume, variable types and distribution, and each of these characteristics imposes constraints upon the choice of applicable algorithms for their visualisation. This has led to an abundance of often disparate algorithmic techniques. Previous work has shown that a hybrid algorithmic approach can be successful in addressing the impact of data volume on the feasibility of multidimensional scaling (MDS). This paper presents a system and framework in which a user can easily explore algorithms as well as their hybrid conjunctions and the data flowing through them. Visual programming and a novel algorithmic architecture let the user semi-automatically define data flows and the co-ordination of multiple views of algorithmic and visualisation components. We propose that our approach has two main benefits: significant improvements in run times of MDS algorithms can be achieved, and intermediate views of the data and the visualisation program structure can provide greater insight and control over the visualisation process