COEL: A Web-based Chemistry Simulation Framework

The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage, which is susceptible to loss, lacks searchable structure, and does not support concurrency. Furthermore, simulations are often single-threaded, and user interfaces are non-trivial to use. Therefore there are significant hurdles to conducting efficient and collaborative chemical research. In this paper, we introduce a new enterprise chemistry simulation framework, COEL, which addresses these issues. COEL is the first web-based framework of its kind. A visually pleasing and intuitive user interface, simulations that run on a large computational grid, reliable database storage, and transactional services make COEL ideal for collaborative research and education. COEL's most prominent features include ODE-based simulations of chemical reaction networks and multicompartment reaction networks, with rich options for user interactions with those networks. COEL provides DNA-strand displacement transformations and visualization (and is to our knowledge the first CRN framework to do so), GA optimization of rate constants, expression validation, an application-wide plotting engine, and SBML/Octave/Matlab export. We also present an overview of the underlying software and technologies employed and describe the main architectural decisions driving our development. COEL is available at http://coel-sim.org for selected research teams only. We plan to provide a part of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl

Iris: an Extensible Application for Building and Analyzing Spectral Energy Distributions

Iris is an extensible application that provides astronomers with a user-friendly interface capable of ingesting broad-band data from many different sources in order to build, explore, and model spectral energy distributions (SEDs). Iris takes advantage of the standards defined by the International Virtual Observatory Alliance, but hides the technicalities of such standards by implementing different layers of abstraction on top of them. Such intermediate layers provide hooks that users and developers can exploit in order to extend the capabilities provided by Iris. For instance, custom Python models can be combined in arbitrary ways with the Iris built-in models or with other custom functions. As such, Iris offers a platform for the development and integration of SED data, services, and applications, either from the user's system or from the web. In this paper we describe the built-in features provided by Iris for building and analyzing SEDs. We also explore in some detail the Iris framework and software development kit, showing how astronomers and software developers can plug their code into an integrated SED analysis environment.Comment: 18 pages, 8 figures, accepted for publication in Astronomy & Computin

Making non-volatile memory programmable

Byte-addressable, non-volatile memory (NVM) is emerging as a revolutionary memory technology that provides persistence, near-DRAM performance, and scalable capacity. By using NVM, applications can directly create and manipulate durable data in place without the need for serialization out to SSDs. Ideally, through NVM, persistent applications will be able to maintain crash-consistency at a minimal cost. However, before this is possible, improvements must be made at both the hardware and software level to support persistent applications. Currently, software support for NVM places too high of a burden on the developer, introducing many opportunities for mistakes while also being too rigid for compiler optimizations. Likewise, at the hardware level, too little information is passed to the processor about the instruction-level ordering requirements of persistent applications; this forces the hardware to require the use of coarse fences, which significantly slow down execution. To help realize the promise of NVM, this thesis proposes both new software and hardware support that make NVM programmable. From the software side, this thesis proposes a new NVM programming model which relieves the programmer from performing much of the accounting work in persistent applications, instead relying on the runtime to perform error-prone tasks. Specifically, within the proposed model, the user only needs to provide minimal markings to identify the persistent data set and to ensure data is updated in a crash-consistent manner. Given this new NVM programming model, this thesis next presents an implementation of the model in Java. I call my implementation AutoPersist and build my support into the Maxine research Java Virtual Machine (JVM). In this thesis I describe how the JVM can be changed to support the proposed NVM programming model, including adding new Java libraries, adding new JVM runtime features, and augmenting the behavior of existing Java bytecodes. In addition to being easy-to-use, another advantage of the proposed model is that it is amenable to compiler optimizations. In this thesis I highlight two profile-guided optimizations: eagerly allocating objects directly into NVM and speculatively pruning control flow to only include expected-to-be taken paths. I also describe how to apply these optimizations to AutoPersist and show they have a substantial performance impact. While designing AutoPersist, I often observed that dependency information known by the compiler cannot be passed down to the underlying hardware; instead, the compiler must insert coarse-grain fences to enforce needed dependencies. This is because current instruction set architectures (ISA) cannot describe arbitrary instruction-level execution ordering constraints. To fix this limitation, I introduce the Execution Dependency Extension (EDE), and describe how EDE can be added to an existing ISA as well as be implemented in current processor pipelines. Overall, emerging NVM technologies can deliver programmer-friendly high performance. However, for this to happen, both software and hardware improvements are necessary. This thesis takes steps to address current the software and hardware gaps: I propose new software support to assist in the development of persistent applications and also introduce new instructions which allow for arbitrary instruction-level dependencies to be conveyed and enforced by the underlying hardware. With these improvements, hopefully the dream of programmable high-performance NVM is one step closer to being realized

Emergent Frameworks for Decision Support Systems

Knowledge is generated and accessed from heterogeneous spaces. The recent advances in in-formation technologies provide enhanced tools for improving the efficiency of knowledge-based decision support systems. The purpose of this paper is to present the frameworks for developing the optimal blend of technologies required in order to better the knowledge acquisition and reuse in large scale decision making environments. The authors present a case study in the field of clinical decision support systems based on emerging technologies. They consider the changes generated by the upraising social technologies and the challenges brought by the interactive knowledge building within vast online communities.Knowledge Acquisition, CDDSS, 2D Barcodes, Mobile Interface

PlinyCompute: A Platform for High-Performance, Distributed, Data-Intensive Tool Development

This paper describes PlinyCompute, a system for development of high-performance, data-intensive, distributed computing tools and libraries. In the large, PlinyCompute presents the programmer with a very high-level, declarative interface, relying on automatic, relational-database style optimization to figure out how to stage distributed computations. However, in the small, PlinyCompute presents the capable systems programmer with a persistent object data model and API (the "PC object model") and associated memory management system that has been designed from the ground-up for high performance, distributed, data-intensive computing. This contrasts with most other Big Data systems, which are constructed on top of the Java Virtual Machine (JVM), and hence must at least partially cede performance-critical concerns such as memory management (including layout and de/allocation) and virtual method/function dispatch to the JVM. This hybrid approach---declarative in the large, trusting the programmer's ability to utilize PC object model efficiently in the small---results in a system that is ideal for the development of reusable, data-intensive tools and libraries. Through extensive benchmarking, we show that implementing complex objects manipulation and non-trivial, library-style computations on top of PlinyCompute can result in a speedup of 2x to more than 50x or more compared to equivalent implementations on Spark.Comment: 48 pages, including references and Appendi

Programming Persistent Memory

Beginning and experienced programmers will use this comprehensive guide to persistent memory programming. You will understand how persistent memory brings together several new software/hardware requirements, and offers great promise for better performance and faster application startup times—a huge leap forward in byte-addressable capacity compared with current DRAM offerings. This revolutionary new technology gives applications significant performance and capacity improvements over existing technologies. It requires a new way of thinking and developing, which makes this highly disruptive to the IT/computing industry. The full spectrum of industry sectors that will benefit from this technology include, but are not limited to, in-memory and traditional databases, AI, analytics, HPC, virtualization, and big data. Programming Persistent Memory describes the technology and why it is exciting the industry. It covers the operating system and hardware requirements as well as how to create development environments using emulated or real persistent memory hardware. The book explains fundamental concepts; provides an introduction to persistent memory programming APIs for C, C++, JavaScript, and other languages; discusses RMDA with persistent memory; reviews security features; and presents many examples. Source code and examples that you can run on your own systems are included. What You’ll Learn Understand what persistent memory is, what it does, and the value it brings to the industry Become familiar with the operating system and hardware requirements to use persistent memory Know the fundamentals of persistent memory programming: why it is different from current programming methods, and what developers need to keep in mind when programming for persistence Look at persistent memory application development by example using the Persistent Memory Development Kit (PMDK) Design and optimize data structures for persistent memory Study how real-world applications are modified to leverage persistent memory Utilize the tools available for persistent memory programming, application performance profiling, and debugging Who This Book Is For C, C++, Java, and Python developers, but will also be useful to software, cloud, and hardware architects across a broad spectrum of sectors, including cloud service providers, independent software vendors, high performance compute, artificial intelligence, data analytics, big data, etc