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

TrIMS: Transparent and Isolated Model Sharing for Low Latency Deep LearningInference in Function as a Service Environments

Deep neural networks (DNNs) have become core computation components within low latency Function as a Service (FaaS) prediction pipelines: including image recognition, object detection, natural language processing, speech synthesis, and personalized recommendation pipelines. Cloud computing, as the de-facto backbone of modern computing infrastructure for both enterprise and consumer applications, has to be able to handle user-defined pipelines of diverse DNN inference workloads while maintaining isolation and latency guarantees, and minimizing resource waste. The current solution for guaranteeing isolation within FaaS is suboptimal -- suffering from "cold start" latency. A major cause of such inefficiency is the need to move large amount of model data within and across servers. We propose TrIMS as a novel solution to address these issues. Our proposed solution consists of a persistent model store across the GPU, CPU, local storage, and cloud storage hierarchy, an efficient resource management layer that provides isolation, and a succinct set of application APIs and container technologies for easy and transparent integration with FaaS, Deep Learning (DL) frameworks, and user code. We demonstrate our solution by interfacing TrIMS with the Apache MXNet framework and demonstrate up to 24x speedup in latency for image classification models and up to 210x speedup for large models. We achieve up to 8x system throughput improvement.Comment: In Proceedings CLOUD 201

A Peer-to-Peer Middleware Framework for Resilient Persistent Programming

The persistent programming systems of the 1980s offered a programming model that integrated computation and long-term storage. In these systems, reliable applications could be engineered without requiring the programmer to write translation code to manage the transfer of data to and from non-volatile storage. More importantly, it simplified the programmer's conceptual model of an application, and avoided the many coherency problems that result from multiple cached copies of the same information. Although technically innovative, persistent languages were not widely adopted, perhaps due in part to their closed-world model. Each persistent store was located on a single host, and there were no flexible mechanisms for communication or transfer of data between separate stores. Here we re-open the work on persistence and combine it with modern peer-to-peer techniques in order to provide support for orthogonal persistence in resilient and potentially long-running distributed applications. Our vision is of an infrastructure within which an application can be developed and distributed with minimal modification, whereupon the application becomes resilient to certain failure modes. If a node, or the connection to it, fails during execution of the application, the objects are re-instantiated from distributed replicas, without their reference holders being aware of the failure. Furthermore, we believe that this can be achieved within a spectrum of application programmer intervention, ranging from minimal to totally prescriptive, as desired. The same mechanisms encompass an orthogonally persistent programming model. We outline our approach to implementing this vision, and describe current progress.Comment: Submitted to EuroSys 200

Kernel arquitecture for CAD/CAM in shipbuilding enviroments

The capabilities of complex software products such as CAD/CAM systems are strongly supported by basic information technologies related with data management, visualization, communication, geometry modeling and others related with the development process. These basic information technologies are involved in a continuous evolution process, but over recent years this evolution has been dramatic. The main reason for this has been that new hardware capabilities (including graphic cards) are available at very low cost, but also a contributing factor has been the evolution of the prices of basic software. To take advantage of these new features, the existing CAD/CAM systems must undergo a complete and drastic redesign. This process is complicated but strategic for the future evolution of a system. There are several examples in the market of how a bad decision has lead to a cul-de-sac (both technically and commercially). This paper describes what the authors consider are the basic architectural components of a kernel for a CAD/CAM system oriented to shipbuilding. The proposed solution is a combination of in-house developed frameworks together with commercial products that are accepted as standard components. The proportion of in-house frameworks within this combination of products is a key factor, especially when considering CAD/CAM systems oriented to shipbuilding. General-purpose CAD/CAM systems are mainly oriented to the mechanical CAD market. For this reason several basic products exist devoted to geometry modelling in this context. But these basic products are not well suited to deal with the very specific geometry modelling requirements of a CAD/CAM system oriented to shipbuilding. The complexity of the ship model, the different model requirements through its short and changing life cycle and the many different disciplines involved in the process are reasons for this inadequacy. Apart from these basic frameworks, specific shipbuilding frameworks are also required. This second layer is built over the basic technology components mentioned above. This paper describes in detail the technological frameworks which have been used to develop the latest FORAN version.Postprint (published version

Map-Based Transparent Persistence for Very Large Models

International audienceThe progressive industrial adoption of Model-Driven Engineering (MDE) is fostering the development of large tool ecosystems like the Eclipse Modeling project. These tools are built on top of a set of base technologies that have been primarily designed for small-scale scenarios, where models are manually developed. In particular, efficient runtime manipulation for large-scale models is an under-studied problem and this is hampering the application of MDE to several industrial scenarios.In this paper we introduce and evaluate a map-based persistence model for MDE tools. We use this model to build a transparent persistence layer for modeling tools, on top of a map-based database engine. The layer can be plugged into the Eclipse Modeling Framework, lowering execution times and memory consumption levels of other existing approaches. Empirical tests are performed based on a typical industrial scenario, model-driven reverse engineering, where very large software models originate from the analysis of massive code bases. The layer is freely distributed and can be immediately used for enhancing the scalability of any existing Eclipse Modeling tool