PyCARL: A PyNN Interface for Hardware-Software Co-Simulation of Spiking Neural Network

We present PyCARL, a PyNN-based common Python programming interface for hardware-software co-simulation of spiking neural network (SNN). Through PyCARL, we make the following two key contributions. First, we provide an interface of PyNN to CARLsim, a computationally-efficient, GPU-accelerated and biophysically-detailed SNN simulator. PyCARL facilitates joint development of machine learning models and code sharing between CARLsim and PyNN users, promoting an integrated and larger neuromorphic community. Second, we integrate cycle-accurate models of state-of-the-art neuromorphic hardware such as TrueNorth, Loihi, and DynapSE in PyCARL, to accurately model hardware latencies that delay spikes between communicating neurons and degrade performance. PyCARL allows users to analyze and optimize the performance difference between software-only simulation and hardware-software co-simulation of their machine learning models. We show that system designers can also use PyCARL to perform design-space exploration early in the product development stage, facilitating faster time-to-deployment of neuromorphic products. We evaluate the memory usage and simulation time of PyCARL using functionality tests, synthetic SNNs, and realistic applications. Our results demonstrate that for large SNNs, PyCARL does not lead to any significant overhead compared to CARLsim. We also use PyCARL to analyze these SNNs for a state-of-the-art neuromorphic hardware and demonstrate a significant performance deviation from software-only simulations. PyCARL allows to evaluate and minimize such differences early during model development.Comment: 10 pages, 25 figures. Accepted for publication at International Joint Conference on Neural Networks (IJCNN) 202

Actors: The Ideal Abstraction for Programming Kernel-Based Concurrency

GPU and multicore hardware architectures are commonly used in many different application areas to accelerate problem solutions relative to single CPU architectures. The typical approach to accessing these hardware architectures requires embedding logic into the programming language used to construct the application; the two primary forms of embedding are: calls to API routines to access the concurrent functionality, or pragmas providing concurrency hints to a language compiler such that particular blocks of code are targeted to the concurrent functionality. The former approach is verbose and semantically bankrupt, while the success of the latter approach is restricted to simple, static uses of the functionality. Actor-based applications are constructed from independent, encapsulated actors that interact through strongly-typed channels. This paper presents a first attempt at using actors to program kernels targeted at such concurrent hardware. Besides the glove-like fit of a kernel to the actor abstraction, quantitative code analysis shows that actor-based kernels are always significantly simpler than API-based coding, and generally simpler than pragma-based coding. Additionally, performance measurements show that the overheads of actor-based kernels are commensurate to API-based kernels, and range from equivalent to vastly improved for pragma-based annotations, both for sample and real-world applications

Beyond XSPEC: Towards Highly Configurable Analysis

We present a quantitative comparison between software features of the defacto standard X-ray spectral analysis tool, XSPEC, and ISIS, the Interactive Spectral Interpretation System. Our emphasis is on customized analysis, with ISIS offered as a strong example of configurable software. While noting that XSPEC has been of immense value to astronomers, and that its scientific core is moderately extensible--most commonly via the inclusion of user contributed "local models"--we identify a series of limitations with its use beyond conventional spectral modeling. We argue that from the viewpoint of the astronomical user, the XSPEC internal structure presents a Black Box Problem, with many of its important features hidden from the top-level interface, thus discouraging user customization. Drawing from examples in custom modeling, numerical analysis, parallel computation, visualization, data management, and automated code generation, we show how a numerically scriptable, modular, and extensible analysis platform such as ISIS facilitates many forms of advanced astrophysical inquiry.Comment: Accepted by PASP, for July 2008 (15 pages

An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

The essence of component-based design and coordination

Is there a characteristic of coordination languages that makes them qualitatively different from general programming languages and deserves special academic attention? This report proposes a nuanced answer in three parts. The first part highlights that coordination languages are the means by which composite software applications can be specified using components that are only available separately, or later in time, via standard interfacing mechanisms. The second part highlights that most currently used languages provide mechanisms to use externally provided components, and thus exhibit some elements of coordination. However not all do, and the availability of an external interface thus forms an objective and qualitative criterion that distinguishes coordination. The third part argues that despite the qualitative difference, the segregation of academic attention away from general language design and implementation has non-obvious cost trade-offs.Comment: 8 pages, 2 figures, 3 table

Parallel Computation in Econometrics: A Simplified Approach

Parallel computation has a long history in econometric computing, but is not at all wide spread. We believe that a major impediment is the labour cost of coding for parallel architectures. Moreover, programs for specific hardware often become obsolete quite quickly. Our approach is to take a popular matrix programming language (Ox), and implement a message-passing interface using MPI. Next, object-oriented programming allows us to hide the specific parallelization code, so that a program does not need to be rewritten when it is ported from the desktop to a distributed network of computers. Our focus is on so-called embarrassingly parallel computations, and we address the issue of parallel random number generation.Code optimization; Econometrics; High-performance computing; Matrix-programming language; Monte Carlo; MPI; Ox; Parallel computing; Random number generation.

Towards Python-based Domain-specific Languages for Self-reconfigurable Modular Robotics Research

This paper explores the role of operating system and high-level languages in the development of software and domain-specific languages (DSLs) for self-reconfigurable robotics. We review some of the current trends in self-reconfigurable robotics and describe the development of a software system for ATRON II which utilizes Linux and Python to significantly improve software abstraction and portability while providing some basic features which could prove useful when using Python, either stand-alone or via a DSL, on a self-reconfigurable robot system. These features include transparent socket communication, module identification, easy software transfer and reliable module-to-module communication. The end result is a software platform for modular robots that where appropriate builds on existing work in operating systems, virtual machines, middleware and high-level languages.Comment: Presented at DSLRob 2011 (arXiv:1212.3308