Towards Energy Consumption Verification via Static Analysis

In this paper we leverage an existing general framework for resource usage verification and specialize it for verifying energy consumption specifications of embedded programs. Such specifications can include both lower and upper bounds on energy usage, and they can express intervals within which energy usage is to be certified to be within such bounds. The bounds of the intervals can be given in general as functions on input data sizes. Our verification system can prove whether such energy usage specifications are met or not. It can also infer the particular conditions under which the specifications hold. To this end, these conditions are also expressed as intervals of functions of input data sizes, such that a given specification can be proved for some intervals but disproved for others. The specifications themselves can also include preconditions expressing intervals for input data sizes. We report on a prototype implementation of our approach within the CiaoPP system for the XC language and XS1-L architecture, and illustrate with an example how embedded software developers can use this tool, and in particular for determining values for program parameters that ensure meeting a given energy budget while minimizing the loss in quality of service.Comment: Presented at HIP3ES, 2015 (arXiv: 1501.03064

Symbolic and analytic techniques for resource analysis of Java bytecode

Recent work in resource analysis has translated the idea of amortised resource analysis to imperative languages using a program logic that allows mixing of assertions about heap shapes, in the tradition of separation logic, and assertions about consumable resources. Separately, polyhedral methods have been used to calculate bounds on numbers of iterations in loop-based programs. We are attempting to combine these ideas to deal with Java programs involving both data structures and loops, focusing on the bytecode level rather than on source code

Optimizing I/O for Big Array Analytics

Big array analytics is becoming indispensable in answering important scientific and business questions. Most analysis tasks consist of multiple steps, each making one or multiple passes over the arrays to be analyzed and generating intermediate results. In the big data setting, I/O optimization is a key to efficient analytics. In this paper, we develop a framework and techniques for capturing a broad range of analysis tasks expressible in nested-loop forms, representing them in a declarative way, and optimizing their I/O by identifying sharing opportunities. Experiment results show that our optimizer is capable of finding execution plans that exploit nontrivial I/O sharing opportunities with significant savings.Comment: VLDB201

Eliminating Network Protocol Vulnerabilities Through Abstraction and Systems Language Design

Incorrect implementations of network protocol message specifications affect the stability, security, and cost of network system development. Most implementation defects fall into one of three categories of well defined message constraints. However, the general process of constructing network protocol stacks and systems does not capture these categorical con- straints. We introduce a systems programming language with new abstractions that capture these constraints. Safe and efficient implementations of standard message handling operations are synthesized by our compiler, and whole-program analysis is used to ensure constraints are never violated. We present language examples using the OpenFlow protocol

ASCR/HEP Exascale Requirements Review Report

This draft report summarizes and details the findings, results, and recommendations derived from the ASCR/HEP Exascale Requirements Review meeting held in June, 2015. The main conclusions are as follows. 1) Larger, more capable computing and data facilities are needed to support HEP science goals in all three frontiers: Energy, Intensity, and Cosmic. The expected scale of the demand at the 2025 timescale is at least two orders of magnitude -- and in some cases greater -- than that available currently. 2) The growth rate of data produced by simulations is overwhelming the current ability, of both facilities and researchers, to store and analyze it. Additional resources and new techniques for data analysis are urgently needed. 3) Data rates and volumes from HEP experimental facilities are also straining the ability to store and analyze large and complex data volumes. Appropriately configured leadership-class facilities can play a transformational role in enabling scientific discovery from these datasets. 4) A close integration of HPC simulation and data analysis will aid greatly in interpreting results from HEP experiments. Such an integration will minimize data movement and facilitate interdependent workflows. 5) Long-range planning between HEP and ASCR will be required to meet HEP's research needs. To best use ASCR HPC resources the experimental HEP program needs a) an established long-term plan for access to ASCR computational and data resources, b) an ability to map workflows onto HPC resources, c) the ability for ASCR facilities to accommodate workflows run by collaborations that can have thousands of individual members, d) to transition codes to the next-generation HPC platforms that will be available at ASCR facilities, e) to build up and train a workforce capable of developing and using simulations and analysis to support HEP scientific research on next-generation systems.Comment: 77 pages, 13 Figures; draft report, subject to further revisio

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

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

Telescope Bibliographies: an Essential Component of Archival Data Management and Operations

Assessing the impact of astronomical facilities rests upon an evaluation of the scientific discoveries which their data have enabled. Telescope bibliographies, which link data products with the literature, provide a way to use bibliometrics as an impact measure for the underlying data. In this paper we argue that the creation and maintenance of telescope bibliographies should be considered an integral part of an observatory's operations. We review the existing tools, services, and workflows which support these curation activities, giving an estimate of the effort and expertise required to maintain an archive-based telescope bibliography.Comment: 10 pages, 3 figures, to appear in SPIE Astronomical Telescopes and Instrumentation, SPIE Conference Series 844