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Bounding data races in space and time

ACM SIGPLAN Notices 2018年第4期53卷 242-255页

作者： Dolan, Stephen Sivaramakrishnan, K.C. Madhavapeddy, Anil University of Cambridge United Kingdom

ISBN: (纸本)9781450349116

We propose a new semantics for shared-memory parallel programs that gives strong guarantees even in the presence of data races. Our local data race freedom property guarantees that all data-race-free portions of programs exhibit sequential semantics. We provide a straightforward operational semantics and an equivalent axiomatic model, and evaluate an implementation for the OCaml programming language. Our evaluation demonstrates that it is possible to balance a comprehensible memory model with a reasonable (no overhead on x86, ∼0.6% on ARM) sequential performance trade-off in a mainstream programming language. © 2018 ACM.

关键词： computer programming languages

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Female Choice Leads to a Switch in Oval Squid Male Mating Tactics

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BIOLOGICAL BULLETIN 2017年第3期233卷 219-226页

作者： Lin, Chun-Yen Chiao, Chuan-Chin Natl Tsing Hua Univ Inst Mol Med Hsinchu Taiwan Natl Tsing Hua Univ Inst Syst Neurosci Hsinchu Taiwan Natl Tsing Hua Univ Dept Life Sci Hsinchu Taiwan

Oval squids are polyandrous, with one female mating with multiple males during the spawning season. There are two alternative male mating tactics used by Sepioteuthis lessoniana. Larger males place spermatophores at the opening of the oviduct using a male-parallel mating posture, whereas smaller males attach spermatophores around the female buccal membrane using a male-upturned mating posture. If the route of egg transportation is taken into consideration, male-parallel mating would be expected to result in higher fertilization success than male-upturned mating. Although these male mating tactics are largely dependent on the body size of the male relative to that of the female, it is unclear how female choice affects the male's mating tactics and his mating success. Squids are highly visual animals, and they communicate through dynamic body patterning. In the present study, we observed that smaller male squids in captivity would attempt to mate with a larger female using the male-parallel tactic repeatedly, but they failed to be successful most of the time because of a rejection signal by the female. In contrast, when the males switched to the male-upturned tactic, the mating success rate was increased significantly, with much less female rejection signal. This finding suggests that female squids signal their mating receptivity visually and that male squids alter their mating tactics accordingly. This is the evidence to support the hypothesis that the switch in male mating tactics depends on female choice in oval squids and that this is transmitted via visual communication.

关键词： AMTs alternative mating tactics ML mantle length MP male-parallel MU male-upturned Spermatogonia male Switches AMT gene BLOC1S5 gene Oval tactics Squid Body Patterning computer programming languages Female PSMA2 gene Mating Copulation Superconducting quantum interference devices

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Backbone: A Multiphysics Framework for Coupling Nuclear Codes Based on CORBA and MPI

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JOURNAL OF NUCLEAR ENGINEERING AND RADIATION SCIENCE 2017年第1期3卷 011020页

作者： Liu, Yu Nishimura, Michael Seydaliev, Marat Piro, Markus Canadian Nucl Labs Fuel & Fuel Channel Safety Branch Chalk River ON K0J 1J0 Canada Univ Waterloo Dept Comp Sci Waterloo ON N2L 3G1 Canada

Recent trends in nuclear reactor performance and safety analyses increasingly rely on multiscale multiphysics computer simulations to enhance predictive capabilities by replacing conventional methods that are largely empirically based with a more scientifically based methodology. Through this approach, one addresses the issue of traditionally employing a suite of stand-alone codes that independently simulate various physical phenomena that were previously disconnected. Multiple computer simulations of different phenomena must exchange data during runtime to address these interdependencies. Previously, recommendations have been made regarding various approaches for piloting different design options of data coupling for multiphysics systems (Seydaliev and Caswell, 2014, "CORBA and MPI Based "Backbone" for Coupling Advanced Simulation Tools,"AECL Nucl. Rev., 3(2), pp. 83-90). This paper describes progress since the initial pilot study that outlined the implementation and execution of a new distribution framework, referred to as "Backbone," to provide the necessary runtime exchange of data between different codes. The Backbone, currently under development at the Canadian Nuclear Laboratories (CNL), is a hybrid design using both common object request broker architecture (CORBA) and message passing interface (MPI) systems. This paper also presents two preliminary cases for coupling existing nuclear performance and safety analysis codes used for simulating fuel behavior, fission product release, thermal hydraulics, and neutron transport through the Backbone. Additionally, a pilot study presents a few strategies of a new time step controller (TSC) to synchronize the codes coupled through the Backbone. A performance and fidelity comparison is presented between a simple heuristic method for determining time step length and a more advanced third-order method, which was selected to maximize configurability and effectiveness of temporal integration, saving time steps and reducin

关键词： Errors Fuels Simulation computer software computer programming languages Design Safety Coupled codes Control equipment computer programming Nuclear fission

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Estimating Total Mortality Rates from Mean Lengths and Catch Rates in Nonequilibrium Situations

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TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY 2017年第4期146卷 803-815页

作者： Huynh, Quang C. Gedamke, Todd Porch, Clay E. Hoenig, John M. Walter, John F. Bryan, Meaghan Brodziak, Jon Virginia Inst Marine Sci Coll William & Mary POB 1346 Gloucester Point VA 23062 USA Natl Marine Fisheries Serv Southeast Fisheries Sci Ctr 75 Virginia Beach Dr Miami FL 33149 USA Natl Marine Fisheries Serv Pacific Isl Fisheries Sci Ctr 1845 Wasp BlvdBldg 176 Honolulu HI 96818 USA MER Consultants 5521 Southeast Nassau Terrace Stuart FL 34997 USA

A series of estimates of the total mortality rate (Z) can be obtained by using the Beverton-Holt nonequilibrium-based approach of Gedamke and Hoenig (2006) on observations of population mean length over time (ML model). In contrast, only relative mortality rates (not absolute values) can be obtained from a time series of catch rates. We derived the transitional behavior of the catch rate following a change in total mortality in the population. From this derivation, we developed a new-method to estimate Z that utilizes both mean lengths and catch rates (MLCR model). Both theML model and the MLCR model assume constant recruitment in the population. We used a simulation study to test performance when recruitment is variable. Simulations over various scenarios of Z and recruitment variability showed that there may be correlated residuals in the mean lengths and catch rates arising from fluctuations in recruitment. However, the root mean square errors of the Z estimates and the change point (i.e., the year when mortality changed) were smaller in the MLCR model than in the ML model, indicating that the MLCR model can better account for variable recruitment. Both methods were then applied to Mutton Snapper Lutjanus analis in Puerto Rico to illustrate their potential application to assess data-limited stocks. The ML model estimated an increase in Z, but the MLCR model also estimated a subsequent reduction in Z when the catch rate data were considered.

关键词： catch computer programming languages Fishing power Time series ROOT-MEAN-SQUARE ERRORS Mortality zero speed mean length Fisheries data Recruitment Lutjanus analis

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1 ML Wetting Layer upon Ga(As)Sb Quantum Dot (QD) Formation on GaAs Substrate Monitored with Reflectance Anisotropy Spectroscopy (RAS)

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ADVANCES IN OPTOELECTRONICS 2018年第1期2018卷

作者： Fouckhardt, Henning Strassner, Johannes Loeber, Thomas H. Doering, Christoph TUK Phys Dept Integrated Optoelect & Microopt IOE Res Grp POB 3049 D-67653 Kaiserslautern Germany TUK Phys Dept NSC POB 3049 D-67653 Kaiserslautern Germany

III/V semiconductor quantum dots (QD) are in the focus of optoelectronics research for about 25 years now. Most of the work has been done on InAs QD on GaAs substrate. But, e.g., Ga(As)Sb (antimonide) QD on GaAs substrate/buffer have also gained attention for the last 12 years. There is a scientific dispute on whether there is a wetting layer before antimonide QD formation, as commonly expected for Stransky-Krastanov growth, or not. Usually ex situ photoluminescence (PL) and atomic force microscope (AFM) measurements are performed to resolve similar issues. In this contribution, we show that reflectance anisotropy/difference spectroscopy (RAS/RDS) can be used for the same purpose as an in situ, real-time monitoring technique. It can be employed not only to identify QD growth via a distinct RAS spectrum, but also to get information on the existence of a wetting layer and its thickness. The data suggest that for antimonide QD growth the wetting layer has a thickness of 1 ML (one monolayer) only.

关键词： computer programming languages quadrant depression gallium arsenides Photoelectricity ras Oncogene Scientific methods Reflectance anisotropy spectroscopy

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Machine learning applications in cell image analysis

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IMMUNOLOGY AND CELL BIOLOGY 2017年第6期95卷 525-530页

作者： Kan, Andrey Walter & Eliza Hall Inst Med Res Div Immunol 1G Royal Parade Parkville Vic 3052 Australia Univ Melbourne Dept Med Biol Parkville Vic Australia

Machine learning (ML) refers to a set of automatic pattern recognition methods that have been successfully applied across various problem domains, including biomedical image analysis. This review focuses on ML applications for image analysis in light microscopy experiments with typical tasks of segmenting and tracking individual cells, and modelling of reconstructed lineage trees. After describing a typical image analysis pipeline and highlighting challenges of automatic analysis (for example, variability in cell morphology, tracking in presence of clutters) this review gives a brief historical outlook of ML, followed by basic concepts and definitions required for understanding examples. This article then presents several example applications at various image processing stages, including the use of supervised learning methods for improving cell segmentation, and the application of active learning for tracking. The review concludes with remarks on parameter setting and future directions.

关键词： computer programming languages Machine Learning automatic analysis clutter Automated Pattern Recognition parameter setting image analysis

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Improving vulnerability inspection efficiency using active learning

arXiv

引用

arXiv 2018年

作者： Yu, Zhe Theisen, Christopher Williams, Laurie Menzies, Tim Department of Computer Science North Carolina State University Raleigh United States Microsoft Seattle United States

Software engineers can find vulnerabilities with less effort if they are directed towards code that might contain more vulnerabilities. HARMLESS is an incremental support vector machine tool that builds a vulnerability prediction model from the source code inspected to date, then suggests what source code files should be inspected next. In this way, HARMLESS can reduce the time and effort required to achieve some desired level of recall for finding vulnerabilities. The tool also provides feedback on when to stop (at that desired level of recall) while at the same time, correcting human errors by double-checking suspicious files. This paper evaluates HARMLESS on Mozilla Firefox vulnerability data. HARMLESS found 80, 90, 95, 99% of the vulnerabilities by inspecting 10, 16, 20, 34% of the source code files. When targeting 90, 95, 99% recall, HARMLESS could stop after inspecting 23, 30, 47% of the source code files. Even when human reviewers fail to identify half of the vulnerabilities (50% false negative rate), HARMLESS could detect 96% of the missing vulnerabilities by double-checking half of the inspected files. Our results serve to highlight the very steep cost of protecting software from vulnerabilities (in our case study that cost is, for example, the human effort of inspecting 28,750 × 20% = 5,750 source code files to identify 95% of the vulnerabilities). While this result could benefit the mission-critical projects where human resources are available for inspecting thousands of source code files, the research challenge for future work is how to further reduce that cost. The conclusion of this paper discusses various ways that goal might be achieved. Copyright © 2018, The Authors. All rights reserved.

关键词： computer programming languages

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Size-change termination as a contract: Dynamically and statically enforcing termination for higher-order programs

arXiv

引用

arXiv 2018年

作者： Nguyn, Phúc C. Tobin-Hochstadt, Sam Gilray, Thomas van Horn, David University of Maryland College ParkMD United States Indiana University BloomingtonIN United States University of Alabama BirminghamAL United States

Termination is an important but undecidable program property, which has led to a large body of work on static methods for conservatively predicting or enforcing termination. One such method is the size-change termination approach of Lee, Jones, and Ben-Amram, which operates in two phases: (1) abstract programs into "size-change graphs," and (2) check these graphs for the size-change property: the existence of paths that lead to infinite decreasing sequences. We transpose these two phases with an operational semantics that accounts for the run-time enforcement of the size-change property, postponing (or entirely avoiding) program abstraction. This choice has two key consequences: (1) size-change termination can be checked at run-time and (2) termination can be rephrased as a safety property analyzed using existing methods for systematic abstraction. We formulate run-time size-change checks as contracts in the style of Findler and Felleisen. The result compliments existing contracts that enforce partial correctness specifications to obtain contracts for total correctness. Our approach combines the robustness of the size-change principle for termination with the precise information available at run-time. It has tunable overhead and can check for nontermination without the conservativeness necessary in static checking. To obtain a sound and computable termination analysis, we apply existing abstract interpretation techniques directly to the operational semantics, avoiding the need for custom abstractions for termination. The resulting analyzer is competitive with with existing, purpose-built analyzers. Copyright © 2018, The Authors. All rights reserved.

关键词： computer programming languages

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Verifying C11 programs operationally

arXiv

引用

arXiv 2018年

作者： Doherty, Simon Dongol, Brijesh Wehrheim, Heike Derrick, John Department of Computer Science University of Sheffield Department of Computer Science University of Surrey Department of Computer Science University of Paderborn

This paper develops an operational semantics for a release-acquire fragment of the C11 memory model with relaxed accesses. We show that the semantics is both sound and complete with respect to the axiomatic model. The semantics relies on a per-thread notion of observability, which allows one to reason about a weak memory C11 program in program order. On top of this, we develop a proof calculus for invariant-based reasoning, which we use to verify the release-acquire version of Peterson's mutual exclusion algorithm. Copyright © 2018, The Authors. All rights reserved.

关键词： computer programming languages

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2D Stencil Computation on Cyclone V SoC FPGA using OpenCL

2D Stencil Computation on Cyclone V SoC FPGA using OpenCL

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International Conference on Radar, Antenna, Microwave, Electronics, and Telecommunications (ICRAMET)

作者： Iman Firmansyah Yusuf Nur Wijayanto Yoshiki Yamaguchi Graduate School of Systems and Information Engineering University of Tsukuba Tsukuba Japan Research Center for Electronics and Telecommunication Indonesian Institute of Sciences (LIPI) Bandung Indonesia Faculty of Engineering Information and Systems University of Tsukuba Tsukuba Japan

ISBN: (纸本)9781538665206;9781538665190

We present the implementation of a 2D stencil computation on Cyclone V SoC Field Programmable Gate Array (FPGA). The heat equation is chosen as a study case for the 2D stencil problem. To reduce the development time in FPGA programming, OpenCL programming language is employed to develop the kernel for the stencil computation. OpenCL is a framework to develop the kernel that can be executed in heterogeneous platforms such as CPU, DSP, GPU, and FPGA. In the study, we compare the execution time and power consumption between core i5 4300U CPU and Cyclone V FPGA. The experiment shows that the Cyclone V SoC FPGA is faster than a single core i5 4300U CPU in executing the 2D stencil computation. The research also shows that the FPGA consumes low power.

关键词： field programmable gate arrays programming languages system-on-chip Field programmable gate arrays computer programming languages system-on-chip cyclones development time Seeds execution time arithmetic Vanadium central processing units Kernel

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