Event Traces Research Articles

Instrumentation for low noise nanopore-based ionic current recording under laser illumination.

We describe a nanopore-based optofluidic instrument capable of performing low-noise ionic current recordings of individual biomolecules under laser illumination. In such systems, simultaneous optical measurements generally introduce significant parasitic noise in the electrical signal, which can severely reduce the instrument sensitivity, critically hindering the monitoring of single-molecule events in the ionic current traces. Here, we present design rules and describe simple adjustments to the experimental setup to mitigate the different noise sources encountered when integrating optical components to an electrical nanopore system. In particular, we address the contributions to the electrical noise spectra from illuminating the nanopore during ionic current recording and mitigate those effects through control of the illumination source and the use of a PDMS layer on the SiNx membrane. We demonstrate the effectiveness of our noise minimization strategies by showing the detection of DNA translocation events during membrane illumination with a signal-to-noise ratio of ∼10 at 10 kHz bandwidth. The instrumental guidelines for noise minimization that we report are applicable to a wide range of nanopore-based optofluidic systems and offer the possibility of enhancing the quality of synchronous optical and electrical signals obtained during single-molecule nanopore-based analysis.

Openness of Natural Information Processing Systems and Short-Term and Long-Term Memory

In this paper, various types of memory are considered.Development of the nervous system and the brain of organisms ensures expansion of species with more developed brain. Different characteristics of the brain zones have created different conditions for forming traces of events. The various traces of trace events formed in different parts of the brain provided a wider range of functions and brain responses, which contributed to the survival and expansion of species. The work describes the appearance of memory varieties and the causes of these varieties.

Non-Traditional Security Dilemmas: Can Military Operations other than War Intensify Security Competition in Asia?

ABSTRACTCan seemingly benign deployments of armed forces on military operations other than war (MOOTW) – such as humanitarian relief and anti-piracy missions – exacerbate security dilemmas? The security dilemma holds a central role in international relations theory, but existing analyses overlook whether non-traditional security operations drive security competition if perceived as threatening. Despite increased MOOTW participation throughout Asia, scant attention has been paid to the broader strategic implications of these operations. This article proposes a hypothesis in which MOOTW participation exacerbates security competition by revealing military capabilities and providing states with skills that make offensive action easier. The article tests this hypothesis by process tracing events surrounding Japan’s post-3/11 earthquake response. The findings suggest that MOOTW participation intensifies long-term security competition, especially when rising powers are involved.

Indian Seamen and Australian Unions Fighting for Labour Rights: "The Real Facts of the Lascars' Case" of 1939

In 1939, the outbreak of war prompted strikes by Indian seafarers across the empire. This article traces events in Australia as Indian seafarers asserted their labour rights and in doing so contest...

Scalable communication event tracing via clustering

Communication traces help developers of high-performance computing (HPC) applications understand and improve their codes. When run on large-scale HPC facilities, the scalability of tracing tools becomes a challenge. To address this problem, traces can be clustered into groups of processes that exhibit similar behavior. Instead of collecting trace information of each individual node, it then suffices to collect a trace of a small set of representative nodes, namely one per cluster. However, clustering algorithms themselves need to have low overhead, be scalable, and adapt to application characteristics. We devised an adaptive clustering algorithm for large-scale applications called ACURDION that traces the MPI communication of code with O(log P) time complexity. First, ACURDION identifies the parameters that differ across processes by using a logarithmic algorithm called Adaptive Signature Building. Second, it clusters the processes based on those parameters. Experiments show that collecting traces of just nine nodes/clusters suffices to capture the communication behavior of all nodes for a wide set of HPC benchmarks codes while retaining sufficient accuracy of trace events and parameters. In summary, ACURDION improves trace scalability and automation over prior approaches.

JSTrace: Fast reproducing web application errors

JavaScript has become the most popular language for client-side web applications. Due to JavaScript's highly-dynamic and event-driven features, it is challenging to diagnose web application errors. Record-replay techniques are used to reproduce errors in web applications. After a long run, these techniques will record a long event trace that triggers an error. Although the error-related events are few, they are interleaved with other massive error-irrelevant events. It is time-consuming to diagnose errors with long event traces.In this article, we present JSTrace, which effectively removes error-irrelevant events from the long event trace, and further facilitates error diagnosis. Based on fine-grained dependences of JavaScript and DOM instructions, we develop a novel dynamic slicing technique that can remove events irrelevant to the error. We further present rules to remove irrelevant events, which cannot be removed by dynamic slicing. In this process, many events and related instructions are removed without losing the error reproducing accuracy. Our evaluation on 13 real-world web application errors shows that the reduced event traces can faithfully reproduce errors with an average reduction rate of 97%. We further performed case studies on 4 real-world errors, and the result shows that JSTrace is useful to diagnose web application errors.

Monitoring with Parametrized Extended Life Sequence Charts

Runtime verification is a lightweight verification technique that checks whether an execution of a system satisfies a given property. A problem in monitoring specification languages is to express parametric properties, where the correctness of a property depends on both the temporal relations of events, and the data carried by events. In this paper, we introduce parametrized extended live sequence charts (PeLSCs) for monitoring sequences of data-carrying events. The language of PeLSCs is extended from life sequence charts by introducing condition and assignment structures. We develop a translation from PeLSCs into the hybrid logic HL, and prove that the word problem of the PeLSCs is linear with respect to the size of a parametrized event trace. Therefore, the formalism is feasible for on-line monitoring.

Design Evaluation of a Performance Analysis Trace Repository

Parallel and high performance computing experts are obsessed with performance and scalability. Performance analysis and tuning are important and complex but there are a number of software tools to support this. One methodology is the detailed recording of parallel runtime behavior in event traces and their subsequent analysis. This regularly produces very large data sets with their own challenges for handling and data management. This paper evaluates the utilization of the MASi research data management service as a trace repository to store, manage, and find traces in an efficient and usable way. First, we give an introduction to trace technologies in general, metadata in OTF2 traces specifically, and the MASi research data management service. Then, the trace repository is described with its potential for both performance analysts and parallel tool developers, followed with how we implemented it using existing metadata and how it can utilized. Finally, we give an outlook on how we plan to put the repository into productive use for the benefit of researchers using traces.

Indian Seamen and Australian Unions Fighting for Labour Rights: “The Real Facts of the Lascars' Case” of 1939

In 1939, the outbreak of war prompted strikes by Indian seafarers across the empire. This article traces events in Australia as Indian seafarers asserted their labour rights and in doing so contested their exploitative working conditions as “lascars” or the seagoing equivalent of shore-based indentured “coolie” labour. While the Australian government responded in ways that reinforced the “coolie” status of Indian seafarers, the Australian labour movement, most notably the maritime unions, threw their support behind the strikers. The Seamen’s Union of Australia and Waterside Workers’ Federation provided material aid, funded the strikers’ legal costs and, significantly, challenged official and media representations of the Indian seafarers as “coolies” with explanations of their exploitative conditions as “workers.” This action was significant because western seafarers’ lack of support has been seen as contributing to Indian seafarers’ difficulties in challenging their working conditions and status as “lascars.” Showing how Indian and Australian workers together resisted labour categories and fought for political rights complicates prevailing views of the relationship between Australian unions and Asian workers and demonstrates a consistency with the earlier internationalism of Australian maritime unions identified by previous historians.

Identifying the Root Causes of Wait States in Large-Scale Parallel Applications

Driven by growing application requirements and accelerated by current trends in microprocessor design, the number of processor cores on modern supercomputers is increasing from generation to generation. However, load or communication imbalance prevents many codes from taking advantage of the available parallelism, as delays of single processes may spread wait states across the entire machine. Moreover, when employing complex point-to-point communication patterns, wait states may propagate along far-reaching cause-effect chains that are hard to track manually and that complicate an assessment of the actual costs of an imbalance. Building on earlier work by Meira, Jr., et al., we present a scalable approach that identifies program wait states and attributes their costs in terms of resource waste to their original cause. By replaying event traces in parallel both forward and backward, we can identify the processes and call paths responsible for the most severe imbalances, even for runs with hundreds of thousands of processes.

Automated Determining of Manufacturing Properties and Their Evolutionary Changes from Event Traces

Production plants are usually kept in operation for several decades. During this long operational phase operation requirements and other production conditions change frequently. Accordingly, the plants have to be adjusted in behavior and/or structure by adapting software and physics of the plant to avoid degeneration. Unfortunately, in industrial practice, changes, especially smaller ones, are often performed ad-hoc without appropriate adaptation of formal models or documentation. As a consequence, knowledge about the process is only implicitly available and an evaluation of performed changes is often omitted, resulting in sub-optimal production performance. Present research approaches to overcome these deficiencies usually concentrate on (a) manual modelling with manual or automatic analysis on a high level of abstraction; or (b) on automatic model generation from observations without lifting gathered knowledge to easy interpretable indicators. The approach presented in this paper combines both methods (a) and (b) by learning models from observation of input / output signals of the production plant’s control system. Semantics are added by using a priori information modelling which is less tedious compared to modelling the process itself. The learned models are used to automatically detect changes by continuously comparing their behavior with real plant behavior during operation as well as to evaluate performed changes. An analysis of the models results in high-level property values such as key performance indicators or flexibility measures of the production system.

A Subpopulation of Label-Retaining Cells of the Kidney Papilla Regenerates Injured Kidney Medullary Tubules.

SummaryTo determine whether adult kidney papillary label-retaining cells (pLRCs) are specialized precursors, we analyzed their transcription profile. Among genes overexpressed in pLRCs, we selected candidate genes to perform qPCR and immunodetection of their encoded proteins. We found that Zfyve27, which encodes protrudin, identified a subpopulation of pLRCs. With Zfyve27-CreERT2 transgenic and reporter mice we generated bitransgenic animals and performed cell-lineage analysis. Post tamoxifen, Zfyve27-CreERT2 marked cells preferentially located in the upper part of the papilla. These cells were low cycling and did not generate progeny even after long-term observation, thus they did not appear to contribute to kidney homeostasis. However, after kidney injury, but only if severe, they activated a program of proliferation, migration, and morphogenesis generating multiple and long tubular segments. Remarkably these regenerated tubules were located preferentially in the kidney medulla, indicating that repair of injury in the kidney is regionally specified. These results suggest that different parts of the kidney have different progenitor cell pools.

Computing Trace Alignment against Declarative Process Models through Planning

Process mining techniques aim at extracting non-trivial knowledge from event traces, which record the concrete execution of business processes. Typically, traces are "dirty" and contain spurious events or miss relevant events. Trace alignment is the problem of cleaning such traces against a process specification. There has recently been a growing use of declarative process models, e.g., Declare (based on LTL over finite traces) to capture constraints on the allowed task flows. We demonstrate here how state-of-the-art classical planning technologies can be used for trace alignment by presenting a suitable encoding. We report experimental results using a real log from a financial domain.

Lightweight control-flow instrumentation and postmortem analysis in support of debugging

Debugging is difficult and costly. As a programmer looks for a bug, it would be helpful to see a complete trace of events leading to the point of failure. Unfortunately, full tracing is simply too slow to use after deployment, and may even be impractical during testing. We aid post-deployment debugging by giving programmers additional information about program activity shortly before failure. We use latent information in post-failure memory dumps, augmented by low-overhead, tunable run-time tracing. Our results with a realistically-tuned tracing scheme show low enough overhead (0–5 %) to be used in production runs. We demonstrate several potential uses of this enhanced information, including a novel postmortem static slice restriction technique and a reduced view of potentially-executed code. Experimental evaluation shows our approach to be very effective. For example, our analyses shrink stack-sensitive interprocedural static slices by 53–78 % in larger applications.

Ordering Traces Logically to Identify Lateness in Message Passing Programs

Event traces are valuable for understanding the behavior of parallel programs. However, automatically analyzing a large parallel trace is difficult, especially without a specific objective. We aid this endeavor by extracting a trace's logical structure, an ordering of trace events derived from happened-before relationships, while taking into account developer intent. Using this structure, we can calculate an operation's delay relative to its peers on other processes. The logical structure also serves as a platform for comparing and clustering processes as well as highlighting communication patterns in a trace visualization. We present an algorithm for determining this idealized logical structure from traces of message passing programs, and we develop metrics to quantify delays and differences among processes. We implement our techniques in Ravel, a parallel trace visualization tool that displays both logical and physical timelines. Rather than showing the duration of each operation, we display where delays begin and end, and how they propagate. We apply our approach to the traces of several message passing applications, demonstrating the accuracy of our extracted structure and its utility in analyzing these codes.

Synchronization-Core-Based Discovery of Processes with Decomposable Cyclic Dependencies

Traditional process discovery techniques mine process models based upon event traces giving little consideration to workflow relevant data recorded in event logs. The neglect of such information usually leads to incorrect discovered models, especially when activities have decomposable cyclic dependencies. To address this problem, the recorded workflow relevant data and decision tree learning technique are utilized to classify cases into case clusters. Each case cluster contains causality and concurrency activity dependencies only. Then, a set of activity ordering relations are derived based on case clusters. And a synchronization-core-based process model is discovered from the ordering relations and composite cases. Finally, the discovered model is transformed to a BPMN model. The proposed approach is validated with a medical treatment process and an open event log. Meanwhile, a prototype system is presented.

A declarative framework for stateful analysis of execution traces

With newer complex multi-core systems, it is important to understand an application's runtime behavior to be able to debug its execution, detect possible problems and bottlenecks and finally identify potential root causes. Execution traces usually contain precise data about an application execution. Their analysis and abstraction at multiple levels can provide valuable information and insights about an application's runtime behavior. However, with multiple abstraction levels, it becomes increasingly difficult to find the exact location of detected performance or security problems. Tracing tools provide various analysis views to help users to understand their application problems. However, these pre-defined views are often not sufficient to reveal all analysis aspects of the underlying application. A declarative approach that enables users to specify and build their own custom analysis and views based on their knowledge, requirements and problems can be more useful and effective. In this paper, we propose a generic declarative trace analysis framework to analyze, comprehend and visualize execution traces. This enhanced framework builds custom analyses based on a specified modeled state, extracted from a system execution trace and stored in a special purpose database. The proposed solution enables users to first define their different analysis models based on their application and requirements, then visualize these models in many alternate representations (Gantt chart, XY chart, etc.), and finally filter the data to get some highlights or detect some potential patterns. Several sample applications with different operating systems are shown, using trace events gathered from Linux and Windows, at the kernel and user-space levels.

Biogeochemical, Isotopic and Bacterial Distributions Trace Oceanic Abyssal Circulation.

We explore the possibility of tracing routes of dense waters toward and within the ocean abyss by the use of an extended set of observed physical and biochemical parameters. To this purpose, we employ mercury, isotopic oxygen, biopolymeric carbon and its constituents, together with indicators of microbial activity and bacterial diversity found in bottom waters of the Eastern Mediterranean. In this basin, which has been considered as a miniature global ocean, two competing sources of bottom water (one in the Adriatic and one in the Aegean seas) contribute to the ventilation of the local abyss. However, due to a recent substantial reduction of the differences in the physical characteristics of these two water masses it has become increasingly complex a water classification using the traditional approach with temperature, salinity and dissolved oxygen alone. Here, we show that an extended set of observed physical and biochemical parameters allows recognizing the existence of two different abyssal routes from the Adriatic source and one abyssal route from the Aegean source despite temperature and salinity of such two competing sources of abyssal water being virtually indistinguishable. Moreover, as the near-bottom development of exogenous bacterial communities transported by convectively-generated water masses in the abyss can provide a persistent trace of episodic events, intermittent flows like those generating abyssal waters in the Eastern Mediterranean basin may become detectable beyond the availability of concomitant measurements.

Wolf by the Ears: The Missouri Crisis, 1819–1821 by John R. Van Atta

Reviewed by: Wolf by the Ears: The Missouri Crisis, 1819–1821by John R. Van Atta Matthew H. Crocker Wolf by the Ears: The Missouri Crisis, 1819–1821. By John R. Van Atta. Witness to History. (Baltimore: Johns Hopkins University Press, 2015. Pp. xiv, 199. Paper, $19.95, ISBN 978-1-4214-1653-3; cloth, $50.00, ISBN 978-1-4214-1652-6.) Following the precedent established by Louisiana, Mississippi, and Alabama, the territory of Missouri in 1819 petitioned Congress to become a slaveholding state without a second thought. There seemed little question that slavery would continue in the district once statehood was achieved. Indeed, the Louisiana Purchase treaty had guaranteed slavery’s legality in the territory, and by 1819 Missouri’s slave population had surpassed ten thousand. When New York congressman James Tallmadge presented an amendment to the Missouri statehood bill that would abolish slavery over the course of a few years, the southern delegation in Congress rebelled, beginning a three-year political battle that, according to John R. Van Atta, led to “a convergenceof political, economic, and social disturbances—West, South, and North—that brought an end to the old order of American life and suggested the broad outlines of a new one” (p. 4). A united South vigorously came to Missouri’s defense to secure slavery’s place in the republic, articulating a new and powerful rhetorical stance that anticipated the proslavery, “positive good” rationale of the future. In reaction, antislavery northerners saw slavery’s expansion coupled with its latest brazen defense as a threat to an emerging market economy in the North that was shedding its dependence on unfree labor for a free labor force of wage earners. Just as southerners during the crisis embraced a new ideology in slavery’s defense, northerners proceeded to form their own innovative canon based on free labor principles. The result in Congress, as well as in the country at large, was, according to Van Atta, “a widening cultural gulf between North and South . . . . [that] resulted in widespread anxiety that the country might split into not two, but three (or more) separate, distinct, and rival political entities—in the West, the South, and the North” (p. 89). In making his case, Van Atta adds to the historiography of the Missouri controversy by expanding his study beyond the halls of Congress and on to Main Street. We learn not only about the backgrounds and positions taken by some of the major players in the debates, such as James Tallmadge, Henry Clay, and brothers James and Philip P. Barbour, but also about how contrasting communities as diverse as Manhattan, New York, and Boon’s Lick, Missouri, reacted to the crisis. Van Atta also provides a comprehensive overview of the compromise worked out by Henry Clay, which Van Atta characterizes as “making sense at thattime” (p. 4). But, as he traces events, [End Page 919]what made sense in 1820 increasingly did not over the course of the next forty years as the “ convergenceof political, economic, and social disturbances” became too volatile for the political realm to handle. John R. Van Atta has written a fine synthesis on the Missouri crisis that incorporates some of the best scholarship in the field. It serves as a wonderful introduction to the subject. Matthew H. Crocker Keene State College Copyright © 2016 The Southern Historical Association

Online MPI Trace Compression Using Event Flow Graphs and Wavelets

Performance analysis of scientific parallel applications is essential to use High Performance Computing (HPC) infrastructures efficiently. Nevertheless, collecting detailed data of large-scale parallel programs and long-running applications is infeasible due to the huge amount of performance information generated. Even though there are no technological constraints in storing Terabytes of performance data, the constant flushing of such data to disk introduces a massive overhead into the application that makes the performance measurements worthless. This paper explores the use of Event flow graphs together with wavelet analysis and EZW-encoding to provide MPI event traces that are orders of magnitude smaller while preserving accurate information on timestamped events. Our mechanism compresses the performance data online while the application runs, thus, reducing the pressure put on the I/O system due to buffer flushing. As a result, we achieve lower application perturbation, reduced performance data output, and the possibility to monitor longer application runs.