Concurrent Trace Research Articles

The reads-from equivalence for the TSO and PSO memory models

The verification of concurrent programs remains an open challenge due to the non-determinism in inter-process communication. One recurring algorithmic problem in this challenge is the consistency verification of concurrent executions. In particular, consistency verification under a reads-from map allows to compute the reads-from (RF) equivalence between concurrent traces, with direct applications to areas such as Stateless Model Checking (SMC). Importantly, the RF equivalence was recently shown to be coarser than the standard Mazurkiewicz equivalence, leading to impressive scalability improvements for SMC under SC (sequential consistency). However, for the relaxed memory models of TSO and PSO (total/partial store order), the algorithmic problem of deciding the RF equivalence, as well as its impact on SMC, has been elusive. In this work we solve the algorithmic problem of consistency verification for the TSO and PSO memory models given a reads-from map, denoted VTSO-rf and VPSO-rf, respectively. For an execution of n events over k threads and d variables, we establish novel bounds that scale as n k +1 for TSO and as n k +1 · min( n k 2 , 2 k · d ) for PSO. Moreover, based on our solution to these problems, we develop an SMC algorithm under TSO and PSO that uses the RF equivalence. The algorithm is exploration-optimal , in the sense that it is guaranteed to explore each class of the RF partitioning exactly once, and spends polynomial time per class when k is bounded. Finally, we implement all our algorithms in the SMC tool Nidhugg, and perform a large number of experiments over benchmarks from existing literature. Our experimental results show that our algorithms for VTSO-rf and VPSO-rf provide significant scalability improvements over standard alternatives. Moreover, when used for SMC, the RF partitioning is often much coarser than the standard Shasha-Snir partitioning for TSO/PSO, which yields a significant speedup in the model checking task.

Novel Fluorescent Mitochondria-Targeted Probe MitoCLox Reports Lipid Peroxidation in Response to Oxidative Stress In Vivo.

A new mitochondria-targeted probe MitoCLox was designed as a starting compound for a series of probes sensitive to cardiolipin (CL) peroxidation. Fluorescence microscopy reported selective accumulation of MitoCLox in mitochondria of diverse living cell cultures and its oxidation under stress conditions, particularly those known to cause a selective cardiolipin oxidation. Ratiometric fluorescence measurements using flow cytometry showed a remarkable dependence of the MitoCLox dynamic range on the oxidation of the sample. Specifically, MitoCLox oxidation was induced by low doses of hydrogen peroxide or organic hydroperoxide. The mitochondria-targeted antioxidant 10-(6′-plastoquinonyl)decyltriphenyl-phosphonium (SkQ1), which was shown earlier to selectively protect cardiolipin from oxidation, prevented hydrogen peroxide-induced MitoCLox oxidation in the cells. Concurrent tracing of MitoCLox oxidation and membrane potential changes in response to hydrogen peroxide addition showed that the oxidation of MitoCLox started without a delay and was complete during the first hour, whereas the membrane potential started to decay after 40 minutes of incubation. Hence, MitoCLox could be used for splitting the cell response to oxidative stress into separate steps. Application of MitoCLox revealed heterogeneity of the mitochondrial population; in living endothelial cells, a fraction of small, rounded mitochondria with an increased level of lipid peroxidation were detected near the nucleus. In addition, the MitoCLox staining revealed a specific fraction of cells with an increased level of oxidized lipids also in the culture of human myoblasts. The fraction of such cells increased in high-density cultures. These specific conditions correspond to the initiation of spontaneous myogenesis in vitro, which indicates that oxidation may precede the onset of myogenic differentiation. These data point to a possible participation of oxidized CL in cell signalling and differentiation.

An efficient algorithm for match pair approximation in message passing

Asynchronous message passing paradigm is commonly used in high performance computing (HPC). Message non-determinism makes the error detection in message passing programs very difficult. The prior work uses an over-approximation of the precise match pair records (each is a pair of a send and a receive that may potentially match in the runtime) to capture all possible message communication in a concurrent trace program (CTP). Symbolic model checking with such a set of match pairs is able to witness program properties including deadlock, message race, and zero-buffer compatibility. However, the approach is inefficient because of the exponential ways of match pair resolution, where most of them are non-feasible for property witnessing. This paper presents an effective under-approximation algorithm that is able to shrink the generated match pair set, thus prune most non-feasible match pairs. The algorithm first sections each process in a CTP such that each potential sender distributes roughly a bounded number of sends to match the same number of receives in the process, and then approximating the match pairs for the sends and receives in each section independently by a few simple rules with ranking. Novelty in the work is that the algorithm has the flexibility to generate the match pair set with various size based on the user input. This paper further presents that the precise match pairs for any CTP can be generated with a bounded input. The experiments over a set of benchmarks show that the symbolic model checking with the algorithm in this paper outperforms the state-of-the-art tools such that the runtime performance of property witnessing is drastically reduced as all the properties are witnessed with a small set of match pairs generated by the new algorithm. The results also show that the algorithm is able to scale to a program that employs a high degree of message non-determinism and/or a high degree of deep communication.

A Constraint-Aware Optimization Method for Concurrency Bug Diagnosis Service in a Distributed Cloud Environment

The advent of cloud computation and big data applications has enabled data access concurrency to be prevalent in the distributed cloud environment. In the meantime, security issue becomes a critical problem for researchers to consider. Concurrency bug diagnosis service is to analyze concurrent software and then reason about concurrency bugs in them. However, frequent context switches in concurrent program execution traces will inevitably impact the service performance. To optimize the service performance, this paper presents a static constraint-aware method to simplify concurrent program buggy traces. First, taking the original buggy trace as the operation object, we calculate the maximal sound dependence relations based on the constraint models. Then, we iteratively check the dependent constraints and move forward current event to extend thread execution intervals. Finally, we obtain the simplified trace that is equivalent to the original buggy trace. To evaluate our approach, we conduct a set of experiments on 12 widely used Java projects. Experimental results show that our approach outperforms other state-of-the-art approaches in terms of execution time.

Causality-based Model Checking

Model checking is usually based on a comprehensive traversal of the state space. Causality-based model checking is a radically different approach that instead analyzes the cause-effect relationships in a program. We give an overview on a new class of model checking algorithms that capture the causal relationships in a special data structure called concurrent traces. Concurrent traces identify key events in an execution history and link them through their cause-effect relationships. The model checker builds a tableau of concurrent traces, where the case splits represent different causal explanations of a hypothetical error. Causality-based model checking has been implemented in the ARCTOR tool, and applied to previously intractable multi-threaded benchmarks.

Succinct Representation of Concurrent Trace Sets

We present a method and a tool for generating succinct representations of sets of concurrent traces. We focus on trace sets that contain all correct or all incorrect permutations of events from a given trace. We represent trace sets as HB-Formulas that are Boolean combinations of happens-before constraints between events. To generate a representation of incorrect interleavings, our method iteratively explores interleavings that violate the specification and gathers generalizations of the discovered interleavings into an HB-Formula; its complement yields a representation of correct interleavings. We claim that our trace set representations can drive diverse verification, fault localization, repair, and synthesis techniques for concurrent programs. We demonstrate this by using our tool in three case studies involving synchronization synthesis, bug summarization, and abstraction refinement based verification. In each case study, our initial experimental results have been promising. In the first case study, we present an algorithm for inferring missing synchronization from an HB-Formula representing correct interleavings of a given trace. The algorithm applies rules to rewrite specific patterns in the HB-Formula into locks, barriers, and wait-notify constructs. In the second case study, we use an HB-Formula representing incorrect interleavings for bug summarization. While the HB-Formula itself is a concise counterexample summary, we present additional inference rules to help identify specific concurrency bugs such as data races, define-use order violations, and two-stage access bugs. In the final case study, we present a novel predicate learning procedure that uses HB-Formulas representing abstract counterexamples to accelerate counterexample-guided abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure refines the abstraction to eliminate multiple spurious abstract counterexamples drawn from the HB-Formula.

基于遗传算法的多核芯片并发追踪调试方法

Trace-based debugging technologies need connect trace signals to trace buffer with additional infrastructure, which not only consumes the limited on chip resource, but also results in the problem of signal integration. Reusing network-on-chip eliminates the problems. But it is still a challenge problem that how to determine the locations of trace buffer under the limitations of link bandwidth and transmission power. We formulate it as P-Median problem which is NP-hard. Then a method based on generic algorithm is proposed. It can optimize the location number of trace buffers and transmission power simultaneously. Experimental results show that multiple trace buffer locations can increase the number of concurrent trace signals in contrast to centralized trace buffer. Compared to previous method, the proposed method can deducing the locations of trace buffer and reducing the transmission power efficiently.

Effects of OEF/OIF-Related Physical and Emotional Co-Morbidities on Associative Learning: Concurrent Delay and Trace Eyeblink Classical Conditioning

This study examined the performance of veterans and active duty personnel who served in Operation Enduring Freedom and/or Operation Iraqi Freedom (OEF/OIF) on a basic associative learning task. Eighty-eight individuals participated in this study. All received a comprehensive clinical evaluation to determine the presence and severity of posttraumatic stress disorder (PTSD) and traumatic brain injury (TBI). The eyeblink conditioning task was composed of randomly intermixed delay and trace conditioned stimulus (CS) and unconditioned stimulus (US) pairs (acquisition) followed by a series of CS only trials (extinction). Results revealed that those with a clinical diagnosis of PTSD or a diagnosis of PTSD with comorbid mTBI acquired delay and trace conditioned responses (CRs) to levels and at rates similar to a deployed control group, thus suggesting intact basic associative learning. Differential extinction impairment was observed in the two clinical groups. Acquisition of CRs for both delay and trace conditioning, as well as extinction of trace CRs, was associated with alcoholic behavior across all participants. These findings help characterize the learning and memory function of individuals with PTSD and mTBI from OEF/OIF and raise the alarming possibility that the use of alcohol in this group may lead to more significant cognitive dysfunction.

Contingency awareness in human aversive conditioning involves the middle frontal gyrus

In contrast to the wealth of data describing the neural mechanisms underlying classical conditioning, we know remarkably little about the mechanisms involved in acquisition of explicit contingency awareness. Subjects variably acquire contingency awareness in classical conditioning paradigms, in which they are able to describe the temporal relationship between a conditioned cue and its outcome. Previous studies have implicated the hippocampus and prefrontal cortex in the acquisition of explicit knowledge, although their specific roles remain unclear. We used functional magnetic resonance imaging to track the trial-by-trial acquisition of explicit knowledge in a concurrent trace and delay conditioning paradigm. We show that activity in bilateral middle frontal gyrus and parahippocampal gyrus correlates with the accuracy of explicit contingency awareness on each trial. In contrast, amygdala activation correlates with conditioned responses indexed by skin conductance responses (SCRs). These results demonstrate that brain regions known to be involved in other aspects of learning and memory also play a specific role, reflecting on each trial the acquisition and representation of contingency awareness.

Trace Element Biology: The Knowledge Base and its Application for the Nutrition of Individuals and Populations

Impressive strides are being made in the understanding of trace element metabolism and function. This is underscored by the many contributions in these proceedings. However, not so impressive are: i) the precise recognition of mild trace element deficiencies and how to establish their functional consequences, possibly confounded by concurrent trace element inadequacies, are difficult to assess, ii) approaches to the quantitative determination of requirements for trace elements remain unsatisfactory and archaic, in so many ways, iii) our understanding of the extent of the biological basis for the variation in requirements among apparently similar individuals is poor, and iv) much needs to be learned about the quantitative extent to which genetic, epigenetic and dietary factors interact to determine the nutritional phenotype. Some ideas are presented as to how we might embrace, in the context of a reconstructive approach, the exciting new knowledge and related techniques emerging during the postgenome era and develop new paradigms for assessing trace element needs and status, and for establishing effective nutrient intake under different conditions of complex genotype-environment interactions. Metabolites are functional cellular entities and I also urge a vigorous application of metabolomics and of metabolic profiling that is closely linked with genomics, proteomics, trace element kinetics and system analysis, as components of the new integrative paradigm. We need to understand the system and its strategy, not only the molecular details of its component parts and its individual controls. An interdisciplinary research and teaching enterprise will be necessary to best achieve this aim. All of this is related to our common goal to promote, through expanded biological knowledge and its effective application, the enhanced role of trace elements for human well-being.

Concurrent Quantification of Quinolinic, Picolinic, and Nicotinic Acids Using Electron-Capture Negative-Ion Gas Chromatography–Mass Spectrometry

Quinolinic, picolinic, and nicotinic acids and nicotinamide are end products of the kynurenine pathway from l-tryptophan and are intermediates in the biosynthesis of nicotinamide adenine dinucleotide. These compounds are involved in complex interrelationships with inflammatory and apoptotic responses associated with neuronal cell damage and death in the central nervous system. To facilitate the study of these compounds, we have utilized gas chromatography–mass spectrometry in electron capture negative ionization mode for their concurrent trace quantification in a single sample. Deuterium-labeled quinolinic, picolinic, and nicotinic acids were used as internal standards and the compounds were converted to their hexafluoroisopropyl esters prior to chromatography. Nicotinamide was readily quantified after conversion to nicotinic acid using gas-phase hydrolysis—a process which did not affect the deuterated internal standards. The on-column limit of quantification was less than 1 fmol for each of the analytes and calibration curves were linear. A packed column liner was used in the gas chromatograph inlet to effectively eliminate sample interference effects in the analysis of trace (femtomolar) levels of quinolinic acid. The method enables rapid and specific concurrent quantification of quinolinic, picolinic, and nicotinic acids in tissue extracts and physiological and culture media.

Ion exchange in zeolites. Part 3.—Hydrolysis and trace45Ca2+and22Na+exchanges in zeolites X and Y

The effects of hydrolysis on concurrent trace 45Ca2+ and 22Na+ exchanges have been studied in the Na forms (trace Ca2+ exchange) and the Ca forms (trace Na+ exchange) of zeolites X and Y in NaNO3(Na forms) and Ca(NO3)2(Ca forms) solutions at different concentrations. Based on the mass-action formulations of Gaines and Thomas, equations were derived for the prediction of hydrolysis and the trace exchange equilibria (distribution coefficient KD) in the zeolites. Predictions of hydrolysis equilibria (pH, Ca2+ and Na+ concentrations) were good in most cases, but for the trace Ca2+ and Na+ equilibria, KD predictions failed significantly at low concentrations of the macro-ions as a strong decrease in selectivities for the trace ions took place. In theory, this could be explained by the presence of suspended zeolite particles, which could not be removed by centrifugation, in solution. The presence of such suspensions in solution could not, however, be established.

Effect of CS Duration on Trace Conditioning of Mental Retardates

The importance of CS duration in concurrent trace conditioning of the GSR and eyelid response was investigated with 32 retardates. Four treatment groups completed a 2-day training procedure involving habituation, acquisition, and extinction. Irrespective of response class, a long CS (1000 msec.) resulted in better conditioning than did a CS with a shorter duration (100 msec.). This finding could not be accounted for by either interstimulus or trace interval differences.