1,618 research outputs found

    Prompt Application-Transparent Transaction Revalidation in Software Transactional Memory

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    Software Transactional Memory (STM) allows encapsulating shared-data accesses within transactions, executed with atomicity and isolation guarantees. The assessment of the consistency of a running transaction is performed by the STM layer at specific points of its execution, such as when a read or write access to a shared object occurs, or upon a commit attempt. However, performance and energy efficiency issues may arise when no shared-data read/write operation occurs for a while along a thread running a transaction. In this scenario, the STM layer may not regain control for a considerable amount of time, thus not being able to early detect if such transaction has become inconsistent in the meantime. To tackle this problem we present an STM architecture that, thanks to a lightweight operating system support, is able to perform a fine-grain periodic (hence prompt) revalidation of running transactions. Our proposal targets Linux and x86 systems and has been integrated with the open source TinySTM package. Experimental results with a port of the TPC-C benchmark to STM environments show the effectiveness of our solution

    Model-Based Proactive Read-Validation in Transaction Processing Systems

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    Concurrency control protocols based on read-validation schemes allow transactions which are doomed to abort to still run until a subsequent validation check reveals them as invalid. These late aborts do not favor the reduction of wasted computation and can penalize performance. To counteract this problem, we present an analytical model that predicts the abort probability of transactions handled via read-validation schemes. Our goal is to determine what are the suited points-along a transaction lifetime-to carry out a validation check. This may lead to early aborting doomed transactions, thus saving CPU time. We show how to exploit the abort probability predictions returned by the model in combination with a threshold-based scheme to trigger read-validations. We also show how this approach can definitely improve performance-leading up to 14 % better turnaround-as demonstrated by some experiments carried out with a port of the TPC-C benchmark to Software Transactional Memory

    Preemptive Software Transactional Memory

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    In state-of-the-art Software Transactional Memory (STM) systems, threads carry out the execution of transactions as non-interruptible tasks. Hence, a thread can react to the injection of a higher priority transactional task and take care of its processing only at the end of the currently executed transaction. In this article we pursue a paradigm shift where the execution of an in-memory transaction is carried out as a preemptable task, so that a thread can start processing a higher priority transactional task before finalizing its current transaction. We achieve this goal in an application-transparent manner, by only relying on Operating System facilities we include in our preemptive STM architecture. With our approach we are able to re-evaluate CPU assignment across transactions along a same thread every few tens of microseconds. This is mandatory for an effective priority-aware architecture given the typically finer-grain nature of in-memory transactions compared to their counterpart in database systems. We integrated our preemptive STM architecture with the TinySTM package, and released it as open source. We also provide the results of an experimental assessment of our proposal based on running a port of the TPC-C benchmark to the STM environment

    The global spread and invasion capacities of alien ants

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    Many alien species are neither cultivated nor traded but spread unintentionally, and their global movements, capacities to invade ecosystems, and susceptibility to detection by biosecurity measures are poorly known.1,2,3,4 We addressed these key knowledge gaps for ants, a ubiquitous group of stowaway and contaminant organisms that include some of the world’s most damaging invasive species.5,6,7,8,9,10 We assembled a dataset of over 146,000 occurrence records to comprehensively map the human-mediated spread of 520 alien ant species across 525 regions globally. From descriptions of the environments in which species were collected within individual regions—such as in imported cargoes, buildings, and outdoor settings—we determined whether different barriers to invasion had been overcome11 and classified alien ant species under three levels of invasion capacity corresponding to increasing biosecurity threat. We found that alien species of different invasion capacities had different sources and sinks globally. For instance, although the diversity of indoor-confined species peaked in the Palearctic realm, that of species able to establish outdoors peaked in the Nearctic and Oceanian realms, and these mainly originated from the Neotropical and Oriental realms. We also found that border interceptions worldwide missed two-thirds of alien species with naturalization capacity, many associated with litter and soil. Our study documents the vast spread of alien ants globally while highlighting avenues for more targeted biosecurity responses, such as prioritizing the screening of imports from regions that are diversity hotspots for species of high invasion capacity and improving the detection of cryptic alien invertebrates dwelling in substrates.journal articl

    The Global Ant Biodiversity Informatics (GABI) database: synthesizing data on the geographic distribution of ant species (Hymenoptera: Formicidae)

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    The global distribution patterns of most vertebrate groups and several plant groups have been described and analyzed over the past few years, a development facilitated by the compilation of important databases. Similar efforts are needed for large insect groups that constitute he majority of global biodiversity. As a result of this lack of information, invertebrate taxa are often left out of both large-scale analyses of biodiversity patterns and large-scale efforts in conservation planning and prioritization. Here, we introduce the first comprehensive global database of ant species distributions, the Global Ant Biodiversity Informatics (GABI) database, based on the compilation of 1.72 million records extracted from over 8811 publications and 25 existing databases. We first present the main goals of the database, the methodology used to build the database, is well as its limitations and challenges. Then, we discuss how different fields of ant biology may benefit from utilizing this tool. Finally, we emphasize the importance of future participation of myrmecologists to improve the database and use it to identify and fill holes in our knowledge of ant biodiversity.published_or_final_versio

    Isotropic reconstruction of 3D fluorescence microscopy images using convolutional neural networks

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    Fluorescence microscopy images usually show severe anisotropy in axial versus lateral resolution. This hampers downstream processing, i.e. the automatic extraction of quantitative biological data. While deconvolution methods and other techniques to address this problem exist, they are either time consuming to apply or limited in their ability to remove anisotropy. We propose a method to recover isotropic resolution from readily acquired anisotropic data. We achieve this using a convolutional neural network that is trained end-to-end from the same anisotropic body of data we later apply the network to. The network effectively learns to restore the full isotropic resolution by restoring the image under a trained, sample specific image prior. We apply our method to 33 synthetic and 33 real datasets and show that our results improve on results from deconvolution and state-of-the-art super-resolution techniques. Finally, we demonstrate that a standard 3D segmentation pipeline performs on the output of our network with comparable accuracy as on the full isotropic data
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