scholarly journals Evolution of the LHCb Continuous Integration system

2020 ◽  
Vol 245 ◽  
pp. 05039
Author(s):  
Robert Currie ◽  
Rosen Mataev ◽  
Marco Clemencic
Keyword(s):  
Recent Work ◽  
Resource Use ◽  
Immediate Feedback ◽  
Integration System ◽  
Continuous Integration ◽  
On Demand ◽  
Current State ◽  
Automatic Code ◽  
Code Quality ◽  
Feedback Time

The physics software stack of LHCb is based on Gaudi and is comprised of about 20 interdependent projects, managed across multiple GitLab repositories. At present, the continuous integration (CI) system used for regular building and testing of this software is implemented using Jenkins and runs on a cluster of about 300 cores. LHCb CI pipelines are python-based and relatively modern with some degree of modularity, i.e. the separation of test jobs from build jobs. However, these still suffer from obsoleted design choices that prevent improvements to scalability and reporting. In particular, the resource use and speed have not been thoroughly optimized due to the predominant use of the system for nightly builds, where a feedback time of 8 hours is acceptable. We describe recent work on speeding up pipelines by aggressively splitting and parallelizing checkout, build and test jobs and caching their artifacts. The current state of automatic code quality integration, such as coverage reports, is shown. This paper presents how feedback time from change (merge request) submission to build and test reports is reduced from “next day” to a few hours by dedicated on-demand pipelines. Custom GitLab integration allows easy triggering of pipelines, including linked changes to multiple projects, and provides immediate feedback as soon as ready. Reporting includes a comparison to tests on a unique stable reference build, dynamically chosen for every set of changes under testing. This work enables isolated testing of changes that integrates well into the development workflow, leaving nightly testing primarily for integration tests.

Four challenges for cognitive neuroscience and the cortico-hippocampal division of memory

2003 ◽  
Vol 26 (6) ◽  
pp. 681-682
Author(s):  
Harry Howard
Keyword(s):  
Independent Component Analysis ◽  
Recent Work ◽  
Cognitive Neuroscience ◽  
Principle Component Analysis ◽  
Pattern Analysis ◽  
Component Analysis ◽  
Independent Component ◽  
Principle Component ◽  
Complementary Methods ◽  
Current State

Jackendoff's criticisms of the current state of theorization in cognitive neuroscience are defused by recent work on the computational complementarity of the hippocampus and neocortex. Such considerations lead to a grounding of Jackendoff's processing model in the complementary methods of pattern analysis effected by independent component analysis (ICA) and principle component analysis (PCA).

scholarly journals LHCb Continuous Integration and Deployment system: a message based approach

2019 ◽  
Vol 214 ◽  
pp. 05001 ◽  
Author(s):  
Stefan-Gabriel Chitic ◽  
Ben Couturier ◽  
Marco Clemencic ◽  
Joel Closier
Keyword(s):  
Distributed System ◽  
File System ◽  
Source Code ◽  
Priority Queues ◽  
Integration System ◽  
Continuous Integration ◽  
System A ◽  
Event Based ◽  
New System

A continuous integration system is crucial to maintain the quality of the 6 millions lines of C++ and Python source code of the LHCb software in order to ensure consistent builds of the software as well as to run the unit and integration tests. Jenkins automation server is used for this purpose. It builds and tests around 100 configurations and produces in the order of 1500 built artifacts per day which are installed on the CVMFS file system or potentially on the developers’ machines. Faced with a large and growing number of configurations built every day, and in order to ease inter-operation between the continuous integration system and the developers, we decided to put in place a flexible messaging system. As soon as the built artifacts have been produced, the distributed system allows their deployment based on the priority of the configurations. We will describe the architecture of the new system, which is based on RabbitMQ messaging system (and the pika Python client library), and uses priority queues to start the LHCb software integration tests and to drive the installation of the nightly builds on the CVMFS file system. We will also show how the introduction of an event based system can help with the communication of results to developers.

scholarly journals A Comparison of Neuropathy Quality of Life Tools: Norfolk QOL-DN, PN-QOL-97, and NeuroQOL-28

2021 ◽  
Vol 9 (11) ◽  
Author(s):  
Jennifer Brown ◽  
Sheri Colberg ◽  
Shane Pribesh ◽  
Kimberly Baskette ◽  
Aaron Vinik
Keyword(s):  
Sural Nerve ◽  
Time Constraints ◽  
Immediate Feedback ◽  
Early Screening ◽  
Subclinical Neuropathy ◽  
Feedback Time ◽  
Sural Nerves ◽  
Screening Measures

Aims To explore the effectiveness of the Norfolk QOL-DN (QOL-DN), PN-QOL-97, and NeuroQOL-28 as tools for early detection of diabetic peripheral neuropathy in overweight, obese, and inactive (OOI), prediabetes (PD), and type 2 diabetes (T2D) individuals. Methods Thirty-four adults were divided by A1C [(10 OOI, 13 PD, and 11 T2D] and the sural nerves were tested bilaterally via NC-Stat DPN Check, conducting a sural nerve conduction study (NCS). Participants were individually timed, filling out questionnaires (QOL-DN, NeuroQOL-28, and PN-QOL-97) at a self-selected pace. Data were analyzed and compared to NCS findings to determine the best instrument for early neuropathy detection, usability in screening settings, and application for individuals with OOI, PD, and T2D. Results Abnormal NCS results were obtained from 27 individuals, of which 25 were bilateral and symmetrical. Confirmed DSPN criteria were met for 24, and 1 case met criteria for subclinical neuropathy. Normal NCS findings, reported symptoms, and reduced bilateral sensation were found in 7 cases. The QOL-DN and NeuroQOL-28 significantly predict neuropathy criteria in OOI, PD, and T2D subjects. Analyses revealed the QOL-DN as the quickest for completion (M=5.17; SD=1.83), followed by the NeuroQOL-28 (M=5.58; SD=3.56), and the PN-QOL-97 (M=13.23; SD=3.606). Conclusions The QOL-DN and NeuroQOL-28 are valid early screening measures for DPN detection. Time completion studies revealed that the QOL-DN and NeuroQOL-28 may be used as excellent short screening measures, completed in approximately 6 minutes or less, with reasonable scoring for both. The NeuroQOL-28 is a better fit for immediate feedback, time constraints, or limited staff. Future investigations should evaluate these tools for detection in DPN-prone individuals and in subclinical populations screenings.

scholarly journals Mobilities III

2016 ◽  
Vol 41 (3) ◽  
pp. 375-381 ◽  
Author(s):  
Peter Merriman
Keyword(s):  
Recent Work ◽  
Academic Work ◽  
Final Report ◽  
Current State ◽  
State Of The Field

In this final report on mobilities, I discuss research published between late 2014 and early 2016, focusing upon three key themes. I examine how recent work on medical bodies and race advances long-standing concerns with the mobile body. I then trace emerging philosophical and political writings on the themes of speed and ‘accelerationism’, before examining the contributions of mobility historians and transport historians to academic work on mobility. I conclude with some thoughts about the multi-disciplinary nature of contemporary mobilities research and the current state of the field.

scholarly journals Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform

2016 ◽  
Vol 22 (3) ◽  
pp. 238-249 ◽  
Author(s):  
Ioannis K. Moutsatsos ◽  
Imtiaz Hossain ◽  
Claudia Agarinis ◽  
Fred Harbinski ◽  
Yann Abraham ◽  
...  
Keyword(s):  
Image Processing ◽  
Open Source ◽  
High Throughput Screening ◽  
High Performance ◽  
Heterogeneous Data ◽  
Scientific Data ◽  
Source Image ◽  
Integration System ◽  
Continuous Integration ◽  
Processing Platform

High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an “off-the-shelf,” open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community.

The Sharing Economy

2018 ◽  
Vol 14 (1) ◽  
pp. 351-366 ◽  
Author(s):  
Bronwen Morgan
Keyword(s):  
Social Science ◽  
Urban Governance ◽  
Sharing Economy ◽  
Property Law ◽  
Science Literature ◽  
On Demand ◽  
Current State ◽  
Legal Literature ◽  
Equal Importance ◽  
Social Science Literature

The sharing economy is an emergent field of scholarship. This review explores two clusters of debate regarding the sharing economy and seeks to discern the lines of a productive dialogue between them. It suggests that the current state of scholarship on law in the sharing economy is a complex and asymmetrical mix of narrative articulation and empirical exploration. The first cluster focuses on an on-demand commercial vision of the sharing economy and is generating an exploding legal literature largely not grounded on empirical research. This coexists with an emergent social science literature focused on a solidarity-inflected version of the sharing economy, which, however, pays little or no explicit attention to law or legality. Each cluster of debate is first separately explored, after which three sites of détente are identified where these trajectories edge toward each other: urban governance, sociolegal accounts of the interplay between enterprise diversity and regulation, and reconfigurations of property law. Common to all three is an appreciation of collective economic agency as of equal importance to regulatory responses.

Histone variants and histone modifications: A structural perspective

2001 ◽  
Vol 79 (6) ◽  
pp. 693-708 ◽  
Author(s):  
Juan Ausió ◽  
D Wade Abbott ◽  
Xiaoying Wang ◽  
Susan C Moore
Keyword(s):  
Recent Work ◽  
Histone Modifications ◽  
Posttranslational Modifications ◽  
Structural Component ◽  
Functional Role ◽  
Short Range ◽  
Histone Variants ◽  
Current State ◽  
Functional Implications ◽  
Different Levels

In this review, we briefly analyze the current state of knowledge on histone variants and their posttranslational modifications. We place special emphasis on the description of the structural component(s) defining and determining their functional role. The information available indicates that this histone "variability" may operate at different levels: short-range "local" or long-range "global", with different functional implications. Recent work on this topic emphasizes an earlier notion that suggests that, in many instances, the functional response to histone variability is possibly the result of a synergistic structural effect.Key words: histone variants, posttranslational modifications, chromatin.

scholarly journals Effects of stochasticity on the length and behaviour of ecological transients

2021 ◽  
Author(s):  
Alan Hastings ◽  
Karen C. Abbott ◽  
Kim Cuddington ◽  
Tessa Francis ◽  
Ying-Cheng Lai ◽  
...  
Keyword(s):  
Recent Work ◽  
General Framework ◽  
Random Processes ◽  
Ecological Systems ◽  
Transient Dynamics ◽  
Asymptotic State ◽  
Systematic Treatment ◽  
Current State ◽  
Ecological Understanding ◽  
Deterministic Processes

AbstractThere is a growing recognition that ecological systems can spend extended periods of time far away from an asymptotic state, and that ecological understanding will therefore require a deeper appreciation for how long ecological transients arise. Recent work has defined classes of deterministic mechanisms that can lead to long transients. Given the ubiquity of stochasticity in ecological systems, a similar systematic treatment of transients that includes the influence of stochasticity is important. Stochasticity can of course promote the appearance of transient dynamics by preventing systems from settling permanently near their asymptotic state, but stochasticity also interacts with deterministic features to create qualitatively new dynamics. As such, stochasticity may shorten, extend, or fundamentally change a system’s transient dynamics. Here, we describe a general framework that is developing for understanding the range of possible outcomes when random processes impact the dynamics of ecological systems over realistic time scales. We emphasize that we can understand the ways in which stochasticity can either extend or reduce the lifetime of transients by studying the interactions between the stochastic and deterministic processes present, and we summarize both the current state of knowledge and avenues for future advances.

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