bluuebunny/crossref_metadata_2025 huggingface dataset:
Selective degradation of plasmid-derived mRNAs by MCPIP1 RNase
Authors: Qian Yisong , Li Xiuzhen , Miao Ruidong , Liu Shufeng , Xin Hong-Bo , Huang Xiaotian , Wang Tony T. , Fu Mingui
Published: September 2019

Detection and degradation of foreign nucleic acids is an ancient form of host defense. However, the underlying mechanisms are not completely clear. MCPIP1 is an endoribonuclease and an important regulator in both innate and adaptive immunity by targeting inflammatory mRNA degradation. Here we report that MCPIP1 RNase can also selectively detect and degrade the mRNAs encoded by transfected plasmids. In transient transfection, MCPIP1 expression potently degraded the mRNA from exogenously transfected vectors, which is independent on the vector, genes and cell types used. Conversely, the expression of transfected plasmids in MCPIP1-null cells is significantly higher than that in wild-type cells. Interestingly, overexpression of MCPIP1 or MCPIP1 deficiency does not affect the expression of the exogenous genes incorporated into the host genome in a stable cell line or the global gene expression of host genome. This ability is not associated with PKR/RNase L system, as PKR inhibitors does not block MCPIP1-mediated mRNA degradation of exogenously transfected genes. Lastly, expression of MCPIP1 suppressed replication of Zika virus in infected cells. The study may provide a model for understanding the antiviral mechanisms of MCPIP1, and a putative tool to increase the expression of transfected exogenous genes.
A well-balanced scheme for the simulation tool-kit A-MaZe: implementation, tests, and first applications to stellar structure
Authors: Popov M. V. , Walder R. , Folini D. , Goffrey T. , Baraffe I. , Constantino T. , Geroux C. , Pratt J. , Viallet M. , Käppeli R.
Published: September 2019

Characterizing stellar convection in multiple dimensions is a topic at the forefront of stellar astrophysics. Numerical simulations are an essential tool for this task. We present an extension of the existing numerical tool-kit A-MaZe that enables such simulations of stratified flows in a gravitational field. The finite-volume based, cell-centered, and time-explicit hydrodynamics solver of A-MaZe was extended such that the scheme is now well-balanced in both momentum and energy. The algorithm maintains an initially static balance between gravity and pressure to machine precision. Quasi-stationary convection in slab-geometry preserves gas energy (internal plus kinetic) on average, despite strong local up- and down-drafts. By contrast, a more standard numerical scheme is demonstrated to result in substantial gains of energy within a short time on purely numerical grounds. The test is further used to point out the role of dimensionality, viscosity, and Rayleigh number for compressible convection. Applications to a young sun in 2D and 3D, covering a part of the inner radiative zone, as well as the outer convective zone, demonstrate that the scheme meets its initial design goal. Comparison with results obtained for a physically identical setup with a time-implicit code show qualitative agreement.
Detection and characterisation of 54 massive companions with the SOPHIE spectrograph
Authors: Kiefer F. , Hébrard G. , Sahlmann J. , Sousa S. G. , Forveille T. , Santos N. , Mayor M. , Deleuil M. , Wilson P. A. , Dalal S. , Díaz R. F. , Henry G. W. , Hagelberg J. , Hobson M. J. , Demangeon O. , Bourrier V. , Delfosse X. , Arnold L. , Astudillo-Defru N. , Beuzit J.-L. , Boisse I. , Bonfils X. , Borgniet S. , Bouchy F. , Courcol B. , Ehrenreich D. , Hara N. , Lagrange A.-M. , Lovis C. , Montagnier G. , Moutou C. , Pepe F. , Perrier C. , Rey J. , Santerne A. , Ségransan D. , Udry S. , Vidal-Madjar A.
Published: September 2019

Context. Brown dwarfs (BD) are substellar objects intermediate between planets and stars with masses of ~13–80 MJ. While isolated BDs are most likely produced by gravitational collapse in molecular clouds down to masses of a few MJ, a non-negligible fraction of low-mass companions might be formed through the planet-formation channel in protoplanetary discs. The upper mass limit of objects formed within discs is still observationally unknown, the main reason being the strong dearth of BD companions at orbital periods shorter than 10 yr, also known as the BD desert.

Aims. To address this question, we aim at determining the best statistics of companions within the 10–100 MJ mass regime and located closer than ~10 au to the primary star, while minimising observation and selection bias.

Methods. We made extensive use of the radial velocity (RV) surveys of northern hemisphere FGK stars within 60 pc of the Sun, performed with the SOPHIE spectrograph at the Observatoire de Haute-Provence. We derived the Keplerian solutions of the RV variations of 54 sources. Public astrometric data of the HIPPARCOS and Gaia missions allowed us to constrain the masses of the companions for most sources. We introduce GASTON, a new method to derive inclination combining RVs and Keplerian and astrometric excess noise from Gaia DR1.

Results. We report the discovery of 12 new BD candidates. For five of them, additional astrometric data led to a revision of their mass in the M-dwarf regime. Among the seven remaining objects, four are confirmed BD companions, and three others are likely also in this mass regime. Moreover, we report the detection of 42 M-dwarfs within the range of 90 MJ–0.52 M⊙. The resulting M sin i-P distribution of BD candidates shows a clear drop in the detection rate below 80-day orbital period. Above that limit, the BD desert appears rather wet, with a uniform distribution of the M sin i. We derive a minimum BD-detection frequency around Solar-like stars of 2.0 ± 0.5%.
Dust production in the debris disk around HR 4796 A
Authors: Olofsson J. , Milli J. , Thébault P. , Kral Q. , Ménard F. , Janson M. , Augereau J.-C. , Bayo A. , Beamín J. C. , Henning Th. , Iglesias D. , Kennedy G. M. , Montesinos M. , Pawellek N. , Schreiber M. R. , Zamora C. , Carbillet M. , Feautrier P. , Fusco T. , Madec F. , Rabou P. , Sevin A. , Szulágyi J. , Zurlo A.
Published: September 2019

Context. Debris disks are the natural by-products of the planet formation process. Scattered or polarized light observations are mostly sensitive to small dust grains that are released from the grinding down of bigger planetesimals.

Aims. High angular resolution observations at optical wavelengths can provide key constraints on the radial and azimuthal distribution of the small dust grains. These constraints can help us better understand where most of the dust grains are released upon collisions.

Methods. We present SPHERE/ZIMPOL observations of the debris disk around HR 4796 A, and we modeled the radial profiles along several azimuthal angles of the disk with a code that accounts for the effect of stellar radiation pressure. This enabled us to derive an appropriate description for the radial and azimuthal distribution of the small dust grains.

Results. Even though we only modeled the radial profiles along, or close to, the semi-major axis of the disk, our best-fit model is not only in good agreement with our observations but also with previously published datasets (from near-infrared to sub-mm wavelengths). We find that the reference radius is located at 76.4 ± 0.4 au, and the disk has an eccentricity of 0.076−0.010+0.016 with the pericenter located on the front side of the disk (north of the star). We find that small dust grains must be preferentially released near the pericenter to explain the observed brightness asymmetry.

Conclusions. Even though parent bodies spend more time near the apocenter, the brightness asymmetry implies that collisions happen more frequently near the pericenter of the disk. Our model can successfully reproduce the shape of the outer edge of the disk without requiring an outer planet shaping the debris disk. With a simple treatment for the effect of the radiation pressure, we conclude that the parent planetesimals are located in a narrow ring of about 3.6 au in width.
LHCb MiniDAQ control system
Authors: Granado Cardoso Luís , Gaspar Clara , Viana Barbosa João , Alessio Federico , Jost Beat , Neufeld Niko , Frank Markus , Schwemmer Rainer , Durante Paolo
Published: September 2019

LHCb is one of the 4 experiments at the LHC accelerator at CERN,
specialized in B-physics. During the next long shutdown period, the LHCb
experiment will be upgraded to a trigger-less readout system with a full software trigger in order to be able to record data with a much higher instantaneous luminosity. To achieve this goal, the upgraded systems for Timing and Fast Control (TFC) and Data Acquisition (DAQ) will have new electronic boards and a new software stack will be introduced for data acquisition. In the development stage, all these components are housed in servers named MiniDAQ. These new components will need to be integrated in an upgraded Experiment Control System (ECS) based on the WinCC OA SCADA and the CERN JCOP framework. The ECS provides full monitoring and control for all these subsystems and many important features like configuration recipes and automated actions. This paper describes the implementation of the upgraded ECS and its component fwMiniDAQ, which integrates all the new developments and can be easily distributed to the sub-detector developers and configured for their various setups.
The CMS Event-Builder System for LHC Run 3 (2021-23)
Authors: André Jean-Marc , Behrens Ulf , Branson James , Brummer Philipp , Cittolin Sergio , Da Silva Gomes Diego , Darlea Georgiana-Lavinia , Deldicque Christian , Demiragli Zeynep , Dobson Marc , Doualot Nicolas , Erhan Samim , Fulcher Jonathan , Gigi Dominique , Gładki Maciej , Glege Frank , Gomez-Ceballos Guillelmo , Hegeman Jeroen , Holzner André , Lettrich Michael , Mečionis Audrius , Meijers Frans , Meschi Emilio , Mommsen Remigius K , Morović Srećko , O’Dell Vivian , Orsini Luciano , Papakrivopoulos Ioannis , Paus Christoph , Petrucci Andrea , Pieri Marco , Rabad Dinyar , Rácz Attila , Rapševičius Valdas , Reis Thomas , Sakulin Hannes , Schwick Christoph , Šimelevičius Dainius , Stankevičius Mantas , Vazquez Velez Cristina , Wernet Christian , Zejdl Petr
Published: September 2019

The data acquisition system (DAQ) of the CMS experiment at the CERN Large Hadron Collider (LHC) assembles events of 2MB at a rate of 100 kHz. The event builder collects event fragments from about 750 sources and assembles them into complete events which are then handed to the High-Level Trigger (HLT) processes running on O(1000) computers. The aging eventbuilding hardware will be replaced during the long shutdown 2 of the LHC taking place in 2019/20. The future data networks will be based on 100 Gb/s interconnects using Ethernet and Infiniband technologies. More powerful computers may allow to combine the currently separate functionality of the readout and builder units into a single I/O processor handling simultaneously 100 Gb/s of input and output traffic. It might be beneficial to preprocess data originating from specific detector parts or regions before handling it to generic HLT processors. Therefore, we will investigate how specialized coprocessors, e.g. GPUs, could be integrated into the event builder. We will present the envisioned changes to the event-builder compared to today’s system. Initial measurements of the performance of the data networks under the event-building traffic pattern will be shown. Implications of a folded network architecture for the event building and corresponding changes to the software implementation will be discussed.
Improving data quality monitoring via a partnership of technologies and resources between the CMS experiment at
CERN and industry
Authors: Azzolin Virginia , Andrews Michael , Cerminara Gianluca , Dev Nabarun , Jessop Colin , Marinelli Nancy , Mudholkar Tanmay , Pierini Maurizio , Pol Adrian , Vlimant Jean-Roch
Published: September 2019

The Compact Muon Solenoid (CMS) experiment dedicates significant effort to assess the quality of its data, online and offline. A real-time data quality monitoring system is in place to spot and diagnose problems as promptly as possible to avoid data loss. The a posteriori evaluation of processed data is designed to categorize it in terms of their usability for physics analysis. These activities produce data quality metadata. The data quality evaluation relies on a visual inspection of the monitoring features. This practice has a cost in term of human resources and is naturally subject to human arbitration. Potential limitations are linked to the ability to spot a problem within the overwhelming number of quantities to monitor, or to the lack of understanding of detector evolving conditions. In view of Run 3, CMS aims at integrating deep learning technique in the online workflow to promptly recognize and identify anomalies and improve data quality metadata precision. The CMS experiment engaged in a partnership with IBM with the objective to support, through automatization, the online operations and to generate benchmarking technological results. The research goals, agreed within the CERN Openlab framework, how they matured in a demonstration applic tion and how they are achieved, through a collaborative contribution of technologies and resources, are presented
A cluster-finding algorithm for free-streaming data
Authors: Friese Volker
Published: September 2019

In position-sensitive detectors with segmented readout (pixels or strips), charged particles activate in general several adjacent read-out channels. The first step in the reconstruction of the hit position is thus to identify clusters of active channels associated to one particle crossing the detector. In conventionally triggered systems, where the association of raw data to events is given by a hardware trigger, this is an easy-to-solve problem. It, however, becomes more involved in untriggered, free-streaming read-out systems like the one employed by the CBM experiment. Here, the time coordinate of the single-channel measurement must be taken into account to decider whether neighbouring active channels belong to a cluster. A simple extension of well-known cluster finding algorithms is not satisfactory because of involving increasing combinatorics, which are prohibitive for reconstruction in real-time. In this article, a cluster-finding solution for the Silicon Tracking System of the CBM experiment is presented which avoids any combinatorics or loops over detector channels. Its execution time is thus independent on the size of the data packages (time slices) delivered by the data acquisition, making it suitable for being used in online reconstruction.
FELIX: the new detector interface for the ATLAS experiment
Authors: Ilic Nikolina , Vermeulen Jos , Kolos Serguei
Published: September 2019

During the next major shutdown from 2019-2020, the ATLAS experiment at the LHC at CERN will adopt the Front-End Link eXchange (FELIX) system as the interface between the data acquisition, detector control and TTC (Timing, Trigger and Control) systems and new or updated trigger and detector front-end electronics. FELIX will function as a router between custom serial links from front end ASICs and FPGAs to data collection and processing components via a commodity switched network. Links may aggregate many slower links or be a single high bandwidth link. FELIX will also forward the LHC bunch-crossing clock, fixed latency trigger accepts and resets received from the TTC system to front-end electronics. The FELIX system uses commodity server technology in combination with FPGA-based PCIe I/O cards. The FELIX servers will run a software routing platform serving data to network clients. Commodity servers connected to FELIX systems via the same network will run the new Software Readout Driver (SW ROD) infrastructure for event fragment building and buffering, with support for detector or trigger specific data processing, and will serve the data upon request to the ATLAS High-Level Trigger for Event Building and Selection. This proceeding will cover the design and status of FELIX and the SW ROD.
The ProtoDUNE Single Phase Detector Control System
Authors: Kehrli Antoine , Lehmann Miotto Giovanna , Pons Xavier , Ravat Sylvain , Rodriguez Manuel J.
Published: September 2019

This paper presents the Detector Control System (DCS) that has been designed and implemented for the NP04 experiment at CERN. NP04, also known as protoDUNE Single Phase (SP), aims at validating the engineering processes and detector performance of a large Liquid Argon (LAr) Time Projection Chamber (TPC) in view of the DUNE experiment. Built at the CERN Neutrino Platform (NP) facilities, it started to operate in September 2018 after two years of construction and commissioning, using a tertiary beam of the CERN SPS accelerator. After an overall description of the distributed control architecture that has been chosen for the control of this experiment, focus will be put on describing the software system design, based on the CERN control frameworks UNICOS and JCOP (built on top of WINCC OA). The knowledge acquired during the operation of the DCS is discussed and future work are presented.
The Prompt Processing System and Data Quality Monitoring in the ProtoDUNE-SP Experiment
Authors: Potekhin Maxim
Published: September 2019

The DUNE Collaboration is conducting an experimental program (named protoDUNE) which involves a beam test of two large-scale prototypes of the DUNE Far Detector at CERN operating in 2018-2019. The volume of data to be collected by the protoDUNE-SP (the single-phase detector) will amount to a few petabytes and the sustained rate of data sent to mass storage is in the range of a few hundred MB per second. After collection the data is committed to storage at CERN and transmitted to Fermi National Accelerator Laboratory in the US for processing, analysis and long-term preservation. The protoDUNE experiment requires substantial Data Quality Monitoring capabilities in order to ascertain the condition of the detector and its various subsystems. We present the design of the protoDUNE Prompt Processing System, its deployment at CERN and its performance during the data challenges and actual data taking.
Experience with Shifter Assistant - an intelligent tool to help operations of ATLAS TDAQ System in LHC Run 2
Authors: Kazarov Andrei , Corso-Radu Alina , Avolio Giuseppe
Published: September 2019

The Trigger and DAQ (TDAQ) system of the ATLAS experiment is a complex distributed computing system, composed of O(10, 000) of applications running on more than 2,500 computers. The system is operated by a crew of operators on shift. An important aspect of operations is to minimize the downtime of the system caused by runtime failures, such as human errors, unawareness or miscommunication. The paper describes recent developments in one of the intelligent TDAQ frameworks, the Shifter Assistant (SA) and summarizes the experience of it's use in operations of ATLAS during LHC Run 2. SA is a framework whose main aim is to automatize routine system checks, error detection and diagnosis, events correlations etc. in order to help the operators react to runtime problems promptly and effectively. The tool is based on CEP (Complex Event Processing) technology. It constantly processes this stream of operational events (O(100 kHz)) over a set of “directives” (or rules) in the knowledge base, producing human-oriented alerts and making shifters aware of the operational issues. More than 200 directives were developed by TDAQ and ATLAS detector experts for different domains. In this paper we also describe different types of directives which were developed in course of Run 2, and present few examples of most interesting and challenging ones, demonstrating the power of CEP for this type of applications.
The ATLAS trigger menu design for higher luminosities in Run 2
Authors: Montejo Berlingen Javier
Published: September 2019

ATLAS utilizes a two-level trigger system in Run-2 to reduce the bunch-crossing rate of 40 MHz to an average recording rate of about 1 kHz. Events are selected based on physics signatures such as presence of energetic leptons, photons, jets or large missing energy. Despite the limited time available for processing collision events, the trigger system is able to exploit topological information as well as multi-variate methods, for example for b-tagging or tau identification. The ATLAS trigger menu specifies which triggers are used during data taking and how much rate a given trigger is allocated. For 2018 data taking, the trigger selections and menus have been improved to handle expected luminosities above 2 × 1034 cm−2 s−1 and to ensure robustness in the presence of multiple interactions per bunch crossing (pile-up).
The Continuously Running iFDAQ of the COMPASS Experiment
Authors: Ondᔉej šubrt , Bodlák Martin , Frolov Vladimir , Huber Stefan , Jandek Matouš , Jarý Vladimίr , Konorov Igor , Květoň Antonίn , Levit Dmytro , Nový Josef , Steffen Dominik , Tomsa Jan , Virius Miroslav
Published: September 2019

Recently, a stability of Data Acquisition System (DAQ) has become a vital precondition for a successful data taking in high energy physics experiments. The intelligent, FPGA-based Data Acquisition System (iFDAQ) of the
COMPASS experiment at CERN is designed to be able to readout data at the maximum rate of the experiment and runsin a mode without any stops. DAQ systems fulfilling such requirements reach the efficiency up to 99%. The newly
introduced continuously running mode enables to collect data without a necessity of any other user intervention.Such mode affects all processes of the iFDAQ with high emphasis on timing and precise synchronization. However,
every undesirable interruption of data taking can potentially result in a possible loss of physics data. Running24/7 puts stress on reliability and robustness of the system. Therefore, the improvement of the iFDAQ stability had to come first. The continuously running mode and the improved iFDAQ stability helped to collect more physicsdata in the Run 2017. In the paper, we present the continuously running mode in more detail and discuss the overall iFDAQ stability.
Alice Overwatch: Online Monitoring and Data Quality Assurance Using Hlt Data
Authors: Ehlers Raymond , Mulligan James
Published: September 2019

ALICE Overwatch is a project started in late 2015 to provide augmented online monitoring and data quality assurance utilizing time-stamped QA histograms produced by the ALICE High Level Trigger. The system receives the data via ZeroMQ, stores it for later review, enriches it with detector specific functionality, and visualizes it via a web application. These provided capabilities are complementary to the existing Data Quality Monitoring system. In addition to basic visualization, additional processing options are accessible to the user, including requests for data within a particular time range or reprocessing of a particular run with different processing parameters. For example, the first ten minutes of a particular run could be investigated for a transient hot trigger channel.

Due to similarities between the Overwatch architecture and that which will be used for Quality Control (QC) in LHC Run 3 and beyond, Overwatch will also be utilized to develop and test various QC components during LHC Run 2. Some of the areas of QC development include a new trending and alarm framework. We report on the project᠙s design, development, and status.
Presentation layer of CMS Online Monitoring System
Authors: André Jean-Marc , Behrens Ulf , Branson James , Brummer Philipp , Cittolin Sergio , Diego Da Silva Gomes , Georgiana-Lavinia Darlea , Deldicque Christian , Demiragli Zeynep , Dobson Marc , Doualot Nicolas , Erhan Samim , Fulcher Jonathan Richard , Gigi Dominique , Gladki Maciej , Glege Frank , Gomez-Ceballos Guillelmo , Hegeman Jeroen , Holzner André , Janulis Mindaugas , Lettrich Michael , Mečionis Audrius , Meijers Frans , Mommsen Remigius K , Morovic Srecko , O’Dell Vivian , Orsini Luciano , Papakrivopoulos Ioannis , Paus Christoph , Petrova Petia , Petrova Petia , Petrucci Andrea , Pieri Marco , Rabady Dinyar , Rácz Attila , Rapševičius Valdas , Reis Thomas , Sakulin Hannes , Schwick Christoph , Šimelevičius Dainius , Stankevičius Mantas , Cristina Vazquez Velez , Wernet Christian , Zejdl Petr
Published: September 2019

The Compact Muon Solenoid (CMS) is one of the experiments at the CERN Large Hadron Collider (LHC). The CMS Online Monitoring system (OMS) is an upgrade and successor to the CMS Web-Based Monitoring (WBM)system, which is an essential tool for shift crew members, detector subsystem experts, operations coordinators, and those performing physics analyses. The CMS OMS is divided into aggregation and presentation layers. Communication between layers uses RESTful JSON:API compliant requests. The aggregation layer is responsible for collecting data from heterogeneous sources, storage of transformed and pre-calculated (aggregated) values and exposure of data via the RESTful API. The presentation layer displays detector information via a modern, user-friendly and customizable web interface. The CMS OMS user interface is composed of a set of cutting-edge software frameworks and tools to display non-event data to any authenticated CMS user worldwide. The web interface tree-like component structure comprises (top-down): workspaces, folders, pages, controllers and portlets. A clear hierarchy gives the required flexibility and control for content organization. Each bottom element instantiates a portlet and is a reusable component that displays a single aspect of data, like a table, a plot, an article, etc. Pages consist of multiple different portlets and can be customized at runtime by using a drag-and-drop technique. This is how a single page can easily include information from multiple online sources. Different pages give access to a summary of the current status of the experiment, as well as convenient access to historical data. This paper describes the CMS OMS architecture, core concepts and technologies of the presentation layer.
Adopting new technologies in the LHCb Gauss simulation framework
Authors: Müller Dominik
Published: September 2019

The increase in luminosity foreseen in the future years of operation of the Large Hadron Collider (LHC) creates new challenges in computing efficiency for all participating experiment. For Run 3 of the LHC, the LHCb collaboration needs to simulate about two orders of magnitude more Monte Carlo events to exploit the increased luminosity and trigger rate. Therefore, the LHCb simulation framework (Gauss) will go through a significant renovation, mostly driven by the upgraded core software framework (Gaudi) and the availability of a multithreaded version of Geant4. The upgraded Gaudi framework replaces single-threaded processing by a multithreaded approach, allowing concurrent execution of tasks with a single event as well as multiple events in parallel. A major task of the required overhaul of Gauss is the implementation of a new interface to the multithreaded version of Geant4.
Recent progress with the top to bottom approach to vectorization in GeantV
Authors: Amadio Guilherme , Ananya  , Apostolakis John , Bandieramonte Marilena , Behera Shiba , Bhattacharyya Abhijit , Brun René , Canal Philippe , Carminati Federico , Cosmo Gabriele , Drohan Vitaliy , Elvira Daniel , Genser Krzysztof , Andrei Gheata  , Mi-haela Gheata , Goulas Ilias , Hariri Farah , Ivanchenko Vladimir , Karpinski Przemislaw , Khattak Gulrukh , Konstantinov Dmitri , Kumawat Harphool , Lima Guilherme , Martínez Castro Jesús , Mendez Patricia , Miranda Aguillar Aldo , Nikolics Katalin , Novak Mihaly , Elena Orlova  , Pedro Kevin , Pokorski Witold , Ribon Alberto , Dmitry Savin  , Ryan Schmitz  , Sehgal Raman , Shadura Oksana , Sharan Shruti , Vallecorsa Sofia , Wenzel Sandro , Yung Jun Soon
Published: September 2019

SIMD acceleration can potentially boost by factors the application throughput. Achieving efficient SIMD vectorization for scalar code with complex data flow and branching logic, goes however way beyond breaking some loop dependencies and relying on the compiler. Since the refactoring effort scales with the number of lines of code, it is important to understand what kind of performance gains can be expected in such complex cases. We started to investigate a couple of years ago a top to bottom vectorization approach to particle transport simulation. Percolating vector data to algorithms was mandatory since not all the components can internally vectorize. Vectorizing low-level algorithms is certainly necessary, but not sufficient to achieve relevant SIMD gains. In addition, the overheads for maintaining the concurrent vector data flow and copy data have to be minimized. In the context of a vectorization R&D for simulation we developed a framework to allow different categories of scalar and vectorized components to co-exist, dealing with data flow management and real-time heuristic optimizations. The paper describes our approach on coordinating SIMD vectorization at framework level, making a detailed quantitative analysis of the SIMD gain versus overheads, with a breakdown by components in terms of geometry, physics and magnetic field propagation. We also present the more general context of this R&D work and goals for 2018.
Local reconstruction algorithms in the cathode strip chambers of CMS
Authors: Paneva Mirena
Published: September 2019

The design of the CMS detector is optimized for muon measurements. The muon system consists of gas ionization detector technologies. Cathode Strip Chambers (CSC) with both tracking and triggering capabilities are installed in the forward region. The first stage of muon reconstruction uses information from individual muon chambers and is thus called local reconstruction, in contrast to a subsequent global reconstruction where the information from all detectors is combined. First, 2-dimensional spatial points (rechits) describing where a muon crosses the CSC layers are built from the electrical signals induced by the charged particle traversing the chamber. Next, from the reconstructed hits, straight-line track segments are built within each chamber. Local reconstruction becomes particularly challenging at high instantaneous luminosities, which are expected at the HL-LHC. The high rate of particles traversing the detectors leads to increased rate of spurious rechits and segments thus increasing the combinatorial backgrounds. In this respect, work on improving the current and developing new algorithms is essential and is in progress. This document presents the existing local reconstruction algorithms used in the CMS cathode strip chambers. Their performance as well as ongoing efforts towards HL-LHC improvements are discussed.
FairRoot and ALICE O2 Multithreading Simulation
Authors: Hˇrivnácˇová Ivana
Published: September 2019

To address the challenges of the major upgrade of the experiment, the ALICE simulations must be able to make efficient use of computing and opportunistic supercomputing resources available on the GRID. The Geant4 transport package, the performance of which has been demonstrated in a hybrid multithreading (MT) and multiprocessing (MPI) environment with up to 1/4 million threads, is therefore of a particular interest.

The O2 simulation framework is based on FairRoot, which itself is based on the Virtual Monte Carlo (VMC). The integration of multithreading into the VMC design and its impact on the Geant4 VMC were presented at CHEP 2014. Geant4 VMC multithreading and the scaling behaviour of the computing time with the number of cores have then been tested using a simplified but realistic multithreaded simulation application.

The focus was then put on the integration of multithreading in FairRoot classes as the necessary step towards multithreading in the FairRoot-based experimental frameworks. The new O2 framework is the first one of which the migration to multithreading is achieved for all actually included detectors. In this paper we present the progress with the integration of multithreading in FairRoot classes, the work for thread-safety in the O2 simulation classes and the experience with the integration of the multithreading mode in testing. We will also discuss plans for the further developments.
Fitting fixed-target and ion collisions in the LHCb Gauss simulation framework
Authors: Massacrier Laure , Popov Dmitry , Robbe Patrick , Winn Michael
Published: September 2019

The LHCb experiment has been operating in various beam configurations in Run 1 and 2 of the LHC, with collisions of lead ion beams or in a fixed-target setup. In order to analyse these data, the Gauss simulation software has been extended to be able to generate events describing these configurations, based mainly on the EPOS event generator. These proceedings give details about the methods employed.
Electromagnetic physics vectorization in the GeantV transport framework
Authors: Amadio Guilherme , Ananya  , Apostolakis John , Bandieramonte Marilena , Behera S.P. , Bhattacharyya Abhijit , Brun Rene , Canal Philippe , Carminati Federico , Cosmo Gabriele , Drohan Vitalji , Elvira Victor Daniel , Genser Krzysztof , Gheata Andrei , Gheata Mihaela , Goulas Ilias , Hariri Farah , Vladimir Ivanchenko , Khattak Gul Ruk , Konstantinov Dmitri , Kumawat Harpool , Lima Jose Guilherme , Castro Jesus Martinez , Mato Pere , Mendez Patricia , Miranda Aguillar Aldo , Nikolics Katalin , Novak Mihaly , Orlova Elena , Pedro Kevin , Pokorski Witold , Ribon Alberto , Savin Dmitry , Schmitz Ryan , Sehgal Raman , Shadura Oksana , Sharan Shruti , Vallecorsa Sofia , Christian Wenzel Sandro , Yung Jun Soon
Published: September 2019

The development of the GeantV Electromagnetic (EM) physics package has evolved following two necessary paths towards code modernization. A first phase required the revision of the main electromagnetic physics models and their implementation. The main objectives were to improve their accuracy, extend them to the new high-energy frontier posed by the Future Circular Collider (FCC) programme and allow a better adaptation to a multi-particle flow. Most of the EM physics models in GeantV have been reviewed from theoretical perspective and rewritten with vector-friendly implementations, being now available in scalar mode in the alpha release. The second phase consists of a thorough investigation on the possibility to vectorise the most CPU-intensive physics code parts, such as final state sampling. We have shown the feasibility of implementing electromagnetic physics models that take advantage of SIMD/SIMT architectures, thus obtaining gains in performance. After this phase, the time has come for the GeantV project to take a step forward towards the final proof of concept. This takes shape through the testing of the full simulation chain (transport + physics + geometry) running in vectorized mode. In this paper we will present the first benchmark results obtained after vectorizing a full set of electromagnetic physics models.
Current and Future Performance of the CMS Simulation
Authors: Pedro Kevin
Published: September 2019

The CMS full simulation using Geant4 has delivered billions of simulated events for analysis during Runs 1 and 2 of the LHC. However, the HL-LHC dataset will be an order of magnitude larger, with a similar increase in occupancy per event. In addition, the upgraded CMS detector will be considerably more complex, with an extended silicon tracker and a high granularity calorimeter in the endcap region. Increases in conventional computing resources are subject to both technological and budgetary limitations, so novel approaches are needed to improve software efficiency and to take advantage of new architectures and heterogeneous resources. Several projects are in development to address these needs, including the vectorized geometry library Vec-Geom and the GeantV transport engine, which uses track-level parallelization. The current computing performance of the CMS simulation will be presented as a baseline, along with an overview of the various optimizations already available for Geant4. Finally, the progress and outlook for integrating VecGeom and GeantV in the CMS software framework will be discussed.
Track Fitting for the Belle II Experiment
Authors: Spataro Stefano
Published: September 2019

The Belle II experiment has started to take data in 2018, studying e+e- collisions at the KEK facility in Tsukuba (Japan), in a center of mass energy range of the Bottomonium states. The tracking system includes a combination of hit measurements coming from the vertex detector, made of pixel detectors and double-sided silicon strip detectors, and acentral drift chamber, inside a solenoid of 1.5 T magnetic field. Once the pattern recognition routines have identified the track candidates, hit measurements are fitted taking into account the different information coming from different detectors, the energy loss in the materials and the inhomogeneity of the magnetic field. Track fitting is performed by the generic track-fitting software GENFIT, which includes a Kalman filter improved by a deterministic annealing filter, in order to reject outlier hits coming from not correctly associated hits by the pattern recognition. Several mass hypotheses are used in the fit, in order to achieve the best track parameter estimation for each particle kind. This article presents the design of the track fitting in the Belle II software, showing results in terms of track parameter estimation as well as computing performances.
Testing and verification of the LHCb Simulation
Authors: Popov Dmitry
Published: September 2019

Monte-Carlo simulation is a fundamental tool for high-energy physics experiments, from the design phase to data analysis. In recent years its relevance has increased due to the ever growing measurements precision. Accuracy and reliability are essential features in simulation and particularly important in the current phase of the LHCb experiment, where physics analysis and preparation for data taking with the upgraded detector need to be performed at the same time. In this paper we will give an overview of the full chain of tests and procedures implemented for the LHCb Simulation software stack to ensure the quality of its results. The tests comprise simple checks to validate new software contributions in a nightlies system as well as more elaborate checks to probe simple physics and software quantities for performance and regression verifications. Commissioning of a new major version of the simulation software for production implies also validating its impact using a few physics anlayses. A new system for Simulation Data Quality (SimDQ) that is being put in place to help in the first phase of commissioning and for fast verification of all samples produced is also discussed.
New techniques for pile-up simulation in ATLAS
Authors: Novak Tadej
Published: September 2019

The high-luminosity data produced by the LHC leads to many proton-proton interactions per beam crossing in ATLAS, known as pile-up. In order to understand the ATLAS data and extract physics results it is important to model these effects accurately in the simulation. As the pile-up rate continues to grow towards an eventual rate of 200 for the HL-LHC, this puts increasing demands on the computing resources required for the simulation and the current approach of simulating the pile-up interactions along with the hard-scatter for each Monte Carlo production is no longer feasible. The new ATLAS “overlay” approach to pile-up simulation is presented. Here a pre-combined set of minimum bias interactions, either from simulation or from real data, is created once and a single event drawn from this set is overlaid with the hard-scatter event being simulated. This leads to significant improvements in CPU time. This contribution will discuss the technical aspects of the implementation in the ATLAS simulation and production infrastructure and compare the performance, both in terms of computing and physics, to the previous approach.
Progress of Geant4 electromagnetic physics developments and applications
Authors: Ivanchenko Vladimir , Bagulya Alexander , Bakr Samer , Bandieramonte Marilena , Bernard Denis , Bordage Marie-Claude , Brown Jeremy , Burkhardt Helmut , Dondero Paolo , Elles Sabine , Grichine Vladimir , Guatelli Susanna , Hariri Farah , Howard Alexander , Incerti Sebastien , Yung Jun Soon , Kadri Omrane , Kyriakou Ioanna , Maire Michel , Mantero Alfonso , Novak Mihaly , Sawkey Daren , Sawkey Daren , Semeniouk Igor , Sokolov Anton , Urban Laszlo
Published: September 2019

We report on developments of the Geant4 electromagnetic physics sub-libraries of Geant4 release 10.4 and beyond. Modifications are introduced to the models of photoelectric effect, bremsstrahlung, gamma conversion, single and multiple scattering. The theory-based Goudsmit-Saunderson model of electron/positron multiple scattering has been recently reviewed and a new improved version, providing the most accurate results for scattering of electrons and positrons, was made available. The updated interfaces, models and configurations have already been integrated into LHC applications and may be useful for any type of simulations.
Producing Madgraph5_aMC@NLO gridpacks and using TensorFlow GPU resources in the CMS HTCondor Global Pool
Authors: Bockelman Brian Paul , Fajardo Hernandez Edgar , Davila Foyo Diego , Hurtado Anampa Kenyi , Aftab Khan Farrukh , Larson Krista , Letts James , Mascheroni Marco , Mason David , Perez-Calero Yzquierdo Antonio , Trendafilovz Ivanov Todor
Published: September 2019

The CMS experiment has an HTCondor Global Pool, composed of more than 200K CPU cores available for Monte Carlo production and the analysis of da.The submission of user jobs to this pool is handled by either CRAB, the standard workflow management tool used by CMS users to submit analysis jobs requiring event processing of large amounts of data, or by CMS Connect, a service focused on final stage condor-like analysis jobs and applications that already have a workflow job manager in place. The latest scenario canbring cases in which workflows need further adjustments in order to efficiently work in a globally distributed pool of resources. For instance, the generation of matrix elements for high energy physics processes via Madgraph5_aMC@NLO and the usage of tools not (yet) fully supported by the CMS software, such as Ten-sorFlow with GPUsupport, are tasks with particular requirements. A special adaption, either at the pool factory level (advertising GPU resources) or at the execute level (e.g: to handle special parameters that describe certain needs for the remote execute nodes during submission) is needed in order to adequately work in the CMS global pool. This contribution describes the challenges and efforts performed towards adaptingsuch workflows so they can properly profit from the Global Pool via CMS Connect.
A simulation tool for ALICE storage and computing resource usage
Authors: Abramyan Armenuhi , Manukyan Narine , Hallyburton Tim , Betev Latchezar , Buncic Predrag , Grigoryan Ara
Published: September 2019

The LHC experiments produce many tens of petabytes of data each year, which must be stored, processed and analyzed. The CPU and storage resources required for these activities are planned for and requested on yearly basis. To make a better resource planning, a more fine-grained time prediction for the resource utilization is necessary, taking into account the LHC running conditions and schedule, the experiment-specific data management policies, scientific conferences demands and other criteria. To that end, we developed a flexible and highly configurable simulation tool, which performs a Discrete Event Simulation of the ALICE data flow processes. The tool consists of a Web GUI, through which the necessary parameters are entered and the results of the simulations are graphically visualized. In this paper, we describe the design of the simulation tool and present the preliminary results.
Addressing Scalability with Message Queues: Architecture and Use Cases for DIRAC Interware
Authors: Krzemien Wojciech , Stagni Federico , Haen Christophe , Mathe Zoltan , McNab Andrew , Zdybal Milosz
Published: September 2019

The Message Queue (MQ) architecture is an asynchronous communication scheme that provides an attractive solution for certain scenarios in a distributed computing model. The introduction of MQ as an intermediate component in-between the interacting processes allows to decouple the end-points making the system more flexible and providing high scalability and redundancy. DIRAC is a general-purpose interware software for distributed computing systems, which offers a common interface to a number of heterogeneous providers and guarantees transparent and reliable usage of the resources. The DIRAC platform has been adapted by several scientific projects, including High Energy Physics communities like LHCb, the Linear Collider and Belle2.

A Message Queue generic interface has been incorporated into the DIRAC framework to help solving the scalability challenges that must be addressed during LHC Run3, starting in 2021. It allows to use the MQ scheme for a message exchange among the DIRAC components or to communicate with third-party services. Within this contribution we describe the integration of MQ systems with DIRAC and several use cases are shown. Message Queues are foreseen to be used in the pilot logging system, and as a backbone of the DIRAC component logging system and monitoring.
ATLAS Grid Workflow Performance Optimization
Authors: Elmsheuser Johannes , Di Girolamo Alessandro , Filipcic Andrej , Limosani Antonio , Schulz Markus , Smith David , Sciaba Andrea , Valassi Andrea
Published: September 2019

The CERN ATLAS experiment grid workflow system manages routinely 250 to 500 thousand concurrently running production and analysis jobs to process simulation and detector data. In total more than 370 PB of data is distributed over more than 150 sites in the WLCG. At this scale small improvements in the software and computing performance and workflows can lead tosignificant resource usage gains. ATLAS is reviewing together with CERN IT experts several typical simulation and data processing workloads for potential performance improvements in terms of memory and CPU usage, disk and network I/O. All ATLASproduction and analysis grid jobs are instrumented to collect many performance metrics for detailed statistical studies using modern data analytics tools like ElasticSearch and Kibana. This presentation will review and explain the performance gains of several ATLAS simulation and data processing workflows and present analytics studies of the ATLAS grid workflows.
ATLAS Global Shares implementation in PanDA
Authors: Barreiro Megino Fernando , Di Girolamo Alessandro , De Kaushik , Maeno Tadashi , Walker Rodney
Published: September 2019

PanDA (Production and Distributed Analysis) is the workload management system for ATLAS across the Worldwide LHC Computing Grid. While analysis tasks are submitted to PanDA by over a thousand users following personal schedules (e.g. PhD or conference deadlines), production campaigns are scheduled by a central Physics Coordination group based on the organization’s calendar. The Physics Coordination group needs to allocate the amount of Grid resources dedicated to each activity, in order to manage sharing of CPU resources among various parallel campaigns and to make sure that results can be achieved in time for important deadlines. While dynamic and static shares on batch systems have been around for a long time, we are trying to move away from local resource partitioning and manage shares at a global level in the PanDA system. The global solution is not straightforward, given different requirements of the activities (number of cores, memory, I/O and CPU intensity), the heterogeneity of Grid resources (site/HW capabilities, batch configuration and queue setup) and constraints on data locality. We have therefore started the Global Shares project that follows a requirements-driven multi-step execution plan, starting from definition of nestable shares, implementing share-aware job dispatch, aligning internal processes with global shares and finally implementing a pilot stream control for controlling the batch slots that keeps late binding. This contribution will explain the development work and architectural changes in PanDA to implement Global Shares, and describe how the Global Shares project has enabled the central control of resources and significantly reduced manual operations.