bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conditions and Alignment Extensions of the DD4hep Detector Description Toolkit
Authors: Frank Markus , Gaede Frank , Petric Marko , Sailer Andre 
Published: September 2019

The detector description is an essential component to analyze data resulting from particle collisions in high energy physics experiments. The interpretation of data from particle collisions typically requires auxiliary data which describe in detail the state of the experiment. These accompanying data include alignment parameters, parameters describing the electronics as well as calibration- and environmental constants. We present a mechanism to manage such data in multiple simultaneous versions depending on their validity. The detector conditions data are made available to the physics algorithms through a number of transient objects grouped to collections. Such a collection represents a coherent slice of all conditions data necessary to process one or several events depending on the valid interval of the slice being the intersection of the individual conditions.
A multi-threaded application may hold several such collections in parallel depending on the time-stamps of the events currently processed. Once prepared, these collections are read-only and can easily be shared between threads with minimal requirements for locking and hence minimal overhead. We deliberately restrained ourselves from providing a persistent data solution, which in the past were fields of expertise of the experiments, but rather provided the necessary hooks to populate the conditions cache. We will present the use-cases that have driven the development, the main design choices and details of the implementation.
Dataclient: a simple interface for scientific data transfers hiding x.509 complexities
Authors: Ciaschini Vincenzo , Morganti Lucia , Tenti Matteo , Pellegrino Carmelo 
Published: September 2019

Since the current data infrastructure of the HEP experiments is based on GridFTP, most computing centres have adapted and based their own access to the data on the X.509. This is an issue for smaller experiments that do not have the resources to train their researchers in the complexities of X.509 certificates and that would prefer an approach based on username/password.
On the other hand, asking computing centres to support different access strategies is not so straightforward, as this would require a significant investment of effort and manpower.
At CNAF-INFN Tier1 we tackled this problem by creating a layer on top of the gridftp client/server, that completely hides the X.509 infrastructure under an authentication/authorization process based on the Kerberos realm of our centre, and therefore based on username/password.
We called this Dataclient. In this article we will describe both the principles that drove its design and its general architecture, together with the measures undertaken to simplify the user experience and maintenance burden.
CERN Tape Archive — from development to production deployment
Authors: Davis Michael C. , Bahyl Vladímir , Cancio Germán , Cano Eric , Leduc Julien , Murray Steven 
Published: September 2019

The first production version of the CERN Tape Archive (CTA) software is planned to be released during 2019. CTA is designed to replace CASTOR as the CERN tape archive solution, to face the scalability and performance challenges arriving with LHC Run–3.
In this paper, we describe the main commonalities and differences between CTA and CASTOR. We outline the functional enhancements and integration steps required to add the CTA tape back-end to an EOS disk storage system. We present and discuss the different deployment and migration scenarios for replacing the five CASTOR instances at CERN, including a description of how the File Transfer Service (FTS) will interface with EOS and CTA.
Scaling the EOS namespace – new developments, and performance optimizations
Authors: Bitzes Georgios , Sindrilaru Elvin Alin , Joachim Peters Andreas 
Published: September 2019

EOS is the distributed storage solution being developed and deployed at CERN with the primary goal of fulfilling the data needs of the LHC and its various experiments. Being in production since 2011, EOS currently manages around 256 petabytes of raw disk space and 3.4 billion files across several instances. Nowadays, EOS is increasingly being used as a distributed filesystem and file sharing platform, which poses scalability challenges on its legacy namespace subsystem, tasked with keeping track of all file and directory metadata on a
particular instance.
In this paper we discuss said challenges, and present our solution which has recently entered production. We made several architectural improvements to the overall system design, the most important of which was introducing QuarkDB, a highly-available datastore capable of serving as the metadata backend for EOS,
tailored to the needs of the namespace.
We also describe our efforts in providing comparable latency and performance to the legacy in-memory implementation, both when reading through the use of extensive caching and prefetching, and when writing through the use of latencyhiding techniques involving a persistent, back-pressured local queue for batching writes towards the QuarkDB backend.
Storage events: distributed users, federation and beyond
Authors: Paul Millar A. , Adeyemi Olufemi , Garonne Vincent , Litvintsev Dmitry , Mkrtchyan Tigran , Rossi Albert , Sahakyan Marina , Starek Jürgen 
Published: September 2019

For federated storage to work well, some knowledge from each storage system must exist outside that system, regardless of the use case. This is needed to allow coordinated activity; e.g., executing analysis jobs on worker nodes with good accessibility to the data.
Currently, this is achieved by clients notifying central services of activity; e.g., a client notifies a replica catalogue after an upload. Unfortunately, this forces end users to use bespoke clients. It also forces clients to wait for asynchronous activities to finish.
dCache provides an alternative approach: storage events. In this approach the storage systems (rather than the clients) become the coordinating service, notifying interested parties of key events.
At DESY, we are investigating storage events along with Apache OpenWhisk and Kubernetes to build a "serverless" cloud, similar to AWS Lambda or Google Cloud Functions, for photon science use cases.
Storage events are more generally useful: catalogues are notified whenever data is uploaded or delete, tape becomes more efficient because analysis can start immediately after the data is on disk, caches can be "smart" fetching new datasets preemptively.
In this paper we will present work within dCache to support a new event-based interface, with which these and other use cases become more efficient.
The ATLAS Wide-Range Database and Application Monitoring
Authors: Vasileva Petya , Formica Andrea , Dimitrov Gancho 
Published: September 2019

In HEP experiments at LHC the database applications often become complex, reflecting the increasingly demanding requirements of the researchers. The ATLAS experiment has several Oracle DB clusters with over 216 database schemes each with its own set of database objects. To effectively monitor them, we designed a modern and portable application with exceptionally good characteristics. Some of them include: A concise view of the most important DB metrics; a list of top SQL statements based on CPU, executions, block reads, etc.; volume growth plots per schema and DB object type; a database jobs section with signalization for failures; and in-depth analysis in case of row-lock contention or DB sessions.
This contribution also describes the technical aspects of the implementation. The project can be separated into three independent layers. The first layer consists in highly-optimized database objects hiding all complicated calculations. The second layer represents a server providing REST access to the underlying database backend. The third layer is a JavaScript/AngularJS web interface. In addition, we will summarize the continuous integration cycle of the application, which uses GitLab-ci pipelines for basic testing, containerization and deployment on the CERN Openshift infrastructure.
Using ZFS to manage Grid storage and improve middleware resilience
Authors: Currie Robert , Li Teng , Washbrook Andrew 
Published: September 2019

ZFS is a powerful storage management technology combining filesystem, volume management and software RAID technology into a single solution. The WLCG Tier-2 computing at Edinburgh was an early adopter of ZFS on Linux, with this technology being used to manage all of our storage systems including servers with aging components. Our experiences of ZFS deployment have been shared with the Grid storage community which has led to additional sites adopting this technology.
ZFS is highly configurable therefore allowing systems to be tuned to give best performance under diverse workloads. This paper highlights our experiences in tuning our systems for best performance when combining ZFS with DPM storage management. This has resulted in reduced system load and better data throughput. This configuration also provides the high redundancy required for managing older storage servers. We also demonstrate how ZFS can be combined with Distributed Replicated Block Device (DRBD) technology to provide a performant and resilient hypervisor solution to host multiple production Grid services.
Bootstrapping a New LHC Data Transfer Ecosystem
Authors: Bockelman Brian , Hanushevsky Andrew , Keeble Oliver , Lassnig Mario , Millar Paul , Weitzel Derek , Yang Wei 
Published: September 2019

GridFTP transfers and the corresponding Grid Security Infrastructure
(GSI)-based authentication and authorization system have been data transfer
pillars of the Worldwide LHC Computing Grid (WLCG) for more than a
decade. However, in 2017, the end of support for the Globus Toolkit - the reference
platform for these technologies - was announced. This has reinvigorated
and expanded efforts to replace these pillars. We present an end-to-end alternate
utilizing HTTP-based WebDAV as the transfer protocol, and bearer tokens for
distributed authorization.
This alternate ecosystem, integrating significant pre-existing work and ideas in
the area, adheres to common industry standards to the fullest extent possible,
with minimal agreed-upon extensions or common interpretations of the core
protocols. The bearer token approach allows resource providers to delegate authorization
decisions to the LHC experiments for experiment-dedicated storage
areas.
This demonstration touches the entirety of the stack - from multiple storage
element implementations to FTS3 to the Rucio data management system. We
show how the traditional production and user workflows can be reworked utilizing
bearer tokens, eliminating the need for GSI proxy certificates for storage
interactions.
Conditions evolution of an experiment in mid-life, without the crisis (in ATLAS)
Authors: Rinaldi Lorenzo , Formica Andrea , Gallas Elizabeth J , Ozturk Nurcan , Roe Shaun 
Published: September 2019

The ATLAS experiment is approaching mid-life: the long shutdown
period (LS2) between LHC Runs 1 and 2 (ending in 2018) and the future collision
data-taking of Runs 3 and 4 (starting in 2021). In advance of LS2, we have
been assessing the future viability of existing computing infrastructure systems.
This will permit changes to be implemented in time for Run 3. In systems with
broad impact such as the conditions database, making assessments now is critical
as the full chain of operations from online data-taking to offline processing
can be considered: evaluating capacity at peak times, looking for bottlenecks,
identifying areas of high maintenance, and considering where new technology
may serve to do more with less.
We have been considering changes to the ATLAS Conditions Database related
storage and distribution infrastructure based on similar systems of other experiments.
We have also examined how new technologies may help and how we
might provide more RESTful services to clients. In this presentation, we give
an overview of the identified constraints and considerations, and our conclusions
for the best way forward: balancing preservation of critical elements of
the existing system with the deployment of the new technology in areas where
the existing system falls short.
Parallel Event Selection on HPC Systems
Authors: Paterno Marc , Kowalkowski Jim , Sehrish Saba 
Published: September 2019

In their recent measurement of the neutrino oscillation parameters,
NOvA uses a sample of approximately 25 million reconstructed spills to search
for electron-neutrino appearance events. These events are stored in an n-tuple
format, in 250 thousand ROOT files. File sizes range from a few hundred KiB to
a few MiB; the full dataset is approximately 1.4 TiB. These millions of events
are reduced to a few tens of events by the application of strict event selection
criteria, and then summarized by a handful of numbers each, which are used in
the extraction of the neutrino oscillation parameters.
The NOvA event selection code is currently a serial C++ program that reads
these n-tuples. The current table data format and organization and the selection/
reduction processing involved provides us with an opportunity to explore
alternate approaches to represent the data and implement the processing. We
represent our n-tuple data in HDF5 format that is optimized for the HPC environment
and which allows us to use the machine’s high-performance parallel
I/O capabilities. We use MPI, numpy and h5py to implement our approach and
compare the performance with the existing approach. We study the performance
implications of using thousands of small files of different sizes as compared
with one large file using HPC resources. This work has been done as part of the
SciDAC project, “HEP analytics on HPC” in collaboration with the ASCR teams
at ANL and LBNL.
GNA: new framework for statistical data analysis
Authors: Fatkina Anna , Gonchar Maxim , Kalitkina Anastasia , Kolupaeva Liudmila , Naumov Dmitry , Selivanov Dmitry , Treskov Konstantin 
Published: September 2019

We report on the status of GNA — a new framework for fitting large-scale physical models. GNA utilizes the data flow concept within which a model is represented by a directed acyclic graph. Each node is an operation on an array (matrix multiplication, derivative or cross section calculation, etc). The framework enables the user to create flexible and efficient large-scale lazily evaluated models, handle large numbers of parameters, propagate parameters’ uncertainties while taking into account possible correlations between them, fit models, and perform statistical analysis.
The main goal of the paper is to give an overview of the main concepts and methods as well as reasons behind their design. Detailed technical information is to be published in further works.
Shared Memory Transport for ALFA
Authors: Rybalchenko Alexey , Klein Dennis , Al-Turany Mohammad , Kollegger Thorsten 
Published: September 2019

The high data rates expected for the next generation of particle physics experiments (e.g.: new experiments at FAIR/GSI and the upgrade of CERN experiments) call for dedicated attention with respect to design of the needed computing infrastructure. The common ALICE-FAIR framework ALFA is a modern software layer, that serves as a platform for simulation, reconstruction and analysis of particle physics experiments. Beside standard services needed for simulation and reconstruction of particle physics experiments, ALFA also provides tools for data transport, configuration and deployment. The FairMQ module in ALFA offers building blocks for creating distributed software components (processes) that communicate between each other via message passing.The abstract "message passing" interface in FairMQ has at the moment three implementations: ZeroMQ, nanomsg and shared memory. The newly developed shared memory transport will be presented, that provides significant per-formance benefits for transferring large data chunks between components on the same node. The implementation in FairMQ allows users to switch between the different transports via a trivial configuration change. The design decisions, im-plementation details and performance numbers of the shared memory transport in FairMQ/ALFA will be highlighted.
REANA: A System for Reusable Research Data Analyses
Authors: Šimko Tibor , Heinrich Lukas , Hirvonsalo Harri , Kousidis Dinos , Rodríguez Diego 
Published: September 2019

The revalidation, reinterpretation and reuse of research data analyses requires having access to the original computing environment, the experimental datasets, the analysis software, and the computational workflow steps which were used by researchers to produce the original scientific results in the first place.
REANA (Reusable Analyses) is a nascent platform enabling researchers to structure their research data analyses in view of enabling future reuse. The analysis is described by means of a YAML file that captures sufficient information about the analysis assets, parameters and processes. The REANA platform consists of a set of micro-services allowing to launch and monitor container-based computational workflow jobs on the cloud. The REANA user interface and the command-line client enables researchers to easily rerun analysis workflows with new input parameters. The REANA platform aims at supporting several container technologies (Docker), workflow engines (CWL, Yadage), shared storage systems (Ceph, EOS) and compute cloud infrastructures (Ku-bernetes/OpenStack, HTCondor) used by the community.
REANA was developed with the particle physics use case in mind and profits from synergies with general reusable research data analysis patterns in other scientific disciplines, such as bioinformatics and life sciences.
Containerized Batch System Monitoring
Authors: Gellrich Andreas , Hartmann Thomas , Lewendel Birgit , Prelogović David , Voss Christian 
Published: September 2019

Running a batch system for grid jobs and for local users, we investigate a generic solution to monitor the resource usages of jobs. We extend a standard toolkit for monitoring container performance metrics also for non-containerized applications, so that we can make easy use of a popular industry solution. By concentrating on the basic kernel features also used by containers frameworks, we envisage to use the same tools on non-containerized batch systems as well as container orchestrators.
For deployment, we encapsulate the tools as Singularity containers and distribute them via CVMFS.
Long-term experiences in keeping balance between safety and usability in research activities in KEK
Authors: Murakami Tadashi , Yuasa Fukuko , Baba Ryouichi , Nakamura Teiji , Hashimoto Kiyoharu , Suzuki Soh Y. , Nishiguchi Mitsuo , Kaneko Toshiaki 
Published: September 2019

This work aims to provide KEK general-purpose network to support various research activities in the fields of high-energy physics, material physics, and accelerator physics. Since the end of the 20th century, on a daily basis, networks experience cyber-attacks and the methods of attack have rapidly evolved to become more sophisticated over the years. Security measures have been developed to mitigate the effects of cyber-attacks. While security measures may improve safety, restrictions might reduce usability. Therefore, we must keep a balance between safety and usability of the network for a smooth running of research activities.
Herein, we present our long-term experience with keeping a balance between safety and usability in KEK research activities. The key points are reasonably ensuring traceability and security management. We have been using security devices, such as firewalls, intrusion detection systems, and vulnerability management systems, to achieve a balance between safety and usability. Also, we present activities of the computer security incident response team (CSIRT) and collaborative activities among research organizations.
Integration and Evaluation of QUIC and TCP-BBR in longhaul Science Data Transfers
Authors: Lopes Raul H. C. , Franqueira Virginia N. L. , Rand Duncan 
Published: September 2019

Two recent and promising additions to the internet protocols are TCP-BBR and QUIC. BBR defines a congestion policy that promises a better control in TCP bottlenecks on long haul transfers and can also be used in the QUIC protocol. TCP-BBR is implemented in the Linux kernels above 4.9. It has been shown, however, to demand careful fine tuning in the interaction, for example, with the Linux Fair Queue. QUIC, on the other hand, replaces HTTP and TLS with a protocol on the top of UDP and thin layer to serve HTTP. It has been reported to account today for 7% of Google’s traffic. It has not been used in server-to-server transfers even if its creators see that as a real possibility.Our work evaluates the applicability and tuning of TCP-BBR and QUIC for data science transfers. We describe the deployment and performance evaluation of TCP-BBR and comparison with CUBIC and H-TCP in transfers through the TEIN link to Singaren (Singapore). Also described is the deployment and initial evaluation of a QUIC server.We argue that QUIC might be a perfect match in security and connectivity to base services that are today performed by the Xroot redirectors.
Erfolgreiche kieferorthopädische Einstellung eines dilazerierten oberen mittleren Inzisivus – ein Fallbericht
Authors: Schubert Michael , Proff Peter , Kirschneck Christian 
Published: September 2019

Zusammenfassung
Hintergrund Verlagerte, dilazerierte Inzisiven sind häufig Folge eines dentalen Traumas im Milchgebiss. Aufgrund z.T. erheblicher funktionell-ästhetischer Einschränkungen ist eine adäquate Therapie indiziert, die neben einer Extraktion mit Lückenschluss, (implantat)prothetischer Versorgung oder Autotransplantation bleibender Zahnkeime auch in einer kombiniert chirurgisch-kieferorthopädischen Einstellung in den Zahnbogen bestehen kann.
Fallvorstellung Bei einem 9-jährigen Patienten mit dilazeriertem Zahn 21, Mesialstand der Seitenzähne im 2. Quadranten sowie tiefem Überbiss mit traumatischem Einbiss der unteren Inzisiven erfolgte im Rahmen einer festsitzenden kieferorthopädischen Multibrackettherapie eine Einstellung des Zahnes 21 in Okklusion nach chirurgischer Freilegung und Traktion mittels des EWC-Systems (Adenta), skelettal verankert über 2 temporäre mediane palatinale Minischrauben an einer BENEslider-Apparatur (PSM Medical Solutions), welche zudem zur Molarendistalisation im 2. Quadranten genutzt wurde.
Schlussfolgerungen Im Fallbericht konnte unter Anwendung einer skelettalen Verankerung und des EWC-Systems im frühen Wechselgebiss ein dilazerierter mittlerer oberer Schneidezahn erfolgreich kieferorthopädisch unter Erhaltung der Zahnvitalität eingestellt werden. Trotz möglicher Risiken (Devitalisierung, Zahnwurzelresorptionen, Ankylosierung) stellt dieses Vorgehen daher bei korrekter biomechanischer Planung eine mögliche zahnerhaltende Therapieoption dar.