Lukas Breitwieser, Ahmad Hesam, Jean de Montigny, Vasileios Vavourakis, Alexandros Iosif, Jack Jennings, Marcus Kaiser, Marco Manca, Alberto Di Meglio, Zaid Al-Ars, Fons Rademakers, Onur Mutlu, Roman Bauer,
Abstract Motivation Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulation platforms do not always take full advantage of modern hardware and often have a field-specific software design. Results We present a novel simulation platform called BioDynaMo that alleviates both of these problems. BioDynaMo features a modular and high-performance simulation engine. We demonstrate that BioDynaMo can be used to simulate use cases in: neuroscience, ...
Tópico(s): Mathematical and Theoretical Epidemiology and Ecology Models
2021 - Oxford University Press | Bioinformatics
I Antcheva, M. Ballintijn, Bertrand Bellenot, Marek Biskup, R. Brun, N. Buncic, Philippe Canal, D. Casadei, Olivier Couet, V Fine, L. Franconi, G. Ganis, A. Gheaţă, David Gonzalez Maline, Minori Goto, J. Iwaszkiewicz, Anna Kreshuk, D. Marcos Segura, R. Maunder, L. Moneta, N. A. Naumann, E. A. J. M. Offermann, V. Onuchìn, S. Panacek, Fons Rademakers, Paul S. Russo, Matevž Tadel,
ROOT is an object-oriented C++ framework conceived in the high-energy physics (HEP) community, designed for storing and analyzing petabytes of data in an efficient way. Any instance of a C++ class can be stored into a ROOT file in a machine-independent compressed binary format. In ROOT the TTree object container is optimized for statistical data analysis over very large data sets by using vertical data storage techniques. These containers can span a large number of files on local disks, the web, ...
Tópico(s): Computational Physics and Python Applications
2009 - Elsevier BV | Computer Physics Communications
M. Ballintijn, Marek Biskup, René Brun, Philippe Canal, Derek Feichtinger, G. Ganis, Günter Kickinger, Andreas Peters, Fons Rademakers,
The Parallel ROOT Facility, PROOF, enables the analysis of much larger data sets on a shorter time scale. It exploits the inherent parallelism in data of uncorrelated events via a multi-tier architecture that optimizes I/O and CPU utilization in heterogeneous clusters with distributed storage. The system provides transparent and interactive access to gigabytes today. Being part of the ROOT framework PROOF inherits the benefits of a performant object storage system and a wealth of statistical and ...
Tópico(s): Data Management and Algorithms
2005 - Elsevier BV | Nuclear Instruments and Methods in Physics Research Section A Accelerators Spectrometers Detectors and Associated Equipment
The ROOT system in an Object Oriented framework for large scale data analysis. ROOT written in C ++, contains, among others, an efficient hierarchical 00 database, a C ++ interpreter. advanced statistical analysis (multi-dimensional histogramming, fitting, minimization, cluster finding algorithms) and visualization tools. The user interacts with ROOT via a graphical user interface, the command line or batch scripts. The command and scripting language is C + + (using the interpreter) and large scripts can be ...
Tópico(s): Advanced Database Systems and Queries
1998 - Belltown Media | Linux journal
The ROOT system in an Object Oriented framework for large scale data analysis. ROOT written in C++, contains, among others, an efficient hierarchical OO database, a C++ interpreter, advanced statistical analysis (multi-dimensional histogramming, fitting, minimization, cluster finding algorithms) and visualization tools. The user interacts with ROOT via a graphical user interface, the command line or batch scripts. The command and scripting language is C++ (using the interpreter) and large scripts ...
Tópico(s): Computational Physics and Python Applications
1997 - Elsevier BV | Nuclear Instruments and Methods in Physics Research Section A Accelerators Spectrometers Detectors and Associated Equipment
R. Brun, P. Bunčić, F. Carminati, A. Morsch, Fons Rademakers, K. Šafařı́k,
Abstract The objective of the offline framework is to reconstruct and analyse the data coming from real interactions. The ALICE Offline framework, AliRoot, has already been used during the production of the Technical Design Reports of each detector to optimise their design and it is currently used to evaluate the physics performance of the full ALICE detector. This paper describes the AliRoot software environment. We wish to put into perspective the main decisions and the organisation of the offline ...
Tópico(s): Particle Detector Development and Performance
2003 - Elsevier BV | Nuclear Instruments and Methods in Physics Research Section A Accelerators Spectrometers Detectors and Associated Equipment
Roman Bauer, Lukas Breitwieser, Alberto Di Meglio, Leonard Johard, Marcus Kaiser, Marco Manca, Manuel Mazzara, Fons Rademakers, Max Talanov, Alexander Tchitchigin,
Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example, biological systems comprise an extremely complex organization and heterogeneous interactions across different spatial and temporal scales. In order to facilitate research on such problems, the BioDynaMo project aims at a general platform for computer simulations for biological ...
Tópico(s): Cloud Computing and Resource Management
2017 - IGI Global | Advances in computational intelligence and robotics book series
M. Arregui, W. Carena, S. Chapeland, P. Csató, E. Dénes, Roberto Divià, B. Eged, P. Jovanović, T. Kiss, V. Lindenstruth, Z. Meggyesi, István Novák, Fons Rademakers, Dieter Roehrich, G. Rubin, D.L. Tarjan, Norbert Tóth, K. Schossmaier, Bernhard Skaali, C. Soós, R. Stock, J. Sulyan, P. Vande Vyvre, A. Vascotto, O. Villalobos Baillie, B.N. Vissy,
The ALICE data acquisition system has been designed to support an aggregate event-building bandwidth of up to 2.5 GByte/s and a storage capability of up to 1.25 GByte/s to mass storage. A general framework called the ALICE Data Acquisition Test Environment (DATE) system has been developed as a basis for prototyping the components of the DAQ. DATE supports a wide spectrum of configurations from simple systems to more complex systems with multiple detectors and multiple event builders. Prototypes of ...
Tópico(s): Distributed and Parallel Computing Systems
2001 - Elsevier BV | Computer Physics Communications
... Review| October 01 1979 Review: Max Havelaar by Fons Rademakers Max HavelaarFons Rademakers Michael Covino Michael Covino Search ... Site Citation Michael Covino; Review: Max Havelaar by Fons Rademakers. Film Quarterly 1 October 1979; 33 (1): 46– ...
Tópico(s): European Cultural and National Identity
1979 - University of California Press | Film Quarterly
... Review| October 01 1979 Review: Max Havelaar by Fons Rademakers Max HavelaarFons Rademakers Michael Covino Michael Covino Search ... Site Citation Michael Covino; Review: Max Havelaar by Fons Rademakers. Film Quarterly 1 October 1979; 33 (1): 46– ...
1979 - University of California Press | Film Quarterly
C Aguado-Sanchez, Jakob Blomer, P. Bunčić, Ioannis Charalampidis, G. Ganis, M Nabozny, Fons Rademakers,
Parallelism aims to improve computing performance by executing a set of computations concurrently. Since the advent of today's many-core machines the full exploitation of the available CPU power has been one of the main challenges. In High Energy Physics (HEP) final data analysis the bottleneck is not only the available CPU but also the available I/O bandwidth. Most of today's HEP analysis frameworks depend on ROOT I/O. In this paper we will discuss the results obtained studying the ROOT I/O performance ...
Tópico(s): Parallel Computing and Optimization Techniques
2011 - IOP Publishing | Journal of Physics Conference Series
I Antcheva, René Brun, Carsten Hof, Fons Rademakers,
A well-designed Graphical User Interface (GUI) has critical importance in any computer application. The user interface is where the end users and the complex system intersect. An effective interface design can make a powerful and complex system, such as ROOT, easy and intuitive to learn and operate. This paper describes the main goals we defined and the design solution we found developing the graphics editor in ROOT.
Tópico(s): Robotics and Automated Systems
2005 - Elsevier BV | Nuclear Instruments and Methods in Physics Research Section A Accelerators Spectrometers Detectors and Associated Equipment
Julien Leduc, João Afonso, Richard J. Bachmann, Vladimír Bahyl, Jorge Camarero Vera, Michael Davis, Pablo Oliver Cortés, Fons Rademakers, Lasse Wardenær, Volodymyr Yurchenko,
The EOS disk + CERN Tape Archive (EOSCTA) service is CERN’s primary physics data long-term storage and archival solution for LHC Run 3. It entered production at CERN during summer 2020 and has since been serving all the LHC and non-LHC workflows involving archival to-and retrieval from tape. The CTA system is a complete redesign of the previous tape software, tape cache and tape workflows, which will need to scale to the data rate requirements of the present LHC activity period, as well as the one ...
Tópico(s): Particle Accelerators and Free-Electron Lasers
2024 - EDP Sciences | EPJ Web of Conferences
Gianmaria Del Monte, Hugo Labrador Gonzalez, Fons Rademakers, Roberto Valverde,
The CERN IT Department is responsible for ensuring the integrity and security of data stored in the IT Storage Services. General storage backends such as EOS, CERNBox and CephFS are used to store data for a wide range of use cases for all stakeholders at CERN, including experiment project spaces and user home directories. In recent years a backup system, cback, was developed based on the open source backup program restic. cback is currently used to backup about 2.5 billion files and 18PB stored ...
Tópico(s): Distributed and Parallel Computing Systems
2024 - EDP Sciences | EPJ Web of Conferences
Michael Davis, João Afonso, Richard J. Bachmann, Vladimír Bahyl, Jorge Camarero Vera, Julien Leduc, Pablo Oliver Cortés, Fons Rademakers, Lasse Wardenær, Volodymyr Yurchenko,
The CERN Tape Archive (CTA) is the successor to CASTOR and the tape backend to EOS. It was designed to meet the needs of archival storage of data from LHC Run–3 and other experimental programmes at CERN. In the wider Worldwide LHC Computing Grid (WLCG), the tape software landscape is quite heterogeneous, but we are entering a period of consolidation. A number of sites have reevaluated their options and are choosing CTA for their future tape archival storage needs. However, CTA’s original mandate imposed ...
Tópico(s): Scientific Computing and Data Management
2024 - EDP Sciences | EPJ Web of Conferences
M. Girone, Andrew Purcell, Alberto Di Meglio, Fons Rademakers, Kristina Gunne, Maria-Athanasia Pachou, Sotirios Pavlou,
LHC Run3 and Run4 represent an unprecedented challenge for HEP computing in terms of both data volume and complexity. New approaches are needed for how data is collected and filtered, processed, moved, stored and analysed if these challenges are to be met with a realistic budget. To develop innovative techniques we are fostering relationships with industry leaders. CERN openlab is a unique resource for public-private partnership between CERN and leading Information Communication and Technology (ICT) ...
Tópico(s): Scientific Computing and Data Management
2017 - IOP Publishing | Journal of Physics Conference Series
Computing in High Energy Physics (HEP) has always required more computing power than could be provided by a single machine. In fact, HEP has been pushing the capabilities of computers since the first mainframes were produced in the early sixties. Every CPU cycle and every last bit of memory and disk has always been used, running data acquisition, simulation, reconstruction and analysis programs.
Tópico(s): Computational Physics and Python Applications
2011 - Springer Nature | The frontiers collection
R. Brun, Dirk Duellmann, G. Ganis, Andrew Hanushevsky, Łukasz Janyst, A. Peters, Fons Rademakers, Elvin Alin Sindrilaru,
The use of proxy caches has been extensively studied in the HEP environment for efficient access of database data and showed significant performance with only very moderate operational effort at higher grid tiers (T2, T3). In this contribution we propose to apply the same concept to the area of file access and analyse the possible performance gains, operational impact on site services and applicability to different HEP use cases. Base on a proof-of-concept studies with a modified XROOT proxy server ...
Tópico(s): Parallel Computing and Optimization Techniques
2011 - IOP Publishing | Journal of Physics Conference Series
R. Brun, Philippe Canal, M. Frank, A. Kreshuk, S. Linev, Paul S. Russo, Fons Rademakers,
For the last several months the main focus of development in the ROOT I/O package has been code consolidation and performance improvements. We introduced a new pre-fetch mechanism to minimize the number of transactions between client and server, hence reducing the effect of latency on the time it takes to read a file both locally and over wide are network. We will review the implementation and how well it works in different conditions (gain of an order of magnitude for remote file access). We will ...
Tópico(s): Distributed and Parallel Computing Systems
2008 - IOP Publishing | Journal of Physics Conference Series
R. Brun, V. Fine, J. Lauret, Fons Rademakers,
Abstract This paper presents the approach and an implementation of the Qt-based low-level graphical plug-in of the ROOT package. In spite of other existing implementations, this work uniquely allows to create applications which can seamlessly use the ROOT GUI classes as well as the Qt Widgets. The current code can be built from a single ROOT-base package and can be assembled for both Unix and Windows OS. No alteration of either user code or core ROOT code is required. An example application using ...
Tópico(s): Gaze Tracking and Assistive Technology
2004 - Elsevier BV | Nuclear Instruments and Methods in Physics Research Section A Accelerators Spectrometers Detectors and Associated Equipment
T. Hakulinen, Fons Rademakers,
A 32-node Meiko CS-2 MIMD machine has been installed at CERN as part of an ESPRIT project funded by the European Community. It is intended that this machine be used by CERN to run codes developed at CERN and elsewhere and to thereby demonstrate the feasibility of using a CS-2 in a demanding high energy physics environment. One part of the project deals with interactive data analysis using PIAF (Parallel Interactive Analysis Facility), a system developed at CERN for carrying out queries on very large ...
Tópico(s): Algorithms and Data Compression
1995 - Springer Science+Business Media | Lecture notes in computer science
Christopher H. Chapman, Upendra Parvathaneni, Sue S. Yom,
... Crossref, Medline, Google Scholar17 Brockstein B, Haraf DJ, Rademaker AW et al. Patterns of failure, prognostic factors ...
Tópico(s): Ear and Head Tumors
2017 - Future Medicine | Future Oncology
Dipti Gupta, Shawn C. Pun, Shivani Verma, Richard M. Steingart,
... 871–876 (1993).Crossref, Medline, CAS, Google Scholar18 Rademaker J, Schoder H, Ariaratnam NS et al. Coronary ...
Tópico(s): Breast Cancer Treatment Studies
2015 - Future Medicine | Future Oncology
... TX: Pro Ed. Google Scholar Logemann, J. A., Rademaker, A. W., Pauloski, B. R., & Kahrilas. P. J. ( ... Rasley, A., Logemann, J. A., Kahrilas, P. J., Rademaker, A. W., Pauloski, B. R., Dodds, W. J. ( ... CrossrefGoogle Scholar Shanahan, T. K., Logemann, J.A., Rademaker, A. W., Pauloski, B. R., Kahrilas, P. J. ( ... Google Scholar Welch, M. W., Logemann, J. A., Rademaker, A. W., Sc Kahrilas, P. J. (1993). Changes ... OutcomesLaurie Wennerholm, Nilsa Rubin Perez, Suzanne Abt, Karen Fon and Kerri Elsabrout Volume 9Issue 2July 2000Pages: 2- ...
Tópico(s): Esophageal and GI Pathology
2000 - American Speech–Language–Hearing Association | Perspectives on Swallowing and Swallowing Disorders (Dysphagia)