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Author |
Gimenez-Alventosa, V.; Gimenez, V.; Oliver, S. |
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Title |
PenRed: An extensible and parallel Monte-Carlo framework for radiation transport based on PENELOPE |
Type |
Journal Article |
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Year |
2021 |
Publication |
Computer Physics Communications |
Abbreviated Journal |
Comput. Phys. Commun. |
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Volume |
267 |
Issue |
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Pages |
108065 - 12pp |
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Keywords |
Radiation transport; Monte Carlo simulation; Electron-photon showers; Parallel computing; MPI; Medical physics |
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Abstract |
Monte Carlo methods provide detailed and accurate results for radiation transport simulations. Unfortunately, the high computational cost of these methods limits its usage in real-time applications. Moreover, existing computer codes do not provide a methodology for adapting these kinds of simulations to specific problems without advanced knowledge of the corresponding code system, and this restricts their applicability. To help solve these current limitations, we present PenRed, a general-purpose, standalone, extensible and modular framework code based on PENELOPE for parallel Monte Carlo simulations of electron-photon transport through matter. It has been implemented in C++ programming language and takes advantage of modern object-oriented technologies. In addition, PenRed offers the capability to read and process DICOM images as well as to construct and simulate image-based voxelized geometries, so as to facilitate its usage in medical applications. Our framework has been successfully verified against the original PENELOPE Fortran code. Furthermore, the implemented parallelism has been tested showing a significant improvement in the simulation time without any loss in precision of results. Program summary Program title: PenRed: Parallel Engine for Radiation Energy Deposition. CPC Library link to program files: https://doi .org /10 .17632/rkw6tvtngy.1 Licensing provision: GNU Affero General Public License (AGPL). Programming language: C++ standard 2011. Nature of problem: Monte Carlo simulations usually require a huge amount of computation time to achieve low statistical uncertainties. In addition, many applications necessitate particular characteristics or the extraction of specific quantities from the simulation. However, most available Monte Carlo codes do not provide an efficient parallel and truly modular structure which allows users to easily customise their code to suit their needs without an in-depth knowledge of the code system. Solution method: PenRed is a fully parallel, modular and customizable framework for Monte Carlo simulations of the passage of radiation through matter. It is based on the PENELOPE [1] code system, from which inherits its unique physics models and tracking algorithms for charged particles. PenRed has been coded in C++ following an object-oriented programming paradigm restricted to the C++11 standard. Our engine implements parallelism via a double approach: on the one hand, by using standard C++ threads for shared memory, improving the access and usage of the memory, and, on the other hand, via the MPI standard for distributed memory infrastructures. Notice that both kinds of parallelism can be combined together in the same simulation. Moreover, both threads and MPI processes, can be balanced using the builtin load balance system (RUPER-LB [30]) to maximise the performance on heterogeneous infrastructures. In addition, PenRed provides a modular structure with methods designed to easily extend its functionality. Thus, users can create their own independent modules to adapt our engine to their needs without changing the original modules. Furthermore, user extensions will take advantage of the builtin parallelism without any extra effort or knowledge of parallel programming. Additional comments including restrictions and unusual features: PenRed has been compiled in linux systems withg++ of GCC versions 4.8.5, 7.3.1, 8.3.1 and 9; clang version 3.4.2 and intel C++ compiler (icc) version 19.0.5.281. Since it is a C++11-standard compliant code, PenRed should be able to compile with any compiler with C++11 support. In addition, if the code is compiled without MPI support, it does not require any non standard library. To enable MPI capabilities, the user needs to install whatever available MPI implementation, such as openMPI [24] or mpich [25], which can be found in the repositories of any linux distribution. Finally, to provide DICOM processing support, PenRed can be optionally compiled using the dicom toolkit (dcmtk) [32] library. Thus, PenRed has only two optional dependencies, an MPI implementation and the dcmtk library. |
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Address |
[Gimenez-Alventosa, V] Univ Politecn Valencia, Inst Instrumentac Imagen Mol I3M, Ctr Mixto CSIC, Cami Vera S-N, Valencia 46022, Spain, Email: vicent.gimenez@i3m.upv.es; |
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Elsevier |
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English |
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ISSN |
0010-4655 |
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Conference |
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Notes |
WOS:000678508900001 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ pastor @ |
Serial |
4907 |
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Author |
Fernandez Casani, A.; Orduña, J.M.; Sanchez, J.; Gonzalez de la Hoz, S. |
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Title |
A Reliable Large Distributed Object Store Based Platform for Collecting Event Metadata |
Type |
Journal Article |
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Year |
2021 |
Publication |
Journal of Grid Computing |
Abbreviated Journal |
J. Grid Comput. |
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Volume |
19 |
Issue |
3 |
Pages |
39 - 19pp |
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Keywords |
Grid computing; Hadoop file system; Object-Based storage |
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Abstract |
The Large Hadron Collider (LHC) is about to enter its third run at unprecedented energies. The experiments at the LHC face computational challenges with enormous data volumes that need to be analysed by thousands of physics users. The ATLAS EventIndex project, currently running in production, builds a complete catalogue of particle collisions, or events, for the ATLAS experiment at the LHC. The distributed nature of the experiment data model is exploited by running jobs at over one hundred Grid data centers worldwide. Millions of files with petabytes of data are indexed, extracting a small quantity of metadata per event, that is conveyed with a data collection system in real time to a central Hadoop instance at CERN. After a successful first implementation based on a messaging system, some issues suggested performance bottlenecks for the challenging higher rates in next runs of the experiment. In this work we characterize the weaknesses of the previous messaging system, regarding complexity, scalability, performance and resource consumption. A new approach based on an object-based storage method was designed and implemented, taking into account the lessons learned and leveraging the ATLAS experience with this kind of systems. We present the experiment that we run during three months in the real production scenario worldwide, in order to evaluate the messaging and object store approaches. The results of the experiment show that the new object-based storage method can efficiently support large-scale data collection for big data environments like the next runs of the ATLAS experiment at the LHC. |
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Address |
[Fernandez Casani, Alvaro; Sanchez, Javier; Gonzalez de la Hoz, Santiago] Univ Valencia, Inst Fis Corpuscular IFIC, Burjassot, Spain, Email: alvaro.fernandez@ific.uv.es; |
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Publisher |
Springer |
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English |
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Edition |
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ISSN |
1570-7873 |
ISBN |
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Area |
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Expedition |
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Conference |
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Notes |
WOS:000692413100001 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ pastor @ |
Serial |
4953 |
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Author |
Holz, S.; Plenter, J.; Xiao, C.W.; Dato, T.; Hanhart, C.; Kubis, B.; Meissner, U.G.; Wirzba, A. |
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Title |
Towards an improved understanding of eta -> gamma*gamma * |
Type |
Journal Article |
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Year |
2021 |
Publication |
European Physical Journal C |
Abbreviated Journal |
Eur. Phys. J. C |
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Volume |
81 |
Issue |
11 |
Pages |
1002 - 15pp |
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Abstract |
We argue that high-quality data on the reaction e(+)e(-) -> pi(+) pi(-) eta will allow one to determine the doubly-virtual form factor eta -> gamma*gamma* in a model-independent way with controlled accuracy. This is an important step towards a reliable evaluation of the hadronic light-by-light scattering contribution to the anomalous magnetic moment of themuon. When analyzing the existing data for e(+) e(-) -> pi(+) pi(-) eta for total energies squared k(2) > 1GeV(2), we demonstrate that the effect of the a(2) meson provides a natural breaking mechanism for the commonly employed factorization ansatz in the doubly-virtual form factor F-eta gamma*gamma* (q(2), k(2)). However, better data are needed to draw firm conclusions. |
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Address |
[Holz, S.; Plenter, J.; Dato, T.; Kubis, B.; Meissner, U-G] Univ Bonn, Helmholtz Inst Strahlen & Kemphys Theorie, D-53115 Bonn, Germany, Email: holz@hiskp.uni-bonn.de; |
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Publisher |
Springer |
Place of Publication |
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Language |
English |
Summary Language |
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Original Title |
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Series Editor |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1434-6044 |
ISBN |
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Area |
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Expedition |
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Conference |
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Notes |
WOS:000718113500001 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ pastor @ |
Serial |
5024 |
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Author |
Otten, S.; Caron, S.; de Swart, W.; van Beekveld, M.; Hendriks, L.; van Leeuwen, C.; Podareanu, D.; Ruiz de Austri, R.; Verheyen, R. |
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Title |
Event generation and statistical sampling for physics with deep generative models and a density information buffer |
Type |
Journal Article |
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Year |
2021 |
Publication |
Nature Communications |
Abbreviated Journal |
Nat. Commun. |
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Volume |
12 |
Issue |
1 |
Pages |
2985 - 16pp |
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Keywords |
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Abstract |
Simulating nature and in particular processes in particle physics require expensive computations and sometimes would take much longer than scientists can afford. Here, we explore ways to a solution for this problem by investigating recent advances in generative modeling and present a study for the generation of events from a physical process with deep generative models. The simulation of physical processes requires not only the production of physical events, but to also ensure that these events occur with the correct frequencies. We investigate the feasibility of learning the event generation and the frequency of occurrence with several generative machine learning models to produce events like Monte Carlo generators. We study three processes: a simple two-body decay, the processes e(+)e(-)-> Z -> l(+)l(-) and pp -> tt<mml:mo><overbar></mml:mover> including the decay of the top quarks and a simulation of the detector response. By buffering density information of encoded Monte Carlo events given the encoder of a Variational Autoencoder we are able to construct a prior for the sampling of new events from the decoder that yields distributions that are in very good agreement with real Monte Carlo events and are generated several orders of magnitude faster. Applications of this work include generic density estimation and sampling, targeted event generation via a principal component analysis of encoded ground truth data, anomaly detection and more efficient importance sampling, e.g., for the phase space integration of matrix elements in quantum field theories. Here, the authors report buffered-density variational autoencoders for the generation of physical events. This method is computationally less expensive over other traditional methods and beyond accelerating the data generation process, it can help to steer the generation and to detect anomalies. |
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Address |
[Otten, Sydney; Caron, Sascha; de Swart, Wieske; van Beekveld, Melissa; Hendriks, Luc; Verheyen, Rob] Radboud Univ Nijmegen, Inst Math Astro & Particle Phys IMAPP, Nijmegen, Netherlands, Email: Sydney.Otten@ru.nl |
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Nature Research |
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English |
Summary Language |
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ISSN |
2041-1723 |
ISBN |
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Notes |
WOS:000658761600003 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ pastor @ |
Serial |
4862 |
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Author |
Wang, E.; Liang, W.H.; Oset, E. |
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Title |
Analysis of the e(+)e(-) -> J/psi D(D)over-bar reaction close to the threshold concerning claims of a chi(c0)(2P) state |
Type |
Journal Article |
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Year |
2021 |
Publication |
European Physical Journal A |
Abbreviated Journal |
Eur. Phys. J. A |
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Volume |
57 |
Issue |
1 |
Pages |
38 - 9pp |
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Abstract |
We analyze the D (D) over bar mass distribution from a recent Belle experiment on the e(+)e(-) -> J/.D (D) over bar reaction, and show that the mass distribution divided by phase sp(c)e does not have a clear peak above the D (D) over bar threshold that justifies the experimental claim of chi(c0)(2P) state from those data. Then we use a unitary formalismwith coupled channels D+ D-, D-0 (D) over bar (0), D-s(D) over bar (s), and eta eta, with some of the interactions taken from a theoretical model, and use the data to fix other parameters. We then show that, given the poor quality of the data, we can get different fits leading to very different D (D) over bar amplitudes, some of them supporting a D (D) over bar bound state and others not. The main conclusion is that the claim for the chi(c0)(2P) state, already included in the PDG, is premature, but refined data can provide very valuable information on the D (D) over bar scattering amplitude. As side effects, we warn about the use of a Breit-Wigner amplitude parameterization close to threshold, and show that the D-s(D) over bar (s) channel plays an important role in this reaction. |
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Address |
[Wang, En; Liang, Wei-Hong; Oset, Eulogio] Guangxi Normal Univ, Dept Phys, Guilin 541004, Peoples R China, Email: wangen@zzu.edu.cn; |
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Thesis |
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Publisher |
Springer |
Place of Publication |
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Editor |
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Language |
English |
Summary Language |
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Original Title |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1434-6001 |
ISBN |
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Area |
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Conference |
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Notes |
WOS:000613544900001 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ pastor @ |
Serial |
4732 |
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