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Lyncs-API: A Python API for Lattice QCD applications

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arXiv 2022年

作者： Bacchio, Simone Finkenrath, Jacob Stylianou, Christodoulos Computation-based Science And Technology Research Center The Cyprus Institute Cyprus

We present Lyncs-API, a Python API for Lattice QCD applications currently under development. Lyncs aims to bring several widely used libraries for Lattice QCD under a common framework. Lyncs flexibly links to libraries for CPUs and GPUs in a way that can accommodate additional computing architectures as these arise, achieving performance-portability for the calculations while maintaining the same high-level workflow. Lyncs distributes calculations using Dask and mpi4py, with bindings to the libraries automatically generated by cppyy. While Lyncs is designed to allow linking to multiple libraries, we focus on a set of targeted packages that include DDalphaAMG, tmLQCD, QUDA and c-lime. More libraries will be added in the future. We also develop generic-purpose tools for facilitating the usage of Python in Lattice QCD and HPC in general. The project is open-source, community-oriented and available on Github. © 2022, CC BY.

关键词： Libraries

Running HMC Simulation with Python via QUDA

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arXiv 2022年

作者： Yamamoto, Shuhei Bacchio, Simone Finkenrath, Jacob Computation-based Science and Technology Research Center The Cyprus Institute Cyprus

Lyncs-API is a Python API for Lattice QCD applications. It is designed as a Python toolkit that allows the user to use and run various lattice QCD libraries while programming in Python. The goal is to provide the user an easy programming experience without scarifying performance across multiple platforms, by preparing a common framework for various softwares for lattice QCD calculations. As such, it contains interfaces to, e.g., c-lime, DDalphaAMG, tmLQCD, and QUDA. In this proceeding, we focus on a Lyncs interface to QUDA, named Lyncs-QUDA, and present a small tutorial on how to use this Python interface to perform a HMC simulation using QUDA. © 2022, CC BY.

关键词： Python

Open science in Lattice Gauge Theory community 39

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Open Science in Lattice Gauge Theory community

39th International Symposium on Lattice Field Theory, LATTICE 2022

作者： Athenodorou, Andreas Bennett, Ed Lenz, Julian Papadopoullou, Elli Computation-based Science and Technology Research Center The Cyprus Institute Cyprus Swansea Academy of Advanced Computing Swansea University Fabian Way SwanseaSA1 8EN United Kingdom ATHENA Research Center Artemidos 6 & Epidavrou Marousi15125 Greece

Open science aims to make scientific research processes, tools and results accessible to all scientific communities, creating trust in science and enabling digital competences to be realized in research, leading to increased innovation. It provides standard and transparent pathways to conducting research and fosters best practices for collecting, analysing, preserving, sharing and reusing data, software, workflows and other outputs through collaborative networks. Open science appears to be becoming the norm with its applications spanning throughout the whole research cycle of a project. The importance of making Open science a reality is nowadays reflected in funding policies, research infrastructure and politics. In these proceedings we present the basic Open science principles explaining briefly best practices for materialising Open science. Subsequently, we present the results of the landscaping survey of Open science in the Lattice Gauge Theories community. Finally, we provide directions in which the Lattice Gauge Theory community could move in order to enhance Openness and FAIRness (Findability, Accessibility, Interoperability, Reusability) in science. © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND 4.0).

关键词： Reusability

A BIBLIOMETRIC OVERVIEW OF OPEN science research 9

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A BIBLIOMETRIC OVERVIEW OF OPEN SCIENCE RESEARCH

9th ECCOMAS Thematic Conference on computational Methods in Structural Dynamics and Earthquake Engineering, COMPDYN 2023

作者： Bakas, Nikolaos P. Athenodorou, Andreas Anastasopoulou, Nana Kyprianou, Katerina Katsikatsos, George Markou, George National Infrastructures for Research and Technology GRNET 7 Kifisias Avenue Athens11523 Greece Computation-based Science and Technology Research Center The Cyprus Institute 20 Konstantinou Kavafi Street Aglantzia Nicosia2121 Cyprus Civil Engineering Department University of Pretoria Private Bag x 20 Hatfield0028 South Africa

Scientific research exhibits a vast increase in terms of published works, as well as produced data, computer codes, and scientific methods. Accordingly, openness is a modern demand in science, and many efforts occur in this direction. The reproducibility of results, data sharing, transparency, and replication are emerging challenges in research, as by following "open science" principles, the research community, as well as society, obtains beneficial outcomes in the best possible way. In this work, we computationally analyse a large volume of papers related to open science. Particularly, we use the Scopus database and search for papers with the term "open science" in the title, abstract or keywords, within the past ten years. In total 4878 papers were identified, in the following categories: Article (N=2770), Conference paper (N=724), Review (N=646), Editorial (N=188), Note (N=176), Book chapter (N=119), Erratum (N=112), Conference review (N=54), Data paper (N=30), Letter (N=29), Book (N=16), and Short survey (N=14). We start with descriptive statistics of the keywor ds appearing in the papers, and continue with inter-items' associations, by computing the contingency matrix. Accordingly, we calculate the objects' potions on the bibliometric map, by using a novel multidimensional scaling algorithm. In order to verify the associations, we permute the contingency matrix to minimise its bandwidth and plot the resulting clusters of keywor ds. Finally, in order to evaluate the evolution of the terms in recent years, we compute the timeseries of the occurrence of keywords and select the ones exhibiting higher trends, based on linear as well as nonlinear model fit. We also compute the normalised timeseries, in order to subtract the overall increase in scientific output. We discuss significant conclusions on open science research, based on a rigorous computational procedure. © 2023 COMPDYN Proceedings. All rights reserved

关键词： Transparency

Investigation of two-particle contributions to nucleon matrix elements 40

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Investigation of two-particle contributions to nucleon matri...

40th International Symposium on Lattice Field Theory, LATTICE 2023

作者： Alexandrou, Constantia Koutsou, Giannis Li, Yan Petschlies, Marcus Pittler, Ferenc Department of Physics University of Cyprus P.O. Box 20537 Nicosia1678 Cyprus Computation-based Science and Technology Research Center The Cyprus Institute 20 Kavafi Str. Nicosia2121 Cyprus Rheinische Friedrich-Wilhelms-Universität Bonn Nußallee 14-16 Bonn53115 Germany

We investigate contributions of excited states to nucleon matrix elements by studying the two- and three-point functions using nucleon and pion-nucleon interpolating fields. This study is carried out using twisted mass fermion ensembles with pion masses 346 MeV and 131 MeV. We compare the results obtained using these two ensembles and show preliminary results for nucleon charges. © Copyright owned by the author(s) under the terms of the Creative Commons.

关键词： Excited states

Implementation of simultaneous inversion of a multi-shifted dirac matrix for twisted-mass fermions within DDαAMG

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arXiv 2022年

作者： Yamamoto, Shuhei Bacchio, Simone Finkenrath, Jacob Computation-based Science And Technology Research Center The Cyprus Institute Aglantzia Nicosia Cyprus

At physical light quark masses, efficient linear solvers are crucial for carrying out the millions of inversions of the Dirac matrix required for obtaining high statistics in quark correlation functions. Adaptive algebraic multi-grid methods have proven to be very efficient in such cases, exhibiting mild critical slowing down towards very light quark masses and outperforming traditional solver methods, such as the conjugate gradient method, at the physical point. We will discuss our implementations of simultaneous inversion of a (degenerate) Dirac matrix for twisted-mass fermions for multiple right-hand-sides (rhs) with multi-shifts and block-Krylov solvers. The implementation is carried out within the community library DDαAMG, which implements aggregation-based Domain Decomposition adaptive algebraic multi-grid methods. The block-Krylov solvers are provided via the Fast Accurate Block Linear krylOv Solver (Fabulous) library and can be used at coarser levels. Our code inverts Dirac matrices with different twisted-mass terms and for multiple rhs simultaneously and is thus also suitable for components within a typical lattice QCD simulation workflow, such as the rational approximation. We show preliminary results on scalability and compare the performance of our implementation when using different Block-Krylov solver techniques. © 2022, CC BY.

关键词： Matrix algebra

The Effect of Loss Functions on Denoising and Reconstructing Sinograms based on Deep Learning Methodologies

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The Effect of Loss Functions on Denoising and Reconstructing...

2021 IEEE Nuclear science Symposium and Medical Imaging Conference, NSS/MIC 2021

作者： Chrysostomou, Charalambos The Cyprus Institute The Computation-Based Science and Technology Research Center 20 Konstantinou Kavafi Street Aglantzia Nicosia2121 Cyprus

ISBN: (数字)9781665421133

ISBN: (纸本)9781665421133

Recent advancements in machine learning and, more specifically, deep learning methodologies showed promising results in Computed tomography (CT) imaging, either by enhancing existing reconstruction methodologies by cleaning the signal from the collected data or used for the complete reconstruction of the images directly from raw data. The loss function used for the training of these deep learning methodologies can significantly impact the training process. This paper compares different deep learning loss functions in the framework of denoising and recon-structing sinograms based on Single-photon emission computed tomography (SPECT) imaging. The loss functions evaluated in the proposed work are Mean Squared Error (MSE), Mean Absolute Error (MAE), Mean Absolute Percentage Error (MAPE), Mean Squared Logarithmic Error (MSLE), Huber, Peak Signal-to-Noise ratio (PSRN) and Structural Similarity Index (SSIM). These loss functions were used to train an identical proposed convolutional-based deep learning methodology to denoise sinograms constructed using software phantoms and compared the results. Furthermore, a study is constructed to measure the reconstructed accuracy of the denoised sinograms and compare the results using the ordered subset expectation maximisation (OSEM) method. based on our analysis, some guidelines are derived for selecting a loss function in denoising data used for inverse problems such as sinogram reconstruction for medical image applications. © 2021 IEEE.

关键词： Inverse problems

DEVELOPING FUNDAMENTAL PERIOD FORMULAE FOR STEEL FRAMED STRUCTURES THROUGH MACHINE LEARNING AND AUTOMATED ALGORITHMS 9

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DEVELOPING FUNDAMENTAL PERIOD FORMULAE FOR STEEL FRAMED STRU...

9th ECCOMAS Thematic Conference on computational Methods in Structural Dynamics and Earthquake Engineering, COMPDYN 2023

作者： Calitz, Duan Markou, George Bakas, Nikolaos Papadrakakis, Manolis University of Pretoria Civil Engineering Department Hatfield Campus South Africa The Cyprus Institute Computation-based Science and Technology Research Center 20 Konstantinou Kavafi Street Aglantzia Nicosia2121 Cyprus National Technical University of Athens Civil Engineering Department Zografou Campus Greece

The fundamental period of a structure is an important intrinsic dynamic property of the structural system response. Current design codes use simplified empirical formulae to estimate the fundamental period, that generally do not account for the influence of plan geometry, cross-sectional properties of the specific structural elements, nor the properties of the soil the structures are founded on, and thus the effects of soil-structure interaction (SSI) are not accounted for. This research work investigates the fundamental period of unbraced steel framed structures of various geometric configurations, and multiple different steel column members, as well as the SSI effect. A new algorithm is also developed for the automated construction and analysis of finite element models. The proposed automated procedure is used to create a dataset that is used to train and test the predictive formulae for computing the fundamental period of steel structures with and without accounting for the SSI effect. The proposed 40-feature formula was found to derive an optimum coefficient of determination (R2) with a value of 99.976% and an error that is less than 2%. © 2023 COMPDYN Proceedings. All rights reserved

关键词： Structural dynamics

The spectrum of open confining strings in the large-Nc limit

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arXiv 2024年

作者： Sharifian, Alireza Athenodorou, Andreas Bicudo, Pedro CeFEMA and Physics Department Instituto Superior Técnico Av. Rovisco Pais Lisboa1049 Portugal Computation-based Science and Technology Research Center The Cyprus Institute Cyprus

We compute the spectra of open flux tubes formed between a static quark-antiquark pair for various gauge groups in the large-Nc limit, focusing on different symmetries manifested by the quantum numbers of angular momentum, parity, and charge conjugation. Specifically, we present spectra from Nc = 3 up to Nc = 6 and for eight different irreducible representations of the symmetry characterizing the flux tube. In this study, we employed an anisotropic Wilson action, a large number of suitable spacial operators, and solved the generalized eigenvalue problem (GEVP) to obtain a significant number of excitations for different combinations of flux tube quantum numbers. The spectra are compared with the Nambu-Goto string model, revealing novel phenomena such as the presence of massive axions in the flux tube spectrum. We find that the mass of the axion in the open flux tube spectra sector is consistent with the mass obtained in the closed flux tube sector. © 2024, CC BY-NC-ND.

关键词： Eigenvalues and eigenfunctions