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Accelerating Communication for Parallel Programming Models on GPU Systems

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arXiv 2021年

作者： Choi, Jaemin Fink, Zane White, Sam Bhat, Nitin Richards, David F. Kale, Laxmikant V. Department of Computer Science University of Illinois Urbana-ChampaignIL United States Charmworks Inc. Illinois United States Center for Applied Scientific Computing Lawrence Livermore National Laboratory CA United States

As an increasing number of leadership-class systems embrace GPU accelerators in the race towards exascale, efficient communication of GPU data is becoming one of the most critical components of high-performance computing. For developers of parallel programming models, implementing support for GPU-aware communication using native APIs for GPUs such as CUDA can be a daunting task as it requires considerable effort with little guarantee of performance. In this work, we demonstrate the capability of the Unified Communication X (UCX) framework to compose a GPU-aware communication layer that serves multiple parallel programming models of the Charm++ ecosystem: Charm++, Adaptive MPI (AMPI), and Charm4py. We demonstrate the performance impact of our designs with microbenchmarks adapted from the OSU benchmark suite, obtaining improvements in latency of up to 10.1x in Charm++, 11.7x in AMPI, and 17.4x in Charm4py. We also observe increases in bandwidth of up to 10.1x in Charm++, 10x in AMPI, and 10.5x in Charm4py. We show the potential impact of our designs on real-world applications by evaluating a proxy application for the Jacobi iterative method, improving the communication performance by up to 12.4x in Charm++, 12.8x in AMPI, and 19.7x in Charm4py. Copyright © 2021, The Authors. All rights reserved.

关键词： Python

Harmony Search: Current Studies and Uses on Healthcare Systems

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arXiv 2022年

作者： Abdulkhaleq, Maryam T. Rashid, Tarik A. Alsadoon, Abeer Hassan, Bryar A. Mohammadi, Mokhtar Abdullah, Jaza M. Chhabra, Amit Ali, Sazan L. Othman, Rawshan N. Hasan, Hadil A. Azad, Sara Mahmood, Naz A. Abdalrahman, Sivan S. Rasul, Hezha O. Bacanin, Nebojsa Vimal, S. Department of Computer Science and Engineering University of Kurdistan Hewler KRI Iraq School of Computing and Mathematics Charles Sturt University Sydney Australia Information Technology Department Sydney Australia Department of Information Technology Kurdistan Institution for Strategic Studies and Scientific Research Sulaimani46001 Iraq Department of Information Technology Lebanese French University KRI Erbil Iraq Computer Science Department College of Science Komar University of Science and Technology KRI Sulaymaniyah Iraq Information Technology College of Commerce University of Sulaimani KRI Sulaymaniyah Iraq Department of Computer Engineering and Technology Guru Nanak Dev University Amritsar India Department of Pharmaceutical Chemistry College of Medicals and Applied Sciences Charmo University Peshawa Street Chamchamal Sulaimani46023 Iraq Singidunum University Danijelova 32 Belgrade11000 Serbia

One of the popular metaheuristic search algorithms is Harmony Search (HS). It has been verified that HS can find solutions to optimization problems due to its balanced exploratory and convergence behavior and its simple and flexible structure. This capability makes the algorithm preferable to be applied in several real-world applications in various fields, including healthcare systems, different engineering fields, and computer science. The popularity of HS urges us to provide a comprehensive survey of the literature on HS and its variants on health systems, analyze its strengths and weaknesses, and suggest future research directions. In this review paper, the current studies and uses of harmony search are studied in four main domains. (i) The variants of HS, including its modifications and hybridization. (ii) Summary of the previous review works. (iii) Applications of HS in healthcare systems. (iv) And finally, an operational framework is proposed for the applications of HS in healthcare systems. The main contribution of this review is intended to provide a thorough examination of HS in healthcare systems while also serving as a valuable resource for prospective scholars who want to investigate or implement this method. © 2022, CC BY.

关键词： Optimization

Fast quantum algorithm for differential equations

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arXiv 2023年

作者： Bagherimehrab, Mohsen Nakaji, Kouhei Wiebe, Nathan Aspuru-Guzik, Alán Chemical Physics Theory Group Department of Chemistry University of Toronto TorontoON Canada Department of Computer Science University of Toronto TorontoON Canada 1-1-1 Umezono Ibaraki Tsukuba305-8568 Japan Quantum Computing Center Keio University 3-14-1 Hiyoshi Kohoku-ku Kanagawa Yokohama223-8522 Japan Pacific Northwest National Laboratory RichlandWA United States Canadian Institute for Advanced Research TorontoON Canada Vector Institute for Artificial Intelligence TorontoON Canada Department of Chemical Engineering & Applied Chemistry University of Toronto TorontoON Canada Department of Materials Science & Engineering University of Toronto TorontoON Canada

Partial differential equations (PDEs) are ubiquitous in science and engineering. Prior quantum algorithms for solving the system of linear algebraic equations obtained from discretizing a PDE have a computational complexity that scales at least linearly with the condition number κ of the matrices involved in the computation. For many practical applications, κ scales polynomially with the size N of the matrices, rendering a polynomial-in-N complexity for these algorithms. Here we present a quantum algorithm with a complexity that is polylogarithmic in N but is independent of κ for a large class of PDEs. Our algorithm generates a quantum state that enables extracting features of the solution. Central to our methodology is using a wavelet basis as an auxiliary system of coordinates in which the condition number of associated matrices is independent of N by a simple diagonal preconditioner. We present numerical simulations showing the effect of the wavelet preconditioner for several differential equations. Our work could provide a practical way to boost the performance of quantum-simulation algorithms where standard methods are used for discretization. © 2023, CC BY.

关键词： Matrix algebra

A directional regularization method for the limited-angle Helsinki Tomography Challenge using the Core Imaging Library (CIL)

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arXiv 2023年

作者： Jørgensen, Jakob Sauer Papoutsellis, Evangelos Murgatroyd, Laura Fardell, Gemma Pasca, Edoardo Department of Applied Mathematics and Computer Science Technical University of Denmark. Richard Petersens Plads Building 324 Kgs. Lyngby2800 Denmark Department of Mathematics The University of Manchester Oxford Road Alan Turing Building ManchesterM13 9PL United Kingdom Finden Ltd Rutherford Appleton Laboratory Harwell Campus DidcotOX11 0QX United Kingdom Scientific Computing Department Science & Technology Facilities Council Rutherford Appleton Laboratory Harwell Campus DidcotOX11 0QX United Kingdom

This article presents the algorithms developed by the Core Imaging Library (CIL) developer team for the Helsinki Tomography Challenge 2022. The challenge focused on reconstructing 2D phantom shapes from limited-angle computed tomography (CT) data. The CIL team designed and implemented five reconstruction methods using CIL (https://***/cil/), an open-source Python package for tomographic imaging. The CIL team adopted a model-based reconstruction strategy, unique to this challenge with all other teams relying on deep-learning techniques. The CIL algorithms showcased exceptional performance, with one algorithm securing the third place in the competition. The best-performing algorithm employed careful CT data pre-processing and an optimization problem with single-sided directional total variation regularization combined with isotropic total variation and tailored lower and upper bounds. The reconstructions and segmentations achieved high quality for data with angular ranges down to 50 degrees, and in some cases acceptable performance even at 40 and 30 degrees. This study highlights the effectiveness of model-based approaches in limited-angle tomography and emphasizes the importance of proper algorithmic design leveraging on available prior knowledge to overcome data limitations. Finally, this study highlights the flexibility of CIL for prototyping and comparison of different optimization methods.1MSC Codes 65R32, 94A08, 65K10 © 2023, CC BY.

关键词： computerized tomography

On the effect of SHPE's social-cognitive leadership theory to Hispanic professionals' leadership self-efficacy (work in progress)

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On the effect of SHPE's social-cognitive leadership theory t...

CoNECD 2021

作者： Rodriguez, Mauro Hasbún, Indhira María Estrada, Jose Luis Renaud, Dora Louise Division of Engineering and Applied Sciences Department of Mechanical and Civil Engineering California Institute of Technology PasadenaCA91125 United States 13181 Crossroads Pkwy N #450 City of Industry CA91746 United States School of Universal Computing Construction and Engineering Education Florida International University MiamiFL33174 United States Shiley-Marcos School of Engineering Department of Computer Science University of San Diego San DiegoCA92110 United States

Despite the rapid growth of Hispanic undergraduate student enrollment into engineering programs, there is limited work on the post-graduation ability of these engineers to succeed in leadership workforce roles. The Society of Hispanic Professional Engineers (SHPE) developed and implemented a leadership framework that integrates McCormick's socio-cognitive leadership theory and SHPE's annual programing. SHPE hosts the annual National Institute of Leadership Advancement (NILA) for its chapter leaders (i.e., university students and engineering professionals). NILA serves as a leadership development intervention for its leaders by developing their individual, community, and organizational leadership skills. The NILA framework and its effect on undergraduate students during NILA 2019 is detailed in the ASEE CoNECD conference proceeding titled, "Social-cognitive leadership theory of SHPE's premier leadership conference for undergraduates and professionals in the STEM workforce." The development of leadership self-efficacy of Hispanic engineering professionals in the workforce that attended NILA 2019 is considered in this work. An internally developed leadership self-efficacy assessment was issued to the attendees pre- and post-NILA. Following the same methods as the student study, the professionals' self-efficacy is analyzed using the leadership factors determined for the students from an Exploratory Factor Analysis. Strategy-oriented leadership was seen to be most increased among the professionals and students. The analysis showed the feasibility of the framework as a unified curriculum for both students and professionals and supplied valuable lessons learned for future NILA assessments. © American Society for Engineering Education, 2021

关键词： Students

Surrogate approximation of the grad-shafranov free boundary problem via stochastic collocation on sparse grids

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arXiv 2021年

作者： Elman, Howard C. Liang, Jiaxing Sánchez-Vizuet, Tonatiuh Department of Computer Science Institute for Advanced Computer Studies University of Maryland College Park United States Applied Mathematics & Statistics and Scientific Computing Program University of Maryland College Park United States Courant Institute of Mathematical Sciences New York University Department of Mathematics The University of Arizona

In magnetic confinement fusion devices, the equilibrium configuration of a plasma is determined by the balance between the hydrostatic pressure in the fluid and the magnetic forces generated by an array of external coils and the plasma itself. The location of the plasma is not known a priori and must be obtained as the solution to a free boundary problem. The partial differential equation that determines the behavior of the combined magnetic field depends on a set of physical parameters (location of the coils, intensity of the electric currents going through them, magnetic permeability, etc.) that are subject to uncertainty and variability. The confinement region is in turn a function of these stochastic parameters as well. In this work, we consider variations on the current intensities running through the external coils as the dominant source of uncertainty. This leads to a parameter space of dimension equal to the number of coils in the reactor. With the aid of a surrogate function built on a sparse grid in parameter space, a Monte Carlo strategy is used to explore the effect that stochasticity in the parameters has on important features of the plasma boundary such as the location of the x-point, the strike points, and shaping attributes such as triangularity and elongation. The use of the surrogate function reduces the time required for the Monte Carlo simulations by factors that range between 7 and over *** Codes 65C30, 65C05, 65N35, 65N99, 65Z05 Copyright © 2021, The Authors. All rights reserved.

关键词： Monte Carlo methods

Emergence of Spacetime from Fluctuations

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arXiv 2023年

作者： Reitz, Marcus Šoda, Barbara Kempf, Achim Jagiellonian University Astronomy and Applied Computer Science Institute of Theoretical Physics Lojasiewicza 11 KrakówPL 30-348 Poland Department of Physics University of Waterloo WaterlooONN2L 3G1 Canada Perimeter Institute for Theoretical Physics WaterlooONN2L 2Y5 Canada Department of Applied Mathematics University of Waterloo WaterlooONN2L 3G1 Canada Institute for Quantum Computing University of Waterloo WaterlooONN2L 3G1 Canada

We use a result of Hawking and Gilkey to define a Euclidean path integral of gravity and matter which has the special property of being independent of the choice of basis in the space of fields. This property allows the path integral to describe also physical regimes that do not admit position bases. These physical regimes are pre-geometric in the sense that they do not admit a mathematical representation of the physical degrees of freedom in terms of fields that live on a spacetime. In regimes in which a spacetime representation does emerge, the geometric properties of the emergent spacetime, such as its dimension and volume, depend on the balance of fermionic pressure and bosonic and gravitational pull. That balance depends, at any given energy scale, on the number of bosonic and fermionic species that contribute, which in turn depends on their masses. This yields an explicit mechanism by which the effective spacetime dimension can depend on the energy scale. © 2023, CC BY.

关键词： Gravitation

AdjointBackMapV2: Precise Reconstruction of Arbitrary CNN Unit’s Activation via Adjoint Operators

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arXiv 2021年

作者： Wan, Qing Cheung, Siu Wun Choe, Yoonsuck School of Computer Science and Technology Zhejiang Gongshang University Zhejiang Province 310018 China Center for Applied Scientific Computing Lawrence Livermore National Laboratory LivermoreCA94550 United States Department of Computer Science & Engineering Texas A&M University College StationTX77843 United States

Adjoint operators have been found to be effective in the exploration of CNN’s inner workings [1]. However, the previous no-bias assumption restricted its generalization. We overcome the restriction via embedding input images into an extended normed space that includes bias in all CNN layers as part of the extended space and propose an adjoint-operator-based algorithm that maps high-level weights back to the extended input space for reconstructing an effective hypersurface. Such hypersurface can be computed for an arbitrary unit in the CNN, and we prove that this reconstructed hypersurface, when multiplied by the original input (through an inner product), will precisely replicate the output value of each unit. We show experimental results based on the CIFAR-10 and CIFAR-100 data sets where the proposed approach achieves near 0 activation value reconstruction error. Copyright © 2021, The Authors. All rights reserved.

关键词： Chemical activation

Dynamical process of a bit-width reduced Ising model with simulated annealing

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arXiv 2023年

作者： Kikuchi, Shuta Togawa, Nozomu Tanaka, Shu Department of Applied Physics and Physico-Informatics Keio University Kanagawa223-8522 Japan Department of Computer Science and Communications Engineering Waseda University Tokyo169-8555 Japan Human Biology-Microbiome-Quantum Research Center WPI-Bio2Q Keio University Tokyo108-8345 Japan Green Computing System Research Organization Waseda University Tokyo162-0042 Japan International Research Frontiers Initiative Tokyo Institute of Technology Tokyo108-0023 Japan

Ising machines have attracted attention as efficient solvers for combinatorial optimization problems, which are formulated as ground-state (lowest-energy) search problems of the Ising model. Due to the limited bit-width of coefficients on Ising machines, the Ising model must be transformed into a bit-width reduced (BWR) Ising model. According to previous research, the bit-width reduction method, which adds auxiliary spins, ensures that the ground state of the BWR Ising model is theoretically the same as the Ising model before bit-width reduction (original Ising model). However, while the dynamical process is closely related to solution accuracy, how the BWR Ising model progresses towards the ground state remains to be elucidated. Therefore, we compared the dynamical processes of these models using simulated annealing (SA). Our findings reveal significant differences in the dynamical process across models. Analysis from the viewpoint of statistical mechanics found that the BWR Ising model has two characteristic properties: an effective temperature and a slow relaxation. These properties alter the temperature schedule and spin flip probability in the BWR Ising model, leading to differences in the dynamical process. Therefore, to obtain the same dynamical process as the original Ising model, we proposed SA parameters for the BWR Ising model. We demonstrated the proposed SA parameters using a square lattice Ising model, in which all coefficients were set uniformly to the same positive values or randomly. Our experimental evaluations demonstrated that the dynamical process of the BWR and original Ising model became closer. © 2023, CC BY.

关键词： Simulated annealing