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21st International Symposium on High Performance computing Systems and Applications, HPCS 2007

作者： Ollivier-Gooch, Carl Diachin, Lori Freitag Shephard, Mark S. Tautges, Timothy Advanced Numerical Simulation Laboratory University of British Columbia Center for Applied Scientific Computing Lawrence Livermore National Laboratory Scientific Computing Research Center Rensselaer Polytechnic Institute Mathematics and Computer Science Division Argonne National Laboratory

ISBN: (纸本)0769528139

Software for numerical solution of partial differential equations requires accessing, manipulating, and often modifying information about the geometry of the computational domain, the mesh used for the simulation, and discrete data stored on that mesh. Typically, applications programmers would prefer to avoid the difficulty and complexity of creating their own modules for tasks like interacting with multiple geometric modelers, mesh adaptation, and optimization algorithms, rightly preferring instead to focus on the problem physics and on studying the physical results that the codeproduces. Ideally, these modules would be provided by experts in CAD modeling, meshing, and optimization, and written so that they can use the application's data regardless of the data structures used by the application. This paper describes a language- and data-structure-independent interface supporting query and modification of mesh data conforming to a general abstract data model. © 2007 IEEE.

关键词： Application programming interfaces (API)

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On the Scalability of computing Genomic Diversity Using SparkLeBLAST: A Feasibility Study

On the Scalability of Computing Genomic Diversity Using Spar...

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2024 IEEE High Performance Extreme computing Conference, HPEC 2024

作者： Prabhu, Ritvik Moussad, Bernard Youssef, Karim Vatai, Emil Feng, Wu-Chun Virginia Tech Department of Computer Science United States Center for Applied Scientific Computing Lawrence Livermore National Laboratory United States Riken Center for Computational Science Japan

ISBN: (纸本)9798350387131

Studying the genomic diversity of viruses can help us understand how viruses evolve and how that evolution can impact human health. Rather than use a laborious and tedious wet-lab approach to conduct a genomic diversity study, we take a computational approach, using the ubiquitous NCBI BLAST and our parallel and distributed SparkLeBLAST, across 53 patients (40,000,000 query sequences) on Fugaku, the world's fastest homogeneous supercomputer with 158,976 nodes, where each code contains a 48-core A64FX processor and 32 GB RAM. To project how long BLAST and SparkLeBLAST would take to complete a genomic diversity study of COVID-19, we first perform a feasibility study on a subset of 50 query sequences from a single COVID-19 patient to identify bottlenecks in sequence alignment processing. We then create a model using Amdahl's law to project the run times of NCBI BLAST and SparkLeBLAST on supercomputing systems like Fugaku. Based on the data from this 50-sequence feasibility study, our model predicts that NCBI BLAST, when running on all the cores of the Fugaku supercomputer, would take approximately 26.7 years to complete the full-scale study. In contrast, SparkLeBLAST, using both our query and database segmentation, would reduce the execution time to 0.026 years (i.e., 22.9 hours) - resulting in more than a 10,000× speedup over using the ubiquitous NCBI BLAST. © 2024 IEEE.

关键词： COVID-19

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A computational framework for Carreau nanomaterial induced by stretchy regime considering Brownian diffusion, viscous dissipation, ferromagnetism and thermophoresis

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Partial Differential Equations in applied Mathematics 2025年 13卷

作者： Hussain, Iftikhar Khan, Waqar Azeem Tabrez, Muhammad Waqas, M. Ibrahim, Talib K. Saidani, Taoufik Kausar, M.S. Zamri, Nurnadiah Abdullaeva, Barno Garalleh, Hakim AL Department of Mathematics Mohi-ud-Din Islamic University Nerian Sharif Jammu and Kashmir Azad 12010 Pakistan School of Mathematics and Statistics Beijing Institute of Technology Beijing 100081 China NUTECH School of Applied Sciences and Humanities National University of Technology Islamabad 44000 Pakistan Faculty of Informatics and Computing Universiti Sultan Zainal Abidin Besut Campus Terengganu Besut 22200 Malaysia Department of Computer Science and Mathematics Lebanese American University Beirut Lebanon Department of Petroleum Engineering College of Engineering Knowledge University Erbil 44001 Iraq Department of Petroleum Engineering Al-Kitab University Altun Kupri Iraq Center for Scientific Research and Entrepreneurship Northern Border University Arar 73213 Saudi Arabia Faculty of Informatics and Computing Universiti Sultan Zainal Abidin (Kampus Gong Badak) Terengganu Kuala Terengganu 21300 Malaysia Department of Mathematics and Information Technologies Vice-Rector for Scientific Affairs Tashkent State Pedagogical University Tashkent Uzbekistan Department of Mathematical Science College of Engineering University of Business and Technology Jeddah 21361 Saudi Arabia

In recent decade, the research in nanotechnology brought the idea of nanofluids which are highly conducting materials. Some important applications of nanofluids are justified in pharmaceutical industry, coolants in vehicles engine, preparation process of various medicines for treatment of fatal diseases like cancer, aircraft industry, latest heat exchangers etc. The ferro particles are special class of nanomaterial which attract variety of interest from the researchers. The objective of current research is to perform the investigation for heat and mass transfer subject to Carreau nanofluid to observe the enhancement of heat transmission phenomena. The induction of magnetic dipole has been observed for thermal transport phenomenon. The flow is causing by stretched surface. A simplified system is obtained by utilizing the dimensionless variables. Physical interpretation of results have been presented. Result showed that temperature profile in presence of ferrofluid fluid boosts up with escalation in thermophoresis parameter, while opposite behavior is noted for power law index. The concentration of ferrofluid showing declining behavior for Schmidt numbers and rises for thermophoresis parameter. © 2024

关键词： Carreau ferrofluid Heat and mass transfer Magnetic dipole Numerical solution

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Topology-based simplification for feature extraction from 3D scalar fields

Topology-based simplification for feature extraction from 3D...

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VIS 05: IEEE Visualization 2005, Proceedings

作者： Gyulassy, Attila Natarajan, Vijay Pascucci, Valerio Bremer, Peer-Timo Hamann, Bernd Institute for Data Analysis and Visualization Dept. of Computer Science University of California Davis Center for Applied Scientific Computing Lawrence Livermore National Laboratory Dept. of Computer Science University of Illinois Urbana Champaign

ISBN: (纸本)0780394623

In this paper, we present a topological approach for simplifying continuous functions defined on volumetric domains. We introduce two atomic operations that remove pairs of critical points of the function and design a combinatorial algorithm that simplifies the Morse-Smale complex by repeated application of these operations. The Morse-Smale complex is a topological data structure that provides a compact representation of gradient flow between critical points of a function. Critical points paired by the Morse-Smale complex identify topological features and their importance. The simplification procedure leaves important critical points untouched, and is therefore useful for extracting desirable features. We also present a visualization of the simplified topology. © 2005 IEEE.

关键词： Feature extraction

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Web service location-allocation using discrete NSGA-II with matrix based genetic operations and a repair mechanism

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Journal of Ambient Intelligence and Humanized computing 2023年第10期14卷 14163-14187页

作者： Verma, Shanu Pant, Millie Snasel, Vaclav Department of Applied Mathematics and Scientific Computing Indian Institute of Technology Roorkee Roorkee247667 India Centre for Artificial Intelligence and Data Science Indian Institute of Technology Roorkee Roorkee247667 India Department of Computer Science VSB-Technical University of Ostrava Ostrava70800 Czech Republic

Web Service Location-Allocation Problem (WSLAP) is an important and challenging NP-hard combinatorial optimization problem where multiple objectives affecting the quality of service (QoS) are to be optimized simultaneously. Most of the existing research articles mainly focus on selecting web service locations that minimize two QoS: total cost and total response time. However, another QoS factor throughput also needs attention when selecting sites for allocating web services. Therefore, we have constructed a new WSLAP model that minimizes the total cost and the total negative quality factor. This negative quality factor considers throughput along with latency to strengthen the QoS of the located web services. Further, three NSGA-II variants, NSGA-II.V1, NSGA-II.V2, and NSGA-II.V3, with a novel matrix-based chromosome representation, are developed to deal with the proposed bi-objective WSLAP model. These algorithms involve matrix-based genetic operations for better exploration and a repair mechanism for tackling infeasibility. The proposed model and algorithms are validated on 24 test instances, out of which 14 are existing, and 10 are newly created with increased web services, user centres and service locations. The experimental results claim that the proposed WSLAP model succeeded in improving the throughput with a comparatively lower total cost. Further, the proposed algorithms outperformed the compared algorithms in terms of hypervolume, inverted generational distance and computational time on 89% of instances. © 2023, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.

关键词： Quality of service

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B-SPLINE CNNS ON LIE GROUPS 8

B-SPLINE CNNS ON LIE GROUPS

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8th International Conference on Learning Representations, ICLR 2020

作者： Bekkers, Erik J. Amsterdam Machine Learning Lab Informatics Institute University of Amsterdam Netherlands Centre for Analysis and Scientific Computing Applied Mathematics and Computer Science Eindhoven University of Technology Netherlands

Group convolutional neural networks (G-CNNs) can be used to improve classical CNNs by equipping them with the geometric structure of groups. Central in the success of G-CNNs is the lifting of feature maps to higher dimensional disentangled representations in which data characteristics are effectively learned, geometric data-augmentations are made obsolete, and predictable behavior under geometric transformations (equivariance) is guaranteed via group theory. Currently, however, the practical implementations of G-CNNs are limited to either discrete groups (that leave the grid intact) or continuous compact groups such as rotations (that enable the use of Fourier theory). In this paper we lift these limitations and propose a modular framework for the design and implementation of G-CNNs for arbitrary Lie groups. In our approach the differential structure of Lie groups is used to expand convolution kernels in a generic basis of B-splines that is defined on the Lie algebra. This leads to a flexible framework that enables localized, atrous, and deformable convolutions in G-CNNs by means of respectively localized, sparse and non-uniform B-spline expansions. The impact and potential of our approach is studied on two benchmark datasets: cancer detection in histopathology slides in which rotation equivariance plays a key role and facial landmark localization in which scale equivariance is important. In both cases, G-CNN architectures outperform their classical 2D counterparts and the added value of atrous and localized group convolutions is studied in detail. © 2020 8th International Conference on Learning Representations, ICLR 2020. All rights reserved.

关键词： Lie groups

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Evaluation of simple causal message logging for large-scale fault tolerant HPC systems

Evaluation of simple causal message logging for large-scale ...

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25th IEEE International Parallel and Distributed Processing Symposium, Workshops and Phd Forum, IPDPSW 2011

作者： Meneses, Esteban Bronevetsky, Greg Kalé, Laxmikant V. Department of Computer Science University of Illinois Urbana IL United States Center for Applied Scientific Computing Lawrence Livermore National Laboratory Livermore CA United States

ISBN: (纸本)9780769543857

The era of petascale computing brought machines with hundreds of thousands of processors. The next generation of exascale supercomputers will make available clusters with millions of processors. In those machines, mean time between failures will range from a few minutes to few tens of minutes, making the crash of a processor the common case, instead of a rarity. Parallel applications running on those large machines will need to simultaneously survive crashes and maintain high productivity. To achieve that, fault tolerance techniques will have to go beyond checkpoint/restart, which requires all processors to roll back in case of a failure. Incorporating some form of message logging will provide a framework where only a subset of processors are rolled back after a crash. In this paper, we discuss why a simple causal message logging protocol seems a promising alternative to provide fault tolerance in large supercomputers. As opposed to pessimistic message logging, it has low latency overhead, especially in collective communication operations. Besides, it saves messages when more than one thread is running per processor. Finally, we demonstrate that a simple causal message logging protocol has a faster recovery and a low performance penalty when compared to checkpoint/restart. Running NAS Parallel Benchmarks (CG, MG, BT and DT) on 1024 processors, simple causal message logging has a latency overhead below 5%. © 2011 IEEE.

关键词： Supercomputers

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Efficient and accurate derivatives for a software process chain in airfoil shape optimization

Efficient and accurate derivatives for a software process ch...

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作者： Bischof, C.H. Bücker, H.M. Lang, B. Rasch, A. Slusanschi, E. Institute for Scientific Computing RWTH Aachen University D-52056 Aachen Germany Applied Computer Science Group University of Wuppertal D-42097 Wuppertal Germany Institute for Scientific Computing RWTH Aachen University Seffenterweg 23 D-52074 Aachen Germany

When using a Newton-based numerical algorithm to optimize the shape of an airfoil with respect to certain design parameters, a crucial ingredient is the derivative of the objective function with respect to the design parameters. In large-scale aerodynamics, this objective function is an output of a computational fluid dynamics program written in a high-level programming language such as Fortran or C. Numerical differentiation is commonly used to approximate derivatives but is subject to truncation and subtractive cancellation errors. For a particular two-dimensional airfoil, we instead apply automatic differentiation to compute accurate derivatives of the lift and drag coefficients with respect to geometric shape parameters. In automatic differentiation, a given program is transformed into another program capable of computing the original function together with its derivatives. In the problem at hand, the objective function consists of a sequence of programs: a MATLAB program followed by two Fortran 77 programs. It is shown how automatic differentiation is applied to a sequence of programs while keeping the computational complexity within reasonable limits. The derivatives computed by automatic differentiation are compared with approximations based on divided differences. © 2004 Elsevier B.V. All rights reserved.

关键词： Airfoils

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Scalable compression and replay of communication traces in massively parallel environments

Scalable compression and replay of communication traces in m...

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21st International Parallel and Distributed Processing Symposium, IPDPS 2007

作者： Noeth, Michael Mueller, Frank Schulz, Martin De Supinski, Bronis R. North Carolina State University Department of Computer Science Raleigh NC 27695-7534 Lawrence Livermore National Laboratory Center for Applied Scientific Computing Livermore CA 94551

ISBN: (纸本)1424409101

Characterizing the communication behavior of large-scale applications is a difficult and costly task due to code/system complexity and their long execution times. An alternative to running actual codes is to gather their communication traces and then replay them, which facilitates application tuning and future procurements. While past approaches lacked lossless scalable trace collection, we contribute an approach that provides orders of magnitude smaller, if not near constant-size, communication traces regardless of the number of nodes while preserving structural information. We introduce intra- and inter-node compression techniques of MPI events and present results of our implementation for BlueGene/L. Given this novel capability, we discuss its impact on communication tuning and beyond. To the best of our knowledge, such a concise representation of MPI traces in a scalable manner combined with deterministic MPI call replay are without any precedence. ©2007 IEEE.

关键词： Parallel processing systems

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Testing GPU Numerics: Finding Numerical Differences Between NVIDIA and AMD GPUs

Testing GPU Numerics: Finding Numerical Differences Between ...

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2024 Workshops of the International Conference for High Performance computing, Networking, Storage and Analysis, SC Workshops 2024

作者： Zahid, Anwar Hossain Laguna, Ignacio Le, Wei Iowa State University Department of Computer Science AmesIA United States Lawrence Livermore National Laboratory Center for Applied Scientific Computing LivermoreCA United States

ISBN: (纸本)9798350355543

As scientific codes are ported between GPU platforms, continuous testing is required to ensure numerical robustness and identify potential numerical differences between platforms. Compiler-induced numerical differences can occur when a program is compiled and run on different GPUs and compilers, and the numerical outcomes are different for the same input. We present a study of compiler-induced numerical differences between NVIDIA and AMD GPUs, two widely used GPUs in HPC clusters. Our approach uses a random program generator (Varity) to generate thousands of short numerical tests in CUDA and HIP, and their inputs;then, we use differential testing to check if the program produced a numerical inconsistency when run on NVIDIA and AMD GPUs, using the same compiler optimization level. We also use the AMD's HIPIFY tool to convert CUDA tests into HIP tests and test if there are numerical inconsistencies induced by HIPIFY. In our study, we generated more than 600,000 tests and found subtle numerical differences occurring between the two classes of GPUs. We found that some of the differences come from (1) math library calls, (2) differences in floating-point precision (FP64 versus FP32), and (3) converting code to HIP with HIPIFY. © 2024 IEEE.

关键词： CUDA Differential testing floating-point HIP random program generation

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