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Parallelization Technique using hybrid programming model

INTERNATIONAL JOURNAL OF ADVANCED COMPUTER SCIENCE AND APPLICATIONS 2021年第2期12卷 682-690页

作者： Algarni, Abdullah Alofi, Abdulraheem Eassa, Fathy King Abdulaziz Univ KAU Dept Comp Sci POB 80221 Jeddah 21589 Saudi Arabia

A multi-core processor is an integrated circuit that contains multiple core processing unit. For more than two decades, the single-core processors dominated the computing environment. The continuous development of hardware and processors led to the emergence of high-performance computers that able to address complex scientific and engineering programs quickly. Besides, running the software codes sequentially increases the execution time in huge and complex programs. The serial code is converted to parallel code to improve the program performances and reduce the execution time. Therefore, parallelization helps programmers solve computing problems efficiently. This study introduced a novel automatic translation tool that converts serial C++ code into a hybrid parallel code. The study analyzed the performance of the proposed S2PMOACC tool using linear algebraic dense matrix multiplication benchmarking. Besides, we introduced Message Passing Interface (MPI) + Open Accelerator (OpenACC) as a hybrid programming model without preliminary knowledge of parallel programming models and dependency analysis of their source code. The research outcomes enhance the program performances and decrease the implementation time. Moreover, our proposed technique offers better performance than other tools.

关键词： Serial code translation parallel code C++ hybrid programming model auto-translation S2PMOACC

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Solution of the Skyrme-Hartree-Fock-Bogolyubov equations in the Cartesian deformed harmonic-oscillator basis. (VII) HFODD (v2.49t): A new version of the program

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COMPUTER PHYSICS COMMUNICATIONS 2012年第1期183卷 166-192页

作者： Schunck, N. Dobaczewski, J. McDonnell, J. Satula, W. Sheikh, J. A. Staszczak, A. Stoitsov, M. Toivanen, P. Lawrence Livermore Natl Lab Div Phys Livermore CA 94551 USA Univ Tennessee Dept Phys & Astron Knoxville TN 37996 USA Oak Ridge Natl Lab Oak Ridge TN 37831 USA Univ Warsaw Fac Phys Inst Theoret Phys PL-00681 Warsaw Poland Univ Jyvaskyla Dept Phys FI-40014 Jyvaskyla Finland Marie Curie Sklodowska Univ Dept Theoret Phys PL-20031 Lublin Poland

We describe the new version (v2.49t) of the code HFODD which solves the nuclear Skyrme-Hartree-Fock (HF) or Skyrme-Hartree-Fock-Bogolyubov (HFB) problem by using the Cartesian deformed harmonic-oscillator basis. In the new version, we have implemented the following physics features: (i) the isospin mixing and projection, (ii) the finite-temperature formalism for the HFB and HF + BCS methods, (iii) the Lipkin translational energy correction method, (iv) the calculation of the shell correction. A number of specific numerical methods have also been implemented in order to deal with large-scale multi-constraint calculations and hardware limitations: (i) the two-basis method for the HFB method, (ii) the Augmented Lagrangian Method CALM) for multi-constraint calculations, (iii) the linear constraint method based on the approximation of the RPA matrix for multi-constraint calculations, (iv) an interface with the axial and parity-conserving Skyrme-HFB code HFBTHO, (V) the mixing of the HF or HFB matrix elements instead of the HF fields. Special care has been paid to using the code on massively parallel leadership class computers. For this purpose, the following features are now available with this version: (i) the Message Passing Interface (MPI) framework, (ii) scalable input data routines, (iii) multi-threading via OpenMP pragmas, (iv) parallel diagonalization of the HFB matrix in the simplex-breaking case using the ScaLAPACK library. Finally, several little significant errors of the previous published version were corrected. New version program summary Program title: HFODD (v2.49t) Catalogue identifier: ADFL_v3_0 Program summary URL: http://***/summaries/ADFL_v3_*** Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence v3 No. of lines in distributed program, including test data, etc.: 190614 No. of bytes in distributed program, including test data, etc.: 985 898 Distribution f

关键词： Hartree-Fock Hartree-Fock-Bogolyubov Skyrme interaction Angular-momentum projection lsospin projection Finite temperature Multi-threading hybrid programming model High-performance computing

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Multicore challenges and benefits for high performance scientific computing

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SCIENTIFIC programming 2008年第4期16卷 277-285页

作者： Nielsen, Ida M. B. Janssen, Curtis L. Sandia Natl Labs Livermore CA 94551 USA

Until recently, performance gains in processors were achieved largely by improvements in clock speeds and instruction level parallelism. Thus, applications could obtain performance increases with relatively minor changes by upgrading to the latest generation of computing hardware. Currently, however, processor performance improvements are realized by using multicore technology and hardware support for multiple threads within each core, and taking full advantage of this technology to improve the performance of applications requires exposure of extreme levels of software parallelism. We will here discuss the architecture of parallel computers constructed from many multicore chips as well as techniques for managing the complexity of programming such computers, including the hybrid message-passing/multi-threading programming model. We will illustrate these ideas with a hybrid distributed memory matrix multiply and a quantum chemistry algorithm for energy computation using Moller-Plesset perturbation theory.

关键词： Multicore technology hybrid programming model multi-threading message-passing matrix multiplay

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A novel cooperative accelerated parallel two-list algorithm for solving the subset-sum problem on a hybrid CPU-GPU cluster

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JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING 2016年第0期97卷 112-123页

作者： Wan, Lanjun Li, Kenli Li, Keqin Hunan Univ Coll Comp Sci & Elect Engn Changsha 410082 Hunan Peoples R China Natl Supercomp Ctr Changsha Changsha 410082 Hunan Peoples R China SUNY Coll New Paltz Dept Comp Sci New Paltz NY 12561 USA

Many parallel algorithms have recently been developed to accelerate solving the subset-sum problem on a heterogeneous CPU-GPU system. However, within each compute node, only one CPU core is used to control one GPU and all the remaining CPU cores are in idle state, which leads to a large number of CPU cores being wasted. In this paper, based on a cost-optimal parallel two-list algorithm, we propose a novel heterogeneous cooperative computing approach to solve the subset-sum problem on a hybrid CPU-GPU cluster, which can make full use of all available computational resources of a cluster. The unbalanced workload distribution and the huge communication overhead are two main obstacles for the heterogeneous cooperative computing. In order to assign the most suitable workload to each compute node and reasonably partition it between CPU and GPU within each node, and minimize the inter-node and intra-node communication costs, we design a communication-avoiding workload distribution scheme suitable for the parallel two-list algorithm. According to this scheme, we provide an efficient heterogeneous cooperative implementation of the algorithm. A series of experiments are conducted on a hybrid CPU-GPU cluster, where each node has two 6-core CPUs and one GPU. The results show that the heterogeneous cooperative computing significantly outperforms the CPU-only or GPU-only computing. (C) 2016 Elsevier Inc. All rights reserved.

关键词： Heterogeneous cooperative computing hybrid CPU-GPU cluster hybrid programming model Subset-sum problem Two-list algorithm Workload distribution

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hybrid parallelization of molecular dynamics simulations to reduce load imbalance

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JOURNAL OF SUPERCOMPUTING 2022年第7期78卷 9184-9215页

作者： Morillo, Julian Vassaux, Maxime Coveney, Peter V. Garcia-Gasulla, Marta Ctr Nacl Supercomp Barcelona Supercomp Ctr Pl Eusebi Guell1-3 Barcelona 08034 Spain UCL Ctr Computat Sci 20 Gordon St London WC1 H0AJ England

The most widely used technique to allow for parallel simulations in molecular dynamics is spatial domain decomposition, where the physical geometry is divided into boxes, one per processor. This technique can inherently produce computational load imbalance when either the spatial distribution of particles or the computational cost per particle is not uniform. This paper shows the benefits of using a hybrid MPI+OpenMP model to deal with this load imbalance. We consider LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator), a prototypical molecular dynamics simulator that provides its own balancing mechanism and an OpenMP implementation for many of its modules, allowing for a hybrid setup. In this work, we extend the current OpenMP implementation of LAMMPS and optimize it and evaluate three different setups: MPI-only, MPI with the LAMMPS balance mechanism, and hybrid setup using our improved OpenMP version. This comparison is made using the five standard benchmarks included in the LAMMPS distribution plus two additional test cases. Results show that the hybrid approach can deal with load balancing problems better and more effectively (50% improvement versus MPI-only for a highly imbalanced test case) than the LAMMPS balance mechanism (only 43% improvement) and improve simulations with issues other than load imbalance.

关键词： Load Balance Parallel computing Molecular dynamics MPI OpenMP hybrid programming model

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An Efficient Parallel Computing Method for the Processing of Large Sensed Data

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AUTOMATIKA 2013年第4期54卷 471-482页

作者： Li, Dandan Ji, Xiaohui Wang, Qun China Univ Geosci Beijing Sch Informat Engn Beijing 100083 Peoples R China

In recent years we witness the advent of the Internet of Things and the wide deployment of sensors in many applications for collecting and aggregating data. Efficient techniques are required to analyze these massive data for supporting intelligent decisions making. Partial differential problems which involve large data are the most common in the engineering and scientific research. For simulations of large-scale three-dimensional partial differential equations, the intensive computation ability and large amounts of memory requirements for modeling are the main research problems. To address the two challenges, this paper provided an effective parallel method for partial differential equations. The proposed approach combines the overlapping domain decomposition strategy and the multi-core cluster technology to achieve parallel simulations of partial differential equations, uses the finite difference method to discretize equations and adopts the hybrid MPI/OpenMP programming model to exploit two-level parallelism on a multi-core cluster. The three-dimensional groundwater flow model with the parallel finite difference overlapping domain decomposition strategy was successfully set up and carried out by the parallel MPI/OpenMP implementation on a multi-core cluster with two nodes. The experimental results show that the proposed parallel approach can efficiently simulate partial differential problems with large amounts of data.

关键词： Data processing Domain decomposition method hybrid programming model Multi-core clusters Finite difference method

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A Locality-based Threading Algorithm for the Configuration-Interaction Method 31

A Locality-based Threading Algorithm for the Configuration-I...

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31st IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPS)

作者： Shan, Hongzhang Williams, Samuel Johnson, Calvin McElvain, Kenneth Lawrence Berkeley Natl Lab Computat Res Div Berkeley CA 94720 USA San Diego State Univ Dept Phys San Diego CA 92182 USA Univ Calif Berkeley Dept Phys Berkeley CA 94720 USA

ISBN: (纸本)9780769561493

The Configuration Interaction (CI) method has been widely used to solve the non-relativistic many-body Schrodinger equation. One great challenge to implementing it efficiently on manycore architectures is its immense memory and data movement requirements. To address this issue, within each node, we exploit a hybrid MPI+OpenMP programming model in lieu of the traditional flat MPI programming model. In this paper, we develop optimizations that partition the workloads among OpenMP threads based on data locality, which is essential in ensuring applications with complex data access patterns scale well on manycore architectures. The new algorithm scales to 256 threads on the 64-core Intel Knights Landing (KNL) manycore processor and 24 threads on dual-socket Ivy Bridge (Xeon) nodes. Compared with the original implementation, the performance has been improved by up to 7x on the Knights Landing processor and 3x on the dual-socket Ivy Bridge node.

关键词： bigstick configuration-interaction method hybrid programming model Ivy bridge knights landing locality-based threading algorithm Manycore MPI multithreading OpenMP

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Techniques for Enabling Highly Efficient Message Passing on Many-Core Architectures 15

Techniques for Enabling Highly Efficient Message Passing on ...

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2015 15th IEEE ACM International Symposium on Cluster Cloud and Grid Computing (CCGrid 2015)

作者： Si, Min Balaji, Pavan Ishikawa, Yutaka Univ Tokyo Tokyo Japan Argonne Natl Lab Argonne IL 60439 USA RIKEN Adv Inst Computat Sci Kobe Hyogo Japan

ISBN: (纸本)9781479980062

Many-core architecture provides a massively parallel environment with dozens of cores and hundreds of hardware threads. Scientific application programmers are increasingly looking at ways to utilize such large numbers of lightweight cores for various programming models. Efficiently executing these models on massively parallel many-core environments is not easy, however and performance may be degraded in various ways. The first author's doctoral research focuses on exploiting the capabilities of many-core architectures on widely used MPI implementations. While application programmers have studied several approaches to achieve better parallelism and resource sharing, many of those approaches still face communication problems that degrade performance. In the thesis, we investigate the characteristics of MPI on such massively threaded architectures and propose two efficient strategies-a multi-threaded MPI approach and a process-based asynchronous model-to optimize MPI communication for modern scientific applications.

关键词： many-core MPI hybrid programming model one-sided asynchronous progress

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A Framework for the Development of Parallel and Distributed Real-Time Embedded Systems

A Framework for the Development of Parallel and Distributed ...

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38th EUROMICRO Conference on Software Engineering and Advanced Applications (SEAA) / 15th EUROMICRO Digital Systems Design (DSD)

作者： Garibay-Martinez, Ricardo Ferreira, Luis Lino Pinho, Luis Miguel Polytech Inst Porto CISTER INESC TEC ISEP Oporto Portugal

ISBN: (纸本)9780769547909

Embedded real-time applications increasingly present high computation requirements, which need to be completed within specific deadlines. But, those applications present highly variable patterns, depending on the data set in a determined instant. The current trend to provide parallel processing in the embedded domain allows providing higher processing power;however, it does not address the variability in the processing pattern. Dimensioning each device for its worst-case scenario implies lower average utilization, and increased available, but unusable, processing in the overall system. A solution for this problem is to extend the parallel execution of the applications, allowing networked nodes to distribute the workload, on peak situations, to neighbour nodes. In this context, this paper proposes a framework to develop parallel and distributed real-time embedded applications, transparently using OpenMP and Message Passing Interface (MPI), within a programming model based on OpenMP. The paper also devises an integrated timing model, which enables the structured reasoning on the timing behaviour of these hybrid architectures.

关键词： real-time parallel execution distributed embedded systems hybrid programming model OpenMP MPI

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Large-scale numerical simulation of laser propulsion by parallel computing

Large-scale numerical simulation of laser propulsion by para...

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2nd International Symposium on Laser Interaction with Matter (LIMIS)

作者： Zeng, Yaoyuan Zhao, Wentao Wang, Zhenghua Natl Univ Def Technol Changsha 410073 Hunan Peoples R China Acad Equipment Beijing 101416 Peoples R China

ISBN: (纸本)9780819496393

As one of the most significant methods to study laser propelled rocket, the numerical simulation of laser propulsion has drawn an ever increasing attention at present. Nevertheless, the traditional serial simulation model cannot satisfy the practical needs because of insatiable memory overhead and considerable computation time. In order to solve this problem, we study on a general algorithm for laser propulsion design, and bring about parallelization by using a two-level hybrid parallel programming model. The total computing domain is decomposed into distributed data spaces, and each partition is assigned to a MPI process. A single step of computation operates in the inter loop level, where a compiler directive is used to split MPI process into several OpenMP threads. Finally, parallel efficiency of hybrid program about two typical configurations on a China-made supercomputer with 4 to 256 cores is compared with pure MPI program. And, the hybrid program exhibits better performance than the pure MPI program on the whole, roughly as expected. The result indicates that our hybrid parallel approach is effective and practical in large-scale numerical simulation of laser propulsion.

关键词： Laser propulsion Numerical simulation Parallel computing HPC MPI OpenMP hybrid programming model Parallel performance

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