• Title/Summary/Keyword: high-performance computing (HPC)

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Shared Memory Model over a Switchless PCIe NTB Interconnect Network

  • Lim, Seung-Ho;Cha, Kwangho
    • Journal of Information Processing Systems
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    • v.18 no.1
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    • pp.159-172
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    • 2022
  • The role of the interconnect network, which connects computing nodes to each other, is important in high-performance computing (HPC) systems. In recent years, the peripheral component interconnect express (PCIe) has become a promising interface as an interconnection network for high-performance and cost-effective HPC systems having the features of non-transparent bridge (NTB) technologies. OpenSHMEM is a programming model for distributed shared memory that supports a partitioned global address space (PGAS). Currently, little work has been done to develop the OpenSHMEM library for PCIe-interconnected HPC systems. This paper introduces a prototype implementation of the OpenSHMEM library through a switchless interconnect network using PCIe NTB to provide a PGAS programming model. In particular, multi-interrupt, multi-thread-based data transfer over the OpenSHMEM shared memory model is applied at the implementation level to reduce the latency and increase the throughput of the switchless ring network system. The implemented OpenSHMEM programming model over the PCIe NTB switchless interconnection network provides a feasible, cost-effective HPC system with a PGAS programming model.

A Preliminary Study on the Performance of Multi-programmed Container-based HPC Workloads (멀티 프로그램화된 컨테이너 기반의 HPC 워크로드 성능에 대한 사전 연구)

  • Yu, Jung-Lok;Yoon, Hee-Jun
    • Proceedings of the Korea Information Processing Society Conference
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    • 2020.11a
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    • pp.84-87
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    • 2020
  • 최근, 응용 프로그램의 이식성, 확장성, 낮은 오버헤드 및 관리의 용이성 등을 제공하는 컨테이너 기술을 고성능 컴퓨팅 (high performance computing, HPC) 환경에 접목하려는 다양한 연구들이 진행되고 있다. 본 논문에서는 멀티 프로그램화된 환경, 즉, 컨테이너 기반의 다수개의 HPC 워크로드들이 동시에 실행되는 환경에서 멀티 프로그래밍 수준, 통신 패턴 및 비율에 따른 HPC 워크로드들의 성능 특성을 분석하고, HPC 워크로드가 실행되는 동일한 컨테이너 그룹에 속한 컨테이너들의 스케쥴링 시간 부조화가 데이터 교환 지연 시간을 증가시키고 그 결과 응용 성능을 크게 저하시킬 수 있음을 확인한다. 또한 HPC 워크로드가 수행되는 동일 그룹 컨테이너들의 CPU 점유 가능값(CPU Shares)을 동적으로 조절하는 휴리스틱을 제안, 적용함으로써, HPC 워크로드의 성능(통신소비시간 최대 약 42.5%, 워크로드 실행시간 최대 약 23.6% 감소)을 크게 향상시킬 수 있음을 확인한다.

Evaluation of Alignment Methods for Genomic Analysis in HPC Environment (HPC 환경의 대용량 유전체 분석을 위한 염기서열정렬 성능평가)

  • Lim, Myungeun;Jung, Ho-Youl;Kim, Minho;Choi, Jae-Hun;Park, Soojun;Choi, Wan;Lee, Kyu-Chul
    • KIPS Transactions on Software and Data Engineering
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    • v.2 no.2
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    • pp.107-112
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    • 2013
  • With the progress of NGS technologies, large genome data have been exploded recently. To analyze such data effectively, the assistance of HPC technique is necessary. In this paper, we organized a genome analysis pipeline to call SNP from NGS data. To organize the pipeline efficiently under HPC environment, we analyzed the CPU utilization pattern of each pipeline steps. We found that sequence alignment is computing centric and suitable for parallelization. We also analyzed the performance of parallel open source alignment tools and found that alignment method utilizing many-core processor can improve the performance of genome analysis pipeline.

Assessment of compressive strength of high-performance concrete using soft computing approaches

  • Chukwuemeka Daniel;Jitendra Khatti;Kamaldeep Singh Grover
    • Computers and Concrete
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    • v.33 no.1
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    • pp.55-75
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    • 2024
  • The present study introduces an optimum performance soft computing model for predicting the compressive strength of high-performance concrete (HPC) by comparing models based on conventional (kernel-based, covariance function-based, and tree-based), advanced machine (least square support vector machine-LSSVM and minimax probability machine regressor-MPMR), and deep (artificial neural network-ANN) learning approaches using a common database for the first time. A compressive strength database, having results of 1030 concrete samples, has been compiled from the literature and preprocessed. For the purpose of training, testing, and validation of soft computing models, 803, 101, and 101 data points have been selected arbitrarily from preprocessed data points, i.e., 1005. Thirteen performance metrics, including three new metrics, i.e., a20-index, index of agreement, and index of scatter, have been implemented for each model. The performance comparison reveals that the SVM (kernel-based), ET (tree-based), MPMR (advanced), and ANN (deep) models have achieved higher performance in predicting the compressive strength of HPC. From the overall analysis of performance, accuracy, Taylor plot, accuracy metric, regression error characteristics curve, Anderson-Darling, Wilcoxon, Uncertainty, and reliability, it has been observed that model CS4 based on the ensemble tree has been recognized as an optimum performance model with higher performance, i.e., a correlation coefficient of 0.9352, root mean square error of 5.76 MPa, and mean absolute error of 4.1069 MPa. The present study also reveals that multicollinearity affects the prediction accuracy of Gaussian process regression, decision tree, multilinear regression, and adaptive boosting regressor models, novel research in compressive strength prediction of HPC. The cosine sensitivity analysis reveals that the prediction of compressive strength of HPC is highly affected by cement content, fine aggregate, coarse aggregate, and water content.

Design and Implementation of National Supercomputing Service Framework (국가 슈퍼컴퓨팅 서비스 프레임워크의 설계 및 구현)

  • Yu, Jung-Lok;Byun, Hee-Jung;Kim, Han-Gi
    • KIISE Transactions on Computing Practices
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    • v.22 no.12
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    • pp.663-674
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    • 2016
  • Traditional supercomputing services suffer from limited accessibility and low utilization in that users(researchers) may perform computational executions only using terminal-based command line interfaces. To address this problem, in this paper, we provide the design and implementation details of National supercomputing service framework. The proposed framework supports all the fundamental primitive functions such as user management/authentication, heterogeneous computing resource management, HPC (High Performance Computing) job management, etc. so that it enables various 3rd-party applications to be newly built on top of the proposed framework. Our framework also provides Web-based RESTful OpenAPIs and the abstraction interfaces of job schedulers (as well as bundle scheduler plug-ins, for example, LoadLeveler, Open Grid Scheduler, TORQUE) in order to easily integrate the broad spectrum of heterogeneous computing clusters. To show and validate the effectiveness of the proposed framework, we describe the best practice scenario of high energy physics Lattice-QCD as an example application.

HPC Technology Through SC20 (SC20를 통해 본 HPC 기술 동향)

  • Eo, I.S.;Mo, H.S.;Park, Y.M.;Han, W.J.
    • Electronics and Telecommunications Trends
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    • v.36 no.3
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    • pp.133-144
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    • 2021
  • High-performance computing (HPC) is the underpinning for many of today's most exciting new research areas, to name a few, from big science to new ways of fighting the disease, to artificial intelligence (AI), to big data analytics, to quantum computing. This report captures the summary of a 9-day program of presentations, keynotes, and workshops at the SC20 conference, one of the most prominent events on sharing ideas and results in HPC technology R&D. Because of the exceptional situation caused by COVID-19, the conference was held entirely online from 11/9 to 11/19 2020, and interestingly caught more attention on using HPC to make a breakthrough in the area of vaccine and cure for COVID-19. The program brought together 103 papers from 21 countries, along with 163 presentations in 24 workshop sessions. The event has covered several key areas in HPC technology, including new memory hierarchy and interconnects for different accelerators, evaluation of parallel programming models, as well as simulation and modeling in traditional science applications. Notably, there was increasing interest in AI and Big Data analytics as well. With this summary of the recent HPC trend readers may find useful information to guide the R&D directions for challenging new technologies and applications in the area of HPC.

Extension of the NEAMS workbench to parallel sensitivity and uncertainty analysis of thermal hydraulic parameters using Dakota and Nek5000

  • Delchini, Marc-Olivier G.;Swiler, Laura P.;Lefebvre, Robert A.
    • Nuclear Engineering and Technology
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    • v.53 no.10
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    • pp.3449-3459
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    • 2021
  • With the increasing availability of high-performance computing (HPC) platforms, uncertainty quantification (UQ) and sensitivity analyses (SA) can be efficiently leveraged to optimize design parameters of complex engineering problems using modeling and simulation tools. The workflow involved in such studies heavily relies on HPC resources and hence requires pre-processing and post-processing capabilities of large amounts of data along with remote submission capabilities. The NEAMS Workbench addresses all aspects of the workflows involved in these studies by relying on a user-friendly graphical user interface and a python application program interface. This paper highlights the NEAMS Workbench capabilities by presenting a semiautomated coupling scheme between Dakota and any given package integrated with the NEAMS Workbench, yielding a simplified workflow for users. This new capability is demonstrated by running a SA of a turbulent flow in a pipe using the open-source Nek5000 CFD code. A total of 54 jobs were run on a HPC platform using the remote capabilities of the NEAMS Workbench. The results demonstrate that the semiautomated coupling scheme involving Dakota can be efficiently used for UQ and SA while keeping scripting tasks to a minimum for users. All input and output files used in this work are available in https://code.ornl.gov/neams-workbench/dakota-nek5000-study.

HTCaaS(High Throughput Computing as a Service) in Supercomputing Environment (슈퍼컴퓨팅환경에서의 대규모 계산 작업 처리 기술 연구)

  • Kim, Seok-Kyoo;Kim, Jik-Soo;Kim, Sangwan;Rho, Seungwoo;Kim, Seoyoung;Hwang, Soonwook
    • The Journal of the Korea Contents Association
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    • v.14 no.5
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    • pp.8-17
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    • 2014
  • Petascale systems(so called supercomputers) have been mainly used for supporting communication-intensive and tightly-coupled parallel computations based on message passing interfaces such as MPI(HPC: High-Performance Computing). On the other hand, computing paradigms such as High-Throughput Computing(HTC) mainly target compute-intensive (relatively low I/O requirements) applications consisting of many loosely-coupled tasks(there is no communication needed between them). In Korea, recently emerging applications from various scientific fields such as pharmaceutical domain, high-energy physics, and nuclear physics require a very large amount of computing power that cannot be supported by a single type of computing resources. In this paper, we present our HTCaaS(High-Throughput Computing as a Service) which can leverage national distributed computing resources in Korea to support these challenging HTC applications and describe the details of our system architecture, job execution scenario and case studies of various scientific applications.

Comparative Analysis of Container for High Performance Computing

  • Lee, Jaeryun;Chae, Yunchang;Tak, Byungchul
    • Journal of the Korea Society of Computer and Information
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    • v.25 no.9
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    • pp.11-20
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    • 2020
  • In this paper, we propose the possibility of using containers in the HPC ecosystem and the criteria for selecting a proper PMI library. Although demand for container has been growing rapidly in the HPC ecosystem, Docker container which is the most widely used has a potential security problem and is not suitable for the HPC. Therefore, several HPC containers have appeared to solve this problem and the chance of performance differences also emerged. For this reason, we measured the performance difference between each HPC container and Docker container through NAS Parallel Benchmark experiment and checked the effect of the type of PMI library. As a result, the HPC container and the Docker container showed almost the same performance as native, or in some cases, rather better performance was observed. In the result of comparison between PMI libraries showed that PMIx was not superior to PMI-2 in all conditions.

Characteristics of HPC(High-performance Computing)-based Parallel Processing on Electromagnetic Scattering Problems (전자파 산란 문제에서의 고성능 컴퓨팅(HPC) 기반 병렬 처리 특성)

  • Cho, Yong-Heui
    • Proceedings of the Korea Contents Association Conference
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    • 2017.05a
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    • pp.37-38
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    • 2017
  • 금속으로 이루어진 긴 선이나 구에 대한 전자파 산란 특성을 계산할 때, 산란 계산 속도를 개선하기 위해 사용하는 고성능 컴퓨팅(HPC) 기반 병렬 처리 특성을 제시한다. 산란 행렬 생성, 가우스 소거법, 산란파 계산 등으로 이루어진 전자파 산란 문제는 병렬 처리를 통해 계산 속도를 높일 수 있다. 산란 문제의 계산 절차를 분석하여 병렬화에 유리한 계산 작업을 분류한 후 OpenMP 기반 병렬화를 적용한다.

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