ON THE CONVERGENCE OF COMPUTATIONAL AND DATA GRIDS

2001 ◽  
Vol 11 (02n03) ◽  
pp. 187-202 ◽  
Author(s):  
DORIAN C. ARNOLD ◽  
SATHISH S. VAHDIYAR ◽  
JACK J. DONGARRA
Keyword(s):  
High Performance ◽  
Distributed Storage ◽  
Computing System ◽  
Data Services ◽  
Tightly Coupled ◽  
Software And Hardware ◽  
Dynamic Storage ◽  
Performance Computing

Great advances in high-performance computing have given rise to scientific applications that place large demands on software and hardware infrastructures for both computational and data services. With these trends the necessity has emerged for distributed systems developers that once distinguished between these elements to acknowledge that indeed computational and data services are tightly coupled and need to be addressed simultaneously. In this article, we compile and discuss several strategies and techniques, like co-scheduling and co-allocation of computational and data services, dynamic storage capabilities, and quality-of-service, that can be used to help resolve some of the aforementioned issues. We present our interactions with a distributed computing system, NetSolve, and a Distributed Storage Infrastructure, IBP, as a case study of how some of these techniques can be effectively deployed and offer experimental evidence from early prototypes that validate our motivation and direction.

scholarly journals Experimenting with reproducibility in bioinformatics

2017 ◽  
Author(s):  
Yang-Min Kim ◽  
Jean-Baptiste Poline ◽  
Guillaume Dumas
Keyword(s):  
High Performance ◽  
Scientific Activity ◽  
Scientific Data ◽  
The Individual ◽  
High Performance Computing Cluster ◽  
Performance Computing ◽  
Scientific Fields ◽  
Research Efficiency

AbstractReproducibility has been shown to be limited in many scientific fields. This question is a fundamental tenet of the scientific activity, but the related issues of reusability of scientific data are poorly documented. Here, we present a case study of our attempt to reproduce a promising bioinformatics method [1] and illustrate the challenges to use a published method for which code and data were available. First, we tried to re-run the analysis with the code and data provided by the authors. Second, we reimplemented the method in Python to avoid dependency on a MATLAB licence and ease the execution of the code on HPCC (High-Performance Computing Cluster). Third, we assessed reusability of our reimplementation and the quality of our documentation. Then, we experimented with our own software and tested how easy it would be to start from our implementation to reproduce the results, hence attempting to estimate the robustness of the reproducibility. Finally, in a second part, we propose solutions from this case study and other observations to improve reproducibility and research efficiency at the individual and collective level.Availabilitylast version of StratiPy (Python) with two examples of reproducibility are available at GitHub [2][email protected]

Hardware Accelerator Integration Tradeoffs for High-Performance Computing: A Case Study of GEMM Acceleration in N-Body Methods

2021 ◽  
Vol 32 (8) ◽  
pp. 2035-2048
Author(s):  
Mochamad Asri ◽  
Dhairya Malhotra ◽  
Jiajun Wang ◽  
George Biros ◽  
Lizy K. John ◽  
...  
Keyword(s):  
High Performance Computing ◽  
High Performance ◽  
Hardware Accelerator ◽  
Performance Computing

GPU-accelerated molecular dynamics: State-of-art software performance and porting from Nvidia CUDA to AMD HIP

2021 ◽  
pp. 109434202110082
Author(s):  
Nikolay Kondratyuk ◽  
Vsevolod Nikolskiy ◽  
Daniil Pavlov ◽  
Vladimir Stegailov
Keyword(s):  
Molecular Dynamics ◽  
High Performance ◽  
Software Performance ◽  
Computing Systems ◽  
Accelerated Molecular Dynamics ◽  
Nvidia Cuda ◽  
Software And Hardware ◽  
Management Capabilities ◽  
Utilization Time ◽  
Performance Computing

Classical molecular dynamics (MD) calculations represent a significant part of the utilization time of high-performance computing systems. As usual, the efficiency of such calculations is based on an interplay of software and hardware that are nowadays moving to hybrid GPU-based technologies. Several well-developed open-source MD codes focused on GPUs differ both in their data management capabilities and in performance. In this work, we analyze the performance of LAMMPS, GROMACS and OpenMM MD packages with different GPU backends on Nvidia Volta and AMD Vega20 GPUs. We consider the efficiency of solving two identical MD models (generic for material science and biomolecular studies) using different software and hardware combinations. We describe our experience in porting the CUDA backend of LAMMPS to ROCm HIP that shows considerable benefits for AMD GPUs comparatively to the OpenCL backend.

A High-Performance Computing System for Probabilistic Weather Forecasts

2019 ◽  
Author(s):  
Weiming Hu ◽  
Guido Cervone ◽  
Vivek Balasubramanian ◽  
Matteo Turilli ◽  
Shantenu Jha
Keyword(s):  
High Performance Computing ◽  
High Performance ◽  
Computing System ◽  
Weather Forecasts ◽  
High Performance Computing System ◽  
Performance Computing

scholarly journals Taxonomic assignment for large-scale metagenomic data on high-perfomance systems

2017 ◽  
Vol 33 (2) ◽  
pp. 119-130
Author(s):  
Vinh Van Le ◽  
Hoai Van Tran ◽  
Hieu Ngoc Duong ◽  
Giang Xuan Bui ◽  
Lang Van Tran
Keyword(s):  
High Performance Computing ◽  
Assignment Problem ◽  
High Performance ◽  
Large Scale ◽  
Computing System ◽  
Metagenomic Data ◽  
Taxonomic Assignment ◽  
High Performance Computing System ◽  
Powerful Approach ◽  
Performance Computing

Metagenomics is a powerful approach to study environment samples which do not require the isolation and cultivation of individual organisms. One of the essential tasks in a metagenomic project is to identify the origin of reads, referred to as taxonomic assignment. Due to the fact that each metagenomic project has to analyze large-scale datasets, the metatenomic assignment is very much computation intensive. This study proposes a parallel algorithm for the taxonomic assignment problem, called SeMetaPL, which aims to deal with the computational challenge. The proposed algorithm is evaluated with both simulated and real datasets on a high performance computing system. Experimental results demonstrate that the algorithm is able to achieve good performance and utilize resources of the system efficiently. The software implementing the algorithm and all test datasets can be downloaded at http://it.hcmute.edu.vn/bioinfo/metapro/SeMetaPL.html.

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