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Graph Visualization for the Analysis of the Structure and Dynamics of Extreme-Scale Supercomputers

Kenneth L. Summers, Thomas Preston Caudell, Kathryn Berkbigler, Brian Bush, Kei Davis, Steve Smith
2004 Information Visualization  
We are exploring the development and application of information visualization techniques for the analysis of new extreme-scale supercomputer architectures.  ...  The scale, complexity, and inherent nonlocality of the structure and dynamics of this hardware, and the systems and applications distributed over it, challenge traditional analysis methods.  ...  Acknowledgements This work was carried out under the auspices of the Department of Energy at Los Alamos National Laboratory under ASCI DisCom2.  ... 
doi:10.1057/palgrave.ivs.9500079 fatcat:c56gwrgaxzau3ihnnhxbqyyt7q

Making Large-Scale Systems Observable - Another Inescapable Step Towards Exascale

2016 Supercomputing Frontiers and Innovations  
for the future system scales.  ...  Predefined monitoring systems and data sources, lack of dynamic on-the-fly reconfiguration, inflexible visualization and screening options are among the most popular issues.  ...  This paper is distributed under the terms of the Creative Commons Attribution-Non Commercial 3.0 License which permits non-commercial use, reproduction and distribution of the work without further permission  ... 
doi:10.14529/jsfi160205 fatcat:4s3raj26zjcyvhia3h4h6uidua

Parsl: Pervasive Parallel Programing in Python [article]

Daniel S. Katz, Yadu Babuji, Anna Woodard, Zhuozhao Li, Ben Clifford, ROHAN KUMAR, Lukasz Lacinski, Ryan Chard, Justin Wozniak, Ian Foster, Michael Wilde, Kyle Chard
2019 Figshare  
a talk presented at Jupyter Community Workshop:Jupyter for Science User Facilities and High Performance Computing11-13 June 2019Berkeley, California  ...  Workflow and resource monitoring and visualization Reproducibility. Capture of workflow provenance in the task graph Jupyter integration.  ...  Extreme-scale workloads -Cosmology simulations, imaging the arctic, genomics analysis -Requirements: millions of tasks, 1000s of nodes (100,000s cores), capacity Interactive and real-time workloads  ... 
doi:10.6084/m9.figshare.8297852 fatcat:wz74iebjl5df5f2p35muuph2om


Steve Petruzza, Aniketh Venkat, Attila Gyulassy, Giorgio Scorzelli, Frederick Federer, Alessandra Angelucci, Valerio Pascucci, Peer-Timo Bremer
2017 SIGGRAPH Asia 2017 Symposium on Visualization on - SA '17  
We evaluate the performance of our system using a leadership-class supercomputer, Shaheen II.  ...  We present a software infrastructure that simplifies end-to-end visualization and analysis of massive data.  ...  This library further allows the user to define visualization and analysis workflows as task graphs that can be executed on local resources for interactive analysis or at scale on HPC systems.  ... 
doi:10.1145/3139295.3139299 pmid:30148289 pmcid:PMC6105268 dblp:conf/siggraph/PetruzzaVGSFAPB17 fatcat:ppcwkpk32jd65arcaw3nrnvzne

Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action [article]

Anda Trifan, Defne Gorgun, Zongyi Li, Alexander Brace, Maxim Zvyagin, Heng Ma, Austin R Clyde, David A Clark, Michael Salim, David Hardy, Tom Burnley, Lei Huang (+21 others)
2021 bioRxiv   pre-print
Consequently, we develop an innovative workflow that bridges the gap between these resolutions, using mesoscale fluctuating finite element analysis (FFEA) continuum simulations and a hierarchy of AI-methods  ...  Conventional tools, e.g., cryo-electron microscopy and all-atom molecular dynamics (AAMD), do not provide sufficiently high resolution or timescale to capture important dynamics of this molecular machine  ...  . • The workow infrastructure also illustrates some limitations in coordinating large le transfers across supercomputing sites that are required for both visualization and analysis. • Our hierarchy of  ... 
doi:10.1101/2021.10.09.463779 fatcat:4oluasz3jbgnvhwryercs6jts4

Scaling applications to massively parallel machines using Projections performance analysis tool

Laxmikant V. Kalé, Gengbin Zheng, Chee Wai Lee, Sameer Kumar
2006 Future generations computer systems  
We also explore the techniques for applying the performance visualization/analysis tool on future generation extreme-scale parallel machines and discuss the scalability issues with Projections. automatically  ...  It uses the remapping capability to do automatic load balancing. The Projections Analysis Framework consists of an instrumentation component and a visualization/analysis tool.  ...  Case Study with MD on Extremely Large Machines: It is clearly quite challenging for molecular dynamics simulation to exploit the enormous compute power of next generation supercomputers.  ... 
doi:10.1016/j.future.2004.11.020 fatcat:hjednzjubnea5ngd2vcezftt7a

Parallel Visualization of Large-scale Unstructured Geophysical Data for the Earth Simulator [chapter]

Li Chen, Issei Fujishiro, Kengo Nakajima
2004 Computational Earthquake Science Part II  
As part of the Earth Simulator project in Japan, the subsystem is effective for the visualization of large-scale geoscientific data, and can be concurrently executed with computation subsystems on the  ...  As part of the Earth Simulator project in Japan, the subsystem is effective for the visualization of large-scale geoscientific data, and can be concurrently executed with computation subsystems on the  ...  Acknowledgments This study was conducted as part of the Solid Earth Platform for Large-Scale Computation project funded by the Japanese Ministry of Education, Culture, Sports, Science and Technology through  ... 
doi:10.1007/978-3-0348-7875-3_10 fatcat:bzkabjmcgngybnmrfko5fhfcwa

A Method for Large-Scale Parallel Simulation of Reactor Structural Mechanics

Longyue Xing, Zhaoshun Wang, Xin Cen, Zhangcheng Jiang, Yang Li
2020 IEEE Access  
Furthermore, we propose a parallel workflow design, function design and architecture design scheme for large-scale parallel simulation of Generation IV reactors structural mechanics based on E-class supercomputer  ...  The structural mechanics simulation in reactor is an extremely complicated problem, which includes statics, fluid-induced vibration and wear.  ...  The experimental results verified the feasibility of our overall design scheme for large-scale simulation of reactor structural mechanics based on the E-class supercomputer, and the correctness of the  ... 
doi:10.1109/access.2020.3037398 fatcat:3oikbg52inf5nbysdead3e7woq

Research trend of large-scale supercomputers and applications from the TOP500 and Gordon Bell Prize

Weimin Zheng
2020 Science China Information Sciences  
In this paper, we review the supercomputers in the latest TOP500 list and seven Gordon Bell Prize applications to show the research trend of the large-scale supercomputers and applications.  ...  We analyze the supercomputers and seven Gordon Bell Prize applications to show the development trend of large-scale supercomputers and applications. We organize the paper as follows.  ...  It can not only visualize material structure at an atomic scale, but also be used for atomic-level modification of matter.  ... 
doi:10.1007/s11432-020-2861-0 fatcat:73afvlh5wneq3oqkj2nlnkv3jy

Heterogeneous Hierarchical Workflow Composition

Orcun Yildiz, Jorge Ejarque, Henry Chan, Subramanian Sankaranarayanan, Rosa M. Badia, Tom Peterka
2019 Computing in science & engineering (Print)  
algorithm, and a visualization library. 1 Such complex workflows require significant effort from scientists to manage the scheduling and data exchange among those tasks.  ...  For instance, the detection of highly turbulent potentially destructive features in plasma physics simulations requires the in situ coupling of two simulation codes, a compression tool, a feature detection  ...  ACKNOWLEDGMENTS This work is a collaboration between Argonne National Laboratory and the Barcelona Supercomputing Center within the Joint Laboratory for Extreme-Scale Computing.  ... 
doi:10.1109/mcse.2019.2918766 fatcat:frwdvwfgxrhzrbzl5q6vxl2aw4

Optimizing parallel performance of unstructured volume rendering for the Earth Simulator

Li Chen, Issei Fujishiro, Kengo Nakajima
2003 Parallel Computing  
As part of the ES project in Japan, the proposed subsystem is effective for the visualization of huge-scale unstructured datasets, and can be concurrent with computation on the same high-performance parallel  ...  node parallelization, and vectorization for each processing element, plus dynamic load balancing.  ...  Acknowledgements This study was conducted as part of the Solid Earth Platform for Large-Scale Computation project funded by the Japanese Ministry of Education, Culture, Sports, Science and Technology through  ... 
doi:10.1016/s0167-8191(02)00251-x fatcat:7igsaghc6rerzjc27433scuv3y

Visualizing Network Traffic to Understand the Performance of Massively Parallel Simulations

A. G. Landge, J. A. Levine, A. Bhatele, K. E. Isaacs, T. Gamblin, M. Schulz, S. H. Langer, Peer-Timo Bremer, V. Pascucci
2012 IEEE Transactions on Visualization and Computer Graphics  
Index Terms-Performance analysis, network traffic visualization, projected graph layouts. the most dominant model for high-performance computing communication.  ...  Here we propose a visualization framework to illustrate and analyze the network traffic of packets on some of the largest simulations performed on modern supercomputers.  ...  This work was also performed under the auspices of the U.S.  ... 
doi:10.1109/tvcg.2012.286 pmid:26357155 fatcat:w4ouppudsfa3zfbmvoftvfjenm

Performance Visualization for Large-Scale Computing Systems: A Literature Review [chapter]

Qin Gao, Xuhui Zhang, Pei-Luen Patrick Rau, Anthony A. Maciejewski, Howard Jay Siegel
2011 Lecture Notes in Computer Science  
Recently the need for extreme scale computing solutions presents demands for powerful and easy to use performance visualization tools.  ...  Then visualization techniques from 21 performance visualization systems are reviewed and discussed, with the hope of shedding light on the design of visualization tools for ultra-large systems.  ...  This research was supported in part by the US National Science Foundation Grant number 0905399, and the CSU Abell Endowment.  ... 
doi:10.1007/978-3-642-21602-2_49 fatcat:6s3m2deu5jed5krhtusx4sildi

Early experiences scaling VMD molecular visualization and analysis jobs on blue waters

John E. Stone, Barry Isralewitz, Klaus Schulten
2013 2013 Extreme Scaling Workshop (xsw 2013)  
We report ongoing progress on porting, tuning, and scaling up the popular molecular visualization and analysis program VMD on the NSF Blue Waters petascale supercomputer.  ...  Extraction of details about the dynamics of biomolecules from terabytes of simulation output requires powerful user-extensible molecular analysis and visualization tools.  ...  Blue Waters is a joint effort of the University of Illinois at Urbana-Champaign and its National Center for Supercomputing Applications (NCSA).  ... 
doi:10.1109/xsw.2013.10 fatcat:czjno62d5ngb3dnmapwqq5yk6q

Advection-Based Sparse Data Management for Visualizing Unsteady Flow

Hanqi Guo, Jiang Zhang, Richen Liu, Lu Liu, Xiaoru Yuan, Jian Huang, Xiangfei Meng, Jingshan Pan
2014 IEEE Transactions on Visualization and Computer Graphics  
The benefits are (1) greatly increasing the scale of local-range analysis (e.g. source-destination queries, streak surface generation) that can fit within any given limit of hardware resources; (2) improving  ...  When computing integral curves and integral surfaces for large-scale unsteady flow fields, a major bottleneck is the widening gap between data access demands and the available bandwidth (both I/O and in-memory  ...  ACKNOWLEDGMENTS The authors would like to thank Prof. Qingdong Cai for providing the TB-scale turbulence simulation data. This work is supported by NSFC No. 61170204.  ... 
doi:10.1109/tvcg.2014.2346418 pmid:26356969 fatcat:4m4nxsxalnhxfaskwlpfmigoim
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