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Autonomous Orchestration of Distributed Discrete Event Simulations in the Presence of Resource Uncertainty

Zhiquan Sui, Matthew Malensek, Neil Harvey, Shrideep Pallickara
2015 ACM Transactions on Autonomous and Adaptive Systems  
Orchestrating the simulations in a distributed setting involves coping with resource uncertainty.  ...  Simulating a wide range of events and conditions provides a more nuanced model, but also increases its computational footprint.  ...  NAADSM is a Monte Carlo model: a simulation is run many times with each run representing one possible way that events could occur in a disease outbreak, which contributes to an overall picture of the probability  ... 
doi:10.1145/2746345 fatcat:uobrjlhibrbkbafz5tjkcah7ge

Quantum Monte Carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond [article]

Anthony Scemama , William Jalby
2012 arXiv   pre-print
framework adapted to all kinds of computational platforms (massively parallel machines, clusters, or distributed grids).  ...  Various strategies to implement efficiently QMC simulations for large chemical systems are presented.  ...  This work was possible thanks to the generous computational support from CALMIP (Université de Toulouse), under the allocation 2011-0510, GENCI under the allocation GEN1738, CCRT (CEA), and PRACE under  ... 
arXiv:1209.6630v2 fatcat:ymr5olx27fby5l5wqcfscsd64y

Predictor@Home: A "Protein Structure Prediction Supercomputer' Based on Global Computing

M. Taufer, Chahm An, A. Kerstens, C.L. Brooks III
2006 IEEE Transactions on Parallel and Distributed Systems  
To address this problem, we developed Predictor@Home, a "structure prediction supercomputer" powered by the Berkeley Open Infrastructure for Network Computing (BOINC) framework and based on the global  ...  In this paper, we describe the protocol we employed for protein structure prediction and its integration into a global computing architecture based on public resources.  ...  The authors wish to thank David Anderson and Rom Walton for their invaluable help with Predictor@Home and the Predictor@Home and BOINC community of volunteers for donating their computing cycles.  ... 
doi:10.1109/tpds.2006.110 fatcat:5uxvljwf5raw3h7m75yakn5h54

Quantum Monte Carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond

Anthony Scemama, Michel Caffarel, Emmanuel Oseret, William Jalby
2013 Journal of Computational Chemistry  
Various strategies to implement efficiently QMC simulations for large chemical systems are presented.  ...  adapted to all kinds of computational platforms (massively parallel machines, clusters, or distributed grids).  ...  This work was possible thanks to the generous computational support from CALMIP (Université de Toulouse), under the allocation 2011-0510, GENCI under the allocation GEN1738, CCRT (CEA), and PRACE under  ... 
doi:10.1002/jcc.23216 pmid:23288704 fatcat:6sugddhrifffvnznskiog2x3ty

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

Rory M. Donovan, Jose-Juan Tapia, Devin P. Sullivan, James R. Faeder, Robert F. Murphy, Markus Dittrich, Daniel M. Zuckerman, Martin Meier-Schellersheim
2016 PLoS Computational Biology  
The WE approach runs an ensemble of parallel trajectories with assigned weights and uses a statistical resampling strategy of replicating and pruning trajectories to focus computational effort on difficult-to-sample  ...  Here, we use WE to orchestrate particle-based kinetic Monte Carlo simulations, which include spatial geometry (e.g., of organelles, plasma membrane) and biochemical interactions among mobile molecular  ...  Acknowledgments The authors gratefully acknowledge helpful conversations with Ernesto Suárez, Lillian Chong, Matthew Zwier, and Joshua Adelman.  ... 
doi:10.1371/journal.pcbi.1004611 pmid:26845334 pmcid:PMC4741515 fatcat:r3jdzbsaerhxrbnxf4wmh5qnfa

Fractionated Software for Networked Cyber-Physical Systems: Research Directions and Long-Term Vision [chapter]

Mark-Oliver Stehr, Carolyn Talcott, John Rushby, Pat Lincoln, Minyoung Kim, Steven Cheung, Andy Poggio
2011 Lecture Notes in Computer Science  
These systems may include a variety of devices that sense and affect their environment and the configuration of the system itself. We call such systems Networked Cyber-Physical Systems (NCPS).  ...  In this paper we lay out research directions centered around a new paradigm for the design of NCPS based on a notion of software fractionation that we are currently exploring which can serve as the basis  ...  Acknowledgments Support from National Science Foundation Grant 0932397 (A Logical Framework for Self-Optimizing Networked Cyber-Physical Systems) and Office of Naval Research Grant N00014-10-1-0365 (Principles  ... 
doi:10.1007/978-3-642-24933-4_7 fatcat:52w7nldn5fc7tjtvla7dbf7kmq

Demystifying the Performance of HPC Scientific Applications on NVM-based Memory Systems [article]

Ivy Peng and Kai Wu and Jie Ren and Dong Li and Maya Gokhale
2020 arXiv   pre-print
Current NVM technologies have lower performance than DRAM and, thus, are often paired with DRAM in a heterogeneous main memory. Recently, byte-addressable NVM hardware becomes available.  ...  Second, we demonstrate that write-aware data placement on uncached-NVM could achieve 2x performance improvement with a 60  ...  We use a general blockstructured AMR framework, BoxLib [3] , for the test. • Monte Carlo methods rely on repeated random data accesses to calculate numerical results.  ... 
arXiv:2002.06499v1 fatcat:m6p6biiqincndb3bfn57lvxtzq

Smart Intra-query Fault Tolerance for Massive Parallel Processing Databases

Yunhong Ji, Yunpeng Chai, Xuan Zhou, Lipeng Ren, Yajie Qin
2019 Data Science and Engineering  
While SQL-on-Hadoop systems can utilize the fault tolerance support of low-level frameworks, such as MapReduce and Spark, their cost-effectiveness is not always acceptable.  ...  Intra-query fault tolerance has increasingly been a concern for online analytical processing, as more and more enterprises migrate data analytical systems from mainframes to commodity computers.  ...  Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long  ... 
doi:10.1007/s41019-019-00114-z fatcat:kwugnnr6dzhq7olonwz7ytqmrq

Software challenges in extreme scale systems

Vivek Sarkar, William Harrod, Allan E Snavely
2009 Journal of Physics, Conference Series  
Carlson is a member of the research staff at the IDA Center for Computing Sciences where, since 1990, his focus has been on applications and system tools for large-scale parallel and distributed computers  ...  Dr His research areas include advanced VLSI and nano technologies, non von Neumann models of programming and execution, parallel algorithms and applications, and their impact on massively parallel computer  ...  Increasingly, ecologists are turning to stochastic optimization techniques such as simulated annealing, or the use of various implementations of Markov Chain Monte Carlo to simulate posterior probability  ... 
doi:10.1088/1742-6596/180/1/012045 fatcat:iukutry2dvbitfdh6ng7kgz564

Rugged free-energy landscapes in disordered spin systems [article]

D. Yllanes
2011 arXiv   pre-print
We also introduce Tethered Monte Carlo, a general strategy for the study of systems with rugged free-energy landscapes.  ...  These systems have been studied by means of large-scale Monte Carlo simulations, exploiting a variety of platforms, which include the Janus special-purpose supercomputer.  ...  For the Monte Carlo simulation, the strategy has been mainly one of sheer brute force.  ... 
arXiv:1111.0266v1 fatcat:mrobpb3hwbhvlpoxe4idxijbma

Generic Workload Management System Using Condor-Based Pilot Factory In Panda Framework

Po-Hsiang Chiu, Torre Wenaus
2010 Zenodo  
applied in the PanDA architecture, PanDA-PF WMS, with the goal of providing a more generic yet efficient resource allocating strategy.  ...  To address these issues and provide a cleaner abstraction of the Grid with the potential of generalizing into arbitrary resource-sharing environment, this paper proposes a new Condor-based pilot mechanism  ...  We also thank the PAS and RACF Groups at the Physics Department in Brookhaven National Laboratory for their feedback, guidance and assistance in the required software systems and computing facilities.  ... 
doi:10.5281/zenodo.1071934 fatcat:2wj33xua4rcp5ofzlvf6whbfuy

Dependable embedded systems

2008 2008 6th IEEE International Conference on Industrial Informatics  
Titles in the Series cover a focused set of embedded topics relating to traditional computing devices as well as hightech appliances used in newer, personal devices, and related topics.  ...  This Series addresses current and future challenges pertaining to embedded hardware, software, specifications and techniques.  ...  Hideharu Amano at Keio University and its partnering institutions. It was a tremendous help to see to possibilities of FDSOI in silicon very early on.  ... 
doi:10.1109/indin.2008.4618103 fatcat:hal6brsgsjg5rlo3u5xil46pxi

Cloud resource management: towards efficient execution of large-scale scientific applications and workflows on complex infrastructures

Nelson Mimura Gonzalez, Tereza Cristina Melo de Brito Carvalho, Charles Christian Miers
2017 Journal of Cloud Computing: Advances, Systems and Applications  
In parallel, as science relies on the analysis of very large data sets, data management and processing must be performed in a scalable and automated way.  ...  Cloud computing evolved from the concept of utility computing, which is defined as the provision of computational and storage resources as a metered service.  ...  This led to selection of 113 works related to resource management and task scheduling with the majority focusing on cloud computing and a few works on distributed systems, such as [51] and [105] .  ... 
doi:10.1186/s13677-017-0081-4 fatcat:oy36rd3zerc2rfx7rhpdqxvkte

Construction of Artistic Design Patterns Based on Improved Distributed Data Parallel Computing of Heterogeneous Tasks

Yao Sun, Gengxin Sun
2022 Mathematical Problems in Engineering  
of heterogeneous parallel computing, designs a heterogeneous parallel computing architecture, and deploys a heterogeneous parallel computing architecture.  ...  In terms of storage resources, the computing system adopts distributed storage as a whole. The CPU-GPU heterogeneous parallel in the desktop system adopts virtual unified storage.  ...  Julien Bert et al. use CPU-GPU heterogeneous computing to accelerate Monte Carlo simulation (MCS), which enables the application of MCS in medical imaging and particle therapy through the acceleration  ... 
doi:10.1155/2022/3890255 fatcat:jnybktiryjhxhbvhwlul2nk7ly

Exa-Dune – Flexible PDE Solvers, Numerical Methods and Applications [article]

Peter Bastian, Mirco Altenbernd, Nils-Arne Dreier, Christian Engwer, Jorrit Fahlke, René Fritze, Markus Geveler, Dominik Göddeke, Oleg Iliev, Olaf Ippisch, Jan Mohring, Steffen Müthing, Mario Ohlberger, Dirk Ribbrock, Nikolay Shegunov (+1 others)
2019 arXiv   pre-print
a heterogeneous massively parallel architecture.  ...  choice of the coarse/fine scale and the overlap region as well as the combination of local reduced basis multiscale methods and the multilevel Monte-Carlo algorithm.  ...  functions to simulate strongly heterogeneous systems.  ... 
arXiv:1911.01492v2 fatcat:ureqbuj3pjfu3k27wayt7cu7xy
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