Filters








809 Hits in 0.79 sec

Highly Optimized Full-Core Reactor Simulations on Summit [article]

Paul Fischer, Elia Merzari, Misun Min, Stefan Kerkemeier, Yu-Hsiang Lan, Malachi Phillips, Thilina Rathnayake, April Novak, Derek Gaston, Noel Chalmers, Tim Warburton
2021 arXiv   pre-print
Nek5000/RS is a highly-performant open-source spectral element code for simulation of incompressible and low-Mach fluid flow, heat transfer, and combustion with a particular focus on turbulent flows in complex domains. It is based on high-order discretizations that realize the same (or lower) cost per gridpoint as traditional low-order methods. State-of-the-art multilevel preconditioners, efficient high-order time-splitting methods, and runtime-adaptive communication strategies are built on a
more » ... st OCCA-based kernel library, libParanumal, to provide scalability and portability across the spectrum of current and future high-performance computing platforms. On Summit, Nek5000/RS has recently achieved an milestone in the simulation of nuclear reactors: the first full-core computational fluid dynamics simulations of reactor cores, including pebble beds with > 350,000 pebbles and 98M elements advanced in less than 0.25 seconds per Navier-Stokes timestep. With carefully tuned algorithms, it is possible to simulate a single flow-through time for a full reactor core in less than six hours on all of Summit.
arXiv:2110.01716v1 fatcat:xyrw6jbwwfcexn2fnv2gwic47y

MOOSE: A parallel computational framework for coupled systems of nonlinear equations

Derek Gaston, Chris Newman, Glen Hansen, Damien Lebrun-Grandié
2009 Nuclear Engineering and Design  
Systems of coupled, nonlinear partial differential equations often arise in simulation of nuclear processes. MOOSE: Multiphysics Object Oriented Simulation Environment, a parallel computational framework targeted at solving these systems, is presented. As opposed to traditional data-flow oriented computational frameworks, MOOSE is founded on the mathematical principle of Jacobian-free Newton-Krylov (JFNK) solution methods. Utilizing the mathematical structure present in JFNK, physics are
more » ... ized into "Kernels" allowing for rapid production of new simulation tools. In addition, systems are solved fully coupled and fully implicit employing physics based preconditioning which allows for great flexibility even with large variance in time scales. A summary of the mathematics, an inspection of the structure of MOOSE, and several representative solutions from applications built on the framework are presented.
doi:10.1016/j.nucengdes.2009.05.021 fatcat:aj54sx3qc5frjfaotjynwcyeca

MOOSE: Enabling Massively Parallel Multiphysics Simulation [article]

Cody J. Permann, Derek R. Gaston, David Andrs, Robert W. Carlsen, Fande Kong, Alexander D. Lindsay, Jason M. Miller, John W. Peterson, Andrew E. Slaughter, Roy H. Stogner, Richard C. Martineau
2019 arXiv   pre-print
Harnessing modern parallel computing resources to achieve complex multi-physics simulations is a daunting task. The Multiphysics Object Oriented Simulation Environment (MOOSE) aims to enable such development by providing simplified interfaces for specification of partial differential equations, boundary conditions, material properties, and all aspects of a simulation without the need to consider the parallel, adaptive, nonlinear, finite-element solve that is handled internally. Through the use
more » ... f interfaces and inheritance, each portion of a simulation becomes reusable and composable in a manner that allows disparate research groups to share code and create an ecosystem of growing capability that lowers the barrier for the creation of multiphysics simulation codes. Included within the framework is a unique capability for building multiscale, multiphysics simulations through simultaneous execution of multiple sub-applications with data transfers between the scales. Other capabilities include automatic differentiation, scaling to a large number of processors, hybrid parallelism, and mesh adaptivity. To date, MOOSE-based applications have been created in areas of science and engineering such as nuclear physics, geothermal science, magneto-hydrodynamics, seismic events, compressible and incompressible fluid flow, microstructure evolution, and advanced manufacturing processes.
arXiv:1911.04488v1 fatcat:xgejxipdcvd5ha3kuylnxrtlay

MOOSE: Enabling massively parallel multiphysics simulation

Cody J. Permann, Derek R. Gaston, David Andrš, Robert W. Carlsen, Fande Kong, Alexander D. Lindsay, Jason M. Miller, John W. Peterson, Andrew E. Slaughter, Roy H. Stogner, Richard C. Martineau
2020 SoftwareX  
Harnessing modern parallel computing resources to achieve complex multiphysics simulations is a daunting task. The Multiphysics Object Oriented Simulation Environment (MOOSE) aims to enable such development by providing simplified interfaces for specification of partial differential equations, boundary conditions, material properties, and all aspects of a simulation without the need to consider the parallel, adaptive, nonlinear, finite element solve that is handled internally. Through the use
more » ... interfaces and inheritance, each portion of a simulation becomes reusable and composable in a manner that allows disparate research groups to share code and create an ecosystem of growing capability that lowers the barrier for the creation of multiphysics simulation codes. Included within the framework is a unique capability for building multiscale, multiphysics simulations through simultaneous execution of multiple sub-applications with data transfers between the scales. Other capabilities include automatic differentiation, scaling to a large number of processors, hybrid parallelism, and mesh adaptivity. To date, MOOSE-based applications have been created in areas of science and engineering such as nuclear physics, geothermal science, magneto-hydrodynamics, seismic events, compressible and incompressible fluid flow, microstructure evolution, and advanced manufacturing processes.
doi:10.1016/j.softx.2020.100430 fatcat:g6uq6ezpfraqrcer7rhekiigwi

Order parameter re-mapping algorithm for 3D phase field model of grain growth using FEM

Cody J. Permann, Michael R. Tonks, Bradley Fromm, Derek R. Gaston
2016 Computational materials science  
Phase field modeling (PFM) is a well-known technique for simulating microstructural evolution. To model grain growth using PFM, typically each grain is assigned a unique non-conserved order parameter and each order parameter field is evolved in time. Traditional approaches using a one-to-one mapping of grains to order parameters present a challenge when modeling large numbers of grains due to the computational expense of using many order parameters. This problem is exacerbated when using an
more » ... icit finite element method (FEM), as the global matrix size is proportional to the number of order parameters. While previous work has developed methods to reduce the number of required variables and thus computational complexity and run time, none of the existing approaches can be applied for an implicit FEM implementation of PFM. Here, we present a modular, dynamic, scalable reassignment algorithm suitable for use in such a system. Polycrystal modeling with grain growth and stress require careful tracking of each grain's position and orientation which is lost when using a reduced order parameter set. The method presented in this paper maintains a unique ID for each grain even after reassignment, to allow the PFM to be tightly coupled to calculations of the stress throughout the polycrystal. Implementation details and comparative results of our approach are presented.
doi:10.1016/j.commatsci.2015.12.042 fatcat:rzgopoguk5bhnlzkxudv64uvgu

AcouStick: A Tracked A-Mode Ultrasonography System for Registration in Image-Guided Surgery [chapter]

Calvin R. Maurer, Ronald P. Gaston, Derek L. G. Hill, Michael J. Gleeson, M. Graeme Taylor, Michael R. Fenlon, Philip J. Edwards, David J. Hawkes
1999 Lecture Notes in Computer Science  
Gaston and for supplying the equipment used in this project. P. J. Edwards was supported by the EPSRC GR/L62221. We thank G. Penney for his help and Dr. F.  ... 
doi:10.1007/10704282_104 fatcat:kme65mtfobc7vfzyqt7la7cigu

A Globally-Implicit Computational Framework for Physics-based Simulation of Coupled Thermo-Hydro-Mechanical Problems: Application to Sustainability of Geothermal Reservoirs

Robert Podgorney, Hai Huang, Mitch Plummer, Derek Gaston
2013 SNE Simulation Notes Europe  
This paper highlights the development of a fully-coupled and fully-implicit modeling tool for predicting the dynamics of fluid flow, heat transport, and rock deformation using a GIA named FALCON (Fracturing And Liquid CONvection). The code is developed on a parallel Multiphysics Object Oriented Simulation Environment (MOOSE) computational framework developed at Idaho National Laboratory (INL) for providing finite element solutions of coupled system of nonlinear partial differential equations.
more » ... this paper, a brief overview of the governing equations numerical approach are discussed, and an example simulation of strongly coupled geothermal reservoir behavior is presented.
doi:10.11128/sne.23.tn.10175 fatcat:rcswvbmeczanrh2dniywjl7zda

Physics-based multiscale coupling for full core nuclear reactor simulation

Derek R. Gaston, Cody J. Permann, John W. Peterson, Andrew E. Slaughter, David Andrš, Yaqi Wang, Michael P. Short, Danielle M. Perez, Michael R. Tonks, Javier Ortensi, Ling Zou, Richard C. Martineau
2015 Annals of Nuclear Energy  
The Multiphysics Object Oriented Simulation Environment (MOOSE) developed at Idaho National Laboratory (Gaston et al., 2009) represents an alternative path toward reactor simulation.  ... 
doi:10.1016/j.anucene.2014.09.060 fatcat:e3qtljkw3na7dcbap2j2wrgn2y

A general-purpose hierarchical mesh partitioning method with node balancing strategies for large-scale numerical simulations [article]

Fande Kong, Roy H. Stogner, Derek R. Gaston, John W. Peterson, Cody J. Permann, Andrew E. Slaughter, Richard C. Martineau
2018 arXiv   pre-print
Large-scale parallel numerical simulations are essential for a wide range of engineering problems that involve complex, coupled physical processes interacting across a broad range of spatial and temporal scales. The data structures involved in such simulations (meshes, sparse matrices, etc.) are frequently represented as graphs, and these graphs must be optimally partitioned across the available computational resources in order for the underlying calculations to scale efficiently. Partitions
more » ... ch minimize the number of graph edges that are cut (edge-cuts) while simultaneously maintaining a balance in the amount of work (i.e. graph nodes) assigned to each processor core are desirable, and the performance of most existing partitioning software begins to degrade in this metric for partitions with more than than O(10^3) processor cores. In this work, we consider a general-purpose hierarchical partitioner which takes into account the existence of multiple processor cores and shared memory in a compute node while partitioning a graph into an arbitrary number of subgraphs. We demonstrate that our algorithms significantly improve the preconditioning efficiency and overall performance of realistic numerical simulations running on up to 32,768 processor cores with nearly 10^9 unknowns.
arXiv:1809.02666v2 fatcat:yxfhslx3izbonlh7gyfidyikhi

Gut Microbiome of a Porcine Model of Metabolic Syndrome and HF-pEF

Aoife N O'Donovan, Florence M Herisson, Fiona Fouhy, Paul M Ryan, Derek Whelan, Crystal N. Johnson, Gaston Cluzel, R. Paul Ross, Catherine Stanton, Noel M Caplice
2020 American Journal of Physiology. Heart and Circulatory Physiology  
Metabolic syndrome (MetS) is a combination of cardiovascular risk factors including obesity, hyperlipidemia, hypertension, insulin resistance, non-alcoholic fatty liver disease and diastolic heart failure. This syndrome has been identified as one of the greatest global health challenges of the 21st century. Herein, we examine in a porcine model of diet-induced MetS whether cardiovascular, metabolic, gut microbiota and functional metataxonomic changes mimic those observed in human studies.
more » ... ce pigs with mineralocorticoid-induced hypertension fed a high-fat, salt and sugar diet (HFD) over 12 weeks were assessed for hyperlipidemia, hyperinsulinemia, immunohistologic, echocardiographic and hemodynamic parameters, as well as assessment of microbiome phenotype and functionality through 16S rRNA gene sequencing, phylogenetic and meta-taxonomic analysis. All MetS animals when compared to controls developed obesity, hyperlipidemia, insulin resistance, hypertension, fatty liver, structural cardiovascular changes including left ventricular hypertrophy and left atrial enlargement, and increased circulating saturated fatty acid levels, in keeping with the human phenotype. A reduction in alpha diversity and specific microbiota changes at phylum, family and genus levels also occurred in this model. Moreover, increases in pro-inflammatory bacteria and secondary bile acid producing bacteria were identified, combined with a decrease in enteroprotective bacteria and a reduction of short chain fatty acid (SCFA)-producing bacteria.Together these data suggest that diet and mineralocorticoid-mediated development of biochemical and cardiovascular stigmata of metabolic syndrome in pigs leads to temporal gut microbiome changes that mimic key gut microbial population signatures in human cardiometabolic disease.
doi:10.1152/ajpheart.00512.2019 pmid:32031871 fatcat:shjdwu7fo5f5dfbldhucp263ke

Design and Evaluation of a System for Microscope-Assisted Guided Interventions (MAGI) [chapter]

Philip J. Edwards, Andrew P. King, Calvin R. Maurer, Darryl A. de Cunha, David J. Hawkes, Derek L. G. Hill, Ron P. Gaston, Michael R. Fenlon, Subhash Chandra, Anthony J. Strong, Christopher L. Chandler, Aurelia Richards (+1 others)
1999 Lecture Notes in Computer Science  
The problem of providing surgical navigation using image overlays on the operative scene can be split into four main tasks -calibration of the optical system; registration of preoperative images to the patient; tracking of the display system and patient and display using a suitable visualisation scheme. To achieve a convincing result in the magnified view through the operating microscope high alignment accuracy is required. We have simulated our entire system to establish the major sources of
more » ... ror. We have improved each of the stages involved. The microscope calibration process has been automated. We have introduced bone-implanted markers for registration and incorporated a locking acrylic dental stent (LADS) for patient tracking and/or registration. These improvements have significantly increased the alignment accuracy of our overlays. LADS repositioning on volunteers showed a mean target registration error of 0.7mm. Phantom accuracy is 0.3-0.5mm and clinical overlay errors were 0.5-1.0mm on the bone fiducials and 0.5-4mm on target structures. We have improved the graphical representation of the stereo overlays. The resulting system provides 3D surgical navigation for microscope-assisted guided interventions (MAGI). C. Taylor, A. Colchester (Eds.): MICCAI'99
doi:10.1007/10704282_91 fatcat:yjmmlwxpajhfllsetpxtanhohu

A highly parallel multilevel Newton-Krylov-Schwarz method with subspace-based coarsening and partition-based balancing for the multigroup neutron transport equations on 3D unstructured meshes [article]

Fande Kong, Yaqi Wang, Derek R. Gaston, Cody J. Permann, Andrew E. Slaughter, Alexander D. Lindsay, Richard C. Martineau
2019 arXiv   pre-print
The multigroup neutron transport equations have been widely used to study the motion of neutrons and their interactions with the background materials. Numerical simulation of the multigroup neutron transport equations is computationally challenging because the equations is defined on a high dimensional phase space (1D in energy, 2D in angle, and 3D in spatial space), and furthermore, for realistic applications, the computational spatial domain is complex and the materials are heterogeneous. The
more » ... multilevel domain decomposition methods is one of the most popular algorithms for solving the multigroup neutron transport equations, but the construction of coarse spaces is expensive and often not strongly scalable when the number of processor cores is large. In this paper, we study a highly parallel multilevel Newton-Krylov-Schwarz method equipped with several novel components, such as subspace-based coarsening, partition-based balancing and hierarchical mesh partitioning, that enable the overall simulation strongly scalable in terms of the compute time. Compared with the traditional coarsening method, the subspace-based coarsening algorithm significantly reduces the cost of the preconditioner setup that is often unscalable. In addition, the partition-based balancing strategy enhances the parallel efficiency of the overall solver by assigning a nearly-equal amount of work to each processor core. The hierarchical mesh partitioning is able to generate a large number of subdomains and meanwhile minimizes the off-node communication. We numerically show that the proposed algorithm is scalable with more than 10,000 processor cores for a realistic application with a few billions unknowns on 3D unstructured meshes.
arXiv:1903.03659v1 fatcat:j667z67y4ndh3onhsy5uvfa4ha

Serial Vaccination and the Antigenic Distance Hypothesis: Effects on Influenza Vaccine Effectiveness During A(H3N2) Epidemics in Canada, 2010–2011 to 2014–2015

Danuta M. Skowronski, Catharine Chambers, Gaston De Serres, Suzana Sabaiduc, Anne-Luise Winter, James A. Dickinson, Jonathan B. Gubbay, Kevin Fonseca, Steven J. Drews, Hugues Charest, Christine Martineau, Mel Krajden (+4 others)
2017 Journal of Infectious Diseases  
Background. The antigenic distance hypothesis (ADH) predicts that negative interference from prior season's influenza vaccine (v1) on the current season's vaccine (v2) protection may occur when the antigenic distance is small between v1 and v2 (v1 ≈ v2) but large between v1 and the current epidemic (e) strain (v1 ≠ e). Methods. Vaccine effectiveness (VE) against medically attended, laboratory-confirmed influenza A(H3N2) illness was estimated by test-negative design during 3 A(H3N2) epidemics ()
more » ... in Canada. Vaccine effectiveness was derived with covariate adjustment across v2 and/or v1 categories relative to no vaccine receipt among outpatients aged ≥9 years. Prior vaccination effects were interpreted within the ADH framework. Results. Prior vaccination effects varied significantly by season, consistent with the ADH. There was no interference by v1 in 2010-2011 when v1 ≠ v2 and v1 ≠ e, with comparable VE for v2 alone or v2 + v1: 34% (95% confidence interval [CI] = −51% to 71%) versus 34% (95% CI = −5% to 58%). Negative interference by v1 was suggested in 2012-2013 with nonsignificant reduction in VE when v1 ≈ v2 and v1 ≠ e: 49% (95% CI = −47% to 83%) versus 28% (95% CI = −12% to 54%). Negative effects of prior vaccination were pronounced and statistically significant in 2014-2015 when v1 ≡ v2 and v1 ≠ e: 65% (95% CI = 25% to 83%) versus −33% (95% CI = −78% to 1%). Conclusions. Effects of repeat influenza vaccination were consistent with the ADH and may have contributed to findings of low VE across recent A(H3N2) epidemics since 2010 in Canada.
doi:10.1093/infdis/jix074 pmid:28180277 pmcid:PMC5853783 fatcat:bifooqm33zh5ja7e34ww62itpe

Page 54 of National Union Catalog Vol. 32, Issue [page]

1963 National Union Catalog  
Translated from the French by Derek Coltman.  ...  Paris, Editions musicales ,19667, Leduc, Gaston, 1904- Cours d’économie du développement, Ren d’aprés les notes et avec l’autorisation de Gaston Leduc. Licence 4° année et D. E. S., 1961-1962.  ... 

Torture and war

N Mamode
1996 BMJ (Clinical Research Edition)  
BMJ 1995;311:286-7. (29 July.) 2 Gaston H. Does the spina bifida clinic need an ophthalmologist? Zeitschrift far kinderchirurgie und Grenzgebiete 1985;40 (supp 1):46-50. 3 Gaston H.  ...  DEREK Atrocities in eastern Europe were not mentioned EDrroR,-Derek Summerfield concludes that "The struggle is to get the social order to own up to what is done to reduce human beings to dust, albeit  ... 
doi:10.1136/bmj.312.7022.57a pmid:8555886 pmcid:PMC2349695 fatcat:q5n3qn2u75ghbgrca2pe7jfrqi
« Previous Showing results 1 — 15 out of 809 results